The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The genetic complement of a BACTERIA as represented in its DNA.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
The genetic complement of a plant (PLANTS) as represented in its DNA.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
The genetic complement of MITOCHONDRIA as represented in their DNA.
The complete gene complement contained in a set of chromosomes in a fungus.
The amount of DNA (or RNA) in one copy of a genome.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
The relationships of groups of organisms as reflected by their genetic makeup.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The genetic complement of an insect (INSECTS) as represented in its DNA.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.
The systematic study of the complete DNA sequences (GENOME) of organisms.
The genetic complement of CHLOROPLASTS as represented in their DNA.
Any method used for determining the location of and relative distances between genes on a chromosome.
The genetic complement of a helminth (HELMINTHS) as represented in its DNA.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
The genetic complement of PLASTIDS as represented in their DNA.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.
A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.
Deoxyribonucleic acid that makes up the genetic material of viruses.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The sequential location of genes on a chromosome.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Genotypic differences observed among individuals in a population.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Databases devoted to knowledge about specific genes and gene products.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.
Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Ribonucleic acid that makes up the genetic material of viruses.
The functional hereditary units of VIRUSES.
Sequential operating programs and data which instruct the functioning of a digital computer.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
Deoxyribonucleic acid that makes up the genetic material of plants.
Proteins found in any species of virus.
The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.
Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.
The functional hereditary units of BACTERIA.
The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The functional hereditary units of PLANTS.
The genetic complement of a microorganism as represented in its DNA or in some microorganisms its RNA.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
The parts of a GENOME sequence that are involved with the different functions or properties of genomes as a whole as opposed to those of individual GENES.
Established cell cultures that have the potential to propagate indefinitely.
The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.
Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.
In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Proteins found in any species of bacterium.
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
The process by which a DNA molecule is duplicated.
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Viruses whose hosts are bacterial cells.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. For example, the hallmarks of a transposon are that it is flanked by inverted repeats on each end and the inverted repeats are flanked by direct repeats. The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept.
The portion of an interactive computer program that issues messages to and receives commands from a user.
Genomes of temperate BACTERIOPHAGES integrated into the DNA of their bacterial host cell. The prophages can be duplicated for many cell generations until some stimulus induces its activation and virulence.
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.
Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.
Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.
The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.
Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.
Viruses whose genetic material is RNA.
Self-replicating cytoplasmic organelles of plant and algal cells that contain pigments and may synthesize and accumulate various substances. PLASTID GENOMES are used in phylogenetic studies.
Insertion of viral DNA into host-cell DNA. This includes integration of phage DNA into bacterial DNA; (LYSOGENY); to form a PROPHAGE or integration of retroviral DNA into cellular DNA to form a PROVIRUS.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
The functional genetic units of ARCHAEA.
A plant genus of the family POACEAE. The grain is used for FOOD and for ANIMAL FEED. This should not be confused with KAFFIR LIME or with KEFIR milk product.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)
Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.
Very long DNA molecules and associated proteins, HISTONES, and non-histone chromosomal proteins (CHROMOSOMAL PROTEINS, NON-HISTONE). Normally 46 chromosomes, including two sex chromosomes are found in the nucleus of human cells. They carry the hereditary information of the individual.
Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).
DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.
Directed modification of the gene complement of a living organism by such techniques as altering the DNA, substituting genetic material by means of a virus, transplanting whole nuclei, transplanting cell hybrids, etc.
Low-copy (2-50) repetitive DNA elements that are highly homologous and range in size from 1000 to 400,000 base pairs.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.
Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.
A nucleic acid sequence that contains an above average number of GUANINE and CYTOSINE bases.
Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.
The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.
One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
Genetic loci associated with a QUANTITATIVE TRAIT.
Two identical genes showing the same phenotypic action but localized in different regions of a chromosome or on different chromosomes. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Members of the group of vascular plants which bear flowers. They are differentiated from GYMNOSPERMS by their production of seeds within a closed chamber (OVARY, PLANT). The Angiosperms division is composed of two classes, the monocotyledons (Liliopsida) and dicotyledons (Magnoliopsida). Angiosperms represent approximately 80% of all known living plants.
Deletion of sequences of nucleic acids from the genetic material of an individual.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
A small order of primarily marine fish containing 340 species. Most have a rotund or box-like shape. TETRODOTOXIN is found in their liver and ovaries.
Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
The chromosomal constitution of cells, in which each type of CHROMOSOME is represented twice. Symbol: 2N or 2X.
The number of mutations that occur in a specific sequence, GENE, or GENOME over a specified period of time such as years, CELL DIVISIONS, or generations.
Viruses which lack a complete genome so that they cannot completely replicate or cannot form a protein coat. Some are host-dependent defectives, meaning they can replicate only in cell systems which provide the particular genetic function which they lack. Others, called SATELLITE VIRUSES, are able to replicate only when their genetic defect is complemented by a helper virus.
An aberration in which a chromosomal segment is deleted and reinserted in the same place but turned 180 degrees from its original orientation, so that the gene sequence for the segment is reversed with respect to that of the rest of the chromosome.
The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.
Deliberate breeding of two different individuals that results in offspring that carry part of the genetic material of each parent. The parent organisms must be genetically compatible and may be from different varieties or closely related species.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.
Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).
The protein complement of an organism coded for by its genome.
Distinct units in some bacterial, bacteriophage or plasmid GENOMES that are types of MOBILE GENETIC ELEMENTS. Encoded in them are a variety of fitness conferring genes, such as VIRULENCE FACTORS (in "pathogenicity islands or islets"), ANTIBIOTIC RESISTANCE genes, or genes required for SYMBIOSIS (in "symbiosis islands or islets"). They range in size from 10 - 500 kilobases, and their GC CONTENT and CODON usage differ from the rest of the genome. They typically contain an INTEGRASE gene, although in some cases this gene has been deleted resulting in "anchored genomic islands".
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
Deoxyribonucleic acid that makes up the genetic material of fungi.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
Diseases of plants.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.
The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.
Deoxyribonucleic acid that makes up the genetic material of algae.
Genes whose nucleotide sequences overlap to some degree. The overlapped sequences may involve structural or regulatory genes of eukaryotic or prokaryotic cells.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of MAMMALS.
Retroviruses that have integrated into the germline (PROVIRUSES) that have lost infectious capability but retained the capability to transpose.
An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.
The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.
A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by long, non-contractile tails.
Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Contiguous large-scale (1000-400,000 basepairs) differences in the genomic DNA between individuals, due to SEQUENCE DELETION; SEQUENCE INSERTION; or SEQUENCE INVERSION.

Ribozymes, genomics and therapeutics. (1/9340)

Genome-sequencing projects are proceeding at a rapid pace and determining the function of open reading frames is the next great challenge. Ribozymes with site-specific cleaving activity could aid greatly in this process. High-throughput screening methods to identify optimal target sites for ribozyme cleavage will provide tools for functional genomics as well as therapeutic reagents.  (+info)

Nonmethylated transposable elements and methylated genes in a chordate genome. (2/9340)

The genome of the invertebrate chordate Ciona intestinalis was found to be a stable mosaic of methylated and nonmethylated domains. Multiple copies of an apparently active long terminal repeat retrotransposon and a long interspersed element are nonmethylated and a large fraction of abundant short interspersed elements are also methylation free. Genes, by contrast, are predominantly methylated. These data are incompatible with the genome defense model, which proposes that DNA methylation in animals is primarily targeted to endogenous transposable elements. Cytosine methylation in this urochordate may be preferentially directed to genes.  (+info)

Alternative splicing of transcripts encoding the alpha- and beta-subunits of mouse glucosidase II in T lymphocytes. (3/9340)

Glucosidase II is a processing enzyme of the endoplasmic reticulum that functions to hydrolyze two glucose residues in immature N -linked oligosaccharides attached to newly synthesized polypeptides. We previously reported the cDNA cloning of the alpha- and beta-subunits of mouse glucosidase II from T cells following copurification of these proteins with the highly glycosylated transmembrane protein-tyrosine phosphatase CD45. Subsequent examination of additional cDNA clones, coupled with partial genomic DNA sequencing, has revealed that both subunits are encoded by gene products that undergo alternative splicing in T lymphocytes. The catalytic alpha-subunit possesses two variably expressed segments, box Alpha1, consisting of 22 amino acids located proximal to the amino-terminus, and box Alpha2, composed of 9 amino acids situated between the amino-terminus and the putative catalytic site in the central region of the molecule. Box Beta1, a variably expressed 7 amino acid segment in the beta-subunit of glucosidase II, is located immediately downstream of an acidic stretch near the carboxyl-terminus. Screening of reverse transcribed RNA by polymerase chain reaction confirms the variable inclusion of each of these segments in transcripts obtained from a panel of T-lymphocyte cell lines. Thus, distinct isoforms of glucosidase II exist that may perform specialized functions.  (+info)

An intact sperm nuclear matrix may be necessary for the mouse paternal genome to participate in embryonic development. (4/9340)

We have been interested in determining the minimally required elements in the sperm head that are necessary in order for the paternal genome to participate in embryogenesis. We used an ionic detergent, mixed alkyltrimethylammonium bromide (ATAB), plus dithiothreitol (DTT) to remove the acrosome and almost all of the perinuclear theca, leaving only the sperm nucleus morphologically intact. We also tested the stability of the sperm nuclear matrix by the ability to form nuclear halos. Sperm nuclei washed in freshly prepared 0.5% ATAB + 2 mM DTT completely decondensed when extracted with salt, but nuclei washed in the same buffer that was 1 wk old, and then extracted with salt, produced nuclear halos, indicating stable nuclear matrices. When we treated sperm heads with freshly prepared ATAB+DTT and injected them into oocytes, none of the oocytes developed into live offspring. In contrast, sperm heads treated in the same way but with 1-wk-old ATAB+DTT solution could support development of about 30% of the oocytes to live offspring. Electron microscopy demonstrated that most of the perinuclear theca had been removed in both cases. These data suggest that at least in the mouse, the only component of the spermatozoa that is crucial for participation in embryologic development is the sperm nucleus with a stable nuclear matrix.  (+info)

The prokaryotic beta-recombinase catalyzes site-specific recombination in mammalian cells. (5/9340)

The development of new strategies for the in vivo modification of eukaryotic genomes has become an important objective of current research. Site-specific recombination has proven useful, as it allows controlled manipulation of murine, plant, and yeast genomes. Here we provide the first evidence that the prokaryotic site-specific recombinase (beta-recombinase), which catalyzes only intramolecular recombination, is active in eukaryotic environments. beta-Recombinase, encoded by the beta gene of the Gram-positive broad host range plasmid pSM19035, has been functionally expressed in eukaryotic cell lines, demonstrating high avidity for the nuclear compartment and forming a clear speckled pattern when assayed by indirect immunofluorescence. In simian COS-1 cells, transient beta-recombinase expression promoted deletion of a DNA fragment lying between two directly oriented specific recognition/crossing over sequences (six sites) located as an extrachromosomal DNA substrate. The same result was obtained in a recombination-dependent lacZ activation system tested in a cell line that stably expresses the beta-recombinase protein. In stable NIH/3T3 clones bearing different number of copies of the target sequences integrated at distinct chromosomal locations, transient beta-recombinase expression also promoted deletion of the intervening DNA, independently of the insertion position of the target sequences. The utility of this new recombination tool for the manipulation of eukaryotic genomes, used either alone or in combination with the other recombination systems currently in use, is discussed.  (+info)

Genome reduction in a hemiclonal frog Rana esculenta from radioactively contaminated areas. (6/9340)

A decrease in genome size was found in the hemiclonal hybridogenetic frog Rana esculenta (R. ridibunda x R. lessonae) from areas of radioactive contamination that resulted from the Chernobyl fallout. This genome reduction was of up to 4% and correlated with the background level of gamma-radiation (linear regression corresponded on average to -0.4% per doubling of radiation level). No change in genome size was observed in the coexisting parental species R. lessonae. There was no correlation between genome size and body mass in R. esculenta froglets, which have metamorphosed in the year of the study. The hemiclonal forms may become a suitable object for study on biological significance of individual DNA sequences (and of genome size as a whole) because mutant animals with deletions in a specified genome can arise after a low radiation dose. The proneness to genetic damage makes such forms also a prospective bioindicator of radioactive (and possibly other mutagenic) pollution with the effects of genetic damage conveniently and rapidly monitored by DNA flow cytometry.  (+info)

Sequence analysis of cDNA and genomic DNA, and mRNA expression of the medaka fish homolog of mammalian guanylyl cyclase C. (7/9340)

We isolated the cDNA and genomic DNA encoding a membrane guanylyl cyclase of medaka fish (designated as OlGC6), and determined their complete nucleotide sequences. The open reading frame for OlGC6 cDNA predicted a protein of 1,075 amino acids. Phylogenetic analysis indicated that OlGC6 is a member of the enterotoxin/guanylin receptor family. We also determined the partial genomic structure of the gene of another membrane guanylyl cyclase of medaka fish, OlGC2, which is a member of the natriuretic peptide receptor family. The intron positions relative to the protein-coding sequence are highly conserved in the intracellular domains of OlGC6, OlGC2, mammalian GC-A, and GC-E. Despite their divergent primary structures, some intron positions also seem to be conserved in the extracellular domains of different membrane guanylyl cyclase genes. Northern blot analysis demonstrated that an OlGC6 transcript of 3.9 kb is only present in the intestine, while reverse transcription (RT)-PCR analysis demonstrated that the OlGC6 transcript is present in the kidney, spleen, liver, pancreas, gallbladder, ovary, testis, brain, and eye. RT-PCR also demonstrated that OlGC6 is only expressed zygotically and that transcripts are present from 1 day after fertilization, i.e. long before the intestinal tissues begin to develop.  (+info)

Cloning and characterization of RGS9-2: a striatal-enriched alternatively spliced product of the RGS9 gene. (8/9340)

Regulators of G-protein signaling (RGS) proteins act as GTPase-activating proteins (GAPs) for alpha subunits of heterotrimeric G-proteins. Previous in situ hybridization analysis of mRNAs encoding RGS3-RGS11 revealed region-specific expression patterns in rat brain. RGS9 showed a particularly striking pattern of almost exclusive enrichment in striatum. In a parallel study, RGS9 cDNA, here referred to as RGS9-1, was cloned from retinal cDNA libraries, and the encoded protein was identified as a GAP for transducin (Galphat) in rod outer segments. In the present study we identify a novel splice variant of RGS9, RGS9-2, cloned from a mouse forebrain cDNA library, which encodes a striatal-specific isoform of the protein. RGS9-2 is 191 amino acids longer than the retinal isoform, has a unique 3' untranslated region, and is highly enriched in striatum, with much lower levels seen in other brain regions and no expression detectable in retina. Immunohistochemistry showed that RGS9-2 protein is restricted to striatal neuropil and absent in striatal terminal fields. The functional activity of RGS9-2 is supported by the finding that it, but not RGS9-1, dampens the Gi/o-coupled mu-opioid receptor response in vitro. Characterization of a bacterial artificial chromosome genomic clone of approximately 200 kb indicates that these isoforms represent alternatively spliced mRNAs from a single gene and that the RGS domain, conserved among all known RGS members, is encoded over three distinct exons. The distinct C-terminal domains of RGS9-2 and RGS9-1 presumably contribute to unique regulatory properties in the neural and retinal cells in which these proteins are selectively expressed.  (+info)

Learn all about what the dog genome project is, how it got started and what it can show us. The successful mapping of the dog genome can help in curing both human and canine genetic disorders.
Genome evolution is the process by which a genome changes in structure (sequence) or size over time. The study of genome evolution involves multiple fields such as structural analysis of the genome, the study of genomic parasites, gene and ancient genome duplications, polyploidy, and comparative genomics. Genome evolution is a constantly changing and evolving field due to the steadily growing number of sequenced genomes, both prokaryotic and eukaryotic, available to the scientific community and the public at large. Since the first sequenced genomes became available in the late 1970s, scientists have been using comparative genomics to study the differences and similarities between various genomes. Genome sequencing has progressed over time to include more and more complex genomes including the eventual sequencing of the entire human genome in 2001. By comparing genomes of both close relatives and distant ancestors the stark differences and similarities between species began to emerge as well as ...
The Genome Assembly and Annotation Team carries out genome projects in the classical sense, from design of the de novo sequencing strategy, on through assembly and annotation of the genome.. The team specializes in large eukaryotic genomes and transcriptomes, especially those of animals and plants. Other types of genomes analyzed include those of organelles, endosymbionts, metagenomes and metatranscriptomes, and cancer genomes. Genome assembly is not only difficult due to the sheer size of the data and computational requirements, but also because the biology of genomes is confounded by repetitive elements, polyploidy and variation (single-nucleotide, insertions/deletions, and larger structural variants). The team focuses its efforts on meeting and overcoming these challenges, incorporating new technologies and developing new computational protocols as each project demands.. Annotation of the gene content of the newly assembled genome is key to understanding the genome, once finished. On this ...
The Genome Assembly and Annotation Team carries out genome projects in the classical sense, from design of the de novo sequencing strategy, on through assembly and annotation of the genome.. The team specializes in large eukaryotic genomes and transcriptomes, especially those of animals and plants. Other types of genomes analyzed include those of organelles, endosymbionts, metagenomes and metatranscriptomes, and cancer genomes. Genome assembly is not only difficult due to the sheer size of the data and computational requirements, but also because the biology of genomes is confounded by repetitive elements, polyploidy and variation (single-nucleotide, insertions/deletions, and larger structural variants). The team focuses its efforts on meeting and overcoming these challenges, incorporating new technologies and developing new computational protocols as each project demands.. Annotation of the gene content of the newly assembled genome is key to understanding the genome, once finished. On this ...
DescriptionDe novo Genome assembly and k-mer frequency counting are two of the classical prob- lems of Bioinformatics. k-mer counting helps to identify genomic k-mers from sequenced reads which may then inform read correction or genome assembly. Genome assembly has two major subproblems: contig construction and scaffolding. A contig is a continu- ous sub-sequence of the genome assembled from sequencing reads. Scaffolding attempts to construct a linear sequence of contigs (with possible gaps in between) using paired reads (two reads whose distance on the genome is approximately known). In this the- sis I will present a new computationally efficient tool for identifying frequent k-mers which are more likely to be genomic, and a set of linear inequalities which can improve scaffolding (which is known to be NP-hard) by identifying reliable paired reads. Identifying reliable k-mers from Whole Genome Amplification (WGA) data is more challenging compared to multi-cell data due to the coverage variation ...
SAN DIEGO, Oct. 13, 2016 (GLOBE NEWSWIRE) - BioNano Genomics, the leader in physical genome mapping, together with Howard Hughes Medical Institute (HHMI) Investigator and new Rockefeller University Professor, Erich Jarvis, Ph.D., today announced that his team will use BioNano Genomics Next Generation Mapping (NGM) combined with Pacific Biosciences sequencing technology to construct thousands of vertebrate reference genomes in the Vertebrate Genomes Project.. Dr. Jarviss lab and his collaborator Dr. Olivier Fredrigo, co-director of the Duke University Genome Sequencing Center, performed a systematic evaluation of available DNA sequencing and scaffolding technologies. They concluded that a combination of BioNanos NGM and PacBio sequencing will yield well-structured and informative genome assemblies, making the technologies a very good combination for establishing reference quality genomes.. Dr. Jarvis has purchased an Irys® System for next-generation mapping to play an integral role in ...
Below is a selection of genome projects that are using the Australian Apollo Service. Click on a link to find out more about the research group performing the organism genome annotation project and to access Apollo to view publicly available genome browsers. Publicly available genome browsers do not require a login. For non-public genomes, an account login is required which may be granted by getting in touch with the research group.. If you are an Australian-based researcher and have a genome annotation project you would like to showcase here, please email us the details at [email protected] ...
The Broad Institute has been sequencing a large number of vertebrate genomes with the goals of annotating the human genome, understanding vertebrate genome evolution and leveraging model organisms. These goals align well with some of the goals of the Genome 10K community. The analysis of 29 mammalian genomes has identified 3.6 million conserved elements, accounting for ~4.2% of the human genome. Sequence analysis and comparison with other datasets has allowed a candidate function to be assigned for up to 60% of these elements, including a rich annotation of hundreds of novel RNA structures and synonymous constraint elements within coding genes likely involved in gene regulation. We estimate that 150-200 mammals will be needed to develop a map of constraint at single-base resolution. The Broad has started on this quest by sequencing an additional 30 mammals selected in collaboration with the G10K community. Progress has been rapid; more than half of these genomes already sequenced using ~80x ...
A systematic study of genome context methods: calibration, normalization and combination - Background: Genome context methods have been introduced in the last decade as automatic methods to predict functional relatedness between genes in a target genome using the patterns of existence and relative locations of the homologs of those genes in a set of reference genomes. Much work has been done in the application of these methods to different bioinformatics tasks, but few papers present a systematic study of the methods and their combination necessary for their optimal use. Results: We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor. We find that for most organisms the gene neighbor method outperforms the phylogenetic profile method by as much as 40% in sensitivity, being competitive with the gene cluster method at low sensitivities. Gene fusion is generally the worst performing of the
Generation of wt genomes by excision of the BAC vector from the MCMV BAC genome.After transfection of the MCMV BAC plasmid into eukaryotic cells we expected homologous recombination via the duplicated sequences leading to excision of the vector sequences and generation of a wt genome (see Fig. 2 and Fig. 3A, maps 4 and 5). During construction of the original MCMV BAC plasmid pSM3 we had observed that overlength genomes are not stable in cells (22), suggesting that overlength genomes are poorly packaged into viral capsids. Similar observations have been made for other DNA viruses. An overlength of more than 5% over the adenovirus wt genome leads to unstable genomes (2), and Epstein-Barr virus preferentially packages genomes within a very narrow size range (3). Thus, we expected that even when rare recombination events occur at the created target site, preferential packaging of unit length genomes should lead to an accumulation of viruses with the wt genome.. For reconstitution of virus progeny ...
Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence
The mouse genome database (MGD, http://www.informatics.jax.org/), the international community database for mouse, provides access to extensive integrated data on the genetics, genomics and biology of the laboratory mouse. The mouse is an excellent and unique animal surrogate for studying normal development and disease processes in humans. Thus, MGDs primary goals are to facilitate the use of mouse models for studying human disease and enable the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Core MGD data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and genome coordinates, and comparative gene data focused on mammals. Data are integrated from diverse sources, ranging from major resource centers to individual investigator laboratories and the scientific literature, using a combination of automated processes and
In this exercise you will compare the genomes of two Escherichia coli strains, K12 DH10B and B REL606, using whole genome syntenic comparison and high-resolution analyses of specific genomic regions. These analyses will use CoGes tools [[SynMap]] and [[GEvo]] respectively, and will reveal evolutionary changes between these two genomes that happened after the divergence of their lineages. While the nucleotide sequence of these genomes is identical over large expanses of their genomes, many other types of large-scale genomic change will be discovered including phage insertions, transposon transposition, and genomic insertion, deletion, inversion, and duplication events. The computational tools used to do these analyses can be used for comparing genomes of any organisms. First, you are going to identify syntenic regions between these genomes. Syntenic is defined as two or more genomic regions that share a common ancestry and thus are derived from a common ancestor. To do this, you are going to ...
If you have a question about this talk, please contact .. Anthony Doran1, Thomas Keane1,2, and The Mouse Genomes Project consortium 1Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK 2EMBL-EBI, Wellcome Genome Campus, Hinxton, UK. The Mouse Genomes Project has completed the first draft assembled genome sequences and strain specific gene annotation for twelve classical laboratory and four wild-derived inbred mouse strains (WSB/EiJ, CAST /EiJ, PWK /PhJ, and SPRET /EiJ). These strains include all of the founders of the Collaborative Cross and Diversity Outbred Cross. We used a hybrid approach for genome annotation, combining evidence from the mouse reference Gencode annotation and strain-specific RNA -seq and PacBio cDNA, to identify novel strain-specific gene structures and alleles. Approx. 20,000 protein coding genes and 45,000 transcripts are annotated per strain. As these strains are fully inbred, we used heterozygous SNP density as a marker for highly polymorphic loci, and ...
Despite the recent massive progress in production of vertebrate genome sequence data and large-scale efforts to completely annotate the human genome, we still have scant knowledge of the principles that built genomes in evolution, of genome architecture and its functional organization. This work uses bioinformatics and zebrafish transgenesis to explain a mechanism for the maintenance of long-range conserved synteny across vertebrate genomes and to analyze the arrangement of underlying gene regulation systems. Large mammal-teleost conserved chromosomal segments contain highly conserved non-coding elements (HCNEs), their target genes, as well as phylogenetically and functionally unrelated bystander genes. Target genes are developmental and transcriptional regulatory genes with complex, temporally and spatially regulated expression patterns. Bystander genes are not specifically under the control of the regulatory elements that drive the target genes and are usually expressed in different, less ...
The project was announced on June 11 by MetaMorphix Inc. of Savage, Maryland. The company acquired preliminary (1x) coverage of the cow genome as well as a map of 600,000 cow single nucleotide polymorphisms (SNPs), when it purchased the animal genomics and genotyping business of Celera Genomics of Rockville, Maryland in March. Celera retains a minority business interest in MetaMorphix. Using the preliminary map of likely bovine SNPs, MetaMorphixs genomics division, MMI Genomics in Davis, California, is working with two cattle subsidiaries of the international agribusiness company Cargill to develop a physical map that covers the entire cow genome and also to locate genetic markers associated with cattle traits. Weve taken a different approach than the public projects that are looking into the bovine genome, says Sue Denise, the research and development director of MMI Genomics (formerly the AgGen division of Celera). With this initial sequencing on a substantial amount of the bovine genome, ...
The ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes from release to release, but these measures say nothing about changes to individual annotations, nor do they provide any means to identify annotations in need of manual review. In response, we have developed a suite of quantitative measures to better characterize changes to a genomes annotations between releases, and to prioritize problematic annotations for manual review. We have applied these measures to the annotations of five eukaryotic genomes over multiple releases - H. sapiens, M. musculus, D. melanogaster, A. gambiae, and C. elegans. Our results provide the first detailed, historical overview of how these genomes annotations have changed over the years, and demonstrate the usefulness of these measures for genome
Projects Research Projects GEL personnel and collaborators are currently engaged in a variety of research projects Here we focus on describing our research interests and many of the projects described span multiple funding sources The funding section of this site contains more information about the objectives and attribution for individual grants If you don t see what you are looking for here let us know paul genome wisc edu Genome Projects We are engaged in multiple projects aimed at increasing the number and diversity genome sequences from enterobacteria These include plant pathogenic enterobacteria which remain underrepresented among complete genomes available as well as neglected genera isolated from a wide variety of sources Software and Database Development We have built several tools to assist with annotation and comparative analysis of genome data These include Mauve a widely used multiple genome aligner and the ASAP database The Software section of this web site includes additional ...
I thought you might be interested in looking at dog genome.. http://www.bordercollie.org/boards/topic/8688-dog-genome/?do=findComment&comment=97997 ...
Over the last decade, and especially after the advent of fluorescent in situ hybridization imaging and Chromosome Conformation Capture methods, the availability of experimental data on genome three-dimensional (3D) organization has dramatically increased. We now have access to unprecedented details on how genomes organize within the interphase nucleus. Development of new computational approaches that leverage such data has already resulted in the first 3D structures of genomic domains and genomes. Such approaches expand our knowledge of the chromatin folding principles, which has been classically studied using polymer physics and molecular simulations. 3D Genomes proposes to continue developing computational approaches for integrating experimental data with polymer physics, thereby bridging the resolution gap for structural determination of genomes and genomic domains. Then, such methods will be applied to address outstanding questions in genome biology, which shall provide insight into the ...
Extensive effort is dedicated to genotyping human, plant and animal populations, to uncover genetic relationships and identify genes that regulate clinical and agricultural traits, among many other uses. With the dramatic increase in DNA sequencing throughput and reduction in cost, direct sequencing of reduced genome representations has emerged as an option for genotyping. Reduced genome representations have been typically generated by restriction enzyme digestion, adaptor ligation, and selective PCR amplification, followed by sequencing. However, in addition to requiring a series of sample-specific enzymatic steps, the approach is restricted by the existing enzymes, limiting the flexibility in marker coverage and density. Here an alternative approach is proposed, that uses a two-step PCR, intercalated by a normalization procedure. Briefly, the first PCR reaction begins with the amplification of regions in the genome with primers containing a specific sequence in the 3end, followed by ...
Abstract: The current status of the functional annotations associated with the human genome is in a rudimentary state. The majority of current genome annotations is heavily protein coding gene centric. This focus on protein coding genes intrinsically influences current perceptions of how the genome is structured and is regulated. This view of the genome also has an underlying supposition that transcripts with very little coding potential are not biologically important. However, recent unbiased experiments analyzing the sites of transcription across large sections of the human genome have led to the conclusion that the current human genome annotations can not account for the amounts of empirically detected transcription. (Kapranov, et al. 2002; Rinn, et al., 2003, Kampa, et al., 2004, Martone, et al., 2003, Cawley et al., 2004). Most of the detected unannotated transcription is composed of RNAs with very little coding capacity (,100 aa). These transcripts of unknown function (TUFs) share many ...
2017-02-16 15:06:47] Checking for Bowtie Bowtie version: 2.2.8.0 [2017-02-16 15:06:47] Checking for Bowtie index files (genome).. [2017-02-16 15:06:47] Checking for reference FASTA file [2017-02-16 15:06:47] Generating SAM header for genome [2017-02-16 15:06:47] Preparing reads left reads: min. length=75, max. length=75, 100 kept reads (0 discarded) right reads: min. length=75, max. length=75, 100 kept reads (0 discarded) [2017-02-16 15:06:47] Mapping left_kept_reads to genome genome with Bowtie2 [2017-02-16 15:06:47] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/3) [2017-02-16 15:06:47] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/3) [2017-02-16 15:06:47] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/3) [2017-02-16 15:06:47] Mapping right_kept_reads to genome genome with Bowtie2 [2017-02-16 15:06:47] Mapping right_kept_reads_seg1 to genome genome with Bowtie2 (1/3) [2017-02-16 15:06:48] Mapping right_kept_reads_seg2 to genome genome with Bowtie2 ...
We first determined whether genome build information is consistently supplied along with submissions to public repositories. As a representative example, we examined the records in the GEO and ENCODE databases with the following search criteria. In the GEO database, we examined all the records (one sample per series) that involved high-throughput sequencing submitted after 31 December 2008 for three species: Homo sapiens; Mus musculus; and Drosophila melanogaster. We then checked whether the data-processing section of metadata explicitly mentioned the genome build information, by case-insensitively searching for the following words: {hg17,hg18,hg19,hg38,grch36,grch37,grch38,build37.2,build37.1,build36.3,ncbi35,ncbi36,ncbi37,mm8,mm9,mm10,grcm38,bdgp6,bdgp5,bdgp5.25,build5.41,build5.3,build5,build4.1,dm6,dm3,ncbi}. In the ENCODE database, we examined the metadata file of all records.. Around 23.0% of the queried series records did not contain the genome build information explicitly in the ...
Links to domain combinations containing the Oncogene products superfamily in all genomes. Links for both groups of genomes, such as eukaryotes, bacteria and archaea, and individual genomes are provided.
Links to domain combinations containing the Hypothetical protein VC0424 superfamily in all genomes. Links for both groups of genomes, such as eukaryotes, bacteria and archaea, and individual genomes are provided.
Im looking to have a single FASTA sequence for each chromosome in an organism, but if I check the sequences in panTro5.fa (chimp) that Ive downloaded from UCSC I get a ton of ids like: chr10_NW_015973889v1_random, chr10_NW_015973890v1_random, etc.. What are these and how do I get rid of them? I dont have them in my hg38.fa (human) file because you can download all the chromosomes individually and then assemble them into one fasta, but I dont think you get that option with other genomes.. I need to use the genomes to find hits for viral LTR sequences and the number of hits is important so I dont want to get the same hit in the same region of the genome twice or more.. ...
Recovering the structure of ancestral genomes can be formalized in terms of properties of binary matrices such as the Consecutive-Ones Property (C1P). The Linearization Problem asks to extract, from a given binary matrix, a maximum weight subset of rows that satisfies such a property. This problem is in general intractable, and in particular if the ancestral genome is expected to contain only linear chromosomes or a unique circular chromosome. In the present work, we consider a relaxation of this problem, which allows ancestral genomes that can contain several chromosomes, each either linear or circular. We show that, when restricted to binary matrices of degree two, which correspond to adjacencies, the genomic characters used in most ancestral genome reconstruction methods, this relaxed version of the Linearization Problem is polynomially solvable using a reduction to a matching problem. This result holds in the more general case where columns have bounded multiplicity, which models possibly duplicated
1. Clicking on View Rat Genes Report (3 in RGD Search Result above) provides a list of gene records containing the search term (bold).. 2. The list is tabbed for each species and is exportable (see below).. 3. Descriptive information is presented in columns - the gene symbol links to the gene report page.. 4. Search results can be filtered by genome assembly or by chromosome, and it is sortable by any column heading. Additional searches for the specific data object and species can be performed from this page by entering a different or additional term in the Refine Term box and clicking Update. Search results for other objects such as QTLs and strains, are configured similarly.. ...
Background: Recovering the structure of ancestral genomes can be formalized in terms of properties of binary matrices such as the Consecutive-Ones Property (C1P). The Linearization Problem asks to extract, from a given binary matrix, a maximum weight subset of rows that satisfies such a property. This problem is in general intractable, and in particular if the ancestral genome is expected to contain only linear chromosomes or a unique circular chromosome. In the present work, we consider a relaxation of this problem, which allows ancestral genomes that can contain several chromosomes, each either linear or circular. Result: We show that, when restricted to binary matrices of degree two, which correspond to adjacencies, the genomic characters used in most ancestral genome reconstruction methods, this relaxed version of the Linearization Problem is polynomially solvable using a reduction to a matching problem. This result holds in the more general case where columns have bounded multiplicity, ...
In Genome Biology this week: sequencing breast cancer tumors from genetically engineered mouse models, micro realignments with SRMA, talk recaps from Beyond the Genome, and more.
View Notes - Lecture 2 from PLB 40175 at UC Davis. PLB 113 Lecture 2 II. Genome Organization and Gene Expression A. Plants have big (and small genomes) B. Genomes consist of single (LOW) copy and
The mouse inbred line C57BL/6J is widely used in mouse genetics and its genome has been incorporated into many genetic reference populations. More recently large initiatives such as the International Knockout Mouse Consortium (IKMC) are using the C57BL/6N mouse strain to generate null alleles for all mouse genes. Hence both strains are now widely used in mouse genetics studies. Here we perform a comprehensive genomic and phenotypic analysis of the two strains to identify differences that may influence their underlying genetic mechanisms. We undertake genome sequence comparisons of C57BL/6J and C57BL/6N to identify SNPs, indels and structural variants, with a focus on identifying all coding variants. We annotate 34 SNPs and 2 indels that distinguish C57BL/6J and C57BL/6N coding sequences, as well as 15 structural variants that overlap a gene. In parallel we assess the comparative phenotypes of the two inbred lines utilizing the EMPReSSslim phenotyping pipeline, a broad based assessment encompassing
The NIH is now accepting applications for the Somatic Cell Genome Editing (SCGE) program. The SCGE program aims to improve genome editing technologies to accelerate the translation of this technology into clinical applications and maximize the potential to treat as many diseases as possible. Pending the availability of funds and sufficient numbers of meritorious applications, the NIH expects to fund projects to provide better animal models for assessing genome editing in vivo, tools and assays to detect adverse consequences of genome editing in human cells, new technologies to deliver genome editing machinery into disease relevant cells and tissues in vivo, novel genome editing and engineering systems, and a Dissemination and Coordinating Center. Applications are due April 3, 2018. For additional information on these RFAs visit our Funding Opportunities page.. ...
Curated databases of completely sequenced genomes have been designed independently at the NCBI (RefSeq) and EBI (Genome Reviews) to cope with non-standard annotation found in the version of the sequenced genome that has been published by databanks GenBank/EMBL/DDBJ. These curation attempts were expected to review the annotations and to improve their pertinence when using them to annotate newly released genome sequences by homology to previously annotated genomes. However, we observed that such an uncoordinated effort has two unwanted consequences. First, it is not trivial to map the protein identifiers of the same sequence in both databases. Secondly, the two reannotated versions of the same genome differ at the level of their structural annotation. Here, we propose CorBank, a program devised to provide cross-referencing protein identifiers no matter what the level of identity is found between their matching sequences. Approximately 98% of the 1,983,258 amino acid sequences are matching, allowing
The Mouse the premier animal model for studying human disease the premier animal model for studying human disease > 95% same genes > 95% same genes same diseases, similar reasons (e.g., cancer, hypertension, diabetes, osteoporosis, …) same diseases, similar reasons (e.g., cancer, hypertension, diabetes, osteoporosis, …) 1000s lab strains, diff. characteristics 1000s lab strains, diff. characteristics precise genetic control precise genetic control
Nobody mentioned junk DNA and the resolution of the C-value paradox. Nobody mentioned the small number of genes in the human genome in spite of the fact that a great many articles begin with the claim that this was a shocking discovery [but see False History and the Number of Genes]. Jernej Ule mentioned alternative splicing but nobody else did in spite of the fact that many papers claim that most human genes are capable of making several different proteins. This is also a false claim, IMHO, but youd never know that from reading the journal. Peter Fraser was the only one who mentioned the vast regulatory network of enhancers as claimed by the ENCODE Consortium. If true, that would clearly count as a major discovery. (Its not true.) Eukaryotic genomes are chock full of defective transposons but none of the editors thought that was a key advance in our understanding of the genome ...
The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets.
Symbol: This is the official symbol assigned to this strain according to the strain nomenclature guidelines. This is a combination of strain and substrain designations for inbred strains (or symbol and ILAR code for other strain types).. Strain: The official strain symbol.. Substrain: The official substrain symbol - this can be a collection of ILAR lab codes defining the history of this particular strain. Can also be found in pulldown section below with links to the strain report pages.. Full Name: If the strain has a text name then it is displayed here; this is not visible if no name is associated to the strain, as in this example. Ontology ID: The identification number of the strain ontology term assigned by RGD, linked to the term in the ontology browser. In the strain ontology, rat strains are organized in a hierarchical fashion based on the type of strain and the way they were developed.. Also known as: Old symbols and synonyms that were used for the strain. If a strain is renamed to comply ...
by vulgavis , Jun 16, 2020 , Biology, Genome Biology, Mobile DNA, Nature Communications, Scientific Reports, TE Day, Technology, TEs, transposable elements, Transposons , 0 , ...
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The Department of Genetics and Genome Biology at the University of Leicester occupies a recently-refurbished, modern, purpose-built laboratory space, furnished with up-to-date equipment for the latest molecular genetic methods. We have an array of facilities both in-department and within the College of Life Sciences.
Comparative assembly using multiple genomes.The target genome is shown in the center, aligned to two related genomes, A and B. The DNA sequence of the target di
Highly fragmented reference genomes (with thousands or more short contigs or scaffolds) have been a persistent challenge for our small RNA-seq analysis program ShortStack. During a run, ShortStack needs to retrieve genomic sub-sequences for analysis of predicted RNA secondary structure. This is required to identify MIRNA hairpins. Early on I made the decision to use the samtools faidx function as the engine to retrieve genome sub-sequences. This was just pragmatic and lazy .. samtools was already required for other portions of ShortStacks analysis, and there wasnt a need to reinvent the wheel. However, when we started to do runs against highly fragmented genome assemblies, we found analysis was very slow. The slowness was traced to the samtools faidx function, which is very sensitive to the number of contigs/references.. The first attempt to fix this issue was in version 3.0, when I introduced the use genome-stitching. When the reference genome had more than 50 sequences, and some were , 1Mb ...
ENCODES a protein that exhibits transcription factor binding (ortholog); INVOLVED IN cell growth involved in cardiac muscle cell development (ortholog); cellular response to growth factor stimulus (ortholog); cellular response to hypoxia (ortholog); PARTICIPATES IN platelet-derived growth factor signaling pathway; ASSOCIATED WITH atrial fibrillation (ortholog); Cardiomegaly (ortholog); congenital megabladder (ortholog); FOUND IN nucleus (ortholog)
Two scientists claim to have pushed the boundaries of what can be learned about the ancestral history of the human race from one persons genome. Dr Richard Durbin and Dr Heng Li from the UKs Wellcome Trust Sanger Institute in Cambridge used information from the genomes of only seven people to show that humans living in Europe and China endured a severe population bottleneck between 10,000 and 60,000 years ago.. In the study published in Nature, the scientists used a new statistical technique to analyse differences between alleles within a genome. They found the more similar the alleles, the more recent the genetic separation was between parents - and by calculating the separation date, the researchers were able to estimate past population sizes. Each human genome contains information from the mother and the father, and the differences between these at any place in the genome carry information about its history, Dr Li said.. Scientists have traditionally performed this kind of analysis on ...
Institutions: The Jackson Laboratory. The release of the publicly accessible mouse genome sequence for the C57BL/6J strain of the laboratory mouse represents a landmark event in genome biology. The ability of researchers to use the mouse genome sequence effectively will depend, in large part, on how well the genes and other features identified in the sequence are integrated with the biological data sets available for the mouse that are available from the Mouse Genome Informatics (MGI) database. Model organism databases, such as MGI, have a unique role to play in connecting sequence and biology and in curating these connections for the long term.. The ways in which sequence data are stored and subsequently accessed from MGI are changing rapidly. Results of these significant enhancements to the capacity of the database will better enable the mouse genetics and genomics research communities to find biological meaning in the mouse genome sequence. I will present the status of our sequence-to-biology ...
Lasergene Genomics allows you to quickly and easily perform and edit de novo genome assemblies from any sequencing platform. Click here to find out more!
With an increasing amount of whole genome sequence data becoming available on a daily basis we have an opportunity to study the interactions and dynamics of different organisms on a whole genome level. In the past, reports of horizontal gene transfer have focused mainly on the identification of single genes that show distorted phylogenetic profiles to that of the organism it was isolated from. This study firstly did whole genome comparisons between the rice nuclear and plastid genomes to determine the level and dynamics gene transfer and insertion of the chloroplast ad mitochondrial genomes into that of the nuclear genome of rice. Secondly, it looked to identify sequence similarities between the rice genome and microbial genomes by performing whole genome comparisons between the rice genome and that of several microbial genomes. These sequences were analyzed further to identify possible instances of horizontal transfer of DNA from microbes to the rice genome. Using this approach, this study ...
The genomic sequences of many important Triticeae crop species are hard to assemble and analyse due to their large genome sizes, (in part) polyploid genomes and high repeat content. Recently, the draft genomes of barley and bread wheat were reported thanks to cost-efficient and fast NGS technologies. The genome of barley is estimated to be 5 Gb in size whereas the genome of bread wheat accounts for 17 Gb and harbours an allo-hexaploid genome. Direct assembly of the sequence reads and access to the gene content is hampered by the repeat content. As a consequence, novel strategies and data analysis concepts had to be developed to provide much-needed whole genome sequence surveys and access to the gene repertoires. Here we describe some analytical strategies that now enable structuring of massive NGS data generated and pave the way towards structured and ordered sequence data and gene order. Specifically we report on the GenomeZipper, a synteny driven approach to order and structure NGS survey sequences of
Genome Editing Genome Engineering Industry 2020 Global Market research report studies the latest Genome Editing Genome Engineering industry aspects market size, share, trends, Opportunities and Strategies To Boost Growth, business overview, revenue, demand, marketplace expanding, technological innovations, recent development, and Genome Editing Genome Engineering industry scenario during the forecast period (2020-2025).. The major players profiled in this report include: Thermo Fisher Scientific, Merck , Horizon Discovery , Genscript , Sangamo Therapeutics , Lonza , Editas Medicine , Crispr Therapeutics , Eurofins Scientific , Precision Biosciences. Download Premium Sample of the Report: brandessenceresearch.biz/Request/Sample?ResearchPostId=194333&RequestType=Sample. Global Genome Editing/Genome Engineering Market is valued approximately USD 4.4 billion in 2019 and is anticipated to grow with a healthy growth rate of more than 17.00 % over the forecast period 2020-2027. Genome Engineering ...
Background: Geminivirus (family Geminiviridae) is a prevalent plant virus that imperils agriculture globally, causing serious damage to the livelihood of farmers, particularly in developing countries. The virus evolves rapidly, attributing to its single-stranded genome propensity, resulting in worldwide circulation of diverse and viable genomes. Genomics is a prominent approach taken by researchers in elucidating the infectious mechanism of the virus. Currently, NCBI Viral Genome website is a popular repository of viral genomes that conveniently provides researchers a centralized data source of genomic information. However, unlike the genome of living organisms, viral genomes most often maintain peculiar characteristics that fit into no single genome architecture. By imposing a unified annotation scheme on the myriad of viral genomes may downplay their hallmark features. For example, virion of Begomovirus prevailing in America encapsulates two similar-sized circular genomes and both are required to
Genome amplification through duplication or proliferation of transposable elements has its counterpart in genome reduction, by elimination of DNA or by gene inactivation. Whether loss is primarily due to excision of random length DNA fragments or the inactivation of one gene at a time is controversial. Reduction after whole genome duplication (WGD) represents an inexorable collapse in gene complement. We compare fifteen genomes descending from six eukaryotic WGD events 20-450 Mya. We characterize the collapse over time through the distribution of runs of reduced paralog pairs in duplicated segments. Descendant genomes of the same WGD event behave as replicates. Choice of paralog pairs to be reduced is random except for some resistant regions of contiguous pairs. For those paralog pairs that are reduced, conserved copies tend to concentrate on one chromosome. Both the contiguous regions of reduction-resistant pairs and the concentration of runs of single copy genes on a single chromosome are evidence of
Multiple laboratories now offer clinical whole genome sequencing (WGS). We anticipate WGS becoming routinely used in research and clinical practice. Many institutions are exploring how best to educate geneticists and other professionals about WGS. Providing students in WGS courses with the option to analyze their own genome sequence is one strategy that might enhance students engagement and motivation to learn about personal genomics. However, if this option is presented to students, it is vital they make informed decisions, do not feel pressured into analyzing their own genomes by their course directors or peers, and feel free to analyze a third-party genome if they prefer. We therefore developed a 26-hour introductory genomics course in part to help students make informed decisions about whether to receive personal WGS data in a subsequent advanced genomics course. In the advanced course, they had the option to receive their own personal genome data, or an anonymous genome, at no financial cost to
There are several more eukaryotic genome sequences on the way: mouse, Fugu, zebrafish, rat, rice, dog and more, with further announcements of genome projects likely in the next few years as the genome centers start to look for new projects. Richard Mural (Celera Genomics Inc.) described the 5.5x whole-genome shotgun coverage of the mouse genome generated by Celera http://www.celera.com/. Using three strains of laboratory mouse (129X1/SvJ, A/J, and DBA/2), Celera have identified 2.7 million SNPs where sequence derived from separate strains overlaps and contains discrepancies. Mural also reported the amazingly high rate of SNPs found within strains, one in 10,000 nucleotides across the genome, although under cross-examination by Eric Lander (Whitehead Institute, Cambridge, USA), Mural admitted that many of these SNPs probably reflect sequencing errors.. As expected, Celera have been finding good correlation of synteny between the mouse and human genomes. An interesting general theme emerging from ...
New release of WormBase WS223, Wormpep223 and Wormrna223 Mon Jan 24 12:12:08 GMT 2011 WS223 was built by Paul Davis -===================================================================================- The WS223 build directory includes: genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data genomes/b_malayi: - genome_feature_tables/ sequences/ genomes/c_brenneri: - genome_feature_tables/ sequences/ genomes/c_briggsae: - genome_feature_tables/ sequences/ genomes/c_elegans: - annotation/ genome_feature_tables/ sequences/ genomes/c_japonica: - genome_feature_tables/ sequences/ genomes/c_remanei: - genome_feature_tables/ sequences/ genomes/h_bacteriophora: - genome_feature_tables/ sequences/ genomes/h_contortus: - genome_feature_tables/ sequences/ genomes/m_hapla: - genome_feature_tables/ sequences/ genomes/m_incognita: - sequences/ genomes/p_pacificus: - genome_feature_tables/ sequences/ *annotation/ - contains additional annotations i) confirmed_genes.WS223.gz ...
It turns out that sequencing individual genomes in a population reveals a rich tapestry of variation that is lost when analyzing the average of DNA pooled from larger cell numbers. Kun Zhang, Mike McConnell and Xuyu Cai (Christopher Walsh lab) have been applying single-cell genome sequencing to neuronal cells, finding that a subset of cells can often harbor mutations not seen elsewhere in the brain, creating a patchwork of genotypes. The Single Cell Analyses meeting took place at the same time as The Scripps Institutes Future of Genomic Medicine conference, which focuses on the field of personal genomes. The mosaicism revealed by single-cell genome sequencing serves as an important reminder that each person has not one personal genome, but many.. Perhaps the best known application of single-cell genome sequencing is the tracking of tumor evolution, where the power of single-cell analyses is leveraged against the known genomic instability, and hence within-individual variability, of cancer ...
On July 8th-9th 2016 scientists from around the world will convene in Edinburgh at Dynamic Earth to discuss the progress of the international synthetic yeast genome project as well as other advances in genome engineering including genome assembly methodologies, mammalian synthetic biology, lab automation and software development for synthetic biology (for more details, go to conference website: http://syngenomesconf.cailab.org).. For the past four years, the conference has focused on the ongoing Synthetic Yeast Genome Project (Sc2.0). As the worlds first synthetic, designer eukaryotic genome project, the Synthetic Yeast Genome Project has garnered global attention. The Sc2.0 international consortium is building 16 designer synthetic chromosomes encompassing ~12 million base pairs of DNA, and we are around halfway through this very exciting project.. The conference has been expanded to include a focus on Synthetic Genomes and Engineering Biology. This is a hot topic and we are thrilled to ...
Genome annotation is a tedious task that is mostly done by automated methods; however, the accuracy of these approaches has been questioned since the beginning of the sequencing era. Genome annotation is a multilevel process, and errors can emerge at different stages: during sequencing, as a result of gene-calling procedures, and in the process of assigning gene functions. Missed or wrongly annotated genes differentially impact different types of analyses. Here we discuss and demonstrate how the methods of comparative genome analysis can refine annotations by locating missing orthologues. We also discuss possible reasons for errors and show that the second-generation annotation systems, which combine multiple gene-calling programs with similarity-based methods, perform much better than the first annotation tools. Since old errors may propagate to the newly sequenced genomes, we emphasize that the problem of continuously updating popular public databases is an urgent and unresolved one. Due to the
To construct a new genome assembly we utilized all existing genomic data generated from Cinnamon, a female Abyssinian cat used for all prior genome assemblies (Pontius et al. 2007; Montague et al. 2014), with the exception of felCat4 (Mullikin et al. 2010), which also included reads from multiple breeds and a wild cat (Felis silvestris lybica). The data from prior maps included ∼2 × whole genome coverage of Sanger-based sequencing (6.7 million plasmid and 1.3 million 40 kb fosmid end reads; Pontius et al. 2007), ∼12 × whole genome coverage with 454 sequencing (6 × fragment and 6 × of 3 kb paired-end reads), and Sanger-based end-sequenced BACs (Amplicon Express Felis catus FSCC library) (Montague et al. 2014). Here, we generated ∼20 × coverage of nonoverlapping 100 bp paired-end reads from a single Illumina short-insert (avg. length = 350 bp) library, prepared from Cinnamons DNA, on the HiSeq2000 (SRA Accession numbers SRX478589 and SRX478590). The new Illumina reads were combined ...
Emerging data from the coelacanth genome are beginning to shed light on the origin and evolution of tetrapod genes and noncoding elements. Of particular relevance is the realization that coelacanth retains active copies of transposable elements that once served as raw material for the evolution of new functional sequences in the vertebrate lineage. Recognizing the evolutionary significance of coelacanth genome in this regard, we employed an ab initio search strategy to further classify its repetitive complement. This analysis uncovered a class of interspersed elements (Latimeria Harbinger 1-LatiHarb1) that is a major contributor to coelacanth genome structure and gene content (∼1% to 4% or the genome). Sequence analyses indicate that 1) each ∼8.7 kb LatiHarb1 element contains two coding regions, a transposase gene and a gene whose function is as yet unknown (MYB-like) and 2) copies of LatiHarb1 retain biological activity in the coelacanth genome. Functional analyses verify ...
During sequencing, its possible to specify the variety of base pairs that are read at a moment. Since mobile components are eliminated from eukaryotic genomes so slowly, theyve accumulated to the point at which they now constitute an important section of the genomes of many eukaryotes. buy essay online Theres no correlation between the range of genes and its complexity.. The HMM includes eight or nine homozygous genotype states, based on the amount of founders that contributed to every line. Other genomes are sequenced with the exact same intention of aiding conservation-guided techniques, for exampled the pufferfish genome. They are essential to genetic research.. The majority of these mutations are single nucleotide changes in noncoding parts of the genome and will most likely have minimum functional significance. https://pasadena.edu/campus-life/student-gov-clubs.php This method is apparently dominated by genetic drift caused by small population size, very low recombination prices, and ...
The genome of a female Hereford cow has been sequenced by the Bovine Genome Sequencing and Analysis Consortium, a team of researchers led by the National Institutes of Health and the U.S. Department of Agriculture.[1] It is one of the largest genomes ever sequenced. The results, published in the journal Science on April 24, 2009,[2] are likely to have a major impact on livestock breeding.[3] They were obtained by more than 300 scientists in 25 countries after six years of effort.. The size of the bovine genome is 3 Gb (3 billion base pairs). It contains approximately 22,000 genes of which 14,000 are common to all mammalian species. Bovines share 80 percent of their genes with humans; cows are less similar to humans than rodents (humans and rodents belong to the clade of Supraprimates). They also have about 1,000 genes shared with dogs and rodents but not identified in humans.[4]. The charting of key DNA differences, also known as haplotypes, between several varieties of cattle could allow ...
The grapevine is the fourth flowering plant whose genome sequence has been made public by a French-Italian public consortium that carried out the Whole Genome Shotgun 8X sequence of a quasi-homozygous genotype, PN40024. Recently the 12X version of the genome was completed. All data were generated by paired-end sequencing plasmid, fosmid and BAC libraries of different insert sizes, using Sanger technology. Using 11.91X coverage, an assembly of 499 Mb was obtained, composed of 2,888 super-contigs, 91% of which are anchored on linkage groups. The automatic annotation led to an estimate of 26,347 protein coding gene models. The grape genome was shaped by two ancient whole genome duplications that were not followed by extensive rearrangements, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This sequence allows now to set up powerful integrative approaches for the identification of key genes for important traits in grapevine, to have a ...
Where did this copy of AS originate from? It aligned well with the version of AS from P. aeruginosa and appeared to have a bacterial origin but was not found on the C. ruddii genome or the psyllid mitochondrial genome, both of which have been sequenced. Several lines of evidence ruled out the presence of a second bacterial endosymbiont in this symbiosis and since no plasmids had been reported during DNA sequencing of C. ruddii the source of this sequence appeared to be the nuclear genome of P. venusta itself. The presence of this bacterial sequence in the eukaryotic genome suggests that LGT may have taken place between a bacterial genome and the insect nuclear genome. This would be one explanation for the fact that C. ruddii has only 182 ORFs, which is significantly lower than the predicted minimal bacterial genome. However, it is also possible that C. ruddii uses mitochondrial proteins to survive and so LGT is not the only explanation for the low ORF count. ...
The UMD 3.1 assembly (NCBI assembly accesion GCA_000003055.3), released in December 2009, is the third release of the cow (Bos taurus) assembly from the Center for Bioinformatics and Computational Biology (CBCB) at University of Maryland. The genome sequences were generated using a combination of BAC-by-BAC hierarchical (~11 million reads) and whole-genome shotgun (~24 million reads) sequencing methods, assembled using the Celera Assembler version 5.2. The total length of the UMD3.1 assembly is 2.65Gb. The N50 size is the median sequence length, i.e. 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size for contigs in the UMD3.1 assembly is 103785. The genome assembly represented here corresponds to GenBank Assembly ID GCA_000003055.3. ...
This is the website for the Reed Labs Butterfly Genome Database at Cornell University.. This site provides a portal for searching and browsing high quality butterfly genome assemblies that are annotated with specialized data types including gene expression (e.g. RNA-seq), chromatin structure, and SNP variation. Data will be added on a rolling basis, and we encourage contributions from other research groups.. Blast: Search genome assemblies and gene predictions using Blast. Genome browser links are embedded in Blast result for your convenience.. Genome Browser: We use the UCSC genome browser as the most powerful current interface for manipulating and viewing complex data tracks. On this page you can go directly to any relevant coordinate in any genome we host.. Downloads: Download genome assemblies and accessory data tracks, as well as custom scripts from Reed Lab publications.. Citations: Publications to cite for specific data sets.. Please note that there are many additional lepidopteran ...
To whom it may concern: The completion of the sequencing of the entire DNA of the S. cerevisae genome, is a major event in the history of biology. All those involved are to be congratulated as we now have the first full genetic blueprint of a free living eukaryotic organism. The analysis of these gene products will provide us with a powerful tool for reading the genomes of other eukaryotes, particularly those of higher eukaryotes, which represent the majority of the data currently in the genetic databases. The analysis of the yeast genome is provided a useful framework for the annotation of many of the complete genome projects currently nearing completion, as well as the upcoming human genome. The yeast sequence information used to create this yeast webpage was provided by the GeneQuiz Consortium and the Mips Genome Commission . We have made an initial attempt to integrate these two data structures as well as supplement their annotation with that obtained ,From a set of functionally diagnostic ...
The genes within the genome (genetic code) of cattle need to be identified and defined before variability of these genes among cattle (individuals and breeds) can be identified. One goal is to determine whether such variations when found are associated with enhanced or decreased resistance to infectious diseases. The cattle genome has been largely sequenced (that is, the genetic code read), and now one of the purposes of the international community effort is to annotate the bovine genome (define genes within the genetic code).
Common plasmids are simple DNA molecules which contain a few genes and regulatory elements. Most viral genomes are more complex. For example, the genome of phage lambda contains approximately 50 genes. About 4,000 genes are present in the E. coli genome while there is approximately 1,000 times more DNA in the genome of a mammal. This progression in genome complexity is the topic of this exercise. Here, students compare the electrophoretic patterns of restriction digests of a plasmid, phage lambda DNA, and cow DNA from thymus and kidney as shown in the figure below. The exercise serves as a good introduction for determining the size of DNA molecules and provides an appreciation for the complexity of genomes from different organisms.. ...
Putting the Genome on the Map. The scale of the human genome is staggering. Our 80,000 genes account for only a small part of the delicate thread of three thousand million bases of sequence that we carry on our chromosomes. Encoded within this part of the sequence are the Instructions for making a complete set of proteins that drive all of the processes in our cells. We have almost no idea about what functions, if any, the rest of the sequence might have. Determining the sequence of the human genome - both that of the genes and that of the non-coding regions - is going to tell us much about our biology. However, there is also a lot that we will not be able to fathom from the sequence of the human genome alone. We need to broaden our horizons when thinking about the map of the human genome and the richness of information that we want it to contain. We need to understand how chromosome environment can perturb gene function every bit as effectively as mutation within gene sequence and how ...
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point
Links to domain combinations containing the Amb V allergen superfamily in all genomes. Links for both groups of genomes, such as eukaryotes, bacteria and archaea, and individual genomes are provided.
Health, ... Genome Research ( www.genome.org...Included in this special issue are novel biological insights gained fr...1. Whole-genome and whole-exome sequencing: Searching for the drivers...Cancer is believed to arise through the accumulation of genetic and ep...,Genome,Research,publishes,special,issue:,Cancer,Genomics,medicine,medical news today,latest medical news,medical newsletters,current medical news,latest medicine news
An approximation to the ~4-Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ~90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single bp mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome-pairs have one or two recombinant transfers of length ~40-115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. ...
Thanks to their ability to move around and replicate within genomes, transposable elements (TEs) are perhaps the most important contributors to genome plasticity and evolution. Their detection and annotation are considered essential in any genome sequencing project. The number of fully sequenced genomes is rapidly increasing with improvements in high-throughput sequencing technologies. A fully automated de novo annotation process for TEs is therefore required to cope with the deluge of sequence data. However, all automated procedures are error-prone, and an automated procedure for TE identification and classification would be no exception. It is therefore crucial to provide not only the TE reference sequences, but also evidence justifying their classification, at the scale of the whole genome. A few TE databases already exist, but none provides evidence to justify TE classification. Moreover, biological information about the sequences remains globally poor. We present here the RepetDB database developed
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The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease. This understanding is fundamental for advancing genome biology research and for translating human genome data into clinical utility.
If LUA had a simple genome (like a simple bacterium) and genetic complexity and all the additional information accumulated over the course of evolution, we should be able to trace this accumulation by examining the genomes of different organisms on different levels of complexity. This is a reasonable expectation. (If we wouldnt know about the c-value paradox or about the recent results of actual DNA sequences, one should reasonably expect to see this accumulation, given the Darwinian framework. ) A compelling starting point could be the genome of a sponge. This creature is one of the most simple multicellular organisms. However, the content of the genome of Amphimedon queenslandica - a marine sponge - literally shocked the scientific community.4 This simple creature has a remarkably complex genome with more individual genes than an average bird, but the most stunning part is that they posses genes that shouldnt be in their genome. Sponges dont have a nervous system, yet they have many of the ...
If LUA had a simple genome (like a simple bacterium) and genetic complexity and all the additional information accumulated over the course of evolution, we should be able to trace this accumulation by examining the genomes of different organisms on different levels of complexity. This is a reasonable expectation. (If we wouldnt know about the c-value paradox or about the recent results of actual DNA sequences, one should reasonably expect to see this accumulation, given the Darwinian framework. ) A compelling starting point could be the genome of a sponge. This creature is one of the most simple multicellular organisms. However, the content of the genome of Amphimedon queenslandica - a marine sponge - literally shocked the scientific community.4 This simple creature has a remarkably complex genome with more individual genes than an average bird, but the most stunning part is that they posses genes that shouldnt be in their genome. Sponges dont have a nervous system, yet they have many of the ...
Models were annotated by projecting transcripts annotated by Ensembl from a reference genome, through a BLASTZ DNA alignment of this genome to a reference genome ...
Models were annotated by projecting transcripts annotated by Ensembl from a reference genome, through a BLASTZ DNA alignment of this genome to a reference genome ...
One of most striking discoveries to arise from comparative genomic studies of the human genome is that the majority of functional sequences that have been under purifying selection during mammalian evolution do not encode proteins (1). Specifically, comparative genomics of the human, dog, mouse, and rat (HDMR) has revealed that ≈5-6% of the human genome is under purifying selection, but only 1-2% of this sequence is attributable to protein-coding sequences. The remainder consists of conserved noncoding elements (CNEs). Intense interest has focused on trying to decipher the function of these CNEs, which are likely to control gene regulation, chromosome structure, and other key functions.. Deciphering the function of the CNEs is particularly challenging because the vast majority seem to be unique in the genome; so far, no large families of similar CNEs have been discovered. For example, a study of the mammalian CNEs within a 1.8 Mb region containing the cystic fibrosis gene (CFTR) found the vast ...
A new type of DNA sequencing technology has been developed and used to identify and characterize key regions of the genome called enhancer sequences.1 These are novel DNA features that were once thought to be a part of the so-called junk DNA regions of the genome. These key elements are now proven to be part of the indispensable and irreducibly complex design inherent to proper gene function for all types and categories of genes.. The new technology described in this report is called STARR-seq, or self-transcribing active regulatory region sequencing. This new technique allows for the more effective identification and characterization of enhancer sequences, which help recruit proteins called transcription factors that regulate gene activity. Enhancers are found in the non-protein coding regions of the genome both within and surrounding genes. In the past, enhancers have been difficult to characterize accurately.. This new study adds yet another layer of deduced complexity in the ...
A new type of DNA sequencing technology has been developed and used to identify and characterize key regions of the genome called enhancer sequences.1 These are novel DNA features that were once thought to be a part of the so-called junk DNA regions of the genome. These key elements are now proven to be part of the indispensable and irreducibly complex design inherent to proper gene function for all types and categories of genes.. The new technology described in this report is called STARR-seq, or self-transcribing active regulatory region sequencing. This new technique allows for the more effective identification and characterization of enhancer sequences, which help recruit proteins called transcription factors that regulate gene activity. Enhancers are found in the non-protein coding regions of the genome both within and surrounding genes. In the past, enhancers have been difficult to characterize accurately.. This new study adds yet another layer of deduced complexity in the ...
Genome[edit]. The genome of MAP strain K-10 was sequenced in 2005 and found to consist of a single circular chromosome of ... "The complete genome sequence of Mycobacterium avium subspecies paratuberculosis". Proc Natl Acad Sci USA. 102 (35): 12344-9. ...
... genome data[edit]. *GeneDB Plasmodium knowlesi. References[edit]. *^ Perkins, Susan L.; Jos. J. Schall ( ...
Genome[edit]. The nuclear,[50] mitochondrial[51][52] and chloroplast[53] genomes of British Columbia interior spruce have been ... genome from whole-genome shotgun sequencing data". Bioinformatics. 29 (12): 1492-1497. doi:10.1093/bioinformatics/btt178. PMC ... "Genome Biology and Evolution. 8 (1): 29-41. doi:10.1093/gbe/evv244. PMC 4758241. PMID 26645680.. CS1 maint: multiple names: ... "Picea glauca, whole genome shotgun sequencing project". 13 March 2015.. Cite journal requires ,journal=. (help). ...
Genome[edit]. Hepadnaviruses have very small genomes of partially double-stranded, partially single stranded circular DNA. The ... Endogenous hepatitis B virus genomes have been described in crocodilian, snake and turtle genomes.[7] This suggests that these ... Genomes are circular, around 3.2kb in length. The genome codes for 7 proteins.[1] ... by the viral polymerase to form a complete circular dsDNA genome (called covalently-closed-circular DNA or cccDNA). The genome ...
Single-cell genome (DNA) sequencing[edit]. Single-cell DNA genome sequencing involves isolating a single cell, amplifying the ... Comparing MDA and MALBAC, MDA results in better genome coverage, but MALBAC provides more even coverage across the genome. MDA ... To obtain the methylome readout, the bisulfite-treated sequence is aligned to an unmodified genome. Whole genome bisulfite ... MDA of individual cell genomes results in highly uneven genome coverage, i.e. relative overrepresentation and ...
Genome. The sequencing in 2010 of the genome of the cacao tree may allow yields to be improved.[49] Due to concerns about ... "Chocolate industry avoids collapse as genome published". BBC. 14 November 2010. Archived from the original on 15 November 2010 ...
Genome[edit]. Although two strains of D. lykanthroporepellens have been isolated and characterized, only the type strain BL-DC- ... of the genome of D. lykanthroporepellens is made up of insertion sequence elements, which encode for 74 full or truncated ... The genome was sequenced using both Illumina and 454 sequencing platforms, more specifically an Illumina shotgun library, a 454 ... 9T has had the genome sequenced. Therefore, when referring to D. lykanthroporepellens in this section, all information is only ...
Robertson, John A. (August 2003). "The $1000 Genome: Ethical and Legal Issues in Whole Genome Sequencing of Individuals". The ... "DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP)". National Human Genome Research Institute. Retrieved ... High-throughput (formerly "next-generation") sequencing applies to genome sequencing, genome resequencing, transcriptome ... or genomes of numerous types and species of life, including the human genome and other complete DNA sequences of many animal, ...
Genome[edit]. The full genome of the silkworm was published in 2008 by the International Silkworm Genome Consortium.[10] Draft ... The International Silkworm Genome Consortium (2008). "The genome of a lepidopteran model insect, the silkworm Bombyx mori". ... The genome of the silkworm is mid-range with a genome size around 432 megabase pairs. ... 2004). "The genome sequence of silkworm, Bombyx mori". DNA Research. 11 (1): 27-35. doi:10.1093/dnares/11.1.27. PMID 15141943. ...
Complete genome sequence[edit]. The complete genome of the HeLa cells was sequenced and published on 11 March 2013[39][42] ... "G3: Genes, Genomes, Genetics. 3 (8): 1213-24. doi:10.1534/g3.113.005777. PMC 3737162. PMID 23550136.. ... The HeLa genome has been remarkably stable after years of continuous cultivation; therefore, the genetic alterations detected ... Horizontal gene transfer from human papillomavirus 18 (HPV18) to human cervical cells created the HeLa genome, which is ...
Genome[edit]. Three variants/strains of S. lacrymans have been sequenced by the Joint Genome Institute (JGI) and its ... One genome is from Serpula lacrymans S7.9 (v2.0). The genome assembly is 42.73 Mbp, with a predicted number of 12789 genes. The ... The third genome is from Serpula lacrymans var shastensis SHA21-2 (v1.0). The genome assembly is 45.98 Mbp, with a predicted ... S. lacrymans' genome encodes six annotated polyketide synthases (PKS1-PKS6), 15 nonribosomal peptide synthetases (NPS1-NPS4, ...
... genome sequencing.[7] Their model was also used in designing the Human Genome Project and continues to play an important role ... Post Human Genome Project advancements[edit]. The physical processes and protocols of DNA sequencing have continued to evolve, ... "Genome Research. 10 (7): 1020-1030. doi:10.1101/gr.10.7.1020. PMC 310895. PMID 10899151.. ... 1995). "Whole-genome random sequencing and assembly of haemophilus influenzae Rd". Science. 269 (5223): 496-512. Bibcode: ...
Genome[edit]. The Megavirus chilensis genome is a linear, double-stranded molecule of DNA with 1,259,197 base pairs in length. ... Table1: Largest giant viruses with complete sequenced genomes[edit]. Giant virus name. Genome Length. Genes. Capsid diameter. ... The apparent conclusion is that the genome of these giant viruses originated from an ancestral cellular genome (thus endowed of ... "Genome Biology and Evolution. 3: 737-42. doi:10.1093/gbe/evr048. PMC 3163472. PMID 21705471.. ...
"Lassa virus RefSeq Genome".. *^ Cornu, T. I.; De La Torre, J. C. (2001). "RING Finger Z Protein of Lymphocytic Choriomeningitis ... Structure and genome[edit]. Lassa viruses[12][13] are enveloped, single-stranded, bisegmented, ambisense RNA viruses. Their ... The positive- or plus-sense genome, then makes viral complementary RNA (vcRNA) copies of itself. The RNA copies are a template ... Nucleotide studies of the genome have shown that Lassa has four lineages: three found in Nigeria and the fourth in Guinea, ...
Genome[edit]. The small genome (15 Mb) was recently sequenced [1] and many of the genes are related to plants, though there is ... "Genome Biology. 13: R74. doi:10.1186/gb-2012-13-8-r74. PMC 3491373 . PMID 22925495.. ... "Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green ...
Genome renewal[edit]. The yeast Saccharomyces cerevisiae and Saccharomyces paradoxus have a life cycle that alternates between ... Purging can reduce the average frequency of deleterious alleles across the genome below the value expected in a non-inbred ... Mortimer, Robert K.; Romano, Patrizia; Suzzi, Giovanna; Polsinelli, Mario (December 1994). "Genome renewal: A new phenomenon ...
Genome[edit]. The genome of the black truffle was published in 2010.[10] It contains 125 million base pairs, 58% of the genome ... Francis Martin u. a. (2010), "Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis", Nature ... consists of transposable elements, and the genome contains only 7500 identified protein-encoding genes. During symbiosis, genes ...
... has a positive sense single-stranded RNA genome. The genome consists of a single open reading frame that is ... The negative strand RNA then serves as a template for the production of new positive strand viral genomes. Nascent genomes can ... Kato N (2000). "Genome of human hepatitis C virus (HCV): gene organization, sequence diversity, and variation". Microb. Comp. ... HCV takes over portions of the intracellular machinery to replicate.[31] The HCV genome is translated to produce a single ...
The total genome size of O. volvulus is 1.5x108 BP and contains around 4,000 genes, with genes for collagen and cuticular ... Unnasch, Thomas R; Williams, S.A. (2000). "The genomes of Onchocerca volvulus". International Journal for Parasitology. 30 (4 ...
Organellar genomes[edit]. Plastomes and mitogenomes[edit]. The human mitochondrial genome has retained genes encoding 2 rRNAs, ... Genome comparisons suggest a close relationship between plastids and cyanobacteria.[61]. *Many genes in the genomes of ... genome encoding thousands of proteins.[22] Plastids and mitochondria exhibit a dramatic reduction in genome size when compared ... that have lost their entire organellar genome,[46] non-photosynthetic plastids tend to retain a small genome.[26] There are two ...
"Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison". Genome Research. ... View the dm6 genome assembly in the UCSC Genome Browser.. *Manchester Fly Facility - for the public from the University of ... A March 2000 study by National Human Genome Research Institute comparing the fruit fly and human genome estimated that about 60 ... "G3: Genes,Genomes,Genetics. 6 (10): 3185-3196. doi:10.1534/g3.116.032508. ISSN 2160-1836. PMC 5068940. PMID 27558665.. ...
Polyploidy brings new genomes into a species. For example, Aegilops tauschii brought the D genome into hexaploid wheats, with ... Feldman, M.; Levy, A.A. (2005). "Allopolyploidy - a shaping force in the evolution of wheat genomes". Cytogenetic and Genome ... Genome(s). Genetic (GRIN Taxonomy for Plants [2]). Traditional (Dorofeev et al. 1979 [3]) ... Genome[edit]. Observation of chromosome behaviour during meiosis, and the results of hybridisation experiments, have shown that ...
Genome[edit]. The monarch was the first butterfly to have its genome sequenced.[10]:(p12) The 273-million base pair draft ... A 2015 paper identified genes from wasp bracoviruses in the genome of the North American monarch[21] leading to articles about ... Stensmyr MC, Hansson BS; Hansson (November 2011). "A Genome Befitting a Monarch". Cell. 147 (5): 970-2. doi:10.1016/j.cell. ... The genome provides researchers insights into migratory behavior, the circadian clock, juvenile hormone pathways and microRNAs ...
Nuclear genome[edit]. The small size of its genome, and the fact that it is diploid, makes Arabidopsis thaliana useful for ... The Arabidopsis Genome Initiative (December 2000). "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana ... What Makes Plants Grow? The Arabidopsis genome knows Featured article in Genome News Network ... showing a genome size of approximately 61 Mbp.[35] It was the first plant genome to be sequenced, completed in 2000 by the ...
Genome sequencing[edit]. Sequencing of the chickpea genome has been completed for 90 chickpea genotypes, including several wild ... "Global research team decodes genome sequence of 90 chickpea lines". International Crops Research Institute for the Semi-Arid ... "Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement". Nature Biotechnology. 31 (3): ...
Organellar genomes[edit]. Plastomes and mitogenomes[edit]. The human mitochondrial genome has retained genes encoding 2 rRNAs, ... Genome comparisons suggest a close relationship between plastids and cyanobacteria.[61]. *Many genes in the genomes of ... genome encoding thousands of proteins.[21] Plastids and mitochondria exhibit a dramatic reduction in genome size when compared ... "Genome Biol Evol. 5 (1): 31-44. doi:10.1093/gbe/evs117. PMC 3595030. PMID 23221676.. CS1 maint: Uses authors parameter (link). ...
The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged ... The reasons for the presence of so much noncoding DNA in eukaryotic genomes and the extraordinary differences in genome size, ... Data sets representing entire genomes' worth of DNA sequences, such as those produced by the Human Genome Project, are ... "Genome Biology. 2 (1): REVIEWS3002. doi:10.1186/gb-2001-2-1-reviews3002. PMC 150442. PMID 11178285.. ...
Genome size variation[edit]. Attempts to understand the extraordinary variation in genome size (C-value)-animals vary 7,000 ... Trivers R, Burt A, Palestis BG (February 2004). "B chromosomes and genome size in flowering plants". Genome. 47 (1): 1-8. doi: ... The effect of TEs in the genome is not entirely selfish. Because their insertion into the genome can disrupt gene function, ... TEs that tend to avoid disrupting vital functions in the genome tend to remain in the genome longer, and hence they are more ...
Locations within the genome[edit]. The 3' untranslated region of mRNA labeled 3' UTR. Normally about 700 nucleotides in human ... Brown, TA (2002). Genomes. Oxford: Wiley-Liss.. *^ Schoenherr, CJ; Anderson DJ (3 March 1995). "The neuron-restrictive silencer ... Not much is yet known about silencers but scientists continue to study in hopes to classify more types, locations in the genome ... Eukaryotes have a much larger genome and thus have different methods of gene regulation than in prokaryotes. All cells in a ...
The frequency of gene targeting can be greatly enhanced through genome editing. Genome editing uses artificially engineered ... "Nation Human Genome Research Institute. 2009.. *^ "GM pigs best bet for organ transplant". Medical News Today. 21 September ... Synthetic genome brings new life to bacterium". Science. 328 (5981): 958-9. doi:10.1126/science.328.5981.958. PMID 20488994.. ... Watson JD (2007). Recombinant DNA: Genes and Genomes: A Short Course. San Francisco: W.H. Freeman. ISBN 978-0-7167-2866-5. .. ...
TADs are portion of the DNA molecule that divides the entire genome of an organism into manageable chunks, like districts in a ... Genome Biology 18:149, 7 August 2017. DOI: 10.1186/s13059-017-1278-z ...
Genome position refers to the reference maize chloroplast genome (51). The map was created with OGDraw (52). (B) Ribosome ... roughly half of the subunits of these complexes are encoded by the plastid genome and half by the nuclear genome (3, 4). This ... 2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218- ... Most chloroplast genomes encode one or two proteins that integrate into the inner envelope (CemA and Ycf1). How these proteins ...
... observations and analysis about research on the human genome, including a searchable online database of genome variants. ... Human Genome Variation is an open-access, online-only peer-reviewed journal publishing important discoveries, ... Human Genome Variation is delighted to present its first Collection for the March 2019 issue. Coordinated by the Editor-in- ... Human Genome Variation is delighted to present its first Collection for the March 2019 issue. ...
The genome of a female Hereford cow has been sequenced by the Bovine Genome Sequencing and Analysis Consortium, a team of ... Elsik, C.G. # (2009). Bovine Genome Sequencing and Analysis Consortium. "The genome sequence of taurine cattle: a window to ... "Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds". Science. 324 (5926): 528-532. doi:10.1126 ... "Cow genome unraveled in bid to improve meat, milk". Associated Press. 2009-04-23. Retrieved 2009-04-23.. ...
Genome: The Autobiography of a Species in 23 Chapters Genome: The Autobiography of a Species in 23 Chapters ... Lee M. Silver, reviewing Genome in The New York Times, argues that the books theme is that each individuals genome contains " ... Ridley concludes that the Human Genome Project is largely based on the inaccurate belief that there is one single human genome ... Genome was shortlisted for the Samuel Johnson Prize in 2000.[9] References[edit]. *^ a b Kealey, Terence (2000). "Book Review ...
... Precise and easy ways to rewrite human genes could finally provide the tools that researchers need to understand ... Though genome editing with CRISPR is just a little over a year old, it is already reinventing genetic research. In particular, ... Genome GPS. The biotechnology industry was born in 1973, when Herbert Boyer and Stanley Cohen inserted foreign DNA that they ... With the new genome-editing tools, says Church, rewriting the defective DNA may be possible: "You arent limited to adding back ...
The Alzheimers Genome Project, supported by Cure Alzheimers Fund, aims to identify all genes linked to the disease. Learn ... The Alzheimers Genome Project, supported by Cure Alzheimers Fund, aims to identify all genes linked to the disease. Learn ... Breakthrough Research: The Alzheimers Genome Project - Duration: 4:13. Cure Alzheimers Fund 770 views ... Francis Collins: Building on the human genome sequence - Duration: 1:26. yourgenome 549 views ...
JAPAN is planning a long-term international project to map the rice plants genome. If approved, the project will begin in 1991 ... Rice genome. JAPAN is planning a long-term international project to map the rice. plants genome. If approved, the project will ... pairs which make up the genome. The Rice Genome Council, drawn from universities and national research. institutes, will meet ...
This morning I had a banana genome, an orange genome, two chicken genomes (haploid, of course), and some fried pig genome, on ... Of course, microbes have genomes, too. But I do my best to cook those first. So, what is a genome? Is it a chromosome? Is it ... Later today, I will consume genomes from different kinds of green plants and perhaps even a cow or fish genome. I probably ... This is especially amusing because the human genome isnt quite done. Were primates, too! Why not finish our genome? [I blame ...
Genome A genome is the complete collection of hereditary information for an individual organism. In cellular life forms, the ... Genome Chemistry: Foundations and Applications COPYRIGHT 2004 The Gale Group, Inc.. Genome. An organisms genome is the ... Genome. The genome is the full set of genes or genetic material carried by a particular organism. The size of a genome is ... Genome Genetics Copyright Genetics Society of America. Genome. A genome is the complete collection of hereditary information ...
The horse genome project was a result of the human genome project. We already knew that the size and organization of the genome ... ABOUT THE HORSE GENOME PROJECT The human genome project changed biology forever. A plan was made to sequence the entire human ... HORSE GENOME SEQUENCE COMPLETE. The first draft of the horse genome sequence was recently completed and deposited.... [JAVMA ... HORSE GENOME SEQUENCED. The first genome map of a horse is complete, providing scientists with new tools for investigating ...
The deal has caused Human Genome Project researchers to seek an alternative home for their map. By Kristen Philipkoski. ... A strand of controversy has emerged over Celeras publication arrangement with the journal for the companys human genome map. ... Nature Snatches Genome Map?. Rumors of where the Human Genome Projects groundbreaking research paper will wind up are flying ... In June, the rival genome mapping teams surprised the scientific community by ending an ongoing race to finish the maps, and ...
Federal health officials yesterday launched the biggest genetic research endeavor since the landmark human genome project: an ... The Cancer Genome Atlas is the outgrowth of a year and a half of planning by NIH advisory groups. It would build on the ... The Cancer Genome Atlas, whose total cost could reach $1 billion or more, will for the first time direct the full force of ... Federal health officials yesterday launched the biggest genetic research endeavor since the landmark human genome project: an ...
Researchers play matchmaker with the Human Genome Project data and proteins. By Andy Patrizio. ... The Human Genome Project has mapped the entire human genome, but not the proteins encoded by our genes. Only one-third of the ... Whereas [email protected] is designed to learn how genomes fold into proteins, Genome@Home was launched this week to try and reverse ... then its very likely that the relationship between genome and protein has been found. For example, if an unclassified genome ...
Genome representation: full. GenBank assembly accession: GCA_001400495.1 (latest). RefSeq assembly accession: GCF_001400495.1 ( ...
How does one sequence a genome? As scientists advance in the development of the technology, the process of sequencing a genome ... Whole genome sequencing gives us the ability to detect certain variants of disease. Ideally, with this knowledge, people can ... First, it might help to understand the basics of genome sequencing in general. Every cell in the human body contains a complete ... Genome Mapping By Meg Marinis, Director of Medical Research , Feb 14th, 2013 ...
genome browsers. Genetic Future. Category archives for genome browsers. Next-generation genome browsers. Posted by Daniel ... Jan Aerts discusses the problem of incorporating information on large-scale genomic rearrangements into genome browsers. Genome ... Why you CAN have your $1000 genome - so long as you learn what to do with it. As part of his Gene Week celebration over at ...
... * 1. Workplace Genome * 2. Workplace culture is increasingly important - for c-suites, leadership ... Mapping your Workplace Genome is a good start. But there is no ROI without action. The Workplace Genome Activation Program ... The core of our work starts here... with the Workplace Genome. Find out how to get yours at workxo.com. ... 4. HOW WE SOLVE IT… WorkXO is a Culture Management Firm that uses our groundbreaking model - the Workplace Genome™ - to measure ...
Scholarships for Genome Sciences/Genomics Majors Bullet name award deadline Link • Emmy Noether Award Joe W. and Dorothy ... Matching Genome Sciences/Genomics Colleges Manchester University Four or more years; Private not for profit; $30,450 average ...
The mission of the Cultural Genome Project is to celebrate and commemorate multi-generations of American histories through the ... Through the Cultural Genome Project, we will preserve historical facts but also celebrate the tradition of story-telling and ... The mission of the Cultural Genome Project is to celebrate and commemorate multi-generations of American histories through the ... The mission of the Cultural Genome Project is to celebrate and commemorate multi-generations of American histories through the ...
Genome representation: full. GenBank assembly accession: GCA_001400345.1 (latest). RefSeq assembly accession: GCF_001400345.1 ( ...
Their goal is to figure out the order of all DNA letters (bases) in our genome. ... Many scientists have joined forces on the Human Genome Project. ... in our genome. Since the human genome is more than 3 billion ... To understand how our genome works, scientists compare it to the genomes of mice, flies, worms, and even bacteria. ... Scientists with the Human Genome Project (HGP) study only the human genome. ...
Inside Chinas Genome Factory Sequencing a complete human genome may soon cost less than an iPhone. Will BGI-Shenzhen decode ... Thousands of Genomes. In its scientific work, BGI often acts as the enabler of other peoples ideas. That is the case in a ... Thanks to a series of clever innovations, the cost to read out the DNA in a persons genome has since fallen to just a few ... He says it will pay BGI a fee for each genome it sequences, and will offer the service to parents of young patients with ...
The journal Genome Biology is published by BioMedCentral, and offers free access to primary research articles and a preprint ...
Genome projects typically involve three main phases: DNA sequencing, assembly of DNA to represent original chromosome, and ... Create a reference genome for successive analyses. The development of suitable tools to assist in the genome analysis process ... Connect the main elements of the genome with biological information. It is important to consider how the genome is similar to ... Additionally, the plasmids, phages and resistance genes of the genome can reveal information about the nature of the genome. ...
Aloni, R. and Lancet, D. Conservation anchors in the vertebrate genome. Genome Biol. 6(7):115 (2005).. • Grossman, I., Avidan, ... Genome. Disease Genomics. We have studied the genetics of hereditary diseases for the last 15 years. Currently we apply ... Lander, E. et al., International Human Genome Sequencing Consortium, including Lancet, D. Initial sequencing and analysis of ... the human genome. Nature, 409:860-921 (2001).. • Bargal, R., Avidan, N., Ben-Asher, E., Olender, Z., Zeigler, M., Frumkin, A., ...
Plant genome editing with TALEN and CRISPR Genome editing promises giant leaps forward in advancing biotechnology, agriculture ... Targeted genome engineering in Caenorhabditis elegans The generation of mutants and transgenes are indispensible for biomedical ... In the nematode Caenorhabditis elegans, a series of methods have been developed to introduce genome modifications, including ...
... have specific morphology and contain a relatively complex retroviral genome. Vectors derived from lentiviruses can be used for ... The genome is organized from the 5′ to the 3′ end, and major protein components are contained in gag, pol and env genes. ... Characteristics of the genome. The specificity of the Lentivirus genus is that it contains a diploid single stranded positive ... sense RNA-genome, i.e. has two strands of RNA. It is spherical in shape (80-120 nm), and its genome is found in the complex ...
A star is born: the updated Human Reference Genome. Posted by Vivien Marx , Categories: Genetics & Genomics, Sequencing ... The release of the 38th build of the human reference genome gets a well-deserved rock-star greeting by the scientific community ...
... Johann Greilhuber,1 Jaroslav Doležel,2 Ilia J. Leitch,3 João Loureiro,4 and Jan Suda5,6 ... I. J. Leitch and M. D. Bennett, "Genome size and its uses: the impact of flow cytometry," in Flow Cytometry with Plant Cells: ... J. M. Beaulieu, S. A. Smith, and I. J. Leitch, "On the tempo of genome size evolution in angiosperms," Journal of Botany, vol. ... M. Höfer and A. Meister, "Genome size variation in Malus species," Journal of Botany, vol. 2010, Article ID 480873, 8 pages, ...
  • The genome of a female Hereford cow has been sequenced by the Bovine Genome Sequencing and Analysis Consortium, a team of researchers led by the National Institutes of Health and the U.S. Department of Agriculture . (wikipedia.org)
  • Over the last decade, as DNA-sequencing technology has grown ever faster and cheaper, our understanding of the human genome has increased accordingly. (technologyreview.com)
  • Mikael Flensborg of Qiagen Bioinformatics and Kristina Kermanshahche of Intel share how different configurations of the Intel® Scalable System Framework help optimize genome sequencing performance and workflows. (intel.com)
  • Researchers will then turn to sequencing the more than 100 million base pairs which make up the genome. (newscientist.com)
  • A Massachusetts startup called Noblegen is developing a simplified version of nanopore genome-sequencing technology-a technique that promises high speed and low costs but that usually requires complex instruments to carry out. (technologyreview.com)
  • The "next generation" sequencing technologies offered by companies including Illumina and Pacific Biosciences have come a very long way, says Jeffery Schloss, program director for technology development at the National Human Genome Research Institute, but "they leave a fair amount to be desired. (technologyreview.com)
  • Feist says Noblegen's goal is to aggressively drive down the cost and increase the speed of sequencing whole genomes to a point where it makes economic sense for hospital labs in the next three or four years. (technologyreview.com)
  • We want to deliver whole genome sequencing in the [hospital] lab within the financial constraints of the health-care system," he says. (technologyreview.com)
  • In this way, information from the human genome could be used without the great expense of sequencing the horse genome. (uky.edu)
  • The issue doesn't have anything to do with Celera, it has to do with Science and the fact that we just disagree with data restrictions,' said John McPherson, co-director of the genome sequencing center at Washington University in St. Louis, Missouri. (wired.com)
  • First, it might help to understand the basics of genome sequencing in general. (go.com)
  • But recently, researchers have discovered methods to map out a person's entire genetic sequence, otherwise known as their genome, by sequencing all 20,000 genes at one time. (go.com)
  • As scientists advance in the development of the technology, the process of sequencing a genome literally continues to become faster and less expensive by the day. (go.com)
  • Whole genome sequencing gives us the ability to detect certain variants of disease. (go.com)
  • But now, in order to augment this concept, researchers have turned their attention on whole tumor genome sequencing, which will sequence all genes within a tumor cell (approximately 25-30,000). (go.com)
  • Genome projects typically involve three main phases: DNA sequencing, assembly of DNA to represent original chromosome, and analysis of the representation. (news-medical.net)
  • The recent advances in technology that allow high throughput genomic sequencing to be undertaken quickly and relatively cheaply has propelled the work of genome analysis forward. (news-medical.net)
  • Currently we apply advanced next-generation sequencing (NGS) methodologies i.e. whole human genome sequencing, exome sequencing and sequencing of specific targeted disease-implicated genomic regions. (weizmann.ac.il)
  • With Susie's data as a reference, the researchers took advantage of next-generation sequencing technology to obtain lower resolution data on the genomes of 10 additional orangutans - five from Sumatra and five from Borneo. (bbc.co.uk)
  • WEDNESDAY, May 9 (HealthDay News) -- Researchers have completed the first genome sequencing of melanoma , an aggressive and frequently fatal form of skin cancer . (medicinenet.com)
  • To help arrive at a functional woolly mammoth genome, the researchers at the Broad Institute of MIT and Harvard are sequencing the genome of the African elephant for comparison. (informationweek.com)
  • Below you will find upcoming events at which FDA will either be 1) presenting information on foodborne pathogen whole genome sequencing, its applications, and its positive public health impact, or 2) otherwise participating in discussions related to foodborne pathogen whole genome sequencing. (fda.gov)
  • The information presented by FDA may include but is not limited to experiences and observations drawn from its foodborne pathogen whole genome sequencing research program and the GenomeTrakr network. (fda.gov)
  • Whole Genome Sequencing in Public Health and Food Safety Practice - the 21st century is now! (fda.gov)
  • The session will focus on the expanding role of whole genome sequencing (WGS) technology as part of foodborne disease surveillance and outbreak response. (fda.gov)
  • Whole genome sequencing (WGS) is a cutting-edge technology that FDA has put to a novel and health-promoting use. (fda.gov)
  • FDA is laying the foundation for the use of whole genome sequencing to protect consumers from foodborne illness in countries all over the world. (fda.gov)
  • Whole genome sequencing reveals the complete DNA make-up of an organism, enabling us to better understand variations both within and between species. (fda.gov)
  • Whole genome sequencing performs the same function as PFGE but has the power to differentiate virtually all strains of foodborne pathogens, no matter what the species. (fda.gov)
  • FDA's foods program has been utilizing whole genome sequencing since 2008. (fda.gov)
  • The FDA Foods Whole Genome Sequencing Staff is coordinating efforts by public health officials to sequence pathogens collected from foodborne outbreaks, contaminated food products, and environmental sources. (fda.gov)
  • BERLIN (AP) - Researchers in Germany said Tuesday they have completed the first high-quality sequencing of a Neanderthal genome and are making it freely available online for other scientists to study. (yahoo.com)
  • The DNA spike-in control materials will be used as a benchmark for validation of next-generation sequencing (NGS) pipelines and other platforms intended to identify induced genome editing events. (nist.gov)
  • By 1998 Venter had established Celera Genomics with sequencing capacity fifty times greater than TIGR, and by June 17, 2000, he concluded a ninety percent complete account of the human genome. (encyclopedia.com)
  • Collins drew twenty laboratories worldwide with hundreds of researchers into the International Human Genome Sequencing Consortium, which he directed from his Washington office. (encyclopedia.com)
  • Sequencing the more than 3.7 billion base pairs in the Neanderthal genome took about four years. (nationalgeographic.com)
  • The sequencing of the yeast genome was a major milestone in biology. (brighthub.com)
  • What is Whole Genome Sequencing (WGS) and what analyses are performed using WGS data? (cdc.gov)
  • Whole Genome Sequencing (WGS) generates DNA sequence data for the entire M. tuberculosis genome, which can be used for various applications. (cdc.gov)
  • In 2018, CDC's Division of TB Elimination (DTBE) began universal whole-genome sequencing (WGS) (i.e., sequencing an M. tuberculosis isolate for each U.S. case of culture-confirmed TB). (cdc.gov)
  • A training module on "Whole-genome sequencing for investigation of recent TB transmission in the United States: Current uses and future plans" is available here. (cdc.gov)
  • My lab was involved in the genetic/physically mapping and sequencing of the A. tumefaciens C58 genome (Goodner et al. (google.com)
  • Dulbecco and others in the scientific community grasped that sequencing the human genome, though a monumental achievement itself, would mark just the first step of the quest to fully understand the biology of cancer. (scientificamerican.com)
  • Recent advances in high-throughput DNA sequencing have provided initial glimpses of the nuclear genome of Neandertals as well as other ancient mammals including cave bears and mammoths. (sciencemag.org)
  • The project is doing that through the application of something called genome analysis, including large-scale genome sequencing. (ohsu.edu)
  • As the science and technology progress, Powell says genome sequencing can sometimes detect rare genetic changes that can be associated with rare genetic conditions. (healthline.com)
  • In the future, there may be specific conditions that can be detected using genome sequencing to only look at specific genes (versus sequencing and analyzing all the genes) that will be helpful to know about even in healthy babies. (healthline.com)
  • The process of 'sequencing' a genome, as this is called, is not simple however, as the chromosomes are much too long to sequence in one go. (warwick.ac.uk)
  • DNAnexus offers a platform that takes the raw sequence directly from the sequencing machine, builds the genome, and analyzes the data, and it is able to do all of this work in the cloud. (genengnews.com)
  • Sequencing is the first step toward deciphering this genome and understanding key characteristics for duck breeding. (inra.fr)
  • The decreasing costs of high throughput sequencing has allowed scientists to focus on the duck genome. (inra.fr)
  • Institute of Genomics and Integrative Biology ( http://igib.res.in ), which is a constituent laboratory of the Council of Scientific and Industrial Research ( http://www.csir.res.in ) has completed the whole genome sequencing of a Wildtype Strain of Zebrafish (Danio rerio). (google.com)
  • PASADENA- Two of the key inventions that made possible the monumental task of sequencing the human genome came from the California Institute of Technology. (caltech.edu)
  • These were especially important in the sequencing of the 3 billion DNA base pairs composing the human genome because the inventions speeded up progress on the task. (caltech.edu)
  • This method revolutionized DNA sequencing, ultimately making it possible to launch the Human Genome Project. (caltech.edu)
  • Coupled with some recent advances, the method remained the core for the just-completed phase of sequencing the human genome. (caltech.edu)
  • The Simon research group was also a major contributor to the mapping and sequencing of chromosome 22-a substantial segment of the human genome, which was completed in 1999. (caltech.edu)
  • The results also have serious repercussions for genome-sequencing projects. (redorbit.com)
  • Physical characterization of aquaculture genomes through BAC end sequencing: Peng Xu, Shaolin Wang, and Zhanjiang Liu. (wiley.com)
  • Sequencing the genome: Zhanjiang Liu. (wiley.com)
  • Imagine a test that could give you a glimpse of your future… CNBC reporter Meg Tirrell underwent whole genome sequencing to map her DNA and discovered as many questions as answers. (cnbc.com)
  • Pretty soon, the sexiness of genome sequencing wore off, and it took a bit more to get into a vanity journal. (scienceblogs.com)
  • Any other genome sequencing projects were relegated to lower tier journals. (scienceblogs.com)
  • Now, it appears that even sequencing the genome of charismatic megafauna only gets you a press release. (scienceblogs.com)
  • As TR Gregory points out, the sequencing of the Kangaroo genome was announced in such a manner ( Science by press release ). (scienceblogs.com)
  • Sequencing all or large parts of a baby's genome at birth could reveal genetic variations that increase risk for conditions that occur in childhood or not until adulthood. (medscape.com)
  • Cite this: Genome Sequencing in Newborns Raises Ethical Issues - Medscape - Nov 13, 2019. (medscape.com)
  • To study the ginkgo's extraordinary biology at a genetic and molecular level, sequencing its genome was high up on the wish list of plant biologists. (eurekalert.org)
  • The great interest in the history and biology of gingko, however, made the work of sequencing and assembling the genome a challenge the researchers from China felt worth taking, and one they succeeded in accomplishing. (eurekalert.org)
  • The goal of the WGS project is to collect whole-genome sequencing data from individuals with well-defined phenotypes and existing clinical outcomes data. (nih.gov)
  • The WGS project aims to provide whole-genome sequencing data that researchers can use to identify genetic markers of increased or decreased risk of heart, lung, blood, and sleep disorders, as well as markers that help define disorder subtypes. (nih.gov)
  • The WGS project has performed whole-genome sequencing on over 90,000 participants from over 30 studies. (nih.gov)
  • We also will look for opportunities to integrate whole-genome sequencing with other -omics data. (nih.gov)
  • The development of new technologies has made genome sequencing dramatically cheaper and easier, and the number of complete genome sequences is growing rapidly. (wikipedia.org)
  • Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant Arabidopsis thaliana, the puffer fish, and the bacteria E. coli. (wikipedia.org)
  • New sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine. (wikipedia.org)
  • In prokaryotes, pulsed field gel electrophoresis and complete genome sequencing are the predominant methods of genome size determination. (wikipedia.org)
  • Although sequenced genome data are practically biased toward small genomes, which may compromise the accuracy of the empirically derived correlation, and ultimate proof of the correlation remains to be obtained by sequencing some of the largest eukaryotic genomes, current data do not seem to rule out a possible correlation. (wikipedia.org)
  • Such bona fides should carry over to the complete genome, he says. (newscientist.com)
  • Researchers Wednesday unveiled the first complete genome of an octopus or any species of cephalopod, the class of mollusks also including squid, cuttlefish and nautiluses. (voanews.com)
  • Scientists have assembled the first complete genome of one of humanity's oldest, and least-loved, companions: the bedbug. (amnh.org)
  • Getting an effectively complete genome sequence of a bacterium that lived nearly 700 years ago is incredibly exciting,' said Julian Parkhill, a disease genome expert at the Wellcome Trust Sanger Institute in Britain. (cbc.ca)
  • The first complete genome sequences among all three domains of life were released within a short period during the mid-1990s: The first bacterial genome to be sequenced was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995. (wikipedia.org)
  • Genome size is the total amount of DNA contained within one copy of a single complete genome. (wikipedia.org)
  • Stanford researchers used cryptography to cloak irrelevant genetic information in individuals' genomes while revealing disease-associated mutations. (stanford.edu)
  • It is now possible to scour complete human genomes for the presence of disease-associated genes without revealing any genetic information not directly associated with the inquiry, say Stanford University researchers. (stanford.edu)
  • The researchers hope that routine implementation of their technique will help individuals overcome any qualms about privacy that may keep them from sharing their genome sequences. (stanford.edu)
  • There are now amazing tools in computer science and cryptography that allow researchers to pinpoint only these differences while keeping the remainder of the genome completely private. (stanford.edu)
  • One source who asked not to be identified said that instead of Science the research will be submitted to Nature , but a spokeswoman at the National Human Genome Research Institute , the main organization overseeing the HGP, said the researchers would rather stick with custom and wait until publication to make any announcements. (wired.com)
  • There is currently a lack of robust analysis tools that are able to handle the depth of data in these genome projects and assist researchers in making use of the information. (news-medical.net)
  • This suggests their genomes are closer to that of the putative ancestral great ape, researchers say. (bbc.co.uk)
  • For instance, the researchers saw what she described as a great deal of "structural rearrangement" on the genome. (medicinenet.com)
  • B]y deciphering this genome we could, in theory, generate data that one day may help other researchers to bring the woolly mammoth back to life by inserting the uniquely mammoth DNA sequences into the genome of the modern-day elephant," Schuster said in a statement. (informationweek.com)
  • Researchers announced Wednesday that they've managed to reconstruct the genome of the Black Death, the illness that wiped out around half of Europe's population in just a few years in the mid-1300s. (pbs.org)
  • Researchers announced Thursday that they had completed a "rough-draft" map of the corn genome -- a step they say will help scientists engineer better corn. (pbs.org)
  • A furor developed when researchers working with government money applied for patents on data that merely reports knowledge of what already exists in nature - knowledge of existing DNA sequences - and this led to the 1992 resignation of James Watson (b. 1928) from the directorship of NIH's National Center for Human Genome Research (NCHGR). (encyclopedia.com)
  • By comparing the human and Neanderthal genomes with that of our closest living relative, the chimpanzee, researchers hope to tell which genes changed very recently, giving modern humans an edge. (nationalgeographic.com)
  • But in the Oct. 18 issue of the journal Science, researchers at Yale and Harvard successfully recoded the genome of E. coli to expand viral resistance and allow researchers to more easily introduce new amino acids into the organism. (yaledailynews.com)
  • In the 7 May 2010 issue of Science , an international team of researchers presents the draft sequence of the Neandertal genome composed of over 3 billion nucleotides from three individuals. (sciencemag.org)
  • The researchers sequenced the genome of the California two-spot octopus (scientific name Octopus bimaculoides ), a relatively small, gray-brown species with two iridescent blue spots on each side of its head. (voanews.com)
  • The researchers found relatively few changes in the genome. (cbc.ca)
  • With the advent of the $1,000 genome, researchers find themselves drowning in data. (genengnews.com)
  • The genome of the common duck ( Anas platyrynchos ) was sequenced in its entirety at the Beijing Genomics Institute in China, within the framework of an international project with the participation of INRA researchers. (inra.fr)
  • However, concerns over genetic data privacy may deter individuals from contributing their genomes to scientific studies and could prevent researchers from sharing data with the scientific community. (virginia.edu)
  • COLUMBUS, Ohio - A team of Ohio State University genetics researchers have produced a third map of the human genome, this one containing twice the number of genes proposed by two earlier maps and providing annotations that explain the function of all 66,000 genes. (eurekalert.org)
  • In February, teams of researchers from Celera Genomics, a private biotechnology firm, and counterparts from the Human Genome Project, the federally funded effort to map the genome, published their findings in the prestigious journals Science and Nature respectively. (eurekalert.org)
  • Both earlier reports proposed that the human genome consists of some 35,000 genes, far less than the estimate of 100,000 to 120,000 genes which researchers had long predicted. (eurekalert.org)
  • The Ohio State effort, which involved a team of 13 researchers from the university and a bioinformatics company, adds a third major map of the human genome and may accelerate the use of the genome in the diagnosis and understanding of diseases. (eurekalert.org)
  • For example, the Ohio State researchers used a rodent gene database, which provided evidence for 1,437 possible genes in the human genome. (eurekalert.org)
  • Some researchers are unsettled by the certainty with which the Human Genome Consortium is presenting its lower gene count," said Fred Wright, assistant professor of human cancer genetics and lead author of the paper. (eurekalert.org)
  • Caltech researchers, both current and past, have also been important in promoting the Human Genome Project itself-a project that originally met with scientific skepticism when it was born 12 years ago, particularly when the goal of a fully sequenced human genome by the year 2003 was announced. (caltech.edu)
  • There is an utterly confusing press release out today - Australian First: Kangaroo Genome Mapped: Australian researchers are launching the world first detailed map of the kangaroo genome, completing the first phase of the kangaroo genomics project. (scienceblogs.com)
  • In a bold step for precision medicine, researchers at the National, Heart, Lung, and Blood Institute (NHLBI) today announced they are releasing for study nearly 9,000 whole genomes, courtesy of participants in the Institute's Trans-Omics for Precision Medicine Program (TOPMed). (nih.gov)
  • In 1996, the United States Department of Agriculture (USDA) invited the Horse Genome Project participants to join their program for studying genomics of agriculturally important species. (uky.edu)
  • Earlier this week, the word on the street was the paper from the government-funded consortium would be submitted to the journal Science for simultaneous publication with research from Celera Genomics, a for-profit company that created its own human genome map. (wired.com)
  • The development of suitable tools to assist in the genome analysis process should be a priority for the future to continue the growth of knowledge and understanding the field of genomics. (news-medical.net)
  • It's not enough to just sequence a genome, because by itself it does not tell the full story," said Mark Siddall, one of the paper's corresponding authors and a curator in the Museum's Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics. (amnh.org)
  • Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. (ensembl.org)
  • J. L. Bennetzen, "Maize genome structure and evolution," in Handbook of Maize: Genetics and Genomics , J. L. Bennetzen and S. Hake, Eds. (hindawi.com)
  • SAN FRANCISCO , Sept. 14, 2017 /PRNewswire/ -- Genome Medical , a nationwide genomics medical practice, today announced a program offering expert care and support to family members of individuals found to carry a disease-causing genetic variant. (prnewswire.com)
  • Genome Medical is a nationwide genomics medical practice bringing genetics to everyday life. (prnewswire.com)
  • Aquaculture Genome Technologies comprehensively covers the field of genomics and its applications to the aquaculture industry. (wiley.com)
  • Concept of genome and genomics: Zhanjiang Liu. (wiley.com)
  • The study of the genome is called genomics. (wikipedia.org)
  • This "genome cloaking" technique, devised by biologists, computer scientists and cryptographers at the university, ameliorates many concerns about genomic privacy and potential discrimination based on an individual's genome sequence. (stanford.edu)
  • The first genome map of a horse is complete, providing scientists with new tools for investigating equine disease. (uky.edu)
  • But many scientists believe tha genome information will help them find solutions. (uky.edu)
  • In October 1995, 70 scientists from 20 countries met in Lexington, Kentucky to make a plan for mapping the horse genome. (uky.edu)
  • Many scientists have joined forces on the Human Genome Project. (amnh.org)
  • By learning about our genome, scientists will better understand how our bodies work and how diseases develop. (amnh.org)
  • So, to get a complete picture of our species' DNA, you might think that the Human Genome Project scientists have to study the DNA of millions of people -- not even close! (amnh.org)
  • After the entire human genome is sequenced, scientists still won't know which genes control which traits. (amnh.org)
  • Scientists with the Human Genome Project (HGP) study only the human genome. (amnh.org)
  • To understand how our genome works, scientists compare it to the genomes of mice, flies, worms, and even bacteria. (amnh.org)
  • Scientists have released a draft sequence of the orangutan genome, revealing intriguing clues to the evolution of great apes and humans. (bbc.co.uk)
  • Just in time for global warming, scientists have sequenced the genome of the extinct woolly mammoth, last seen roaming the Earth about 10,000 years ago. (informationweek.com)
  • Scientists have for the first time mapped the entire genome of a cancer patient, in the process finding eight new genetic mutations that led to the woman's leukemia. (pbs.org)
  • A four-year international study of the human genome has prompted scientists to rethink some of their most basic ideas about how DNA functions. (pbs.org)
  • In the Nov. 11 issue of the journal Nature , scientists from the Smithsonian Institution , the University of Copenhagen, BGI-Shenzen, the University of California, Santa Cruz and approximately 100 other institutions report on the genomes of 363 species of birds, including 267 that have been sequenced for the first time. (si.edu)
  • In the meantime, the genome sequence is being made freely available so scientists elsewhere can conduct research on it, he said. (yahoo.com)
  • While scientists have previously modified the genetic code of organisms, they have never successfully recoded the genome in ways that fundamenally alter the organism's biological function. (yaledailynews.com)
  • Several years ago, U.S. scientists launched a hugely ambitious project called the Cancer Genome Atlas. (ohsu.edu)
  • Scientists have yet to map out the full human genome , so any tests done today are incomplete, as they're missing a fundamental part of indisputable science: a full data set. (healthline.com)
  • The draft version of the genome's DNA sequences that was assembled by scientists at the Human Genome Project would then resemble a copy of Ulysses that lacked all punctuation and spacing. (eurekalert.org)
  • Because the process was so slow and required the work of highly skilled technicians, it was clear to most scientists in the mid '80s that it would not be possible to sequence entire genomes by manual methods. (caltech.edu)
  • This includes devising new ways to extract and manipulate information from the human genome sequence and from recently completed genome sequences of important experimental organisms used by scientists in the laboratory, such as the fruit fly, mustard weed, and yeast. (caltech.edu)
  • Scientists at the University of Rochester and the J. Craig Venter Institute have discovered a copy of the genome of a bacterial parasite residing inside the genome of its host species. (redorbit.com)
  • Bacterial DNA is routinely discarded when scientists are assembling invertebrate genomes, yet these genes may very well be part of the organism's genome, and might even be responsible for functioning traits. (redorbit.com)
  • In December 2013, scientists first sequenced the entire genome of a Neanderthal, an extinct species of humans. (wikipedia.org)
  • Jan Aerts discusses the problem of incorporating information on large-scale genomic rearrangements into genome browsers. (scienceblogs.com)
  • Genome browsers such as UCSC and Ensembl are fantastic for presenting many types of genomic information, such as the position and orientation of protein-coding genes or the location of small-scale genetic variants. (scienceblogs.com)
  • Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (East Central Africa). (ebi.ac.uk)
  • To realize this goal FDA is spearheading an international effort to build a network of laboratories that can sequence the genomes of foodborne pathogens and then upload the genomic sequence of the pathogen and the geographic location from which the pathogen was gathered into a publicly accessible database. (fda.gov)
  • Clustered Regularly Interspaced Short Palindromic Repeats, or CRISPRs, have emerged as a next-generation genome-engineering tool because of their ability to cut genomic DNA at precise locations. (prweb.com)
  • Over the past 1 2+ years, my undergrads and I have worked to update the an notation of the C58 genome and to connect genes to cellular functions through a variety of functional genomic approaches (Slater et al. (google.com)
  • This program is a collaboration with the Department of Energy (DOE) Joint Genome Institute (JGI) as part of the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project using the Integrated Microbial Genomes Annotation Collaboration Tool (IMG-ACT). (google.com)
  • In light of this, we performed genome mining and comparative genomic analysis of CNS strains Staphylococcus cohnii subsp. (omicsonline.org)
  • Less than three years after the Human Genome Project's completion, the National Institutes of Health has officially launched the pilot stage of an effort to create a comprehensive catalogue of the genomic changes involved in cancer: The Cancer Genome Atlas (TCGA). (scientificamerican.com)
  • 9 ) engineer the HSV KOS strain genome, leveraging synthetic genomic cloning approaches to rapidly construct HSV variants with combinatorial mutations for functional evaluation. (pnas.org)
  • Overall, Aquaculture Genome Technologies gives a good and comprehensive overview of the principes of genomic tools covering both classical and modern methods, combining clarity and depth besides some space limitations in certain chapters. (wiley.com)
  • Less than half of these genomes are from individuals of non-European descent, creating a valuable genomic resource reflective of the diverse U.S. population. (nih.gov)
  • The first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research. (wikipedia.org)
  • The decreasing cost of genomic mapping has permitted genealogical sites to offer it as a service, to the extent that one may submit one's genome to crowdsourced scientific endeavours such as DNA.LAND at the New York Genome Center, an example both of the economies of scale and of citizen science. (wikipedia.org)
  • A new distributed computing project is comparing gene data with protein structures to determine their genome sequences. (wired.com)
  • One of [email protected]'s tasks is to disassemble and find all of the potential sequences that are used to create that protein. (wired.com)
  • It then takes all of the sequences and compares them to the Human Genome Project database. (wired.com)
  • Also, by determining the sequences that go into creating a protein, [email protected] might someday find ways to cause the proteins that make up bacteria and viruses, such as Staphylococcus and HIV, to break down. (wired.com)
  • So by working with known proteins in viruses, the [email protected] effort can find or test new gene sequences that fold into the viral protein and thus interfere with it, the same way protease inhibitors fight HIV. (wired.com)
  • With [email protected], if the computer is off the network for two weeks, the program will simply continue to work on that same work unit, finding more and more of the sequences used to assemble the protein. (wired.com)
  • Another nice benefit is by being able to compare [email protected] sequences to natural sequences, we'll learn a lot about the process of making proteins,' he said. (wired.com)
  • What remains are different plasmids required for viral particle formation and infectivity (the packaging and the envelope constructs) and sequences for mobilization of viral genome. (news-medical.net)
  • The process of sexual reproduction enables the DNA sequences from the female and male's chromosomes to be intermixed to generate a unique genome in each offspring. (warwick.ac.uk)
  • why, so far, only a small number of plant genome sequences have been published. (warwick.ac.uk)
  • We ended up with a higher estimated number of genes than the other two teams because we compared 13 different gene databases to the DNA sequences in the draft genome produced by the Human Genome Project," said Bo Yuan, head of Ohio State's Division of Human Cancer Genetics bioinformatics group. (eurekalert.org)
  • One of the databases had over 2 million sequences, each of which had to be searched against the entire 2.8 billion base pairs in the genome draft. (eurekalert.org)
  • However, because of its size as well as the presence of an enormous number of repeat sequences, assembling the whole genome sequence would be a difficult task. (eurekalert.org)
  • Wenbin Chen from BGI explains some of the difficulties that they had to overcome: "A huge amount of raw data (~2 TB) was generated, and the computing capability for genome assembly was challenged by both the huge data and the remarkably high proportion of repetitive sequences. (eurekalert.org)
  • He went on to highlight several genome features: "The large genome of ginkgo may have resulted from whole genome duplication and insertion of a remarkably high proportion of repetitive sequences, at least 76.58%, and the longest introns among all sequenced species due to insertions of transposable elements. (eurekalert.org)
  • Currently, the WGS project has released over 30,000 whole genome sequences in dbGAP and approximately 45,000 more will be added to dbGaP in early 2018. (nih.gov)
  • A few months later, the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. (wikipedia.org)
  • Reference genome sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity. (wikipedia.org)
  • Ridley continues his premise in this chapter that the use of simple genetic markers is inadequate to describe the complete function of the genome, or the causation of disease. (wikipedia.org)
  • Though genome editing with CRISPR is just a little over a year old, it is already reinventing genetic research. (technologyreview.com)
  • The initial goal of the Horse Genome Project was limited to making a genetic map for the horse. (uky.edu)
  • All 32 pairs of chromosomes would be identified and genetic landmarks identified on each chromosome so that points of reference could be established to the human genome sequence. (uky.edu)
  • Federal health officials yesterday launched the biggest genetic research endeavor since the landmark human genome project: an ambitious effort to categorize all of the hundreds of molecular glitches that turn normal healthy cells into cancers. (washingtonpost.com)
  • The Cancer Genome Atlas, whose total cost could reach $1 billion or more, will for the first time direct the full force of today's sophisticated genetic technologies to the thorough understanding of a single disease -- one that will eventually strike nearly half of all Americans alive. (washingtonpost.com)
  • A 38,000-year old bone has yielded the world's first complete Neanderthal mitochondrial genome sequence, offering a tantalising glimpse at the genetic changes that separate humans from Neanderthals , which split some 600 millennia ago. (newscientist.com)
  • We will gain insights into many aspects of the history of both Neanderthals and Denisovans, and refine our knowledge about the genetic changes that occurred in the genomes of modern humans after they parted ways with the ancestors of Neanderthals and Denisovans," Paabo said. (yahoo.com)
  • As expected, the genome holds clues to the genetic changes behind the transition from a lobed fin to a tetrapod limb, Amemiya says. (scientificamerican.com)
  • A very large and comprehensive online genetics resource,displaying information from all aspects of genetics today, Human chromosomes, genetic disorders, Genome project and topics of interest. (merlot.org)
  • The wgMLST scheme for TB includes 2,690 different genetic loci, each of which is an individual gene in the genome. (cdc.gov)
  • Genome-wide patterns of genetic variation among elite maize inbred lines," Nature Genetics , vol. 42, no. 11, pp. 1027-1030, 2010. (hindawi.com)
  • Genome Medical's genetic experts-physicians and genetic counselors-deliver consultation services via telemedicine to individuals and medical professionals. (prnewswire.com)
  • Free access to these data could improve the power of genome-wide association studies (GWAS) to identify disease-causing genetic variants and aid the discovery of new drug targets. (virginia.edu)
  • The emerging paradigm is that polyploidy - through alterations in genome structure and gene regulation - generates genetic and phenotypic novelty that manifests itself at the chromosomal, physiological, and organismal levels, with long-term ecological and evolutionary consequences. (springer.com)
  • Such a genome fills a major phylogenetic gap of land plants, and provides key genetic resources to address evolutionary questions like phylogenetic relationships of gymnosperm lineages, evolution of genome and genes in land plants, innovation of developmental traits, evolution of sex as well as history of demography and distribution, resistance and conservation of ginkgo. (eurekalert.org)
  • In the fields of molecular biology and genetics, a genome is all genetic material of an organism. (wikipedia.org)
  • There is a general conception that we can only find meaningful differences by surveying the entire genome," said Bejerano. (stanford.edu)
  • The genome has a large number of transposable elements - non-coding parts of the genome that have an important role in gene regulation - that have been moving around in the genome at a relatively rapid pace. (scientificamerican.com)
  • According to Aerts, such knowledge could be extremely useful: "We can now explore if we can use this lock-and-key system to open up or close off other parts of the genome in a controlled way as well. (eurekalert.org)
  • Sequence assembly is especially complicated in plants because some parts of the genome are repeat copies of other parts. (warwick.ac.uk)
  • Genome: The Autobiography of a Species in 23 Chapters is a 1999 popular science book by the science writer Matt Ridley , published by Fourth Estate. (wikipedia.org)
  • It would be very valuable to sequence more primate genomes to enable more comparative analysis of this kind and thus help us understand the evolution of primates and our own species. (bbc.co.uk)
  • Our data set is 100 times more extensive than any other published data set for an extinct species, demonstrating that ancient DNA studies can be brought up to the same level as modern genome projects. (informationweek.com)
  • It now hopes to compare the new genome sequence to that of other Neanderthals, modern humans and Denisovans - another extinct human species whose genome was previously extracted from remains found in the same Siberian cave. (yahoo.com)
  • A "first draft" of the Neanderthal genome announced today adds to evidence that the extinct human species was lactose intolerant and could have shared some basic language capabilities with modern humans. (nationalgeographic.com)
  • By contrast, a genome is the full set of genes that gives rise to a particular species. (nationalgeographic.com)
  • And now, we've found at least one species where the parasite's entire or nearly entire genome has been absorbed and integrated into the host's. (redorbit.com)
  • Published today in the open-access journal GigaScience , is an article that presents the genome sequence of Ginkgo biloba , the oldest extant tree species. (eurekalert.org)
  • Given its longevity as a species and unique position in the evolutionary tree of life, the ginkgo genome will provide an extensive resource for studies concerning plant defenses against insects and pathogens, and research investigating early events in tree evolution and in evolution overall. (eurekalert.org)
  • The tree's genome is also larger than other plant species known for extremely big genomes, such as maize or orchids. (eurekalert.org)
  • A genome sequence is the complete list of the nucleotides (A, C, G, and T for DNA genomes) that make up all the chromosomes of an individual or a species. (wikipedia.org)
  • Nuclear genome sizes are well known to vary enormously among eukaryotic species. (wikipedia.org)
  • I. J. Leitch and M. D. Bennett, "Genome size and its uses: the impact of flow cytometry," in Flow Cytometry with Plant Cells: Analysis of Genes, Chromosomes and Genomes , J. Doležel, J. Greilhuber, and J. Suda, Eds. (hindawi.com)
  • Work on synthetic genomes has seen the field scale-up from the full synthesis of the small poliovirus genome (2002) ( 1 ), to a complete working synthetic bacterial genome (2010) ( 2 ), and more recently to the construction and validation of multiple rewritten eukaryote chromosomes for the model organism Saccharomyces cerevisiae (2014, 2017) ( 3 ⇓ ⇓ ⇓ ⇓ - 8 ). (pnas.org)
  • The costs and time-scales for assembling entire bacterial genomes and eukaryotic chromosomes mean that synthetic genome engineering is not yet a routine approach to manipulating cells for research or biotechnology. (pnas.org)
  • If the DNA is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be present in a single cell, and if the cells divide faster than the DNA can be replicated, multiple replication of the chromosome is initiated before the division occurs, allowing daughter cells to inherit complete genomes and already partially replicated chromosomes. (wikipedia.org)
  • So while the HGP data may have a gene and a sequence, but not a structure, [email protected] might have a protein and a structure, and if their structures match, then it's very likely that the relationship between genome and protein has been found. (wired.com)
  • For example, if an unclassified genome has the same sequence as a protein used in digestion, then it's possible that the gene is also used in digestion. (wired.com)
  • It is important to consider how the genome is similar to other genomes that are already known, as this can help when establishing the role of the gene. (news-medical.net)
  • The efficiency, versatility and multiplexing capacity of RNA-guided genome engineering using the CRISPR/Cas9 technology enables a variety of applications in plants, ranging from gene editing to the constructi. (biomedcentral.com)
  • Physical and gene map of the green alga Nephroselmis chloroplast genome, showing the typical structural arrangement found in land plants. (tolweb.org)
  • This greatly simplifies the process of gene editing by allowing for rapid, efficient and precise engineering, even with complex genomes. (prweb.com)
  • This Hub is maintained as a result of the gene editing project of the OECD Working Party on Biotechnology, Nanotechnology and Converging Technologies (BNCT ) which is a partner in the genome editing conference. (oecd.org)
  • Now that we can systematically profile genomes, epigenomes and transcriptomes, the challenge is to discover the rules that link DNA sequence with chromatin state and gene expression. (eurekalert.org)
  • They shared a vision of the future in which knowledge of every gene that composes the human genome would be available to any scientist in the world at the click of a computer key. (caltech.edu)
  • Once considered a speciation process common only in plants, polyploidy is now recognized to have played a major role in the structure, gene content, and evolution of most eukaryotic genomes. (springer.com)
  • By the early 1970s, "genome size" was in common usage with its present definition, probably as a result of its inclusion in Susumu Ohno's influential book Evolution by Gene Duplication, published in 1970. (wikipedia.org)
  • However, although there is no longer any paradoxical aspect to the discrepancy between genome size and gene number, the term remains in common usage. (wikipedia.org)
  • Based on currently available completely sequenced genome data (as of April 2009), log-transformed gene number forms a linear correlation with log-transformed genome size in bacteria, archaea, viruses, and organelles combined, whereas a nonlinear (semi-natural logarithm) correlation is seen for eukaryotes. (wikipedia.org)
  • Depending on the size of the genome or chromosome being built, this may require many rounds of assembly, as the typical starting material for DNA assembly projects is almost always fragments of DNA smaller than 15 kb, with these obtained either from commercial synthesis or from PCR amplification of natural DNA regions. (pnas.org)
  • Bacterial artificial chromosome libraries and BAC-based physical mapping of aquaculture genomes: William S. Davidson. (wiley.com)
  • The work is published in Genome Biology . (epfl.ch)
  • Genome Biology 18:149, 7 August 2017. (epfl.ch)
  • The human genome project changed biology forever. (uky.edu)
  • The journal Genome Biology is published by BioMedCentral, and offers free access to primary research articles and a preprint depository to which authors may submit work for free distribution over the web. (scidev.net)
  • Only after the genome of the African elephant has been completed will we be able to make a final assessment about how much of the full woolly-mammoth genome we have sequenced," said Webb Miller, a professor of biology, computer science, and engineering at Penn State, in a statement. (informationweek.com)
  • Genome-scale plant research to address fundamental questions in biology, including processes of economic and/or societal importance. (nsf.gov)
  • The Ohio State report was published today on the website of the journal Genome Biology. (eurekalert.org)
  • A second key invention for the genome project was developed at Caltech by Professor Melvin Simon, chair of Caltech's biology division, and his coworker Hiroaki Shizuya. (caltech.edu)
  • Isaacs and Church also showed that eliminating the UAG codon frees up a protein coding space in an organism's genome, allowing for a more efficient incorporation of non-standard amino acids - amino acids that are not traditionally coded for. (yaledailynews.com)
  • Genome reduction, also known as genome degradation, is the process by which an organism's genome shrinks relative to that of its ancestors. (wikipedia.org)
  • Of dramatic interest is the number of genes in the human genome. (encyclopedia.com)
  • As of December 2017, Mary Ann Liebert, Inc. is no longer the publisher of Gender and the Genome , The Official Journal of the Foundation for Gender-Specific Medicine. (liebertpub.com)
  • The traditional method of curation method uses the Basic Local Alignment Search Tool (BLAST) algorithm to find similarities to annotate the genome. (news-medical.net)
  • TADs are portion of the DNA molecule that divides the entire genome of an organism into manageable chunks, like districts in a city. (epfl.ch)
  • A genome is the complete collection of hereditary information for an individual organism. (encyclopedia.com)
  • The programs, methods and tools developed for the human genome project could be used to study the genetics of any biological organism. (uky.edu)
  • In 1996 Saccharomyces cerevisiae or baker's yeast was the first eukaryotic organism to have its entire nuclear genome sequenced. (brighthub.com)
  • While the assembly strategy is typically more costly and time-consuming than the editing strategy, it allows for many more design changes throughout the genome, including large-scale rearrangements, and its efficiency is not determined by our ability to work with the target organism. (pnas.org)
  • In land plants and green algae, roughly half of the subunits of these complexes are encoded by the plastid genome and half by the nuclear genome ( 3 , 4 ). (pnas.org)
  • This timeline highlights key discoveries about our closest relatives, from early fossil finds to the publication of the draft nuclear genome sequence. (sciencemag.org)
  • Nuclear genome size is typically measured in eukaryotes using either densitometric measurements of Feulgen-stained nuclei (previously using specialized densitometers, now more commonly using computerized image analysis) or flow cytometry. (wikipedia.org)
  • The release of the 38th build of the human reference genome gets a well-deserved rock-star greeting by the scientific community. (nature.com)
  • One person can generate the data, and others can perform related tasks-mapping sequence reads to the reference genome, writing software to analyze the data, and interpreting results. (genengnews.com)
  • Now there is hope in the form of new genome-engineering tools, particularly one called CRISPR. (technologyreview.com)
  • DNA2.0 today announced the release of a set of CRISPR/Cas9 tools for genome editing and engineering. (prweb.com)
  • CRISPR/Cas9 technology has simplified genome editing and enabled many exciting new approaches in a very short time," said Jeremy Minshull, CEO and cofounder of DNA2.0. (prweb.com)
  • Genome editing, and one of its most discussed techniques the CRISPR/Cas9 system, has received increasing attention in the academic press and the wider media. (oecd.org)
  • Apart from comparing the genome homology, size and G + C content, we also showed the presence 10 different CRISPR-cas genes in the CNS strains. (omicsonline.org)
  • For editing, new technologies, such as multiplex automated genome engineering-based targeted mutation ( 10 ) and the new genome editing tools of CRISPR-Cas9 allow existing genomes to be extensively modified toward a target sequence over several generations within their host cells ( 11 ). (pnas.org)
  • Rumors of where the Human Genome Project's groundbreaking research paper will wind up are flying faster than RNA messages. (wired.com)
  • 65 participants at the 2016 NIST Genome Editing Standards Workshop identified pre-competitive standards and measurements needed to establish greater confidence in characterization of genome editing outputs. (nist.gov)
  • In 2016, the same strategy allowed the Venter Institute team to construct a working, rationally reduced Mycoplasma genome with large-scale changes from the natural sequence, including removal of hundreds of genes ( 12 ). (pnas.org)
  • Groundbreaking Journal, Gender and the Genome, To Launch in Summer 2016. (liebertpub.com)
  • In connection with the genetics section they interviewed several members of the Horse Genome Project. (uky.edu)
  • Targeted genome engineering has been described as a "game-changing technology" for fields as diverse as human genetics and plant biotechnology. (biomedcentral.com)
  • The dance is intended to represent the human genome and related topics, including the history of genetics and social implications. (genomeweb.com)
  • University of California Berkeley genetics professor Daniel Rokhsar said genome research is underway on other cephalopods, including the world's largest, the giant squid. (voanews.com)
  • [email protected] is a project at Stanford University to advance the amount knowledge in the field of genetics . (everything2.com)
  • Zebrafish Wild Type Strain Genome was presented at the 6th European Zebrafish Genetics and Development Meeting at Rome, Italy. (google.com)
  • When Bob Waterston became chair of the Department of Genome Sciences in 2002, it was a major coup for UW Medicine. (washington.edu)
  • The Rice Genome Council, drawn from universities and national research institutes, will meet this month to plan the scheme. (newscientist.com)
  • The Boston University lab of Amit Meller, whose technology NobleGen has licensed, received $4.2 million in funding from the National Human Genome Research Institute last September. (technologyreview.com)
  • The horse genome community has met as a part of a USDA National Sponsored Research Project in San Diego, CA every January since 1997. (uky.edu)
  • The planets have aligned to tackle cancer in a comprehensive way that we've never had the tools to do before,' said Francis S. Collins, director of the NIH's National Human Genome Research Institute. (washingtonpost.com)
  • Genome editing promises giant leaps forward in advancing biotechnology, agriculture, and basic research. (biomedcentral.com)
  • The Mid -Career Investigator Awards in Plant Genome Research (MCA-PGR) will be available in FY 2014. (nsf.gov)
  • This program is a continuation of the Plant Genome Research Program (PGRP) that began in FY 1998 as part of the National Plant Genome Initiative (NPGI). (nsf.gov)
  • Yet the research, led by Richard Green and Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, will pave the way for the construction and analysis of the complete Neanderthal genome. (newscientist.com)
  • The genome of a Neanderthal is now there in a form as accurate as that of any person walking the streets today," Svante Paabo, a geneticist who led the research, told The Associated Press in an email. (yahoo.com)
  • The National Institute of Standards and Technology Genome Editing Consortium addresses the measurements and standards needed to increase confidence and lower the risk of utilizing genome editing technologies in research and commercial products. (nist.gov)
  • Whether genome editing will be used in healthcare, agriculture or basic research, robust quantitative measurements are needed to enable high confidence characterization of DNA alterations. (nist.gov)
  • Now the technology exists to finally understand the mysterious code buried in the human genome, but finding the pieces of Kraus's research is more dangerous than anyone imagined. (worldcat.org)
  • The exciting field of genome editing is rapidly advancing and precise genome editing techniques have already become an important tool for both fundamental research and plant biotechnology. (biomedcentral.com)
  • This collection includes both invited reviews and unsolicited research covering all aspects of genome editing technologies as applied to plant research (both for crop plants and model organisms). (biomedcentral.com)
  • The yeast genome has been an important model in a whole host of research efforts. (brighthub.com)
  • This session highlighted case studies and examples of agricultural applications of genome editing, particularly plant varieties or animal breeds that may be on or close to the market or under research and development. (oecd.org)
  • Since the start of this century, a handful of research groups have pursued the synthesis and large-scale engineering of genomes. (pnas.org)
  • The Foundation for Gender-Specific Medicine and Gender and the Genome (Mary Ann Liebert, Inc., publishers) Announce the Robert S. Birch $25,000 Award Competition for the Best Original Research Paper or Commentary. (liebertpub.com)
  • The Center on Children and Families at Brookings is answering these questions with the Social Genome Project, a data-rich model using the best research on what determines success in each stage of the lifecycle. (brookings.edu)
  • In the past, prohibitive costs had left it behind similar research on other genomes such as that of the cow or horse. (inra.fr)
  • The NSF Directorate for Biological Sciences (BIO) has implemented a requirement for submission of full proposals via Research.gov (or Grants.gov) for certain program solicitations, including the Plant Genome Research Program solicitation ( NSF 21-507 ). (nsf.gov)
  • The Plant Genome Research Program (PGRP) supports genome-scale research that addresses challenging questions of biological, societal and economic importance. (nsf.gov)
  • PGRP encourages the development of innovative tools, technologies and resources that empower a broad plant research community to answer scientific questions on a genome-wide scale. (nsf.gov)
  • Some of my research has focused on developing cryptographic methods to protect the privacy of a patient's genome while still enabling useful computations across multiple genomes. (virginia.edu)
  • For nearly a decade, our research group has had the privilege of developing and mining a multi-center, microarray-based, genome-wide expression database of critically ill children ( ≤ 10 years of age) with septic shock. (psu.edu)
  • The Human Genome Project is unique among scientific projects for having set aside, from the beginning, research support for studies of the ethical, legal, and social implications of the new knowledge of human genes that would result. (caltech.edu)
  • Aquaculture Genome Technologies is the quintessential What, When, Why and How-to book for aquatic genome research…an important addition to any science classroom, laboratory or office. (wiley.com)
  • The term "genome size" is often erroneously attributed to a 1976 paper by Ralph Hinegardner, even in discussions dealing specifically with terminology in this area of research (e.g. (wikipedia.org)
  • Confusion was enhanced when the human genome was compared to a yeast cell with 6,000 genes, a fly with 13,000 genes, a worm with 26,000 genes, and a rice cell with 50,000 genes. (encyclopedia.com)
  • The project to sequence the yeast genome got underway in 1989 and the entire code of strain S288c was spelled out in 1996. (brighthub.com)
  • It was extracted from its yeast host and used to transform Mycoplasma cells, resulting in a bacteria growing and dividing with the accepted synthetic genome. (pnas.org)
  • In a recent interview, Dr. Waterston talked about his career and genome sciences. (washington.edu)
  • Dr. Kelley Harris joined Genome Sciences in 2018. (washington.edu)
  • Genome Sciences is pleased to welcome Dr. Brian Beliveau to the department in September 2018 as our newest faculty member. (washington.edu)
  • Retrieved on December 14, 2019 from https://www.news-medical.net/life-sciences/Genome-Analysis.aspx. (news-medical.net)
  • Retrieved on August 17, 2019 from https://www.news-medical.net/life-sciences/Lentivirus-Genome.aspx. (news-medical.net)
  • Genome mapping in animals is now one of the leading disciplines in animal sciences. (springer.com)
  • Say Hello to Chip Skowron III, the Latest Hedge-Funder Charged With Insider Trading [Updated] Over a tip about Human Genome Sciences. (nymag.com)
  • In Caltech's Division of the Humanities and Social Sciences, Professor Daniel Kevles has examined these ethical issues in his book The Code of Codes: Scientific and Social Issues in the Human Genome Project, which he coedited in 1992 with Leroy Hood. (caltech.edu)
  • Finally, viruses (which are noncellular, parasitic "life forms") have genomes of double-stranded DNA, single-stranded DNA, double-stranded RNA, or single-stranded RNA. (encyclopedia.com)
  • However, by stepping down a scale from bacteria to viruses, opportunities quickly arise, even for those viruses with comparatively large genomes, like the double-stranded DNA herpes simplex virus (HSV) type 1 genome, over 150 kb in length. (pnas.org)
  • The genomes of RNA viruses can be either single-stranded RNA or double-stranded RNA, and may contain one or more separate RNA molecules (segments: monopartit or multipartit genome). (wikipedia.org)
  • DNA viruses can have either single-stranded or double-stranded genomes. (wikipedia.org)
  • Although the latter contrasts with the previous view that no correlation exists for the eukaryotes, the observed nonlinear correlation for eukaryotes may reflect disproportionately fast-increasing non-coding DNA in increasingly large eukaryotic genomes. (wikipedia.org)
  • Genomes fluctuate in size regularly, and genome size reduction is most significant in bacteria. (wikipedia.org)
  • The most evolutionarily significant cases of genome reduction may be observed in the eukaryotic organelles known to be derived from bacteria: mitochondria and plastids. (wikipedia.org)
  • Dr. Beliveau develops and applies super-resolution microscopy methods and programmable molecular technologies to map the 3D organization of the genome in single cells. (washington.edu)
  • There are two fundamentally distinct types of cells in the living world, prokaryotic and eukaryotic, and the organization of genomes differs in these two types of cells. (encyclopedia.com)
  • Thus, the physical organization of the genome varies from inter-phase to division phase. (encyclopedia.com)
  • We already knew that the size and organization of the genome was very similar among all mammals. (uky.edu)
  • We could use the information from the human genome to predict the organization and sequence of horse genes. (uky.edu)
  • Polyploidy - whole-genome duplication (WGD) - is a fundamental driver of biodiversity with significant consequences for genome structure, organization, and evolution. (springer.com)
  • You had to sequence something cute and cuddly, something extinct, or a lot of genomes at once. (scienceblogs.com)
  • and FST values were significantly higher for SNPs within the Batwa pygmy phenotype-associated regions than the remainder of the genome, a signature of polygenic adaptation. (ebi.ac.uk)
  • The Genome Properties system consists of a suite of "Properties" which are carefully defined attributes of prokaryotic organisms whose status can be described by numerical values or controlled vocabulary terms for individual completely sequenced genomes. (jcvi.org)
  • The size of the bovine genome is 3 Gb (3 billion base pairs ). (wikipedia.org)
  • The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs. (wikipedia.org)
  • The first draft of the horse genome sequence was recently completed and deposited. (uky.edu)
  • In June, the rival genome mapping teams surprised the scientific community by ending an ongoing race to finish the maps, and announcing together that they each had completed a 'working draft. (wired.com)
  • The genome produced from remains of a toe bone found in a Siberian cave is far more detailed than a previous "draft" Neanderthal genome sequenced three years ago by the same team at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. (yahoo.com)
  • Koonin, who is Caltech's provost, was chair of the JASON study of 1997, which noted to the scientific community that quality standards could be relaxed so that a "rough draft" of the human genome could be made years earlier and still be of great utility. (caltech.edu)
  • The NIST-led Genome Editing Consortium has been established to address these needs. (nist.gov)
  • Proteins in the chloroplast thylakoid membrane system are derived from both the nuclear and plastid genomes. (pnas.org)
  • This genome-wide, high-resolution analysis of the partitioning of chloroplast ribosomes between membrane and soluble fractions revealed that approximately half of the chloroplast-encoded thylakoid proteins integrate cotranslationally and half integrate posttranslationally. (pnas.org)
  • Chloroplast genomes encode ∼37 proteins that integrate into the thylakoid membrane. (pnas.org)
  • Insights into the architecture of ancestral chloroplast genomes. (tolweb.org)
  • The genome includes both the genes (the coding regions) and the noncoding DNA, as well as mitochondrial DNA and chloroplast DNA. (wikipedia.org)
  • Studying the Neanderthal genome will tell us what makes modern humans really modern, and really human," said project collaborator Jean-Jacques Hublin, of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. (nationalgeographic.com)
  • Meanwhile, Bailey wants to sequence the genome of a patient's cancer? (go.com)
  • I understood that they a) made a map, and b) intend to sequence the genome over the next year. (scienceblogs.com)
  • According to the article at www.sciencedaily.com they didn't sequence the genome yet. (scienceblogs.com)
  • His lab at Washington University in St. Louis was also central to the success of the Human Genome Project, which was completed in April 2003. (washington.edu)
  • Ridley concludes that the Human Genome Project is largely based on the inaccurate belief that there is one single human genome. (wikipedia.org)
  • The Alzheimer's Genome Project, supported by Cure Alzheimer's Fund, aims to identify all genes linked to the disease. (youtube.com)
  • JAPAN is planning a long-term international project to map the rice plant's genome. (newscientist.com)
  • The horse genome project was a result of the human genome project. (uky.edu)
  • By the end of the meeting the Horse Genome Project was born. (uky.edu)
  • [email protected] is the second project from Stanford University's chemistry department, which also runs the [email protected] project. (wired.com)
  • The Human Genome Project has mapped the entire human genome, but not the proteins encoded by our genes. (wired.com)
  • Desjarlais does his own genome experiments at Penn State but only has so much computing horse power, so a distributed computing project is the best way to bring a lot of CPUs into the project. (wired.com)
  • The Music Genome Project powers Pandora. (pandora.com)
  • The mission of the Cultural Genome Project is to celebrate and commemorate multi-generations of American histories through the simple, but sometimes forgotten, human interaction of asking and listening. (idealist.org)
  • Through the Cultural Genome Project, we will preserve historical facts but also celebrate the tradition of story-telling and memory-passing. (idealist.org)
  • Whose genome was selected for this important project? (amnh.org)
  • The results of the Human Genome Project are published on the Internet. (amnh.org)
  • It brings together the discoveries from the previous phases of the project to form conclusions, which can offer true value to further our knowledge of the genome and be applied in relevant situations. (news-medical.net)
  • The massive sets of data that have been produced by projects, such as the Human Genome Project, remain largely under-utilized, despite the fact that the project concluded more than a decade ago. (news-medical.net)
  • Chocolate maker Mars Inc. will fund a five year, $10 million project to map the cocoa bean genome -- work that could lead to hardier, higher-yielding crops and better quality chocolate, the company announced Thursday. (pbs.org)
  • The worldwide effort, originally named the Human Genome Initiative but later known as the Human Genome Project or HGP, began in 1987 and was celebrated as complete in 2001. (encyclopedia.com)
  • Nobel laureate Renato Dulbecco penned those words more than 20 years ago in one of the earliest public calls for what would become the Human Genome Project. (scientificamerican.com)
  • thus the project generates artificial genomes that, while not existing in the real world, should produce the same results as the existing genome (since they should produce proteins with the same shape). (everything2.com)
  • The project hopes that by comparing these artificial genomes to natural ones, they will be able to gain a better understanding of genome evolution and how genes and proteins work. (everything2.com)
  • [email protected] has a sister project, [email protected] whose goal is to find the shape of proteins via computer simulation. (everything2.com)
  • The [email protected] project can be found at http://genomeathome.stanford.edu/ . (everything2.com)
  • The Social Genome Project , a model of social mobility over the life cycle, will produce a unique new data set and tool for policy analysis. (brookings.edu)
  • These BACs provided the major input DNA for both the public genome project and Celera. (caltech.edu)
  • David Baltimore, president of Caltech and a Nobel laureate for his work on the genes of viruses, was a highly influential supporter of the Human Genome Project at its inception. (caltech.edu)
  • To shape this unprecedented and complex project, Caltech professors Norman Davidson, Barbara Wold, and Steve Koonin have served in national scientific advisory roles to the genome project in the intervening years. (caltech.edu)
  • Also, Baltimore chaired the National Institutes of Health (NIH) meeting where the human genome project was launched. (caltech.edu)
  • The WGS project has sequenced over 90,000 genomes from over 30 studies, and the project aims to sequence more than 120,000 genomes. (nih.gov)
  • The WGS project released data from over 30,000 genomes through the National Institutes of Health (NIH) Database of Genotypes and Phenotypes (dbGaP). (nih.gov)
  • The Human Genome Project was organized to map and to sequence the human genome. (wikipedia.org)
  • David Reich/Nature The entire genome of the Denisovans was extracted from a tooth and finger bone. (scienceblogs.com)
  • A plan was made to sequence the entire human genome in the late 1980s. (uky.edu)
  • and the University of Tubingen in Germany describe its entire genome. (cbc.ca)
  • But integrating an entire genome was definitely an unexpected find. (redorbit.com)
  • The Cancer Genome Atlas is the outgrowth of a year and a half of planning by NIH advisory groups. (washingtonpost.com)
  • When the software sees a repeated region it cannot tell which of the copies the short fragment came from, so is unable to accurately assemble the whole genome sequence. (warwick.ac.uk)
  • The NHLBI will continue growing this valuable whole-genome sequence public data resource and hopes to sequence over 120,000 individual genomes. (nih.gov)
  • Less glamorously, the newly minted mitochondrial genome offers important technical insights into constructing and verifying far larger ancient genomes. (newscientist.com)
  • The analysis of DNA phase is the final step in genome analysis. (news-medical.net)
  • The team's analysis reveals that the orangutan genome has experienced a slower rate of evolution than those of other great apes, with fewer rearrangements, duplications and repeats in the sequence. (bbc.co.uk)
  • Ending one long-standing argument, analysis of the coelacanth genome clearly shows that it is not the closest living fishy relative to tetrapods, Amemiya says: that honor belongs to the lungfish. (scientificamerican.com)
  • The analysis showed that not all parts of the coelacanth genome are slow to evolve. (scientificamerican.com)
  • Surprisingly, there is a lack of genome analysis data in literature against CNS particularly of human origin. (omicsonline.org)
  • It is employed for all facets in genome analysis in animals and their improvement for benefit of human beings. (springer.com)
  • Here we describe a protocol for large-scale genome-wide analysis that facilitates quality control and population stratification correction in 9K, 13K, and 23K individuals while maintaining the confidentiality of underlying genotypes and phenotypes. (virginia.edu)
  • If we pick a disease to treat using genome editing, we should start with something relatively simple," he says. (technologyreview.com)
  • Targeted genome editing, a method used to alter the DNA of living cells at desired locations, is poised to revolutionize science and medicine. (nist.gov)
  • NIST has brought together experts across the genome editing field including stakeholders in industry, academia and government to assess their measurement needs. (nist.gov)
  • These discussions have identified common pre-competitive measurements and standards needed to establish greater confidence in the characterization of genome editing outputs. (nist.gov)
  • Design and conduct controlled evaluations of existing assays for quantifying on- and off-target genome editing, with a robust and optimal experimental design aimed at assessing the sources of variability, repeatability, and reproducibility within an assay. (nist.gov)
  • Determine the type of metadata that would be needed to be shared, housed, and interrogated from genome editing experiments. (nist.gov)
  • Identify terms and related definitions to form a common genome editing community lexicon. (nist.gov)
  • The efficiency of multiplex editing in plants by the RNA-guided Cas9 system is limited by efficient introduction of its components into the genome and by their activity. (biomedcentral.com)
  • By co-expressing two guide RNAs using dual RNA polymerase promoters, the patent-pending NickaseNinja removes the need for co-transfection of multiple vectors, improving genome editing efficiency and consistency compared with the conventional two vector systems currently available. (prweb.com)
  • The OECD Conference on Genome Editing: Applications in Agriculture - Implications for Health, Environment and Regulation explored the safety and regulatory considerations raised by genome edited products, with the aim to favour a coherent policy approach to facilitate innovation involving genome editing and will bring together policy makers, academia, innovators and other stakeholders involved in the topic. (oecd.org)
  • Genome editing - set of techniques in which specialised enzymes have been modified - can insert, replace or remove DNA from a genome with a high degree of specificity. (oecd.org)
  • The rapidly growing use of genome editing has policy implications and human health and environmental safety considerations. (oecd.org)
  • The meeting report of the OECD conference on ''Genome Editing: Applications in Agriculture-Implications for Health, Environment and Regulation'' includes in-depth summaries of the presentations of each invited speaker given at the Conference. (oecd.org)
  • The Policy Considerations Regarding Genome Editing describes the applications of genome editing, its risk and safety considerations and regulatory aspects. (oecd.org)
  • This session presented background information on genome editing techniques in the broader context. (oecd.org)
  • Science and Legal Experts Debate Future Uses and Impact of Human Genome Editing in Gender and the Genome. (liebertpub.com)
  • Human Genome Variation is delighted to present its first Collection for the March 2019 issue. (nature.com)
  • An international team led by Devin Locke, from the Washington University School of Medicine in St Louis, US, sequenced the full genome of a female Sumatran orangutan named Susie. (bbc.co.uk)
  • A major step toward that goal was the completion in 2007 of the full genome of James D. Watson, one of the co-discoverers of the structure of DNA. (wikipedia.org)
  • Everyone on the planet -- except identical twins -- has a unique genome. (amnh.org)
  • The genome data set now consists of 4 billion DNA bases, but Schuster and his colleagues believe that only 3.3 billion of them belong in the mammoth genome. (informationweek.com)
  • Lastly, I note that Science Now has used the "d-word" with respect to the mammoth genome . (scienceblogs.com)
  • Through this route in 2010, the J. Craig Venter Institute constructed the first completely synthetic bacterial genome ( 2 ). (pnas.org)
  • The Novel Methods for Generating Physical Frameworks for Plant Genomes (GPF-PG) will not be available in FY 2014. (nsf.gov)
  • The precise manipulation of plant genomes relies on the induction of DNA double-strand breaks by site-specific nucleases to initiate DNA repair reactions that are either based on non-homologous end joining (NH. (biomedcentral.com)
  • M. Morgante, "Plant genome organisation and diversity: the year of the junk! (hindawi.com)
  • Because polyploidy is most common and best studied in plants, the book emphasizes plant models, but recent studies of vertebrates and fungi are providing fresh perspectives on factors that allow polyploid speciation and shape polyploid genomes. (springer.com)
  • The ginkgo genome stretches over more than 10 Gb, which is 80 times larger than the "model plant" Arabidopsis thaliana genome. (eurekalert.org)
  • The specificity of the Lentivirus genus is that it contains a diploid single stranded positive sense RNA-genome, i.e. has two strands of RNA. (news-medical.net)
  • Prokaryotes and eukaryotes have DNA genomes. (wikipedia.org)
  • In eukaryotes (but not prokaryotes), genome size is not proportional to the number of genes present in the genome, an observation that was deemed wholly counter-intuitive before the discovery of non-coding DNA and which became known as the "C-value paradox" as a result. (wikipedia.org)
  • The 8th Dorothy Russell Havemeyer Foundation International Equine Genome Mapping Workshop took place near Newmarket, UK from July 22 to 25, 2009. (uky.edu)
  • The series Genome Mapping in Animals will fill this gap. (springer.com)
  • Viruses that belong to the genus Lentivirus of the family Retroviridae are exogenous, have specific morphology and contain a relatively complex retroviral genome. (news-medical.net)
  • Whereas [email protected] is designed to learn how genomes fold into proteins, [email protected] was launched this week to try and reverse engineer known proteins by guessing the genome sequence of their structures. (wired.com)
  • This effort is very much a discovery for the participants, as learning how genomes become proteins is something that's still largely unknown. (wired.com)
  • With the emergence of various molecular techniques in the past 50 years, the genome sizes of thousands of eukaryotes have been analyzed, and these data are available in online databases for animals, plants, and fungi (see external links). (wikipedia.org)
  • We will analyse directly quantitative traits in the cohorts and the selected traits in the extreme samples, and also use imputation down to 0.1% allele frequency to extend the analyses to further sample sets with genome wide genotype data. (ebi.ac.uk)
Genome-Wide Analysis of Alternative Splicing during Dendritic Cell Response to a Bacterial Challenge