Sequence Analysis, DNA
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.
Chromosomes, Artificial, Bacterial
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.
Molecular Sequence Data
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.
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.
Open Reading Frames
A large plant family of the order Asterales, subclass Asteridae, class Magnoliopsida. The family is also known as Compositae. Flower petals are joined near the base and stamens alternate with the corolla lobes. The common name of "daisy" refers to several genera of this family including Aster; CHRYSANTHEMUM; RUDBECKIA; TANACETUM.
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.
DNA Transposable Elements
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.
Repetitive Sequences, Nucleic Acid
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).
Nucleic Acid Renaturation
Terminal Repeat Sequences
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.
Physical Chromosome Mapping
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)
Databases, Nucleic Acid
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.
Gene Transfer, Horizontal
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).
Molecular Sequence Annotation
A plant family of the order Capparales, subclass Dilleniidae, class Magnoliopsida. They are mostly herbaceous plants with peppery-flavored leaves, due to gluconapin (GLUCOSINOLATES) and its hydrolysis product butenylisotrhiocyanate. The family includes many plants of economic importance that have been extensively altered and domesticated by humans. Flowers have 4 petals. Podlike fruits contain a number of seeds. Cress is a general term used for many in the Brassicacea family. Rockcress is usually ARABIS; Bittercress is usually CARDAMINE; Yellowcress is usually RORIPPA; Pennycress is usually THLASPI; Watercress refers to NASTURTIUM; or RORIPPA or TROPAEOLUM; Gardencress refers to LEPIDIUM; Indiancress refers to TROPAEOLUM.
Amino Acid Sequence
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)
Nucleic Acid Hybridization
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)
Sequence Homology, Nucleic Acid
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.
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.
Human Genome Project
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.
Expressed Sequence Tags
Seedless nonflowering plants of the class Filicinae. They reproduce by spores that appear as dots on the underside of feathery fronds. In earlier classifications the Pteridophyta included the club mosses, horsetails, ferns, and various fossil groups. In more recent classifications, pteridophytes and spermatophytes (seed-bearing plants) are classified in the Subkingdom Tracheobionta (also known as Tracheophyta).
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 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).
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)
Technique using an instrument system for making, processing, and displaying one or more measurements on individual cells obtained from a cell suspension. Cells are usually stained with one or more fluorescent dyes specific to cell components of interest, e.g., DNA, and fluorescence of each cell is measured as it rapidly transverses the excitation beam (laser or mercury arc lamp). Fluorescence provides a quantitative measure of various biochemical and biophysical properties of the cell, as well as a basis for cell sorting. Other measurable optical parameters include light absorption and light scattering, the latter being applicable to the measurement of cell size, shape, density, granularity, and stain uptake.
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.
Electrophoresis, Gel, Pulsed-Field
Gel electrophoresis in which the direction of the electric field is changed periodically. This technique is similar to other electrophoretic methods normally used to separate double-stranded DNA molecules ranging in size up to tens of thousands of base-pairs. However, by alternating the electric field direction one is able to separate DNA molecules up to several million base-pairs in length.
DNA Restriction Enzymes
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.
Polymerase Chain Reaction
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.
High-Throughput Nucleotide Sequencing
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.
Gymnosperms are a group of vascular plants whose seeds are not enclosed by a ripened ovary (fruit), in contrast to ANGIOSPERMS whose seeds are surrounded by an ovary wall. The seeds of many gymnosperms (literally, "naked seed") are borne in cones and are not visible. Taxonomists now recognize four distinct divisions of extant gymnospermous plants (CONIFEROPHYTA; CYCADOPHYTA; GINKGOPHYTA; and GNETOPHYTA).
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.
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.
A phylum of photosynthetic EUKARYOTA bearing double membrane-bound plastids containing chlorophyll a and b. They comprise the classical green algae, and represent over 7000 species that live in a variety of primarily aquatic habitats. Only about ten percent are marine species, most live in freshwater.
Deoxyribonucleases, Type II Site-Specific
Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 188.8.131.52.
Interspersed Repetitive Sequences
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.
Electrophoresis, Agar Gel
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.
Sequence Homology, Amino Acid
Nucleic Acid Conformation
Gene Expression Profiling
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.
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.
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.
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).
A large plant genus of the family EUPHORBIACEAE, order Euphorbiales, subclass Rosidae. They have a milky sap and a female flower consisting of a single pistil, surrounded by numerous male flowers of one stamen each. Euphorbia hirta is rarely called milkweed but that name is normally used for ASCLEPIAS.
Oligonucleotide Array Sequence Analysis
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)
A technique for visualizing CHROMOSOME ABERRATIONS using fluorescently labeled DNA probes which are hybridized to chromosomal DNA. Multiple fluorochromes may be attached to the probes. Upon hybridization, this produces a multicolored, or painted, effect with a unique color at each site of hybridization. This technique may also be used to identify cross-species homology by labeling probes from one species for hybridization with chromosomes from another species.
Polymorphism, Single Nucleotide
The branch of science concerned with the interrelationship of organisms and their ENVIRONMENT, especially as manifested by natural cycles and rhythms, community development and structure, interactions between different kinds of organisms, geographic distributions, and population alterations. (Webster's, 3d ed)
Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.
A. senegalensis is one of the few species in Anerococcus whose genome has been sequenced. The genome has a size of 1,790,835 bp ... The first analysis made on Anaerococcus provencensis showed it is susceptible to penicillin G, imipenem, amoxillin, ... Their cells size can differ from 0.6μm to 0.9μm. However, when they are grown using enrinched blood agar their size can go from ... Its genome was sequenced in August 2009. The genus Anaerococcus is one of six genera classified within the group GPAC (Gram- ...
Strictly standardized mean difference
Zhang XHD (2010). "Genome-wide screens for effective siRNAs through assessing the size of siRNA effects". BMC Research Notes. 1 ... Zhang XHD (2011). Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-scale RNAi ... Zhang XHD, Heyse JF (2009). "Determination of sample size in genome-scale RNAi screens". Bioinformatics. 25 (7): 841-44. doi: ... In an HTS assay, one primary goal is to select compounds with a desired size of inhibition or activation effect. The size of ...
... "genome size analyses of Pucciniales reveal the largest fungal genomes". Frontiers in Plant Science. 5: 422. doi:10.3389/fpls. ...
List of Plasmodium species
The genome of Haemoproteus tartakovskyi has been sequenced. Its genome (23.2 megabases) is similar in size to those of ... An analysis of four apicoplast genome-encoded genes (small subunit rRNA, large subunit rRNA and caseinolytic protease C) of ... The branching order suggested by other analyses concurs with an analysis of the mitochondrial genes This latter paper puts the ... The gametocytes are medium-sized Paraplasmodium The schizonts are of medium size. Exoerythrocytic schizonts may be produced in ...
Can handle large and complex genomes of any size. Finally, the GS Amplicon Variant Analyzer aligns reads from amplicon samples ... Life Technologies has released BioScope, a data analysis package for resequencing, ChiP-Seq and transcriptome analysis. It uses ... These techniques formed the base for the completion of the human genome project in 2001. The human genome project spurred the ... GS De Novo Assembler is a tool for de novo assembly of whole-genomes up to 3GB in size from shotgun reads alone or combined ...
Genome Size Estimation Using Flow Cytometry and K-Mer Analyses". Plants. 9 (2): 270. doi:10.3390/plants9020270. ISSN 2223-7747 ... "The commercial history of Cape herbal teas and the analysis of phenolic compounds in historic teas from a depository of 1933". ... Journal of Food Composition and Analysis. 76: 66-73. doi:10.1016/j.jfca.2018.11.001. ISSN 0889-1575. Van Putten, JW (2000). Die ... Journal of Food Composition and Analysis. Elsevier BV. 76: 39-43. doi:10.1016/j.jfca.2018.12.002. ISSN 0889-1575. Krafczyk, ...
1998). "Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta, Prasinophyceae)" J. Phycol. 34 (5): 844-849. ... 2006). "Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features" Proceedings of ... The genome sequence of three members of this genus is available: the 13 Mb nuclear genome of O. tauri RCC4221 published in 2006 ... and its position was later confirmed by analysis of its 18S rDNA. Molecular phylogenetic analysis based on the 18SrDNA sequence ...
1998). "Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta, Prasinophyceae)" J. Phycol. 34 (5): 844-849. ... Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proceedings of the ... tauri genome was sequenced by Derelle et al.. The 12.56 Mb genome organized in 20 chromosomes showed extreme gene density and ... As early as 1998, O. tauri was identified as "a good candidate for biological models such as cell division and/or genome ...
"Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus". The Plant Genome. 8 (3): 1- ... The genus has a 25-fold range in genome size among its species and notably includes some of the smallest known plant genomes. ... More than one genome size has been measured in G. aurea and G. repens, suggesting that di- and tetraploid individuals exist. ... "Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate ...
Zhang XHD (2010). "Genome-wide screens for effective siRNAs through assessing the size of siRNA effects". BMC Research Notes. 1 ... Practical Experimental Design and Data Analysis for Genome-scale RNAi Research, Cambridge University Press" Zhang XHD (2011). ... One issue with the use of t-statistic and associated p-values is that they are affected by both sample size and effect size. ... SSMD directly assesses the size of effects. SSMD has also been shown to be better than other commonly used effect sizes. The ...
ISBN 0-7167-4382-5. Gregory TR (January 2004). "Insertion-deletion biases and the evolution of genome size". Gene. 324: 15-34. ... January 2007). "Somatic microindels: analysis in mouse soma and comparison with the human germline". Hum. Mutat. 28 (1): 69-80 ... "Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)". Genome Biology. 12 (11): R114. doi: ... variation in the human genome". Genome Research. 16 (9): 1182-1190. doi:10.1101/gr.4565806. PMC 1557762. PMID 16902084. ...
Phylogenetic analysis of DNA C-values provides evidence for a small ancestral genome size in flowering plants. Annals of Botany ... The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes Yin-Long Qiu, Jungho Lee, Fabiana Bernasconi ...
Human disease modifier gene
The size and complexity of the human genome make this a challenging task. Methods of identifying modifier loci can be ... 2015). "Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis". ... Their methods exemplify the large sample size required to conduct a statistically powerful analysis capable of identifying loci ... and whole-genome association studies. In an example of a familial linkage study, genotyping and linkage analysis conducted in a ...
Single cell sequencing
"Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles". ... Single-cell genome (DNA) sequencing. 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 ...
Multiple displacement amplification
"Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles". ... The large size of MDA-amplified DNA products also provides desirable sample quality for identifying the size of polymorphic ... MDA has been actively used in whole genome amplification (WGA) and is a promising method for application to single cell genome ... "Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification". ...
"Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis". PLOS ...
Its genome has been sequenced, and has a size of 3.57 Mbp, with 3338 protein-coding genes. Characteristics of S. thermophilum ... However, the sequence of 16S rRNA gene led to the complete phylogenic analysis of S. thermophilum, concluding it was in fact ... The genome of S. thermophilum is not even partially alike other prokaryotic genomes sequenced at this point in time, as ... Although it has no flagella, the genome of S. thermophilum does include a flagella biosynthesis gene cluster. S. thermophilum ...
The genome size was 58.55 Mbp with an estimated 16,549 genes. The T. spiralis genome is the only known nematode genome to be ... "Global Gene Expression Analysis of the Zoonotic Parasite Trichinella spiralis Revealed Novel Genes in Host Parasite Interaction ... The females of T. spiralis are about twice the size of the males, and have an anus found terminally. The vulva is located near ... "Trichinella spiralis". Genome. NCBI. Retrieved 2012-04-19. Mitreva M, Jasmer DP, Zarlenga DS, Wang Z, Abubucker S, Martin J, ...
"Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size". Journal of ... The genome of this phage is very different from that of other mycobacteriophages and is highly mosaic. More than half of its ...
"Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: Genome Clustering, Gene Acquisition, and Gene Size". Journal of ... A selection of 60 mycobacteriophages were isolated and had their genomes sequenced in 2009. These genome sequences were grouped ... In the following years hundreds of additional genomes have been sequenced. Mycobacteriophages have highly mosaic genomes. Their ... Host range analysis shows that not all mycobacteriophages from M. smegmatis infect other strains and only phages in Cluster K ...
A complete genome sequence analysis of Monocercomonoides sp. PA203 from Chinchilla lanigera was conducted. The estimated size ... The genome of Monocercomonoides has approximately 75 million base pairs (75 Mbp), with 16629 predicted protein-coding genes. ... The lack of mitochondria or any mitochondria-related organelles in Monocercomonoides is confirmed by its genome sequence. ... Genes that are typically encoded on mitochondrial genomes (mtDNA) were not found among the assembled scaffold, suggesting ...
Craddock, Elysse M.; Gall, Joseph G.; Jonas, Mark (2016). "Hawaiian Drosophila genomes: size variation and evolutionary ... "Phylogenetic and ecological relationships of the Hawaiian Drosophila inferred by mitochondrial DNA analysis". Molecular ... The genome of Drosophila grimshawi was selected to be one of the landmark 12 Drosophila genomes sequenced in 2007. Since then ... Drosophila 12 Genomes Consortium (2007). "Evolution of genes and genomes on the Drosophila phylogeny". Nature. 450 (7167): 203- ...
... similar genome size, and similar numbers of protein coding and nonprotein coding genes. Further analysis demonstrated about 62 ... The genome of C. briggsae is roughly 100 Mb in size and is predicted to encode about 20,000 genes. The whole genome sequencing ... briggsae Project View the cb3 genome assembly in the UCSC Genome Browser.. ... The genome sequence for C. briggsae was determined in 2003. C. briggsae was initially discovered by Margaret Briggs in 1944. ...
Due to their replicative nature, retrotransposons can increase eukaryotic genome size quickly and survive in eukaryotic genomes ... February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860-921. Bibcode:2001Natur.409..860L ... SanMiguel P, Bennetzen JL (1998). "Evidence that a recent increase in maize genome size was caused by the massive amplification ... There is an estimate of 80-100 active L1s in the reference genome of the Human Genome Project, and an even smaller number of ...
August 1999). "Accommodation of foreign genes into the Sendai virus genome: sizes of inserted genes and viral replication". ... genome characterization and structural protein sequence analysis". Archives of Virology. 153 (9): 1715-23. doi:10.1007/s00705- ... The genome of SeV as genomes of other non segmented negative-stranded RNA viruses has a low rate of homologous recombination ... 3) Sendai virus belongs to a category of viruses that are governed by the "rule of six". SeV genome as genomes of other ...
"Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal ... frame size". PLoS Genet. 5 (4): e1000445. doi:10.1371/journal.pgen.1000445. PMC 2661236. PMID 19343178.. ... 2009). "Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of ... "A genome-wide association study of northwestern Europeans involves the C-type natriuretic peptide signaling pathway in the ...
It was reclassified in the genus Shimwellia based on phylogenetic analyses of its genome sequence. The genome of S. blattae is ... about 4.2 megabases in size, slightly smaller than similar enteric bacteria found in humans. It has 56.5% GC content, ... Genomic analysis suggests that the ability of S. blattae to synthesize vitamin B12 has its origins in horizontal gene transfer ... "Complete Genome Sequence of the B12-Producing Shimwellia blattae Strain DSM 4481, Isolated from a Cockroach". Journal of ...
After cyanobacterium genome analysis, the researchers found that over 30% of the genome was made up of pseudogenes. In addition ... Consistent with our previous rules for reduction in genome size, and incorporation of genes into the host genome, peridinin ... decreased genome size within the organelle and gene integration into the nucleus occurred. Chloroplasts genomes encode 50-200 ... and a 3.9 Mb sized genome. However, most plastids rarely exceed 200 protein coding genes. A recent study sequenced the genome ...
Stetter, Markus G.; Schmid, Karl J (2016-11-03). "Analysis of phylogenetic relationships and genome size evolution of the ... "The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly". The Plant Genome. 9 (1): 0. doi:10.3835/ ... "Squalene Market Size to Exceed USD 240 Million by 2022". Global Market Insights Inc. 27 April 2016. Retrieved 14 December 2016 ... The phylogenies of Amaranthus of maximum parsimony and Bayesian analysis of nuclear and chloroplast genes suggest five clades ...
Quantitative trait locus
INTERSNP - a software for genome-wide interaction analysis (GWIA) of case-control SNP data and analysis of quantitative traits ... For early geneticists, it was not immediately clear that the smooth variation in traits like body size (i.e., Incomplete ... Analysis of variance. The simplest method for QTL mapping is analysis of variance (ANOVA, sometimes called "marker ... Garnier, Sophie, Truong, Vinh, Genome-Wide Haplotype Analysis of Cis Expression Quantitative Trait Loci in Monocytes  ...
... virus genomes contain seven genes including 3'-UTR-NP-VP35-VP40-GP-VP30-VP24-L-5'-UTR. The genomes of the five ... "Virological Analysis: no link between Ebola outbreaks in west Africa and Democratic Republic of Congo". World Health ... about the size of a laptop and solar-powered, allows testing to be done in remote areas. ... Replication of the viral genome results in full-length, positive-strand antigenomes that are, in turn, transcribed into genome ...
Hauber, Mark E. (2014). The Book of Eggs: A Life-Size Guide to the Eggs of Six Hundred of the World's Bird Species. University ... Genetic analysis has shown that certain mallards appear to be closer to their Indo-Pacific relatives while others are related ... but the nuclear genome displays a notable lack of genetic structure. Haplotypes typical of American mallard relatives and ... Also, the population size of the mallard is very large.. Unlike many waterfowl, mallards have benefited from human ...
"Phylogeographic Analysis of the mid-Holocene Mammoth from Qagnax Cave, St. Paul Island, Alaska" (PDF).. ... "Callaway, Ewen (22 September 2011), "First Aboriginal genome sequenced", Nature, Nature News, doi:10.1038/news.2011.551 ... allowing them to shrink the size of the gastrointestinal tract relative to body mass and to increase the brain mass instead.[ ... habitat to shrink in size, resulting in a drop in population. The small populations were then hunted out by Paleolithic humans. ...
This section needs expansion with: Genome size differences between algae and land plants, chloroplast stuff coded by the ... "Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of ... Over time, many parts of the chloroplast genome were transferred to the nuclear genome of the host, a process called ... Many of the chloroplast's protein complexes consist of subunits from both the chloroplast genome and the host's nuclear genome ...
"Genome sequence and analysis of a Propionibacterium acnes bacteriophage". Journal of Bacteriology. 189 (11): 4161-7. doi: ... Boxcar scars are round or ovoid indented scars with sharp borders and vary in size from 1.5-4 mm across. Ice-pick scars are ... a systematic review and meta-analysis". The British Journal of Dermatology (Systematic Review & Meta-Analysis). 173 (5): 1132- ... "Journal of Zhejiang University Science B (Meta-analysis). 13 (3): 192-202. doi:10.1631/jzus.B1100285. PMC 3296070. PMID ...
Both the structures and editing sites are conserved in the coleoid genome and the mutation rates for the sites are severely ... The pupil can be adjusted in size and a retinal pigment screens incident light in bright conditions. ... implied alignment and analysis methods". Journal of Molluscan Studies. 73 (4): 399-410. doi:10.1093/mollus/eym038.. ... The California two-spot octopus has had its genome sequenced, allowing exploration of its molecular adaptations. Having ...
The clutch size is usually two, but occasionally one or three eggs are laid about two days apart. The dull white eggs are ... Analyses showed strong niche separation between Brolgas and sarus cranes by diet. It is likely that their diet in dry season ... "Mitochondrial genome sequences and the phylogeny of cranes (Gruiformes: Gruidae)". Auk. 127 (2): 440-452. doi:10.1525/auk. ... Isotopic analyses of molted feathers in their breeding grounds along the Gulf of Carpentaria showed their diet to be diverse ...
Some whole-genome sequencing studies have shown that PAX8 also targets BRCA1 (carcinogenesis), MAPK pathways (thyroid ... "A comprehensive analysis of PAX8 expression in human epithelial tumors". The American Journal of Surgical Pathology. 35 (6): ... small in size, present in a solid/nested growth pattern and frequently involve vascular invasion. It has been observed that ... Genome Research. 6 (9): 791-806. doi:10.1101/gr.6.9.791. PMID 8889548.. ...
DNA analysis consistently shows that all existing red wolves carry coyote genes. This has caused a problem for Canid taxonomy, ... Wayne, R. & Ostrander, Elaine A. (1999). "Origin, genetic diversity, and genome structure of the domestic dog". BioEssays. 21 ( ... barring size or behavioral constraints) and produce fertile offspring. There are two exceptions: the side-striped jackal and ... Analysis on the haplotype of some coyotes from Texas also detected the presence of male wolf introgression such as Y ...
At 4.7 million nucleotides in length, A1::DQ2 is the second longest haplotype identified within the human genome. A1::DQ2 ... The SNP analysis of the haplotype suggests a potential founding affect of 20,000 years within Europe, though conflicts in ... the average size is 1 centiMorgan (or 1 cM). The average length of these 'haplotypes' are about 1 million nucleotides. ... Castaño-Rodríguez N, Diaz-Gallo LM, Pineda-Tamayo R, Rojas-Villarraga A, Anaya JM (February 2008). "Meta-analysis of HLA-DRB1 ...
The genome size of Brassicaceae compared to that of other Angiosperm families is very small to small (less than 3.425 million ... It has long been clear that the Aethionema are sister of the remainder of the family. One analysis from 2014 represented the ... Brassicaceae (/ˌbræsɪˈkeɪsii/) or Cruciferae (/kruːˈsɪfəri/) is a medium-sized and economically important family of ... Early DNA-analysis showed that the Capparaceae-as defined at that moment-were paraphyletic, and it was suggested to assign the ...
Hartl, D.L., Jones, E.W. (2000) Genetics: Analysis of Genes and Genomes. Fifth Edition. Jones and Bartlett Publishers Inc., pp ... They can be computed from genealogies or estimated from the population size and its breeding properties, but all methods assume ... Griffiths AJ, Miller JH, Suzuki DT, Lewontin RC, Gelbart WM (1999). An introduction to genetic analysis. New York: W. H. ... Historical analysis indicated that a population expansion from just two matrilineal lines was responsible for most of the ...
Ndryshimi mes inspektimeve të "Përdoruesi:Tiimiii/I ftohti i zakonshem"
Sequencing and Analyses of All Known Human Rhinovirus Genomes Reveals Structure and Evolution,url=,journal=Science,language=en, ... image_size =. , field = Semundje infektive. , synonym = I ftofti, nazofaringiti akut viral, nazofaringiti, riniti viral, ... A re-analysis and review,url=,journal=Breastfeeding Review,language=en,volume=18,issue=2,pages=25-32,pmid=20879657,via=}},/ref ... www.cnn.com/2009/HEALTH/02/12/cold.genome/,archivedate=26 April 2009,publisher=CNN,language=en,url-status=live,df=dmy-all}},/ ...
... analyses of c-Jun and DJ-1 proto-oncogenes". Cytogenetic and Genome Research. 127 (2-4): 79-93. doi:10.1159/000297715. PMID ... Extant reptiles range in size from a tiny gecko, Sphaerodactylus ariasae, which can grow up to 17 mm (0.7 in) to the saltwater ... As of 2013, three turtle genomes have been sequenced. The results place turtles as a sister clade to the archosaurs, the ... Once full size, the frequency of shedding drastically decreases. The process of ecdysis involves forming a new layer of skin ...
Fluorescence in situ hybridization
The size of the human genome is so large, compared to the length that could be sequenced directly, that it was necessary to ... genome-wide, at unprecedented resolution. Currently, this type of analysis will only detect gains and losses of chromosomal ... measuring the size of each small fragment using size-exclusion chromatography, and using that information to determine where ... divide the genome into fragments. (In the eventual analysis, these fragments were put into order by digesting a copy of each ...
Process design and analysisEdit. Main article: Process design. A unit operation is a physical step in an individual chemical ... Plant construction is coordinated by project engineers and project managers  depending on the size of the investment. A ... The completion of the Human Genome Project is also seen as a major development, not only advancing chemical engineering but ... Modeling and analysis of transport phenomena is essential for many industrial applications. Transport phenomena involve fluid ...
... relative to a reference genome or averaged over many genomes).. For a benchmark in genetics/genomics data compressors, ... The process of reducing the size of a data file is often referred to as data compression. In the context of data transmission, ... Faxin Yu; Hao Luo; Zheming Lu (2010). Three-Dimensional Model Analysis and Processing. Berlin: Springer. p. 47. ISBN ... Christley S, Lu Y, Li C, Xie X; Lu; Li; Xie (Jan 15, 2009). "Human genomes as email attachments". Bioinformatics. 25 (2): 274-5 ...
Lewontin, R. (2000). It Ain't Necessarily So: The Dream of the Human Genome and other Illusions. New York: NYREV Inc. ISBN 88- ... Tor Nørretranders (1998). "Preface". The user illusion: Cutting consciousness down to size (Jonathan Sydenham translation of ... The first part of their analysis (which the only relevant part to this section) was not meant to discover the types of free ... Without entering into metaphysical speculations, I may perhaps add that an analysis of the very concept of explanation would, ...
The size of the exodus increased during and after the war. The monthly number of boat people arriving in Southeast Asia ... Analysis of Vietnamese Kinh people's genetics show that within the last 800 years there was mixture between a Malay-like ... "Phylogeographic and genome-wide investigations of Vietnam ethnic groups reveal signatures of complex historical demographic ... ethnic Chinese controlled 2492 shops or 41 percent of all the small and medium-sized shops in Saigon-Cholon's nine districts. ...
In some currencies, such as the euro, the pound sterling and the Indian rupee, the size of a note increases with its value. ... Recent advances in mapping of the human genome have identified other genetic causes of low vision or blindness. One such ... a systematic analysis for the Global Burden of Disease Study 2015". Lancet. 388 (10053): 1545-1602. doi:10.1016/S0140-6736(16) ... They use a combination of vision and other senses to learn, although they may require adaptations in lighting or the size of ...
Tree Genetics & Genomes, 12. *^ Meegahakumbura MK, MC Wambulwa, M Li, et al. 2018. Domestication origin and breeding history of ... Leaf size is the chief criterion for the classification of tea plants, with three primary classifications being, Assam type ... plants are not necessarily the evidence of the dualism hypothesis from the researches using the statistical cluster analysis ... characterised by leaves of intermediate size. The Cambod type tea (C. assamica subsp. lasiocaly) was originally considered a ...
The tiny 490,885 base-pair genome of Nanoarchaeum equitans is one-tenth of this size and the smallest archaeal genome known; it ... Comparative analysis of archaeal genomes has also identified several molecular signatures in the form of conserved signature ... "Genome Biol. Evol. 7 (1): 191-204. doi:10.1093/gbe/evu274. PMC 4316627 . PMID 25527841.. ... "Genome Biol. 3 (2): REVIEWS0003. doi:10.1186/gb-2002-3-2-reviews0003. PMC 139013 . PMID 11864374.. ...
Bird of prey
"Whole-genome analyses resolve early branches in the tree of life of modern birds" (PDF). Science. 346 (6215): 1320-1331. doi: ... The true hawks are medium-sized birds of prey that usually belong to the genus Accipiter (see below). They are mainly woodland ... Falcons are medium-size birds of prey with long pointy wings. They belong to the Falconidae family, rather than the ... Based on some comparative analyses, diet breadth also has an effect on the evolution of migratory behaviour in this group, ...
The other types of densification are larger in size compared to a pellet and are compatible with a broad range of input ... Brinkman, N. et al., "Well-to-Wheels Analysis of Advanced/Vehicle Systems", 2005. ... This process includes grinding the raw biomass to an appropriate particulate size (known as hogfuel), which, depending on the ...
"The size and regional distribution of the black population". Lewis Mumford Center. Archived from the original on 12 October ... "Genome-wide patterns of population structure and admixture in West Africans and African Americans". Proceedings of the ... "The trans-Saharan slave trade - clues from interpolation analyses and high-resolution characterization of mitochondrial DNA ...
Pyruvate dehydrogenase (lipoamide) alpha 2
"Genome Res. 14 (10B): 2121-7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334.. ... The entire human complex is 9.5 MDa in size, and has been described as 60-meric, meaning there are over 60 components that are ... it is recommended to perform a detailed biochemical analysis on a muscle biopsy in females with a suspected pyruvate ... 2001). "The sequence of the human genome". Science. 291 (5507): 1304-51. doi:10.1126/science.1058040. PMID 11181995.. ...
Schein, Martin W.; Holmes Orgain (1 November 1953). "A Preliminary Analysis of Garbage as Food for the Norway Rat". Am. J. Trop ... Stories of rats attaining sizes as big as cats are exaggerations, or misidentifications of larger rodents, such as the coypu ... View the rat genome in Ensembl. *View the rn5 genome assembly in the UCSC Genome Browser. ... There is great debate over the size of the population of rats in New York City, with estimates from almost 100 million rats to ...
A phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the ... These plants are large shrubs or small to moderate-sized trees, reaching 5-15 m (16-49 ft) tall, with spiny shoots and ... "Journal of Food and Drug Analysis. 26 (2): S61-S71. doi:10.1016/j.jfda.2018.01.009. ISSN 1021-9498. PMID 29703387.. [permanent ... "Journal of Food and Drug Analysis. 25 (1): 71-83. doi:10.1016/j.jfda.2016.11.008. ISSN 1021-9498. PMID 28911545.. [permanent ...
Genome Size, Antioxidant Potential and Phytochemistry". Planta Medica. 74 (4): 474-81. doi:10.1055/s-2008-1034358. PMID ... Journal of Pharmaceutical and Biomedical Analysis. 63: 120-7. doi:10.1016/j.jpba.2012.01.027. PMID 22342658.. ... "Phytochemical and biological analysis of skullcap (Scutellaria lateriflora L.): a medicinal plant with anxiolytic properties" ...
Genome size determination in peronosporales (Oomycota) by Feulgen image analysis. - PubMed - NCBI
Genome size determination in peronosporales (Oomycota) by Feulgen image analysis.. Voglmayr H1, Greilhuber J. ... Genome size was determined, by nuclear Feulgen staining and image analysis, in 46 accessions of 31 species of Peronosporales ( ... The applicability and limitations of Feulgen photometry are discussed in relation to other methods of genome size determination ... which was used as an internal standard for genome size determination. The linearity of Feulgen absorbance photometry method ...
Genome Editing Market Size, Share, Analysis, Report and Forecast... - Stratistics Market Research Consulting
... the Global Genome Editing market is estimated at $2098.9 million in 2015 and is expected to reach $5367.64 million by 2022... ... Genome Editing Market Size, Share, Analysis, Report and Forecast to 2022. Press Release • Nov 04, 2016 00:14 EDT ... Genome Editing Services. • Software. • Reagents, Enzymes and Consumables. o Delivery Tools. o Genome Editing Tools And Kits. o ... Market share analysis of the top industry players. - Strategic recommendations for the new entrants. - Market forecasts for a ...
Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size. - PubMed -...
Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size.. Hatfull GF1 ... Comparative genomic analysis of sixty mycobacteriophage genomes: Genome clustering, gene acquisition and gene size ... Comparative genomic analysis of sixty mycobacteriophage genomes: Genome clustering, gene acquisition and gene size ... Comparative genomic analysis of sixty mycobacteriophage genomes: Genome clustering, gene acquisition and gene size ...
Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals ...
Meta-analysis of data from 58,265 cattle shows that the genetic architecture underlying stature is similar to that in humans, ... Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals ... P.S. acknowledges funding from the Genome Canada project entitled Whole Genome Selection through Genome Wide Imputation in ... Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor *Jiantao Zhao ...
Power Analysis of C-TDT for Small Sample Size Genome-Wide Association Studies by the Joint Use of Case-Parent Trios and Pairs
... image analysis, epidemiology, immunology, time series analysis, extracellular matrix properties and signalling, and tissue ... Power Analysis of C-TDT for Small Sample Size Genome-Wide Association Studies by the Joint Use of Case-Parent Trios and Pairs. ... Upon considering genome-wide significance level as 0.05, for each sample size, the corrected values which are resulting from ... Finally, the simulation is repeated 100 times for each sample size. Under any sample size, at any simulation repetition, the ...
Genome Engineering Market Growth by 2020- Global Market Analysis, Size, Share, Trends, Key Vendors, Drivers and Forecast |...
The Global Genome Engineering Market report covers the presen ... The Global Genome Engineering Market to GROW at a CAGR of 12.25 ... Genome Engineering Market Growth by 2020- Global Market Analysis, Size, Share, Trends, Key Vendors, Drivers and Forecast. ... The Global Genome Engineering Market report covers the present scenario and the growth prospects of the Genome Engineering for ... Genome Engineering Market Opportunities:. With a purpose of enlightening new entrants about the possibilities in this market, ...
Identification of Molecular Pathways and Candidate Genes Associated With Cocks' Comb Size Trait by Genome-Wide Transcriptome...
Although quantitative trait loci (QTLs) related to comb size have been identified, molecular mechanisms underlying this trait ... Comb Size Trait by Genome-Wide Transcriptome Analysis Sci Rep. 2018 Jan 31;8(1):2015. doi: 10.1038/s41598-018-20373-6. ... Functional annotation analysis revealed that DEGs were involved in cell communication and calcium signaling. Protein-protein ... Our data provide a source for identifying genes and pathways with functions critical to comb size and accelerate studies ...
Genome Analysis > Size Markers > RNA Laboratory Product Directory and Equipment Reviews on...
Size Markers > RNA products in the SelectScience products and suppliers directory ... Read reviews and compare manufacturers of Genome Analysis > ... Flow Injection Analysis Tandem Mass Spectrometry (FIA-MS/MS) in ... MVP RNA is application-ready RNA available in small economical pack sizes. Extensive and rigorous quality control including ...
Insects | Free Full-Text | Estimation of the Whitefly Bemisia tabaci Genome Size Based on k-mer and Flow Cytometric Analyses
K-mer analysis using these sequences revealed that the genome size of the whitefly was ~682.3 Mb. In addition, the flow ... As a starting point to genome sequencing, we report a new estimation of the genome size of the B. tabaci B biotype or Middle ... cytometric analysis estimated the haploid genome size of the whitefly to be ~690 Mb. Considering the congruency between both ... we predict the haploid genome size of B. tabaci MEAM1 to be ~680-690 Mb. Our data provide a baseline for ongoing efforts to ...
Single-Cell Genome Sequencing Market Size, Share & Trends Analysis Report By Product, By Technology (PCR, NGS, qPCR), By...
Trends Analysis Report By Product, By Technology (PCR, NGS, qPCR), By Workflow, By Application, By Disease Area, By End Use, ... Single-Cell Genome Sequencing Market Size, Share & Trends Analysis Report By Product, By Technology (PCR, NGS, qPCR), By ... Single-Cell Genome Sequencing Market Size, Share & Trends Analysis Report By Product, By Technology (PCR, NGS, qPCR), By ... 3.4 Industry Analysis - Porters. Chapter 4 Single-cell Genome Sequencing Categorization: Product Estimates & Trend Analysis. ...
Comparative analysis of genome sizes of Streptococcus thermophilus strains, Russian Journal of Genetics | 10.1134...
"Comparative analysis of genome sizes of Streptococcus thermophilus strains, Russian Journal of Genetics" on DeepDyve, the ... Comparative analysis of genome sizes of Streptococcus thermophilus strains. Comparative analysis of genome sizes of ... genomic fingerprinting analysis has shown variability in both genome size and restriction fragments length. The genomes varied ... genomic fingerprinting analysis has shown variability in both genome size and restriction fragments length. The genomes varied ...
Molecular characterization of Pistacia atlantica Desf. subsp. atlantica (Anacardiaceae) in Algeria: Genome size determination,...
... chromosome count and genetic diversity analysis using SSR markers, Scientia Horticulturae" on DeepDyve, the largest online ... Phylogenetic analysis of DNA C-values provides evidence for a small ancestral genome size in flowering plants ... atlantica MARK (Anacardiaceae) in Algeria: Genome size determination, chromosome count and genetic diversity analysis using SSR ... atlantica MARK (Anacardiaceae) in Algeria: Genome size determination, chromosome count and genetic diversity analysis using SSR ...
Genome Integrity Analysis of Adeno-Associated Viruses (AAV) by Genome Sizing Methodology
... Sponsored by: SCIEX C.E. Credits: P.A ... Discover a Genome Sizing Methodology for Transgene Integrity Analysis of AAV Gene Therapies ... Quantitative western blotting analysis: tips, considerations, and streamlining analysis using Invitrogen iBright Analysis ... errors can happen leading to packaging of truncated genome as well as fragments from host cell genome and plasmid vector. Size ...
Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes |...
Comparative analysis demonstrated that ~57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L ... Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative ... Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate ... Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. ...
Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis | BMC Bioinformatics | Full Text
In this study, an Integrated Genome Sizing (IGS) approach is adopted to speed up multiple whole genome analysis in high- ... storing raw sequence reads to perform large-scale genome analysis pose hardware challenges. Despite advancement in genome ... Using a single reference pilot genome, NA12878, we compared the NGS process time between Maha-Fs (NFS SATA hard disk drive) and ... The implementation of IGS can leverage the ability of HPC systems to analyze multiple genomes simultaneously. We believe this ...
Genome Wide Analysis of Drug-Induced Torsades de Pointes: Lack of Common Variants with Large Effect Sizes - UCL Discovery
Genome Wide Analysis of Drug-Induced Torsades de Pointes: Lack of Common Variants with Large Effect Sizes. PLoS One , 8 (11) , ... Genome Wide Analysis of Drug-Induced Torsades de Pointes: Lack of Common Variants with Large Effect Sizes ... Genome Wide Analysis of Drug-Induced Torsades de Pointes: Lack of Common Variants with Large Effect Sizes. ... With these sample sizes, there is 80% power to detect a variant at genome-wide significance with minor allele frequency of 10% ...
Dynamics of genome size evolution in birds and mammals | PNAS
2003) Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes. Genome Res ... Cytological haploid genome sizes are from ref. 32. There were no reported genome sizes for two species, so the size of the ... There were no reported genome sizes for 2 mammals and 11 bird species (genome size in italic), so the size of the closest ... 53) and avian (46) genomes, we characterize genome size evolution in mammals and birds through an integrated analysis of DNA ...
Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
The largely continuous genome assembly will be useful for comparative genomics and offers an opportunity to look into regions ... Though ,500 eukaryotic genome sequences are available in public repositories, the majority are highly fragmented with ... population structure of the species was analysed based on low-coverage genome sequence information from 61 individuals ... Author Summary We describe the genome assembly of Asian seabass (Lates calcarifer), a marine teleost with aquaculture relevance ...
Drosophila Genome Size Larger than Estimated, Says Celera Genomics | GenomeWeb
... genome, have said that the organism now appears to be larger than originally thought. ... In Science this week: genomic analysis of ancient and modern horses indicates population turnover, and more. ... Drosophila Genome Size Larger than Estimated, Says Celera Genomics Aug 27, 1999 ... Combining CNV and SNV Analysis for Genomic Diagnostics on a Single Sample and Platform. ...
Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful...
Differential gene expression analysis may discover a set of genes too large to easily investigate, so a means of ranking genes ... Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci. ... standardized effect sizes are used. Cohens d is one such standardized effect size. Cohens d is the ratio of an effect size to ... Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010; ...
Frontiers | Prophylactic Bacteriophage Administration More Effective than Post-infection Administration in Reducing Salmonella...
Determination of Phage Genome Size by Agarose Gel Electrophoresis. The relatively small genome of PSE made it possible to use ... The analysis of phage nucleic acid suggested that PSE is a DNA phage as the genome was completely digested by DNase I, but ... and determination of phage genome size (B). Lanes contained the following: 1, digested genome of PSE with DNase I; 2, un-cut ... The estimated genome size of PSE was approximately 35.72 kb (Figure 5). Two restriction enzymes used in this study, EcoRI and ...
A Genome-Wide Association Study Identifies Multiple Regions Associated with Head Size in Catfish | G3: Genes | Genomes |...
2007 PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81(3): 559-575. ... A Genome-Wide Association Study Identifies Multiple Regions Associated with Head Size in Catfish. Xin Geng, Shikai Liu, Jun Yao ... A Genome-Wide Association Study Identifies Multiple Regions Associated with Head Size in Catfish. Xin Geng, Shikai Liu, Jun Yao ... A Genome-Wide Association Study Identifies Multiple Regions Associated with Head Size in Catfish. Xin Geng, Shikai Liu, Jun Yao ...
Genome size analyses of Pucciniales reveal the largest fungal genomes<...
Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome ... Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome ... Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome ... Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome ...
Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis. -...
Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis.. ... Forty-Three Loci Associated with Plasma Lipoprotein Size, Concentration, and Cholesterol Content in Genome-Wide Analysis ... Forty-Three Loci Associated with Plasma Lipoprotein Size, Concentration, and Cholesterol Content in Genome-Wide Analysis ... Among 36 loci with genome-wide significance (P,5x10(-8)) in primary and secondary analysis, ten (PCCB/STAG1 (3q22.3), GMPR/ ...
Pleiotropic loci underlying bone mineral density and bone size identified by a bivariate genome-wide association analysis -...
Pleiotropic loci underlying bone mineral density and bone size identified by a bivariate genome-wide association analysis H ... Pleiotropic loci underlying bone mineral density and bone size identified by a bivariate genome-wide association analysis H ... Methods: We conducted a bivariate genome-wide association (GWA) analysis of hip BMD and hip BS in 6180 participants from 5 ... a bivariate genome-wide association analysis. Wei XT, Feng GJ, Zhang H, Xu Q, Ni JJ, Zhao M, Yang XL, Tian Q, Shen H, Hai R, ...
Analysis of Genome Size of Sixteen Coffea arabica Cultivars Using Flow Cytometry in: HortScience Volume 54 Issue 6 (2019)
HuangH.TongY.ZhangQ.J.GaoL.Z.2013Genome size variation among and within Camellia species by using flow cytometric analysisPLoS ... CarvalhoC.R.ClarindoW.R.2011Flow cytometric analysis using SYBR Green I for genome size estimation in coffeeActa Histochem.113 ... SiskoM.IvancicA.BohanecB.2003Genome size analysis in the genus Cucurbita and its use for determination of interspecific hybrids ... Flow cytometric analysis using SYBR Green I for genome size estimation in coffee. Acta Histochem.. 113. 221. 225. ), false ...
Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing | BMC Genomics | Full...
... comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size ... holocanthus has a low gene density and repeat elements rich genome. Genome size variation between D. holocanthus and the smooth ... A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp) in D. holocanthus genome is ... The length difference of intron is consistent with the genome size variation between D. holocanthus and the smooth pufferfish. ...
Genome size and ploidy level among wild and cultivated Prunus taxa in Slovakia | SpringerLink
Doležel J, Greilhuber J, Suda J (2007) Flow cytometry with plant cells: analysis of genes, chromosomes and genomes. WILEY-VCH ... Doležel J, Bartoš J (2005) Plant DNA Flow Cytometry and Estimation of Nuclear Genome Size. Ann Bot 95:99-110CrossRefPubMed ... Siljak-Yakovlev S, Pustahija F, Šolić EM, Bogunić F, Muratović E, Bašić N, Catrice O, Brown SC (2010) Towards a genome size and ... The aim of the study was to define genome sizes and find differences between closely related taxa within Prunus spinosa sensu ...
Global Genome Sequencing Equipment Market Analysis By Key Players, Industry Growth, Size, Share, Trends, Sales Forecast To 2025...
Genome Sequencing Equipment, Genome Sequencing Equipment industry, Genome Sequencing Equipment market, Genome Sequencing ... Genome Sequencing Equipment Market Segment, Genome Sequencing Equipment market Share, Genome Sequencing Equipment market Size, ... Genome Sequencing Equipment market Analysis, Genome Sequencing Equipment Market Application, Genome Sequencing Equipment Market ... Global Genome Sequencing Equipment Market Analysis By Key Players, Industry Growth, Size, Share, Trends, Sales Forecast To 2025 ...
Genomic analysis of uncultured marine viral communities | PNAS
Effect of Varying Average Genome Size on Model Predictions.. To study the effect of the genome size on the predictions of the ... but most calculations found M similar in size to the predicted value for the 50-kb genome size given in Table 2. ... 75 fragments of 663 bp to constitute an average sized marine phage genome of 50 kb, Chao1 predicts 423 different viral genomes ... The best fit b parameter was very similar for all genome sizes. Because of the error associated with the M parameter, there was ...
GenesSequenceFlow cytometryGeneSequencesPhylogeneticChromosomesHuman genomeSpeciesPlant genomesGeneticGWAS2017AnnotationLociEvolutionGenomicsMajor determinant of genome sizeGenomic analysisEvolutionaryEukaryotesOrganismsDifferencesReference genomeMethods of genome size determinationPerformed a genome-wideGeneticsTaxaBiologyDiploidFluorescence in situ hybrCompletely sequencedSmall genomesBacterial GenomesCorrelation between genome sizePlastidViral genomesTotal genome sizeCharacterize the genomeDiversityPloidyHigh-throughputOrganismSingle-cell genomeNucleotideDeterminationStudyEukaryotic genomeData2020DraftCytogeneticFungalTransposable element
- Genome clustering facilitates the identification of genes that are in greatest genetic flux and are more likely to have been exchanged horizontally in relatively recent evolutionary time. (nih.gov)
- Although mycobacteriophage genes exhibit a smaller average size than genes of their host (205 residues compared with 315), phage genes in higher flux average only 100 amino acids, suggesting that the primary units of genetic exchange correspond to single protein domains. (nih.gov)
- There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals. (nature.com)
- Derived variants at six genes explain nearly half of size reduction in dog breeds. (nature.com)
- Our data provide a source for identifying genes and pathways with functions critical to comb size and accelerate studies involving molecular mechanisms of this sexual ornament. (nih.gov)
- Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. (nature.com)
- Differential gene expression analysis may discover a set of genes too large to easily investigate, so a means of ranking genes by biological interest level is desired. (biomedcentral.com)
- A common default presentation of differential expression analysis results is to list genes in order of an "FDR adjusted p value. (biomedcentral.com)
- Head size genetic loci were mapped in catfish to genomic regions with candidate genes involved in bone development. (g3journal.org)
- Comparative analysis indicated that homologs of several candidate genes are also involved in skull morphology in various other species ranging from amphibian to mammalian species, suggesting possible evolutionary conservation of those genes in the control of skull morphologies. (g3journal.org)
- In total, 776 kb of non-redundant sequences without gap representing 0.1% of the D. holocanthus genome were identified, and 77 distinct genes were predicted. (biomedcentral.com)
- A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp) in D. holocanthus genome is significantly longer than that in the smooth pufferfish genome (435 bp). (biomedcentral.com)
- Additionally, because viral genomes contain genes (e.g., holins, lysozyme) that must be disrupted before cloning, we have not been able to create a representative cosmid library from these communities. (pnas.org)
- Genomes of these viruses are ≈200 kb long, have highly conserved central regions coding for replication and assembly machinery, and have more variable terminal ends that contain genes involved in host range determination and pathogenesis ( 1 ). (cdc.gov)
- In this context, "genome size" was being used in the sense of genotype to mean the number of genes. (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)
- orange, genes present only in En. (asm.org)
- gray, genes absent from both genomes. (asm.org)
- Complete list of genes in the genome of Endomicrobium proavitum (Data Set S1) and genes of " Ca. Endomicrobium trichonymphae" strain Rs-D17 that have no homologs in Endomicrobium proavitum (Data Set S2). (asm.org)
- Sharon Browning of the University of Washington and colleagues developed a method to estimate historical effective population size, which is the number of individuals who pass on their genes to the next generation, to reveal the shifting demographic history of U.S. populations during the last several thousand years. (eurekalert.org)
- By looking at genome-wide data from several hundred individuals from a population, scientists can learn not only the current effective population size, but also the sizes of the ancestral populations that once contributed their genes. (eurekalert.org)
- The Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched analysis suggested that some of the genes were significantly associated with the sex determination process of P. bungeana , such as those involved in tryptophan metabolism, zeatin biosynthesis, and cysteine and methionine metabolism, and the phenylpropanoid biosynthesis pathways. (mdpi.com)
- Chloroplast genome evolution seems to have evolved in a punctuated fashion, with episodes of loss involving suites of genes or tRNAs followed by stabilization of gene content in major clades. (biomedcentral.com)
- Genome size compared to number of genes. (wikipedia.org)
- Then they compared these known grass genes to direct ancestors of wheat, whose genomes are much simpler than modern wheat cereal grasses. (nsf.gov)
- Analysis of genes disrupted by the transforming DNA will lead to new information regarding the basis for the infection of sugarbeet by this pathogen. (usda.gov)
- Several genomic markers have been associated with body size traits and genes have been identified as causative candidates in humans, dog and cattle. (pubmedcentralcanada.ca)
- A limited number of related GWAS have been performed in various sheep breeds and have identified genomic regions and candidate genes that partly account for body size variability. (pubmedcentralcanada.ca)
- A guilt-by-association-based (GBA) prioritization analysis (PA) was performed to identify the most plausible functional candidate genes. (pubmedcentralcanada.ca)
- GBA-based PA identified 39 genes that were significantly associated with gene networks relevant to body size traits. (pubmedcentralcanada.ca)
- The results of this GWAS provide evidence for 39 causative candidate genes across nine chromosomal regions for body size traits, some of which are novel and some are previously identified candidates from other studies (e.g. (pubmedcentralcanada.ca)
- The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. (springer.com)
- Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references. (springer.com)
- Candidate genes are prioritized based on enrichment analyses in pathways related to the phenotype (e.g., neuronal activity regulation) or some other disease feature shared by the genes (e.g., expression in the brain). (biomedcentral.com)
- Regardless of the study design, the analysis with respect to functional convergence follows a similar (and largely separable) design: genes selected as hits are tested for the presence of some joint signature with the null provided by genes which are not hits. (biomedcentral.com)
- With the genome sequenced, researchers have begun to search for genes responsible for the organism's capacity to adapt and break down a variety of waste products. (genomenewsnetwork.org)
- The development of assays for quantitative analysis of the relative transcript levels of ABC transporter genes by real-time reverse transcription-PCR (RT-PCR) might provide important information about multidrug resistance in filamentous fungi. (asm.org)
- Genomics is a discipline in genetics that studies the genome composition of organisms and the precise structure of genes and their expression and regulation. (hindawi.com)
- Here, we summarize advances in aquatic plant genomics with a focus on molecular markers, the genes related to photosynthesis and stress tolerance, comparative study of genomes and genome/transcriptome sequencing technology. (hindawi.com)
- In addition to identifying associations with genes previously implicated with measures of glucose metabolism in nonpregnant populations, we identified two novel genome-wide significant associations: 2-h plasma glucose and HKDC1 , and fasting C-peptide and BACE2 . (diabetesjournals.org)
- Charlesworth B (1996) The changing sizes of genes. (els.net)
- Phylogenetic relationships in the order Ericales s.l.: analyses of molecular data from five genes from the plastid and mitochondrial genomes. (semanticscholar.org)
- Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. (semanticscholar.org)
- During latency, viral genomes exist as extrachromosomal episomes in the nucleus and, being largely silenced by host-driven methylation of CpG island motifs, are only able to express a small subset of genes including latent proteins with oncogenic potential and viral miRNAs . (thefreedictionary.com)
- In a recent genome wide association study, polymorphisms in the DSCAM and CNTNAP2 genes were reported to be related with susceptibility of AIS. (jove.com)
- Synteny analysis revealed a high level of homology between gilthead sea bream genes. (csic.es)
- Transcriptional analyses across six different tissues (anterior and posterior intestine, skeletal muscle, liver, gills, spleen) indicated that gene duplication preferentially affected genes expressed in two or more tissues. (csic.es)
- Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and Mycobacterium rhodesiae NBB3, while it is more distant to M. smegmatis mc2 155. (diva-portal.org)
- Individual genome sequences were concatenated into a single sequence arranged such that related genomes were adjacent to each other. (nih.gov)
- We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. (nature.com)
- Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution. (nature.com)
- The use of whole genome sequence has increased recently with rapid progression of next-generation sequencing (NGS) technologies. (biomedcentral.com)
- However, storing raw sequence reads to perform large-scale genome analysis pose hardware challenges. (biomedcentral.com)
- The approach splits a genome (GRCh37) into 630 chunks (fragments) wherein multiple chunks can simultaneously be parallelized for sequence analyses across cohorts. (biomedcentral.com)
- The declining cost of generating a DNA sequence is promoting an increase in the uptake of whole genome sequencing (WGS), especially when applied to the human genome. (biomedcentral.com)
- On the other hand, the genome-wide association studies (GWAS) [ 2 ] and the HapMap project [ 3 , 4 ] have already characterized many sequence variants and their association to match disease phenotypes. (biomedcentral.com)
- To optimize the computational environment for genetic analysis, we present Integrated Genome Sizing (IGS), a method that splits a full genome sequence into tiny sizable fragments to speed-up genome analysis. (biomedcentral.com)
- Firstly, the genome sizing uses a concept of storing and localizing sequence data, which seeks to reduce the size of input data for improving the system performance. (biomedcentral.com)
- A chunk is a nucleotide sequence with an average size of approximately 5 MB. (biomedcentral.com)
- In addition, population structure of the species was analysed based on low-coverage genome sequence information from 61 individuals representing diverse geographic locations stretching from North-Western India across South-East Asia and Australia to Papua New Guinea. (plos.org)
- The results also showed that it would be possible to sequence the entire genome of an uncultured marine viral community. (pnas.org)
- While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. (slideshare.net)
- We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. (slideshare.net)
- Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes. (slideshare.net)
- Sequencing of the BAC ends generated 12.6 Mb of random sequence representative of the genome. (nih.gov)
- Our study represents a crucial step in the perspective of the determination and study of the whole Bg tritici genome sequence. (nih.gov)
- The ability to quickly sequence the human genome in the future may have significant impacts on medicine. (wikibooks.org)
- Comparative analysis of the protective antigen gene sequence in 25 diverse strains found only five differences across 2,500 nucleotides ( 18 ). (asm.org)
- This volume focuses on the latest methods used to sequence, assemble, and analyze insect genomes. (springer.com)
- bioinformatics analysis of epigenetic modifications, high-throughput scanning of insect genomes (TEEseq) for the presence of endosymbionts, and leveraging genome sequence information to design RNAi strategies. (springer.com)
- The impact of the research already has been considerable because the authors provided the sequence and analyses directly to users in industry and academia to jumpstart uses as soon as the genome analysis was generated in August 2010. (nsf.gov)
- Theoretically, genome sizes can be determined by DNA sequencing at the highest resolution at nucleotide level, however sequence data do not cover the whole genome owing to unresolvable gaps and the omission of centromeres and telomeres. (royalsocietypublishing.org)
- They have obtained a draft genome sequence, which is practically sufficient for comparison with the genomes of other organisms. (eurekalert.org)
- The draft genome sequence is deposited at the DNA Data Bank of Japan (DDBJ*3)) and available through the International Nucleotide Sequence Database Collaboration (INSDC). (eurekalert.org)
- We are now in a position to answer those questions with the genome sequence. (genomenewsnetwork.org)
- We believe the best way to understand a genome is to bring together as many experts as possible to analyze the sequence,' says Galagan. (genomenewsnetwork.org)
- Quantitative nucleic acid sequence analysis has had an important role in many fields of biological research. (asm.org)
- Complete Plastid Genome Sequence of the Basal Asterid Ardisia polysticta Miq. (semanticscholar.org)
- Genome sequence of Pasteurella multocida subsp. (cambridge.org)
- We have recently received NIH funding to sequence 10-20 Mb of the Leishmania genome over the next 5 years. (bio.net)
- The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution. (ipk-gatersleben.de)
- Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea. (ipk-gatersleben.de)
- We present the complete genome sequence for the IV, phlei CCUG21000(T) type strain and the draft genomes for four additional strains. (diva-portal.org)
- The size difference is attributed partly to large bacteriophage sequence fragments in the M. phlei RIVM genome. (diva-portal.org)
- Using four proteogenomic pipelines (integrated transcriptomic-proteomic, Peppy, Enosi, and ProteoAnnotator) on publicly available RNA-sequence and MS proteomics data, we discovered 363 novel peptides in rat brain microglia representing novel proteoforms for 249 gene loci in the rat genome. (mcponline.org)
- Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). (unl.pt)
- In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. (unl.pt)
- In the present work, genome size of 16 cultivars was assessed through high-resolution flow cytometry (FCM). (ashs.org)
- We estimated genome size using flow cytometry in 84 populations of 67 Artemisia species and one population of Crossostephium chinense . (wiley.com)
- 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)
- He has pioneered the use of flow cytometry in plant science for the analysis of nuclear genome size and regularly holds international training courses on the subject. (wiley.com)
- He has constantly been developing novel techniques to study plant genomes, among them many methods based on flow cytometry. (wiley.com)
- Bennett MD, Price HJ and Johnston JS (2008) Anthocyanin inhibits propidium iodide DNA fluorescence in Euphorbia pulcherrima: implications for genome size variation and flow cytometry. (els.net)
- Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size. (nih.gov)
- Sukhodolets, V. 2007-07-23 00:00:00 Twenty-five Streptococcus thermophilus isolates were analyzed using pulse-field gel electrophoresis (PFGE) and gene restriction profile analysis techniques. (deepdyve.com)
- Expanding the number of controls and a gene-based analysis did not yield significant associations. (ucl.ac.uk)
- Here, the effect size of interest is generally the log 2 fold change (LFC) in the relative RNA abundance of each gene between two groups of biological samples. (biomedcentral.com)
- Compared with the smooth pufferfish, D. holocanthus has a low gene density and repeat elements rich genome. (biomedcentral.com)
- It has been postulated that progressive gene loss, primarily at the terminal ends of the genome, has been a driving force behind the evolution of these viruses ( 7 ). (cdc.gov)
- 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)
- Based on the sequenced genomes and gene annotations of 31 plant and algal species in Phytozome version 8.0 ( http://www.phytozome.net/ ), we examined TRs in a genome-wide scale, characterized their distributions and motif features, and explored their putative biological functions. (g3journal.org)
- B) Organization of the gene sets encoding the [FeFe]-hydrogenases in En. (asm.org)
- Genome-wide association identifies ATOH7 as a major gene determining human optic disc size. (sanger.ac.uk)
- The gene comparison also revealed a wheat genome that has undergone genetic loss as a consequence of domestication. (nsf.gov)
- A gene transfer technology useful for gene ablation in this haploid fungus, as well as for gene introduction and analysis, was developed using Agrobacterium tumefacies strain EHA105. (usda.gov)
- 8 ) showed that the combination of the cloning and expression of recombinant protein fragments with immunohistochemistry analysis could be used for systematic protein expression and subcellular localization describing distribution and expression of putative gene products in normal tissues as well as in common cancers and other forms of diseased tissues. (mcponline.org)
- 2013) Convergent gene loss following gene and genome duplications creates single‐copy families in flowering plants. (els.net)
- Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis was repeatedly carried out to verify the linkage of AIS with SNPs rs2222973 in the DSCAM gene and rs11770843 in the CNTNAP2 gene. (jove.com)
- It also provided training in the use of free web tools for clustering and gene set analysis. (otago.ac.nz)
- Single gene analysis resulted in six distinct clusters. (ilri.org)
- A large degree of recent and lineage-specific gene duplications were found, that were mainly enriched in functions related to genome transposition, immune response and response to stimulus. (csic.es)
- This fact makes gilthead sea bream an interesting model for the study of gene repertoire expansion strategies complementary to fish whole genome duplication events. (csic.es)
- K-mer analysis using these sequences revealed that the genome size of the whitefly was ~682.3 Mb. (mdpi.com)
- We took advantage of the recent availability of genome sequences for a wide range of species to investigate the mechanism underlying genome size equilibrium over the past 100 million years. (pnas.org)
- 500 eukaryotic genome sequences are available in public repositories, the majority are highly fragmented with incomplete assemblies, which explains why considerable effort and resources are often spent to improve their quality after publication. (plos.org)
- Genome size variation between D. holocanthus and the smooth pufferfish exhibits as length variation between homologous region and different accumulation of non-homologous sequences. (biomedcentral.com)
- A total of 73 sequences of nrDNA ITS and 3′-ETS were newly generated and analysed, together with previously published sequences, to address the evolution of genome size in a phylogenetic framework. (wiley.com)
- Analysis of BAC-end sequences revealed a massive invasion of transposable elements accounting for at least 85% of the genome. (nih.gov)
- So far about 92.3% of the genome has been sequenced, but its difficult to determine due to non-coding sequences of DNA or "junk" DNA. (wikibooks.org)
- Phylogenetic analyses of the glucose 6-phosphate transporter UhpC (Fig. S1), the catalytic subunit of the ferredoxin/flavodoxin dependent 2-oxoacid oxidoreductases (Fig. S2), the catalytic subunit (EchE) of [NiFe]-hydrogenases (Fig. S3), isopropylmalate/citramalate/homocitrate synthases (Fig. S4), transporter proteins for aromatic amino acids, proline, and serine (Fig. S5), and amino acid sequences of ThiE and ThiH (Fig. S6). (asm.org)
- We don't know (yet) how big the market for whole genome sequences will be, or what impact preconception carrier testing might have, but at the moment it is clear that the market for DTC genetic testing is much smaller than expected or than one might surmise from all the media attention. (genomesunzipped.org)
- However, Chlamydomonas and land plants are distantly related with a divergence time of a billion years, so the genome sequences of green algae, closer to land plants, was of clear interest. (eurekalert.org)
- Transposable elements are DNA sequences with the capacity to move within a genome. (exlibris.ch)
- By 2005, on the systematic analysis of the spacer sequences separating the individual direct repeats showed their extrachromosomal and phage-associated origins (19,20). (thefreedictionary.com)
- Differences in 2C values were detected among some lineages, as well as an increase of genome size heterogeneity in subgenera whose phylogenetic relationships are still unclear. (wiley.com)
- Genbank numbers of species included in the phylogenetic analysis. (wiley.com)
- Phylogenetic analysis of the alcohol dehydrogenase AdhE. (asm.org)
- proavitum and strain Rs-D17 and in bacteria with the most closely related orthologs identified in the phylogenetic analysis. (asm.org)
- For a detailed phylogenetic analysis of ThiH and ThiE, see Fig. S7 in the supplemental material. (asm.org)
- 1998. Phylogenetic analysis of DNA C-values provides evidence for a small ancestral genome size in flowering plants. (wikipedia.org)
- Currently, dozens of different molecular markers have been employed to assess genetic diversity for phylogenetic analysis and to identify germplasm. (hindawi.com)
- Although broad‐scale patterns suggest a negative correlation between effective population size and genome size, comparative phylogenetic methods and comparisons of focal taxa have not suggested repeated shifts in genome size are tied to repeated changes in effective population size. (els.net)
- Only minor differences were observed between the different phylogenetic analyses, including branch lengths and additional duplicate or triplicate subclustering. (ilri.org)
- Phylogenetic analysis based on the full genomes supported these clusters. (ilri.org)
- Phylogenetic analysis very commonly produces several alternative trees for a given set of taxa. (newton.ac.uk)
- Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. (nature.com)
- Genome-wide association studies (GWAS) have allowed the mapping of quantitative trait loci (QTL) controlling head shapes in eight chromosomes in dogs. (g3journal.org)
- These analyses are fundamental in the design of control specimens present C-heterochromatic blocks in most of campaigns because their results will help determine the their 22 chromosomes, whereas non-Andean specimens have only 4-7 autosomes with C-banding. (cdc.gov)
- In this study, size and GC content of all chromosomes are measured from the flow karyotypes of GGA, TSC and CNI. (royalsocietypublishing.org)
- Analysis of chromosome GC content in each of these three species shows a higher GC content in smaller chromosomes than in larger chromosomes. (royalsocietypublishing.org)
- Based on our more precise measurements, we find similar genome sizes in chicken, turtle and crocodile, and a relatively higher GC content in the smaller chromosomes of these three species. (royalsocietypublishing.org)
- An electrophoretic karyotype of C. beticola isolate 98-23 revealed the presence of 7-8 chromosomes ranging from ~0.5 megabases to ~5.5 megabases in size, comparable to the size range for the related soybean pathogen, C. kikuchii. (usda.gov)
- Leishmania is a protozoan parasite with a total genome size of 36 Mb, spread over 36 chromosomes. (bio.net)
- Karyotypes of more than 3400 species/subspecies are arranged here by fish systematics and include a list of genome size, sex chromosomes, B chromosomes, polyploidy, and locality of material fish, among others. (epa.gov)
- A set of cytogenetic markers allows the precise identification of all A-genome chromosomes in diploid and polyploid wheat. (ipk-gatersleben.de)
- The assembly comprised 5,039 scaffolds that span 1.24 Gb of the expected 1.59 Gb complete genome size, with 932 scaffolds (~732 Mb) anchored to 24 chromosomes. (csic.es)
- Furthermore, recent advances in biotechnology lead to genome-wide association studies (GWAS) and, in turn, enable genotyping hundreds of thousands of single nucleotide polymorphisms (SNPs) for a human genome [ 1 ]. (hindawi.com)
- Despite advancement in genome analytic platforms, efficient approaches remain relevant especially as applied to the human genome. (biomedcentral.com)
- A famous example is the human genome through the Human Genome Project. (wikibooks.org)
- The human genome project was an international scientific research effort to fully map out the human genome. (wikibooks.org)
- The genome size was estimated to be large (about 2 Gbp, about two-thirds of the human genome). (eurekalert.org)
- Genome size was determined, by nuclear Feulgen staining and image analysis, in 46 accessions of 31 species of Peronosporales (Oomycota), including important plant pathogens such as Bremia lactucae, Plasmopara viticola, Pseudoperonospora cubensis, and Pseudoperonospora humuli. (nih.gov)
- Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. (nature.com)
- There have been substantial advances in the ability to generate draft genome assemblies for many crop species, as well as in dense genotyping platforms to underpin whole-genome prediction 7 . (nature.com)
- However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. (pnas.org)
- Additionally, the fixation probability of slightly deleterious deletions or insertions would be higher in species with smaller effective population sizes, where natural selection acts less efficiently ( 3 , 8 ). (pnas.org)
- We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. (plos.org)
- The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics. (plos.org)
- With aquaculture fish species, head size is also important for economic reasons because it has a direct impact on fillet yield. (g3journal.org)
- Species evolve to have different head shapes and sizes in response to their environments, and in relation to their behavior and mode of survival. (g3journal.org)
- As a companion species, dogs have been artificially bred and selected to have hundreds of breeds, with various overall sizes and various head shapes and sizes ( Schoenebeck and Ostrander 2013 ). (g3journal.org)
- Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. (unl.pt)
- Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. (biomedcentral.com)
- Another striking characteristic of the genome size is that it can vary greatly among different taxonomic categories and even among closely related species. (biomedcentral.com)
- Genome size variation among closely related species is also prevalent and significant. (biomedcentral.com)
- Bureš P, Wang YF, Horová L, Suda J (2004) Genome Size Variation in Central European Species of Cirsium (Compositae) and their Natural Hybrids. (springer.com)
- Nuclear genome sizes are well known to vary enormously among eukaryotic species. (wikipedia.org)
- Among the 31 species, no significant correlation was detected between the TR density and genome size. (g3journal.org)
- Different from nuclear genomes, mitochondrial genomes appear to prefer mononucleotide repeats (A/T) first and dinucleotide repeats (AT) next in 16 investigated plant species ( Kuntal and Sharma 2011 ). (g3journal.org)
- The cluster analysis revealed two distinct genetic groups for the six populations that were sampled in this endemic species, which might be caused by the fragmentation of habitats and long-term geographic isolation among different populations. (mdpi.com)
- Nuclear genome size is highly variable within Cuscuta , particularly within subgenus Grammica , and in some cases may indicate the existence of cryptic species in this large clade of morphologically similar species. (biomedcentral.com)
- Nearly all species of Cuscuta retain some photosynthetic ability, most likely for nutrient apportionment to their seeds, while complete loss of photosynthesis and possible loss of the entire chloroplast genome is limited to a single small clade of outcrossing species found primarily in western South America. (biomedcentral.com)
- All species examined had chlorophyllous ovules and gynoecia except C. chilensis , for which two different flower morphs with gynoecia of various shapes, sizes and colors were examined. (biomedcentral.com)
- In this study, we present whole-genome sequencing data of 104 P. pacificus strains and the draft assembly of the obligate outcrossing sister species P. exspectatus . (genetics.org)
- The animal genome database provides genome size data for 4972 species, including the chicken ( Gallus gallus domesticus , GGA) with a genome size of 1.25 pg equivalent to 1.2 Gb [ 1 ]. (royalsocietypublishing.org)
- Despite the large differences in genome size between these three species according to the database, GGA macrochromosomes, comprising about 70 per cent of the genome, show extensive homology in the karyotypes of TSC and CNI by chromosome painting [ 2 ]. (royalsocietypublishing.org)
- In this study, we use flow karyotypes of GGA, TSC and CNI as representative species of birds, turtles and crocodiles to measure each chromosome size and GC content. (royalsocietypublishing.org)
- Syngenta has a patent pending in 115 countries that, if approved, would give it a multi-genome monopoly over at least 40 plant species. (etcgroup.org)
- However, attempts at estimating effective population sizes ( Ne ) are particularly challenging in bacteria due to their extremely large census populations sizes, varying rates of recombination and arbitrary species boundaries. (springer.com)
- Population dynamics dictate the evolution of species, such that organisms with large effective population sizes ( Ne ) evolve under effective selection, preventing most deleterious alleles to reach fixation in the population, and those with small Ne are more susceptible to genetic drift, whereby alleles can sometimes reach fixation irrespective of their adaptive value. (springer.com)
- It is a composite quantitative trait that has been studied with high-throughput genomic methods, i.e. genome-wide association studies (GWAS) in various mammalian species. (pubmedcentralcanada.ca)
- The other taxa of cultivated potato contain varying ploidy levels (2 X -5 X ), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. (springer.com)
- That the genomes of closely related species vary so much in size raises a lot of biological questions,' says Galagan. (genomenewsnetwork.org)
- In addition, the findings of genetic diversity based on SSR analysis may contribute to establishing conservation programs for some endangered species. (hindawi.com)
- Here, we report the assembly and characterization of the Zostera muelleri genome, a southern hemisphere temperate species. (plantphysiol.org)
- The extent and causes of between‐species changes in transposable element activity should be characterised, to better understand the drivers of genome expansion. (els.net)
- Ai B, Wang ZS and Ge S (2012) Genome size is not correlated with effective population size in the Oryza species. (els.net)
- Preface -- Availability of fish karyotypes -- Fish vouchering and identification -- Classification of the extant fishes -- Historical transition of numbers of karyotyped species/subspecies -- Relationship between karyotype and genome size -- Database of karyotypes: How to use the database -- References -- Journal list -- Index. (epa.gov)
- Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species. (ipk-gatersleben.de)
- Polyploidy is a key factor in the evolution of higher plants and plays an important role in the variation of plant genomes, leading to speciation in some cases. (wiley.com)
- Genlisea nigrocaulis , with 86 Mbp one of the smallest plant genomes, and the 18-fold larger genome of G. hispidula (1,550 Mbp) possess identical chromosome numbers (2 n = 40) but differ considerably in chromatin organization, nuclear and cell size. (frontiersin.org)
- He has studied plant genomes for almost 30 years and is an expert on intraspecific variation of genome size. (wiley.com)
- The present book gives an overview of the impact of transposable elements on plant genomes and explains how to recognize and study transposable elements, e.g. by using state-of-the-art strategies like 'new generation sequencing. (exlibris.ch)
- Field cress ( Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. (nature.com)
- Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. (nature.com)
- However, the importance of genetic mapping and molecular cytogenetics remain undiminished, both in supporting these technologies, and in addressing fundamental biological questions related to genome and karyotype evolution. (nature.com)
- Consequently, the 1000 Genomes Project [ 1 ] in the past had integrated the functional spectrum of human genetic variation for approximately 1092 genomes. (biomedcentral.com)
- Here we used genome-wide association analysis to search for common predisposing genetic variants. (ucl.ac.uk)
- Variation in genome sizes may not always occur at a level where natural selection is strong enough to prevent genetic drift to determine their fate (neutral or effectively neutral variation) ( 3 ). (pnas.org)
- SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. (plos.org)
- However, little is known about the underlying genetic basis of head size. (g3journal.org)
- One approach is the analysis of genome size in these cultivars as a proxy to study its genetic variability. (ashs.org)
- Genome size, defined as the total amount of DNA contained within the haploid chromosome set of an organism, is not only one of the most fundamental genetic properties of living organisms, but also is one of the most mysterious biological traits. (biomedcentral.com)
- Therefore, studies on the One important approach used to establish genetic vari- changes that have taken place in such domestication and ation in T. infestans is cytogenetic analysis. (cdc.gov)
- Size really matters: prior to the era of large genome-wide association studies, the large effect sizes reported in small initial genetic studies often dwindled towards zero (that is, an odds ratio of one) as more samples were studied. (genomesunzipped.org)
- And indeed, in the last four years the genetics community has identified thousands of associations between genetic variants and disease that consistently and robustly replicate, thanks to the crucial innovation of genome-wide association studies done on thousands of individuals. (genomesunzipped.org)
- We present here a genetic linkage map based on analysis of genetic markers in 73 individuals from a single F 2 family, offspring of a cross between H. m. cythera from western Ecuador and H. m. melpomene from French Guiana. (genetics.org)
- The work is a major breakthrough in understanding an exceptionally large and complex genome, and it lays strong foundations for improving wheat through breeding practices and genetic engineering, say researchers. (nsf.gov)
- The analysis has translated this genetic data into accessible tools that will accelerate breeding and the discovery of varieties with better disease resistance and stress tolerance,' said Klaus Mayer from the Helmholtz-Zentrum Munich, who studies environmental health issues in Germany and participated in the analysis. (nsf.gov)
- This discrepancy between predicted and observed population sizes suggests that demographic fluctuations and other mechanisms contribute to the loss of a large part of their genetic diversity. (springer.com)
- 2019 ). The availability of the two potato reference genomes, along with expression data, has facilitated genetic profiling of different potato varieties, particularly in the identification of structural variants such as single nucleotide polymorphisms (SNPs) and larger copy number variations (CNVs). (springer.com)
- To identify genetic loci associated with measures of maternal metabolism obtained during an oral glucose tolerance test at ∼28 weeks' gestation, we performed a genome-wide association study of 4,437 pregnant mothers of European ( n = 1,367), Thai ( n = 1,178), Afro-Caribbean ( n = 1,075), and Hispanic ( n = 817) ancestry, along with replication of top signals in three additional European ancestry cohorts. (diabetesjournals.org)
- Fine‐scale investigation of the mutational and population‐genetic properties of both small and large insertions and deletions should help advance our understanding of how and why genome size evolution has occurred. (els.net)
- Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. (ipk-gatersleben.de)
- We report a draft genome assembly for the teleost gilthead sea bream (Sparus aurata), reconstructed by combination of short- and long-read high-throughput sequencing, and genetic linkage maps. (csic.es)
- GWAS data used on the Zebrafish Mutation Project Web site comes from http://www.genome.gov/gwastudies/ . (sanger.ac.uk)
- GWAS data comes from http://www.genome.gov/gwastudies/ . (sanger.ac.uk)
- Here, we conducted a GWAS in Frizarta dairy sheep with phenotypic data from 10 body size measurements and genotypic data (from Illumina ovineSNP50 BeadChip) for 459 ewes. (pubmedcentralcanada.ca)
- Trio and quad studies are used mainly in WES and WGS study designs, while large case and control cohorts are required for signals in genome-wide association studies (GWAS). (biomedcentral.com)
- In 2017, the global Genome Editing/Genome Engineering market size was million US$ and it is expected to reach million US$ by the end of 2025, with a CAGR of during 2018-2025. (reportsnreports.com)
-  In 2017, a major improvement to this technique, called WGA-X, was introduced by taking advantage of a thermostable mutant of the phi29 polymerase, leading to better genome recovery from individual cells, in particular those with high G+C content. (wikipedia.org)
- 2017 ). The first publicly available potato reference genome was derived from a doubled monoploid clone of S. tuberosum group Phureja (DM1-3), which was sequenced and assembled by the Potato Genome Sequencing Consortium (PGSC 2011 ). (springer.com)
- Partitioning heritability by functional annotation using genome-wide association summary statistics. (nature.com)
- Functional annotation analysis revealed that DEGs were involved in cell communication and calcium signaling. (nih.gov)
- Transposable element annotation in completely sequenced eukaryote genomes. (exlibris.ch)
- This is an incredibly versatile organism,' says James Galagan, who led the annotation and analysis effort at the Whitehead Institute Center for Genome Research in Cambridge, Massachusetts. (genomenewsnetwork.org)
- Genome annotation and functional genomics have developed rapidly and penetrated into many areas of life science, profoundly affecting the future development and direction of research. (hindawi.com)
- Genome-wide detection of proteoforms in the brain would enable better genome annotation of protein coding regions. (mcponline.org)
- Although quantitative trait loci (QTLs) related to comb size have been identified, molecular mechanisms underlying this trait remain mostly unknown. (nih.gov)
- Comparative analysis demonstrated that ~57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. (nature.com)
- Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis. (cdc.gov)
- Thus, genome-wide associations identified novel loci involved with lipoprotein metabolism-including loci that affect the NMR-based measures of concentration or size of LDL, HDL, and VLDL particles-all characteristics of lipoprotein profiles that may impact disease risk but are not available by conventional assay. (cdc.gov)
- Loci with distinct classes of SNP associations among lipoprotein fractions with genome-wide significance. (cdc.gov)
- Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. (sanger.ac.uk)
- Multiple-locus VNTR analysis (MLVA) uses the combined power of multiple alleles at several marker loci. (asm.org)
- Genome-wide significant loci: how important are they? (springer.com)
- Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population. (sanger.ac.uk)
- Expansion of a collection of sequenced phage genomes to a total of 60-all infecting a common bacterial host-provides further insight into their diversity and evolution. (nih.gov)
- Deciphering the forces and mechanisms modulating genome size is central to our understanding of molecular evolution, but the subject has been understudied in mammals and birds. (pnas.org)
- Our data provide evidence for an "accordion" model of genome size evolution in birds and mammals, whereby the amount of DNA gained by transposable element expansion, which greatly varies across lineages, was counteracted by DNA loss through large segmental deletions. (pnas.org)
- Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. (pnas.org)
- These findings support a unified "accordion" model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. (pnas.org)
- On the other hand, a number of correlative associations between genome size and phenotypic traits, such as cell size ( 9 , 10 ) and metabolic rate associated with powered flight ( 11 , 12 ), suggest that natural selection and adaptive processes also shape genome size evolution. (pnas.org)
- Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish. (biomedcentral.com)
- Genome size variation appears to have resulted from a number of different processes over evolution time. (biomedcentral.com)
- The gain and loss of non-coding DNA are considered to be the main force behind the gradual accumulation of genome size variation over evolution time. (biomedcentral.com)
- This also allows one to analyze the chromosomal structure, the effects of evolution upon the genome, and protein structures and functions. (wikibooks.org)
- The monophyletic carnivorous genus Genlisea (Lentibulariaceae) is characterized by a bi-directional genome size evolution resulting in a 25-fold difference in nuclear DNA content. (frontiersin.org)
- This is one of the largest ranges found within a genus so far and makes Genlisea an interesting subject to study mechanisms of genome and karyotype evolution. (frontiersin.org)
- We use the phylogeny to interpret morphological and plastid genome evolution within the genus. (biomedcentral.com)
- This map forms the basis for future comparative linkage analysis of color pattern evolution in Heliconius. (genetics.org)
- However, GGA macrochromosomes show extensive homology in the karyotypes of the red eared slider ( Trachemys scripta elegans , TSC) and the Nile crocodile ( Crocodylus niloticus , CNI), and bird and reptile genomes have been highly conserved during evolution. (royalsocietypublishing.org)
- evidence for karyotypic conservation, chromosome repatterning, and genome size evolution. (amphibiaweb.org)
- For example, heterogeneous samples, rare cell types, cell lineage relationships, mosaicism of somatic tissues, analyses of microbes that cannot be cultured, and disease evolution can all be elucidated through single cell sequencing. (wikipedia.org)
- Together, these results point to a new model of genome architecture evolution in prokaryotes, in which pan-genome sizes, not individual genome sizes, are governed by drift-barrier evolution. (springer.com)
- MITEs, miniature elements with a major role in plant genome evolution. (exlibris.ch)
- Neutral, nearly neutral and adaptive models for the evolution of genome size have been proposed, but strong evidence for the general importance of any of these models remains lacking, and improved understanding of factors driving the activity of TEs should also be considered. (els.net)
- The importance of ancient whole genome duplication events in genome size evolution, particularly in plants, remains to be fully resolved. (els.net)
- Direct estimates of mutational patterns do not suggest that the relative rate and size of small insertion/deletion events are major contributors to genome size evolution. (els.net)
- Ågren JA and Wright SI (2011) Co‐evolution between transposable elements and their hosts: a major factor in genome size evolution? (els.net)
- 2009) Exceptional diversity, non‐random distribution, and rapid evolution of retroelements in the B73 maize genome. (els.net)
- Chalopin D, Naville M, Plard F, Galiana D and Volff JN (2015) Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. (els.net)
- Genome Biology and Evolution 7 (2): 567-580. (els.net)
- Genome stability and evolution: attempting a holistic view. (ipk-gatersleben.de)
- Comparative genome analysis reveals divergent genome size evolution in a carnivorous plant genus. (ipk-gatersleben.de)
- The largely continuous genome assembly will be useful for comparative genomics and offers an opportunity to look into regions less explored such as tandem repeats (the core component of centromeres and telomeres). (plos.org)
- The Human Mitochondrial Genome: From Basic Biology to Disease offers a comprehensive, up-to-date examination of human mitochondrial genomics, connecting basic research to translational medicine across a range of disease types. (researchandmarkets.com)
- In this review, progress in aquatic plant genomics research involving development and application of molecular markers, comparative genomics, functional genomics, and genome sequencing, as well as future prospects, is summarized. (hindawi.com)
- The Otago Genomics & Bioinformatics Facility became an Illumina Propel-certified service provider utilising high-throughput Illumina HiSeq 2500 and MiSeq sequencing platforms, and a Nanostring nCounter Analysis System Core Facility for New Zealand. (otago.ac.nz)
- The facility offered a team of skilled genomics and bioinformatics specialists providing a complete package of project design, data generation, and analysis for researchers. (otago.ac.nz)
Major determinant of genome size1
- Transposable elements and other repetitive DNA represent a major determinant of genome size variation. (els.net)
- In Science this week: genomic analysis of ancient and modern horses indicates population turnover, and more. (genomeweb.com)
- Here we report a genomic analysis of two uncultured marine viral communities. (pnas.org)
- Following a brief introduction that highlights general considerations when analyzing plant cells by flow cytometric methods, the book goes on to discuss examples of application in plant genetics, genomic analysis, cell cycle analysis, marine organism analysis and breeding studies. (wiley.com)
- Details of the genomic analysis are in this week's Nature magazine. (nsf.gov)
- We approached this as perhaps the supreme challenge for genomic analysis with next-gen sequencing, and are delighted to have contributed to this first major step in the physical characterization of the wheat genome,' said Richard McCombie, genetics professor at Cold Spring Harbor Laboratory. (nsf.gov)
- The nature and relative importance of the molecular mechanisms and evolutionary forces underlying genome size variation has been the subject of intense research and debate ( 1 ⇓ ⇓ ⇓ ⇓ ⇓ - 7 ). (pnas.org)
- Sequencing genomes allow scientists to identify homologous proteins and establish evolutionary relationships. (wikibooks.org)
- 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)
- 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)
- Tandem repeats (TRs) extensively exist in the genomes of prokaryotes and eukaryotes. (g3journal.org)
- Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. (biomedcentral.com)
- In diploid organisms, genome size is often used interchangeably with the term C-value. (wikipedia.org)
- The size of the genome represents one of the most strikingly variable yet poorly understood traits in eukaryotic organisms. (els.net)
- In this study, RNA sequencing (RNA-seq) was employed to compare whole transcriptomic differences between two groups of Partridge Shank chickens that are divergent in comb sizes. (nih.gov)
- Since then, great efforts have been devoted to the analysis of head shapes and sizes in dogs in order to understand the genomic basis underlying the large differences ( Schoenebeck and Ostrander 2013 ). (g3journal.org)
- The aim of the study was to define genome sizes and find differences between closely related taxa within Prunus spinosa sensu lato mentioned in previous works. (springer.com)
- The differences in historical effective sizes between these populations can be useful for understanding why individual groups face different health and disease risks. (eurekalert.org)
- Because different study designs are distinguishable by their differences in effect size, this also provides a unified means of incorporating the impact of study design into the analysis of convergence. (biomedcentral.com)
- Similarity analyses were performed using the index of Bray-Curtis, significant differences between samples being determined by the non parametric test of ANOSIM. (bioone.org)
- There were large differences in the relative genome lengths of the isolates as calculated on the basis of the gel pictures. (asm.org)
- Although the rat, mouse, and human genomes are comparable in size ( 8 ), there are large differences in the number of annotated proteins or transcripts ( Table I ). The relatively smaller number of annotations for the rat genome limits its utility as a model organism for studying human diseases. (mcponline.org)
- DM1-3 was soon followed by the reference genome of a S. chacoense clone, M6 (Leisner et al. (springer.com)
- A comparison of 12 monoploid and doubled monoploid clones derived from S. tuberosum accessions, to the DM1-3 reference genome, showed that great heterogeneity in the genomes and that a large portion of their genomes are affected by CNVs (Hardigan et al. (springer.com)
- Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping and Oxford Nanopore technologies. (ipk-gatersleben.de)
Methods of genome size determination2
- The applicability and limitations of Feulgen photometry are discussed in relation to other methods of genome size determination (CHEF gel electrophoresis, reassociation kinetics, genomic reconstruction) that have been previously applied to Oomycota. (nih.gov)
- In prokaryotes, pulsed field gel electrophoresis and complete genome sequencing are the predominant methods of genome size determination. (wikipedia.org)
Performed a genome-wide2
- In this study, we performed a genome-wide association study using the catfish 250K SNP array with backcross hybrid catfish to map the QTL for head size (head length, head width, and head depth). (g3journal.org)
- We performed a genome-wide association study of 17 lipoprotein measures determined by NMR together with LDL-C, HDL-C, triglycerides, ApoA1, and ApoB in 17,296 women from the Women's Genome Health Study (WGHS). (cdc.gov)
- Illumina next generation sequencers at the National Institute of Genetics, Japan, were used for most of genome sequencing. (eurekalert.org)
- Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. (pnas.org)
- Thus, establishing an integrated view of the contribution of gain and loss of DNA to genome size variation (or lack thereof) remains an important goal in genome biology (e.g., refs. (pnas.org)
- Hieronder staan het programma en de vakomschrijvingen van MSc Marine Biology: Research Klik op de naam van een vak in een schema om naar de omschrijving te gaan. (rug.nl)
- Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense . (springer.com)
Fluorescence in situ hybr1
- Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre , L. heterophyllum Benth. (nature.com)
- All genomes are on a circular chromosome and have been completely sequenced. (asm.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)
- i ) Genomic-based methods used to estimate Ne rely on segregating alleles at neutral sites, but since selection might potentially be acting on every nucleotide position in bacterial genomes [ 6 ], identification of strictly neutral sites is challenging. (springer.com)
Correlation between genome size1
- We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. (slideshare.net)
- Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic Plant Hydnora visseri (Hydnoraceae). (semanticscholar.org)
- Viral genomes often contain modified nucleotides that cannot be directly cloned into Escherichia coli . (pnas.org)
Total genome size1
- Phylogenetically corrected correlations (independent contrasts) between total genome size and genomic properties. (els.net)
Characterize the genome1
- Studies were carried out to better characterize the genome of C. beticola and to provide methods for genome manipulation. (usda.gov)
- We therefore assessed genome diversity of viruses in 60 samples obtained from humans with primary and secondary cases of infection from 2005 through 2007. (cdc.gov)
- The genome of M. acetivorans reveals extensive metabolic and physiological diversity. (genomenewsnetwork.org)
- For example, SSR analysis of an aquatic macrophyte Sparganium emersum revealed significant genotypic diversity between populations in two rivers, the Swalm and Rur. (hindawi.com)
- We confirmed that the increase in 2C values in Artemisia polyploids was not proportional to ploidy level, but 1Cx genome size tended to decrease significantly when high ploidy levels were reached. (wiley.com)
- The challenge for antibody-based proteomics is to move from a conventional protein-by-protein approach into a high throughput mode to allow chromosome wide analysis ( 6 , 7 ). (mcponline.org)
- The use of tissue microarrays (TMAs) generated from multiple biopsies combined into single paraffin blocks enabled high throughput analysis of protein expression in various tissues and organs ( 2 ). (mcponline.org)
- 10 ) showed that high throughput analysis of protein expression can be performed with a standard set of tissue microarrays representing both normal and cancer tissues. (mcponline.org)
- Although mass spectrometry (MS)-based proteomics provides a high-throughput method to probe proteins from biological samples, challenges remain in the analysis of MS data to harness its full power. (mcponline.org)
- Accordingly, we re-analyzed publicly available proteomics data and integrated it with high-throughput transcriptomics data to refine rat genome annotations. (mcponline.org)
-  In the context of microbiomes, a genome from a single unicellular organism is referred to as a single amplified genome (SAG). (wikipedia.org)
- The global single-cell genome sequencing market size is expected to reach USD 2.49 billion by 2025, registering a CAGR of 14.64% during the forecast period. (researchandmarkets.com)
- Earlier, single-cell genome sequencing market was dominated by PCR and microarray technologies. (researchandmarkets.com)
- Furthermore, rising number of single-cell genome sequencing centers & associated facilities worldwide is fostering growth prospects. (researchandmarkets.com)
- This figure illustrates steps involved in workflow of single cell genome sequencing. (wikipedia.org)
- for example, the 6 genomes in Cluster D share more than 97.5% average nucleotide similarity with one another. (nih.gov)
- Relation between amount of DNA (deoxyribonucleic acid) gained/lost due to small indels (calculated as the total size of small insertions minus the total size of small deletions) per single nucleotide mutation and genome size, from direct estimation of insertion and deletion events in mutation studies. (els.net)
- Genome size determination in peronosporales (Oomycota) by Feulgen image analysis. (nih.gov)
- This is 0.041- to 0.144-fold that of Glycine max (soybean, 1C = 1.134 pg), which was used as an internal standard for genome size determination. (nih.gov)
- Size determination of rAAV genome offers insights in assessing the transgene integrity of the rAAV. (labroots.com)
- Both are time consuming and with limited precision and resolution on size determination. (labroots.com)
- He is a taxonomist specializing in plant biosystematics, including genome size determination and has co-authored a book on taxonomy analysis. (wiley.com)
- In this paper, a simulation study is carried out to estimate the power and false positive rate of this test across different sample sizes for a family-based genome-wide association study. (hindawi.com)
- In this study, an Integrated Genome Sizing (IGS) approach is adopted to speed up multiple whole genome analysis in high-performance computing (HPC) environment. (biomedcentral.com)
- The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (plos.org)
- The " Global Genome Sequencing Equipment Market " study outlines the market landscape and its growth prospects in the coming years, as well as the leading companies operating in this market. (clarkcountyblog.com)
- The study examines the top 10 most powerful companies in the global Genome Sequencing Equipment Market, including their company profile, operations, financial analysis, SWOT analysis, and Genome Sequencing Equipment Market products and services. (clarkcountyblog.com)
- This study is focused on the market side of genome editing and provides a comprehensive review of genome editing technologies, along with updates on the latest related progress in the field. (bccresearch.com)
- As the first systematic examination of TRs in plant and green algal genomes, our study showed that TRs displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation in plants and green algae. (g3journal.org)
- In the current study, researchers developed a method for estimating past effective population size and used it to analzye data from nine populations enrolled in a Latino health study, and from African-American and European-American populations in Pittsburgh and Memphis. (eurekalert.org)
- Funding: The analyses in this study were supported by NIH research grants GM099568 and HG005701 (funding received by SRB). (eurekalert.org)
- On Twitter, Daniel and Joe dismissed this study out of hand due to its small sample size (n = 23), leading Ed to update his post. (genomesunzipped.org)
- This finding was notable at the time for the size of the study, which involved a total of over 500 individuals from four cohorts, and the effect size of the identified variant-in a population initially identified as low-risk for heart attack, the variant had an odds ratio of over 3 (with a corresponding p-value less than 0.0001). (genomesunzipped.org)
- Targeted at beginners as well as experienced users, this handy reference explains the benefits and uses of flow cytometery in the study of plants and their genomes. (wiley.com)
- To study and forecast the market size of Genome Editing/Genome Engineering in global market. (reportsnreports.com)
- The genome size of C. beticola estimated from the study is ~26-28 Mb. (usda.gov)
- In the present study, we reveal the genome of Chara braunii *1), which is considered to have separated from land plants 550 to 750 million years ago. (eurekalert.org)
- Meta-analysis within each of these study designs is routine, whether using raw data or summary statistics, but combining results across study designs is atypical. (biomedcentral.com)
- The proposed method was successfully applied to depict the kinetic profiles of PhIP, 4'-OH-PhIP, and their precursors in pork model, reducing the analysis time and cost in the kinetic study. (jove.com)
- The size and scope of projects expanded greatly, and included a genome wide association study involving over 1500 genotyping arrays. (otago.ac.nz)
- The first eukaryotic genome to be sequenced is that of Saccharomyces cerevisiae ( S. cerevisiae ) in 1996, and it is commonly known as brewer's yeast. (wikibooks.org)
- The low coefficients of variation (usually between 5 and 10%), repeatability of the results, and compatibility with CHEF data prove the resolution power of Feulgen image analysis. (nih.gov)
- Our data provide a baseline for ongoing efforts to assemble and annotate the B. tabaci genome. (mdpi.com)
- Although many sequenced genomes already exist, whole genome and exome sequencing projects [ 5 ] have doubled with more data expected to accumulate in the future. (biomedcentral.com)
- However, processing the data is computationally resource-intensive, since numerous intermediate analyses require different applications, often having a large size of input data. (biomedcentral.com)
- One area this shift has not yet occurred is in differential expression analysis of microarray and RNA-Seq data. (biomedcentral.com)
- He kindly shared his data with us, and agreed to an exchange here on Genomes Unzipped. (genomesunzipped.org)
- The problem is how to go about estimating a market size when there is precious little data, and the companies are all privately owned? (genomesunzipped.org)
- The raw data of the wheat genome is like having tens of billions of scrabble letters,' said Neil Hall, a lead researcher at the University of Liverpool's Centre for Genome Research in the United Kingdom. (nsf.gov)
- These data suggest that a common ancestor of birds, turtles and crocodiles had a small genome size and a chromosomal size-dependent GC bias, distinct from the squamate lineage. (royalsocietypublishing.org)
-  Like typical NGS experiments, the protocols of single cell sequencing generally contain the following steps: isolation of a single cell, nucleic acid extraction and amplification, sequencing library preparation, sequencing and bioinformatic data analysis. (wikipedia.org)
- Using nextgen sequencing data to investigate genome size variation and transposable element content. (exlibris.ch)
- The results are presented as a publicly available protein atlas database, and the data suggest that it should be possible to extend this analysis to most or all human proteins. (mcponline.org)
- A valuable tool for medical and biological research can thus be envisioned as a complement to genome and transcript profiling data. (mcponline.org)
- During its infancy the facility provided assistance with rudimentary data analysis, including data normalisation and simple statistical analysis. (otago.ac.nz)
- In 2006 Dr Mik Black was employed by the University to assist meeting the evolving need for more complex data analysis. (otago.ac.nz)
- By visual inspection, the numbers of restriction fragments and overall banding pattern similarity in the three groups of isolates showed interlaboratory concordance, but centralized computer analysis of data from four laboratories yielded percent similarity values of only 85% for the group of identical isolates. (asm.org)
- Our integrative multi-omics data analysis not only enables the discovery of new proteoforms but also generates an improved reference for human disease studies in the rat model. (mcponline.org)
- The Global Genome Engineering Market to GROW at a CAGR of 12.25% during the period 2016-2020. (medgadget.com)
- The Global Genome Engineering Market report covers the present scenario and the growth prospects of the Genome Engineering for 2016-2020. (medgadget.com)
- Overall, the report provides an in-depth insight of 2016-2020 global Genome Engineering industry covering all important parameters. (medgadget.com)
- To date, neither a linkage map nor molecular cytogenetic analysis has ever been developed for L. campestre . (nature.com)
- Different transposable element accumulation is responsible for genome size variation between D. holocanthus and the smooth pufferfish. (biomedcentral.com)