Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The relationships of groups of organisms as reflected by their genetic makeup.
Two identical genes showing the same phenotypic action but localized in different regions of a chromosome or on different chromosomes. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
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)
Low-copy (2-50) repetitive DNA elements that are highly homologous and range in size from 1000 to 400,000 base pairs.
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.
An aberration in which an extra chromosome or a chromosomal segment is made.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
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.
Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
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.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
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.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
Any method used for determining the location of and relative distances between genes on a chromosome.
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.
The functional hereditary units of PLANTS.
The genetic complement of a plant (PLANTS) as represented in its DNA.
A portion of the animal phylum Chordata comprised of the subphyla CEPHALOCHORDATA; UROCHORDATA, and HYPEROTRETI, but not including the Vertebrata (VERTEBRATES). It includes nonvertebrate animals having a NOTOCHORD during some developmental stage.
Genotypic differences observed among individuals in a population.
Phylum in the domain Eukarya, comprised of animals either with fully developed backbones (VERTEBRATES), or those with notochords only during some developmental stage (CHORDATA, NONVERTEBRATE).
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.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190)
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The systematic study of the complete DNA sequences (GENOME) of organisms.
The complete gene complement contained in a set of chromosomes in a fungus.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).
A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales.
Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.
The asymmetrical segregation of genes during replication which leads to the production of non-reciprocal recombinant strands and the apparent conversion of one allele into another. Thus, e.g., the meiotic products of an Aa individual may be AAAa or aaaA instead of AAaa, i.e., the A allele has been converted into the a allele or vice versa.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
The sequential location of genes on a chromosome.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
A 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.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.
A genus of pufferfish commonly used for research.
A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.
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).
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.
Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
The functional hereditary units of INSECTS.
The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
Higher plants that live primarily in terrestrial habitats, although some are secondarily aquatic. Most obtain their energy from PHOTOSYNTHESIS. They comprise the vascular and non-vascular plants.
A small aquatic oviparous mammal of the order Monotremata found in Australia and Tasmania.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
A small order of primarily marine fish containing 340 species. Most have a rotund or box-like shape. TETRODOTOXIN is found in their liver and ovaries.
Self-replicating, short, fibrous, rod-shaped organelles. Each centriole is a short cylinder containing nine pairs of peripheral microtubules, arranged so as to form the wall of the cylinder.
Common name for a family of eel-shaped jawless fishes (Myxinidae), the only family in the order MYXINIFORMES. They are not true vertebrates.
Animals that have no spinal column.
A superfamily of proteins that share a highly conserved MADS domain sequence motif. The term MADS refers to the first four members which were MCM1 PROTEIN; AGAMOUS 1 PROTEIN; DEFICIENS PROTEIN; and SERUM RESPONSE FACTOR. Many MADS domain proteins have been found in species from all eukaryotic kingdoms. They play an important role in development, especially in plants where they have an important role in flower development.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
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.
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.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Proteins obtained from species of fish (FISHES).
Changes in biological features that help an organism cope with its ENVIRONMENT. These changes include physiological (ADAPTATION, PHYSIOLOGICAL), phenotypic and genetic changes.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.
The functional hereditary units of FUNGI.
Family of the suborder HAPLORHINI (Anthropoidea) comprising bipedal primate MAMMALS. It includes modern man (HOMO SAPIENS) and the great apes: gorillas (GORILLA GORILLA), chimpanzees (PAN PANISCUS and PAN TROGLODYTES), and orangutans (PONGO PYGMAEUS).
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.
Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.
A kingdom of eukaryotic, heterotrophic organisms that live parasitically as saprobes, including MUSHROOMS; YEASTS; smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi, commonly known as molds, refer to those that grow as multicellular colonies.
Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.
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.
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.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
A 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).
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
The only genus in the family Oryziinae, order BELONIFORMES. Oryzias are egg-layers; other fish of the same order are livebearers. Oryzias are used extensively in testing carcinogens.
A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.
The genetic complement of an insect (INSECTS) as represented in its DNA.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.
An exotic species of the family CYPRINIDAE, originally from Asia, that has been introduced in North America. They are used in embryological studies and to study the effects of certain chemicals on development.
The cell center, consisting of a pair of CENTRIOLES surrounded by a cloud of amorphous material called the pericentriolar region. During interphase, the centrosome nucleates microtubule outgrowth. The centrosome duplicates and, during mitosis, separates to form the two poles of the mitotic spindle (MITOTIC SPINDLE APPARATUS).
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
Photosensitive proteins in the membranes of PHOTORECEPTOR CELLS such as the rods and the cones. Opsins have varied light absorption properties and are members of the G-PROTEIN-COUPLED RECEPTORS family. Their ligands are VITAMIN A-based chromophores.
Common name for the only family (Petromyzontidae) of eellike fish in the order Petromyzontiformes. They are jawless but have a sucking mouth with horny teeth.
Congenital structural abnormalities of the DIGESTIVE SYSTEM.
Databases devoted to knowledge about specific genes and gene products.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Deoxyribonucleic acid that makes up the genetic material of plants.
The splitting of an ancestral species into daughter species that coexist in time (King, Dictionary of Genetics, 6th ed). Causal factors may include geographic isolation, HABITAT geometry, migration, REPRODUCTIVE ISOLATION, random GENETIC DRIFT and MUTATION.
The only species of a cosmopolitan ascidian.
The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.
Photosensitive proteins expressed in the ROD PHOTORECEPTOR CELLS. They are the protein components of rod photoreceptor pigments such as RHODOPSIN.
The reciprocal exchange of segments at corresponding positions along pairs of homologous CHROMOSOMES by symmetrical breakage and crosswise rejoining forming cross-over sites (HOLLIDAY JUNCTIONS) that are resolved during CHROMOSOME SEGREGATION. Crossing-over typically occurs during MEIOSIS but it may also occur in the absence of meiosis, for example, with bacterial chromosomes, organelle chromosomes, or somatic cell nuclear chromosomes.
A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.
The amount of DNA (or RNA) in one copy of a genome.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The parts of the gene sequence that carry out the different functions of the GENES.
Abnormal number or structure of chromosomes. Chromosome aberrations may result in CHROMOSOME DISORDERS.
A genus of small free-living nematodes. Two species, CAENORHABDITIS ELEGANS and C. briggsae are much used in studies of genetics, development, aging, muscle chemistry, and neuroanatomy.
The functional hereditary units of HELMINTHS.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
A genus of parasitic nematodes that occurs in mammals including man. Infection in humans is either by larvae penetrating the skin or by ingestion of uncooked fish.
Structures within the CELL NUCLEUS of insect cells containing DNA.
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
The female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in human and other male-heterogametic species.
A species of nematode that is widely used in biological, biochemical, and genetic studies.
The morning glory family of flowering plants, of the order Solanales, which includes about 50 genera and at least 1,400 species. Leaves are alternate and flowers are funnel-shaped. Most are twining and erect herbs, with a few woody vines, trees, and shrubs.
Members of the phylum Arthropoda, composed of organisms having a hard, jointed exoskeleton and paired jointed legs. It includes the class INSECTS and the subclass ARACHNIDA, many species of which are important medically as parasites or as vectors of organisms capable of causing disease in man.
Group of fish under the superorder Acanthopterygii, separate from the PERCIFORMES, which includes swamp eels, mullets, sticklebacks, seahorses, spiny eels, rainbowfishes, and KILLIFISHES. The name is derived from the six taxa which comprise the group. (From, 8/4/2000)
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
The genetic complement of a BACTERIA as represented in its DNA.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.
A receptor tyrosine kinase that is involved in HEMATOPOIESIS. It is closely related to FMS PROTO-ONCOGENE PROTEIN and is commonly mutated in acute MYELOID LEUKEMIA.
The functional hereditary units of BACTERIA.
A general term for single-celled rounded fungi that reproduce by budding. Brewers' and bakers' yeasts are SACCHAROMYCES CEREVISIAE; therapeutic dried yeast is YEAST, DRIED.
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)
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Subnormal intellectual functioning which originates during the developmental period. This has multiple potential etiologies, including genetic defects and perinatal insults. Intelligence quotient (IQ) scores are commonly used to determine whether an individual has an intellectual disability. IQ scores between 70 and 79 are in the borderline range. Scores below 67 are in the disabled range. (from Joynt, Clinical Neurology, 1992, Ch55, p28)
This single species of Gorilla, which is a member of the HOMINIDAE family, is the largest and most powerful of the PRIMATES. It is distributed in isolated scattered populations throughout forests of equatorial Africa.
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)
A group of ALKALOIDS, characterized by a nitrogen-containing necine, occurring mainly in plants of the BORAGINACEAE; COMPOSITAE; and LEGUMINOSAE plant families. They can be activated in the liver by hydrolysis of the ester and desaturation of the necine base to reactive electrophilic pyrrolic CYTOTOXINS.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
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.
Family of slender threadlike aquatic plants, in the order CHARALES, phylum STREPTOPHYTA, that are closely related to LAND PLANTS.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
An aberration in which a chromosomal segment is deleted and reinserted in the same place but turned 180 degrees from its original orientation, so that the gene sequence for the segment is reversed with respect to that of the rest of the chromosome.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
Genes that encode highly conserved TRANSCRIPTION FACTORS that control positional identity of cells (BODY PATTERNING) and MORPHOGENESIS throughout development. Their sequences contain a 180 nucleotide sequence designated the homeobox, so called because mutations of these genes often results in homeotic transformations, in which one body structure replaces another. The proteins encoded by homeobox genes are called HOMEODOMAIN PROTEINS.
Proteins found in any species of insect.
Any fluid-filled closed cavity or sac (CYSTS) that is lined by an EPITHELIUM and found in the ESOPHAGUS region.
A genus of ascomycetous fungi of the family Saccharomycetaceae, order SACCHAROMYCETALES.
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.
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.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.
The reproductive organs of plants.
A genus of the family HYLOBATIDAE consisting of six species. The members of this genus inhabit rain forests in southeast Asia. They are arboreal and differ from other anthropoids in the great length of their arms and very slender bodies and limbs. Their major means of locomotion is by swinging from branch to branch by their arms. Hylobates means dweller in the trees. Some authors refer to Symphalangus and Nomascus as Hylobates. The six genera include: H. concolor (crested or black gibbon), H. hoolock (Hoolock gibbon), H. klossii (Kloss's gibbon; dwarf siamang), H. lar (common gibbon), H. pileatus (pileated gibbon), and H. syndactylus (siamang). H. lar is also known as H. agilis (lar gibbon), H. moloch (agile gibbon), and H. muelleri (silvery gibbon).
Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.
A group of elongate elasmobranchs. Sharks are mostly marine fish, with certain species large and voracious.
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
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).
Deletion of sequences of nucleic acids from the genetic material of an individual.
A plant genus of the family SALICACEAE. Balm of Gilead is a common name used for P. candicans, or P. gileadensis, or P. jackii, and sometimes also used for ABIES BALSAMEA or for COMMIPHORA.
A myelin protein that is the major component of the organic solvent extractable lipoprotein complexes of whole brain. It has been the subject of much study because of its unusual physical properties. It remains soluble in chloroform even after essentially all of its bound lipids have been removed. (From Siegel et al., Basic Neurochemistry, 4th ed, p122)
A technique of operations research for solving certain kinds of problems involving many variables where a best value or set of best values is to be found. It is most likely to be feasible when the quantity to be optimized, sometimes called the objective function, can be stated as a mathematical expression in terms of the various activities within the system, and when this expression is simply proportional to the measure of the activities, i.e., is linear, and when all the restrictions are also linear. It is different from computer programming, although problems using linear programming techniques may be programmed on a computer.
A plant genus of the family Plantaginaceae. Members contain DEFICIENS PROTEIN.
A large family of narrow-leaved herbaceous grasses of the order Cyperales, subclass Commelinidae, class Liliopsida (monocotyledons). Food grains (EDIBLE GRAIN) come from members of this family. RHINITIS, ALLERGIC, SEASONAL can be induced by POLLEN of many of the grasses.
Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.
Actual loss of portion of a chromosome.
A type of chromosomal aberration involving DNA BREAKS. Chromosome breakage can result in CHROMOSOMAL TRANSLOCATION; CHROMOSOME INVERSION; or SEQUENCE DELETION.
An enzyme that catalyzes the phosphorylation of the guanidine nitrogen of arginine in the presence of ATP and a divalent cation with formation of phosphorylarginine and ADP. EC
A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.
Different forms of a protein that may be produced from different GENES, or from the same gene by ALTERNATIVE SPLICING.
A specific pair of GROUP D CHROMOSOMES of the human chromosome classification.
Sequential operating programs and data which instruct the functioning of a digital computer.
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.
The light chain subunits of clathrin.
Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.
Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).
A subphylum of chordates intermediate between the invertebrates and the true vertebrates. It includes the Ascidians.
Mapping of the KARYOTYPE of a cell.
Proteins found in any species of bacterium.

The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes. (1/2949)

The nuclear receptor (NR) superfamily is the most abundant class of transcriptional regulators encoded in the Caenorhabditis elegans genome, with >200 predicted genes revealed by the screens and analysis of genomic sequence reported here. This is the largest number of NR genes yet described from a single species, although our analysis of available genomic sequence from the related nematode Caenorhabditis briggsae indicates that it also has a large number. Existing data demonstrate expression for 25% of the C. elegans NR sequences. Sequence conservation and statistical arguments suggest that the majority represent functional genes. An analysis of these genes based on the DNA-binding domain motif revealed that several NR classes conserved in both vertebrates and insects are also represented among the nematode genes, consistent with the existence of ancient NR classes shared among most, and perhaps all, metazoans. Most of the nematode NR sequences, however, are distinct from those currently known in other phyla, and reveal a previously unobserved diversity within the NR superfamily. In C. elegans, extensive proliferation and diversification of NR sequences have occurred on chromosome V, accounting for > 50% of the predicted NR genes.  (+info)

Phytochrome D acts in the shade-avoidance syndrome in Arabidopsis by controlling elongation growth and flowering time. (2/2949)

Shade avoidance in higher plants is regulated by the action of multiple phytochrome (phy) species that detect changes in the red/far-red ratio (R/FR) of incident light and initiate a redirection of growth and an acceleration of flowering. The phyB mutant of Arabidopsis is constitutively elongated and early flowering and displays attenuated responses to both reduced R/FR and end-of-day far-red light, conditions that induce strong shade-avoidance reactions in wild-type plants. This indicates that phyB plays an important role in the control of shade avoidance. In Arabidopsis phyB and phyD are the products of a recently duplicated gene and share approximately 80% identity. We investigated the role played by phyD in shade avoidance by analyzing the responses of phyD-deficient mutants. Compared with the monogenic phyB mutant, the phyB-phyD double mutant flowers early and has a smaller leaf area, phenotypes that are characteristic of shade avoidance. Furthermore, compared with the monogenic phyB mutant, the phyB-phyD double mutant shows a more attenuated response to a reduced R/FR for these responses. Compared with the phyA-phyB double mutant, the phyA-phyB-phyD triple mutant has elongated petioles and displays an enhanced elongation of internodes in response to end-of-day far-red light. These characteristics indicate that phyD acts in the shade-avoidance syndrome by controlling flowering time and leaf area and that phyC and/or phyE also play a role.  (+info)

Inheritance of nuclear DNA markers in gynogenetic haploid pink salmon. (3/2949)

We describe the inheritance of 460 PCR-based loci in the polyploid-derived pink salmon (Oncorhynchus gorbuscha) genome using gynogenetic haploid embryos. We detected a length polymorphism in a growth hormone gene (GH-2) intron that is caused by an 81 bp insertion homologous to the 3' end of the salmonid short interspersed repetitive element (SINE) SmaI. Such insertion polymorphisms within species bring into question the use of SINEs as phylogenetic markers. We confirmed that a microsatellite locus encodes a PCR-null allele that is responsible for an apparent deficit of heterozygotes in a population sample from Prince William Sound. Another set of microsatellite primers amplified alleles of the same molecular weight from both loci of a duplicated pair. In our analysis of several PCR-based multilocus techniques, we failed to detect evidence of comigrating fragments produced by duplicated loci. Segregation analysis of PCR-based markers using gynogenetic haploid embryos ensures that the interpretation of molecular variation is not complicated by heterozygosity, diploidy, or gene duplication. We urge investigators to test the inheritance of polymorphisms in salmonids prior to using them to measure genetic variation.  (+info)

Truncated RanGAP encoded by the Segregation Distorter locus of Drosophila. (4/2949)

Segregation Distorter (SD) in Drosophila melanogaster is a naturally occurring meiotic drive system in which the SD chromosome is transmitted from SD/SD+ males in vast excess over its homolog owing to the induced dysfunction of SD+-bearing spermatids. The Sd locus is the key distorting gene responsible for this phenotype. A genomic fragment from the Sd region conferred full distorting activity when introduced into the appropriate genetic background by germline transformation. The only functional product encoded by this fragment is a truncated version of the RanGAP nuclear transport protein. These results demonstrate that this mutant RanGAP is the functional Sd product.  (+info)

Genetic and biochemical characterization of phosphofructokinase from the opportunistic pathogenic yeast Candida albicans. (5/2949)

We have used the two PFK genes of Saccharomyces cerevisiae encoding the alpha and beta-subunit of the enzyme phosphofructokinase (Pfk) as heterologous probes to isolate fragments of the respective genes from the dimorphic pathogenic fungus Candida albicans. The complete coding sequences were obtained by combining sequences of chromosomal fragments and fragments obtained by inverse polymerase chain reaction (PCR). The CaPFK1 and CaPFK2 comprise open reading frames of 2961 bp and 2838 bp, respectively, encoding Pfk subunits with deduced molecular masses of 109 kDa and 104 kDa. The genes presumably evolved by a duplication event from a prokaryotic type ancestor, followed by another duplication. Heterologous expression in S. cerevisiae revealed that each gene alone was able to complement the glucose-negative phenotype of a pfk1 pfk2 double mutant. In vitro Pfk activity in S. cerevisiae was not only obtained after coexpression of both genes, but also in conjunction with the respective complementary subunits from S. cerevisiae. This indicates the formation of functional hetero-oligomers consisting of C. albicans and S. cerevisiae Pfk subunits. In C. albicans, specific Pfk activity was shown to decrease twofold upon induction of hyphal growth. CaPfk cross-reacts with a polyclonal antiserum raised against ScPfk and displays similar allosteric properties, i.e. inhibition by ATP and activation by AMP and fructose 2,6-bisphosphate.  (+info)

Comparisons of genomic structures and chromosomal locations of the mouse aldose reductase and aldose reductase-like genes. (6/2949)

Aldose reductase (AR), best known as the first enzyme in the polyol pathway of sugar metabolism, has been implicated in a wide variety of physiological functions and in the etiology of diabetic complications. We have determined the structures and chromosomal locations of the mouse AR gene (Aldor1) and of two genes highly homologous to Aldor1: the fibroblast growth factor regulated protein gene (Fgfrp) and the androgen regulated vas deferens protein gene (Avdp). The number of introns and their locations in the mouse Aldor1 gene are identical to those of rat and human AR genes and also to those of Fgfrp and Avdp. Mouse Aldor1 gene was found to be located near the Cald1 (Caldesmon) and Ptn (Pleiotropin) loci at the proximal end of chromosome 6. The closely related genes Fgfrp and Avdp were also mapped in this region of the chromosome, suggesting that these three genes may have arisen by a gene duplication event.  (+info)

Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4. (7/2949)

As part of the European Scientists Sequencing Arabidopsis program, a contiguous region (396607 bp) located on chromosome 4 around the APETALA2 gene was sequenced. Analysis of the sequence and comparison to public databases predicts 103 genes in this area, which represents a gene density of one gene per 3.85 kb. Almost half of the genes show no significant homology to known database entries. In addition, the first 45 kb of the contig, which covers 11 genes, is similar to a region on chromosome 2, as far as coding sequences are concerned. This observation indicates that ancient duplications of large pieces of DNA have occurred in Arabidopsis.  (+info)

Molecular cloning and characterization of the human topoisomerase IIalpha and IIbeta genes: evidence for isoform evolution through gene duplication. (8/2949)

Human DNA topoisomerase II is essential for chromosome segregation and is the target for several clinically important anticancer agents. It is expressed as genetically distinct alpha and beta isoforms encoded by the TOP2alpha and TOP2beta genes that map to chromosomes 17q21-22 and 3p24, respectively. The genes display different patterns of cell cycle- and tissue-specific expression, with the alpha isoform markedly upregulated in proliferating cells. In addition to the fundamental role of TOP2alpha and TOP2beta genes in cell growth and development, altered expression and rearrangement of both genes are implicated in anticancer drug resistance. Here, we report the complete structure of the human topoisomerase IIalpha gene, which consists of 35 exons spanning 27.5 kb. Sequence data for the exon-intron boundaries were determined and examined in the context of topoisomerase IIalpha protein structure comprising three functional domains associated with energy transduction, DNA breakage-reunion activity and nuclear localization. The organization of the 3' half of human TOP2beta, including sequence specifying the C-terminal nuclear localization domain, was also elucidated. Of the 15 introns identified in this 20 kb region of TOP2beta, the first nine and the last intron align in identical positions and display the same phases as introns in TOP2alpha. Though their extreme 3' ends differ, the striking conservation suggests the two genes diverged recently in evolutionary terms consistent with a gene duplication event. Access to TOP2alpha and TOP2beta gene structures should aid studies of mutations and gene rearrangements associated with anticancer drug resistance.  (+info)

Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage. Duplications arise from an event termed unequal crossing-over that occurs during meiosis between misaligned homologous chromosomes.The chance of this happening is a function of the degree of sharing of repetitive elements between two chromosomes. The products of this recombination are a duplication at the site of the exchange and a reciprocal deletion. Ectopic recombination is typically mediated by sequence similarity at the duplicate ...
The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions. By analysing 67 completely sequenced plant genomes 775 myosins were identified and manually assembled. Phylogenetic trees of the myosin motor domains revealed orthologous and paralogous relationships and were consistent with recent species trees. Based on the myosin inventories and the phylogenetic trees, we have identified duplications of the entire myosin motor protein family at timings consistent with 23 WGDs, that had been reported before. We also predict 6 WGDs based on further protein family duplications. Notably, the myosin data support the two recently reported WGDs in the common ancestor of all
We found overall support for the hypothesis that gene duplication and/or retention rates are higher in pancrustaceans, the group with the highest disparity of optical-types. We examined the sensitivity of this overall conclusion in three different ways. First, we compared pancrustaceans to both non-arthropod protostomes and to vertebrates. Second, for each of these comparisons, we estimated gene duplication rates using three different denominators: total gene duplications, overall genetic distance, and divergence time estimates from molecular clock analyses. These different denominators are necessary to understand the influence of different modes of genome evolution on our conclusions, such as the multiple genome duplications known in vertebrates. Third, we examined (both separately and together) duplication rates of genes from different eye-gene categories (developmental versus phototransduction genes), allowing us to test whether one category was the primary driver of the overall rates. For ...
Abstract: The fact that there are four homeobox (Hox) clusters in most vertebrates but only one in invertebrates is often cited as evidence for the hypothesis that two rounds of genome duplication by polyploidization occurred early in vertebrate history. In addition it has been observed in humans and other mammals that numerous gene families include paralogs on two or more of the four Hox-bearing chromosomes (the chromosomes bearing the Hox clusters; i.e. human chromosomes 2 7 12 and 17) and the existence of these paralogs has been taken as evidence that these genes were duplicated along with the Hox clusters by polyploidization. We tested this hypothesis by phylogenetic analysis of 42 gene families including members on two or more of the human Hox-bearing chromosomes. In 32 of these families there was evidence against the hypothesis that gene duplication occurred simultaneously with duplication of the Hox clusters. Phylogenies of 14 families supported the occurrence of one or more gene ...
Gene duplication is considered a major driving force for evolution of genetic novelty, thereby facilitating functional divergence and organismal diversity, including the process of speciation. Animals, fungi and plants are major eukaryotic kingdoms and the divergences between them are some of the most significant evolutionary events. Although gene duplications in each lineage have been studied extensively in various contexts, the extent of gene duplication prior to the split of plants and animals/fungi is not clear. Here, we have studied gene duplications in early eukaryotes by phylogenetic relative dating. We have reconstructed gene families (with one or more orthogroups) with members from both animals/fungi and plants by using two different clustering strategies. Extensive phylogenetic analyses of the gene families show that, among nearly 2,600 orthogroups identified, at least 300 of them still retain duplication that occurred before the divergence of the three kingdoms. We further found evidence that
Translocated chromosomal duplications occur spontaneously in many organisms; segmental duplications of large chromosomal regions are expected to result in phenotypic changes because of gene dosage effects. Therefore, experimentally generated segmental duplications in targeted chromosomal regions can be used to study phenotypic changes and determine the functions of unknown genes in these regions. Previously, we performed tandem duplication of a targeted chromosomal segment in Aspergillus oryzae. However, in tandem chromosomal duplication, duplication of chromosomal ends and multiple chromosomal duplication are difficult. In this study, we aimed to generate fungal strains with a translocated duplication or triplication of a targeted chromosomal region via break-induced replication. Double-strand breaks were introduced into chromosomes of parental strains by treating protoplast cells with I-SceI meganuclease. Subsequently, strains were generated by nonreciprocal translocation of a 1.4-Mb duplicated region
Translocated chromosomal duplications occur spontaneously in many organisms; segmental duplications of large chromosomal regions are expected to result in phenotypic changes because of gene dosage effects. Therefore, experimentally generated segmental duplications in targeted chromosomal regions can be used to study phenotypic changes and determine the functions of unknown genes in these regions. Previously, we performed tandem duplication of a targeted chromosomal segment in Aspergillus oryzae. However, in tandem chromosomal duplication, duplication of chromosomal ends and multiple chromosomal duplication are difficult. In this study, we aimed to generate fungal strains with a translocated duplication or triplication of a targeted chromosomal region via break-induced replication. Double-strand breaks were introduced into chromosomes of parental strains by treating protoplast cells with I-SceI meganuclease. Subsequently, strains were generated by nonreciprocal translocation of a 1.4-Mb duplicated region
Members of the YidC/Oxa1/Alb3 protein family facilitate the insertion, folding and assembly of proteins of the inner membranes of bacteria and mitochondria and the thylakoid membrane of plastids. All homologs share a conserved hydrophobic core region comprising five transmembrane domains. On the basis of phylogenetic analyses, six subgroups of the family can be distinguished which presumably arose from three independent gene duplications followed by functional specialization. During evolution of bacteria, mitochondria and chloroplasts, subgroup-specific regions were added to the core domain to facilitate the association with ribosomes or other components contributing to the substrate spectrum of YidC/Oxa1/Alb3 proteins. ...
Gene loss pattern after teleost-specific whole genome duplication. Figure 2. Gene loss pattern after teleost-specific whole genome duplication.. A: Species tree showing major vertebrate groups and their evolutionary relationships.. B: The comparison of genomes between two species with the coloured lines showing corresponding genes between human and medaka (upper circle) and between zebrafish and medaka (lower circle). The structure is quite different between human and medaka, while it is similar between zebrafish and medaka.. C: Gene loss pattern showing the two-phase loss of duplicate genes in teleost fishes. A and C use the same timeline.. The results of this study suggest that approximately 80% of the duplicate genes were lost in the first 60 million years after the whole genome duplication event (Fig. 2C). Considering that the first vertebrates appeared on Earth about 500 million years ago (Fig. 2A), 60 million years is a very short time. Dr Inoue states that it is possible that genome ...
Whole-genome duplication (WGD) events have shaped the history of many evolutionary lineages. One such duplication has been implicated in the evolution of teleost fishes, by far the most species-rich vertebrate clade. After initial controversy, there is now solid evidence that such event took place in the common ancestor of all extant teleosts. It is termed teleost-specific (TS) WGD. After WGD, duplicate genes have different fates. The most likely outcome is non-functionalization of one duplicate gene due to the lack of selective constraint on preserving both. Mechanisms that act on preservation of duplicates are subfunctionalization (partitioning of ancestral gene functions on the duplicates), neofunctionalization (assigning a novel function to one of the duplicates) and dosage selection (preserving genes to maintain dosage balance between interconnected components). Since the frequency of these mechanisms is influenced by the genes properties, there are over-retained classes of genes, such as ...
Van de Peer, Y. and Meyer, A. (2005). Large-scale gene and ancient genome duplications. In The Evolution of the Genome (edited by T.R. Gregory). Elsevier, San Diego, pp. 329- ...
TY - JOUR. T1 - 40 Mb duplication in chromosome band 5p13.1p15.33 with 800 kb terminal deletion in a foetus with mild phenotypic features. AU - Izzo, A.. AU - Genesio, R.. AU - Ronga, V.. AU - Nocera, V.. AU - Marullo, L.. AU - Cicatiello, R.. AU - Sglavo, G.. AU - Paladini, D.. AU - Conti, A.. AU - Nitsch, L.. PY - 2012/2. Y1 - 2012/2. N2 - Large duplication of the short arm of chromosome 5 is a rare condition normally associated to severe phenotype anomalies including heart and brain malformations. We report a prenatal case of a large 5p duplication with sub-telomeric deletion in a foetus with very mild phenotypic abnormalities. Foetal ultrasonographic examination at 22 weeks of gestation showed short femur, clubfeet, pielectasy, and facial dysmorphisms. Chromosome investigations revealed an inverted duplication of the short arm of chromosome 5 from 5p13.1 to 5p15.33 and a 800 kb deletion at 5pter. The absence of severe anomalies such as cardiac and cerebral defects, observed so far in all ...
Transmembrane glycerol transport is an ancient biophysical property that evolved in selected subfamilies of water channel (aquaporin) proteins. Here, we conducted broad level genome (,550) and transcriptome (,300) analyses to unravel the duplication history of the glycerol-transporting channels (glps) in Deuterostomia. We found that tandem duplication (TD) was the major mechanism of gene expansion in echinoderms and hemichordates, which, together with whole genome duplications (WGD) in the chordate lineage, continued to shape the genomic repertoires in craniates. Molecular phylogenies indicated that aqp3-like and aqp13-like channels were the probable stem subfamilies in craniates, with WGD generating aqp9 and aqp10 in gnathostomes but aqp7 arising through TD in Osteichthyes. We uncovered separate examples of gene translocations, gene conversion, and concerted evolution in humans, teleosts, and starfishes, with DNA transposons the likely drivers of gene rearrangements in paleotetraploid ...
Genome amplification through duplication or proliferation of transposable elements has its counterpart in genome reduction, by elimination of DNA or by gene inactivation. Whether loss is primarily due to excision of random length DNA fragments or the inactivation of one gene at a time is controversial. Reduction after whole genome duplication (WGD) represents an inexorable collapse in gene complement. We compare fifteen genomes descending from six eukaryotic WGD events 20-450 Mya. We characterize the collapse over time through the distribution of runs of reduced paralog pairs in duplicated segments. Descendant genomes of the same WGD event behave as replicates. Choice of paralog pairs to be reduced is random except for some resistant regions of contiguous pairs. For those paralog pairs that are reduced, conserved copies tend to concentrate on one chromosome. Both the contiguous regions of reduction-resistant pairs and the concentration of runs of single copy genes on a single chromosome are evidence of
Gene duplication provide a means to evolve novel biological functions and changes in protein functions may then provide different evolutionary constraints on duplicated genes. Functional divergence of a protein family can occur after major evolutionary events such as gene duplication or speciation. Some of them result in different evolutionary rates at certain amino acid residues, which is termed type I functional divergence [33, 34]. To estimate functional divergence in the vertebrate anoctamin family, we have conducted pair-wise functional divergence analysis between anoctamin paralogous genes using DIVERGE [35]. Table 1 shows the coefficient of functional divergence (θ) of pair-wise comparisons between the members of the anoctamin family. All comparisons showed θ , 0 with p , 0.05, suggesting that a site-specific rate shift after gene duplication is a common phenomenon in the evolution of the anoctamin family. Further analysis was subsequently focused on ano1/ano2, and ano1/ano4. Amino ...
This finding appeared online Oct. 4, 2009, in Nature Genetics and was done by researchers at the National Cancer Institute (NCI), part of the National Institutes of Health, and their colleagues.. That an inherited duplication of a gene is responsible for the development of a familial form of cancer is an important finding, said Rose Yang, Ph.D., NCI, one of the lead authors of the study.. Usual types of gene mutations and gene duplications are permanent changes to the DNA that a person inherits from parents. These changes often alter the expression of the affected gene in ways that lead to cancer and other diseases. The new finding highlights the importance of CNVs, as well as typical specific genetic mutations, in the genetic development of cancer.. Chordoma affects about 1 in every 1 million people in the United States, with about 300 new cases diagnosed each year. Those affected with the disease usually develop a tumor at the base of the skull, or at any point along the spinal column ...
With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million y …
Results Large duplications involving one complete domain or both domains are associated with either SRS or BWS, depending on the parental origin of the duplication. Genotype-phenotype correlation studies of partial duplications within the telomeric domain demonstrate the prominent role of IGF2, rather than H19, in the control of growth. Furthermore, it highlights the role of CDKN1C within the centromeric domain and suggests that the expected overexpression of KCNQ1OT1 from the paternal allele (in partial paternal duplications, excluding CDKN1C) does not affect the expression of CDKN1C. ...
Background: Duplications are very common in the evolution of plant genomes, explaining the high number of members in plant gene families. New genes born after duplication can undergo pseudogenization, neofunctionalization or subfunctionalization. Rice is a model for functional genomics research, an important crop for human nutrition and a target for biofortification. Increased zinc and iron content in the rice grain could be achieved by manipulation of metal transporters. Here, we describe the ZINC-INDUCED FACILITATOR-LIKE (ZIFL) gene family in plants, and characterize the genomic structure and expression of rice paralogs, which are highly affected by segmental duplication. Results: Sequences of sixty-eight ZIFL genes, from nine plant species, were comparatively analyzed. Although related to MSF_1 proteins, ZIFL protein sequences consistently grouped separately. Specific ZIFL sequence signatures were identified. Monocots harbor a larger number of ZIFL genes in their genomes than dicots, probably ...
Gene duplication is closely associated with the evolution of genes with new functions (Force et al., 1999; Hughes, 1999). After gene duplication, for example, one of the genes may be released from functional constraints, enabling it to accumulate mutations and to acquire a new function (neofunctionalization). Alternatively, several functions controlled by an ancestral gene may be partitioned into two genes produced by gene duplication (subfunctionalization). Repetitious gene duplication produces many genes from a single ancestral gene and gives rise to the diversification of gene function into multigene families. In some cases, a gene may lose its function and accumulate mutations as a pseudogene (nonfunctionalization).. The study of floral homeotic mutants in model eudicots, such as Arabidopsis thaliana and Antirrhinum majus, has established the ABC model, which explains the genetic mechanism underlying floral organ specification. The ABC model proposes that three classes of genes, termed A, B, ...
Ohno postulated that gene duplication plays a major role in evolution in his classic book Evolution by Gene Duplication (1970).[1] While subsequent research has overwhelmingly confirmed the key role of gene duplication in molecular evolution, research to evaluate Ohnos model for the preservation of duplicate genes (now termed neofunctionalization) is ongoing and very active. He also discovered in 1956 that the Barr body of mammalian female nuclei was in fact a condensed X chromosome.[2] In Evolution by Gene Duplication, he also suggested that vertebrate genome is the result of one or more entire genome duplications; variations of this idea have come to be known as the 2R hypothesis (also called Ohnos hypothesis). He indicated that mammalian X chromosomes are conserved among species;[3] it has been referred to as Ohnos law. He also popularized the term junk DNA for segments of the DNA that have no known function.[4][5] In 1986, Ohno authored a paper published in Immunogenetics that explored ...
While the rise of single-molecule sequencing systems has enabled an unprecedented rise in the ability to assemble complex regions of the genome, long segmental duplications in the genome still remain a challenging frontier in assembly. Segmental duplications are at the same time both gene rich and prone to large structural rearrangements, making the resolution of their sequences important in medical and evolutionary studies. Duplicated sequences that are collapsed in mammalian de novo assemblies are rarely identical; after a sequence is duplicated, it begins to acquire paralog specific variants. In this paper, we study the problem of resolving the variations in multicopy long-segmental duplications by developing and utilizing algorithms for polyploid phasing. We develop two algorithms: the first one is targeted at maximizing the likelihood of observing the reads given the underlying haplotypes using discrete ma- trix completion. The second algorithm is based on correlation clustering and ...
BACKGROUND: Oxidative phosphorylation is central to the energy metabolism of the cell. Due to adaptation to different life-styles and environments, fungal species have shaped their respiratory pathways in the course of evolution. To identify the main mechanisms behind the evolution of respiratory pathways, we conducted a phylogenomics survey of oxidative phosphorylation components in the genomes of sixty fungal species. RESULTS: Besides clarifying orthology and paralogy relationships among respiratory proteins, our results reveal three parallel losses of the entire complex I, two of which are coupled to duplications in alternative dehydrogenases. Duplications in respiratory proteins have been common, affecting 76% of the protein families surveyed. We detect several instances of paralogs of genes coding for subunits of respiratory complexes that have been recruited to other multi-protein complexes inside and outside the mitochondrion, emphasizing the role of evolutionary tinkering. CONCLUSIONS: ...
Article 1 Reciprocal deletion and duplication at 2q23.1 indicates a role for MBD5 in autism spectrum disorder Sureni V Mullegama et al. The European Journal of Human Genetics (2013), 1-7 This article describes a new chromosome duplication syndrome, 2q23.1 duplication. This duplication includes the MBD5 gene, the same gene involved in the 2q23.1 deletion syndrome.…
Xp11.22 duplications have been reported to contribute to nonsyndromic intellectual disability (ID). The HUWE1 gene has been identified in all male Xp11.22 duplication patients and is associated with nonsyndromic ID. Currently, few Xp11.22 duplication cases have been reported in the Chinese population, with limited knowledge regarding the role of other genes in this interval. We investigated four unrelated Chinese male Xp11.22 duplication patients, performed a comprehensive clinical evaluation for the patients and discussed the role of other genes in this interval. All patients presented with similar clinical features, including ID, speech impairments and motor delay, which were mostly consistent with those of the Xp11.22 duplication described previously. We searched and compared all cases and noted that one of the probands (Family 1) and DECIPHER case 263,219, who carried small overlapping duplications at Xp11.22 that only covered the entire HSD17B10 gene, also suffered from ID, suggesting the important
In plants, tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci. Recent studies suggest that duplicate genes diverge predominantly through the partitioning of expression and that breadth of gene expression is related to the rate of gene duplication and protein sequence evolution. Here, we utilize expressed sequence tag (EST) data to study gene duplication and expression patterns in the monosaccharide transporter (MST) gene family across the land plants. In Arabidopsis, there are 53 MST genes that form seven distinct subfamilies. We created profile hidden Markov models of each subfamily and searched EST databases representing diverse land plant lineages to address the following questions: 1) Are homologs of each Arabidopsis subfamily present in the earliest land plants? 2) Do expression patterns among subfamilies and individual genes within subfamilies differ across lineages? 3) Has gene duplication within each lineage resulted in lineage-specific
Whole-genome duplication (WGD) is usually followed by gene loss and karyotype repatterning. Despite evidence of new adaptive traits associated with WGD, the underpinnings and evolutionary significance of such genome fractionation remain elusive. Here, we use Buckler mustard (Biscutella laevigata) to infer processes that have driven the retention of duplicated genes after recurrent WGDs. In addition to the b- and a-WGD events shared by all Brassicaceae, cytogenetic and transcriptome analyses revealed two younger WGD events that occurred at times of environmental changes in the clade of Buckler mustard (Biscutelleae): a mesopolyploidy event from the late Miocene that was followed by considerable karyotype reshuffling and chromosome number reduction and a neopolyploidy event during the Pleistocene. Although a considerable number of the older duplicates presented signatures of retention under positive selection, the majority of retained duplicates arising from the younger mesopolyploidy WGD event ...
BACKGROUND: Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. A relatively recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. However, little is known about the consequences of this duplication at the level of the genome, the epigenome, and gene expression. RESULTS: The X. laevis genome consists of two subgenomes, referred to as L (long chromosomes) and S (short chromosomes), that originated from distinct diploid progenitors. Of the parental subgenomes, S chromosomes have degraded faster than L chromosomes from the point of genome duplication until the present day. Deletions appear to have the largest effect on pseudogene formation and loss of regulatory regions. Deleted regions are enriched for long DNA repeats and the flanking regions have high alignment scores, suggesting that non-allelic homologous recombination has ...
Sequence variations in the gene products PYPAF1/CIAS1 and NOD2/CARD15 have been associated with several autoinflammatory diseases that, although clinically different, share a similar inflammatory pathophysiology. A multiple sequence alignment of homologous proteins demonstrates that some of the missense variants are located in highly conserved regions of the NTPase domain and possibly impair NTP-hydrolysis. Intriguingly, one of the variations, which is found identically in PYPAF1 and NOD2, is located at the same alignment position. Our findings suggest that evolutionary gene duplication can give rise to disease families because variants affect conserved sequence in a similar fashion ...
P.2205 left column: Gene Duplications: Much of the genomes of flies and worms consists of duplicated genes [investigators] next asked how these paralogs are arranged. The frequency of local gene duplications and the number of their constituent genes differ widely between fly and worm, although in both genomes most paralogs are dispersed. The fly genome contains half the number of local gene duplications relative to C. elegans (ref 4), and these gene clusters are distributed randomly along the chromosome arms in C. elegans there is a concentration of gene duplications in the recombinogenic segments of the autosomal arms (ref 1). In both organisms, approximately 70% of duplicated gene pairs are on the same strand (306 out of 417 for D. melanogaster and 581 out of 826 for C. elegans ...
Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of families and superfamilies of proteins suggest a history of gene duplication and divergence during evolution. Genome encoded protein families, their size and functional composition, reflect metabolic potentials of the organisms they are found in. Comparing protein families of different organisms give insight into functional differences and similarities. Equivalent enzyme families with metabolic functions were selected from the genomes of four experimentally characterized bacteria belonging to separate genera. Both similarities and differences were detected in the protein family memberships, with more similarities being detected among the more closely related organisms. Protein family memberships reflected known metabolic characteristics of the organisms. Differences in divergence of functionally characterized enzyme family members accounted for
The process of evolution is of both scientific and medical interest. This thesis presents several studies using complete genomic reference sequences, comparative genomic data, and intraspecific diversity data to study the two key processes of evolution: mutation and selection.. Large duplications, deletions, inversions, and translocations of DNA contribute to genomic variation both between and within species. Human chromosomes 15 and 17 contain a high percentage of dispersed, recently duplicated sequences. Examination of the relationships between these sequences showed that the majority of all duplications within each chromosome could be linked through core sequences that are prone to duplication. Comparison to orthologous sequences in other mammals allowed a reconstruction of the ancestral state of the human chromosomes, revealing that regions of rearrangement specific to the human lineage are highly enriched in chromosome-specific duplications. Comparison to copy number variation data from ...
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Abstract Background It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple subgenomes derived from genome duplications, we need to relax the traditional requirements of one-to-one syntenic matchings of genomic regions in order to reflect one-to-many or more generally many-to-many matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this quota-based ...
Seven times in On the Origin of Species, Darwin invoked the concept that nature does not make leaps. Over 50 years after Darwins treatise was published, and now 100 years ago, an article published in the first year of the fledgling journal GENETICS discussed a situation in which nature does in fact make leaps-the origin of novel morphologies after a jump in genomic content by genome duplication (Tupper and Bartlett 1916). Genome duplication appears to have shaped vertebrate evolution in two rounds before the divergence of fish and mammalian lineages (Holland et al. 1994; Dehal and Boore 2005). It was previously known that gene families are often larger in teleosts than in mammals, but it was unclear if this condition arose due to excess preservation of tandem duplicates or to an additional genome duplication event, as suggested by S. Ohno (Ohno 1970). To resolve this question, we used genetic mapping to find the genomic locations of duplicated gene pairs in zebrafish. We found that gene pairs ...
Deletion of individual antibiotic resistance genes found within the variable region of integrons is demonstrated. Evidence for gene duplications and rearrangements resulting from the insertion of gene units at new locations is also presented. Deletion, duplication, and rearrangement occur only in the presence of the integron-encoded DNA integrase. These events are precise and involve loss or gain of one or more complete insert units or gene cassettes. This confirms the recent definition of gene cassettes as consisting of the gene coding sequences, all except the last 7 bases of the 59-base element found at the 3 end of the gene, and the core site located 5 to the gene (Hall et al., Mol. Microbiol. 5:1941-1959, 1991) and demonstrates that individual gene cassettes are functional units which can be independently mobilized. Both deletions and duplications can be generated by integrase-mediated cointegrate formation followed by integrase-mediated resolution involving a different pair of sites. ...
Certain types of gene families, such as those encoding most families of transcription factors, maintain their chromosomal syntenic positions throughout angiosperm evolutionary time. Other nonsyntenic gene families are prone to deletion, tandem duplication, and transposition. Here, we describe the chromosomal positional history of all genes in Arabidopsis thaliana throughout the rosid superorder. We introduce a public database where researchers can look up the positional history of their favorite A. thaliana gene or gene family. Finally, we show that specific gene families transposed at specific points in evolutionary time, particularly after whole-genome duplication events in the Brassicales, and suggest that genes in mobile gene families are under different selection pressure than syntenic genes. ...
Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S., Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.. Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it ...
Published on 2/1/2010. Vaglio A, Milunsky A, Quadrelli A, Huang XL, Maher T, Mechoso B, Martínez S, Pagano S, Bellini S, Costabel M, Quadrelli R. Clinical, cytogenetic, and molecular characterization of a girl with some clinical features of Down syndrome resulting from a pure partial trisomy 21q22.11-qter due to a de novo intrachromosomal duplication. Genet Test Mol Biomarkers. 2010 Feb; 14(1):57-65. PMID: 20143912.. Read at: PubMed ...
Ive done similar analyses of a variety of ancient genomes. For instance, StoraFörvar11, or SfF11, from Mesolithic Sweden came out 3/4 La Brana-1 and 1/4 MA-1, which translates to 3/4 Western European Hunter-Gatherer (WHG) and 1/4 Ancient North Eurasian (ANE), and lines up well with results reported recently for Swedish hunter-gatherers in scientific literature. You can see the full analysis StoraFörvar11 and a couple of other ancient genomes at the links below ...
QC saga continues.... from bad to worse - posted in Macroarray and Microarray: I wasnt sure whether I should have this in my previous post as this is a different issue. I still havent been able to fix the QC issues and as this is an optional control in the kit were seeing if getting bad QC score still allows us to detect deletion/duplication events. So Ive tried it on control samples that have one gene that contains a duplication/deletion, and did these in duplicates. T...
Some aspects of the work of our group on the human and mouse immunoglobulin κ genes are reviewed. The human κ locus contains a large duplication: a 600 kb C κ-proximal copy with 40 V κ genes is found in the close vicinity of a 440 kb C κ-distal copy with 36 very similar, but not identical, V κ genes. The chimpanzee has only the C κ -proximal copy of the locus. The κ locus of the mouse is close to 3.2 Mb in size, of which 3.1 Mb have been cloned in four contigs, leaving three small gaps of together about 90 kb; 140 V κ genes and pseudogenes were localized and sequenced. In parallel to the elucidation of the structure of the κ loci, the mechanisms of the V-J rearrangement, somatic hypermutation and κ gene expression were studied. Various polymorphisms were detected in the human population and a number of haplotypes defined. in addition to the V κ genes within the loci numerous V κ orphons were localized on different chromosomes. Comparing the κ loci of different species allows some ...
Germline mutations in the CDH1 (E-cadherin gene) gene have been reported in families with a hereditary predisposition to breast cancer and gastric cancer. Sequencing and deletion/duplication analyses of the CDH1 gene will identify individuals at risk for CHD1-related cancers ...
If a word is labeled in RED, that means that it is defined under the Basic Genetics tab. Check out this link, to understand some of these terms better and to gain more genetic knowledge. My child just received a diagnosis of 2q23.1 deletion/duplication disorder. What do I do next? If you have received these results by someone…
This method does not reliably detect mosaic variants; large deletions; large duplications, inversions, or other rearrangements; or deep intronic variants. It may be affected by allele dropout, it may not allow determination of the exact numbers of T/A or microsatellite repeats, and it does not allow any conclusion as to whether two heterozygous variants are present on the same or on different chromosome copies.. This test was developed, and its performance characteristics determined, by LabCorp. It has not been cleared or approved by the US Food and Drug Administration (FDA). The FDA has determined that such clearance or approval is not necessary. ...
45 Years old patient presented with left ischiorectal space pain along with swelling. MRI perineum was done that revealed a soft tissue mass lesion in left ischiorectal space ...
Evolution is driven by changes in genes. Sometimes genes are inadvertently duplicated during replication. This provides an extra copy that is free to vary through mutation, sometimes providing extended function. A good example is the family of hemoglobin genes in mammals. Members of a family which arose through duplication can also mutate and lose function. This module lets you explore these scenarios. The guide for this is in Dropbox (you dont need an account in Dropbox to get these, but its handy free cloud storage.) The guide can be downloaded here ...
Gupta, K., Galhotra, R. and Saggar, K. (2013) Yo-Yo Reflux in Partial Duplication of Ureter A Diagnosis on the Color and Pulse Doppler Study. Muller Journal of Medical Sciences and Research, 4, 116-188.
Euteleost fishes seem to have more copies of many genes than their tetrapod relatives. Three different mechanisms could explain the origin of these extra fish genes. The duplicates may have been produced during a fish-specific genome duplication event. A second explanation is an increased rate of independent gene duplications in fish. A third possibility is that after gene or genome duplication events in the common ancestor of fish and tetrapods, the latter lost more genes. These three hypotheses have been tested by phylogenetic tree reconstruction. Phylogenetic analyses of sequences from human, mouse, chicken, frog (Xenopus laevis), zebrafish (Danio rerio) and pufferfish (Takifugu rubripes) suggest that ray-finned fishes are likely to have undergone a whole genome duplication event between 200 and 450 million years ago. We also comment here on the evolutionary consequences of this ancient genome duplication ...
We present the first detailed genome-wide analysis of recent segmental duplication content of the bovine genome. Global studies of segmental duplication content have become an effective measure to assess one aspect of the quality of whole-genome sequence assemblies [1, 51]. Regions of recent segmental duplication remain one of the greatest challenges to finishing a genome assembly. The underlying problem is the same--the correct placement and resolution of large sequence that can be assigned to multiple positions within the genome. An initial assessment of bovine segmental duplication content therefore provides an important level of annotation for the user of genome sequence information in the design and interpretation of future experiments. Moreover, these initial analyses precisely delineate potential regions where whole-genome shotgun or a BAC-enrichment strategy will provide insufficient information for biologists. These regions include gene families important in immunity, digestion, ...
νgW is a homozygous lethal mutation killing embryos prior to formation of the syncitial blastoderm. In heterozygous condition it causes duplications of the posterior wing, ranging from very small duplications of the axillary cord and alar lobe to large duplications including much of the wing blade and the posterior row of bristles. No anterior margin structures are ever observed. The thorax is sometimes slightly abnormal, but rarely shows large duplications. The size of the wing is related to the number of pattern elements deleted or duplicated.. Heterozygous νgW flies also show homoeosis of the haltere to wing. This occurs in the capitellum, where wing blade is observed, but no wing margin structures are found. As with the bithorax (bx) mutation which transforms anterior haltere to anterior wing this aspect of the phenotype is repressed by the Contrabithorax (Cbx) mutation. The transformed haltere discs show more growth than wild-type haltere discs.. Flies heterozygous for νgW also show a ...
7q11.23 duplication syndrome is a condition that can cause a variety of neurological and behavioral problems as well as other abnormalities.. People with 7q11.23 duplication syndrome typically have delayed development of speech and motor skills such as crawling and walking. Speech problems and abnormalities in the way affected individuals walk and stand may persist throughout life. People with this condition may also have weak muscle tone (hypotonia) and abnormal movements, such as involuntary movements of one side of the body that mirror intentional movements of the other side. About one-fifth of people with 7q11.23 duplication syndrome experience seizures.. Intellectual development varies widely in 7q11.23 duplication syndrome. The majority of people with this condition have low-average to average intelligence. Intellectual disability or borderline intellectual ability occur in about one-third of affected individuals. Rarely, people with this disorder have above-average ...
Comparative Genomics/Transcriptomics. Trostle, Alex [1], Goyal, Anshu [1], Galuska, Sally [1], Reardon, Chris [1], Tiley, George [2], Ellis, Jake [1], Li, Zheng [3], Sutherland, Brittany [4], Barker, Michael [3]. Machine learning approaches for the inference of WGDs from gene age distributions.. The inference of whole genome duplications (WGDs) from gene age distributions or Ks plots is frequently more of an art than exact science. Ancient WGDs leave characteristic peaks of gene duplication in Ks plots that are often relatively easy to identify by eye. However, depending on the data source, Ks estimation method, variation in gene birth and death rates, gene retention rates, and other variables, these peaks may not always appear to be prominent. Most of the statistical approaches applied to this problem often search for a peak of duplication that is statistically significant relative to a null background or fit normal distributions to a range of Ks values. Diagnosing WGDs in these cases can often ...
The evolutionary mechanism, fate and function of duplicate genes in various taxa have been widely studied; however, the mechanism underlying the maintenance and divergence of duplicate genes in Danio rerio remains largely unexplored. Whether and how the divergence of DNA methylation between duplicate pairs is associated with gene expression and evolutionary time are poorly understood. In this study, by analyzing bisulfite sequencing (BS-seq) and RNA-seq datasets from public data, we demonstrated that DNA methylation played a critical role in duplicate gene evolution in zebrafish. Initially, we found promoter a methylation of duplicate genes generally decreased with evolutionary time measured by synonymous substitution rate between paralogous duplicates (Ks). Importantly, promoter methylation of duplicate genes was negatively correlated with gene expression. Interestingly, for 665 duplicate gene pairs, one gene was consistently promoter methylated while the other was unmethylated across nine ...
We present a global comparison of differences in content of segmental duplication between human and chimpanzee, and determine that 33% of human duplications (| 94% sequence identity) are not duplicated in chimpanzee, including some human disease-causing duplications. Combining experimental and co …
Using computer programmes, he produced a comparative map that revealed duplications unique to each of these four genomes, along with those that are shared between them. The map showed that about a third of the duplications in the human genome are unique to us, and most of the remaining duplications are ones we share with chimps. The rate at which these duplications cropped up had greatly accelerated in the part of the primate family tree that includes humans and the African great apes. These rates doubled and hit their peak in the last common ancestor of ourselves and chimpanzees. As a result, both chimps and humans have far more of these doubles than either orang-utans or macaques. This burst of activity coincided with a time when other types of mutation, such as changes to single nucleotides, were slowing down. Marques-Bonet thinks that these accelerated rates of gene duplication played a pivotal role in the success and evolution of the great apes. More duplications, genes and a puzzling ...
Using computer programmes, he produced a comparative map that revealed duplications unique to each of these four genomes, along with those that are shared between them. The map showed that about a third of the duplications in the human genome are unique to us, and most of the remaining duplications are ones we share with chimps. The rate at which these duplications cropped up had greatly accelerated in the part of the primate family tree that includes humans and the African great apes. These rates doubled and hit their peak in the last common ancestor of ourselves and chimpanzees. As a result, both chimps and humans have far more of these doubles than either orang-utans or macaques. This burst of activity coincided with a time when other types of mutation, such as changes to single nucleotides, were slowing down. Marques-Bonet thinks that these accelerated rates of gene duplication played a pivotal role in the success and evolution of the great apes. More duplications, genes and a puzzling ...
Ben Creisler [email protected] A number of recent non-dino papers that may be of interest: In open access: Philip C. J. Donoghue and Joseph N. Keating (2014) Early vertebrate evolution. Palaeontology (advance online publication) DOI: 10.1111/pala.12125 Debate over the origin and evolution of vertebrates has occupied biologists and palaeontologists alike for centuries. This debate has been refined by molecular phylogenetics, which has resolved the place of vertebrates among their invertebrate chordate relatives, and that of chordates among their deuterostome relatives. The origin of vertebrates is characterized by wide-ranging genomic, embryologic and phenotypic evolutionary change. Analyses based on living lineages suggest dramatic shifts in the tempo of evolutionary change at the origin of vertebrates and gnathostomes, coincident with whole-genome duplication events. However, the enriched perspective provided by the fossil record ...
Duplication is one of the most important mechanisms for evolving gene or genome complexity. Exploring how duplicated genes or genomic regions evolve has become the cornerstone of modern evolutionary theory. In Eukaryotes, over 30% of all genes are confirmed to derive directly from duplication. In the era of genomic data explosion since year two thousand, the flood of complete genome sequences from multiple species significantly facilitated its study. For example, the long debated two round hypothesis of genome duplication in the early stage of vertebrate evolution has been demonstrated via comparing several invertebrate and vertebrate genomes.; In my study I focus on the duplication process from three different aspects: DNA sequence, transcriptional regulation, and gene function. I emphasize the dynamics of the duplication process, e.g. how duplication played a role in the adaptation of the species.; At the DNA sequence level, I modeled how duplicated microsatellites evolve. When a ...
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Abstract: Using genomic information from mosquito, red flour beetle, honeybee, mouse, and sea anemone, we have studied the molecular evolution of 91 Drosophila genes involved in eye primordium determination, retinal differentiation, and phototransduction. Our results show that the majority of these gene sequences predate the diversification of endopterygote insects. However, all three functional groups contain a conspicuous fraction of evolutionarily younger genes, which originated by tandem duplication in the lineage leading to Drosophila, whereas gene duplications are rare in other insect lineages. We conclude that the retention of duplicated genes spiked during the early diversification of the higher Diptera possibly due to an extended period of exceptional population size reduction. Genetic data suggest that gene duplication played an important role in the evolution of visual performance in the fast flying higher Diptera by spatial or intracellular subfunctionalization. Developmental gene ...
Gene duplication and loss are predicted to be at least of the order of the substitution rate and are key contributors to the development of novel gene function and overall genome evolution. Although it has been established that proteins evolve more rapidly after gene duplication, we were interested in testing to what extent this reflects causation or association. Therefore, we investigated the rate of evolution prior to gene duplication in chordates. Two patterns emerged; firstly, branches, which are both preceded by a duplication and followed by a duplication, display an elevated rate of amino acid replacement. This is reflected in the ratio of nonsynonymous to synonymous substitution (mean nonsynonymous to synonymous nucleotide substitution rate ratio [Ka:Ks]) of 0.44 compared with branches preceded by and followed by a speciation (mean Ka:Ks of 0.23). The observed patterns suggest that there can be simultaneous alteration in the selection pressures on both gene duplication and amino acid ...
Catostomid fishes (suckers) have duplicate copies of the growth hormone gene and other nuclear genes, due to a genome duplication event early in the groups history. Yet, paralogs of GH in suckers are more than 90% conserved in nucleotide (nt) and amino acid (aa) sequence. Within paralogs across species, variation in nt and aa sequence averages 3.33% and 4.46% for GHI, and 3.22% and 2.43% for GHII, respectively. Selection tests suggest that the two GH paralogs are under strong purifying selection. Consensus trees from phylogenetic analysis of GH coding region data for 23 species of suckers, other cypriniform fishes and outgroups resolved cypriniform relationships and relationships among GHI sequences of suckers more or less consistently with analyses based on other molecular data. However, the analysis failed to resolve all sucker GHI and GHII sequences as monophyletic sister groups. This unexpected topology did not differ significantly from topologies constrained to make all GH sequences monophyletic.
In our phylogeny, two V. vinifera proteins and four P. trichocarpa proteins group in the lignification-related R2R3-MYB clade. The P. trichocarpa genes encoding these proteins are located on LG_1 (PtrMYB002 and PtrMYB003) and LG_IX (PtrMYB020 and PtrMYB021) in regions that are thought to be the paralogous product of the recent salicoid whole genome duplication event (Tuskan et al., 2006). The P. trichocarpa proteins are most similar to E. gunnii MYB2 and to the V. vinifera members of this clade. Three of the four Populus R2R3-MYB genes exhibit high levels of transcript accumulation in xylem tissue (Fig. 5B), suggesting that function in this tissue has been retained for most family members since the duplication event. The transcript abundance profile also suggests that, like their counterparts in other plant species, these transcription factors also function in xylem-based processes, perhaps also regulating genes encoding enzymes of the lignin biosynthetic pathway. The retention of these apparent ...
In the last years pioneer studies have presented first analysis methods for genome data in a disease context. Several data quality control and statistical methods are now well established and more and more data is available for application. This weeks studies point out the importance of thinking outside the box as well as data dissecting from a different perspective.. Ohnologs and CNVs. Is a specific class of genes overrepresented in large recurrent pathogenic CNVs? Using an evolutionary genetic approach, McLysaght and colleagues demonstrate that ohnologs are overrepresented in pathogenic CNVs in their recent PNAS study. Ohnologs are genes retained after ancestral whole-genome duplication events. McLysaght and colleagues suggest that ohnologs represent critical dosage-sensitive elements of the genome and are possibly responsible for some of the deleterious phenotypes observed for pathogenic CNVs. In the field of epilepsy genetics, we usually identify a huge amount of truncating mutations in an ...
1850-1998, Duplication on album leaves & A4 stockcards noted medium better values, etc, mint hinged, MNH and used, mixed to v.fine ...
2p duplications fall into a category of chromosome disorders in which a segment of chromosome 2 is duplicated or copied. This means instead of two copies of the genes in this segment, each cell of the body now has three copies. These extra copies of genetic information may cause multiple birth defects and developmental issues. Duplications generally arise by random chance (de novo), but also can be the result of inheriting a chromosome error from the parents.. Individuals with 2p duplications generally have a similar appearance of a prominent forehead, a triangular shaped mouth, wide spaced eyes, slanted back ears, and a thin upper lip. This appearance, in addition to slow body growth and feeding difficulties, typically alerts the parents that someone might be wrong. The condition is officially diagnosed with a genetic test that allows the specialist to see that a specific portion of the chromosome is duplicated.. Symptoms of 2p duplications may include developmental delays, intellectual ...
2p duplications fall into a category of chromosome disorders in which a segment of chromosome 2 is duplicated or copied. This means instead of two copies of the genes in this segment, each cell of the body now has three copies. These extra copies of genetic information may cause multiple birth defects and developmental issues. Duplications generally arise by random chance (de novo), but also can be the result of inheriting a chromosome error from the parents.. Individuals with 2p duplications generally have a similar appearance of a prominent forehead, a triangular shaped mouth, wide spaced eyes, slanted back ears, and a thin upper lip. This appearance, in addition to slow body growth and feeding difficulties, typically alerts the parents that someone might be wrong. The condition is officially diagnosed with a genetic test that allows the specialist to see that a specific portion of the chromosome is duplicated.. Symptoms of 2p duplications may include developmental delays, intellectual ...
Give up? No, its not from some creationist tripe. This is actually from the Preface of a well respected book within evolutionary genetics: Susumu Ohnos Evolution by Gene Duplication published in 1970. Yes, even thirty five years ago evolutionary biologists did not need intelligent designers to tell them that natural selection is not the be all, end all of evolutionary forces. Weve known it all along, and without gene duplication (via retrotransposition, segmental duplication, and whole genome duplication) evolution would have ceased with the simplest of all prokaryotes. You see, its easy to attack a caricature of evolutionary theory consisting of only random mutation and natural selection, but thats just a straw man. Understanding evolution to any extent requires one to examine more than just the pop culture concept of Darwin. Natural selection on allelic mutations cannot explain much beyond within population variation and speciation; to truly appreciate the amazing diversity of life on ...
Here we describe the occurrence of distal chromosome 16p11.2 duplications in nearly 1% of patients with AIS, a common paediatric musculoskeletal disorder whose aetiology is largely unexplained. The chromosome 16p11.2 region was previously proposed as a candidate locus for AIS based on linkage data.32 33 This complex chromosomal region has undergone a recent, rapid integration of segmental duplications followed by adaptive evolution that has occurred since the split between the human/great ape lineage and orangutans, approximately 12 million years ago.34 This regions richness in segmental duplications predisposes it to recurrent rearrangements.35 The proximal 600 kb region (29.5-30.1 Mb) defined by breakpoints 4-5 (BP4-BP5; OMIM #611913) harbours the TBX6 gene and has been previously associated with congenital scoliosis,19 while the distal 220 kb BP2-BP3 region (28.7-28.9 Mb) reported here in AIS has not been previously associated with any skeletal phenotype. Deletion of the proximal region is ...
p,The heat-shock protein 90 (HSP90) acts as a chaperone by ensuring proper maturation and folding of its client proteins. The HSP90 capacitor hypothesis holds that interactions with HSP90 allow proteins to accumulate mutations while maintaining function. Following this logic, HSP90 clients would be predicted to show relaxed selection compared with nonclients. In this study, we identify a new HSP90 client in the plant steroid hormone pathway: the transcription factor BES1. Its closest paralog, BZR1, is not an HSP90 client. This difference in HSP90 client status in two highly similar proteins enabled a direct test of the capacitor hypothesis. We find that BES1 shows relaxed selection compared to BZR1, hallmarks of neo- and subfunctionalization, and dynamic HSP90 client status across independent evolutionary paths. These results suggested that HSP90's influence on gene evolution may be detectable if we compare gene duplicates because duplicates share most other properties influencing ...
Common models for the evolution of duplicated genes after genome duplication are subfunctionalization, neofunctionalization, and pseudogenization. Although the crucial roles of cis-regulatory mutations in subfunctionalization are well-documented, their involvement in pseudogenization and/or neofunctionalization remains unclear. We addressed this issue by investigating the evolution of duplicated homeobox genes, six6.L and six6.S, in the allotetraploid frog Xenopus laevis. Based on a comparative expression analysis, we observed similar eye-specific expression patterns for the two loci and their single ortholog in the ancestral-type diploid species Xenopus tropicalis. However, we detected lower levels of six6.S expression than six6.L expression. The six6.S enhancer sequence was more highly diverged from the orthologous enhancer of X. tropicalis than the six6.L enhancer, and showed weaker activity in a transgenic reporter assay. Based on a phylogenetic analysis of the protein sequences, we observed ...
Like most Archaea, the hypersaline-adapted organism Halobacterium salinarum exhibits characteristics from all three domains of life, including a eukaryotic histone protein, a universal propensity to genetic rearrangements, and homologs of bacterial cell division proteins. Here we investigate the ancestral function of histone protein in the Archaea. Transcriptomics, proteomics, and phenotypic assays of histone mutants determine that histone regulates gene expression and cell shape but not genome compaction in H. salinarum. We further explore the regulation of gene expression on a genome-wide scale through the study of genomic instability. Genomic deletions and duplications are detected through the meta-analysis of 1154 previously published gene expression arrays and 48 chromatin immunoprecipitation arrays. We discover that a 90 kb duplication event in the megaplasmid pNRC100 directly leads to increased gene expression, and find evidence that the chromosome is far more unstable than previously ...
PfCCp1 and PfCCp2 have similar architectures and are paralogs arising via relatively recent gene duplication after domain accretion. C. parvum also has paralogs, CpCCp1 and CpCCp2, and thus the gene duplication event likely occurred before the divergence of the apicomplexan genera. Within PfCCp1 and PfCCp2, we identified three predicted polysaccharide-binding domains, namely ricin, discoidin, and levanase-type lectin domains (26, 27). COOH terminal to these modules are two copies of an apicomplexan-specific cysteine-rich module (herein termed ApicA) that has not been identified in any other gene. Between the discoidin and levanase lectin domains there are two distinct cysteine-rich modules, the described animal- and fungal-specific LCCL domain (28), and a novel module, termed NEC, which appears in a wide range of animal proteins such as neurexins (29), fibrillar collagen α globular domain (30) from vertebrates and sponges, and the fibrinogen family of proteins (31). The NEC domain has not been ...
The globin gene superfamily as a model system. A second area of research is geared towards understanding the role of gene duplication and whole-genome duplication in the evolution of key physiological innovations. Gene duplication is thought to play an extremely important role in the evolution of novel protein and pathway functions. However, there is still much debate about the specific evolutionary mechanisms that are responsible for the initial retention and subsequent functional divergence of duplicated genes. The globin gene superfamily is an ideal model system for investigating these issues because it is one of the most intensively studied multigene families from the standpoint of molecular genetics and phylogenetic history. The globin gene families also provide an excellent example of the kind of physiological versatility that can be attained through functional and regulatory divergence of duplicated genes that encode different subunit polypeptides of the same multimeric protein. For ...
Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many ...
To determine the basis for the persistence of functional gene duplicates in the genome, three scientists at the Institute of Molecular Systems Biology at the Swiss Federal Institute of Technology in Zürich have collaborated on the largest systematic analysis of duplicated gene function to date. Using an integrative combination of computational and experimental approaches, they classified duplicate pairs of genes involved in yeast metabolism into four functional categories: (1) back-up, where a duplicate gene copy has acquired the ability to compensate in the absence of the other copy, (2) subfunctionalization, where a duplicate copy has evolved a completely new, non-overlapping function, (3) regulation, where the differential regulation of duplicates fine-tunes pathway usage, and (4) gene dosage, where the increased expression provided by the duplicate gene copy augments production of the corresponding protein.. Their results, which appear in the October issue of the journal Genome Research, ...
The purpose of this book is to present a new mechanistic theory of mutation-driven evolution based on recent advances in genomics and evolutionary developmental biology. The theory asserts, perhaps somewhat controversially, that the driving force behind evolution is mutation, with natural selection being of only secondary importance. The word mutation is used to describe any kind of change in DNA such as nucleotide substitution, gene duplication/deletion, chromosomal change, and genome duplication. A brief history of the principal evolutionary theories (Darwinism, mutationism, neo-Darwinism, and neo-mutationism) that preceded the theory of mutation-driven evolution is also presented in the context of the last 150 years of research. However, the core of the book is concerned with recent studies of genomics and the molecular basis of phenotypic evolution, and their relevance to mutation-driven evolution. In contrast to neo-Darwinism, mutation-driven evolution is capable of explaining real ...
Comparative Genomics: Gene and Genome Duplication. What are the molecular, phenotypic, and taxonomic outcomes of gene and whole genome duplication? We use two gene families, opsins and olfactory receptors, as models to answer these questions. Most of the opsin research involves fishes including guppies, the four-eyed fish, sticklebacks, various flatfish and zebrafish. The research on olfactory receptors (ORs) involves cnidarians, sea urchins and amphioxus. Recently weve added gene duplication and cancer evolution, and gene colinearity (conserved synteny) to our research repertoire. I also co-supervise graduate students who study tube worm population genetics and protein-protein interaction networks.. ...
THE genomes of most organisms contain multiple copies of genes that are closely related in structure and function. Such gene families can arise from tandem duplications, as in the case of the HOX, hemoglobin, and keratin clusters in animals, or from polyploidization events such as those presumed to have preceded the origin of vertebrates (Ohno 1970; Morizotet al. 1991; Lundin 1993; Hollandet al. 1994; Amoreset al. 1998; Pébusqueet al. 1998), brewers yeast (Wolfe and Shields 1997; Seoighe and Wolfe 1998), and many plant species (Lewis 1979). The mechanism that preserves a large proportion of duplicate genes for long time periods, however, is unclear. The classical model predicts that duplicate genes initially have fully overlapping, redundant functions, such that one copy may shield the second copy from natural selection, if gene dosage is not critical. Because deleterious mutations occur much more frequently than beneficial mutations (Lynch and Walsh 1998), the classical model predicts that ...
Analysis of genomes shows that many gene copies are found lying next to each other, linked head to tail in an arrangement called a tandem repeat. This may occur because of errors of the normal recombination machinery that is responsible for DNA repair and crossing over during meiosis. Tandem repeats are susceptible to amplification, which is the further increase in the number of copies. This can occur during crossing over. Normal crossing over pairs up identical segments on homologous chromosomes, and then exchanges them. If the chromosomes each have a tandem repeat, the crossover machinery may line up incorrectly, leaving one homologue with three gene copies and one with only one. Repeating this process over ensuing generations can lead to dozens of extra gene copies.. Duplication of much larger portions of a genome is also possible, including whole chromosomes (called chromosomal aberrations) and even the entire genome (called polyploidy). In each case, the number of copies of a gene ...
Purpose: : To test for copy number variants in the CHM gene. Choroideremia (CHM) is an X-linked progressive chorioretinal degenerative disease that affects 1 in 50,000 males. CHM results from relative deficiency or absence of Rab escort protein-1 which is encoded by the CHM gene; however, the exact pathogenesis remains to be determined. Through genetic studies, we have determined that CHM can arise from partial and complete deletions, insertions, frameshifts, point mutations (missense and nonsense) and splice site mutations in the CHM gene. Methods: : Case control, non-randomized, study design. One female and eight male subjects were identified with fundus features consistent with a clinical diagnosis of CHM. In all cases, previous sequencing of the coding region and adjacent intronic splice sites had not found a mutation. We designed a multiplex ligation-dependent probe amplification (MLPA) assay kit for the detection of copy number variants in the CHM gene. Using this MLPA assay, we tested the ...
Failure to Diagnose Chromosome 12q duplication syndrome including overlooked symptoms and complications for under-diagnosed medical conditions.
Spinal Muscular Atrophy (SMA) is the second most common autosomal recessive genetic disorder with a 1:50 carrier frequency. Deletion /duplication change...
An understanding of the factors favoring the maintenance of duplicate genes in microbial genomes is essential for developing models of microbial evolution. A genome-scale flux-balance analysis of the metabolic network of Saccharomyces cerevisiae has suggested that gene duplications primarily provide increased enzyme dosage to enhance metabolic flux because the incidence of gene duplications in essential genes is no higher than that in nonessential genes. Here, we used genome-scale metabolic models to analyze the extent of genetic and biochemical redundancy in prokaryotes that are either specialists, with one major mode of energy generation, or generalists, which have multiple metabolic strategies for conservation of energy. Surprisingly, the results suggest that generalists, such as Escherichia coli and Bacillus subtilis, are similar to the eukaryotic generalist, S. cerevisiae, in having a low percentage (,10%) of essential genes and few duplications of these essential genes, whereas metabolic ...
This study has systematically evaluated the total pool of genomic mutations arising in 737 E. coli lines subjected to daily single-cell bottlenecks for 1−2 mo. After WGS, we detected thousands of mutational events, including point mutations, indels, prophage deletions, and large duplications, as well as their responses to sublethal concentrations of norfloxacin with or without the presence of DNA repair systems such as MMR and DNA oxidative-damage repair. Our findings demonstrate the power and resolution of MA techniques for ascertaining the consequences of exogenous factors for replication fidelity and damage repair, paving the way for future work on the mutagenic consequences of other antibiotics and other means of microbial intervention.. Numerous checks on the nature of mutations accumulated in this MA setting indicate that this experimental design cleanly separates the response of the mutation rate to antimicrobial dosage from the downstream issue of which specific mutations confer ...
Background Great gene figures in herb genomes reflect polyploidy and major gene duplication events. into paralogous protein families respectively. Singleton and paralogous family genes differed substantially in their likelihood of encoding a protein of known or putative function; 26% and Ritonavir 66% of singleton genes compared to 73% and 96% of the paralogous family genes encode a known or putative protein in rice and Arabidopsis respectively. Furthermore a major skew in the distribution of specific gene function was observed; a total of 17 Gene Ontology groups in both rice and Arabidopsis were statistically significant in their differential distribution between paralogous family and singleton proteins. In contrast to mammalian organisms we found that duplicated genes in rice and Arabidopsis tend to have more alternate splice forms. Using data from Massively Parallel Signature Sequencing we show that a significant portion of the duplicated genes in rice show divergent expression although a ...
The DiagHunter and GenoPix2D applications work together to enable genomic comparisons and exploration at both genome-wide and single-gene scales. DiagHunter identifies homologous regions (synteny blocks) within or between genomes. DiagHunter works efficiently with diverse, large datasets to predict extended and interrupted synteny blocks and to generate graphical and text output quickly. GenoPix2D allows interactive display of synteny blocks and other genomic features, as well as querying by annotation and by sequence similarity.
As part of our mission, Dup15q Alliance seeks to unite families, researchers, and professionals; and promote research, awareness, and understanding of chromosome 15q11.2-13.1 duplication syndrome and related disorders. Dup15q Alliance formally endorses and funds research and collaborates with researchers interested in research on chromosome 15q duplications by disseminating research information and promoting opportunities for Dup15q Alliance families to participate in research studies.. ...
Authors: Dearborn DC, Gager AB, McArthur AG, Gilmour ME, Mandzhukova E, Mauck RA.. Mol Ecol. 2016 Sep;25(17):4355-67.. Genes of the major histocompatibility complex (MHC) exhibit heterozygote advantage in immune defence, which in turn can select for MHC-disassortative mate choice. However, many species lack this expected pattern of MHC-disassortative mating. A possible explanation lies in evolutionary processes following gene duplication: if two duplicated MHC genes become functionally diverged from each other, offspring will inherit diverse multilocus genotypes even under random mating. We used locus-specific primers for high-throughput sequencing of two expressed MHC Class II B genes in Leachs storm-petrels, Oceanodroma leucorhoa, and found that exon 2 alleles fall into two gene-specific monophyletic clades. We tested for disassortative vs. random mating at these two functionally diverged Class II B genes, using multiple metrics and different subsets of exon 2 sequence data. With good ...
... greatly facilitating the evolutionary studies of gene regulation after gene duplication or speciation. Gene duplications can ... The gene duplication rate in C. elegans is on the order of 10−7 duplications/gene/generation, that is, in a population of 10 ... Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is ... It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of ...
Chromosome 2q31.1 duplication syndrome is a protein that in humans is encoded by the DUP2Q31.1 gene. "Human PubMed Reference ... "Entrez Gene: Chromosome 2q31.1 duplication syndrome". Retrieved 2016-07-25. Sandholm N, McKnight AJ, Salem RM, Brennan EP, ... v t e (Articles with short description, Short description matches Wikidata, Genes on human chromosome, All stub articles, Human ...
Ohno postulated that gene duplication plays a major role in evolution in his classic book Evolution by Gene Duplication (1970 ... everything." Gene duplication Paleopolyploidy Susumu Ohno (1970). Evolution by gene duplication. Springer-Verlag. ISBN 0-04- ... In Evolution by Gene Duplication, he also suggested that vertebrate genome is the result of one or more entire genome ... While subsequent research has overwhelmingly confirmed the key role of gene duplication in molecular evolution, research to ...
Molecular evolution Gene duplication Gene conversion Pseudogenes Ancestral gene resurrection Bovinae Ribonuclease A ENCODE ... Among different models that exist, one model suggests that after the gene duplication, among the two copies of genes, one will ... Gene conversion is of two types - interallelic and interlocus gene conversions. The resurrection of seminal RNase gene function ... Ohno, S. (1970). Evolution by gene duplication. NY: Springer. ISBN 0-04-575015-7. Benner, S.A (1990). Bioorganic Chemistry ...
Evolution by Gene Duplication. London: Allen and Unwin, ISBN 0-04-575015-7. Watson JM, Riggs A, Graves JA (1992). "Gene mapping ... Additionally, for individual gene loci, a number of X-linked genes are common through mammalian species. Examples include ... Genes on the long arm of the human X are contained in the monotreme X and genes on the short arm of the human X are distributed ... Chloride channel gene (CLCN4) was mapped to the human X but on chromosome 7 of C57BL/6 mice, species of Mus musculus, though ...
A Continuation of Spetner v. Max - discusses the B-cell hypermutation model; role of gene duplication; interpretations of the ... and gene families as examples of duplication, mutation and selection. a review of Lee Spetner's "NOT BY CHANCE!" by Gert ... Spetner, L. M. (1970). "Natural selection versus gene uniqueness". Nature. 226 (5249): 948-949. Bibcode:1970Natur.226..948S. ...
Gene duplication may occur via cis-duplication or trans duplication. Cis-duplication, or intrachromosomal duplication, entails ... some genes may be lost. Loss of genes is dependent of the number of genes originating in the gene cluster. In the four gene ... When gene duplication occurs to produce a gene cluster, one or multiple genes may be duplicated at once. In the case of the Hox ... It postulates that gene clusters were formed as a result of gene duplication and divergence. These gene clusters include the ...
Sets of genes formed in this way compose a gene family. Gene duplications and losses within a family are common and represent a ... Gene dosage Gene expression Gene family Gene nomenclature Gene patent Gene pool Gene redundancy Genetic algorithm Haplotype ... These genes appear either from gene duplication within an organism's genome, where they are known as paralogous genes, or are ... There are two types of molecular genes: protein-coding genes and noncoding genes. During gene expression, the DNA is first ...
Maeda N, Yang F, Barnett DR, Bowman BH, Smithies O (1984). "Duplication within the haptoglobin Hp2 gene". Nature. 309 (5964): ... Erickson LM, Kim HS, Maeda N (1993). "Junctions between genes in the haptoglobin gene cluster of primates". Genomics. 14 (4): ... Maeda N (1985). "Nucleotide sequence of the haptoglobin and haptoglobin-related gene pair. The haptoglobin-related gene ... the latter one having arisen due to the partial duplication of Hp1 gene. Three genotypes of Hp, therefore, are found in humans ...
Chromosome 17q12 duplication syndrome is a protein in humans that is encoded by the DUP17Q12 gene. "Human PubMed Reference:". ... "Entrez Gene: Chromosome 17q12 duplication syndrome". Retrieved 2013-02-16. v t e (Articles with short description, Short ... Genes on human chromosome 17, All stub articles, Human chromosome 17 gene stubs). ... description matches Wikidata, Genes on human chromosome, ...
Gottlieb, L. D.; Weeden, N. F. (1979). "Gene duplication and phylogeny in Clarkia". Evolution. 33 (4): 1024-1039. doi:10.2307/ ... Odrzykoski, I. J.; Gottlieb, L. D. (1984). "Duplication of genes coding 6-phosphogluconate dehydrogenase in Clarkia(Onagraceae ... Gene exchange between species must be restricted if they are to maintain genetic integrity, but, as we have seen, such ... A by-product of this accumulation of structural rearrangements has been the establishment of strong barriers to gene exchange ...
A gene duplication model". Journal of Molecular Biology. 206 (2): 313-21. doi:10.1016/0022-2836(89)90481-6. PMID 2541254. ... "DNMT1". Gene Symbol Report. HUGO Gene Nomenclature Committee. Retrieved 2012-09-27. Chen T, Ueda Y, Xie S, Li E (October 2002 ... "DNMT3B". Gene Symbol Report. HUGO Gene Nomenclature Committee. Retrieved 2012-09-27. Barau J, Teissandier A, Zamudio N, Roy S, ... "DNMT3L". Gene Symbol Report. HUGO Gene Nomenclature Committee. Retrieved 2012-09-27. Kho MR, Baker DJ, Laayoun A, Smith SS ( ...
... can result from gene duplication. Such duplication events are responsible for many sets of paralogous genes. ... Gene redundancy most often results from Gene duplication. Three of the more common mechanisms of gene duplication are ... Gene duplication events can also be detected by looking at increases in gene duplicates. A good example of using gene ... This paper studies how one KCS gene evolved into an entire gene family via duplication events. The number of redundant genes in ...
Both gene duplication and lateral gene transfer have the capacity to bring about relatively large changes that are saltational ... Serres, M. H.; Kerr AR, McCormack TJ, Riley M. (2009).Evolution by leaps: gene duplication in bacteria. Biology Direct 4: 46. ... ISBN 0262600692 Serres, M. H.; Kerr, A. R.; McCormack, T. J.; Riley, M. (2009). Evolution by leaps: gene duplication in ... Freeling, M. (2009). Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or ...
In some gene families, this process is very fast, caused by random events of gene duplication and gene deletion and generates ... Recent molecular data indicate that many sets of interacting genes such as Hox genes, immunoglobulin genes, and histone genes ... gene duplication, and gene inactivation, he predicted that higher organisms contain a large number of duplicate genes and ... Nei, M (1969). "Gene duplication and nucleotide substitution in evolution". Nature. 221 (5175): 40-42. Bibcode:1969Natur.221... ...
... gene duplication, lateral gene transfer, and transposable elements (jumping genes). The neutral theory of molecular evolution, ... ISBN 978-0-632-04708-6 Serres, M. H.; Kerr, A. R.; McCormack, T. J.; Riley, M. (2009). "Evolution by leaps: gene duplication in ... In modern epigenetics, biologists observe that phenotypes depend on heritable changes to gene expression that do not involve ... doi:10.1111/j.1502-3931.1989.tb01332.x. Wagner, Günter P., Homology, Genes, and Evolutionary Innovation. Princeton University ...
She is also known for her studies on gene expression of phototransduction proteins, duplication events in opsin genes, the ... Her studies have also sought to elucidate the role and emergence of double gene duplication events in opsin protein expression ... As Briscoe herself has addressed, gene duplication and mutation events in opsins more broadly account for a large fraction of ... Briscoe, A. D. (2001). "Functional diversification of lepidopteran opsins following gene duplication". Molecular Biology and ...
Hurles, Matthew (13 July 2004). "Gene Duplication: The Genomic Trade in Spare Parts". PLOS Biology. 2 (7): e206. doi:10.1371/ ... Gene flow involves the exchange of genes between populations and between species. The presence or absence of gene flow ... Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer. Horizontal gene transfer ... This is important because most new genes evolve within gene families from pre-existing genes that share common ancestors. For ...
Susumu Ohno, Author of "Evolution by gene duplication". Ph.D. in Veterinary Science in 1949. Hirohide Hamashima, Director of ...
"Venom evolution through gene duplications". Gene. 496 (1): 1-7. doi:10.1016/j.gene.2012.01.009. PMID 22285376. GBD 2013 ... Snake venom may have originated with duplication of genes that had been expressed in the salivary glands of ancestors. Venom is ... Extensive research on platypuses shows that their toxin was initially formed from gene duplication, but data provides evidence ... "Restriction and Recruitment-Gene Duplication and the Origin and Evolution of Snake Venom Toxins". Genome Biology and Evolution ...
Wong ES, Belov K (March 2012). "Venom evolution through gene duplications". Gene. 496 (1): 1-7. doi:10.1016/j.gene.2012.01.009 ... Therefore, conotoxin genes experience less selection against mutations (like gene duplication and nonsynonymous substitution), ... thus cone snails are under constant selective pressure to maintain polymorphism in these genes because failing to evolve and ... "Adaptive radiation of venomous marine snail lineages and the accelerated evolution of venom peptide genes". Ann. N. Y. Acad. ...
... this gene and SULT1A4 arose from a segmental duplication. This gene is the most centromeric of the four sulfotransferase genes ... Exons of this gene overlap with exons of a gene that encodes a protein containing GIY-YIG domains (GIYD1). Three alternatively ... The gene structure (number and length of exons) is similar among family members. This gene encodes a phenol sulfotransferase ... "Entrez Gene: SULT1A3 sulfotransferase family, cytosolic, 1A, phenol-preferring, member 3". Weinshilboum RM, Otterness DM, Aksoy ...
"Functional characterization of a human histone gene cluster duplication". Gene. 342 (1): 35-40. doi:10.1016/j.gene.2004.07.036 ... This gene is found in a histone cluster on chromosome 1. This gene is one of four histone genes in the cluster that are ... This gene is intronless and encodes a member of the histone H4 family. Transcripts from this gene lack polyA tails; instead, ... "Entrez Gene: HIST2H4A histone cluster 2, H4a". Green L, Van Antwerpen R, Stein J, et al. (1984). "A major human histone gene ...
Gossmann TI, Schmid KJ (October 2011). "Selection-driven divergence after gene duplication in Arabidopsis thaliana". Journal of ... Sex-biased genes are genes with expression exclusive to one sex and provide a potential means of rapid evolution in a species. ... Male and female sex-biased genes of A. thaliana have major differences in expression and function. Male genes expressed in the ... On the other hand, approximately 196 genes have been identified to associate with the female gametophyte. The genes identified ...
"Frequent occurrence of CYP2D6 gene duplication in Saudi Arabians". Pharmacogenetics. 7 (3): 187-91. doi:10.1097/00008571- ... Yasukochi Y, Satta Y (2011). "Evolution of the CYP2D gene cluster in humans and four non-human primates". Genes & Genetic ... Annotated PGx Gene Information for CYP2D6 Human CYP2D6 genome location and CYP2D6 gene details page in the UCSC Genome Browser ... 2010). "CYP2D6 gene variants: association with breast cancer specific survival in a cohort of breast cancer patients from the ...
Natural gene duplication plays a major role in evolution. It is also implicated in several forms of human cancer including ... Amplification of the genes encoded by these amplicons generally increases transcription of those genes and ultimately the ... or naturally through gene duplication. In this context, amplification refers to the production of one or more copies of a ... This works similarly in the fungal domain with the 18S rRNA gene as well as the ITS1 non-coding region. Irrespective of the ...
The family evolved via two separate gene duplication events. The initial duplication gave rise to two genes one of subsequently ... The second duplication appears to have occurred via an unequal crossing over event. The GypA gene itself consists of 7 exons ... The MiV and MiV(J.L.) genes are arranged in the same 5' alpha-delta 3' frame whereas Sta gene is in a reciprocal 5'delta-alpha ... Kudo S, Fukuda M (1989). "Structural organization of glycophorin A and B genes: glycophorin B gene evolved by homologous ...
"Functional characterization of a human histone gene cluster duplication". Gene. 342 (1): 35-40. doi:10.1016/j.gene.2004.07.036 ... This gene is found in a histone cluster on chromosome 1. This gene is one of four histone genes in the cluster that are ... This gene is intronless and encodes a member of the histone H2A family. Transcripts from this gene lack polyA tails but instead ... "Entrez Gene: HIST2H2AA3 histone cluster 2, H2aa3". Allen BS, Stein JL, Stein GS, Ostrer H (June 1991). "Single-copy flanking ...
Mekalanos JJ (1983). "Duplication and amplification of toxin genes in Vibrio cholerae". Cell. 35 (1): 253-63. doi:10.1016/0092- ... His early work as an independent researcher led to the identification of toxR, a gene that affects the expression of the ... the demonstration of the presence of duplications of the toxin operon in different strains of Vibrio cholerae that could ...
Sankoff D, Zheng C, Zhu Q (May 2010). "The collapse of gene complement following whole genome duplication". BMC Genomics. 11 (1 ... in addition to altering gene products if inserted into a gene, also alter promoter activity for genes if inserted upstream of ... Therefore, discordant gene trees are only evidence of introgression if a gene tree produced by excess allele sharing between ... Genome-wide incompatibilities have been identified in Xipophorous fish, chimeric genes and mutations of orthologous genes cause ...
The protein encoded by this gene shares similarity with the product of Drosophila syd gene, required for the functional ... 2005). "The sequence and analysis of duplication-rich human chromosome 16". Nature. 432 (7020): 988-94. Bibcode:2004Natur.432.. ... Studies of the similar gene in mouse suggested that this protein may interact with and regulate the activity of numerous ... "Entrez Gene: MAPK8IP3 mitogen-activated protein kinase 8 interacting protein 3". Matsuura, Hiroshi; Nishitoh Hideki; Takeda ...
Park, Gene (September 17, 2020). "PlayStation CEO Jim Ryan says more PlayStation 5 units will be available than PS4s in 2013". ... and the duplication of data across the medium in order to reduce load times. An important goal was to find ways to reduce ...
These genes are used and reused, occasionally by duplication but far more often by being applied unchanged to new functions. ... In turn, these regulatory genes turn out to be based on a very old set of highly conserved genes which Carroll nicknames the ... He introduces the evo-devo gene toolkit. 4. Making Babies: 25,000 Genes, Some Assembly Required Carroll looks at how a fruit ... "evolution of form is very much a matter of teaching old genes to make new genes." The review in BioScience noted that the book ...
Avramopoulos D, Wang R, Valle D, Fallin MD, Bassett SS (April 2007). "A novel gene derived from a segmental duplication shows ... Human ASAH2B genome location and ASAH2B gene details page in the UCSC Genome Browser. Brandenberger R, Wei H, Zhang S, et al. ( ... v t e (Articles with short description, Short description matches Wikidata, Genes on human chromosome 10, All stub articles, ... 2B or ASAH2B is a ceramidase enzyme which in humans is encoded by the ASAH2B gene. ASAH2B shows reduced expression with ...
In general, the binding of pRb to E2F inhibits the E2F target gene expression of certain G1/S and S transition genes including ... These events include the duplication of its DNA (DNA replication) and some of its organelles, and subsequently the partitioning ... Several gene expression studies in Saccharomyces cerevisiae have identified 800-1200 genes that change expression over the ... However, for reasons related to gene copy number effects, possession of extra copies of certain genes is also deleterious to ...
... evidence for evolution of gastrin by gene duplication". Proceedings of the National Academy of Sciences of the United States of ... In humans, the GAS gene is located on the long arm of the seventeenth chromosome (17q21). Gastrin is a linear peptide hormone ... Lund T, Geurts van Kessel AH, Haun S, Dixon JE (May 1986). "The genes for human gastrin and cholecystokinin are located on ... Lund T, Geurts van Kessel AH, Haun S, Dixon JE (May 1986). "The genes for human gastrin and cholecystokinin are located on ...
... likely due to both whole genome duplication and other forms of gene duplication; the ubiquitin, SUMO, ATG8, and MUB families ... One additional protein, known as FUBI, is encoded as a fusion protein in the FAU gene, and is proteolytically processed to ... Yeh ET, Gong L, Kamitani T (May 2000). "Ubiquitin-like proteins: new wines in new bottles". Gene. 248 (1-2): 1-14. doi:10.1016/ ... Recently, a seemingly complete set of genes corresponding to a eukaryote-like ubiquitin pathway was identified in an uncultured ...
Powers: Self-duplication by absorbing kinetic energy. Quicksilver / Pietro Maximoff (voiced by Paul Haddad) - Quicksilver guest ... Shaman / Michael Twoyoungmen (voiced by Don Francks) Puck / Eugene Milton Judd (voiced by Don Francks) Powers: Superhuman ...
The cause of M2DS is a duplication of the MECP2 or Methyl CpG binding protein 2 gene located on the X chromosome (Xq28). The ... "MECP2 Duplication Syndrome". Reference, Genetics Home. "MECP2 duplication syndrome". Genetics Home Reference. "Van Wright ... Gene expression, Chromosome instability syndromes, Autosomal duplications, Disorders causing seizures). ... MECP2 duplication syndrome (M2DS) is a rare disease that is characterized by severe intellectual disability and impaired motor ...
In a 22 February 1962 memorandum to the Secretary of the Air Force, Eugene Zuckert, the Secretary of Defense, Robert McNamara, ... which decried it as a wasteful duplication of facilities, given that the recently completed US$154 million (equivalent to $957 ... Homer 2019, p. 2. Zuckert, Eugene (25 August 1962). "Memorandum for Director, Manned Orbiting Laboratory (MOL) Program - ...
The APG II system placed the family in Malpighiales, based on a DNA sequence for the rbcL gene from Whittonia. This sequence ... increased diversification rates often follow whole genome duplications". New Phytologist. 207 (2): 454-467. doi:10.1111/nph. ... a 5-gene, 567-taxon analysis of angiosperms". BMC Evolutionary Biology. 9 (1): 61. doi:10.1186/1471-2148-9-61. PMC 2674047. ... as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales". Genome Biology and Evolution. 8 (7): ...
... gene duplication and loss between the two species differs by 6.4%. There are also differences in the genetic networks and ... The changes include around 35 million base-pair changes, 689 genes gained and 86 lost, the increase in brain mass, as well as ...
2007). "A novel gene derived from a segmental duplication shows perturbed expression in Alzheimer's disease". Neurogenetics. 8 ... "Entrez Gene: ASAH2 N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2". Human ASAH2 genome location and ASAH2 gene ... 2004). "Neutral ceramidase gene: role in regulating ceramide-induced apoptosis". Gene. 315: 113-22. doi:10.1016/S0378-1119(03) ... 1994). "The addition of 5'-coding information to a 3'-directed cDNA library improves analysis of gene expression". Gene. 146 (2 ...
This duplication is the fourth of its kind to happen in the evolutionary lineage of the salmonids, with two having occurred ... Around half of the duplicated protein-coding genes have been deleted, but all apparent miRNA sequences still show full ... This divergence was marked by a whole-genome duplication event in the ancestral salmonid, where the diploid ancestor became ... This more precise dating and examination of the salmonid whole-genome duplication event has allowed more speculation on the ...
Schlieper D, Oliva MA, Andreu JM, Löwe J (June 2005). "Structure of bacterial tubulin BtubA/B: evidence for horizontal gene ... Hinchcliffe EH, Sluder G (May 2001). ""It takes two to tango": understanding how centrosome duplication is regulated throughout ... Rosette C, Karin M (March 1995). "Cytoskeletal control of gene expression: depolymerization of microtubules activates NF-kappa ... which has provided information on the differential expression of the genes depending on the presence of these factors. This ...
February 1994). "Olfactory receptor gene cluster on human chromosome 17: possible duplication of an ancestral receptor ... The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and ... "Entrez Gene: OR1G1 olfactory receptor, family 1, subfamily G, member 1". Sanz G, Thomas-Danguin T, Hamdani EH, Le Poupon C, ... Olfactory receptor 1G1 is a protein that in humans is encoded by the OR1G1 gene. Olfactory receptors interact with odorant ...
... is one of a number of Bio* projects designed to reduce code duplication. Examples of such projects that fall under Bio ... This module is focused on the creation of gene sequence objects from the core module. This is realized by supporting the ... GTF files generated by GeneMark GFF2 files generated by GeneID GFF3 files generated by Glimmer Then the gene sequence objects ... names are familiar and make sense to biologists and also provide a concrete representation of the steps in going from a gene ...
"XX male sex reversal with genital abnormalities associated with a de novo SOX3 gene duplication". American Journal of Medical ... that resulted from a heterozygous mutation in the SOX18 gene. The SOX18 gene has a major role in the formation of blood and ... The SOX3 gene encodes a protein that is similar but distinct to the testis-determining factor (TDF), also known as sex- ... also led to the description of an SRY negative type of XX male sex reversal that resulted from a duplication of the SOX3 gene ...
"HGNC database of human gene names - HUGO Gene Nomenclature Committee". HGNC - TERC HGNC - DKC1 HGNC - TEP1 NCBI ... thus avoiding cell death as long as the conditions for their duplication are met. Many cancer cells are considered 'immortal' ... siRNA treatment can function similar to traditional gene therapy by destroying the mRNA products of particular genes, and ... However, the genes that have mutated in these diseases all have roles in the repair of DNA damage and the increased DNA damage ...
A large reason for this diversification is because of gene duplications and tandem duplications, which have helped contribute ... Genes that have this element seem to require it for the gene to be transcribed in sufficient quantities. It is frequently ... Whereas in animals each NF-Y subunit is encoded by a single gene, there has been a diversification in plants in both structure ... Full gene expression occurs when transcription activator proteins bind to each module within the regulatory promoter. Protein ...
... see KSHV/HHV8 genes). Products of these viral genes include: 1) LANA-1, which inhibits host cells' p53 protein thereby reducing ... duplications, inversions, translocations), aneuploidy (i.e. increases or decreases in the number of chromosomes), and the ... The cells may also express many of the structural and non-structural gene abnormalities cited in the Pathophysiology section. ... abnormal expression of genes that may or may not be a result of the preceding structural gene changes. Potentially important ...
v t e (Genes on human chromosome 2, All stub articles, Human chromosome 2 gene stubs). ... "Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q". Genomics. 60 (3): 295-308. ... "Entrez Gene: CIAO1 cytosolic iron-sulfur protein assembly 1 homolog (S. cerevisiae)". Gari K, León Ortiz AM, Borel V, Flynn H, ... Probable cytosolic iron-sulfur protein assembly protein CIAO1 is a protein that in humans is encoded by the CIAO1 gene. CIAO1 ...
The duplication-which undermines the security of a one-time system-was discovered, and attempts to lessen its impact were made ... The VENONA Project was initiated on February 1, 1943, by Gene Grabeel, an American mathematician and cryptanalyst, under orders ...
Sutcliffe JS, Han MK, Amin T, Kesterson RA, Nurmi EL (2003). "Partial duplication of the APBA2 gene in chromosome 15q13 ... the murine Fe65 gene (Apbb1), and the human Fe65-like gene (APBB2): genes encoding phosphotyrosine-binding domain proteins that ... v t e (Genes on human chromosome 15, All stub articles, Human chromosome 15 gene stubs). ... This gene product is believed to be involved in signal transduction processes. It is also regarded as a putative vesicular ...
Sequencing may be performed on a single gene, a group of genes (panel testing), most of the coding region or exons (whole exome ... Deletion/duplication testing is a type of testing designed to detect larger areas of the genetic code that are missing or extra ... while others involve many genes or are a complex mix of genes and environment. There are many different types of genetic ... By identifying gene changes that may increase risk to develop a certain condition, a person can be screened earlier and more ...
... differs from other defensin genes by an extra 83-base segment that is apparently the result of a recent duplication ... "The gene encoding the human corticostatin HP-4 precursor contains a recent 86-base duplication and is located on chromosome 8 ... "Entrez Gene: DEFA4; defensin, alpha 4, corticostatin (Homo sapiens)". Wu Z, Ericksen B, Tucker K, Lubkowski J, Lu W (September ... 11 (3): 232-8. doi:10.1038/gene.2010.1. PMID 20237496. Kim E, Lee JE, Namkung JH, Kim PS, Kim S, Shin ES, et al. (April 2009 ...
It has been hypothesized that the clustering of EDC genes occurred due to duplication events which were evolutionarily favored ... The epidermal differentiation complex (EDC) is a gene complex comprising over fifty genes encoding proteins involved in the ... 37 genes had been identified as members of the EDC. The number rose to 43 in 2002, and by 2012 a total of 57 genes were ... The proteins encoded by EDC genes are closely related in terms of function, and evolutionarily they belong to three distinct ...
So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes. The following is a ... 2004). "The sequence and analysis of duplication-rich human chromosome 16" (PDF). Nature. 432 (7020): 988-94. Bibcode:2004Natur ... generally CG-rich and gene rich; acen Centromere. var: Variable region; stalk: Stalk. Gilbert F (1999). "Disease genes and ... Pertea M, Salzberg SL (2010). "Between a chicken and a grape: estimating the number of human genes". Genome Biol. 11 (5): 206. ...
Mutations in maize promoters affect the expression of the promoter genes in a plant-organ-specific manner. A duplication of the ... The TATA box has a binding site for the transcription factor of the PG2 gene. This gene produces PG2 serum, which is used as a ... Similarly, in humans only 24% of genes have promoter regions containing the TATA box. Genes containing the TATA-box tend to be ... Gene. 389 (1): 52-65. doi:10.1016/j.gene.2006.09.029. PMC 1955227. PMID 17123746. Bae SH, Han HW, Moon J (2015). "Functional ...
This new understanding of the apple genome will help scientists identify genes and gene variants that contribute to resistance ... has 17 chromosomes which were found to be derived from an ancestor with 9 chromosomes that experienced genome-wide duplication ... and more genes than the human genome which has about 25,000 genes. The modern apple ... Understanding the genes behind these characteristics will help scientists perform more knowledgeable selective breeding. Since ...
The duplication of APBA2 sequences in this region adds to a complex picture of different low copy repeats present across this ... Partial duplication of the APBA2 gene in chromosome 15q13 corresponds to duplicon structures BMC Genomics. 2003 Apr 29;4(1):15. ... Adjacent to APBA2 maps a gene termed KIAA0574. The protein encoded by this gene is weakly homologous to a protein termed X123 ... Conclusion: The duplication of APBA2 sequences in this region adds to a complex picture of different low copy repeats present ...
Emerging Human Metapneumovirus Gene Duplication Variants in Patients with Severe Acute Respiratory Infection, China, 2017-2019 ... Emerging Human Metapneumovirus Gene Duplication Variants in Patients with Severe Acute Respiratory Infection, China, 2017-2019 ...
... plants were saving an extra copy of certain genes-or so say Brad Chapman and his colleagues in a recent paper that ... Over the course of three Arabidopsis duplications, genes reduced back to single status after the γ duplication are usually ... how is the evolution of a gene sequence affected by the presence of an extra copy of that gene from a genome duplication event ... GENE CLASSES FOLLOW DIFFERENT FATES AFTER PLANT GENOME DUPLICATION by heatherramsey Any student who has lost hours of work to a ...
Fates of genes after duplication : sublocalization and regulatory neofunctionalization Tay, Yii Van Abstract. Gene duplication ... Gene duplication has supplied the raw material for novel gene functions and evolutionary innovations in plants. Duplicated ... Regulatory neofunctionalization involves changes in expression patterns of a gene after duplication. The goals for the second ... Regulatory neofunctionalization involves changes in expression patterns of a gene after duplication. The goals for the second ...
... ... Title : Emerging Human Metapneumovirus Gene Duplication Variants in Patients with Severe Acute Respiratory Infection, China, ... HMPV genotype A2c variants 111 nt and 180 nt duplications predominated, demonstrating their continuing geographic spread. ...
OC gene is likely to have appeared from MGP through a tandem gene duplication that occurred concomitantly with the appearance ... Animals, Bone and Bones, Calcium-Binding Proteins, Evolution, Molecular, Extracellular Matrix Proteins, Gene Duplication, Gene ... with OC following a gene duplication strategy while MGP variability was obtained mostly by the use of multiple promoters and ... Both OC and MGP share similar structural features, both in terms of protein domains and gene organization. ...
Gene Ontology) enrichment analysis of the gene composition of each ancestral genome, allowing us to characterize the subseq ... We then addressed the question of which expanded gene families and gained genes are potentially involved in adaptation to ... Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because ...
... including clear signals in gene families that form tandem intra-chromosomal clusters. Taken together, my analyses implicate IGC ... Interlocus gene conversion (IGC) is a recombination-based mechanism that results in the unidirectional transfer of short ... Interlocus gene conversion explains at least 2.7 % of single nucleotide variants in human segmental duplications. Access & ...
Whole genome sequencing of field isolates reveals a common duplication of the Duffy binding protein gene in Malagasy Plasmodium ... gene. A survey of Malagasy patients infected with P. vivax showed that the PvDBP duplication was present in numerous locations ... PvDBP duplication prevalence was highest in west-central Madagascar sites where the highest frequencies of P. vivax-infected, ... Additionally, the PvDBP duplication was observed in travelers seeking treatment of vivax malaria upon returning home. ...
Phenotypic suppression of the Drosophila mitochondrial disease-like mutant tko25t by duplication of the mutant gene in its ... Phenotypic suppression of the Drosophila mitochondrial disease-like mutant tko25t by duplication of the mutant gene in its ... exhibiting almost wild-type phenotype and containing overlapping segmental duplications including the mutant allele, plus a ... second mitoribosomal protein gene, mRpL14. Ectopic, expressed copies of tko25t and mRpL14 conferred no phenotypicsuppression. ...
... gene duplication and recombination all contribute to the diversity of MHC class Ia genes. These findings broaden our knowledge ... The goal of the present study was to isolate MHC class I genes from two Rhacophoridae species (Rhacophorus omeimontis and ... The available evidence suggests that these 27 sequences all belong to classical MHC class I (MHC Ia) genes. Although several ... In addition, signals of positive selection were found in Rhacophoridae MHC class Ia genes. Amino acid sites strongly suggested ...
The gene duplication process has exhibited much larger promiscuity in the. Home / Uncategorized / The gene duplication process ... polyploidization also entails the coordinated duplication of the structural gene and linked gene duplication occasions where in ... In this paper, I focus on the diversity of the gene GW 4869 price duplication process whereby fresh genes are created by ... It also provided the 1st theoretical framework for the evolution of novel gene function by one copy following gene duplication ...
Analysis of fish ZP1/ZPB homologous genes - evidence for both genome duplication and species-specific amplification models of ... Analysis of fish ZP1/ZPB homologous genes - evidence for both genome duplication and species-specific amplification models of ...
Phylogenetic and molecular evolution analyses found evidence that gene deletions and duplications as well as concerted ... Loricrin is the main protein component of the mammalian CE and is encoded for by a gene located within the EDC. Recently, genes ... We found that loricrin is present within the EDC of all species investigated, and that three loricrin genes were present in ... Many of the substrates of cornification are encoded by linked genes located at a conserved genetic locus known as the epidermal ...
MECP2 duplication syndrome is a condition that occurs almost exclusively in males and is characterized by moderate to severe ... The MECP2 gene is always included in this duplication, and other genes may also be involved, depending on the size of the ... MECP2 duplication syndrome is caused by a genetic change in which there is an extra copy of the MECP2 gene in each cell. This ... MECP2 duplication syndrome is inherited in an X-linked pattern. The gene associated with this condition is located on the X ...
Dive into the research topics of Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in ... Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals. ...
Gene Deletion, Gene Duplication, Humans, In Situ Hybridization, Fluorescence, Infant, Male, Models, Genetic, Pedigree, ... Deletion and duplication of the adenomatous polyposis coli gene resulting from an interchromosomal insertion involving 5( ... Deletion and duplication of the adenomatous polyposis coli gene resulting from an interchromosomal insertion involving 5( ...
Emerging Human Metapneumovirus Gene Duplication Variants in Patients with Severe Acute Respiratory Infection, China, 2017-2019 ... Emerging Human Metapneumovirus Gene Duplication Variants in Patients with Severe Acute Respiratory Infection, China, 2017-2019 ...
We also focus on the evolutionary tinkering of these clock genes and compare and contrast the neuronal basis for behavioural ... Once gene duplication occurs, the selective constraints on the new copy are reduced, allowing the new copy (or both) to evolve ... Kopelman et al98 found that gene duplication and splicing are inversely correlated in the human and mouse genomes, with large ... Cycling gene products and negative feedback. The products of the per and tim genes, RNA and proteins, cycle in abundance in the ...
This test can be used to detect the presence or absence of large deletions in the HBA1 or HBA2 gene in patients or their family ... This assay can be used instead of southern blot analysis to determine the total number of intact alpha globin genes. ...
Segmental duplication is shown to be responsible for the expansion of ZmHSFs. Most of the ZmHSFs are localized inside the ... Gene ontology and protein-protein interaction analysis indicated a major role of ZmHSFs in resistance to environmental stress ... Gene structure and protein motif analysis supported the results obtained through the phylogenetic analysis. ... Thus, a comprehensive genome-wide identification analysis was performed to identify HSFs genes in the maize genome. The current ...
... in copy numbers of MEDLE family secreted proteins and insulinase-like proteases indicate that telomeric gene duplications could ... These genomes had complete synteny in gene organization and 96.86-97.0% and 99.72-99.83% nucleotide sequence similarities to ... reveals occurrence of genetic recombination in virulent Cryptosporidium hominis subtypes and telomeric gene duplications in ... reveals occurrence of genetic recombination in virulent Cryptosporidium hominis subtypes and telomeric gene duplications in ...
Gene duplication in the epigenomic era. / Zheng, Deyou.. In: Epigenetics : official journal of the DNA Methylation Society, Vol ... Gene duplication in the epigenomic era. In: Epigenetics : official journal of the DNA Methylation Society. 2008 ; Vol. 3, No. 5 ... Gene duplication in the epigenomic era. Epigenetics : official journal of the DNA Methylation Society. 2008 Sep;3(5):250-253. ... Zheng, D. (2008). Gene duplication in the epigenomic era. Epigenetics : official journal of the DNA Methylation Society, 3(5), ...
gene duplication to enable genetic programming to concurrently evolve both the architecture and work-performing steps of a ... begins with a gene duplication and that gene duplication is {"}the major force of evolution.{"} This paper describes six new ... Gene Duplication to Enable Genetic Programming to Concurrently Evolve Both the Architecture and Work-Performing Steps of a ... title = "Gene Duplication to Enable Genetic Programming to Concurrently Evolve Both the Architecture and Work-Performing Steps ...
Segmental duplications in the human genome are selectively enriched for genes involved in immunity, although the phenotypic ... abstract = "Segmental duplications in the human genome are selectively enriched for genes involved in immunity, although the ... N2 - Segmental duplications in the human genome are selectively enriched for genes involved in immunity, although the ... AB - Segmental duplications in the human genome are selectively enriched for genes involved in immunity, although the ...
Test ID CASRG CASR Full Gene Sequencing with Deletion/Duplication, Varies Ordering Guidance. Targeted testing for familial ... Testing for the CASR gene as part of a customized panel is available. For more information, see CGPH / Custom Gene Panel, ... In the parathyroid glands, an increase in serum calcium results in downregulation of gene expression of the main short-term ... variants (also called site-specific or known mutations testing) is available for the genes on this panel. See FMTT / Familial ...
We have optimized all our processes to accept a wide range of samples, always adapting to each case ...
Complexity of Gene Expression Evolution after Duplication: Protein Dosage Rebalancing. Igor B. Rogozin ... Modulation at Age of Onset in Tunisian Huntington Disease Patients: Implication of New Modifier Genes. Dorra Hmida-Ben Brahim ... Generalized Portrait of Cancer Metabolic Pathways Inferred from a List of Genes Overexpressed in Cancer. Eugenia Poliakov , ... Using new understanding of genes and pathways to develop powerful new therapeutic approaches to disease ...
Palmgren M, Sørensen DM, Hallström BM, Säll T, Broberg K. Evolution of P2A and P5A ATPases: ancient gene duplications and the ... Evolution of P2A and P5A ATPases : ancient gene duplications and the red algal connection to green plants revisited. In: ... Dive into the research topics of Evolution of P2A and P5A ATPases: ancient gene duplications and the red algal connection to ... Evolution of P2A and P5A ATPases : ancient gene duplications and the red algal connection to green plants revisited. / Palmgren ...
  • Deletion and duplication of the adenomatous polyposis coli gene resulting from an interchromosomal insertion involving 5(q22q23.3) in the father. (
  • In this retrospective study , nine cases (five with microdeletion and four with microduplication) are reported with 6q26 deletion disrupting the PARK2 gene . (
  • Mechanisms of Rh-negativity in these ethnic groups may include gene deletion, gene rearrangement, gene duplication, and gene mutation. (
  • Single gene sequencing, deletion/duplication analysis and targeted variant analysis is also available for this gene. (
  • Extent of the deletion/duplication should be specified using the genomic description (g.). "-" indicates the variant described on genomic level does not affect the coding DNA reference sequence. (
  • Blueprint Genetics' Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis. (
  • FISH mapping further narrowed the region of deletion of chromosome 4 to 39.6 centimorgans (cM) and the region of duplication to 10-35 cM. (
  • However, a true acknowledgement of the part of gene duplication in the creation of radically modified structures would not be forthcoming until the introduction of the genomic revolution. (
  • One of evolutionary molecular biology fundamental issues is to discover genomic duplication events and their correspondence to the species tree. (
  • The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. (
  • The genomic loci for FABP genes were diverse and their genomic structure varied. (
  • Use of genomic DNA reference materials has generally worked well for tests targeting one or a few genes but presents challenges for assuring the quality of sequencing tests with more than a few genes. (
  • It can be challenging for individual laboratories to recognize the clinically relevant variant spectrum and have knowledge of difficult to sequence genomic regions, such as those with high GC content, highly homologous genes, or repetitive sequences for all genes included in the test. (
  • Whole genome duplication (WGD) provides new genetic material for genome evolution. (
  • Functional divergence of Populus MYB158 and MYB189 gene pair created by whole genome duplication[J]. J Syst Evol, 2022, 60(1): 169-185. (
  • Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. (
  • The evolution of duplicated genes after whole-genome duplication (WGD) has been studied extensively. (
  • Targeted testing for familial variants (also called site-specific or known mutations testing) is available for the genes on this panel. (
  • HMPV genotype A2c variants 111 nt and 180 nt duplications predominated, demonstrating their continuing geographic spread. (
  • Recently, unique HMPV variants possessing a 180 nt duplication (nt-dup) in the G gene, first reported in Spain, and a 111 nt-dup in the G gene, first reported Japan ( 5 , 8 , 9 ), followed by Croatia and Guangdong, China ( 10 , 11 ). (
  • No clear differences in clinical signs and symptoms were apparent among the patients infected with duplication variants compared with other HMPV viruses. (
  • Variants in the ABCB11 gene also result in a condition known as benign recurrent intrahepatic cholestasis (BRIC2). (
  • Alternatively spliced transcript variants encoding different isoforms have been found for this gene. (
  • Belted mice have sequence variants in the Adamts20 gene encoding a secreted metalloprotease [ 16 ], which was shown to be required for melanoblast survival [ 17 ]. (
  • Accumulations of TEs (TE islands) comprising 7.18% of the genome evolve faster than other regions with regard to single-nucleotide variants, gene/exon duplications and deletions and gene homology. (
  • Over the last decade, genetic testing has evolved from examining a few well-defined variants in one or a few genes to the capability to examine much of the human genome using next generation sequencing (NGS). (
  • As part of this study, the ClinGen Variant Curation Expert Panels nominated 546 variants found in 84 disease associated genes ( link to table of genes ), including common pathogenic and difficult to detect variants. (
  • For paleologs, single-nucleotide polymorphisms (single base-pair differences in otherwise identical stretches of DNA) tend to fall in the third codon position, where they are unlikely to alter the amino acid in the functional protein, whereas mutations retained by singleton genes usually do alter the protein product. (
  • Chromosomal rearrangements of the type may actually provide a mechanism for achieving more rapid and extensive changes in protein structure in evolution than are possible by point mutations even when preceded by gene duplication. (
  • Ohno postulated that single-copy genes with essential functions are actively policed by purifying natural selection that serves to remove newly-acquired forbidden mutations that may compromise the ancestral gene function. (
  • This active removal of fresh mutations by single-copy genes in turn precludes GW 4869 price them from exploring fresh evolutionary space (and gain of novel functions). (
  • The gene duplication process, by creating a redundant locus, concurrently (i) permits the uninterrupted maintenance of the ancestral function by one copy and (ii) enables the extra, initially redundant copy to accumulate mutations that facilitate its rebirth as a new gene with a hitherto non-existent function (neofunctionalization) or hasten its degeneration into a nonsense, DNA foundation sequence [16, 20] or pseudogene (nonfunctionalization). (
  • Heterozygous mutations in the gene encoding noggin affect human joint morphogenesis. (
  • Also includes mutations in the protein-coding region that neither alter the amino acid sequence nor are predicted to significantly affect exon splicing, and base pair alterations in non-coding portions of the gene that have been demonstrated to have no deleterious effect on the length or stability of the mRNA transcript. (
  • Casewell suspects snake venom originated when variations in existing genetic material-duplications and other mutations-produced toxic products. (
  • Biologists think that mutations such as duplication of these "good" genes led to the production of toxins now found in snake venom. (
  • ABSTRACT Approximately 5%-10% of all breast cancers are inherited as the result of germline mutations in the BRCA1 gene. (
  • Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. (
  • All mutations are rare events, but mutation frequencies vary from organism to organism and from gene to gene within a given organism. (
  • Subsequent mutations in one of the two copies of the gene might not have an adverse effect on sur- vival because the other copy of the gene would continue to produce functional protein. (
  • Expression of p63 is almost exclusively restricted to epithelial cells, mutations in this gene are infrequent, and its expression is increased in a variety of solid tumors, particularly those of the head and neck area 12,13 . (
  • Certain MHC class I genes that display a very high level of genetic diversity [ 3 , 4 ] are called classical MHC class I genes or MHC class Ia genes [ 2 ]. (
  • 13] succinctly complete the evolutionary potential of such radically changed gene duplicatesWe claim that proteins with radically transformed properties could be formed because of the one genetic event of a chromosomal rearrangement regarding nonintegral amounts of genes. (
  • In this paper, I focus on the diversity of the gene GW 4869 price duplication process whereby fresh genes are created by incorporating genetic tracts from previously existing genes and also noncoding DNA (intergenic and intronic), and the evolutionary effects of this promiscuity inherent in the gene duplication process. (
  • Many of the substrates of cornification are encoded by linked genes located at a conserved genetic locus known as the epidermal differentiation complex (EDC). (
  • This relationship between CCL3L1 dose and altered HIV/AIDS susceptibility points to a central role for CCL3L1 in HIV/AIDS pathogenesis and indicates that differences in the dose of immune response genes may constitute a genetic basis for variable responses to infectious diseases. (
  • The G gene, around 654-867 nt acids sequence length, is the most variable nucleotide sequence in the whole genome of HMPV and has been widely used to study HMPV genetic variation ( 3 - 5 ). (
  • In this study, we investigated the prevalence of HMPV associated with patients with severe acute respiratory infection (SARI) and identified genetic variations in the G gene of HMPV in Luohe, in Henan Province, China, during 2017-2019. (
  • This is the case in particular in the presence of lateral genetic transfer (LGT), whereby a gene is inherited from a distant species rather than an immediate ancestor. (
  • Biologist Ann Gauger looked at one of the initially strongest arguments against Adam and Eve from human genetic diversity (HLA genes) and found the evidence is compatible with our descending from an initial couple. (
  • The use of 2 different gene-specific probes can detect translocations too small to detect by normal karyotyping, such as when genetic material from the c- abl oncogene on chromosome 9 is inserted into the BCR gene on chromosome 22 as occurs in chronic myelogenous leukemia. (
  • Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. (
  • If whole genes were sometimes duplicated by the mechanisms described in the previous section, the bearer of the duplication would have a surplus of genetic information that might be turned to good use. (
  • Genetic testing for the HPS1 gene, which most commonly occurs in Puerto Ricans, exists. (
  • Although entire genome sequences are available for numerous species, lack of reverse genetic tools has hindered cross-species comparisons of gene function. (
  • Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. (
  • Genome-wide approaches to epidermal function include short interfering RNA-based genetic screens in cultured human epidermal cells 8 and RNA interference-mediated gene knockdown via in utero microinjection of lentiviral vectors 9 . (
  • Germline or somatic GPR101 duplication leads to X-linked acrogigantism: a clinico-pathological and genetic study. (
  • Segmental duplications in the human genome are selectively enriched for genes involved in immunity, although the phenotypic consequences for host defense are unknown. (
  • Recent research shows that duplications in the human genome play a role in a variety of diseases, including autism, schizophrenia, and mental retardation. (
  • Duplicate genes from organisms as diverse as Xenopus, Arabidopsis and Saccaromyces actually show unexpected similarity even long after the original duplication event. (
  • 2006) take advantage of information from genome sequencing of Arabidopsis and rice to explore the nature of singleton and duplicate genes from the same genome duplication event. (
  • While it seems that the rice lineage went through only one such duplication, Arabidopsis bears evidence of three (α, β and γ, where α is the most recent). (
  • By following the fate of Arabidopsis genes over each of these duplications, Chapman et al. (
  • Over the course of three Arabidopsis duplications, genes reduced back to single status after the γ duplication are usually reduced to singletons again after the α and β events as well. (
  • The goals for the second part of my thesis were to study expression patterns of duplicated genes in Arabidopsis thaliana and to analyze the selective forces acting on the genes of interest. (
  • Thus for example, in Arabidopsis thaliana , over-retained genes are involved in basic cellular machinery, nucleotide-sugar metabolism, signal transduction or regulatory functions, while the diploidized genes are involved in DNA repair, tRNA ligation or defense ( Blanc and Wolfe, 2004 ). (
  • KEY MESSAGE: Overexpression of the tea plant gene CsbZIP18 in Arabidopsis impaired freezing tolerance, and CsbZIP18 is a negative regulator of ABA signaling and cold stress. (
  • 2006). But not all species whose progenitors experienced genome duplication actually have twice the normal number of chromosomes. (
  • Comparison of major histocompatibility complex (MHC) genes across vertebrate species can reveal molecular mechanisms underlying the evolution of adaptive immunity-related proteins. (
  • The goal of the present study was to isolate MHC class I genes from two Rhacophoridae species ( Rhacophorus omeimontis and Polypedates megacephalus ) and examine their evolution. (
  • We found that loricrin is present within the EDC of all species investigated, and that three loricrin genes were present in birds. (
  • Estimation of species trees from multiple genes is complicated by processes such as incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer, that result in gene trees that differ fr. (
  • It is shown that a species phylogeny can be reconstructed correctly from gene trees even when, on each gene, each edge of the species tree has a constant probability of being the location of an HGT event. (
  • It is shown that not taking into account this inter-dependency relationships (co- evolutionary relationships) during the inference of gene trees results in an overestimation of the differences between gene trees as well as between gene tree and species tree. (
  • Inconsistency of Species Tree Methods under Gene Flow. (
  • Here, we surveyed chromatin architecture and gene expression during desiccation in these two closely related species to identify regulatory dynamics underlying the distinct desiccation tolerance strategies in grasses. (
  • illustrates how these deficiencies affect the composition and function of gut microbiota, and further, how different species realize changes in gene expression and cellular metabolism to cope with micronutrient shortages. (
  • The loss/retention of duplicated genes is not a random process and, from studies in various plant species, it appears to depend on gene functional category. (
  • Only in genomes of two cnidarian species could FABP genes not be identified. (
  • These results demonstrate that both gene duplication and post-transcriptional modifications are used to generate diverse FABPs in species studied. (
  • They rely on a probability model for the evolution of gene families on a species tree with WGDs. (
  • Both methods use multiple gene families across multiple species. (
  • Identification of multicomponent histidine-aspartate phosphorelay system controlling flagellar and motility gene expression in Geobacter species. (
  • We established a broadly applicable strategy using zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) for targeted disruption of endogenous genes and cis-acting regulatory elements in diverged nematode species. (
  • We developed efficient procedures for targeted, heritable disruption of genes and cis-acting regulatory elements in the model nematode Caenorhabditis elegans and applied them to C. briggsae , a species diverged by 15 to 30 million years. (
  • Regulation of two highly similar genes, omcB and omcC, in a 10 kb chromosomal duplication in Geobacter sulfurreducens. (
  • Even if all genes remain intact after a chromosomal break, serious problems may occur. (
  • The team examined clinical samples from blood, skin and amniotic fluid of nine patients with chromosomal breaks but without damage to known genes. (
  • Recently, genes resembling mammalian loricrin, along with several other proteins most likely involved in CE formation, have been identified within the EDC of birds and several reptiles. (
  • Its genome is ≈13.2 kb, containing 8 genes encoding 9 proteins. (
  • Although MYB158 and MYB189 proteins could repress the same structural genes involved in lignin, cellulose, and xylan biosynthesis, the two proteins had their own specific regulatory targets. (
  • The RHD and RHCE genes encode proteins such that each crosses the red cell membrane 12 times, with 6 protein loops on the exterior of the cell membrane. (
  • A tandem array of early light induced proteins (ELIPs) had massive shifts in gene expression and chromatin openness under desiccation in only O. thomaeum , and ELIPs acquired a novel desiccation related cis-regulatory motif, reflecting regulatory neofunctionalization during the evolution of desiccation tolerance. (
  • Snake venom is not a single substance but a cocktail of proteins encoded by many different genes. (
  • Genes encoding venom proteins are located at multiple locations in the king cobra's genome. (
  • They include duplicate copies of genes that produce nontoxic proteins in the stomach, spleen, testes, and ovaries. (
  • There are four main gene families that create venom proteins in the King Cobra, and they have all expanded hugely compared to other parts of the genome," Casewell explains. (
  • Fatty acid-binding proteins (FABPs) are a family of fatty acid-binding small proteins essential for lipid trafficking, energy storage and gene regulation. (
  • Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. (
  • 2006) set out to address intriguing, unanswered questions of molecular evolution: how is the evolution of a gene sequence affected by the presence of an extra copy of that gene from a genome duplication event? (
  • Phylogenetic and molecular evolution analyses found evidence that gene deletions and duplications as well as concerted evolution has shaped the evolution of avian loricrins. (
  • Molecular evolution of Coq1 gene family in eukaryotes [J]. J Syst Evol, 2017, 55(5): 417-425. (
  • Model based calculations of the codon substitution rate of the human genes included in these segments agree with the molecular clock duplication time-scale prediction. (
  • One method relies on aligned molecular sequences and the other simply uses information on gene counts. (
  • GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies ( Molecular Function , Biological Process , and Cellular Component ), a reference, and an evidence code. (
  • This stands in stark contrast with the classical prediction that duplicate genes rather than singletons will show more drastic (i.e., protein-altering) changes in their DNA sequences. (
  • Sublocalization, which is a type of subfunctionalization based on protein subcellular relocalization, happens when the products of the duplicate genes are each directed to only one of two subcellular locations that were previously targeted by the single ancestral gene. (
  • Our findings provide new insights into the evolutionary and functional divergence of WGD-derived duplicate genes. (
  • For deletions/duplications extending beyond the reference transcript resp. (
  • About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. (
  • Much evidence suggests many pseudogenes are functional, and not "nonfunctional" genes. (
  • Pseudogenes are DNA sequences that resemble functional genes but seem to have no purpose. (
  • Pseudogenes are DNA sequences that appear similar to functional genes, but contain important defects that appear to make them incapable of producing a functioning protein (Proudfoot 1980). (
  • The gene is located near two cytochrome P450 pseudogenes on chromosome 22q13.1. (
  • It predicts that paleologous duplicates will undergo fewer changes than singleton genes do in their nucleotide and amino acid sequences. (
  • The available evidence suggests that these 27 sequences all belong to classical MHC class I (MHC Ia) genes. (
  • Phylogenetic tree generated by maximum-likelihood method of HMPV G gene sequences (red) from patients with SARI admitted to Luohe Central Hospital, Luohe, China, during October 2017-June 2019, and reference sequences. (
  • Ordinary structural genes are made of DNA sequences that contain coded information for making a particular protein molecule. (
  • They lack introns (spacer sequences within a gene) and certain regulatory sequences located in front of the gene, they often terminate in a series of adenines, and are flanked by direct repeats. (
  • Snake genomes may be prone to gene duplications because their many repeated nucleotide sequences, coauthor David Pollock suggests. (
  • Now that we have the complete genome sequences of both (and other monkeys) it is possible to look for the protein coding genes which separate us. (
  • The duplication occurs on the short (p) arm of the chromosome in a region designated 17p12-17p11.2. (
  • Two separate genes for the Rh system are found on chromosome 1. (
  • These increase the chance of chromosome misalignment during DNA replication and increase the chance of duplications. (
  • Fig. 1: Standard G-banded karyotype: each chromosome has a characteristic banding pattern, allowing the identification of gross duplications, deletions, additions and translocations. (
  • Gene-specific probes, also known as "locus specific," bind to single areas of a chromosome, whether a gene, or a repetitive sequence such as a centromere or telomere. (
  • Such locus- specific probes can detect abnormal duplication of a gene ( Fig. 2 ) or chromosome. (
  • Both expression bias and expression equivalence were observed at the transcriptomic level in these homoeologous regions: out of the 89 homoeologous gene pairs expressed in both regions, 40% showed bias (higher transcript accumulation) toward the homoeologs on chromosome 10. (
  • Clementi M, Tenconi R, Turolla L, Silvan C, Bortotto L, Artifoni L. Apparent CHARGE association and chromosome anomaly: chance or contiguous gene syndrome. (
  • Exon deletions exist in the dystrophin gene Xp21 (X-chromosome, short arm p, region 2, band 1). (
  • The chromosome on the right acquired an additional piece by duplication of a section of DNA, which is apparent by the additional band (arrow). (
  • Duplication of the proximal region of chromosome 4 occurred in 22% of the spontaneously-occurring high-invasive cells strains and 83% of the chemically-induced high-invasive cell culrures. (
  • Regulatory neofunctionalization involves changes in expression patterns of a gene after duplication. (
  • In the parathyroid glands, an increase in serum calcium results in downregulation of gene expression of the main short-term regulator of calcium homeostasis, parathyroid hormone (PTH), as well as diminished secretion of already synthesized PTH. (
  • The RAI1 gene provides instructions for making a protein that helps regulate the activity (expression) of other genes. (
  • Research suggests that duplications involving this gene lead to higher-than-normal amounts of the RAI1 protein, which disrupts the expression of genes that influence brain and craniofacial development and the sleep-wake cycle. (
  • Populus MYB158 could act as the upstream regulator of secondary cell wall NAC master switch and directly represses the expression of the SND1-B2 gene. (
  • In both grasses, we observed a strong association between nearby chromatin accessibility and gene expression in desiccated tissues compared to well-watered, reflecting an unusual chromatin stability under anhydrobiosis. (
  • Integration of chromatin accessibility (ATACseq) and expression data (RNAseq) revealed a core desiccation response across these two grasses including many genes with binding sites for the core seed development transcription factor ABI5. (
  • 4 Even regulatory genes associated with expression of the venom-producing genes are responsible for benign functions in other organs such as the pancreas. (
  • Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the resistance phenotype. (
  • Chemical RNA modifications, collectively referred to as the "epitranscriptome," are essential players in fine-tuning gene expression. (
  • A non-random distribution of gene families, larvae/adult specific gene expression and signs of differential methylation in TE islands indicate intragenomic differences in regulation, evolutionary rates and coalescent effective population size. (
  • The M allele impacts canine coat color by altering the expression of the PMEL gene which is primarily located in eumelanosomes that produce and store eumelanin (black pigment). (
  • Alteration in copy number and expression of these genes may play a functional role in lung cancer development. (
  • Fig. 2: Visualization of genes using locus-specific FISH probes: red signals (see arrows) hybridized to the chromosomes of a metaphase cell and an adjacent interphase nucleus demonstrate normal numbers of the cyclin D1 gene. (
  • Polyploidy and Gene Duplication: copying existing genes or chromosomes. (
  • To study the functions of large numbers of genes in vivo 2 requires a shift from gene-specific to genome-wide approaches. (
  • Gene duplication has supplied the raw material for novel gene functions and evolutionary innovations in plants. (
  • The goals of the first part of my project were to study changes in protein subcellular localization (relocalization) after gene duplication by finding cases of sublocalization and further characterizing them from an evolutionary perspective. (
  • I identified and analyzed multiple cases of sublocalization of the APX and PP5 genes by doing RT-PCR experiments and then performing phylogenetic analyses and sequence rate analyses to further characterize the genes from an evolutionary perspective. (
  • Knowledge regarding the evolutionary patterns and mechanisms associated with amphibian MHC genes remains limited. (
  • The evolutionary mechanisms contributing to the diversity of MHC class I genes are of significant interest in the study of MHC evolution. (
  • Second, I discuss the many flavours of gene duplicates from both DNA- and RNA-mediated mutational occasions and explore their particular prospect of the creation of Rabbit Polyclonal to NDUFB10 evolutionary improvements and biological diversity. (
  • Third, I explore the many scenarios under which gene paralogs can get away homogenization by ectopic gene transformation, rendering them absolve to evolve along novel evolutionary trajectories and believe divergent functions. (
  • Evolution of the 4-coumarate:coenzyme A ligase ( 4CL ) gene family: Conserved evolutionary pattern and two new gene classes in gymnosperms [J]. J Syst Evol, 2012, 50(3): 195-205. (
  • Modern data sets often contain a large number of genes which can complicate the reconstruction problem due to the fact that different genes may undergo different evolutionary histories. (
  • Duplications are really important from an evolutionary perspective because they add a lot of variation to the genome," says Tomas Marques-Bonet , a scientist in Evan Eichler's lab at the University of Washington, in Seattle, who led the research. (
  • For example, it's not yet clear whether the duplications that occurred during this time period conferred an evolutionary advantage on their bearers. (
  • Duplications are likely to have very different evolutionary properties than single-letter changes. (
  • We're watching a series of at least gene duplications with subsequent modifications build the brain that is unique to us over relatively rapid evolutionary times. (
  • Comparison of the genomes of the king cobra with the Burmese python and other vertebrates reveals that the snakes have duplicate copies of lots of genes that ordinarily produce nontoxic products. (
  • In this case, one of the parental genomes is more likely to retain genes and has a higher gene density than the other(s) genome(s). (
  • Availability of the complete genomes of 34 invertebrates, together with transcriptomes and ESTs, allowed us to systematically investigate the gene structure and alternative splicing of FABP genes over a wide range of phyla. (
  • Hominid Specific genes (HS genes) result which result from recent gene duplications in hominid/human genomes. (
  • A recent paper [ Neuron vol. 111 pp. 65 - 80 '23 ] discusses CROCCP2 (you don't want to know what the acronym stands for) which is one of several genes in this family with at least 6 copies in various hominid genomes. (
  • This test can be used to detect the presence or absence of large deletions in the HBA1 or HBA2 gene in patients or their family members suspected of having alpha thalassemia or who are carriers of alpha globin deletions. (
  • These extra copies of genes have long been viewed as prime real estate for the evolution of new gene functions. (
  • And does the effect of a paleologous copy on gene evolution depend on the type of gene in question? (
  • It also provided the 1st theoretical framework for the evolution of novel gene function by one copy following gene duplication. (
  • First, I describe the canonical model of gene duplicate evolution as envisioned by Ohno and delineate its major tenets and also its failure to encapsulate the entire complexity of the gene duplication procedure as uncovered by whole-genome sequence data. (
  • Evolution of Snake Venom: A New Use for Old Genes? (
  • It could be that this just lets the snake deliver more of the same toxins, but it's also highly likely that these duplications led to the evolution of new functions. (
  • Regions of DNA prone to duplication may have played a vital role in human evolution. (
  • Scientists are hesitant to speculate about precisely how the acceleration in the rate of duplication arose in the human and chimp lineage, and how it affected human evolution. (
  • Gene duplication is a great way for evolution to work quickly. (
  • In this project I performed experimental evolution of a small RNA virus to asses the stability of changes in its genome architecture (relocation, duplication and insertion of foreign genes). (
  • The possibility that the eta globin pseudogene provides a binding site for a molecule involved in gene regulation has not been ruled out. (
  • Genes retained in several copies were mainly involved in response to stress, signaling, or transcription regulation. (
  • The distinct organization of TE islands, their gene composition and their regulation by the genome adds compelling evidence for the role of TEs as players in differentiation, adaptation and speciation. (
  • 2006). Nevertheless, the classical model based on functional divergence and subfunctionalization is not the whole story of duplicated genes. (
  • Owing to technical limitations, a large-scale high-throughput systematic functional screen for genes involved in skin homeostasis was not feasible until recently. (
  • Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. (
  • Here we have performed structure/function analyses of DOR guided by identification of conserved regions in the DOR gene family by phylogenetic reconstructions. (
  • This assay can be used instead of southern blot analysis to determine the total number of intact alpha globin genes. (
  • Either way, genes retained as duplicates are expected to show more severe changes to amino acid sequence than genes for which only a single copy is kept. (
  • Likewise, genes duplicated in the γ event usually show up as duplicates following the α and β events. (
  • Not only are some genes preferentially retained as duplicates, but the differences between these duplicates are fewer and less severe than between homologous singleton genes in related ecotypes or subspecies. (
  • Analyses of entire populations of young gene duplicates recognized from whole-genome sequence data have established that the duplication process shows little respect for gene boundaries and may spawn remarkably varied units of duplication products with varying examples of structural resemblance to the ancestral copy. (
  • Such gene duplicates may have persisted in the genome of venomous snakes, the authors suggest, because toxins produced when those genes were expressed in the salivary and accessory glands provided selective advantages in obtaining prey. (
  • Studies published so far include limited sequence data from organisms close to the hypothesized genome duplications. (
  • Comparing areas of DNA duplication in the genome sequence, researchers found a burst in the rate of duplications right before orangutans split from the tree, and a second burst before chimps and humans diverged, according to research published today in the journal Nature . (
  • The belt-associated variant was a copy number variant (CNV) involving the quadruplication of a 6 kb non-coding sequence located approximately 16 kb upstream of the TWIST2 gene. (
  • O. thomaeum had a unique set of desiccation induced genes and regulatory elements associated with photoprotection, pigment biosynthesis, and response to high light, reflecting its adaptation of homoiochlorophyly. (
  • A reading frame or in-frame mutation hypothesis has been proposed to explain abnormal translation of the dystrophin gene. (
  • The frequency of mutation is usually much lower than one mutation per 104 base pairs per DNAduplication, and sometimes as low as one mutation per 109 base pairs per duplication. (
  • In addition, scientists can now create custom-designed gene microarrays to quickly detect a large number of specific duplications. (
  • Direct correlation between rates of anaerobic respiration and levels of mRNA for key respiratory genes in Geobacter sulfurreducens. (
  • those genes can then mutate separately. (
  • The extra gene might mutate over and over again without ill effect because its original function would be fulfilled by the original copy. (
  • The duplicated region always contains at least two genes, RAI1 and PMP22 . (
  • In addition, while single-letter changes may make a particular protein more or less effective by slightly tweaking its structure, duplications that create additional copies of specific genes free up the new copies to evolve an entirely new purpose. (
  • Such a screen would facilitate the identification of novel genes that are involved in skin homeostasis, cancer, aging, infection, wound repair and sensation. (
  • Researchers believe that having an extra copy of both of these genes underlies the characteristic features of YUHAL syndrome. (
  • Researchers suggest that by co-opting more and more genes for the production of more and more toxins, snakes like the king cobra's ancestors stayed a step ahead of their prey and produced increasingly complex biological weapons. (
  • The human-specific NOTCH2NL genes increase the self-renewal potential of human cortical progenitors (meaning more brain cell can result from them). (
  • The challenge for improvement of crop varieties is determining how quantitative resistance genes apply to a specific pathogen. (
  • These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. (
  • We found significant nuclear gene tree conflict as well as cytonuclear discordance. (
  • thus, ligand and antagonist seem to have evolved from a common ancestral gene. (
  • A complex structural rearrangement involving duplication of the KIT gene was identified in belted pigs, whose belt includes the forelimbs and is localized more cranially than the one in Adamts20 mutant mice [ 18 , 19 ]. (
  • Processes occurring in various organisms by which new genes are copied. (
  • The M Locus (Merle) coat color test reliably determines if a dog carries the M (merle insertion variant) Allele of the PMEL gene. (
  • Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes. (
  • Duplicated genes can have different fates over time such as neofunctionalization and subfunctionalization. (
  • Subfunctionalization: splitting functions of a gene into two genes doesn't add information. (