The relationships of groups of organisms as reflected by their genetic makeup.
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.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
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.
Sequential operating programs and data which instruct the functioning of a digital computer.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The 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.
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 sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
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.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
Genotypic differences observed among individuals in a population.
In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)
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.
Computer-based representation of physical systems and phenomena such as chemical processes.
The systematic study of the complete DNA sequences (GENOME) of organisms.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
Databases devoted to knowledge about specific genes and gene products.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
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.
The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
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 arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.
A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
The genetic complement of a BACTERIA as represented in its DNA.
Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
A field of study concerned with the principles and processes governing the geographic distributions of genealogical lineages, especially those within and among closely related species. (Avise, J.C., Phylogeography: The History and Formation of Species. Harvard University Press, 2000)
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.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
The genetic complement of MITOCHONDRIA as represented in their DNA.
The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.
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.
Any method used for determining the location of and relative distances between genes on a chromosome.
The genomic analysis of assemblages of organisms.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Deoxyribonucleic acid that makes up the genetic material of plants.
Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.
The portion of an interactive computer program that issues messages to and receives commands from a user.
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.
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.
That part of the genome that corresponds to the complete complement of EXONS of an organism or cell.
The genetic complement of a plant (PLANTS) as represented in its DNA.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.
Deoxyribonucleic acid that makes up the genetic material of fungi.
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.
A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.
The functional hereditary units of BACTERIA.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.
Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
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.
Organized activities related to the storage, location, search, and retrieval of information.
Software designed to store, manipulate, manage, and control data for specific uses.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)
Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.
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.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
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.
Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.
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)
Information application based on a variety of coding methods to minimize the amount of data to be stored, retrieved, or transmitted. Data compression can be applied to various forms of data, such as images and signals. It is used to reduce costs and increase efficiency in the maintenance of large volumes of data.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
A phylum of fungi which have cross-walls or septa in the mycelium. The perfect state is characterized by the formation of a saclike cell (ascus) containing ascospores. Most pathogenic fungi with a known perfect state belong to this phylum.
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.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
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 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.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
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.
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).
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Self-replicating cytoplasmic organelles of plant and algal cells that contain pigments and may synthesize and accumulate various substances. PLASTID GENOMES are used in phylogenetic studies.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
The functional hereditary units of PLANTS.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
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.
The change in gene frequency in a population due to migration of gametes or individuals (ANIMAL MIGRATION) across population barriers. In contrast, in GENETIC DRIFT the cause of gene frequency changes are not a result of population or gamete movement.
Proteins found in any species of bacterium.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
A collective genome representative of the many organisms, primarily microorganisms, existing in a community.
The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.
A large, subclass of arachnids comprising the MITES and TICKS, including parasites of plants, animals, and humans, as well as several important disease vectors.
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.
Procedures for identifying types and strains of fungi.
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.
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.
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.
Techniques for standardizing and expediting taxonomic identification or classification of organisms that are based on deciphering the sequence of one or a few regions of DNA known as the "DNA barcode".
The sequential location of genes on a chromosome.
Integrated set of files, procedures, and equipment for the storage, manipulation, and retrieval of information.
Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.
The variety of all native living organisms and their various forms and interrelationships.
An optical disk storage system for computers on which data can be read or from which data can be retrieved but not entered or modified. A CD-ROM unit is almost identical to the compact disk playback device for home use.
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)
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 genus of the family Lemuridae consisting of five species: L. catta (ring-tailed lemur), L. fulvus, L. macaco (acoumba or black lemur), L. mongoz (mongoose lemur), and L. variegatus (white lemur). Most members of this genus occur in forested areas on Madagascar and the Comoro Islands.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
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 determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Short tracts of DNA sequence that are used as landmarks in GENOME mapping. In most instances, 200 to 500 base pairs of sequence define a Sequence Tagged Site (STS) that is operationally unique in the human genome (i.e., can be specifically detected by the polymerase chain reaction in the presence of all other genomic sequences). The overwhelming advantage of STSs over mapping landmarks defined in other ways is that the means of testing for the presence of a particular STS can be completely described as information in a database.
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 genetic complement of CHLOROPLASTS as represented in their DNA.
The application of molecular biology to the answering of epidemiological questions. The examination of patterns of changes in DNA to implicate particular carcinogens and the use of molecular markers to predict which individuals are at highest risk for a disease are common examples.
A phylum of fungi that produce their sexual spores (basidiospores) on the outside of the basidium. It includes forms commonly known as mushrooms, boletes, puffballs, earthstars, stinkhorns, bird's-nest fungi, jelly fungi, bracket or shelf fungi, and rust and smut fungi.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
The fruiting 'heads' or 'caps' of FUNGI, which as a food item are familiarly known as MUSHROOMS, that contain the FUNGAL SPORES.
The number of mutations that occur in a specific sequence, GENE, or GENOME over a specified period of time such as years, CELL DIVISIONS, or generations.
The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.

## Novel regulation of the homeotic gene Scr associated with a crustacean leg-to-maxilliped appendage transformation. (1/277092)

Homeotic genes are known to be involved in patterning morphological structures along the antero-posterior axis of insects and vertebrates. Because of their important roles in development, changes in the function and expression patterns of homeotic genes may have played a major role in the evolution of different body plans. For example, it has been proposed that during the evolution of several crustacean lineages, changes in the expression patterns of the homeotic genes Ultrabithorax and abdominal-A have played a role in transformation of the anterior thoracic appendages into mouthparts termed maxillipeds. This homeotic-like transformation is recapitulated at the late stages of the direct embryonic development of the crustacean Porcellio scaber (Oniscidea, Isopoda). Interestingly, this morphological change is associated with apparent novelties both in the transcriptional and post-transcriptional regulation of the Porcellio scaber ortholog of the Drosophila homeotic gene, Sex combs reduced (Scr). Specifically, we find that Scr mRNA is present in the second maxillary segment and the first pair of thoracic legs (T1) in early embryos, whereas protein accumulates only in the second maxillae. In later stages, however, high levels of SCR appear in the T1 legs, which correlates temporally with the transformation of these appendages into maxillipeds. Our observations provide further insight into the process of the homeotic leg-to-maxilliped transformation in the evolution of crustaceans and suggest a novel regulatory mechanism for this process in this group of arthropods.  (+info)

## The Drosophila kismet gene is related to chromatin-remodeling factors and is required for both segmentation and segment identity. (2/277092)

The Drosophila kismet gene was identified in a screen for dominant suppressors of Polycomb, a repressor of homeotic genes. Here we show that kismet mutations suppress the Polycomb mutant phenotype by blocking the ectopic transcription of homeotic genes. Loss of zygotic kismet function causes homeotic transformations similar to those associated with loss-of-function mutations in the homeotic genes Sex combs reduced and Abdominal-B. kismet is also required for proper larval body segmentation. Loss of maternal kismet function causes segmentation defects similar to those caused by mutations in the pair-rule gene even-skipped. The kismet gene encodes several large nuclear proteins that are ubiquitously expressed along the anterior-posterior axis. The Kismet proteins contain a domain conserved in the trithorax group protein Brahma and related chromatin-remodeling factors, providing further evidence that alterations in chromatin structure are required to maintain the spatially restricted patterns of homeotic gene transcription.  (+info)

## The homeobox gene Pitx2: mediator of asymmetric left-right signaling in vertebrate heart and gut looping. (3/277092)

Left-right asymmetry in vertebrates is controlled by activities emanating from the left lateral plate. How these signals get transmitted to the forming organs is not known. A candidate mediator in mouse, frog and zebrafish embryos is the homeobox gene Pitx2. It is asymmetrically expressed in the left lateral plate mesoderm, tubular heart and early gut tube. Localized Pitx2 expression continues when these organs undergo asymmetric looping morphogenesis. Ectopic expression of Xnr1 in the right lateral plate induces Pitx2 transcription in Xenopus. Misexpression of Pitx2 affects situs and morphology of organs. These experiments suggest a role for Pitx2 in promoting looping of the linear heart and gut.  (+info)

## Mrj encodes a DnaJ-related co-chaperone that is essential for murine placental development. (4/277092)

We have identified a novel gene in a gene trap screen that encodes a protein related to the DnaJ co-chaperone in E. coli. The gene, named Mrj (mammalian relative of DnaJ) was expressed throughout development in both the embryo and placenta. Within the placenta, expression was particularly high in trophoblast giant cells but moderate levels were also observed in trophoblast cells of the chorion at embryonic day 8.5, and later in the labyrinth which arises from the attachment of the chorion to the allantois (a process called chorioallantoic fusion). Insertion of the ROSAbetageo gene trap vector into the Mrj gene created a null allele. Homozygous Mrj mutants died at mid-gestation due to a failure of chorioallantoic fusion at embryonic day 8.5, which precluded formation of the mature placenta. At embryonic day 8.5, the chorion in mutants was morphologically normal and expressed the cell adhesion molecule beta4 integrin that is known to be required for chorioallantoic fusion. However, expression of the chorionic trophoblast-specific transcription factor genes Err2 and Gcm1 was significantly reduced. The mutants showed no abnormal phenotypes in other trophoblast cell types or in the embryo proper. This study indicates a previously unsuspected role for chaperone proteins in placental development and represents the first genetic analysis of DnaJ-related protein function in higher eukaryotes. Based on a survey of EST databases representing different mouse tissues and embryonic stages, there are 40 or more DnaJ-related genes in mammals. In addition to Mrj, at least two of these genes are also expressed in the developing mouse placenta. The specificity of the developmental defect in Mrj mutants suggests that each of these genes may have unique tissue and cellular activities.  (+info)

## A Drosophila doublesex-related gene, terra, is involved in somitogenesis in vertebrates. (5/277092)

The Drosophila doublesex (dsx) gene encodes a transcription factor that mediates sex determination. We describe the characterization of a novel zebrafish zinc-finger gene, terra, which contains a DNA binding domain similar to that of the Drosophila dsx gene. However, unlike dsx, terra is transiently expressed in the presomitic mesoderm and newly formed somites. Expression of terra in presomitic mesoderm is restricted to cells that lack expression of MyoD. In vivo, terra expression is reduced by hedgehog but enhanced by BMP signals. Overexpression of terra induces rapid apoptosis both in vitro and in vivo, suggesting that a tight regulation of terra expression is required during embryogenesis. Terra has both human and mouse homologs and is specifically expressed in mouse somites. Taken together, our findings suggest that terra is a highly conserved protein that plays specific roles in early somitogenesis of vertebrates.  (+info)

## Requirement of a novel gene, Xin, in cardiac morphogenesis. (6/277092)

A novel gene, Xin, from chick (cXin) and mouse (mXin) embryonic hearts, may be required for cardiac morphogenesis and looping. Both cloned cDNAs have a single open reading frame, encoding proteins with 2,562 and 1,677 amino acids for cXin and mXin, respectively. The derived amino acid sequences share 46% similarity. The overall domain structures of the predicted cXin and mXin proteins, including proline-rich regions, 16 amino acid repeats, DNA-binding domains, SH3-binding motifs and nuclear localization signals, are highly conserved. Northern blot analyses detect a single message of 8.9 and 5.8 kilo base (kb) from both cardiac and skeletal muscle of chick and mouse, respectively. In situ hybridization reveals that the cXin gene is specifically expressed in cardiac progenitor cells of chick embryos as early as stage 8, prior to heart tube formation. cXin continues to be expressed in the myocardium of developing hearts. By stage 15, cXin expression is also detected in the myotomes of developing somites. Immunofluorescence microscopy reveals that the mXin protein is colocalized with N-cadherin and connexin-43 in the intercalated discs of adult mouse hearts. Incubation of stage 6 chick embryos with cXin antisense oligonucleotides results in abnormal cardiac morphogenesis and an alteration of cardiac looping. The myocardium of the affected hearts becomes thickened and tends to form multiple invaginations into the heart cavity. This abnormal cellular process may account in part for the abnormal looping. cXin expression can be induced by bone morphogenetic protein (BMP) in explants of anterior medial mesoendoderm from stage 6 chick embryos, a tissue that is normally non-cardiogenic. This induction occurs following the BMP-mediated induction of two cardiac-restricted transcription factors, Nkx2.5 and MEF2C. Furthermore, either MEF2C or Nkx2.5 can transactivate a luciferase reporter driven by the mXin promoter in mouse fibroblasts. These results suggest that Xin may participate in a BMP-Nkx2.5-MEF2C pathway to control cardiac morphogenesis and looping.  (+info)

## Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (7/277092)

On the basis of developmental gene expression, the vertebrate central nervous system comprises: a forebrain plus anterior midbrain, a midbrain-hindbrain boundary region (MHB) having organizer properties, and a rhombospinal domain. The vertebrate MHB is characterized by position, by organizer properties and by being the early site of action of Wnt1 and engrailed genes, and of genes of the Pax2/5/8 subfamily. Wada and others (Wada, H., Saiga, H., Satoh, N. and Holland, P. W. H. (1998) Development 125, 1113-1122) suggested that ascidian tunicates have a vertebrate-like MHB on the basis of ascidian Pax258 expression there. In another invertebrate chordate, amphioxus, comparable gene expression evidence for a vertebrate-like MHB is lacking. We, therefore, isolated and characterized AmphiPax2/5/8, the sole member of this subfamily in amphioxus. AmphiPax2/5/8 is initially expressed well back in the rhombospinal domain and not where a MHB would be expected. In contrast, most of the other expression domains of AmphiPax2/5/8 correspond to expression domains of vertebrate Pax2, Pax5 and Pax8 in structures that are probably homologous - support cells of the eye, nephridium, thyroid-like structures and pharyngeal gill slits; although AmphiPax2/5/8 is not transcribed in any structures that could be interpreted as homologues of vertebrate otic placodes or otic vesicles. In sum, the developmental expression of AmphiPax2/5/8 indicates that the amphioxus central nervous system lacks a MHB resembling the vertebrate isthmic region. Additional gene expression data for the developing ascidian and amphioxus nervous systems would help determine whether a MHB is a basal chordate character secondarily lost in amphioxus. The alternative is that the MHB is a vertebrate innovation.  (+info)

## Mechanisms of GDF-5 action during skeletal development. (8/277092)

Mutations in GDF-5, a member of the TGF-beta superfamily, result in the autosomal recessive syndromes brachypod (bp) in mice and Hunter-Thompson and Grebe-type chondrodysplasias in humans. These syndromes are all characterised by the shortening of the appendicular skeleton and loss or abnormal development of some joints. To investigate how GDF-5 controls skeletogenesis, we overexpressed GDF-5 during chick limb development using the retrovirus, RCASBP. This resulted in up to a 37.5% increase in length of the skeletal elements, which was predominantly due to an increase in the number of chondrocytes. By injecting virus at different stages of development, we show that GDF-5 can increase both the size of the early cartilage condensation and the later developing skeletal element. Using in vitro micromass cultures as a model system to study the early steps of chondrogenesis, we show that GDF-5 increases chondrogenesis in a dose-dependent manner. We did not detect changes in proliferation. However, cell suspension cultures showed that GDF-5 might act at these stages by increasing cell adhesion, a critical determinant of early chondrogenesis. In contrast, pulse labelling experiments of GDF-5-infected limbs showed that at later stages of skeletal development GDF-5 can increase proliferation of chondrocytes. Thus, here we show two mechanisms of how GDF-5 may control different stages of skeletogenesis. Finally, our data show that levels of GDF-5 expression/activity are important in controlling the size of skeletal elements and provides a possible explanation for the variation in the severity of skeletal defects resulting from mutations in GDF-5.  (+info)

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Although sequenced genome data are practically biased toward small genomes, which may compromise the accuracy of the ... With the emergence of various molecular techniques in the past 50 years, the genome sizes of thousands of eukaryotes have been ... Based on currently available completely sequenced genome data (as of April 2009), log-transformed gene number forms a linear ... The loss of large section of genomes could in fact lead to a loss in promotor sequences. This could in fact pushed the ...
... analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. ... He then joined the Departments of Integrative Biology and Microbiology and Molecular Biology at Brigham Young University as an ... His lab also focuses on the development and testing of methods for DNA sequence analysis, including leading methods in ... Louis in 1993, for research supervised by Alan Templeton on the molecular systematics and evolutionary biology in the crayfish ...
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Another sequenced species, S. tokodaii has a circular chromosome as well but is slightly smaller with 2,694,756 bp. Both ... Sulfolobus is now used as a model to study the molecular mechanisms of DNA replication in Archaea. And because the system of ... Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information. Retrieved 2007-03-19. J.P. ... In 2001, the first genome sequence of Sulfolobus, Sulfolobus solfataricus P2, was published. In P2's genome, the genes related ...
Corporation and Quest Diagnostics to develop a solution for scoring genetic variation for next generation sequencing data (NGS ... The software has been cited in thousands of scientific molecular biology publications and is one of several tools for systems ... IPA can be used with or without data. IPA helps researchers analyze data derived from expression and SNP microarrays, ... QIAGEN Silicon Valley's first product, IPA, was introduced in 2003, and is used to help researchers analyze omics data and ...
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Three-dimensional structural data have shown that a TPR region forms two antiparallel alpha-helices. TPR motifs that are ... TTC39B is expected to have a molecular binding function as well as a role in lipid regulation; the phenotype as well as the ... "NetPhos 2.0 Server". Center for Biological Sequence Analysis. Retrieved 13 May 2013. "SUMOsp 2.0 - SUMOylation Site Prediction ... The data indicates that TTC39B as causal genes for lipid regulation. GRCh38: Ensembl release 89: ENSG00000155158 - Ensembl, May ...
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... accurate 1.89-Mb genome sequence of Francisella tularensis subsp. holarctica strain FSC200, isolated in 1998 in the Swedish ... Molecular Sequence Data * Sequence Analysis, DNA * Sweden * Tularemia / microbiology* Substances * DNA, Bacterial ... Genome sequence of Francisella tularensis subspecies holarctica strain FSC200, isolated from a child with tularemia J Bacteriol ... Here we report the complete, accurate 1.89-Mb genome sequence of Francisella tularensis subsp. holarctica strain FSC200, ...
Methods in molecular biology, computer analysis of sequence data. Totowa (NJ): Humana; 1994. p. 307-18. ... We sequenced the glmM genes of 47 randomly selected isolates. The glmM phylogenetic trees based on the neighbor-joining (data ... Multilocus sequence typing (MLST) tools were used to delineate clusters of strains by using sequence output available from the ... Mosaicism of the hspA 3â€²-end sequences. * Figure 3. Neighbor-joining unrooted dendrogram for hspA sequences. The tree includes ...
Combining data from public-health interviews and molecular sequencing creates a powerful new tool for understanding communities ... Analyzing HIV molecular sequence data can also identify networks of potential transmission partners. Among named partner ... Supplementing named partner data with molecular data might detect HIV transmission networks not elucidated through traditional ... linkages where both people had an HIV sequence available, 33.8 percent also had a molecular linkage and were deemed plausible ...
... based on parsimony and likelihood analyses of nuclear EF-1Î± sequence data. Molecular Phylogenetics and Evolution. 13: 605-618. ... Amalgamation of molecular and morphological data for the Xeromelissinae. A. Ponte. Honours Thesis. 2012-2013. Diploid male ... Bayesian analysis of molecular data for the Xeromelissinae. M. Miklasevskaja. Honours Thesis. 2013-2014. Fluctuating asymmetry ... "Resolving conflict between molecular and morphological data: The systematic position of Coelioxoides." OE3C, Toronto, Canada 14 ...
However, the accuracy of current VS models heavily relies on three-dimensional (3D) structures obtained through molecular ... A sequence-based virtual screening method uses natural language processing algorithms and optimized deep K-embedding strategies ... To address this issue, we introduce a sequence-based virtual screening (SVS) as another generation of VS models that ... Furthermore, an in-house small molecular Transformer was trained with over 700 million sequence data24. However, none of these ...
A positive quantitative or qualitative nucleic acid test result or molecular sequence data for an HIV-1 genotypic drug- ... and retrieving HIV-related data), was developed for use with surveillance data to report epidemiologic trends. Identification ... Data from CDCs NHSS collected through December 2018.. â€  Diagnoses in NHSS with no evidence of an HIV-2, HIV-2 probable but ... Data from CDCs NHSS collected through December 2018.. â€  Diagnoses in NHSS with no evidence of HIV-2, HIV-2 probable but not ...
Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. ... as a natural response to the increasing demand of data analysis of many experimental scientists wishing to add a molecular ... Tools included in Phylemon cover a wide yet selected range of programs: from the most basic for multiple sequence alignment to ... Phylemon -- A suite of web tools for molecular evolution, phylogenetics and phylogenomics. URL: ...
Additionally, we explore data generated from molecular dynamics simulations along with next-generation sequencing of directed ... We seek to develop technologies for diagnostic and research applications at the nano and molecular level using both in vitro ... The Yang group is actively exploring opportunities in the interface between computational chemical biology and data science. My ... Recently, we have become interested in using our technology to understand the molecular basis of health disparities in ...
"Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets". Mol Biol Evol. 14 (3): 248 ... Technology has even advanced so as to allow the communication of mass data upon request and over great distance through data- ... In this way data networks are important to the continuing development of language; changing it as just as Gutenberg did with ... Full genome sequencing has resulted in the conclusion that "after 6.5 [million] years of separate evolution, the differences ...
Within Heliconius the relationships presented here are based on molecular sequence data for 3 mtDNA and 4 nuclear gene regions ... Inferences from multilocus DNA sequence data. Biological Journal of the Linnean Society in press. ... Click on an image or a media link to access the media data window, which provides the relevant licensing information. For the ... Click on an image to view larger version & data in a new window ... Click on an image to view larger version & data in a new window ...
Molecular Biology (Splice-junction Gene Sequences). Sequential, Domain-Theory Classification Categorical 3190 ... About Citation Policy Donate a Data Set Contact Repository Web View ALL Data Sets ...
Molecular Sequence Data. *Phylogeny. *Sequence Alignment. *Zebrafish/genetics*. *Zebrafish/immunology. PubMed. 20865040 Full ... A diversity of sequences similar to CXCL8 was reported in fish, but their evolutionary relationships and functional homology ... PRINCIPAL FINDINGS: We screened fish genomes to seek for sequences related to CXCL8. A first lineage was retrieved in all ...
By interfacing single cell sequence data with the molecular tools at our disposal, this project will enhance understanding of ... 9. Next-generation sequencing; 10. Multiplex biosensor platforms and LFD development.. Internationally Renowned Experts. * ... This work provides a blueprint for a new approach to metazoan biology that allows single-cell data to support a better ... This project will exploit new single-cell transcriptome data for liver fluke to drive predictions of cell functions that ...
Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 ... The PHYLogeny Inference Package is a package of programs for inferring phylogenies (evolutionary trees) from sequences. Methods ...
Molecular Sequence Data, Mutation, NF-kappa B, Promoter Regions, Genetic, Transcription, Genetic, Virus Replication", ... keywords = "Base Sequence, Binding Sites, Cell Line, Cytomegalovirus, Enhancer Elements, Genetic, Gene Deletion, Gene ... These data reveal the robustness of the regulatory network controlling the MIEP enhancer. ... These data reveal the robustness of the regulatory network controlling the MIEP enhancer.", ...
1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, ... Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours. Laleh Haghverdi, View ORCID ... The presence of batch effects is a well-known problem in experimental data analysis, and single- cell RNA sequencing (scRNA-seq ... Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours ...
Diversification of Neoaves: integration of molecular sequence data and fossils. Biology Letters doi:10.1098/rsbl.2006.0523 ... Read a story about the Pritzker Laboratory for Molecular Systematics and Evolution at the Field Museum. ... the most exhilarating moment of the meeting was delivered by scientists who were using mtDNA and nuclear data to shed light ...
... speakers emphasized measures such as data harmonization and the need for longitudinal data collection. ... At the NCIs Childhood Cancer Data Initiative Symposium, ... Retrospective whole-genome sequence data from 10,000 study ... The database started in June with prospective data from 685 patients who had undergone clinical genomic sequencing, and data ... The idea is to give researchers and clinicians, who may not have access to high-tech sequencing resources, data that can help ...
... has been determined by elucidation of the cDNA sequence encoding the protein kina ... data&figures Data & Figures. contents Contents. supplements Supplements. references References. related&metrics Related & ... Use of DNA sequence and mutant analyses and antisense oligodeoxynucleotides to examine the molecular basis of nonmuscle myosin ... Use of DNA sequence and mutant analyses and antisense oligodeoxynucleotides to examine the molecular basis of nonmuscle myosin ...
Knowledge of the molecular pathways altered in tumor cells, coupled with a wealth of genetic sequencing data from individual ... Molecular knowledge breeds smarter, more precise therapies.. Infections caused by antibiotic-resistant bacteria-and their ...
Analysis of DNA/RNA/protein sequence data, including mutagenic processes, molecular evolution and systematics, codon usage, ... Molecular design, synthesis and fermentation technology. Theoretical, computational, synthetic and applied approaches to the ... BTEC 5P51 Molecular Virology (also offered as BIOL 5P51) A seminar course on virus-host interaction, productive cycle, effect ... Emphasis on the molecular/biochemical tools used to study these pathways. Note: course taught in conjunction with BIOL/BCHM/ ...
Bolger, A. M.; Lohse, M.; Usadel, B.: Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 (15), pp. ... Algorithm-driven Artifacts in median polish summarization of Microarray data. BMC Bioinformatics 11, p. 553 (2010) ...
A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data. BMC Research Notes 3: 320.. Olsson, S ... More to the point, Merget & Wolf were using that most wretched of molecular methods, neighbour joining, and despite their use ... the various Lembophyllaceae lack any reliable shared morphological characters and are united on the basis of molecular data ( ... Supporters of the latter point to the low levels of morphological and molecular differentiation between individuals from ...
Data, Molecular Sequence Data, Molecular Sequencing Molecular Sequencing Data Sequence Data, Molecular Sequencing Data, ... Data, Molecular Sequence. Data, Molecular Sequencing. Molecular Sequencing Data. Sequence Data, Molecular. Sequencing Data, ... Molecular Sequence Data - Preferred Concept UI. M0013986. Scope note. Descriptions of specific amino acid, carbohydrate, or ... numbers for sequences deposited in a molecular sequence databank such as GenBank or for the presence of molecular sequences in ...
Examples of big data include the following: diagnostic medical imaging, DNA sequencing and other molecular technologies, ... Public Health Approach to Big Data in the Age of Genomics: How Can we Separate Signal from Noise?. The term Big Data is used to ... describe massive volumes of both structured and unstructured data that is so large and complex it is difficult to process and ... big data - Genomics and Precision Health Blog ... Categories big data, epidemiology, evidence-based medicine, ...
... obtain sequence data and re-analyze those data as described above. Molecular markers: We will use the following molecular ... Those data will be added to a data set of available sequences for each marker and a concatenated data set of the three markers ... Sequence data for the three molecular markers described below will be obtained for each accession. ... unpublished data). We are now sequencing ycf1 and have a number of sequences from various accessions of Medicago that show a ...
Molecular Sequence Analysis, Motifs, and Pattern Matching â€¢Biological Databases, Data Management, Data Integration, and Data ... Statistical Analysis of Molecular Sequences â€¢Cheminformatics and Computer-Aided Drug Design â€¢Molecular Docking and Modeling ... Big Data Analytics and High-Performance Computing in Bioinformatics and Computational Biology â€¢Comparative, Structural, ... molecular biology, biochemistry, genetics, medicine, microbiology, and others) to submit papers describing original work ...
• With advanced techniques in data collecting, processing, analyzing, and representing, modern computational biology can study biological processes at extraordinary scales and multiple dimensions. (nature.com)
• This work provides a blueprint for a new approach to metazoan biology that allows single-cell data to support a better understanding of complex living systems. (qub.ac.uk)
• The idea is to give researchers and clinicians, who may not have access to high-tech sequencing resources, data that can help them better understand the biology of pediatric cancers and make treatment decisions for patients. (genomeweb.com)
• 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. (bvsalud.org)
• BSB 2021 would like to attract participation from academic and industrial researchers, both in the exact sciences (computer science, mathematics, and statistics) and the life sciences (molecular biology, biochemistry, genetics, medicine, microbiology, and others) to submit papers describing original work related to the topics indicated below. (wikicfp.com)
• He received his B.S. in biochemistry and molecular biology from Peking University and his Ph.D. in computational biology from Baylor College of Medicine. (agbt.org)
• Critical Reviews in Biochemistry and Molecular Biology. (cdc.gov)
• There are significant structural features in the viral genomic RNA that could, by themselves, explain the retention of the ORF10 nucleotide sequences without the need for a functional protein product. (bvsalud.org)
• Trimmomatic: a flexible trimmer for Illumina sequence data. (mpg.de)
• Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1. (cdc.gov)
• The School of Biological Sciences provides PhD and MPhil (research degree) programmes in subjects ranging from basic biochemistry, molecular genetics and cancer research, to agricultural science, marine ecology and the economic evaluation of ecosystem services and food retailing. (qub.ac.uk)
• The study, published in the journal Nature Genetics, is the largest of its kind to date and uses whole-genome sequencing data from more than 120 patients with malignant pleural mesothelioma. (who.int)
• If precision medicine approaches are to become part of routine healthcare, doctors and other healthcare providers will need to know more about molecular genetics and biochemistry. (medlineplus.gov)
• To assess the genetic diversity and relationships between the isolates, we sequenced two housekeeping genes ( glmM and hspA ). (cdc.gov)
• Knowledge of the molecular pathways altered in tumor cells, coupled with a wealth of genetic sequencing data from individual patients' changing cancer. (the-scientist.com)
• nmMLCK is distinct from and larger than smooth muscle MLCK (smMLCK), although their extended DNA sequence identity is suggestive of a close genetic relationship not found with skeletal muscle MLCK. (rupress.org)
• Dr. Shen currently directs National Institutes of Health-funded research programs that integrate genomics data to predict functional impact of genetic variation by machine learning and identify genetic causes of human diseases. (agbt.org)
• Additionally, drugs that are developed to treat conditions based on molecular or genetic variations are likely to be expensive. (medlineplus.gov)
• The molecular data and relative distribution of these species in relation to their vectorial capacity and the epidemiology of malaria in the region are discussed. (who.int)
• These data provide insight into zoonotic reservoirs of human-infective T. trichiura and will support future efforts toward the implementation of genomic epidemiology of this globally important helminth. (bvsalud.org)
• Epidemiology and Molecular Characteristics of mcr-9 in Citrobacter spp. (cdc.gov)
• This was confirmed by the high similarity (99.2%-100%) of their sequences with those available in GenBank. (who.int)
• Descripciones de secuencias especÃ­ficas de aminoÃ¡cidos, carbohidratos o nucleÃ³tidos que han aparecido en publicaciones o estÃ¡n incluidas y actualizadas en bancos de datos como el GENBANK, el Laboratorio Europeo de BiologÃ­a Molecular (EMBL), la FundaciÃ³n Nacional de InvestigaciÃ³n BiomÃ©dica (NBRF) u otros archivos de secuencias. (bvsalud.org)
• The PHYLogeny Inference Package is a package of programs for inferring phylogenies (evolutionary trees) from sequences. (debian.net)
• The analysis of 20 mutant MLCKs indicates that the autoinhibitory and CaM recognition activities are centered in distinct but functionally coupled amino acid sequences (residues 1,068-1,080 and 1,082-1,101, respectively). (rupress.org)
• Also and they were told about the aim of the molecular similarity has been observed study, and were informed that the data between IRRET amino acid sequence which would be used for scientific purposes only. (who.int)
• This technique involves using information from molecular tests used in routine clinical care that determine the sequences of HIV viral genes to help clinicians pick the best HIV treatment regimen for their patient. (cdc.gov)
• Sequencing of viral RNA in the lungs of hamsters infected with ORF10KO virus revealed that this virus frequently reverts to WT. (bvsalud.org)
• Medical Microbiology & through molecular mimicry mechanism. (who.int)
• Initially illnesses were reported only in the genome sequencing of clinical and environmental samples from the outbreak revealed a new V. parahaemolyticus northern cities of Peru (Cajamarca, Chiclayo, and Piura), clone. (cdc.gov)
• St. Jude Children's Research Hospital's bioinformatics group recently launched the St. Jude Cloud , a repository of pediatric clinical genome sequencing data available in real time. (genomeweb.com)
• The database started in June with prospective data from 685 patients who had undergone clinical genomic sequencing, and data from an additional 273 people was made available in July. (genomeweb.com)
• The initiative is aiming to provide researchers with high-quality whole-genome, exome, and transcriptome data from consenting St. Jude patients. (genomeweb.com)
• 2014), a method to identify rare copy number variants from exome sequencing data, and gMVP (Zhang et al. (agbt.org)
• ABSTRACT A diagnostic polymerase chain reaction (PCR) assay using species-specific primers and direct sequencing was used to identify members of the Anopheles maculipennis complex in the north-west and central regions of the Islamic Republic of Iran. (who.int)
• Specimens were collected from 9 provinces during 2 seasonal activities in 2001-2002, identified morphologically and subjected to PCR assay and direct sequencing. (who.int)
• Tim Triche, co-director for the Center of Personalized Medicine at Children's Hospital Los Angeles (CHLA), has also started a data collection effort related to his center's use of a targeted sequencing panel that he and his team at CHLA have developed in partnership with Thermo Fisher Scientific, called the Oncomine Childhood Cancer Research Assay, or OncoKids. (genomeweb.com)
• A Custom Hepatitis A Virus Assay for Whole-Genome Sequencing. (cdc.gov)
• Tools included in Phylemon cover a wide yet selected range of programs: from the most basic for multiple sequence alignment to elaborate statistical methods of phylogenetic reconstruction including methods for evolutionary rates analyses and molecular adaptation. (pitt.edu)
• Public Health Approach to Big Data in the Age of Genomics: How Can we Separate Signal from Noise? (cdc.gov)
• Using whole-genome sequencing of geographically distributed worms collected from human and other primate hosts, together with ancient samples preserved in archaeologically-defined latrines and deposits dated up to one thousand years old, we present the first population genomics study of T. trichiura. (bvsalud.org)
• The Rare Cancers Genomics Team at IARC has used sequencing data to uncover sources of molecular variation in malignant pleural mesothelioma, paving the way for a revised classification system that could change the manner in which the disease is diagnosed and treated. (who.int)
• H. pylori is one of the most genetically diverse bacterial species, displaying from 2.7% to 8.0% of DNA sequence polymorphism ( 14 - 16 ). (cdc.gov)
• We have routinely obtained DNA sequence data from matK and nrDNA ITS from a wide variety of temperate legumes in addition to many species of Medicago (Steele et al. (elsevier.com)
• New computational methods including FALCON and Assemblytics for assembling and analyzing the genomes of different species using single molecule sequencing, especially plant and animal species, to study their evolution and adaption. (agbt.org)
• As convergent evolution is common in coinhabiting parasites, a mitochondrial gene sequence (cox1) and ribosomal gene sequence (ITS1) were used to identify species similar to Trichuris from Chinese serow. (bvsalud.org)
• Here we report the complete, accurate 1.89-Mb genome sequence of Francisella tularensis subsp. (nih.gov)
• Whole-genome sequence contigs clone ST-3, which also originated in Asia ( 8 , 12 ). (cdc.gov)
• Retrospective whole-genome sequence data from 10,000 study participants is also available in the repository. (genomeweb.com)
• Small, 2011) and is based on results of phylogenetic analyses of a variety of molecular markers (Steele et al, 2010) and low coverage whole genome sequence data (Yoder et al. (elsevier.com)
• Tracing Foodborne Botulism Events Caused by Clostridium botulinum in Xinjiang Province, China, Using a Core Genome Sequence Typing Scheme. (cdc.gov)
• To explore this question further we made two recombinant viruses, firstly a control virus (WT) based on the genome sequence of the original Wuhan isolate and with the inclusion of the early D614G mutation in the Spike protein. (bvsalud.org)
• MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing. (cdc.gov)
• Sequence data for the three molecular markers described below will be obtained for each accession. (elsevier.com)
• It has been conceived as a natural response to the increasing demand of data analysis of many experimental scientists wishing to add a molecular evolution and phylogenetics insight into their research. (pitt.edu)
• His innovative biotechnologies and computational tools to study the sequence and function of genomes are advancing the understanding of the structure, evolution, and function of genomes for medicine - particularly autism spectrum disorders, cancer, and other human diseases - and agriculture. (agbt.org)
• Analysis of the sequences of housekeeping genes ( atpD , scoB , glnA and recA ) showed that strains cluster according to their geographic origins ( 15 , 20 ). (cdc.gov)
• The presence of batch effects is a well-known problem in experimental data analysis, and single- cell RNA sequencing (scRNA-seq) is no exception. (biorxiv.org)
• The first primary structure for a nonmuscle myosin light chain kinase (nmMLCK) has been determined by elucidation of the cDNA sequence encoding the protein kinase from chicken embryo fibroblasts, and insight into the molecular mechanism of calmodulin (CaM) recognition and activation has been obtained by the use of site-specific mutagenesis and suppressor mutant analysis. (rupress.org)
• Analysis of enzyme chimeras, random mutations, inverted sequences, and point mutations in the 1,082-1,101 region demonstrates its functional importance for CaM recognition but not autoinhibition. (rupress.org)
• NGMLR and Sniffles are long-read sequencing analysis methods to study the longer fragments of DNA, a breakthrough that may yield critical information about how cancer genomes evolve. (agbt.org)
• At Baylor, Shen led the analysis of the first human genome sequenced by next-generation technologies. (agbt.org)
• Public health staff may also identify a cluster by using molecular data analysis. (cdc.gov)
• Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. (pitt.edu)
• Use of DNA sequence and mutant analyses and antisense oligodeoxynucleotides to examine the molecular basis of nonmuscle myosin light chain kinase autoinhibition, calmodulin recognition, and activity. (rupress.org)
• this change is supported by phylogenetic analyses of a number of molecular markers including nrDNA ITS and matK and other nuclear-encoded genes (Bena et al. (elsevier.com)
• The main purpose of the CKQ questionnaire was to collect data on factors which may cause transient elevations in CPK (a history of recent injury or heavy physical exertion) so that data analysts can account for such cases in their analyses of the relationship of CPK to health conditions. (cdc.gov)
• PRINCIPAL FINDINGS: We screened fish genomes to seek for sequences related to CXCL8. (zfin.org)
• Supported by underpinning technological expertise in cutting edge molecular, genomic, transcriptomic/proteomic and metabolomic methods, the goal of the theme is to transform Agri-Food systems so that they benefit both human nutrition and health while simultaneously reducing the greenhouse gases emissions from livestock production systems, protecting ecological resources, supporting livelihoods and affordable foods, and upholding social, cultural, and ethical values. (qub.ac.uk)
• NEW YORK - Large genomic databases for adult cancers, such as The Cancer Genome Atlas, have pioneered the collection of petabytes worth of genomic, epigenomic, transcriptomic, and proteomic data. (genomeweb.com)
• When it comes to pediatric cancer, there is no such similar genomic data repository. (genomeweb.com)
• First, there will be an opportunity to aggregate that data into an ever-larger â€¦ database of genomic features encountered in childhood cancer," Triche said in an interview. (genomeweb.com)
• Strain relationships within the family were determined by analyzing allelic variation at both loci and building phylogenetic trees and by using multilocus sequence typing. (cdc.gov)
• tern of dominance afterwards because of the presence of In silico multilocus sequence typing (MLST) by multiple serotypes. (cdc.gov)
• This project will exploit new single-cell transcriptome data for liver fluke to drive predictions of cell functions that support growth and virulence. (qub.ac.uk)
• We compared the sequences of two housekeeping genes ( hspA and glmM ) from these clones with those of 131 unrelated strains from patients living in different geographic regions. (cdc.gov)
• Clonal descent has been demonstrated by comparing alleles of genes such as vacA , flaA , and flaB of isolates infecting members of the same family ( 10 - 12 ) and by sequencing three housekeeping genes ( ureI , atpA , and ahpC ) ( 13 ). (cdc.gov)
• Data were acquired using unbiased data-independent mass spectrometry (MS). Statistically significant and measures were processed in ProteinLynx Global Server and sequenced using in-house software EndogeSeq against selective subsets of a mouse UniProt protein database. (cdc.gov)
• The functioning of NSP12 was dependent on the T-complex protein Ring Complex, a molecular chaperone. (bvsalud.org)
• standards of the responsible committee on Proteus mirabilis is thought to contribute in RA development in susceptible individuals human experimentation (institutional and through molecular mimicry mechanism. (who.int)
• A diversity of sequences similar to CXCL8 was reported in fish, but their evolutionary relationships and functional homology with their human homolog remain unclear. (zfin.org)
• To conduct the strategy, agencies first use data routinely reported to health departments to identify where HIV prevention and treatment services and other interventions are urgently needed. (cdc.gov)
• The Kim group works in the areas of complex molecule synthesis and catalysis, focusing on the design of novel ligands and catalysts that enable site selective reactivity in highly oxidized systems by leveraging phenomena like molecular recognition and non-covalent directing effects. (vanderbilt.edu)
• The term Big Data is used to describe massive volumes of both structured and unstructured data that is so large and complex it is difficult to process and analyze. (cdc.gov)
• Antibiotic resistance surveillance of Klebsiella pneumoniae complex is affected by refined MALDI-TOF identification, Swiss data, 2017 to 2022. (cdc.gov)
• When a group of people have similar molecular HIV sequences, it suggests that little time has passed between when HIV was acquired and transmitted. (cdc.gov)
• Our data suggests that the retention of a functional ORF10 sequence is highly desirable for SARS-CoV-2 infection of hamsters and affects the virus's ability to propagate in the lower respiratory tract. (bvsalud.org)
• We seek to develop technologies for diagnostic and research applications at the nano and molecular level using both in vitro and in vivo systems.The Haselton Laboratory is an active participant in LIGHT, which aims to accelerate the development of global health technologies in a multidisciplinary research environment addressing the needs of patients and physicians in low-resource settings. (vanderbilt.edu)
• Alongside TCGA, the National Cancer Institute developed data hubs and coordination centers that paved the way for data harmonization and standardization, so that anyone accessing these various databases or uploading information to them started on the same baseline. (genomeweb.com)
• Though several research centers and children's hospitals have begun to collect and disseminate data on their own, there aren't any agreed-upon standards from one database to another, like there are with adult cancer databases. (genomeweb.com)
• In order to begin developing a model of data federation that's more in-line with what's been created for adult cancer databases, the NCI last week convened a meeting of stakeholders from academia, government, industry, and advocacy organizations for the Childhood Cancer Data Initiative (CCDI) Symposium, to discuss the challenges unique to pediatric cancer data and how to solve them. (genomeweb.com)
• They also needed databases to store large amounts of patient data efficiently. (medlineplus.gov)
• We demonstrate the superiority of our approach over existing methods on a range of simulated and real scRNA-seq data sets. (biorxiv.org)
• More to the point, Merget & Wolf were using that most wretched of molecular methods, neighbour joining, and despite their use of a large number of source taxa it is difficult to accord their results much significance. (fieldofscience.com)
• Technologies such as sequencing large amounts of DNA are expensive to carry out (although the cost of sequencing is decreasing). (medlineplus.gov)
• The resulting infrastructure is one that allows users to not only access and download the raw data, but also work within the ecosystem to analyze it, according to Alexander Gout, a bioinformatician at St. Jude who worked on building the cloud. (genomeweb.com)
• For accessions suspected of being misidentified we will first re-isolate DNA from the voucher specimen and again, obtain sequence data and re-analyze those data as described above. (elsevier.com)
• data include patient demographic characteristics, HIV transmission risk category, and laboratory test results. (cdc.gov)
• These sequences are then reported to the health department and may be used to identify similar sequences circulating in their jurisdiction. (cdc.gov)
• Further, CHLA and Thermo Fisher are looking to share the data from OncoKids with other cancer researchers and clinicians. (genomeweb.com)
• To describe the percentage of diagnoses for which an HIV-1/HIV-2 differentiation test result was reported and to categorize HIV type based on laboratory test results, 2010-2017 data from CDC's National HIV Surveillance System (NHSS) were analyzed. (cdc.gov)
• Treatment of chicken and mouse fibroblasts with antisense oligodeoxynucleotides based on the cDNA sequence results in an apparent decrease in MLCK levels, an altered morphology reminiscent of that seen in v-src-transformed cells, and a possible effect on cell proliferation. (rupress.org)
• By interfacing single cell sequence data with the molecular tools at our disposal, this project will enhance understanding of selected parasite cells, particularly stem cells, and drive new drug target discovery and validation pipelines for parasite control. (qub.ac.uk)
• But for my money, the most exhilarating moment of the meeting was delivered by scientists who were using mtDNA and nuclear data to shed light upon a group of birds known as nine-primaried oscines -- tanagers, cardinals and grosbeaks, New World sparrows, New World blackbirds, and wood-warblers. (typepad.com)
• The NIH Precision Medicine Initiative channel on YouTube offers videos of talks by leading experts on various aspects of the project, including issues related to data collection and sharing, storing data in electronic health records, and participant protection. (medlineplus.gov)
• The Precision Medicine Initiative has information about its Privacy and Trust Principles and Data Security Policy Principles and Framework . (medlineplus.gov)