Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Bayes Theorem: 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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Models, Genetic: 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.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Sequence Alignment: 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.Likelihood Functions: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Fossils: Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Markov Chains: 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.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Computational Biology: 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.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Genetic Variation: Genotypic differences observed among individuals in a population.Monte Carlo Method: 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)Amino Acid Sequence: 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 Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Sequence Homology, Nucleic Acid: 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.Species Specificity: 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.DNA, Ribosomal Spacer: 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, Nucleic Acid: 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.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Cloning, Molecular: 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.Classification: The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.Sequence Analysis: 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.Internet: 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.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.RNA, Ribosomal, 28S: Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Phylogeography: 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)Sequence Analysis, Protein: 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.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Genetics, Population: 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.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Metagenomics: The genomic analysis of assemblages of organisms.DNA: 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).Genome, Human: 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.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Databases, Factual: 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.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Gene Library: 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.Cluster Analysis: 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.Exome: That part of the genome that corresponds to the complete complement of EXONS of an organism or cell.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.INDEL Mutation: 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.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Genetic Speciation: 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.Human Genome Project: A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.Genes, Bacterial: The functional hereditary units of BACTERIA.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Haplotypes: 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.RNA, Ribosomal, 5.8S: Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Genes: 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.Information Storage and Retrieval: Organized activities related to the storage, location, search, and retrieval of information.Database Management Systems: Software designed to store, manipulate, manage, and control data for specific uses.Open Reading Frames: 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).Geography: 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, rRNA: 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.DNA Primers: 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.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.DNA, Chloroplast: Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.DNA, Complementary: 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, Mitochondrial: 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.Multigene Family: 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)Data Compression: 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.Bacteria: 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.Ascomycota: 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.Proteins: 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.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Mutation: 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.Sequence Homology: 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.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.ComputersAngiosperms: 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.Codon: 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).DNA, Intergenic: 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.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Plastids: 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.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Genes, Plant: The functional hereditary units of PLANTS.RNA, Ribosomal: 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)Conserved Sequence: 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.Gene Flow: 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.Bacterial Proteins: Proteins found in any species of bacterium.Microsatellite Repeats: 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).Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.South AmericaPlants: 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.Metagenome: A collective genome representative of the many organisms, primarily microorganisms, existing in a community.Computer Graphics: 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.Acari: A large, subclass of arachnids comprising the MITES and TICKS, including parasites of plants, animals, and humans, as well as several important disease vectors.Recombination, Genetic: 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.Mycological Typing Techniques: Procedures for identifying types and strains of fungi.Polymorphism, Genetic: 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.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Genomic Library: 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).Models, Statistical: 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.Chromosomes, Artificial, Bacterial: 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.DNA Barcoding, Taxonomic: 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".Gene Order: The sequential location of genes on a chromosome.Information Systems: Integrated set of files, procedures, and equipment for the storage, manipulation, and retrieval of information.Multilocus Sequence Typing: 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.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.CD-ROM: 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.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Lemur: 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.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Escherichia coli: 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.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Sequence Tagged Sites: 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.Physical Chromosome Mapping: Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.Molecular Epidemiology: 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.Basidiomycota: 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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.North AmericaFruiting Bodies, Fungal: The fruiting 'heads' or 'caps' of FUNGI, which as a food item are familiarly known as MUSHROOMS, that contain the FUNGAL SPORES.Mutation Rate: 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.Transcriptome: 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)

*Mitochondrial DNA

Data from the comparisons is used to construct a network of relationships among the sequences, which provides an estimate of ... Molecular and cellular biology portal Molecular Anthropology portal Evolutionary biology portal. ... Although most of them focus on sequence data, some of them include phylogenetic or functional information. MitoSatPlant: ... Moreover, there is data supporting the involvement of helix-distorting intrinsically curved regions and long G-tetrads in ...

*List of phylogenetic tree visualization software

... phylogenetic inference and data visualization for sequence based typing methods". BMC Bioinformatics. 13: 7. doi:10.1186/1471- ... Molecular Biology and Evolution. 33 (8): 2163-6. doi:10.1093/molbev/msw080. PMC 4948708 . PMID 27189561. Retrieved 21 April ... a software environment for sequence data". Nucleic Acids Res. 32 (4): 1363-71. doi:10.1093/nar/gkh293. PMC 390282 . PMID ... a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization". Bioinformatics. doi: ...

*Ancestral reconstruction

Rather than inferring the ancestral DNA sequence, one may be interested in the larger-scale molecular structure and content of ... The majority of these software packages are designed for analyzing genetic sequence data. For example, PAML is a collection of ... These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the ... HyPhy, Mesquite, and MEGA are also software packages for the phylogenetic analysis of sequence data, but are designed to be ...

*Phylogenesis

Phylogenetics is the branch of life science concerned with the analysis of molecular sequencing data to study evolutionary ... These terms may be confused with the term phylogenetics, the application of molecular - analytical methods (i.e. molecular ... genetic sequencing data and computational phylogenetics are now commonly used and the parsimony criterion has been abandoned by ... such as DNA sequences or overall morpho-anatomical, ethological, and other characteristics. The result of these analyses is a ...

*Molecular phylogenetics

... is one aspect of molecular systematics, a broader term that also includes the use of molecular data in ... Typical molecular systematic analyses require the sequencing of around 1000 base pairs. At any location within such a sequence ... provides a molecular clock for dating divergence. Molecular phylogeny uses such data to build a "relationship tree" that shows ... ISBN 0-41202-231-1. Soltis, P.S., Soltis, D.E., and Doyle, J.J. (1998) Molecular Systematics of Plants II: DNA Sequencing. ...

*Protein primary structure

Peptides can be directly sequenced, or inferred from DNA sequences. Large sequence databases now exist that collate known ... Despite these data and later evidence that proteolytically digested proteins yielded only oligopeptides, the idea that proteins ... CS1 maint: Multiple names: authors list (link) Hausman, Robert E.; Cooper, Geoffrey M. (2004). The cell: a molecular approach. ... Sequence families are often determined by sequence clustering, and structural genomics projects aim to produce a set of ...

*Structural alignment software

Sippl, M.; Wiederstein, M. (2012). "Detection of spatial correlations in protein structures and molecular complexes". Structure ... Sequence-based alignment Pair -- Pairwise Alignment (2 structures *only*); Multi -- Multiple Structure Alignment (MStA); C-Map ... a web application for highly accurate screening of spatial resiudue patterns in protein structure data". Bioinformatics. 32: ... Algorithms for Molecular Biology. 7 (4): 4. doi:10.1186/1748-7188-7-4. PMC 3298807 . PMID 22336468. Minami, S.; Sawada K.; ...

*DNA nanoball sequencing

"State of the art de novo assembly of human genomes from massively parallel sequencing data". Human genomics. 4 (4): 271-7. doi: ... The high-molecular-weight DNA, often several megabase pairs long, is sonicated to break the DNA double-strands at random ... DNA nanoball sequencing is a high throughput sequencing technology that is used to determine the entire genomic sequence of an ... used DNA nanoball sequencing to sequence the genomes of a family of four relatives and were able to identify SNPs that may be ...

*Mormopterus

Molecular sequencing data indicates that Mormopterus is paraphyletic. The closest relatives of M. kalinowski are members of ... "Toward a Molecular Phylogeny for the Molossidae (Chiroptera) of the Afro-Malagasy Region". Acta Chiropterologica. 13 (1): 1-16 ...

*Near passerine

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... However, molecular data does not support the traditional arrangement; it is now clear that "near passerines" and "higher ... Johansson, Ulf S. & Ericson, Per G. P. (2003): Molecular support for a sister group relationship between Pici and Galbulae ( ...

*Hamerkop

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ...

*New World vulture

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-7. doi:10.1098/rsbl.2006.0523. PMC 1834003 . ... This was criticized, and an early DNA sequence study was based on erroneous data and subsequently retracted. There was then an ... They were especially common in the gut with Clostridia DNA sequence counts between 26% and 85% relative to total sequence ... Retrieved 3 August 2010 Avise, J. C.; Nelson, W. S. & Sibley, C. G. (1994) "DNA sequence support for a close phylogenetic ...

*Turkey vulture

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 1-5. doi:10.1098/rsbl.2006.0523. PMC 1834003 . ... Media related to Turkey vulture at Wikimedia Commons Data related to Cathartes aura at Wikispecies Turkey vultures on eNature. ... 1991). Phylogeny and Classification of Birds: A Study in Molecular Evolution. Yale University Press. ISBN 0-300-04085-7. ... Molecular Phylogenetics and Evolution. 37 (2): 327-346. doi:10.1016/j.ympev.2005.04.010. ISSN 1055-7903. PMID 15925523. ...

*Columbaves

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature (2015). doi:10.1038/nature15697 ...

*Jacamar

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... "Molecular support for a sister group relationship between Pici and Galbulae (Piciformes sensu Wetmore 1960" (PDF). Journal of ...

*Aequorlitornithes

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... 22 October 2015). "A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing". Nature. 526 (7574 ...

*Galbuli

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... Johansson, Ulf S.; Ericson, Per G.P. (2003). "Molecular support for a sister group relationship between Pici and Galbulae ( ... Witt, C.C. (2004), Rates of Molecular Evolution and their Application to Neotropical Avian Biogeography, Ph.D. dissertation, ...

*Puffbird

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... Molecular investigation of the Bucconidae in 2004 indicated that the nunlets (genus Nonnula) diverged from the common ancestor ... Johansson, Ulf S. & Ericson, Per G.P. (2003). "Molecular support for a sister group relationship between Pici and Galbulae ( ... Witt, C.C. (2004), Rates of Molecular Evolution and their Application to Neotropical Avian Biogeography, Ph.D. dissertation, ...

*Pici (taxon)

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... Johansson, Ulf S. & Ericson, Per G.P. (2003). "Molecular support for a sister group relationship between Pici and Galbulae ( ...

*Otidimorphae

... integration of molecular sequence data and fossils". Biology Letters. rsbl.royalsocietypublishing.org. 2 (4): 543-547. doi: ...

*Mirandornithes

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... Molecular Phylogenetics and Evolution. 30 (1): 140-151. doi:10.1016/S1055-7903(03)00159-3. PMID 15022765. Mayr, G. (February ...

*Tadarida

Molecular sequence data indicates Tadarida is not a monophyletic taxon. The closest relative of Tadarida aegyptiaca of Africa ... "Toward a Molecular Phylogeny for the Molossidae (Chiroptera) of the Afro-Malagasy Region". Acta Chiropterologica. 13 (1): 1-16 ...

*Pelecaniformes

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... but molecular and morphological studies indicate they are not such close relatives. They have been placed in their own orders, ...

*Cretaceous-Paleogene extinction event

December 2006). "Diversification of Neoaves: integration of molecular sequence data and fossils". Biol. Lett. 2 (4): 543-7. doi ... Based on molecular sequencing and fossil dating, Neoaves appeared to radiate after the K-Pg boundary. They even produced giant ... At present the most informative sequence of dinosaur-bearing rocks in the world from the K-Pg boundary is found in western ... In North America, the data suggests massive devastation and mass extinction of plants at the K-Pg boundary sections, although ...

*Psittacopasserae

... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... The group was proposed following an alignment of nuclear intron sequences by Shannon Hackett et al. in 2008, it was formally ... However, the technique requires very extensive genomic data - in the 2011 paper, approximately 200,000 retroposon-containing ...

*Phyllanthaceae

"Molecular phylogenetic analysis of Euphorbiaceae sensu stricto based on plastid and nuclear DNA sequences and ovule and seed ... "Delimitation of Sauropus (Phyllanthaceae) Based on Plastid matK and Nuclear Ribosomal ITS DNA Sequence Data." Annals of Botany ... "Molecular phylogenetics of Phyllanthaceae: evidence from plastid matK and nuclear PHYC sequences". American Journal of Botany. ... based on nrITS and plastid matK DNA sequence data". American Journal of Botany. 93 (4): 637-655. doi:10.3732/ajb.93.4.637. PMID ...

*Lesser yellow-headed vulture

... integration of molecular sequence data and fossils" (PDF). Biology Letters. 2 (4): 543-7. doi:10.1098/rsbl.2006.0523. PMC ... ISBN 0-19-854012-4. Sibley, Charles G.; Jon E. Ahlquist (1991). Phylogeny and Classification of Birds: A Study in Molecular ... Phylogeny and Classification of Birds: A Study in Molecular Evolution. Yale University Press. ISBN 0-300-04085-7. Accessed 2007 ...
Evolution of a species specific determinant essay, buy custom Evolution of a species specific determinant essay paper cheap, Evolution of a species specific determinant essay paper sample, Evolution of a species specific determinant essay sample service online
In 2000 H. van den Berg published eleven articles. In 2001 H. van den Berg published five articles, published one book - monograph and published one chapter. In 2002 H. van den Berg published seven articles, published three chapters and published one book - monograph . In 2004 H. van den Berg published four articles. In 2005 H. van den Berg published three articles and published one chapter. In 2006 H. van den Berg published six articles. In 2007 H. van den Berg published seven articles. In 2009 H. van den Berg published one article. In 2010 H. van den Berg published three articles. In 2011 H. van den Berg published six articles. In 2012 H. van den Berg published two articles. In 2013 H. van den Berg published four articles. ...
We report the sequence of a 4.5-kb cDNA clone isolated from a human melanoma library which bears high amino acid sequence identity to the yeast mitochondrial (mt) DNA polymerase (Mip1p). This cDNA contains a 3720-bp open reading frame encoding a predicted 140-kDa polypeptide that is 43% identical to Mip1p. The N-terminal part of the sequence contains a 13 glutamine stretch encoded by a CAG trinucleotide repeat which is not found in the other DNA polymerases gamma (Pol gamma). Multiple amino acid sequence alignments with Pol gamma from Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia pastoris, Drosophila melanogaster, Xenopus laevis and Mus musculus show that these DNA polymerases form a family strongly conserved from yeast to man and are only loosely related to the Family A DNA polymerases. ...
A short sequence of predominantly basic amino acids Pro-Pro-Lys-Lys-Lys-Arg-Lys-Val from SV40 Large T is responsible for the normal nuclear location of the protein. Alteration of Lys-128 to each of six different residues other than Arg renders Large T cytoplasmic, whereas single amino acid changes in the surrounding region impair but do not prevent nuclear accumulation. When transposed to the amino terminus of cytoplasmic Large T species, or Escherichia coli β-galactosidase or of chicken muscle pyruvate kinase, the sequence around Lys-128 of Large T is able to direct the recipient protein to the nucleus. This demonstrates that these amino acids can be sufficient for nuclear location and can act as a nuclear location signal. A computer search of over 2500 proteins reveals that some other nuclear proteins (for example, BK virus Large T, SV40 VP2 and adenovirus 72kDa DNA binding protein) contain very similar basic tracts, but so too do some presumed non-nuclear proteins (for example, poliovirus ...
Alazawi W, Heath H, et al. Stat2 loss leads to cytokine-independent, cell-mediated lethality in LPS-induced sepsis. Proc Natl Acad Sci U S A 110(21):8656-8661, 2013 [95].. Arnold, ES, SC Ling, et al. ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP- 43. Proc Natl Acad Sci U S A 110(8):E736- E745, 2013 [96].. Burdick RC, Hu WS, Pathak VK. Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes. Proc Natl Acad Sci U S A 110(49):E4780-E4789, 2013 [97].. Chen J, Feigenbaum L, et al. Insulin-dependent diabetes induced by pancreatic beta cell expression of IL-15 and IL-15R alpha. Proc Natl Acad Sci U S A 110(33):13534- 13539, 2013 [98].. Feng MQ, Gao W, et al. Therapeutically targeting glypican-3 via a conformation-specific single-domain antibody in hepatocellular carcinoma. Proc Natl Acad Sci U S A 110(12):E1083-E1091, 2013 [99].. Kim TS, Park JE, Shukla A, Choi S, Murugan RN, Lee JH, Ahn M, Rhee K, ...
Neural cell adhesion molecules (NCAMs) are cell surface glycoproteins that appear to mediate cell-cell adhesion. In vertebrates NCAMs exist in at least three different polypeptide forms of apparent molecular masses 180, 140, and 120 kD. The 180- and 140-kD forms span the plasma membrane whereas the 120-kD form lacks a transmembrane region. In this study, we report the isolation of NCAM clones from an adult rat brain cDNA library. Sequence analysis indicated that the longest isolate, pR18, contains a 2,574 nucleotide open reading frame flanked by 208 bases of 5 and 409 bases of 3 untranslated sequence. The predicted polypeptide encoded by clone pR18 contains a single membrane-spanning region and a small cytoplasmic domain (120 amino acids), suggesting that it codes for a full-length 140-kD NCAM form. In Northern analysis, probes derived from 5 sequences of pR18, which presumably code for extracellular portions of the molecule hybridized to five discrete mRNA size classes (7.4, 6.7, 5.2, 4.3, ...
RFC 7035 Relative Location October 2013 reference and relative locations while providing a baseline that is as accurate as possible. Both the baseline and the reference location are defined as either a geodetic location [OGC.GeoShape] or a civic address [RFC4776]. If the baseline location was expressed as a geodetic location, the reference MUST be geodetic. If the baseline location was expressed as a civic address, the reference MUST be civic. Baseline and reference locations MAY also include dynamic location information [RFC5962]. The relative location can be expressed using a point (2- or 3-dimensional) or a shape that includes uncertainty: circle, sphere, ellipse, ellipsoid, polygon, prism, or arc-band. Descriptions of these shapes can be found in [RFC5491]. Optionally, a reference to a map document can be provided. The reference is a URI [RFC3986]. The document could be an image or dataset that represents a map, floor plan, or other form. The type of document the URI points to is described ...
The M2 protein of the influenza A virus is a homotetrameric transmembrane proton channel implicated in several stages of the viral replication process. Each of its 97-residue monomers is known to include a transmembrane α-helix. but the structures of the N- and C-terminal domains have not yet been solved. A significant barrier to an atomic level understanding of the M2 protein is the difficulty associated with expression and purification of the full-length protein, which has primarily been studied in the form of truncated constructs covering the amphipathic helix and a short C-terminal segment. This C-terminal segment, which includes residues 46-62, has been shown for a truncated version of the protein to consist of an amphipathic helix lying on the membrane surface. Here, we present SDSL-EPR structural studies using full-length M2 constructs to examine sites 50-54 in the proposed amphipathic helix region of M2. Using power saturation data for the protein reconstituted into vesicles and CW ...
Membrane organization describes the orientation of a protein with respect to the membrane and can be determined by the presence, or absence, and organization within the protein sequence of two features: endoplasmic reticulum signal peptides and alpha-helical transmembrane domains. These features allow protein sequences to be classified into one of five membrane organization categories: soluble intracellular proteins, soluble secreted proteins, type I membrane proteins, type II membrane proteins, and multi-spanning membrane proteins. Generation of protein isoforms with variable membrane organizations can change a proteins subcellular localization or association with the membrane. Application of MemO, a membrane organization annotation pipeline, to the FANTOM3 Isoform Protein Sequence mouse protein set revealed that within the 8,032 transcriptional units (TUs) with multiple protein isoforms, 573 had variation in their use of signal peptides, 1,527 had variation in their use of transmembrane domains, and
Аннотация доклада: A new algorithm Zebra and a corresponding web-server have been developed to systematically study diverse protein superfamilies and identify the subfamily-specific positions (SSPs) - conserved only within functional subfamilies but different between them - that seem to be responsible for different substrate specificity, catalytic activity, stability, etc. [1]. It is known from experimental enzymology that mutations in the active site can change enantioselectivity, substrate specificity and catalytic promiscuity more effectively than distant ones. However, both close and distant mutations can be important for activity and stability thus highlighting complexity of evolutionary adaptation. Therefore, to identify functionally important SSPs a novel scoring function is suggested that incorporates structural information as well as physicochemical and residue conservation in protein subfamilies. The algorithm does not require pre-defined subfamilies and can propose ...
Human cellular nucleic acid binding protein (CNBP) is a zinc finger DNA binding protein of unknown function. The human CNBP cDNA was used as a probe to isolate four structurally distinct but highly homologous mouse liver cDNA clones. Each of the mouse clones exhibited extraordinary sequence conservation with human CNBP cDNA, and the predicted mouse amino acid sequence identities with human CNBP protein ranged from 99 to 100%. Genetic mapping of CNBP genes in interspecific and intersubspecific mouse backcrosses revealed two loci that hybridize to CNBP cDNA at high stringency, located on chromosomes 5 and 6. The subcellular distribution of the CNBP protein was characterized with a specific polyclonal antibody generated against a synthetic peptide from the carboxyl terminus. CNBP was found in the cytosol and the endoplasmic reticulum in subcellular fractions from mouse liver, but was undetectable in nuclear fractions. These data suggest that CNBP is a member of a highly conserved family of
Professional Journals. Robinson, D. (2015) The difficulty with inclusive pedagogy in teacher education: some more thoughts on the way forward. Teaching and Teacher Education, 61, pp 164-178.. Garner, P. and Robinson, D. (2000) Which SEN books to primary school teachers find Influential? British Journal of Special Education, 27 (2) pp.87-92. Goodey, C. and Robinson, D. (2017). The inclusion phobia and teacher education: Scaling the problem. Teaching and teacher education. Pending. Research Reports. Adams, L, Tindle, A., Basran, S., Dobie, S., Thomson, Robinson, D. and Shepherd, C. (2017) Education Health and Care Plans: a survey user experiences. London: DfE. Robinson, D., Moore, N. & Parker, G (2016) An evaluation of BookTrust additional needs resources. Institute of Education: University of Derby.. Moore, N., Sahar, A., Robinson, D. & Hoare, M. (2016) Young Enterprise: Evalauting the impact of the Team programme. Derby: International Centre for Guidance Studies, University of Derby.. Robinson, ...
Affects function: The variants effect on the proteins function, in the format Reported/Curator concluded; + indicating the variant affects function, +? probably affects function, +* affects function, not associated with individuals disease phenotype, # affects function, not associated with any known disease phenotype, - does not affect function, -? probably does not affect function, ? effect unknown, . effect not classified ...
Affects function: The variants effect on the proteins function, in the format Reported/Curator concluded; + indicating the variant affects function, +? probably affects function, +* affects function, not associated with individuals disease phenotype, # affects function, not associated with any known disease phenotype, - does not affect function, -? probably does not affect function, ? effect unknown, . effect not classified ...
The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A resolution by x-ray crystallography. The bipartite structure of PurR consists of an amino-terminal DNA-binding domain and a larger carboxyl-terminal corepressor binding and dimerization domain that is similar to that of the bacterial periplasmic binding proteins. The DNA-binding domain contains a helix-turn-helix motif that makes base-specific contacts in the major groove of the DNA. Base contacts are also made by residues of symmetry-related alpha helices, the "hinge" helices, which bind deeply in the minor groove. Critical to hinge helix-minor groove binding is the intercalation of the side chains of Leu54 and its symmetry-related mate, Leu54, into the central CpG-base pair step. These residues thereby act as "leucine levers" to pry open the minor groove and kink the purF operator by 45 degrees. ...
The DNA sequence of the whole of the short unique region (U S ) and that of part of the short terminal repeat (TR S ) of herpesvirus of turkeys (HVT) were determined. HVT U S is 8·6 kbp long and contains eight potential open reading frames (ORFs). Seven of these have counterparts in the U S of herpes simplex virus type 1 (HSV-1). The homologous proteins include US1, US2, US10, protein kinase (US3) and the glycoproteins gD, gI and gE. In addition, HVT contains one ORF which has a counterpart in the U S of Marek's disease virus (MDV) but is not homologous to any other known herpesvirus gene. Although HVT and MDV proteins encoded by U S genes have evident similarities with proteins encoded by alphaherpesviruses, multiple alignment analysis of predicted amino acid sequences show that HVT proteins are more closely related to MDV proteins than to homologous proteins of mammalian alphaherpesviruses. The percentage amino acid identity between HVT and MDV U S -encoded proteins ranges from 35 to 65, the
Appropriate C-terminal cleavage of a CTL epitope by the proteasome is a crucial step in the formation of precursor peptides leading to MHC presentable TCR ligands. A single residue exchange, flanking the C-terminal amino acid, obliterates accurate proteasome-mediated cleavage. This leads to the generation of peptide precursors that are neither suitable for TAP translocation nor for MHC class I binding. In this case an N to D exchange is caused by a single nucleotide mutation (N = AAC or AAT codon; D = GAC or GAT codon). An alternative explanation for the lack of epitope presentation of the Friend homologue could be the lower MHC class I-binding affinity. The Friend sequence harbors an alternative anchor residue Y instead of F, the binding affinity of the peptide for the MHC class I-Kb molecule has been studied in detail and published in our previous paper (31). The binding affinity of the Y peptide is ∼5-fold lower than that of the F peptide. However, the affinity of this peptide is still very ...
Philus transformation. Proc Natl Acad Sci U S A 79: 2393 2397. 47. Duffin PM, Seifert HS DNA uptake sequence-mediated enhancement of transformation in Neisseria
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 ...
The Runt related transcription factors (RUNX) are recognized as key players in suppressing or promoting tumor growth. RUNX3, a member of this family, is known as a tumor suppressor in many types of cancers, although such a paradigm was challenged by some researchers. The TGF-β pathway governs major upstream signals to activate RUNX3. RUNX3 protein consists of several regions and domains. The Runt domain is a conserved DNA binding domain and is considered as the main part of RUNX proteins since. Herein, we compared the effects of Runt domains and full-Runx3 in cell viability by designing two constructs of Runx3, including N-terminal region and Runt domain. We investigated the effect of full-Runx3, N-t, and RD on growth inhibition in AGS, MCF-7, A549, and HEK293 cell lines which are different in TGF-β sensitivity, in the absence and presence of TGF-β. The full length RUNX3 did not notably inhibit growth of these cell lines while, the N-t and RD truncates showed different trends in these cell lines.
When inferring phylogenetic relationships, not all sites in a sequence alignment are equally informative. One recently proposed approach that takes advantage of this inequality relies on sites that contain amino acids whose replacement requires multiple substitutions. Identifying these so-called RGC_CAM substitutions (after Rare Genomic Changes as Conserved Amino acids-Multiple substitutions) requires that, first, at any given site in the amino acid sequence alignment, there must be a minimum of two different amino acids; second, each amino acid must be present in at least two taxa; and third, the amino acids must require a minimum of two nucleotide substitutions to replace each other. Although theory suggests that RGC_CAM substitutions are expected to be rare and less likely to be homoplastic, the informativeness of RGC_CAM substitutions has not been extensively evaluated in biological data sets. We investigated the quality of RGC_CAM substitutions by examining their degree of homoplasy and internode
Effect: The variants effect on the proteins function, in the format R/C where R is the value reported by the source and C is the value concluded by the curator; + indicating the variant affects function, +? probably affects function, +* affects function, not associated with individuals disease phenotype, # affects function, not associated with any known disease phenotype, - does not affect function, -? probably does not affect function, ? effect unknown, . effect not classified ...
NCAM in vertebrates and its related molecules, apCAM in Aplysia, fasciclin II in Drosophila, and OCAM in mammals, play key roles in various aspects of brain development and functions. In this study, we have identified and characterized three members of the NCAM gene family in zebrafish, designated as zNCAM, zOCAM, and zPCAM. Three molecules exhibit similar domain organization: an amino-terminal signal peptide, five immunoglobulin-like domains, two fibronectin type III-like domains, a transmembrane segment, and a carboxy-terminal cytoplasmic region. A novel molecule zPCAM is most closely related to zNCAM with 66% amino acid identity. Diversity in the extracellular region of zPCAM is generated by insertion of two different types of variable alternatively spliced exons. In situ hybridization analysis revealed that three molecules were specifically expressed by the central and peripheral nervous systems from early developmental stages in region-specific and cell-type-specific manners. For example, ...
Interactions between GPCRs and their cognate G proteins are known to involve several different domains on both the receptor and the G protein heterotrimer. Within Gα, the best characterized GPCR contact site is the extreme C terminus where residues at positions -3 and -4 are particularly important for specific receptor recognition (Conklin et al., 1993, 1996; Kostenis et al., 1997c; Bahia et al., 1998; Blahos et al., 1998; Liu et al., 2002). We have recently demonstrated the importance of the linker I region of Gαq proteins in constraining the fidelity of receptor recognition. A highly conserved glycine residue in linker I (glycine 66) regulates coupling selectivity indirectly by playing a role in the specificity of nucleotide exchange within Gαq induced by ligand-activated GPCRs (Heydorn et al., 2004). Here, we analyzed 1) the relationship between the linker I region and the extreme C terminus of Gα in determining selective GPCR coupling and 2) whether different GPCRs use different Gα ...
The Arabidopsis thaliana R2R3-MYB transcription factor MYB12 is a light-inducible, flavonol-specific activator of flavonoid biosynthesis. The transactivation activity of the AtMYB12 protein was analyzed using a C-terminal deletion series in a transient A. thaliana protoplast assay with the goal of mapping the activation domain (AD). Although the deletion of the last 46 C-terminal amino acids did not affect the activation capacity, the deletion of the last 98 amino acids almost totally abolished transactivation of two different target promoters. A domain swap experiment using the yeast GAL4 DNA-binding domain revealed that the region from positions 282 to 328 of AtMYB12 was sufficient for transactivation. In contrast to the R2R3-MYB ADs known thus far, that of AtMYB12 is not located at the rearmost C-terminal end of the protein. The AtMYB12 AD is conserved in other experimentally proven R2R3-MYB flavonol regulators from different species ...
Lower vertebrate species, including Xenopus laevis, exhibit restricted antibody diversity relative to higher vertebrates. We have analyzed more than 180 VH gene-containing recombinant clones from an unamplified spleen cDNA library by selective sequencing of JH and CH positive clones following iterative hybridization screening with family-specific VH probes, 11 unique families of VH genes, each associated with a unique genomic Southern blot hybridization pattern, are described and compared. Considerable variation in the number of hybridizing components detected by each probe is evident. The nucleotide sequence difference between VH families is as great as, if not more than, that reported in other systems, including representatives of the mammalian, avian, and elasmobranch lineages. Some Xenopus Ig gene families encode alternative amino acids at positions that are otherwise invariant or very rarely substituted in known Igs. Furthermore, variations in complementarity determining region sequences ...
Two distinct IL-1 receptors have been identified as shown by the cloning studies of Sims and coworkers. Both receptors are members of the immunoglobulin superfamily. The type I receptor is an 80 kDa transmembrane protein, 552 amino acids long, with a single 22 amino acid transmembrane region and a long cytoplasmic tail of 213 amion acids. Its extracellular ligand-binding region consists of three immunoglob-ulin-like domains. The type II receptor is a 60 kDa protein and is similar to the type I receptor in its extracellular and transmembrane regions. The type II receptor has a short cytoplasmic tail of 29 amino acids and is incapable of signal transduction. The type II receptor actually competitively inhibits IL-1 activity by acting as a decoy receptor for IL-1, and regulates the level of extracellular IL-1.. IL-1 acts on target cells by binding with high affinity (Kd of 10~10 m) to IL-1 type I receptors. Type I receptors are found on T cells, endothelial cells, hepatocytes, fibroblasts and ...
Alternative splicing of transcripts from a single gene is often used as a mechanism for generating protein variants with diverse functions (reviewed by McKeown, 1992). In the case of transcription factor genes, alternative splicing frequently gives rise to protein isoforms with distinct or even opposing transcriptional activities (reviewed by Foulkes and Sassone‐Corsi, 1992). However, few cases are known where the DNA sequence specificity of a transcription factor is altered by alternative splicing. Pax6 belongs to this class of genes which normally code for transcription factors with modular DNA‐binding domains such as the mammalian WT‐1, the Drosophila Tramtrack and CF2 zinc finger proteins (Bickmore et al., 1992; Gogos et al., 1992; Read and Manley, 1992). Here we have demonstrated that a second Pax gene, Pax8, also codes for alternative splice products with drastically different DNA‐binding specificities.. The paired domain is a bipartite DNA‐binding region consisting of an ...
Nine integrin alpha subunits contain an additional domain (termed A or I) that is inserted into the head region, where it plays a central role in ligand binding: thus, recombinant I domains recapitulate many of the ligand-binding properties of the intact integrin. The first crystal structure of an I domain shows that it adopts the dinucleotide-binding fold, with a central mostly parallel beta sheet surrounded on both sides by amphipathic alpha helices. At the C-terminal end of the beta sheet is a conserved metal binding site that has been called the metal ion-dependent adhesion site, or MIDAS motif. Mutagenesis studies have shown that the MIDAS motif and exposed side chains on the surrounding surface are required for ligand binding, and are thus likely to form the ligand contact sites. Comparison between two different crystal forms of the alphaM-I domain led to the proposal that affinity regulation occurs via changes in metal coordination at the MIDAS motif that are linked to tertiary changes ...
A new kind of high avidity binding molecule, termed peptabody was made by harnessing the result of multivalent interaction. 85 kDa, with interchain disulfide bonds. Pab-S could be dissociated under denaturing and reducing circumstances and reassociated like a pentamer with full-binding activity. This intrinsic feature has an easy method to mix Pab substances with two different peptide specificities, creating heteropentamers with bispecific and/or chelating properties thus. binding actions for different receptors. A robust method of developing artificial ligands emerges by MCC950 sodium novel inhibtior the testing of huge phage libraries, displaying billions of different polypeptide sequences fused with coat proteins on the surface of filamentous bacteriophage (1, 2). For example, isolation of new peptide ligands allowed the mapping of antibody binding sites, the characterization of important residues in HLA-DR molecules, and the identification of protease substrates or inhibitors (for review see ...
Hematopoietic antigen receptors such as the TCR, the B cell receptor, or Fc receptors are generally composed of at least two different subunits, one representing the ligand binding site, the other being responsible for signal transduction after receptor engagement. The molecular structure of these two subunits reflects their different tasks for eliciting cellular responses. Thus, the ligand binding site normally comprises a long extracellular domain (serving as recognition element), an α-helical transmembrane domain that carries at least one charged amino acid, and a very short cytoplasmic segment devoid of any signaling motifs. In contrast, the signal-transducing component is composed of a very short extracellular domain (lacking an external ligand), a transmembrane domain that also contains a charged amino acid (to allow stable interaction with the ligand binding subunit), and a comparably long cytoplasmic tail carrying particular amino acid motifs, which are necessary for signal ...
Nox2/gp91phox (where phox is phagocyte oxidase) is the catalytic membrane subunit of the NADPH oxidase, an enzyme complex found in phagocytic leucocytes which catalyses the formation of superoxide anion (O2•−), a reactive oxygen species involved in the host defence against pathogens. It is an integral membrane protein of 570 amino acids, which is predicted to contain multiple transmembrane domains [1,2]. The N-terminal part of the protein was shown to be involved in haem binding through histidine residues 101, 115, 209 and 222, located in helices III (101 and 115) and V (209 and 222) [3]. After proteolytic treatment of partially purified cytochrome b558, a spectrally stable fragment comprising the whole N-terminus and ending at amino acids 320 or 363 was recovered [4]. gp91phox has been proposed to contain the binding sites for the NADPH oxidase prosthetic group, FAD, and the substrate, NADPH [5,6]. Based on a weak primary structure similarity between the C-terminal domain of gp91phox and ...
The alpha 2 protein, the product of the MAT alpha 2 gene, is a regulator of cell type in the yeast Saccharomyces cerevisiae. It represses transcription of a group of cell type-specific genes by binding to an operator located upstream of each target gene. Fifteen in-frame deletions within the coding region of the MAT alpha 2 gene were constructed. The deletion alleles were examined for phenotypes conferred in vivo, and the encoded mutant proteins were assayed for ability to bind specifically to the operator in vitro. This analysis has revealed that the sequence-specific DNA-binding domain of alpha 2 is located within a region of 68 amino acids. This region of alpha 2 has significant homology with the homeo domain, a conserved sequence found in the products of several Drosophila homeotic and segmentation genes. In addition, there is a class of mutant alpha 2 proteins that binds tightly and specifically to the operator in vitro, but fails to repress transcription in vivo ...
Highly conserved amino acid residues are highlighted by vertical shading in the Pfam view. The first thing you should notice is that there are very few amino acids that are invariant. The conserved residue on the left (blue) is tryptophan (W). Its present in most of the globins from different species but not all. Look at the other positions and note that in most cases a variety of different amino acid residues can be substituted. Sometimes only hydrophobic residues (blue) can be found at a particular site and sometimes there are other restricted choices. Lots of insertions and deletions (dots) can be tolerated without major disruption to the overall three-dimensional structure ...
GWAS and more recently whole-exome/genome sequencing have generated a massive expansion in the number of candidate disease genes. Animal models will have an essential role in validating candidate genes and understanding their role in pathobiology. Advances in targeted genome engineering with TALENs and CRISPRs now makes it feasible for individual laboratories to generate heritable and precise sequence modifications of their gene of interest in any organism. Zebrafish are an attractive model system because they share the vast majority of human disease genes. Genome editing tools such as CRISPR-Cas9 and TALENs permit heritable and precise sequence modification of the genome. In this session I will discuss the strengths and weaknesses of the new genome editing tools and compare these methods to existing gene knock-down approaches. I will provide a brief overview of how we are applying these exciting genome editing tools to generate more informative models of human disease.. ...
1. Shu HB,Agranoff A, Nabel EG, Leung K, Neish AS, Collins , Nabel GJ* (1993).Differential regulation of VCAM-1 gene expression by specific NF-kB subunits in endothelial and epithelial cells. Mol Cell Biol13:6283-6289.. 2. Shu HB, Li Z, Palacios MJ, Li Q, Joshi HC* (1995). A transient association of g-tubulin at the midbody is required for the completion of cytokinesis during the mammalian cell division. J Cell Sci108: 2955-2962.. 3. Shu HB, Joshi HC* (1995). g-Tubulin can both neacleate microtubule assembly and self-assemble into tubular structures in mammalian cells. J Cell Biol130:1137-1147.. 4. Hsu H, Shu HB,Pan MG, Goeddel DV* (1996). TRADD-TRAF2 and TRADD-FADD interactions define two distinct TNF receptor-1 signal transduction pathways. Cell84:299-308.. 5. Shu HB,Takeuchi M, Goeddel DV* (1996). The TNF receptor 2 signal transducers TRAF2 and c-IAP1 are components of the TNF receptor 1 signaling complex. P Natl Acad Sci USA93:13973-13978.. 6. Shu HB,Halpins DR, Goeddel DV* (1997). Casperis ...
We have mapped determinants for species‐specific interactions of Par components (Figure 6). Operon repression involves a specific interaction between ParA and the operator DNA. The specific determinant includes a HTH motif in the N‐terminal region of ParA and probably contacts the operator directly. Direct binding of ParA to the operator sequence has been shown previously (Davis et al., 1992).. Specific enhancement of repression by ParB was shown to be due to a protein-protein interaction with ParA rather than direct recognition of the operator by ParB. This is consistent with the observation that ParB does not appear to bind to the operator by itself, and does not cause any qualitative modification of the footprint of ParA bound to operator DNA (Davis et al., 1992). The ParA-ParB interaction involves determinants in the C‐terminal region of ParA and the N‐terminal end of ParB (Figure 6). ParA and ParB interact directly in vitro (Davis et al., 1992). Thus it is likely that the mapped ...
The tumor suppressor protein, p53, is mutated or dysregulated in nearly all human cancers(1). The amino terminal domains are essential for transcriptional activation in stressed cells and play a vital role in cell cycle regulation, apoptosis and senescence. The transactivation (TAD) and proline rich domains in this region are dynamic and intrinsically disordered; lacking stable secondary or tertiary structure. This region contains multiple binding sites; arguably, the most significant of these is for p53s negative regulator, the E3 ligase, MDM2. An important, but less understood interaction involving the single stranded DNA binding protein, RPA70A, is hypothesized to be involved in maintaining genome integrity(2-4). Additionally, the amino terminus contains an important single nucleotide polymorphism that has demonstrated different affinity for MDM2 and is of significant biological importance in the induction of apoptosis (5). Isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR)
K(v)3.4 belongs to the shaw subfamily of shaker-type potassium channels. It conducts fast inactivating, high threshold currents in the central nervous system and in fast-twitch skeletal muscle fibers. The corresponding mouse gene, Kcnc4, consists of five exons spanning a region of 20 kb. Approximately 700 bp of regulatory sequence were delineated. It is GC rich and lacks typical TATA and CAAT motifs. Instead, seven Sp-1 and three E-box elements define putative regulatory sequences. The mouse K(v)3.4 mRNA has a size of 3639 bp, 1120 bp of which are 3 untranslated region. A transcript initiated from an alternative 5-exon was identified by RACE and verified by genomic analysis. This isoform, designated K(v)3.4d, is predominantly expressed in skeletal muscle and probably results from alternative promoter usage. It encodes a channel protein with a novel N-terminal cytoplasmic domain. It lacks the conserved sequence motifs encoding the shaw-type tetramerization domain and the ball peptide, which ...
Comparative genomics is a powerful means of uncovering important functional DNA elements through DNA sequence conservation [63], but identification of mouse Dxz4 was initially discovered not through primary DNA sequence conservation but instead through conservation of DNA sequence organization within a syntenic region of the mouse genome. This work led to the subsequent identification of DXZ4 in a diverse group of distantly related mammals. DNA sequence comparisons revealed a highly conserved region within each DXZ4 monomer that corresponds to the CTCF binding motif that is bound by CTCF in all mammals tested thus far. Furthermore, the highly conserved sequence immediately adjacent to the Ctcf consensus site suggests a second DNA binding protein may associate alongside Ctcf. Therefore, on the basis of conservation, several features of DXZ4 appear to have functional importance in eutherian mammals: CTCF binding, tandem-repeat organization, expression, and location downstream of PLS3.. In primates ...
Evidence that the transcriptional unit identified corresponds to fl(2)d: Several lines of evidence indicate that the transcriptional unit described above corresponds to fl(2)d. First, the site of P-element insertion in the fl(2)dP mutant disrupts the longer Fl(2)d ORF (Figures 2A and 4A). Second, sequence analysis of genomic DNA from fl(2)d1 flies, a recessive temperature-sensitive mutant of fl(2)d, revealed a single G to A nucleotide change at nucleotide position 939. This results in an amino acid change from aspartic acid to asparagine at position 180 of the longer version of Fl(2)d ORF (Figure 4, A and B). Third, sequence analysis of genomic DNA from fl(2)d2/+ heterozygous flies also revealed DNA alterations that are consistent with the stronger, non-sex-specific phenotype associated with this mutation (Granadinoet al. 1992). Because fl(2)d2 is lethal in homozygosis, DNA from fl(2)d2/+ heterozygous flies was amplified by PCR to generate products that span the complete ORF. The profile of the ...
Press release about the Basel Committee issuing final guidelines on identification and management of step-in risk (25 October 2017). The Basel Committee on Banking Supervision released today the final Guidelines on identification and management of step-in risk. Step-in risk refers to the risk that a bank provides financial support to an entity beyond, or in the absence of, its contractual obligations should the entity experience financial stress.
We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment ...
On Feb 8, 2012, at 8:52 AM, Brad Kemper wrote: , On Feb 8, 2012, at 1:28 AM, Alex Mogilevsky ,[email protected], wrote: , ,,, From: Brad Kemper [mailto:[email protected]] ,,, Sent: Tuesday, February 07, 2012 6:34 PM ,,, ,,, What it the purpose of this restriction? If authors wants that behavior, they can ,,, just set position:relative on the first block. Why must it be prescribed as a ,,, containing block? ,, ,, Set position:relative on first region or root element of named flow? , , Im confused by the question, because root element of named flow is meaningless to me (or, has been meaningless, or should be meaningless). The root of any HTML document Id the HTML element viewport, and there is only one root per document. , , I had meant that the author could set position:relative on first region, instead of the first region being the ICB. It seems like that would amount to the same effect, except that it wouldnt be mandatory (the author could leave the first region as static, and ...
TALE represents the largest effector family and functions in transcriptional activation of plant genes. Their unique structure encompasses a DNA-binding region that enables TALEs to bind specifically to the promoter region on DNA. Their binding specificity can be predictable since two hypervariable amino acids within the repeat domain known as repeat variable di-residues (RVDs) determine the nucleotide to which the particular repeat binds (Boch et al., 2009).. The repetitive nature of TALE DNA-binding domains led to the binding code being deciphered in 2009 (Boch et al., 2009). As shown in Fig. 3, amino acids at positions 12 and 13 within a 34-amino acid repeat are called RVDs, which direct nucleotide specificity on the target DNA. The tandem polymorphic amino acid repeats of TALEs are located in the central DNA-binding region. Each RVD recognizes a single DNA base and different RVDs have variable affinity for different nucleotides. The four most common RVDs are HD, NG, NI, and NN, specifying C, ...
The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins [(PUBMED:7667876), (PUBMED:9482716), (PUBMED:1882418)]. It mediates protein-protein interactions and the assembly of multiprotein complexes [(PUBMED:14659697)]. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs ...
We often think of DNA binding sites as dictating the particular transcription factor that will bind and in that way determining how transcription is regulated. However, evidence is accumulating that the interaction provides additional information and may actually allosterically modify the bound transcription factor. Leung et al. noted unusual conservation of binding sites for the transcription factor NF-κB in human and mouse genes and therefore tested the effects of single nucleotide changes on gene regulation at such a site. In mouse 3T3 cells infected with lentivirus that permitted modification of the endogenous gene promoter, a single nucleotide change was found to have no effect on binding of the transcription factor, but rather to alter the requirement for a particular coactivator, IRF3. The authors suggest that conformational changes in the bound NF-κB molecule likely account for altered preference for cofactors when bound to different promoters. T. H. Leung, A. Hoffmann, D. Baltimore, ...
Shop Kelch repeat and BTB domain-containing protein ELISA Kit, Recombinant Protein and Kelch repeat and BTB domain-containing protein Antibody at MyBioSource. Custom ELISA Kit, Recombinant Protein and Antibody are available.
In the present study, we cloned, sequenced, and generated specific antibodies for immunolocalization, and assayed functional activity of two closely related homologues of Kir4.2 that are expressed in rat hepatocytes. These results extend the recent cloning of a Kir4.2 from whole mouse liver (22). Although Kir4.2 mRNA was not detected on Northern blot analyses of embryonic mouse liver (27), this likely resulted from an inability to detect rare messages such as K+ channels in nonexcitable tissue and/or the tissue developmental stage. Nonconducting human and guinea pig transcripts have also been cloned (6, 25). The overall sequence identity at the amino acid level is 90%. The biophysical properties of Kir4.2 make it a suitable candidate for the functional data accumulated regarding K+ fluxes in the intact liver and isolated hepatocytes. Furthermore, whole cell currents of short-term cultured rat hepatocytes exhibit characteristics of moderately inwardly rectifying K+ channels (12) such as ...
Epitope tags are short peptide sequences that are easily recognized by tag-specific antibodies. Due to their small size, epitope tags do not affect the tagged proteins biochemical properties. Most often, sequences encoding the epitope tag are included with target DNA at the time of cloning to produce fusion proteins containing the epitope tag sequence. This allows anti-epitope tag antibodies to serve as universal detection reagents for any tag-containing protein produced by recombinant means. This means that anti-epitope tag antibodies are a useful alternative to generating specific antibodies to identify, immunoprecipitate or immunoaffinity purify a recombinant protein. The anti-epitope tag antibody is usually functional in a variety of antibody-dependent experimental procedures. Expression vectors producing epitope tag fusion proteins are available for a variety of host expression systems including bacteria, yeast, insect and mammalian cells. Rockland Immunochemicals produces anti-epitope tag
Big MAP kinase 1 (BMK1), also known as ERK5, is a mitogen-activated protein (MAP) kinase member whose biological role is largely undefined. The activity of BMK1 in rat smooth muscle cells is up-regulated by oxidants. A constitutively active form of the MAP kinase kinase, MEK5(D), is described which selectively activates BMK1 but not other MAP kinases in vivo. Through utilization of MEK5(D), it has been determined that a member of the MEF2 transcription factor family, MEF2C, is a protein substrate of BMK1. BMK1 dramatically enhances the transactivation activity of MEF2C by phosphorylating a serine residue at amino acid position 387 in this transcription factor. Serum is also a potent stimulator of BMK1-induced MEF2C phosphorylation, since a dominant-negative form of BMK1 specifically inhibits serum-induced activation of MEF2C. One consequence of MEF2C activation is increased transcription of the c-jun gene. Taken together, these results strongly suggest that in some cell types the MEK5/BMK1 MAP ...
Short-chain dehydrogenases/reductases (SDRs) constitute a large family of NAD(P)(H)-dependent oxidoreductases, sharing sequence motifs and displaying similar mechanisms. SDR enzymes have critical roles in lipid, amino acid, carbohydrate, cofactor, hormone and xenobiotic metabolism as well as in redox sensor mechanisms. Sequence identities are low, and the most conserved feature is an alpha/beta folding pattern with a central beta sheet flanked by 2 - 3 alpha-helices from each side, thus a classical Rossmannfold motif for nucleotide binding. The conservation of this element and an active site, often with an Asn-Ser-Tyr-Lys tetrad, provides a platform for enzymatic activities encompassing several EC classes, including oxidoreductases, epimerases and lyases. The common mechanism is an underlying hydride and proton transfer involving the nicotinamide and typically an active site tyrosine residue, whereas substrate specificity is determined by a variable C-terminal segment. Relationships exist with ...
We present data on the interaction of arginine-rich peptides of human immunodeficiency virus (HIV-Tat) with tRNAPhe of Saccharomyces cerevisiae. We have found that tRNA forms complexes with the Tat1 peptide of amino acid sequence GRKKRRQRRRA and its mutants where R is replaced by D-arginine, citrulline or ornithine. The structure of tRNA-Tat1 complex was probed by specific RNases digestions and Pb2+-induced cleavage of phosphodiester bond of guanosine. The nucleotide sequence UGGG located in the dihydrouridine loop of tRNAPhe binds to Tat peptide and therefore is specifically protected against RNases and is not hydrolyzed by Pb2+ ion. It seems that the peptide-RNA complex formation depends on direct recognition of guanine moieties of tRNA with arginine residues. These interactions are similar to those observed in many DNA-protein complexes, but are different from those previously observed for TAR RNA-Tat complexes.. Keywords: Tat peptides; TAR RNA; tRNAPhe; Protein-nucleic acids interactions; ...
The RFC is the predominant route of entry of MTX and endogenous reduced folates into most mammalian cells. The open reading frame of the RFC cDNA predicts a protein with a molecular mass of 65 kDa. The RFC is an integral membrane protein that, based on predictions by hydropathy plotting, consists of 12 putative transmembrane-spanning domains flanked by NH2 and COOH termini and a long internal loop between transmembrane domains 6 and 7 localized adjacent to the cytoplasm. In this study, rabbit polyclonal antisera was generated against a 16-mer MAP peptide, corresponding to a sequence localized to a highly antigenic region between transmembrane domains 6 and 7 (adjacent to the internal loop). The antibody was used to characterize the expression of RFC in human tumor cell lines.. Western analysis of membrane preparations isolated from a panel of cell lines by sucrose density gradient centrifugation demonstrated an approximately 60-kDa membrane protein in the CCRF-CEM, MCF, malignant fibrous ...
article{818070, abstract = {Caspase-3 and -7 are considered functionally redundant proteases with similar proteolytic specificities. We performed a proteome-wide screen on a mouse macrophage lysate using the N-terminal combined fractional diagonal chromatography technology and identified 46 shared, three caspase-3-specific, and six caspase-7-specific cleavage sites. Further analysis of these cleavage sites and substitution mutation experiments revealed that for certain cleavage sites a lysine at the P5 position contributes to the discrimination between caspase-7 and -3 specificity. One of the caspase-7-specific substrates, the 40 S ribosomal protein S18, was studied in detail. The RPS18-derived P6-P5 undecapeptide retained complete specificity for caspase-7. The corresponding P6-P1 hexapeptide still displayed caspase-7 preference but lost strict specificity, suggesting that P residues are additionally required for caspase-7-specific cleavage. Analysis of truncated peptide mutants revealed that ...
Exponential growth in genome sequencing, which allows scientists to determine the linear sequence of amino acids (residues) in protein molecules encoded by genes, has yielded a conundrum.. There were more than 69 million protein sequences identified in life forms ranging from humans to bacteria in the Uniprot database, as of June 2014, up from less than 10 million at the start of 2010. But at least half of those have uncertain, unknown, or incorrectly annotated functions.. In other words, despite approaches that include automated comparisons of the discovered proteins sequence data, their specific chemical and biological functions either cannot be determined or have been mislabeled. This is because closely related proteins (those with high sequence similarity) can have different functions, and unrelated proteins can have similar functions. The problem becomes ever more significant and self-perpetuating as newly discovered proteins are assigned incorrect function due to their similarity with ...
[48 Pages Report] Check for Discount on Interleukin 1 Receptor Type 1 (CD121 Antigen Like Family Member A or Interleukin 1 Receptor Alpha or p80 or CD121a or IL1R1) - Pipeline Review, H2 2017 report by Global Markets Direct. Interleukin 1 Receptor Type 1 (CD121 Antigen Like Family Member...
Antibodies for proteins involved in glycerol biosynthetic process pathways, according to their Panther/Gene Ontology Classification
Ligand stimulation of growth factor receptors with intrinsic protein-tyrosine kinase activity initiates the assembly of multienzyme signalling complexes. This is mediated by binding of proteins with src homology 2 (SH2) domains to receptor autophosphorylation sites. Among the proteins involved in complex formation is phosphatidylinositol (PI) 3-kinase, a heterodimeric enzyme composed of 85 kDa and 110 kDa subunits, which binds to receptor (and non-receptor) phosphotyrosine residues through the two SH2 domains in the p85 subunit. p85 acts as an adaptor protein and possibly a regulator of the p110 catalytic subunit that phosphorylates phosphoinositides at the D-3 position of the inositol ring. p85 subunit is composed of several distinct functional domains: one SH3 and two SH2 domains, a p110 binding site and a region with homology to BCR. Expression of these domains in E. coli as GST-fusion proteins has allowed definition by nuclear magnetic resonance (NMR) of three-dimensional structures for the ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the ...
Molecules of one protein being expressed in more than one subcellular compartment is a common phenomenon in eukaryotic cells, and is referred to as dual localization or dual targeting (Kisslov et al., 2014). Differently localized proteins, but with identical or nearly identical protein sequence, are defined as echoforms or echoproteins. Echoforms exhibit the same or in some cases, surprisingly distinct activities and functions in each subcellular location (Raza, 2011; Yogev and Pines, 2011). Our previous studies (Li et al., 2011) have identified both mitochondria and cytosol as subcellular expression sites of GSTZ1, based on immunoreactivity, enzyme reaction, and partial protein sequence (,15%). However, the enzyme properties of liver mitochondrial GSTZ1 were incompletely understood. Considering the importance of mitochondrial GSTZ1 to DCA metabolism, in this study we extended our investigation on mitochondrial GSTZ1 using human samples. One of the aims was to investigate the developmental ...
Cancer Research Laboratory, University of Western Ontario, London, Canada. A mouse mRNA, provisionally designated 5B10, has been cloned based on its inducibility by serum in quiescent murine fibroblasts. Here we report the full-length complementary DNA sequence and a partial characterization. There are about five copies of the gene in the mouse genome. Sequence analysis of the 5B10 coding region reveals 94 and 97% amino acid identity to human and rat calcyclin, respectively. Although the coding region has been highly conserved during evolution of the rodent and human genomes, the untranslated flanking sequences differ significantly. A protein of Mr about 8000 was produced by in vitro translation of the mRNA transcribed in vitro from 5B10 complementary DNA in a riboprobe vector. An antiserum raised against a portion of the predicted human calcyclin protein cross-reacted with this mouse protein. 5B10 mRNA was found in greatest amount in organs containing proliferating cells, e.g., epidermis, skin, ...
View Notes - Organic_Molecules_II from BIOL 1201 at LSU. all nucleotides have the same basic structure Nucleic Acids: are polymers of nucleotides bonded together through condensation reactions.
The BURP domain-containing protein family is defined by its conserved amino acid motif whose name is based on four typical members, BNM2, USP, RD22, and PG1β. BURP domain-containing proteins have so far only been found in plants, suggesting that their functions may be plant specific. Generally, the BURP family proteins consist of several modules: an N-terminal hydrophobic domain, a presumptive transit peptide; a variable internal region containing either a short conserved segment or other segments; an optional segment consisting of repeated units which is unique to each member; and the BURP domain at the C-terminus [1].. BURP domain-containing proteins were classified into four subfamilies, BNM2-like, USP-like, RD22-like, and PG1β-like [2]. All members of each subfamily contain BURP domain at the C-terminal region. Within the domain there are several conserved amino acid residues, including four cystein-histidine repeats and one tryptophan residue. The spacing between the four CH residues is ...
Chang C, Simmons DT, Martin MA and Mora PT (1979) Identification and partial characterization of new antigens from simian virus 40-transformed mouse cells. J Virol 31: 463-471.. Crawford LV, Pim DC and Bulbrook RD (1982) Detection of antibodies against the cellular protein p53 in sera from patients with breast cancer. Int. J. Cancer 30: 403-408.. Crawford L (1983) The 53,000-dalton cellular protein and its role in transformation. Int. Rev. Exp. Path. 25: 1-50.. De Leo AB, Jay G, Appella E, Dubois GC, Law LW and Old LJ (1979) Detection of a transformation-related antigen in chemically induced sarcomas and other transformed cells of the mouse. Proc Natl Acad Sci USA 76: 2420-2424.. Kress M, May E, Cassingena R and May P (1979) Simian Virus 40-transformed cells express new species of proteins precipitable by anti-simian virus 40 serum. J. Virol. 31: 472-483.. Lane DP and Crawford LV (1979) T antigen is bound to a host protein in SV40-transformed cells. Nature 278: 261-263.. Linzer DIH and Levine AJ ...
In mammals, the most poorly understood P-type ATPases are those of the P(5) subfamily. To begin characterization of the mammalian P(5)-ATPases, BLAST searches of DNA sequence databases were performed. Five genes were identified in the mouse, human, dog, and rat genomes, and the coding sequences of the mouse genes, termed Atp13a1-Atp13a5, were determined. The intron/exon organization of Atp13a1 differs entirely from those of Atp13a2-5, which are closely related. Amino acid sequence comparisons between the five mouse and two yeast P(5)-ATPases suggest that Atp13a1 is orthologous to the yeast Cod1 gene and that Atp13a2-5 are orthologous to yeast Yor291w ...
Bozzetti M, Massari S, Finelli P, Meggio F, Pinna LA, et al. 1995. The Ste locus, a component of the parasitic cry-Ste system of Drosophila melanogaster, encodes a protein that forms crystals in primary spermatocytes and mimics properties of the β subunit of casein kinase 2. Proc Natl Acad Sci USA 92: 6067-6071 ...
Highly purified Cited-2 recombinant proteins and full length proteins. Browse our Cited-2 recombinant proteins and full length proteins backed by our 100% Guarantee.
Most of the genes involved in the development of multicellular eukaryotes encode large, multidomain proteins. To decipher the major trends in the evolution of these proteins and make functional predictions for uncharacterized domains, we applied a strategy of sequence database search that includes construction of specialized data sets and iterative subsequence masking. This computational approach allowed us to detect previously unnoticed but potentially important sequence similarities. Developmental gene products are enriched in predicted nonglobular regions as compared to unbiased sets of eukaryotic and bacterial proteins. Developmental genes that act intracellularly, primarily at the level of transcription regulation, typically code for proteins containing highly conserved DNA-binding domains, most of which appear to have evolved before the radiation of bacteria and eukaryotes. We identified bacterial homologues, namely a protein family that includes the Escherichia coli universal stress ...
chromosomes, although some members are genetically linked together. For example CD90(Thy-l), CD-56(NCAM) and CD3e, y and 8 are all found on chromosome 11 at band position q23.. One commonly used approach for sequence comparisons with known members of the superfamily utilizes the Dayhoff ALIGN program which scores similarities between the candidate sequence and several sequences from accepted Ig gene superfamily members. The alignments used for such sequence comparisons need careful consideration, taking into account such factors as the 3 strand/loop organization and the repertoire of conserved amino acids. No residue is invariant in all Ig-related domains and the primary structure of the Ig-type domains can be very different. This is vividly illustrated by the Ig variable region genes where even proteins encoded by the same gene family are sometimes ,20% similar. Three domain patterns have been identified in the Ig gene superfamily, namely the V-, CI- and C2-related domains. Each domain consists ...
Discussion. The novel αA-crystallin mutation G98R was identified and reported in an Indian family by Santhiya et al. [37]. G98R is the only mutation in αA-crystallin associated with cataract where a positively charged amino acid replaces the uncharged amino acid in the native protein. The other known mutations in αA-crystallin, such as R116C, R41C, and R21L have a substitution of a uncharged amino acid [30-32]. Therefore, we investigated the effect of the G98R mutation on the structure and function of αA-crystallin. Using a site-directed mutagenesis method, we constructed the αAG98R mutant and expressed it in E. coli cells. The mutant αA-crystallin protein was expressed but the recombinant protein formed inclusion bodies. The protein from the inclusion bodies was solubilized with urea and refolded. Interestingly, the urea-refolded mutant proteins stayed in soluble form. We observed that when the recombinant protein was extracted within 2 h of IPTG induction G98R was present in both ...
DNA constructs and protein interaction assays. All constructs were generated by subcloning PCR amplification products into appropriate vectors, and each construct was verified by automated DNA sequencing. cDNA fragments encoding the C terminus of the D1 (residues 365-446), D2 (residues 428-443), D3 (residues 385-400), D4 (residues 370-387), and D5 (residues 360-477) receptors were ligated into the yeast GAL4 DNA-binding domain expression vector pAS2-1 (Clontech, Palo Alto, CA). For the D2 receptor screen, the D2-pAS2-1 bait plasmid and the human brain cDNA library in the GAL4 activation domain vector pACT2 (Clontech) were simultaneously cotransformed into the yeast strain MaV103 as previously described (Lin et al., 2001). Positive clones were identified by growth on Leu−/Trp−/His−/Ura−selection plates. Protein interaction was assayed for by β-galactosidase activity via the nitrocellulose filter lift method (Lin et al., 2001).. To identify the sites of interaction between D2 or D3 ...
We have analyzed in detail the transcription pattern of the putative apoptotic gene Pdcd2 [9] and the tightly linked Tbp gene, a key factor in transcription initiation of all eukaryotes [32].. One new alternative Pdcd2 transcript, arising by alternative splicing, and at least three new transcripts of Tbp originated by alternative polyadenylation have been identified in the mouse. The presence of the alternative Pdcd2 mRNA was also found in human [GenBank: NM_144781] and chicken. Although the mechanism and structure of these transcripts is different, in all three species the alternative Pdcd2 transcript encodes the MYND zinc-finger domain but not the highly conserved CT domain, suggesting the biological importance of such truncated protein. The function of the alternative Pdcd2 product can be deduced from the reported study of cell-cycle regulation [14]. The cell line used has a mutation in the HCFC1 gene, causing an arrest of the cell growth at the non-permissive temperature. Transfection of a ...
ID LACI_ECOLI Reviewed; 360 AA. AC P03023; O09196; P71309; Q2MC79; Q47338; DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot. DT 19-JUL-2003, sequence version 3. DT 20-MAR-2007, entry version 87. DE Lactose operon repressor. GN Name=lacI; OrderedLocusNames=b0345, JW0336; OS Escherichia coli. OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=562; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX MEDLINE=78246991; PubMed=355891; DOI=10.1038/274765a0; RA Farabaugh P.J.; RT "Sequence of the lacI gene."; RL Nature 274:765-769(1978). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Chen J., Matthews K.K.S.M.; RL Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases. RN [3] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Marsh S.; RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases. RN [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / MG1655 / ATCC 47076; RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., ...
When does chemical elaboration induce a ligand to change its binding mode? Malhotra S et al. J Med Chem, 2016, 60(1):128-145.. Application of off-rate screening in the identification of novel pan-isoform inhibitors of pyruvate dehydrogenase kinase. Brough PA et al. J Med Chem, 2017, 60(6):2271-2286.Non-coding RNAs as drug targets. Matsui M et al. Nat Rev Drug Discov, 2017, 16(3):167-179.. Drugging RAS: know the enemy. Papke B et al. Science, 2017, 355(6330):1158-1163.. RON kinase: a target for treatment of cancer-induced bone destruction and osteoporosis. Andrade K et al. Sci Transl Med, 2017, 9(374).. Dual-activity PI3K-BRD4 inhibitor for the orthogonal inhibition of MYC to block tumor growth and metastasis. Andrews FH et al. Proc Natl Acad Sci USA, 2017, 114(7):E1072-E1080.. Inhibition of the GAS6/AXL pathway augments the efficacy of chemotherapies. Kariolis MS et al. J Clin Invest. 2017, 127(1):183-198.. The MCL1 inhibitor S63845 is tolerable and effective in diverse cancer models. Kotschy A ...
Spectrin, the major component of the erythroid membrane skeleton, is a long, asymmetrical rodlike protein that interacts with several other proteins to form a two-dimensional membrane skeleton. Progress in several laboratories over the past few years including substantial partial peptide and nucleotide sequence determination has greatly enhanced our knowledge of the structural properties of this large molecule (heterodimer = 465,000 daltons). The alpha and beta subunits are homologous with approximately 30% identity. They are aligned in an antiparallel side-to-side orientation with the amino- and carboxy-termini near opposite physical ends of the molecule. The predominant structural feature elucidated from sequencing this large molecule is the nearly universal occurrence in both subunits of a single type of repetitive structure. The periodicity of this homologous structure is exactly 106 amino acid residues. As many as 36 homologous, but nonidentical, repeats exist and comprise more than 90% of ...
Autoantibodies to IA-2 in type 1 diabetes are associated with HLA-DR4, suggesting influences of HLA-DR4-restricted T cells on IA-2-specific B cell responses. The aim of this study was to investigate possible T-B cell collaboration by determining whether autoantibodies to IA-2 epitopes are associated with T cell responses to IA-2 peptides presented by DR4. T cells secreting the cytokines IFN-γ and IL-10 in response to seven peptides known to elicit T cell responses in type 1 diabetes were quantified by cytokine ELISPOT in HLA-typed patients characterized for Abs to IA-2 epitopes. T cell responses were detected to all peptides tested, but only IL-10 responses to 841-860 and 853-872 peptides were associated with DR4. Phenotyping by RT-PCR of FACS-sorted CD45RO(hi) T cells secreting IL-10 in response to these two peptides indicated that these expressed GATA-3 or T-bet, but not FOXP3, consistent with these being Th2 or Th1 memory T cells rather than of regulatory phenotype. T cell responses to the same two
Based on these observations and the results presented here, we propose a model for the functional diversification of duplicated members of transcription factor families (Fig. 5). After duplication of an ancestral gene X, one of the copies (Y) may accumulate mutations in the C-terminus, while retaining features such as DNA binding, essential for its function as a transcription factor, in the upstream coding regions. Apart from in frame insertions/deletions and single nucleotide substitutions, mutations in the coding sequence at the 3 end will also induce frameshifts, as such masking the ancestral origin of the motif at the protein level. While most frameshift mutations will be deleterious for the existing function, in specific cases they may yield novel functional C-terminal motifs. The three cases we have described are perfect examples of such a neo-functionalization process. This widens the emerging view that plant transcription factors evolve mainly by changes in cis-regulatory elements that ...
Rabbit polyclonal Guanine nucleotide-binding protein subunit beta-like protein antibody. Validated in WB and tested in Recombinant fragment. Immunogen corresponding to recombinant full length protein.
Alternative pre-mRNA splicing is a widespread mechanism contributing to the diversity of gene expression. The number of newly detected alternatively spliced transcripts has continuously risen, and distinct biological functions have been attributed to some protein isoforms resulting from these mRNA variants. We report on the detection of a novel alternatively spliced transcript of the human interleukin-4 receptor alpha (IL-4R-alpha) chain, which has been called IL-4R-alpha-IT mRNA. A premature stop codon due to omission of one exon in the membrane-proximal region of the cytoplasmic domain leads to an mRNA variant, which encodes an intracellular truncated receptor protein lacking domains which are essential for signal transduction. The investigation of the biological function of the IL-4Ra splice variants in a suitable mouse cell system showed, that the truncated receptor variant is not able to mediate cell proliferation or prevention of apoptosis. Bone marrow and peripheral blood samples from ...
Biochemical Roles of Eukaryotic Cell Surface Macromolecules By Abhijit Chakrabarti, Avadhesha Surolia 2015 | 424 Pages | ISBN: 3319112791 | PDF | 14 MB Biochemical Roles of Eukaryotic Cell S
This work demonstrates a highly nonrandom distribution of specific genes relative to nuclear domains enriched in splicing factors and poly(A)+ RNA, and provides evidence for the direct involvement of these in pre-mRNA metabolism. As investigated in hundreds of diploid fibroblasts, human collagen I alpha 1 and beta-actin DNA/RNA showed a very high degree of spatial association with SC-35 domains, whereas three nontranscribed genes, myosin heavy chain, neurotensin, and albumin, showed no such preferential association. Collagen I alpha 1 RNA accumulates within the more central region of the domain, whereas beta-actin RNA localizes at the periphery. A novel approach revealed that collagen RNA tracks are polarized, with the entire gene at one end, on the edge of the domain, and the RNA extending into the domain. Intron 26 is spliced within the RNA track at the domain periphery. Transcriptional inhibition studies show both the structure of the domain and the genes relationship to it are not dependent upon
A composite including a polymeric film having a first generally planar major surface and an opposite second major surface defined by a multiplicity of elongate parallel contiguous ridge portions. The ridge portions each have a generally triangular cross section and elongate obscured and transmitting second major surface portions intersecting at the apex of the ridge with the obscured second major surface portion being on the side of the ridge generally facing a first end of the sheet and the transmitting second major surface portions being on the side of the ridge portions adjacent a second end of the sheet. The film can provide visual transmission between its first major surface and the transmitting second major surface portions while coatings along the obscured second major surface portions prevent viewing of visual images through the film; whereas the composite can also provide light transmission between the first major surface and the transmitting second major surface portions, while the coatings
Find great deals for Progress in Polyamine Research: Novel Biochemical, Pharmacological, and Clinical Aspects by Springer-Verlag New York Inc. (Paperback, 2012). Shop with confidence on eBay!
This report addresses bacteria source tracking activities to support allocations of loadings. This report includes information on study area, characteristics, materials and methods of bacterial source tracking, and results and findings of the source tracking study ...
The strongest correlation between MYC and TCF7L2 expression was observed for assay "ex13-14" of TCF7L2 (r = 0.57- 0.60, p , 10-6), followed by assay "ex11-13" (r = 0.52-0.54, p , 10-6). The weakest correlation was detected for assay "ex11-13a" (r = 0.10 - 0.15, p = 0.12 - 0.28) (Table 1). These assays detect alternative splicing forms that include combinations of exons 11-13-14 and 11-13a-14 in the C-terminal end of the TCF7L2 transcripts (GenBank accession numbers FJ010174 and FJ010167). Both protein isoforms encoded by these splicing forms have long C-terminal reading frames (E-tails) with binding sites for the C-terminal binding protein (CtBP) involved in post-translational regulation of TCF7L2 expression [21, 22]. Protein fragments encoded by the alternative exons 13 and 13a share 68% identity (17 amino acids of 25, Figure 2). The form with exons 11-13-14 encodes a 30-amino-acid highly conserved motif with a CRAR F signature protein sequence, while in the form with exons 11-13a-14 this ...
multiple choice questions and answers on biology e.g. The chromosomes as thread like structures in nucleus was first described by:
Subject: Degenerate PCR...a complication.. From: Alejandro Abuin, aabuin at bcm.tmc.edu Date: 8 Feb 1994 15:42:01 GMT In article ,2j8bs9$pvg at gazette.bcm.tmc.edu, Alejandro Abuin, aabuin at bcm.tmc.edu writes: , Well, I want to do degenerate oligo PCR from a very conserved region of ,a particular cDNA in the mouse. My problem is that the region between my ,hypothetical degenerate primers has been conserved IN SIZE from E.coli to ,humans...and there probably are several genes belonging to this family in ,the mouse...(one so far cloned). , , If I do degenerate PCR across this region, it seems like all fragments ,will be of the same size, no matter what family member Im amplifying. ,The SIZE conservation is 100% from E.coli to humans, including yeast and ,the known mouse cDNA. How would you go about separating different species ,from a pool of PCR products of the same size? , , Any ideas would be greatly appreciated... , , Alex An interesting problem. You definitely need to incorporate some type ...
Edman degradation, N-terminal protein sequencing, was the method of choice for protein ID prior to the advent of mass spectrometry based ID. Edman degradation is still a very powerful technique. With Edman sequencing amino acids are cleaved from the N-terminus of a peptide or protein and each amino acid is then chromatographed using a 20 to 50 min HPLC gradient. Identification is based on correlating the retention time of the eluting amino acid to a standard chromatogram. The power of this technique is that the exact sequence can often be determined, and there is no confusion as in MS with amino acids having isobaric mass. The technique is simple and powerful and....slow and usually it only identifies one protein at a time. On average it takes about seven cycles of the sequencer to uniquely identify a protein in a sequence database, if you are running a 50 min gradient, thats about six hours! Identification of proteins by mass spectrometry uses peptide masses or the MS/MS fragmentation of a ...
THANK YOU DOUG! dont ya just love this contraption!!! Doug Neubauer wrote: , In article ,3ACC996B.CE408820 at Mail.TJU.Edu,, Mark.Haynes at Mail.TJU.Edu wrote: , ,Hello all, , ,I am looking for information about secondary markers (cd28, ctla4, , ,cd40l) on human T cells. I want to know what differences there are , ,between virgin and non-virgin Ts regarding expression. I know that , ,ctla4 is low to negligible unless the cell is stimulated and I plan to , ,compare un-stimulated to anti-cd3 stimulated but I dont know about the , ,other molecules. , ,If someone could send refs or point me to the answers I would be , ,grateful , ,thanx , ,markH. , ,I , , , , Not sure if this is what youre looking for, here are some articles , on phenotype/function vs. naive/effector/memory t cells: , , Functional differences between memory and naive CD8 T cells., , Cho, et al., Proc Natl Acad Sci USA 1999 Mar 16;96(6):2976-81 (PMID:10077622) , , T cell memory: heterogeneity and mechanisms., , Farber, Clin ...
Couthouis J, Hart MP, Shorter J, DeJesus-Hernandez M, Erion R, Oristano R, Liu AX, Ramos D, Jethava N, Hosangadi D, Epstein J, Chiang A, Diaz Z, Nakaya T, Ibrahim F, Kim HJ, Solski JA, Williams KL, Mojsilovic-Petrovic J, Ingre C, Boylan K, Graff-Radford NR, Dickson DW, Clay-Falcone D, Elman L, McCluskey L, Greene R, Kalb RG, Lee VM, Trojanowski JQ, Ludolph A, Robberecht W, Andersen PM, Nicholson GA, Blair IP, King OD, Bonini NM, Van Deerlin V, Rademakers R, Mourelatos Z, Gitler AD: A yeast functional screen predicts new candidate ALS disease genes. Proc Natl Acad Sci USA 108(52): 20881-90, Dec 2011 ...
Putative uncharacterized protein ITGA6 (Integrin, alpha 6, isoform CRA_b) contains a PF00357 domain.. Putative uncharacterized protein ITGA6 (Integrin, alpha 6, isoform CRA_b) contains a PF01839 domain.. Putative uncharacterized protein ITGA6 (Integrin, alpha 6, isoform CRA_b) contains a PF01839 domain.. Putative uncharacterized protein ITGA6 (Integrin, alpha 6, isoform CRA_b) contains a PF01839 domain.. Putative uncharacterized protein ITGA6 (Integrin, alpha 6, isoform CRA_b) contains a PF08441 domain.. Putative uncharacterized protein ITGA6 (Integrin, alpha 6, isoform CRA_b) is proteolytically cut by u-plasminogen activator (S01.231) cleavage. PSSR-RRVN.. ...
Not only do HCV quasispecies sequences express variability in different regions of the genomes, but isolates also differ among themselves. All isolates separate into phylogenetically-related clusters called subtypes. One or several subtypes can be classified into several major types that show similarities over 65-75% of the total genome. The term genotype is used generically to refer to subtypes, types or both. Use of the term genotype to describe quasispecies variants is not appropriate. Eleven HCV genomes are known to exist21 as well as more than 90 subtypes,22 with more subtypes being discovered at a continuous rate. 21. Several screening tests have been developed to identify HCV genotype, and include reverse hybridization line probe assay restriction fragment length polymorphism (RFLP) of the PCR amplicons, and nested PCR with genotype-specific parameters to the core region.. The optimal genotyping region is reported to be the 5 untranslated region (UR) because of high conservation ...
Typical steps in a complete analysis of gene expression. (by row): (1) Filtering empty spots; (2) double scan resolution; (3) Lowess estimation of parameters; (
It was noted recently that regions of homology to the NRSE occur within both the AVP and oxytocin coding and intronic regions, which were hypothetically suggested to play a role in hypothalamic transcriptional regulation (4) . However, the AVP NRSE-like motif we describe here is adjacent to the transcriptional start site. This mimics the structural architecture of the PPT gene, where the restricted, neuron-specific expression is mediated by a dominant repressor element located at the same position (8) . 4 We therefore predicted it would exert a major influence on transcription initiation. It was proposed recently that the NRSE can in fact have a dual function, as both silencer and enhancer, determined by the proximity of the motif to the TATA box (18) . Thus, the location of the NRSE-like motif in both the AVP and PPT promoters raises the possibility that, rather than acting solely as a repressor, this element could also mediate an enhancer function, as described recently for the nicotinic ...
The dual specificity tyrosine phosphorylated and regulated kinase (DYRK) family of protein kinases is a group of evolutionarily conserved protein kinases that have been characterized as regulators of growth and development in mammals, Drosophila and lower eukaryotes. In the present study, we have characterized three splicing variants of DYRK1B (DYRK1B-p65, DYRK1B-p69 and DYRK1B-p75) with different expression patterns and enzymic activities. DYRK1B-p65 and DYRK1B-p69 exhibited similar, but not identical, patterns of expression in mouse tissues, with the highest protein levels found in the spleen, lung, brain, bladder, stomach and testis. In contrast, DYRK1B-p75 was detected specifically in skeletal muscles, in the neuronal cell line GT1-7 and also in differentiated, adipocyte-like 3T3-L1 cells, but not in undifferentiated 3T3-L1 preadipocytes. A comparison of the mouse and human Dyrk1b genomic and cDNA sequences defined the alternative splicing events that produce the variants of DYRK1B. In ...
BioAssay record AID 2415 submitted by Johns Hopkins Ion Channel Center: Mode of Action - subtype specificity assay for ztz240, a potentiator of KCNQ2 potassium channels.
Genetic susceptibility to autoimmunity is frequently associated with specific MHC alleles. Diabetogenic MHC class II molecules, such as human HLA-DQ8 and mouse I-Ag7, typically have a small, uncharged amino acid residue at position 57 of their β chain (β57); this results in the absence of a salt bridge between β57 and Argα76, which is adjacent to the P9 pocket of the peptide-binding groove. However, the influence of Argα76 on the selection of the TCR repertoire remains unknown, particularly when the MHC molecule binds a peptide with a neutral amino acid residue at position P9. Here, we have shown that diabetogenic MHC class II molecules bound to a peptide with a neutral P9 residue primarily selected and expanded cells expressing TCRs bearing a negatively charged residue in the first segment of their complementarity determining region 3β. The crystal structure of one such TCR in complex with I-Ag7 bound to a peptide containing a neutral P9 residue revealed that a network of favorable ...
Looking for online definition of putative RNA-binding protein 11 in the Medical Dictionary? putative RNA-binding protein 11 explanation free. What is putative RNA-binding protein 11? Meaning of putative RNA-binding protein 11 medical term. What does putative RNA-binding protein 11 mean?
Looking for online definition of nonpolar amino acid in the Medical Dictionary? nonpolar amino acid explanation free. What is nonpolar amino acid? Meaning of nonpolar amino acid medical term. What does nonpolar amino acid mean?
Neck Pain Phillips, Chiropractic Treatment Phillips, Sciatic Nerve Pain Phillips, Advanced Chiropractic Phillips, Chiropracter Phillips, Stenosis Phillips, Chiropractic Clinic Phillips, Stiff Neck Phillips, Sciatic Nerve Phillips, Back Pain Phillips, Family Chiropractic Phillips, Slipped Disc Phillips, Chiropractor Phillips, Lower Back Pain Phillips, Sciatica Pain Relief Phillips, Chiropractor Near Me Phillips, Sciatica Symptoms Phillips, Spinal Stenosis Phillips, Herniated Disc Phillips, Chiropractor Massage Phillips, Sciatica Phillips, Best Chiropractor Phillips, Pediatric Chiropractor Phillips, Chiropractic Care Phillips, Pinched Nerve Phillips, Chiropractic Phillips, Chiropractic Adjustment Phillips
An accurate method based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been developed for quantitative analysis of calcitonin and insulin in different commercially available pharmaceutical products. Tryptic peptides derived from these polypeptides were chemically modified at their C-terminal lysine-residues with 2-methoxy-4,5-dihydro-imidazole (light tagging) as standard and deuterated 2-methoxy-4,5-dihydro-imidazole (heavy tagging) as internal standard (IS). The heavy modified tryptic peptides (4D-Lys tag), differed by four atomic mass units from the corresponding light labelled counterparts (4H-Lys tag). The normalized peak areas (the ratio between the light and heavy tagged peptides) were used to construct a standard curve to determine the concentration of the analytes. The concentrations of calcitonin and insulin content of the analyzed pharmaceutical products were accurately determined, and less than 5% error was obtained between the ...
BACKGROUND Sequence type 131 (ST131) is a predominant lineage among extraintestinal pathogenic Escherichia coli. It plays a major role in the worldwide dissemination of extended-spectrum β-lactamase (ESBL)-producing E. coli. The ST131 pandemic is mainly the result of clonal expansion of the single well-adapted subclone H30-Rx, which is acquired in hospitals more frequently than other ESBL-producing E. coli clones. AIM To develop a rapid method using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify ST131 for infection control purposes. METHODS Peak biomarkers of ST131 were identified from the mass spectrum profiles of 109 E. coli isolates (including 50 ST131 isolates). FINDINGS The models accurately identified ST131 isolates from mass spectrum profiles obtained with and without protein extraction. CONCLUSIONS The rapid identification of ST131 isolates with MALDI-TOF MS can be easily implemented in the laboratory, and could help to target
TY - JOUR. T1 - Partial nucleotide sequence of the Murray Valley encephalitis virus genome. Comparison of the encoded polypeptides with yellow fever virus structural and non-structural proteins. AU - Dalgarno, Lynn. AU - Trent, Dennis W.. AU - Strauss, James H.. AU - Rice, Charles M.. PY - 1986/2/5. Y1 - 1986/2/5. N2 - The sequence of 5400 bases corresponding to the 5′-terminal half of the Murray Valley encephalitis virus genome has been determined. The genome contains a 5′ non-coding region of about 97 nucleotides, followed by a single continuous open reading frame that encodes the structural proteins followed by the non-structural proteins. Amino acid sequence homology between the Murray Valley encephalitis and yellow fever (Rice et al., 1985) polyproteins is 42% over the region sequenced. The start points of the various Murray Valley encephalitis virus-coded proteins have been assigned on the basis of this homology and a consistent set of potential proteolytic cleavage sites identified, ...
TY - JOUR. T1 - The transmembrane sequence of human histocompatibility leukocyte antigen (HLA)-C as a determinant in inhibition of a subset of natural killer cells. AU - Davis, Daniel M.. AU - Mandelboim, Ofer. AU - Luque, Isabel. AU - Baba, Eishi. AU - Boyson, Jonathan. AU - Strominger, Jack L.. PY - 1999/4/19. Y1 - 1999/4/19. N2 - Molecular interactions with the extracellular domains of class I major histocompatibility complex proteins are major determinants of immune recognition that have been extensively studied both physically and biochemically. However, no immunological function has yet been placed on the transmembrane or cytoplasmic amino acid sequences of these proteins despite strict conservation of unique features within each class I major histocompatibility complex locus. Here we report that lysis by a subset of natural killer (NK) cells inhibited by target cell expression of human histocompatibility leukocyte antigen (HLA)-Cw6 or -Cw7 was not inhibited by expression of chimeric ...
In this paper, the taxonomy of the genus Arthrobacter is discussed, from its first description in 1947 to the present state. Emphasis is given to intrageneric phylogeny and chemotaxonomic characteristics, concentrating on quinone systems, peptidoglycan compositions and polar lipid profiles. Internal groups within the genus Arthrobacter indicated from homogeneous chemotaxonomic traits and corresponding to phylogenetic grouping and/or high 16S rRNA gene sequence similarities are highlighted. Furthermore, polar lipid profiles and quinone systems of selected species are shown, filling some gaps concerning these chemotaxonomic traits. Based on phylogenetic groupings, 16S rRNA gene sequence similarities and homogeneity in peptidoglycan types, quinone systems and polar lipid profiles, a description of the genus Arthrobacter sensu lato and an emended description of Arthrobacter roseus are provided. Furthermore, reclassifications of selected species of the genus Arthrobacter into novel genera are proposed,

The detection of linkage disequilibrium in molecular sequence data. | GeneticsThe detection of linkage disequilibrium in molecular sequence data. | Genetics

The detection of linkage disequilibrium in molecular sequence data. Message Subject (Your Name) has forwarded a page to you ... The detection of linkage disequilibrium in molecular sequence data.. R C Lewontin ... The detection of linkage disequilibrium in molecular sequence data.. R C Lewontin ... The detection of linkage disequilibrium in molecular sequence data.. R C Lewontin ...
more infohttps://www.genetics.org/content/140/1/377?ijkey=c09c9498d8e53981b1eacf519f770e83293a6cd1&keytype2=tf_ipsecsha

Experts and Doctors on molecular sequence data in Houston, United StatesExperts and Doctors on molecular sequence data in Houston, United States

Genomes and Genes about Experts and Doctors on molecular sequence data in Houston, United States ... You are here: Locale , United States , Texas , Experts and Doctors on molecular sequence data in Houston, United States ... Experts and Doctors on molecular sequence data in Houston, United States. Summary. Locale: Houston, United States ... Our data further support the notion of molecular heterogeneity of galactosemia and suggest that galactosemia mutations and GALT ...
more infohttp://www.labome.org/locale/united/texas/experts-and-doctors-on-molecular-sequence-data-in-houston--united-states-21797.html

SEView: a Java applet for browsing molecular sequence data - InfoscienceSEView: a Java applet for browsing molecular sequence data - Infoscience

Independence from the source datas format is achieved through a description language and ad hoc translators, which make the ... SEView is a Java applet that represents known or predicted elements of a protein or nucleotide sequence. It replaces or ... SEView: a Java applet for browsing molecular sequence data Junier, T. ; Bucher, P. ... SEView is a Java applet that represents known or predicted elements of a protein or nucleotide sequence. It replaces or ...
more infohttps://infoscience.epfl.ch/record/114865?ln=en

Geneious | Bioinformatics Solutions for the Analysis of Molecular Sequence DataGeneious | Bioinformatics Solutions for the Analysis of Molecular Sequence Data

Empowering you to achieve a mastery of biology with software that transforms biological data into knowledge and actionable ... A powerful and comprehensive suite of molecular biology and NGS analysis tools. ...
more infohttps://www.geneious.com/

Experts and Doctors on molecular sequence data in Cambridge, England, United KingdomExperts and Doctors on molecular sequence data in Cambridge, England, United Kingdom

Genomes and Genes about Experts and Doctors on molecular sequence data in Cambridge, England, United Kingdom ... You are here: Locale , United Kingdom , England , Experts and Doctors on molecular sequence data in Cambridge, England, United ... Experts and Doctors on molecular sequence data in Cambridge, England, United Kingdom. Summary. Locale: Cambridge, England, ... Genomic sequence analysis revealed a circular double-stranded DNA sequence of 157,834 bp, encoding 198 proteins and 3 tRNAs. ...
more infohttp://www.labome.org/locale/united/england/experts-and-doctors-on-molecular-sequence-data-in-cambridge--england--united-kingdom-24868.html

Bayesian hypothesis testing of four-taxon topologies using molecular sequence data. - Semantic ScholarBayesian hypothesis testing of four-taxon topologies using molecular sequence data. - Semantic Scholar

... develop Bayesian inference to determine the posterior probability that a four-taxon topology is correct given the sequence data ... The reconstruction of phylogenetic trees from molecular sequences presents unusual problems for statistical inference. For ... Bayesian hypothesis testing of four-taxon topologies using molecular sequence data.. *. Janet S. Sinsheimer, Jessica A Lake, ... article{Sinsheimer1996BayesianHT, title={Bayesian hypothesis testing of four-taxon topologies using molecular sequence data.}, ...
more infohttps://www.semanticscholar.org/paper/Bayesian-hypothesis-testing-of-four-taxon-topologi-Sinsheimer-Lake/ef225102073d649dbad37a623b9016751f199a20

EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth...EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth...

EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth ... EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth ... EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth ... EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth ...
more infohttp://dl.ndl.go.jp/info:ndljp/pid/10487822?tocOpenedNodeIds=info%3Andljp%2Fpid%2F10387530%7Cinfo%3Andljp%2Fpid%2F10389965%7Cinfo%3Andljp%2Fpid%2F10387530%3F20%2F2005%7Cinfo%3Andljp%2Fpid%2F10387530%3F20&viewMode=&tocOpenNodeId=info%3Andljp%2Fpid%2F10387530%3F20%2F2006

EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth...EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth...

EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth ... EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth ... EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth ... EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth ...
more infohttp://dl.ndl.go.jp/info:ndljp/pid/10487822?tocOpenedNodeIds=info%3Andljp%2Fpid%2F10387530%7Cinfo%3Andljp%2Fpid%2F10389965%7Cinfo%3Andljp%2Fpid%2F10387530%3F20%2F2005%7Cinfo%3Andljp%2Fpid%2F10387530%3F20&

Experts and Doctors on molecular sequence data in DenmarkExperts and Doctors on molecular sequence data in Denmark

Publications about Experts and Doctors on molecular sequence data in Denmark ... Experts and Doctors on molecular sequence data in Denmark. Summary. Locale: Denmark ... You are here: Locale , Experts and Doctors on molecular sequence data in Denmark ... The data suggest that the purified human GalNAc-transferase is a novel member of a family of polypeptide GalNAc-transferases, ...
more infohttp://labome.ru/locale/experts-and-doctors-on-molecular-sequence-data-in-denmark-21506.html

UCI Machine Learning Repository: Molecular Biology (Promoter Gene Sequences) Data Set: SupportUCI Machine Learning Repository: Molecular Biology (Promoter Gene Sequences) Data Set: Support

View ALL Data Sets Molecular Biology (Promoter Gene Sequences) Data Set Below are papers that cite this data set, with context ... Return to Molecular Biology (Promoter Gene Sequences) data set page. Ken Tang and Ponnuthurai N. Suganthan and Xi Yao and A. ... of real credit card transactions and two molecular biology sequence analysis data sets, were used in our experiments. The ... The six data sets are landsat, optdigits, vehicle, DNA thyroid disease and vowel data sets. Landsat. The Landsat data set is ...
more infohttp://archive.ics.uci.edu/ml/support/Molecular+Biology+

9781627035132: Deep Sequencing Data Analysis (Methods in Molecular Biology) - AbeBooks: 16270351339781627035132: Deep Sequencing Data Analysis (Methods in Molecular Biology) - AbeBooks: 1627035133

Methods in Molecular Biology) (9781627035132) and a great selection of similar New, Used and Collectible Books available now at ... 1. Deep Sequencing Data Analysis (Methods in Molecular Biology) Published by Humana Press (2013) ... Authoritative and practical, Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data ... Authoritative and practical, Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data ...
more infohttps://www.abebooks.com/9781627035132/Deep-Sequencing-Data-Analysis-Methods-1627035133/plp

Molecular biology: Coordination of sequence data<...Molecular biology: Coordination of sequence data<...

Molecular biology : Coordination of sequence data. / Lesk, Arthur.. In: Nature, Vol. 314, No. 6009, 01.12.1985, p. 318-319.. ... Molecular biology : Coordination of sequence data. In: Nature. 1985 ; Vol. 314, No. 6009. pp. 318-319. ... Molecular biology: Coordination of sequence data. Nature. 1985 Dec 1;314(6009):318-319. https://doi.org/10.1038/314318b0 ... Lesk, A. (1985). Molecular biology: Coordination of sequence data. Nature, 314(6009), 318-319. https://doi.org/10.1038/314318b0 ...
more infohttps://pennstate.pure.elsevier.com/en/publications/molecular-biology-coordination-of-sequence-data

Eurosurveillance | S-OtrH3N2 viruses: use of sequence data for description of the molecular characteristics of the viruses and...Eurosurveillance | S-OtrH3N2 viruses: use of sequence data for description of the molecular characteristics of the viruses and...

With the help of data generated from the World Health Organization Collaborating Centre for Reference and Research on Influenza ... S-OtrH3N2 viruses: use of sequence data for description of the molecular characteristics of the viruses and their relatedness ... S-OtrH3N2 viruses: use of sequence data for description of the molecular characteristics of the viruses and their relatedness ... 4 Institut Pasteur, Unit of Molecular Genetics of RNA Viruses, Department of Virology, Paris France 5 French National Centre ...
more infohttp://www.eurosurveillance.org/content/10.2807/ese.16.50.20039-en

A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards: From Sequencer to Electronic Health...A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards: From Sequencer to Electronic Health...

A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards: From Sequencer to Electronic Health ... A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards: From Sequencer to Electronic Health ... A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards : From Sequencer to Electronic Health ... title = "A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards: From Sequencer to ...
more infohttps://nebraska.pure.elsevier.com/en/publications/a-model-information-management-plan-for-molecular-pathology-seque

Molecular systematics of Craterellus: cladistic analysis of 
  nuclear LSU rDNA sequence data | Mycological Research |...Molecular systematics of Craterellus: cladistic analysis of nuclear LSU rDNA sequence data | Mycological Research |...

... nuclear LSU rDNA sequence data - Volume 104 Issue 4 - Mattias DAHLMAN, Eric DANELL, Joseph W. SPATAFORA ... Views captured on Cambridge Core between ,date,. This data will be updated every 24 hours. ... Molecular systematics of Craterellus: cladistic analysis of ...
more infohttps://www.cambridge.org/core/journals/mycological-research/article/molecular-systematics-of-craterellus-cladistic-analysis-of-nuclear-lsu-rdna-sequence-data/87B0E3412A7371F6374D681CEC708EE5

Abstract 5592: Molecular classification of triple negative breast cancer via RNA-sequencing data | Cancer ResearchAbstract 5592: Molecular classification of triple negative breast cancer via RNA-sequencing data | Cancer Research

Abstract 5592: Molecular classification of triple negative breast cancer via RNA-sequencing data. Kevin J. Thompson, Xiaojia ... Molecular classification of triple negative breast cancer via RNA-sequencing data. [abstract]. In: Proceedings of the 105th ... Abstract 5592: Molecular classification of triple negative breast cancer via RNA-sequencing data ... Abstract 5592: Molecular classification of triple negative breast cancer via RNA-sequencing data ...
more infohttp://cancerres.aacrjournals.org/content/74/19_Supplement/5592

DAMBE 5.3.48 - Sequence Data Analysis in Molecular Biology and EvolutionDAMBE 5.3.48 - Sequence Data Analysis in Molecular Biology and Evolution

... data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically ... Posted by admin at 8:32 am Tagged with: Analysis, DAMBE, Evolution, Molecular Biology, Sequence Data 2,645 views. Sorry, the ... DAMBE 5.3.48 - Sequence Data Analysis in Molecular Biology and Evolution. DNA / Genome Analysis ... Molecular Biology and Evolution 30:1720-1728. Xia, X., and Xie. Z., 2001. DAMBE: Data analysis in molecular biology and ...
more infohttp://www.mybiosoftware.com/dambe-5-2-31-sequence-data-analysis-molecular-biology-evolution.html

BIOINFTool: Bioinformatics and sequence data analysis in molecular biology using MatlabBIOINFTool: Bioinformatics and sequence data analysis in molecular biology using Matlab

... Mabrouk, Mai S.; Hamdy, Marwa; Mamdouh ... BIOINFTool: Bioinformatics and sequence data analysis in molecular biology using Matlab. Login ... genome sequences, and gene expression data. Techniques developed by computer scientists have enabled researchers at Celera ... resources that aid in the analysis of data. We can use these tools to analyze the data and interpret the results in a ...
more infohttp://dspace.must.edu.eg/handle/123456789/222

In silico discovery of human natural anti... & related info | MendeleyIn silico discovery of human natural anti... & related info | Mendeley

Molecular Sequence Data. *Proteome/*genetics. *RNA, Antisense/*genetics. *Sequence Alignment/*methods. *Sequence Analysis, RNA ... Based on microarray data from Stanford Microarray Database, two hNAT pairs were found to display significant inverse expression ... RESULTS: We have identified 568 NATs from human RefSeq RNA sequences. Among them, 403 NATs are reported for the first time, and ... UTR sequences, supporting the regulatory role of UTRs. Among a total of 535 NAT pairs related with splice variants, 77.4% (414/ ...
more infohttps://www.mendeley.com/research-papers/silico-discovery-human-natural-antisense-transcripts/

Three distinct types of GnRH rece... preview & related info | MendeleyThree distinct types of GnRH rece... preview & related info | Mendeley

Here we present data demonstrating that at least three types of GnRHR are expressed in a single... ... Molecular Sequence Data. *Pituitary Gland. *Pituitary Gland: chemistry. *Protein Isoforms. *Protein Isoforms: chemistry ... Here we present data demonstrating that at least three types of GnRHR are expressed in a single diploid species, the bullfrog. ...
more infohttps://www.mendeley.com/research-papers/three-distinct-types-gnrh-receptor-characterized-bullfrog/

The Master Registry of Oncology Outcomes Associated With Testing and Treatment - Full Text View - ClinicalTrials.govThe Master Registry of Oncology Outcomes Associated With Testing and Treatment - Full Text View - ClinicalTrials.gov

Molecular Sequence Data. Databases, Genetic. High-Throughput Nucleotide Sequencing. Massively-Parallel Sequencing. ... Real-world data in the molecular era-finding the reality in the real world. Clin Pharmacol Ther. 2016 Feb;99(2):186-97. doi: ... This is a multi-institutional effort to aggregate detailed genetic (and molecular) data in connection with treatments and ... Any patient whose tumor has been sequencing using a multiplex method such as next-generation sequencing including hot-spot, ...
more infohttps://clinicaltrials.gov/ct2/show/NCT04028479?term=adenoid+cystic+carcinoma&

Predicting demographic group structures based on DNA sequence data. | Mullins Molecular Retrovirology LabPredicting demographic group structures based on DNA sequence data. | Mullins Molecular Retrovirology Lab

Predicting demographic group structures based on DNA sequence data. Molecular biology and evolution. , 20(7), 1168-80. (pubmed) ... Several studies have focused on the evolution of HIV-1, but there is little information to link sequence similarities and ... Using standard phylogenetic and phenetic techniques on 100 HIV-1 subtype B sequences, we were able to show some correlation ... The ability to infer relationships between groups of sequences, either by searching for their evolutionary history or by ...
more infohttps://mullinslab.microbiol.washington.edu/publications/640-Predicting-demographic-group-structures-based-on-DNA-sequence-data

A. Jonathan Shaw, Professor of Biology and Curator of Bryophytes, Duke HerbariumA. Jonathan Shaw, Professor of Biology and Curator of Bryophytes, Duke Herbarium

Molecular Sequence Data • Mosses • Mutation • New York • New Zealand • North America • Ovule • Phylogeny • Phytochrome • Plant ... We utilize DNA sequence data from the nuclear, chloroplast, and mitochondrial genomes to infer historical processes of ... Our data base presently includes nucleotide sequences from multiple loci representing some 500-600 accessions of peatmosses. ... Sequence Alignment • Sequence Analysis, DNA • Soil • Species Specificity • Sphagnopsida • Transcriptome • Tropical Climate. ...
more infohttp://fds.duke.edu/db/aas/Herbarium/brophytes/shaw

Francois M. Lutzoni, Professor of Biology and Curator of Lichens, Duke HerbariumFrancois M. Lutzoni, Professor of Biology and Curator of Lichens, Duke Herbarium

Molecular Sequence Data • North America • North Carolina • Open Reading Frames • Panama • Parmeliaceae • Pattern Recognition, ... Sequence Alignment • Sequence Analysis, DNA • Sequence Homology • Sequence Homology, Nucleic Acid • Software • Species ... Rydholm, C; Dyer, PS; Lutzoni, F, DNA sequence characterization and molecular evolution of MAT1 and MAT2 mating-type loci of ... Automatic Data Processing • Bacteria • Base Sequence • Bayes Theorem • Biodiversity • Biological Evolution • British Columbia ...
more infohttps://fds.duke.edu/db/aas/Herbarium/francois.lutzoni
  • ITHACA, N.Y.--( BUSINESS WIRE )-- Rheonix Inc. , a developer of fully automated molecular testing solutions, will highlight its Encompass Optimum ™ workstation at the Association for Molecular Pathology (AMP) Annual Meeting Nov. 10-12 in Charlotte, North Carolina. (businesswire.com)
  • abstract = "Incorporating genetic variant data into the electronic health record (EHR) in discrete computable fashion has vexed the informatics community for years. (elsevier.com)
  • Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of necessary materials and reagents, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls. (abebooks.com)
  • Using tree construction, MDS, and newly developed likelihood assignment methods on the original 100 samples we sequenced, and also on a set of blinded samples, we were able to predict demographic/risk group membership at a rate statistically better than by chance alone. (washington.edu)
  • 2008. (Methods in Molecular Biology, Volume 452). (koeltz.com)
  • When sequenced on the Illumina platform, the resulting libraries yielded NGS sequence data indistinguishable from the labor-intensive methods previously employed by the facility. (businesswire.com)
  • These membranes are then probed as many times as there are types of tags in the original pools, producing, in each cycle of probing, autoradiographs similar to those from standard DNA sequencing methods. (harvard.edu)
  • It is shown that more power can be achieved by increasing the length of sequence determined than by increasing the number of genomes sampled for the same total work. (genetics.org)
  • Interpreting relationships of human immunodeficiency virus type 1 (HIV-1) sequences can be challenging because of their rapidly evolving genomes, but it may also lead to a better understanding of the underlying biology. (washington.edu)
  • We utilize DNA sequence data from the nuclear, chloroplast, and mitochondrial genomes to infer historical processes of biodiversification. (duke.edu)
  • The ability to infer relationships between groups of sequences, either by searching for their evolutionary history or by comparing their sequence similarity, can be a crucial step in hypothesis testing. (washington.edu)
  • With the help of data generated from the World Health Organization Collaborating Centre for Reference and Research on Influenza at the United States Centers for Disease Control and Prevention*, we provide here information on the swine-origin triple reassortant influenza A(H3N2) viruses detected in human cases in the north-east of the United States. (eurosurveillance.org)
  • Includes a daily case report and sequence summary for Influenza A (H1N1). (dmoztools.net)
  • Overview of influenza, case definitions, vaccine information (including the Influenza Vaccination Pocket Information Guide), and surveillance data with influenza activity levels. (dmoztools.net)
  • Lina B , Bouscambert M , Enouf V , Rousset D , Valette M , van der Werf S . S-OtrH3N2 viruses: use of sequence data for description of the molecular characteristics of the viruses and their relatedness to previously circulating H3N2 human viruses. (eurosurveillance.org)
  • Such predictions of demographic epidemiology based on sequence information may become valuable in assigning different treatment regimens to infected individuals. (washington.edu)
  • That method identified statistically significant correlations between the viral sequences and the risk factors of men who engage in sex with men and individuals who engage in sex with injection drug users or use injection drugs themselves. (washington.edu)
  • The detection of linkage disequilibrium in molecular sequence data. (genetics.org)
  • once the raw specimen is loaded, the fully automated, high-efficiency system performs all sample preparation and molecular detection on the workstation. (businesswire.com)
  • Third, the molecular laboratory is challenged to monitor its sequencing processes for nonrandom process variation and other quality metrics. (elsevier.com)
  • Bayesian hypothesis testing of four-taxon topologies using molecular sequence data. (semanticscholar.org)
  • The aim of this work is to organize data in a way that allows researchers to access existing information and to submit new entries as they are produced. (must.edu.eg)
  • For TNBC patients who fail standard chemotherapy, there are a lack of novel drug therapies, given the absence of well-defined molecular targets. (aacrjournals.org)
  • Dr. Montagna will present data showing use of the Rheonix Chemistry and Reagent Device (CARD ® ) technology in a user-defined molecular assay that simultaneously detects 20 targets for STIs. (businesswire.com)
  • Studies of genetic variation in natural populations at the sequence level usually show that most polymorphic sites are very asymmetrical in allele frequencies, with the rarer allele at a site near fixation. (genetics.org)
  • As a result, clinicians often struggle to find historical gene sequence results on a series of oncology patients within the EHR that might influence the care of the current patient. (elsevier.com)
  • This is a multi-institutional effort to aggregate detailed genetic (and molecular) data in connection with treatments and physician reported outcomes in patients with advanced cancer. (clinicaltrials.gov)
  • and Boosting won the best accuracy on 4 data sets (i.e., hepatitis, lymph, sick and splice). (uci.edu)
  • These included techniques for compressing of data generated, Chromatin Immunoprecipitation (ChIP-seq), and various approaches for the identification of sequence variants. (abebooks.com)
  • The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) apparatuses which, in essence, read billions of nucleotides per reaction. (abebooks.com)
  • Rheonix will present data from a user-defined assay for sexually transmitted infections (STIs), as well as data that demonstrates new capabilities of its system in next-generation sequencing (NGS) library preparation. (businesswire.com)
  • Johansson, Ulf S. & Ericson, Per G. P. (2003): Molecular support for a sister group relationship between Pici and Galbulae (Piciformes sensu Wetmore 1960). (wikipedia.org)
  • The collections represent a central resource for bryological research at Duke, and we are actively integrating molecular investigations with field work and collections- based approaches. (duke.edu)
  • Data generated by this effort demonstrates that, in addition to detecting the presence of viral RNA, the system can distinguish early immunoglobulin M (IgM) antibodies from late immunoglobulin G (IgG) antibodies, thus providing more information on a patient's stage of infection. (businesswire.com)
  • The increasing demand for DNA sequences can be met by replacement of each DNA sample in a device with a mixture of N samples so that the normal throughput is increased by a factor of N. Such a method is described. (harvard.edu)
  • Study record managers: refer to the Data Element Definitions if submitting registration or results information. (clinicaltrials.gov)
  • Report of a study on the need for a global surveillance program to provide data needed for allocation of scarce healthcare resources. (dmoztools.net)
  • An article authored by Montagna, " Automating Molecular LDTs ," was featured in the October issue of Clinical Lab Products . (businesswire.com)
  • To help identify more subtle relationships between the viral sequences, the method of multidimensional scaling (MDS) was performed. (washington.edu)