The relationships of groups of organisms as reflected by their genetic makeup.
A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Sequential operating programs and data which instruct the functioning of a digital computer.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
Genotypic differences observed among individuals in a population.
In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Computer-based representation of physical systems and phenomena such as chemical processes.
The systematic study of the complete DNA sequences (GENOME) of organisms.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
Databases devoted to knowledge about specific genes and gene products.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.
A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
The genetic complement of a BACTERIA as represented in its DNA.
Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
A field of study concerned with the principles and processes governing the geographic distributions of genealogical lineages, especially those within and among closely related species. (Avise, J.C., Phylogeography: The History and Formation of Species. Harvard University Press, 2000)
A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
The genetic complement of MITOCHONDRIA as represented in their DNA.
The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Any method used for determining the location of and relative distances between genes on a chromosome.
The genomic analysis of assemblages of organisms.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Deoxyribonucleic acid that makes up the genetic material of plants.
Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.
The portion of an interactive computer program that issues messages to and receives commands from a user.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
That part of the genome that corresponds to the complete complement of EXONS of an organism or cell.
The genetic complement of a plant (PLANTS) as represented in its DNA.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.
Deoxyribonucleic acid that makes up the genetic material of fungi.
The splitting of an ancestral species into daughter species that coexist in time (King, Dictionary of Genetics, 6th ed). Causal factors may include geographic isolation, HABITAT geometry, migration, REPRODUCTIVE ISOLATION, random GENETIC DRIFT and MUTATION.
A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.
The functional hereditary units of BACTERIA.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.
Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
Organized activities related to the storage, location, search, and retrieval of information.
Software designed to store, manipulate, manage, and control data for specific uses.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)
Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Information application based on a variety of coding methods to minimize the amount of data to be stored, retrieved, or transmitted. Data compression can be applied to various forms of data, such as images and signals. It is used to reduce costs and increase efficiency in the maintenance of large volumes of data.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
A phylum of fungi which have cross-walls or septa in the mycelium. The perfect state is characterized by the formation of a saclike cell (ascus) containing ascospores. Most pathogenic fungi with a known perfect state belong to this phylum.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
Members of the group of vascular plants which bear flowers. They are differentiated from GYMNOSPERMS by their production of seeds within a closed chamber (OVARY, PLANT). The Angiosperms division is composed of two classes, the monocotyledons (Liliopsida) and dicotyledons (Magnoliopsida). Angiosperms represent approximately 80% of all known living plants.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Self-replicating cytoplasmic organelles of plant and algal cells that contain pigments and may synthesize and accumulate various substances. PLASTID GENOMES are used in phylogenetic studies.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
The functional hereditary units of PLANTS.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
The change in gene frequency in a population due to migration of gametes or individuals (ANIMAL MIGRATION) across population barriers. In contrast, in GENETIC DRIFT the cause of gene frequency changes are not a result of population or gamete movement.
Proteins found in any species of bacterium.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
A collective genome representative of the many organisms, primarily microorganisms, existing in a community.
The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.
A large, subclass of arachnids comprising the MITES and TICKS, including parasites of plants, animals, and humans, as well as several important disease vectors.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
Procedures for identifying types and strains of fungi.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.
DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.
Techniques for standardizing and expediting taxonomic identification or classification of organisms that are based on deciphering the sequence of one or a few regions of DNA known as the "DNA barcode".
The sequential location of genes on a chromosome.
Integrated set of files, procedures, and equipment for the storage, manipulation, and retrieval of information.
Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.
The variety of all native living organisms and their various forms and interrelationships.
An optical disk storage system for computers on which data can be read or from which data can be retrieved but not entered or modified. A CD-ROM unit is almost identical to the compact disk playback device for home use.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
A genus of the family Lemuridae consisting of five species: L. catta (ring-tailed lemur), L. fulvus, L. macaco (acoumba or black lemur), L. mongoz (mongoose lemur), and L. variegatus (white lemur). Most members of this genus occur in forested areas on Madagascar and the Comoro Islands.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Short tracts of DNA sequence that are used as landmarks in GENOME mapping. In most instances, 200 to 500 base pairs of sequence define a Sequence Tagged Site (STS) that is operationally unique in the human genome (i.e., can be specifically detected by the polymerase chain reaction in the presence of all other genomic sequences). The overwhelming advantage of STSs over mapping landmarks defined in other ways is that the means of testing for the presence of a particular STS can be completely described as information in a database.
Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)
The genetic complement of CHLOROPLASTS as represented in their DNA.
The application of molecular biology to the answering of epidemiological questions. The examination of patterns of changes in DNA to implicate particular carcinogens and the use of molecular markers to predict which individuals are at highest risk for a disease are common examples.
A phylum of fungi that produce their sexual spores (basidiospores) on the outside of the basidium. It includes forms commonly known as mushrooms, boletes, puffballs, earthstars, stinkhorns, bird's-nest fungi, jelly fungi, bracket or shelf fungi, and rust and smut fungi.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
The fruiting 'heads' or 'caps' of FUNGI, which as a food item are familiarly known as MUSHROOMS, that contain the FUNGAL SPORES.
The number of mutations that occur in a specific sequence, GENE, or GENOME over a specified period of time such as years, CELL DIVISIONS, or generations.
The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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TY - JOUR. T1 - A new usage of functionalized oligodeoxynucleotide probe for site-specific modification of a guanine base within RNA. AU - Onizuka, Kazumitsu. AU - Taniguchi, Yosuke. AU - Sasaki, Shigeki. PY - 2010/1/29. Y1 - 2010/1/29. N2 - Site-specific modification of RNA is of great significance to investigate RNA structure, function and dynamics. Recently, we reported a new method for sequence-and cytosine-selective chemical modification of RNA based on the functional group transfer reaction of the 1-phenyl-2-methylydene-1,3-diketone unit of the 6-thioguanosine base incorporated in the oligodeoxynucleotide probe. In this study, we describe that the functionality transfer rate is greatly enhanced and the selectivity is shifted to the guanine base when the reaction is performed under alkaline conditions. Detailed investigation indicated that the 2-amino group of the enolate form of rG is the reactant of the functionality transfer reaction. As a potential application of this efficient ...
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 ...
A New Approach for DNA Sequence Similarity Analysis based on Triplets of Nucleic Acid Bases: 10.4018/978-1-60960-064-8.ch006: Similarity analysis of DNA sequences is a fundamental research area in Bioinformatics. The characteristic distribution of L-tuple, which is the tuple of
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, ...
Using rigorous statistical methods, we have identified and evaluated unusual properties of the distribution of charged residues within the sequences of eukaryotic cellular transcription factors. Virtually all transcription factors, including GAL4, c-Jun, C/EBP, CREB, Oct-1, Oct-2, Sp1, Egr-1, CTF-1, steroid and thyroid hormone receptors, and others, carry one or more highly significant charge clusters. For the most part these clusters (conserved within families of homologous proteins) are of positive net charge but contain also substantial numbers of acidic residues. Predominantly basic charge clusters are often, but not exclusively, associated with DNA-binding domains, and vice versa. Negative charge clusters of note occur only in the yeast protein PHO4 and in the proteins encoded at the Drosophila loci zeste (zeta) and knrl. This dearth of statistically significant negative charge clusters raises questions with respect to the generality of acidic activation domains. A number of sequences ...
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 ...
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
The majority of mammalian genes produce multiple transcripts resulting from alternative splicing (AS) and/or alternative transcription initiation (ATI) and alternative transcription termination (ATT). Comparative analysis of the number of alternative nucleotides, isoforms, and introns per locus in genes with different types of alternative events suggests that ATI and ATT contribute to the diversity of human and mouse transcriptome even more than AS. There is a strong negative correlation between AS and ATI in 5′ untranslated regions (UTRs) and AS in coding sequences (CDSs) but an even stronger positive correlation between AS in CDSs and ATT in 3′ UTRs. These observations could reflect preferential regulation of distinct, large groups of genes by different mechanisms: 1) regulation at the level of transcription initiation and initiation of translation resulting from ATI and AS in 5′ UTRs and 2) posttranslational regulation by different protein isoforms. The tight linkage between AS in CDSs ...
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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 ...
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 ...
Many receptors involved in clathrin-mediated protein transport through the endocytic and secretory pathways of yeast and animal cells share common features. They are all type I integral membrane proteins containing cysteine-rich lumenal domains and cytoplasmic tails with tyrosine-containing sorting signals. The cysteine-rich domains are thought to be involved in ligand binding, whereas the cytoplasmic tyrosine motifs interact with clathrin-associated adaptor proteins during protein sorting along these pathways. In addition, tyrosine-containing signals are required for the retention and recycling of some of these membrane proteins to the trans-Golgi network. Here we report the characterization of an approximately 80-kD epidermal growth factor receptor-like type I integral membrane protein containing all of these functional motifs from Arabidopsis thaliana (called AtELP for A. thaliana Epidermal growth factor receptor-Like Protein). Biochemical analysis indicates that AtELP is a membrane protein ...
TY - JOUR. T1 - Potential bias of fungal 18S rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil. AU - Anderson, Ian C. AU - Campbell, C. D.. AU - Prosser, James Ivor. PY - 2003. Y1 - 2003. N2 - Four fungal 18S rDNA and internal transcribed spacer (ITS) polymerase chain reaction (PCR) primer pairs were tested for their specificity towards target fungal DNA in soil DNA extracts, and their ability to assess the diversity of fungal communities in a natural grassland soil was compared. Amplified PCR products were cloned, and approximate to 50 clones from each library were sequenced. Phylogenetic analysis and database searches indicated that each of the sequenced cloned DNA fragments was of fungal origin for each primer pair, with the exception of the sequences generated using the 18S rDNA primers nu-SSU-0817 and nu-SSU-1196, where 35 of the 50 sequenced clones represented soil invertebrates. Although some of the primers have previously ...
By directed mutagenesis, we constructed a set of seven TEM-1 derivatives containing single replacements in each one of the amino acids substituted in naturally occurring extended-spectrum TEM beta-lactamases. The exact contribution of each mutation to the resistance phenotype was determined. In addition, mutant enzyme production and stabilities were studied. Five of seven mutations determined to some extent variations in cephalosporin and/or monobactam activity. Dramatic changes in the hydrolysis of ceftazidime and aztreonam occurred when a serine was at position 164. Changes at positions 104, 238, and 240 showed more leaky variation in activity towards cephalosporins and aztreonam. Replacements at positions 237 and 265 caused no variation in susceptibility to cephalosporins. Interestingly, the change from Gln to Lys at position 39 found in TEM-2, classically considered a neutral change, slightly but consistently increased the MIC of ceftazidime and aztreonam. The in vitro construction of ...
Three members of Brassica napus TRANSPARENT TESTA 2 (BnTT2) gene family encoding potential R2R3-MYB regulatory proteins of proanthocyanidin biosynthesis were isolated. BnTT2-1, BnTT2-2, and BnTT2-3 are 1102 bp with two introns, and have a 938-bp full-length cDNA with a 260 amino acid open reading frame. They share 98.2-99.3% nucleotide and 96.5-98.5% amino acid identities to each other, and are orthologous to Arabidopsis thaliana TT2 (AtTT2) with 74.1-74.8% nucleotide and 71.1-71.8% amino acid identities. An mRNA type of BnTT2-2 was found to contain unspliced intron 2 and encode a premature protein. They all have an alternative polyadenylation site. BnTT2-1 and BnTT2-3 also have an alternative transcription initiation site. Aligned with AtTT2, their 5 untranslated regions (UTRs) are astonishingly conserved, and two conserved regions were also found in their 3 UTRs. Oligonucleotide deletion leads to double-start codons of them. Resembling AtTT2, BnTT2 proteins are nuclear-located R2R3-MYB ...
The 54-kDa subunit of the mammalian signal recognition particle (SRP54) binds to the signal sequences of nascent secretory and transmembrane proteins and facilitates their cotranslational targeting to the membrane translocation apparatus in the endoplasmic reticulum (ER). A 48-kDa Escherichia coli protein that shares extensive sequence similarity with SRP54 was identified in homology searches. Recent genetic experiments by Phillips and Silhavy [Phillips, G. J. & Silhavy, T. J. (1992) Nature (London) 359, 744-746] have shown that depletion of this protein, designated Ffh (fifty-four homolog), leads to a significant secretory defect in vivo. We demonstrate here that Ffh is structurally and functionally related to SRP54 by virtue of its ability to mimic closely its mammalian counterpart in several established biochemical assays, thereby suggesting that it plays a direct role in protein export. Ffh assembled efficiently with mammalian SRP components into a chimeric ribonucleoprotein [SRP(Ffh)] and ...
TY - JOUR. T1 - Characterization of a family of related cellular transcription factors which can modulate human immunodeficiency virus type 1 transcription in vitro. AU - Yoon, Jong-Bok. AU - Li, Gen. AU - Roeder, Robert G.. PY - 1994/1/1. Y1 - 1994/1/1. N2 - LBP-1 is a cellular protein which binds strongly to sequences around the human immunodeficiency virus type 1 (HIV-1) initiation site and weakly over the TATA box. We have previously shown that LBP-1 represses HIV-1 transcription by inhibiting the binding of TFIID to the TATA box. Four similar but distinct cDNAs encoding LBP-1 (LBP-1a, -b, -c, and -d) have been isolated. These are products of two related genes, and each gene encodes two alternatively spliced products. Comparison of the amino acid sequence of LBP- 1 with entries in the available protein data bases revealed the identity of LBP-1c to α-CP2, an α-globin transcription factor. These proteins are also homologous to Drosophila melanogaster Elf-1/NTF-1, an essential transcriptional ...
Inverse polymerase chain reaction (Inverse PCR) is a variant of the polymerase chain reaction that is used to amplify DNA with only one known sequence. One limitation of conventional PCR is that it requires primers complementary to both termini of the target DNA, but this method allows PCR to be carried out even if only one sequence is available from which primers may be designed. Inverse PCR is especially useful for the determination of insert locations. For example, various retroviruses and transposons randomly integrate into genomic DNA. To identify the sites where they have entered, the known, internal viral or transposon sequences can be used to design primers that will amplify a small portion of the flanking, external genomic DNA. The amplified product can then be sequenced and compared with DNA databases to locate the sequence which has been disrupted. The inverse PCR method involves a series of restriction digests and ligation, resulting in a looped fragment that can be primed for ...
Chang, E., et al. N-Terminal Amino Acid Sequence Determination of Proteins by N-Terminal Dimethyl Labeling: Pitfalls and Advantages When Compared with Edman Degradation Sequence Analysis. Journal of Biomolecular Technology. 27(2). 07/03/2016.. ...
Proteins (/ˈproʊˌtiːnz/ or /ˈproʊti.ɪnz/) are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific three-dimensional structure that determines its activity.. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino ...
The invention provides a method for determining an amino acid sequence motif for a phosphorylation site of a protein kinase. In the method of the invention, a protein kinase is contacted with an oriented degenerate peptide library, peptides within the library which are substrates for the kinase are converted to phosphopeptides and the phosphopeptides are separated from non-phosphorylated peptides. The isolated phosphopeptides are sequenced and an amino acid sequence motif for the phosphorylation site is determined based upon the relative abundance of different amino acids residues at each degenerate position. The invention also provides peptide substrates for protein kinase A, cell cycle control kinases, src family kinases, the EGF receptor and p92.sup.c-fps/fes based upon amino acid sequence motifs for the phosphorylation sites of these kinases.
Purified glucocorticoid receptorhormone complex from rat liver cytosol binds specifically to cloned mouse mammary tumor virus long terminal repeats in vitro. Proc Natl Acad Sci USA 1982; 79:5157-61. Moore DD, Marks AR, Buckley DI, Kapler G, Payvar F, Goodman HM. The first intron of the human growth hormone gene contains a binding site for glucocorticoid receptor. Proc Natl Acad Sci USA 1985; 82:699-702. Bechet D. Control of gene expression by steroid hormones. Reprod Nutr Develop 1986; 26:1025-55. Endocrinology 1981; 108:1533-7. King WJ, DeSombre ER, Jensen EV, Greene GL. Comparison of immunocytochemical and steroid-bind:ing assays for estrogen receptor in human breast tumors. Cancer Res 1985; 45:293-304. Pertschuk LP, Eisenberg KB, Carter AC, Fcldman JG. Immunohistologic localization of estrogen receptors in breast cancer with monoclonal antibodies. Cancer 1985; 55:1513-8. Perrot-Applanat M, Groyer-Picard MT, Lorenzo F, et al. Immunocytochemical study with monoclonal antibodies to progesterone ...
A cDNA library prepared from the mouse osteoblastic cell line MC3T3-E1 was screened for the presence of specifically expressed genes by employing a combined subtraction hybridization/differential screening approach. A cDNA was identified and sequenced which encodes a protein designated osteoblast-specific factor 2 (OSF-2) comprising 811 amino acids. OSF-2 has a typical signal sequence, followed by a cysteine-rich domain, a fourfold repeated domain and a C-terminal domain. The protein lacks a typical transmembrane region. The fourfold repeated domain of OSF-2 shows homology with the insect protein fasciclin I. RNA analyses revealed that OSF-2 is expressed in bone and to a lesser extent in lung, but not in other tissues. Mouse OSF-2 cDNA was subsequently used as a probe to clone the human counterpart. Mouse and human OSF-2 show a high amino acid sequence conservation except for the signal sequence and two regions in the C-terminal domain in which in-frame insertions or deletions are observed, ...
Preparation of LPA Receptor cDNA Plasmids and Expression. The entire coding regions of LPA1 (1,095 bp, GenBank accession number Y09479), LPA2 (1,149 bp, GenBank accession number AF011466), and LPA3 (1,148 bp, GenBank accession number AF127138) were amplified from human cDNA library by RT-PCR. The respective amplified fragment was subcloned into the EcoRI site of pEFneo eukaryotic expression vector (Kon et al., 1999; Sato et al., 2000), and each DNA sequence was confirmed. The primers used for the RT-PCR were as follows. The 5′primers contained an EcoRI site, a Kozak sequence (CCACC), and the N-terminal region of the respective receptor. The 3′-primers contained an EcoRI site and a stop codon in addition to the C-terminal region of the respective receptor. CHO cells or RH7777 cells were transfected with pEFneo empty vector alone or the pEFneo vector containing human LPA1, human LPA2, or human LPA3 by electroporation, and the neomycin-resistant cells (G418 sulfate at 1 mg/ml for CHO cells and ...
The complete nucleotide sequence of an isolate of puma lentivirus (PLV-14) was obtained by an inverse polymerase chain reaction (I-PCR) technique and confirmed by conventional PCR. Both methods were used to amplify overlapping regions of proviral DNA, for cloning and sequencing, from genomic DNA isolated from PLV-14 infected Florida puma (Felis concolor coryi) peripheral blood mononuclear cells (PBMC). The provirus has a total length of 9100 nucleotides and the genomic organization of presumed protein coding regions are similar to those seen in other members of the lentivirus family, i.e., three large open reading frames gag, pol, and env as well as smaller intergenic regions that apparently encode regulatory proteins vif and 3′ rev by positional and sequence similarity to those seen in other lentiviruses. Two additional open reading frames were identified in the env region and their function (if any) is unknown. The length of the PLY-14 long terminal repeat (LTR) was found to be shorter than the LTRs
37 CFR 1.822(c)(5) provides that nucleotide sequences shall only be represented by a single strand, in the 5′ to 3′ direction, from left to right. That is, double stranded nucleotides shall not be represented in the sequence listing. A double stranded nucleotide may be represented as two single stranded nucleotides, and any relationship between the two may be shown in the drawings. The procedures for presenting and numbering amino acid sequences are set forth in 37 CFR 1.822(d). Two alternatives are presented for numbering amino acid sequences. Amino acid sequences may be numbered with respect to the identification of the first amino acid of the first mature protein or with respect to the first amino acid appearing at the amino terminal. The numbering procedure for nucleotides is set forth in 37 CFR 1.822(c)(6). Sequences that are circular in configuration are intended to be encompassed by these rules, and the numbering procedures described above remain applicable with the exception that the ...
CombAlign is a new Python code that generates a gapped, multiple structure-based sequence alignment (MSSA) given a set of pairwise structure-based sequence alignments. CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related structures. The method for combining multiple pairwise alignments is straightforward, involving the recording of pre-computed residue-residue correspondences between positions on the reference protein and each compared structure, and insertion of non-redundant gaps, as needed, to reflect amino-acid deletions or structural divergence in the reference relative to one or more compared structures.. CombAlign is not intended for use in applications for which greater benefit would be provided using a multiple structure alignment as generated by the vast majority of open-source programs [20], nor does it propose to address matters of protein evolution or function ...
en] AmiD is the fifth identified N-acetylmuramoyl-l-alanine zinc amidase of Escherichia coli. This periplasmic lipoprotein is anchored in the outer membrane and has a broad specificity. AmiD is capable of cleaving the intact peptidoglycan (PG) as well as soluble fragments containing N-acetylmuramic acid regardless of the presence of an anhydro form or not, unlike the four other amidases, AmiA, AmiB, AmiC, and AmpD, which have some specificity. AmiD function is, however, not clearly established but it could be part of the enzymatic machinery involved in the PG turnover in E. coli. We solved three structures of the E. coli zinc amidase AmiD devoid of its lipidic anchorage: the holoenzyme, the apoenzyme in complex with the substrate anhydro-N-acetylmuramic-acid-l-Ala-gamma-d-Glu-l-Lys, and the holoenzyme in complex with the l-Ala-gamma-d-Glu-l-Lys peptide, the product of the hydrolysis of this substrate by AmiD. The AmiD structure shows a relatively flexible N-terminal extension that allows an easy ...
The serine-proteinase domain is responsible for the proteolytic events that occur during complement activation. The sequences of nine serine proteinases of known crystal structure were compared with the serine-proteinase sequences in the six complement proteins C1r, C1s, C2, factor B, factor I and factor D to assess the degree of structural homology of the latter with the crystal structures. All sequence insertions and deletions were readily located at the protein surface. The internal location of disulphide bridges and the surface location of putative glycosylation sites are compatible with this structure. Secondary-structure predictions for the sequences were fully consistent with the crystal structures. It is concluded that the double subdomain beta-sheet motif is retained in the complement sequences, but that localized differences are observed for factor I, C2 and factor B. ...
Specific cis-acting sequences within the carlavirus potato virus S (PVS) genomic RNA molecule appear to control gene expression at the translational level. Two sequences have been investigated, the untranslated sequence upstream from the initiation codon of the viral coat protein gene, designated VTE and the 5 untranslated leader sequence from the genomic RNA molecule (PVS 5). In vitro and in vivo, either of these sequences enhance the translation of a downstream open reading frame when provided as the untranslated leader in a transcript molecule. Translational enhancement was also detected at the transgenic plant level. Both PVS sequences were deleted in an attempt to identify the core regulatory element responsible for this translational enhancement phenomenon. Results indicate that in vitro and in vivo, the functional motif is contained within the 5 promixal portion of both sequences. When the sequences of these important regions were compared, a homologous block of nucleotides was ...
The role of the cytoplasmic domain of the human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins in virus replication was investigated. Deletion of residues 840 to 856 at the carboxyl terminus of gp41 reduced the efficiency of virus entry during an early step in the virus life cycle between CD4 binding and formation of the DNA provirus without affecting envelope glycoprotein synthesis, processing, or syncytium-forming ability. Deletion of residues amino terminal to residue 846 was associated with decreased stability of envelope glycoproteins made in COS-1 cells, but this phenotype was cell type dependent. The cytoplasmic domain of gp41 was not required for the incorporation of the HIV-1 envelope glycoproteins into virions. These results suggest that the carboxyl terminus of the gp41 cytoplasmic domain plays a role in HIV-1 entry other than receptor binding or membrane fusion. The cytoplasmic domain of gp41 also affects the stability of the envelope glycoprotein in some cell types. ...
The fine specificity of T cell recognition of peptide analogues of the influenza nucleoprotein epitope, NP 383-391 SRYWAIRTR, was studied using HLA B27-restricted influenza-specific cytotoxic T cell (CTL) clones, of defined T cell receptor (TcR) usage, derived from unrelated individuals following natural infection. Even conservative amino acid substitutions of the peptide residues P4, P7 and P8 influenced CTL recognition. These side chains are probably directly contacted by the TcR. CTL clones which used the TcR V alpha 14 gene segment (but not those using TcR V alpha 12) were also sensitive to P1 substitutions, suggesting that the TcR alpha chain of these clones lies over the N terminus of bound peptide, and that the footprint of certain TcR can span all exposed residues of a peptide bound to a major histocompatibility complex class I molecule. These results, taken together with previous structural and functional data, suggest that, for nonamer peptides bound to HLA B27, P1, P4 and P8 are flag
We have taken a comprehensive approach to the generation of novel DNA binding zinc finger domains of defined specificity. Herein we describe the generation and characterization of a family of zinc finger domains developed for the recognition of each of the 16 possible 3-bp DNA binding sites having the sequence 5-GNN-3. Phage display libraries of zinc finger proteins were created and selected under conditions that favor enrichment of sequence-specific proteins. Zinc finger domains recognizing a number of sequences required refinement by site-directed mutagenesis that was guided by both phage selection data and structural information. In many cases, residues not expected to make base-specific contacts had effects on specificity. A number of these domains demonstrate exquisite specificity and discriminate between sequences that differ by a single base with >100-fold loss in affinity. We conclude that the three helical positions -1, 3, and 6 of a zinc finger domain are insufficient to allow for ...
cDNA clones coding for the β subunit of rat brain type II Ca2+/calmodulin-dependent protein kinase were isolated and sequenced. The clones, including one containing the entire coding region, hybridize at high stringency to a single band of poly(A)+ RNA of length 4.8 kilobases. The subunit coded for by the clones was identified by in vitro transcription of the cDNA followed by translation of the resulting RNA. The DNA sequence of the clones contains a single long open reading frame (1626 nucleotides) coding for a protein of 542 amino acids with a molecular weight of 60,333, the amino-terminal half of which is homologous to several other protein kinases. Potential ATP- and calmodulin-binding domains were identified. Two independent clones contain an identical 45-nucleotide deletion, relative to the clones described above, resulting in a shorter open reading frame coding for a protein of molecular weight 58,000. This suggests that the minor, 58-kDa β subunit of the type II ...
Key publications. Semenza, G.L, Nejfelt, M.K., Chi, S.M. & Antonarakis, S.E. (1991). Hypoxia-inducible nuclear factors bind to an enhancer element located 3 to the human erythropoietin gene. Proc Natl Acad Sci USA, 88, 5680-5684. Wang, G.L., Jiang, B.-H., Rue, E.A. & Semenza, G.L. (1995). Hypoxia-inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated by cellular O2 tension. Proc Natl Acad Sci USA, 92, 5510-5514. Maxwell, P.H., Wiesener, M.S., Chang, G.-W., Clifford, S.C., Vaux, E.C., Cockman, M.E., Wykoff, C.C., Pugh, C.W., Maher, E.R. & Ratcliffe, P.J. (1999). The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis. Nature, 399, 271-275. Ivan, M., Kondo, K., Yang, H., Kim, W., Valiando, J., Ohh, M., Salic, A., Asara, J.M., Lane, W.S. & Kaelin Jr., W.G. (2001) HIFa targeted for VHL-mediated destruction by proline hydroxylation: Implications for O2 sensing. Science, 292, 464-468. Jaakkola, P., Mole, D.R., Tian, Y.-M., Wilson, M.I., ...
CDC23 is required in Saccharomyces cerevisiae for cell cycle progression through the G2/M transition. The CDC23 gene product contains tandem, imperfect repeats, termed tetratricopeptide repeats, (TPR) units common to a protein family that includes several other nuclear division CDC genes. In this report we have used mutagenesis to probe the functional significance of the TPR units within CDC23. Analysis of truncated derivatives indicates that the TPR block of CDC23 is necessary for the function or stability of the polypeptide. In-frame deletion of a single TPR unit within the repeat block proved sufficient to inactivate CDC23 in vivo, though this allele could rescue the temperature-sensitive defect of a cdc23 point mutant by intragenic complementation. By both in vitro and in vivo mutagenesis techniques, 17 thermolabile cdc23 alleles were produced and examined. Fourteen alleles contained single amino acid changes that were found to cluster within two distinct mutable domains, one of which ...
CDC23 is required in Saccharomyces cerevisiae for cell cycle progression through the G2/M transition. The CDC23 gene product contains tandem, imperfect repeats, termed tetratricopeptide repeats, (TPR) units common to a protein family that includes several other nuclear division CDC genes. In this report we have used mutagenesis to probe the functional significance of the TPR units within CDC23. Analysis of truncated derivatives indicates that the TPR block of CDC23 is necessary for the function or stability of the polypeptide. In-frame deletion of a single TPR unit within the repeat block proved sufficient to inactivate CDC23 in vivo, though this allele could rescue the temperature-sensitive defect of a cdc23 point mutant by intragenic complementation. By both in vitro and in vivo mutagenesis techniques, 17 thermolabile cdc23 alleles were produced and examined. Fourteen alleles contained single amino acid changes that were found to cluster within two distinct mutable domains, one of which ...
positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process - Ontology Report - Rat Genome Database
...COLLEGE STATION - Functional amino acids play a critical role in the d...In a journal article appearing in the American Society for Nutrition (... We need to move forward and capitalize on the potential of functional...A functional amino acid is an amino acid that can regulate key metabol...,AgriLife,scientist:,Functional,amino,acids,regulate,key,metabolic,pathways,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
Glutathione transferase genes (GST) are candidate genes for Parkinsons disease because they are involved with the metabolism of pesticides, dopamine, and glutathione. Recent reports have suggested an association between Parkinsons disease and polymorphisms of GSTP1 1 orGSTM1 andGSTT1.2 Recently we discovered a new polymorphic site in the zeta class G→T (GSTZ1) gene.3 This consists of a C6T transition at nucleotide 245 in exon 5 that results in an amino acid change at position 82 from methionine to threonine. The T substitution occurs in 14% of white people. We have previously reported two other polymorphic sites at nucleotides 94 and 124 in exon 3.4 There are now thought to be four alleles of GSTZ1:Z1*A(A94A124C245),Z1*B(A94G124C245),Z1*C(G94G124C245,) andZ1*D(G94G124T245). Here we investigated the association of Parkinsons disease, pesticide exposure, and theseGSTZ1 polymorphisms.. DNA was extracted from blood samples collected from patients with Parkinsons disease and matched controls as ...
Human immunodeficiency virus type 1 (HIV-1) accessory genes including nef, vif, and vpr are important factors that determine the replication and pathogenesis of HIV-1. The state of activation is also important for the replication of HIV-1. We evaluated the properties of nef-, vif-, and vpr-minus macrophage-tropic HIV-1(JR) CSF in primary CD4+ Th1- or Th2-like cell cultures which had been activated through CD3 molecules in the presence of interleukin-2 (IL-2) and IL-12 (Th1-like culture) or IL-4 (Th2-like culture), respectively. In activated Th1- or Th2-like cultures, replication of nef-minus HIV-1(JR-CSF) was markedly lower than that of wild-type HIV-1. Subsequent analysis by site-directed mutagenesis showed that (i) the presence of an acidic amino acid-rich domain (amino acid residues 72 to 75) in the Nef protein was critical for the enhancement of viral DNA synthesis, resulting in increased virus growth rate, and (ii) prolines that form part of Src homology 3 binding domain were not essential ...
Search PubMed for more publications by Chris Todd Hittinger. RESEARCH PUBLICATIONS (& equal contributions, @corresponding author). Libkind D &, Hittinger CT &, Valério E, Gonçalves C, Dover J, Johnston M, Gonçalves P, Sampaio JP. Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proc Natl Acad Sci USA 108: 14539-44.. Scannell DR&, Zill [email protected], Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger [email protected] 2011. The awesome power of yeast evolutionary genetics: New genome sequences and strain resources for the Saccharomyces sensu stricto genus. G3 Genes Genomes Genet 1: 11-25.. Hittinger CT, Gonçalves P, Sampaio JP, Dover J, Johnston M, Rokas A. 2010. Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature 464: 54-8.. Hittinger CT, Johnston M, Tossberg JT, Rokas A. 2010. Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proc Natl Acad Sci USA 107: 1476-81.. Gibbons ...
RNA degradation is important for the regulation of gene expression. Despite the identification of proteins and sequences related to deadenylation-dependent RNA degradation in plants, endonucleolytic cleavage-dependent RNA degradation has not been studied in detail. Here, we developed truncated RNA end sequencing in Arabidopsis thaliana to identify cleavage sites and evaluate the efficiency of cleavage at each site. Although several features are related to RNA cleavage efficiency, the effect of each feature on cleavage efficiency has not been evaluated by considering multiple putative determinants in A. thaliana. Cleavage site information was acquired from a previous study, and cleavage efficiency at the site level (CSsite value), which indicates the number of reads at each cleavage site normalized to RNA abundance, was calculated. To identify features related to cleavage efficiency at the site level, multiple putative determinants (features) were used to perform feature selection using the Least
Analysis of the heteromeric DNA binding protein GABP has revealed the interaction of two distinct peptide sequence motifs normally associated with proteins located in different cellular compartments. The alpha subunit of GABP contains an 85-amino acid segment related to the Ets family of DNA binding proteins. The ETS domain of GABP alpha facilitates weak binding to DNA and, together with an adjacent segment of 37 amino acids, mediates stable interaction with GABP beta. The beta subunit of GABP contains four imperfect repeats of a sequence present in several transmembrane proteins including the product of the Notch gene of Drosophila melanogaster. These amino-terminal repeats of GABP beta mediate stable interaction with GABP alpha and, when complexed with GABP alpha, directly contact DNA. These observations provide evidence for a distinct biochemical role for the 33-amino acid repeats, and suggest that they may serve as a module for the generation of specific dimerization interfaces. ...
TY - JOUR. T1 - The study of biogenesis and secretion of alkaline phosphatase and its mutant forms in Escherichia coli. I. Introduction of mutations into alkaline phosphatase gene. AU - Karamyshev, A. L.. AU - Shlyapnikov, M. G.. AU - Khmelnitsky, M. I.. AU - Nesmeyanova, M. A.. AU - Ksenzenko, V. N.. PY - 1994. Y1 - 1994. N2 - Various mutations in E. coli alkaline phosphatase gene were obtained by oligonucleotide-directed mutagenesis. They result in amino acid substitutions in the signal peptide cleavage site [Val for Ala(-1)] and in the N terminus of mature polypeptide chain: Ala for Arg(+1) and Gln for Glu(+4); Gln for Glu(+4). Enzyme activity was observed in all E. coli strains transformed by plasmids with cloned mutant genes. In addition, an amber mutation was introduced into the Arg(+1) position, and the synthesis of mutant alkaline phosphatase was shown in E. coli strains containing suppressor tRNAs specific for Ser, Gln, Tyr, Leu, Ala, Glu, Phe, Gly, His, Pro, and Cys.. AB - Various ...
Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the local secondary structures of proteins based only on knowledge of their amino acid sequence. The secondary structure of proteins is determined by the pattern of hydrogen bonding. A large number of servers and tools are used to predict the secondary structure analysis.. Protein secondary structure refers to the local conformation proteins polypeptide backbone. There are two regular secondary structure states, α-helix (H) and β-strand (E), and one irregular secondary structure type, the coil region (C). Sander developed a secondary structure assignment method Dictionary of Secondary Structure of Proteins (DSSP)3, which automatically assigns secondary structure into eight states (H, E, B, T, S, L, G, and I) according to hydrogen-bonding patterns. These eight states are often further simplified into three states of helix, sheet and coil. The most widely used convention is that helix is designated as G, ...
p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class=publication>Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href=>Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...
TY - JOUR. T1 - Genes within genes. T2 - independent expression of phage T4 intron open reading frames and the genes in which they reside.. AU - Gott, J. M.. AU - Zeeh, A.. AU - Bell-Pedersen, D.. AU - Ehrenman, Karen. AU - Belfort, M.. AU - Shub, D. A.. PY - 1988/1/1. Y1 - 1988/1/1. N2 - The td, nrdB, and sunY introns of bacteriophage T4 each contain a long open reading frame (ORF). These ORFs are preceded by functional T4 late promoters and, in the case of the nrdB intron ORF, a functional middle promoter. Expression of phage-encoded intron ORF-lacZ fusions indicates that these T4 genes are highly regulated. The lack of translation of these ORFs from early pre-mRNAs can be accounted for by the presence of secondary structures that are absent from the late RNAs. Because translation of the intron ORFs could disrupt core structural elements required for pre-mRNA splicing, such regulation may be necessary to allow expression of the genes in which they reside.. AB - The td, nrdB, and sunY introns ...
Accurate sequence alignments of distantly related proteins are crucial for the better understanding of proteins at their family/superfamily level. However, such alignments of distantly related proteins are often hard to obtain by automatic multiple sequence alignment programs. Hence, we suggest a protocol that permits the reliable sequence alignment of distantly related proteins whose structural information is available. This protocol employs two stages of structure-based sequence alignments in order to obtain reliable alignments. The method proposed is clearly suited to work for protein structural members with distant relationships. We further propose a novel assessment of the derived alignments using the measurements of the structural variations and the percentage secondary structural equivalences. This structure-based sequence alignment protocol can be employed for a single superfamily or for a large number of structural domain superfamilies in a near-automatic and rapid manner.. Development ...
BACKGROUND: There is an increasing need to develop bioinformatic tools to organise and analyse the rapidly growing amount of nucleotide and amino acid sequence data in organisms ranging from viruses to eukaryotes. FINDING: A simple sequence editor (SSE) was developed to create an integrated environment where sequences can be aligned, annotated, classified and directly analysed by a number of built-in bioinformatic programs. SSE incorporates a sequence editor for the creation of sequence alignments, a process assisted by integrated CLUSTAL/MUSCLE alignment programs and automated removal of indels. Sequences can be fully annotated and classified into groups and annotated of sequences and sequence groups and access to analytical programs that analyse diversity, recombination and RNA secondary structure. Methods for analysing sequence diversity include measures of divergence and evolutionary distances, identity plots to detect regions of nucleotide or amino acid homology, reconstruction of sequence changes,
1 Motivating the need for optimal sequence alignments Note that this actually combines two objectives of optimal sequence alignments: (i) use the score of the alignment o infer homology; (ii) use
Antiprotease targeting : altered specificity of α1-antitrypsin by amino acid replacement at the reactive centre Academic Article ...
The supernumerary subunit g is found in all mitochondrial ATP synthases. Most of the conserved amino acid residues are present in the membrane C-terminal part of the protein that contains a dimerization motif GXXXG. In yeast, alteration of this motif leads to the loss of subunit g and of supramolecular structures of the ATP synthase with concomitant appearance of anomalous mitochondrial morphologies. Disulfide bond formation involving an engineered cysteine in position 109 of subunit g and the endogenous cysteine 28 of subunit e promoted g + g, e + g, and e + e adducts, thus revealing the proximity in the mitochondrial membrane of several subunits e and g. Disulfide bond formation between two subunits g in mitochondria increased the stability of an oligomeric structure of the ATP synthase in digitonin extracts. These data suggest the participation of the dimerization motif of subunit g in the formation of supramolecular structures and is in favor of the existence of ATP synthase associations, in ...
The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity. We developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of 12 amino acid residues from the CLE motif in a site-weight dependent manner. In total, 2156 CLE candidates-including 627 novel candidates-were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach
Protein kinase CK2 (CK2) is a ubiquitous serine/threonine kinase with multiple cellular functions in vertebrates including apoptosis, differentiation, proliferation, survival, tumorigenesis, signal transduction, immune regulation and inflammation. In the current study, the catalytic and regulatory subunit homologs of Litopenaeus vannamei protein kinase CK2 (LvCK2α and LvCK2ß) were cloned and characterized. LvCK2α has a full-length cDNA sequence of 1764 bp with a 1053 bp open reading frame (ORF) encoding a putative protein of 351 amino acids, which contains a typical serine/threonine kinase domain. On the other hand, LvCK2ß has a 1394 bp full-length cDNA with an ORF of 663 bp encoding a protein with 221 amino acids, which contains a Casein kinase II regulatory subunit domain. Sequence and phylogenetic analysis revealed that LvCK2 was evolutionary related with the CK2 of invertebrates. Quantitative reverse transcription PCR (RT-qPCR) analysis showed that LvCK2α and LvCK2ß transcripts were ...
TY - JOUR. T1 - Recurrent sequence exchange between homeologous grass chromosomes. AU - Wicker, Thomas. AU - Wing, Rod A.. AU - Schubert, Ingo. N1 - Publisher Copyright: © 2015 John Wiley & Sons Ltd. Copyright: Copyright 2016 Elsevier B.V., All rights reserved.. PY - 2015/11/1. Y1 - 2015/11/1. N2 - All grass species evolved from an ancestor that underwent a whole-genome duplication (WGD) approximately 70 million years ago. Interestingly, the short arms of rice chromosomes 11 and 12 (and independently their homologs in sorghum) were found to be much more similar to each other than other homeologous regions within the duplicated genome. Based on detailed analysis of rice chromosomes 11 and 12 and their homologs in seven grass species, we propose a mechanism that explains the apparently younger age of the duplication in this region of the genome, assuming a small number of reciprocal translocations at the chromosome termini. In each case the translocations were followed by unbalanced ...
Evidence for subdivisions from sequence and morphological data. Molecular Phylogenetics and Evolution 39: 16-32. ... Groombridge 1982 , title=The IUCN Amphibia - Reptilia Red Data Book *^ Bradford 2017 ,title= Health Survey Including Selected ... Molecular Phylogenetics and Evolution. 60: 183-191. doi:10.1016/j.ympev.2011.03.026. PMID 21459152.. ...
2019) based on molecular sequence data. Sites and ages of specimen (complete list): Casimba, Cuba ~1.8 Mya-11,000 years ago. ...
... integration of molecular sequence data and fossils". Biol. Lett. 2 (4): 543-7. doi:10.1098/rsbl.2006.0523. PMC 1834003. PMID ... Based on molecular sequencing and fossil dating, Neoaves appeared to radiate after the K-Pg boundary.[23][155] They even ... "Molecular Biology and Evolution. 23 (6): 1144-1155. doi:10.1093/molbev/msj124. PMID 16533822.. CS1 maint: Multiple names: ... At present the most informative sequence of dinosaur-bearing rocks in the world from the K-Pg boundary is found in western ...
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ...
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi: ...
... integration of molecular sequence data and fossils" (PDF). Biology Letters. 2 (4): 1-5. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... Phylogeny and Classification of Birds: A Study in Molecular Evolution. Yale University Press. ISBN 0-300-04085-7. Accessed ... Biologists can then use this data to deduce which birds are at risk of lead poisoning. ... Molecular Biology and Evolution. 24 (1): 269-280. CiteSeerX doi:10.1093/molbev/msl158. PMID 17062634.. ...
Integration of molecular sequence data and fossils" (PDF). Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC ... Molecular studies such as DNA-DNA hybridization (Sibley & Ahlquist, 1990)[full citation needed] and sequence analyses fail to ... 1990): Distribution and taxonomy of the birds of the world: A Study in Molecular Evolution. Yale University Press, New Haven, ... "Molecular Phylogenetics and Evolution. 30 (1): 140-151. doi:10.1016/S1055-7903(03)00159-3. PMID 15022765.. ...
... based on nuclear and mitochondrial sequence data". Molecular Phylogenetics and Evolution. 29 (1): 126-138. doi:10.1016/S1055- ... a congruence analysis of heterogeneous mitochondrial and nuclear DNA sequence data". Molecular Phylogenetics and Evolution. 31 ... Advances in molecular biology and improved paleobiogeographical data gradually are revealing a clearer picture of passerine ... taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data" (PDF). Proceedings of the Royal Society B ...
"The phylogenetic relationships of the extant pelicans inferred from DNA sequence data". Molecular Phylogenetics and Evolution. ... However, trees derived from genetic data disagree. In 1990, Charles Sibley and John E. Ahlquist's Unweighted Pair Group Method ... with Arithmetic Mean (UPGMA) tree based on DNA-DNA hybridization data found that the American white pelican, the pink-backed ...
e.g. Ericson et al., Diversification of Neoaves: integration of molecular sequence data and fossils, Biol Lett. 2007 Jun 22;3(3 ... "that is probably misplaced in the current phylogenetic listing but for which data indicating proper placement are not yet ...
New insights from multilocus sequence data", 41(1) Genetics and Molecular Biology (2018). ... Scholars rely on archaeological data and written records from settlers from Europe. Most scholars writing at the end of the ... The University of Kansas, DNA sequences suggest 250 people made up original Native American founding population (2018/05/01) ... "Amateur website, but reports data from scholarly sources.. *Jeffrey Amherst and Smallpox Blankets "Lord Jeffrey Amherst's ...
... 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 ... "An unbiased molecular approach using 3′-UTRs resolves the avian family-level tree of life". Molecular Biology and Evolution ( ... Johansson, Ulf S. & Ericson, Per G. P. (2003): Molecular support for a sister group relationship between Pici and Galbulae ( ...
... 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 ... ISBN 0-300-04969-2 Sibley, Charles G., and Jon E. Ahlquist (1991) Phylogeny and Classification of Birds: A Study in Molecular ...
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 1-5. doi:10.1098/rsbl.2006.0523. PMC 1834003. PMID ... 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. ... and classification of the Accipitridae based on DNA sequences of the RAG-1 exon". Journal of Avian Biology. 38 (5): 587-602. ...
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... "An unbiased molecular approach using 3'UTRs resolves the avian family-level tree of life". Molecular Biology and Evolution: 143 ... sequenced 3-prime untranslated region (3'UTR) from 429 species and 379 genera of birds found support of Columbaves in their ... A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature (2015). doi:10.1038/nature15697 ...
... 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 ...
... 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 ...
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... More recent molecular studies support their grouping together in Eurypygimorphae, which is usually recovered as the sister ... 2015) A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526, 569-573. Suh, ...
... 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. 56 (2): 698-706. doi:10.1016/j.ympev.2010.04.016. PMID 20399870. v t e. ... using targeted next-generation DNA sequencing". Nature. 526 (7574): 569-573. Bibcode:2015Natur.526..569P. doi:10.1038/ ...
... 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, ...
... 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, ...
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... An unbiased molecular approach using 3'UTRs resolves the avian family-level tree of life. Molecular Biology and Evolution. ...
... 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 ( ...
Molecular sequence data exist for two families: Vampyrellidae and Leptophyridae. Frequently, Vampyrella is the only genus ...
... 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 ...
6 July 2006). "Diversification of Neoaves: integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547 ... "LC White-bellied Go-away-bird Criniferoides leucogaster". BirdLife International Data Zone. 2019. Dale A. Zimmerman, Birds of ...
Molecular sequence data indicate 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 ...
... 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, ...
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, many species of birds (the Neoaves group in particular) appeared to radiate ... 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 ...
... 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 ...
More reference expression data. Gene ontology. Molecular function. • transcription factor activity, sequence-specific DNA ... RNA polymerase II regulatory region sequence-specific DNA binding. • DNA binding. • sequence-specific DNA binding. • ... transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding. • RNA ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
Nuclear and mitochondrial sequence data reveal the major lineages of starlings, mynas and related taxa. Molecular Phylogenetics ... 1990): Distribution and taxonomy of the birds of the world: A Study in Molecular Evolution. Yale University Press, New Haven, ... Hunt, Jeffrey S.; Bermingham, Eldredge; & Ricklefs, Robert E. (2001): Molecular systematics and biogeography of Antillean ...
The sequence has been published on the website OpenAshDieBack and offers clues to how the fungus infects trees. The study has ... Gross, A.; Grünig, C. R.; Queloz, V.; Holdenrieder, O. (2012). "A molecular toolkit for population genetic investigations of ... "National Biodiversity Data Centre. Retrieved 5 November 2012.. *^ ... Teams from The Sainsbury Laboratory (TSL) and the John Innes Centre in Norwich sequenced the genome of the fungus in December ...
Once a region of DNA is identified as contributing to a phenotype, it can be sequenced. The DNA sequence of any genes in this ... INTERSNP - a software for genome-wide interaction analysis (GWIA) of case-control SNP data and analysis of quantitative traits ... Methods in Molecular Biology, Springer US, pp. 15-25, doi:10.1007/978-1-4939-9865-4_3, ISBN 9781493998654. , PMID 31541435. ... This can be done using BLAST, an online tool that allows users to enter a primary sequence and search for similar sequences ...
Corporation and Quest Diagnostics to develop a solution for scoring genetic variation for next generation sequencing data (NGS ... The software has been cited in thousands of scientific molecular biology publications and is one of several tools for systems ... IPA can be used with or without data. IPA helps researchers analyze data derived from expression and SNP microarrays, ... QIAGEN Silicon Valley's first product, IPA, was introduced in 2003, and is used to help researchers analyze omics data and ...
... inferred from mtDNA data". Molecular Phylogenetics and Evolution. 29 (2): 250-257. doi:10.1016/S1055-7903(03)00096-4. PMID ... An analysis of mitochondrial DNA sequences published in 2003 confirmed that the black-billed magpie and the yellow-billed ... Molecular Phylogenetics and Evolution. 65 (2): 562-572. doi:10.1016/j.ympev.2012.07.011. PMID 22842292.. ...
The statistics of data thereby obtained are much worse than those obtained through transmission tomography. A normal PET data ... 2003). "11C-metomidate PET imaging of adrenocortical cancer". European Journal of Nuclear Medicine and Molecular Imaging. 30 (3 ... Because the two scans can be performed in immediate sequence during the same session, with the patient not changing position ... Also, FBP treats the data deterministically-it does not account for the inherent randomness associated with PET data, thus ...
There is a regularity in these angles and they follow the numbers in a Fibonacci sequence: 1/2, 2/3, 3/5, 5/8, 8/13, 13/21, 21/ ... Walls, R. L. (25 January 2011). "Angiosperm leaf vein patterns are linked to leaf functions in a global-scale data set". ... On the basis of molecular genetics, Eckardt and Baum (2010) concluded that "it is now generally accepted that compound leaves ...
Genome-sequencing showed that this outbreak was not related to the 2014-15 West Africa Ebola virus outbreak, but was the same ... Klenk, Hans-Dieter; Feldmann, Heinz (2004). Ebola and Marburg viruses: molecular and cellular biology (Limited preview). ... "Ebolavirus - Pathogen Safety Data Sheets". Public Health Agency of Canada. 17 September 2001. Archived from the original on 20 ... Genome sequencing suggests that this outbreak, the 11th outbreak since the virus was first discovered in the country in 1976, ...
Mitochondrial DNA data for the D-loop sequence suggests that mallards may have evolved in the general area of Siberia. Mallard ... "Molecular Phylogenetics and Evolution. 70: 402-411. doi:10.1016/j.ympev.2013.08.008. ISSN 1095-9513. PMID 23994490.. ... McCracken, Kevin G.; Johnson, William P.; Sheldon, Frederick H. (2001). "Molecular population genetics, phylogeography, and ... Molecular Ecology (published January 2013). 22 (1): 41-55. doi:10.1111/mec.12098. PMID 23110616.. ...
More reference expression data. Gene ontology. Molecular function. • ion channel activity. • benzodiazepine receptor activity. ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-45. doi:10.1038/ ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
"Molecular Biology of the Cell. 6 (5): 509-24. doi:10.1091/mbc.6.5.509. PMC 301212 . PMID 7545030.. ... Preclinical data support the notion that Substance P is an important element in pain perception. The sensory function of ... Huston JP, Hasenöhrl RU, Boix F, Gerhardt P, Schwarting RK (1993). "Sequence-specific effects of neurokinin substance P on ... Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). ...
The California two-spot octopus has had its genome sequenced, allowing exploration of its molecular adaptations.[151] Having ... Relevant data at Google Ngram Viewer.. *^ "Octopus". 2014. Retrieved 4 February 2014.. ... Octopuses and other coleoid cephalopods are capable of greater RNA editing (which involves changes to the nucleic acid sequence ... Strugnell, J.; Nishiguchi, M. K. (2007). "Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) inferred from ...
"Journal of Molecular Biology. 409 (1): 28-35. doi:10.1016/j.jmb.2011.02.041. PMC 3108490. PMID 21371478.. ... Yale University's data strongly suggest a model in which TipN regulates the orientation of the polarity axis by providing a ... In 2010, the Caulobacter NA1000 strain was sequenced and all differences with the CB15 "wild type" strain were identified.[6] ... Detailed study of the molecular development of these cells as they progress through the cell cycle has enabled researchers to ...
... taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proceedings of the Royal Society B. 269: ... Evidence on their evolution comes from comparative anatomy, the fossil record and molecular biology. It is thought that the ...
More reference expression data. Gene ontology. Molecular function. • DNA binding. • sequence-specific DNA binding. • ... RNA polymerase II core promoter sequence-specific DNA binding. • RNA polymerase II transcription factor activity, sequence- ... "Molecular and Cellular Biology. 21 (2): 524-33. doi:10.1128/MCB.21.2.524-533.2001. PMC 86614. PMID 11134340.. ... "Molecular and Cellular Biology. 13 (10): 6024-35. doi:10.1128/mcb.13.10.6024. PMC 364662. PMID 8413205.. ...
A new classification and linear sequence based on molecular data can be found in an article by Christenhusz et al.[7] ... Phylogeny of the Pinophyta based on cladistic analysis of molecular data.[5] ... In discussing the data obtained from the one 11 m tall white spruce, Fraser et al. (1964)[16] speculated that if the ... but recent research into DNA sequences suggests that this interpretation leaves the Pinales without Taxales as paraphyletic, ...
Molecular and Cellular Probes. 31: 22-27. doi:10.1016/j.mcp.2016.08.003. PMID 27523487. Archived (PDF) from the original on 20 ... "Lyme Disease Data and surveillance". Lyme Disease. Centers for Disease Control and Prevention. 5 February 2019. Archived from ... revealed the presence of the DNA sequence of Borrelia burgdorferi making him the earliest known human with Lyme disease.[242] ... "Molecular Medicine. 14 (3-4): 205-12. doi:10.2119/2007-00091.Rupprecht. PMC 2148032. PMID 18097481. Archived from the original ...
Recent molecular data from rRNA,[4] and from mtDNA,[5] show that these living agnathans are monophyletic. There are about 100 ... 28S and 18S ribosomal DNA sequences support the monophyly of lampreys and hagfishes. Molecular Biology and Evolution 15 (12): ... Molecular phylogenetics and evolution. 22, 2, 184-192. [4] *↑ Janvier, Philippe 2010. MicroRNAs revive old views about jawless ... Complete mitochondrial DNA of the hagfish, Eptatretus burgeri: the comparative analysis of mitochondrial DNA sequences strongly ...
"National Nuclear Data Center: Brookhaven National Laboratory. Retrieved 4 October 2012.. *^ Patton, I. Jocelyn; Waldbauer, L. J ... 8).[66] Upon heating of KC8, the elimination of potassium atoms results in the conversion in sequence to KC24, KC36, KC48 and ... in a molecular dynamics (MD) simulation study". Biophys. Chem. 120 (1): 1-9. doi:10.1016/j.bpc.2005.10.002. PMID 16253415.. ... Allred, A. L. (1961). "Electronegativity values from thermochemical data". J. Inorg. Nucl. Chem. 17 (3-4): 215-221. doi:10.1016 ...
"Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix". ... 2] [3] മോളിക്കുലർ ഫൈലൊ ജെനെറ്റിക്സ്(Molecular phylogenetics) ഇവ ഇരു കുടുബമാണെന്ന് ഉറപ്പിച്ചു [4][5] For example, some ... Kimball, R. T.; Braun, E. L.; Zwartjes, P. W.; Crowe, T. M.; Ligon, J. D. (1999). "A molecular phylogeny of the pheasants and ... partridges suggests that these lineages are not monophyletic". Molecular Phylogenetics and Evolution. 11 (1): 38-54. doi: ...
... based on nucleotide sequence data. Journal of Avian Biology 36: 222-234. ... inferred from mtDNA data. Molecular Phylogenetics and Evolution 29: 250-257. ...
Sequence-tagged site (STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are most often ... "Evaluation of the GenBank, EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates That ... The GenBank database includes additional data sets that are constructed mechanically from the main sequence data collection, ... Upon receipt of a sequence submission, the GenBank staff examines the originality of the data and assigns an accession number ...
Hall, J.C.; Sytsma, K.J.; Iltis, H.H. (2002). "Phylogeny of Capparaceae and Brassicaceae based on chloroplast sequence data". ... based on molecular and pollen data, and the description of a new family of Brassicales, Borthwickiaceae" (PDF). Taxon. 61 (3): ... The small Eurasian weed Arabidopsis thaliana is widely used as model organism in the study of the molecular biology of ... Although a substantial effort was made through molecular phylogenetic studies, the relationships within the Brassicaceae have ...
More reference expression data. Gene ontology. Molecular function. • DNA binding. • sequence-specific DNA binding. • ... "Molecular and Cellular Biology. 20 (9): 3102-15. doi:10.1128/MCB.20.9.3102-3115.2000. PMC 85605. PMID 10757795.. ... "Molecular and Cellular Biology. 19 (2): 1182-9. doi:10.1128/mcb.19.2.1182. PMC 116047. PMID 9891052.. ... "Molecular and Cellular Biology. 18 (8): 4471-87. doi:10.1128/mcb.18.8.4471. PMC 109033. PMID 9671457.. ...
... molecular) and fossil (morphological) data to obtain its results.[25] ... As of 2013, three turtle genomes have been sequenced.[33] The results place turtles as a sister clade to the archosaurs, the ... Hideyuki Mannena & Steven S.-L. Li (1999). "Molecular evidence for a clade of turtles". Molecular Phylogenetics and Evolution. ... Classically, turtles were considered to be related to the primitive anapsid reptiles.[32] Molecular work has usually placed ...
It is optical molecular imaging for hemoglobin both oxygenated and deoxygenated. The technology uses laser in the same way ... A laser detector measures the intensity drop and the data is collected as the laser detector moves across the breast creating a ...
Datum osnivanja. 1988 .. Vrsta. Domaćin i uređivač niza baza podataka, relevantnih za biotehnologiju i biomedicinu i važan je ... "Sense from Sequences: Stephen F. Altschul on Bettering BLAST". 2000. Arhivirano s originala, 7. 10. 2007.. ... Journal of Molecular Biology. 215 (3): 403-410. doi:10.1016/s0022-2836(05)80360-2. PMID 2231712.. ... 8. 2007). GenBank: The Nucleotide Sequence Database. National Center for Biotechnology Information (US) - preko www.ncbi.nlm. ...
Science In Medicine: The JCI Textbook Of Molecular Medicine. Jones & Bartlett Learning. pp. 1061 ff. ISBN 0763750832.. ... On this doctrine events throughout eternity have been foreordained by some supernatural power in a causal sequence.. ... Others have argued that data such as the Bereitschaftspotential undermine epiphenomenalism for the same reason, that such ... Wagenaar, W. A. (1972). "Generation of random sequences by human subjects: A critical survey of literature". Psychological ...
a b c d e Kai Müller, Thomas Borsch (2005): Phylogenetics of Amaranthaceae using matK/trnK sequence data - evidence from ... Molecular Phylogenetic Analysis Of Nuclear And Chloroplast Data Sets And A Revised Classification. - International Journal of ... Ivonne Sánchez del-Pino, Thomas Borsch, Timothy J. Motle (2009): trnL-F and rpl16 Sequence Data and Dense Taxon Sampling Reveal ... a b Gudrun Kadereit, Evgeny V. Mavrodiev, Elizabeth H. Zacharias, Alexander P. Sukhorukov (2010): Molecular phylogeny of ...
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 ...
... 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 ...
Locale about Experts and Doctors on molecular sequence data in Switzerland ... Experts and Doctors on molecular sequence data in Switzerland. Summary. Locale: Switzerland ... You are here: Locale , Experts and Doctors on molecular sequence data in Switzerland ... Based on these data we propose to assign species rank to six CSP of P. fortinii: P. turiciensis, P. letzii, P. europaea, P. ...
Research Topics about Experts and Doctors on molecular sequence data in Belgium ... Experts and Doctors on molecular sequence data in Belgium. Summary. Locale: Belgium ... You are here: Locale , Experts and Doctors on molecular sequence data in Belgium ... Our data indicate that TAXI-I belongs to a newly identified class of plant proteins for which a molecular function as glycoside ...
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 ...
Molecular EcologyVolume 19, Issue 7, Version of Record online: 8 MAR 2010. ...
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 ...
Rheonix will present data from a user-defined assay for STIs and data that demonstrates new capabilities of its Encompass ... Rheonix to Present Data on User-Defined Tests and Next-Generation Sequencing Library Preparation with its Automated Molecular ... When sequenced on the Illumina platform, the resulting libraries yielded NGS sequence data indistinguishable from the labor- ... Rheonix will present data from a user-defined assay for STIs and data that demonstrates new capabilities of its Encompass ...
... The breadth and scope of the ORIEN Avatar clinical and molecular data enables the discovery of a wide array of DNA and RNA ... Virtual Molecular Tumor Board Series: What to Do with a Negative Molecular Panel Case. ...
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 ...
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 ...
The Genomics & Sequencing Data Integration, Analysis and Visualization Symposium is a part of the Molecular Medicine Tri- ... Molecular Medicine Tri-Conference: Genomics & Sequencing Data Integration, Analysis and Visualization Symposium. ... As data shifts between research, sequencing labs, and the clinic, there is an ever-increasing volume of information generated ... Globus Genomics is a robust, scale on-demand solution that provides end-to-end research data management for Next-Gen Sequencing ...
Bioinformatics: Volume 1: Data, Sequence Analysis and Evolution. 2008. (Methods in Molecular Biology, Volume 452). illus. XII, ... Examines a selection of methods involving the generation and organization of data, including sequence data, RNA and protein ... structures, microarray expression data and functional annotations, methods for discovering the functional components of genomes ...
The plastid and nuclear data were therefore combined in order to analyse the data sets together. The molecular data does not ... Molecular systematics of the Western Cape genus Serruria Salisb. (Proteaceae L.) based on DNA sequence data. De Villiers, ... Based upon the strong monophyly of Serruria, DNA sequence data were collected for 53 of the 55 species from the plastid (rps16 ... Die plastied- en kern-data is derhalwe gekombineer om die datastelle saam te kan analiseer. Die molekulêre data ondersteun nie ...
... 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.}, ...
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. ... Lesk, A. (1985). Molecular biology: Coordination of sequence data. Nature, 314(6009), 318-319. ...
To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here ... We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype. ... Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We ... The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere ...
The nucleotide sequence of a 300-bp fragment of the ITS2 was determined by direct sequencing and nucleotide divergence used for ... The resulting phylogenetic tree expressing interspecific relationships in genusTetranychus agrees with morphological data. The ... DNA sequence data were used to examine phylogenetic relationships between six species of economically important Tetranychidae ... Molecular approach in spider mites (Acari: Tetranychidae): Preliminary data on ribosomal DNA sequences. @article{ ...
Start Over You searched for: Subjects Molecular Sequence Data ✖Remove constraint Subjects: Molecular Sequence Data Subjects ... Amino Acid Sequence. Base Sequence. Genes, Homeobox. Molecular Sequence Data. Archival Collection:. The Marshall W. Nirenberg ... Amino Acid Sequence. Cloning, Molecular. Genes, Homeobox. RNA, Messenger. Molecular Sequence Data. Archival Collection:. The ... Molecular Sequence Data. Amino Acid Sequence. Archival Collection:. The Marshall W. Nirenberg Papers (Profiles in Science). ...
Molecular phylogeny of the genus Arum (Araceae) inferred from multi-locus sequence data and AFLPs ... Molecular phylogeny of the genus Arum (Araceae) inferred from multi-locus sequence data and AFLPs ... inferred from multi-locus sequence data and AFLPs. Taxon, 59(2), 405-415. doi:10.1002/tax.592006. ... Linz, J., Stökl, J., Urru, I., Krügel, T., Stensmyr, M. C., & Hansson, B. S. (2010). Molecular phylogeny of the genus Arum ( ...
Research Containing: Molecular Sequence Data. Space Environmental Factor Impacts upon Murine Colon Microbiota and Mucosal ... The transcriptional response of spaceflight-grown P. aeruginosa was compared with our previous data for this organism grown in ...
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, ...
Amino Acid Sequence Subjects Molecular Sequence Data ✖Remove constraint Subjects: Molecular Sequence Data Genre Articles ✖ ... Amino Acid Sequence. Base Sequence. Genes, Homeobox. Molecular Sequence Data. Archival Collection:. Profiles in Science. 3. The ... Amino Acid Sequence. Cloning, Molecular. Genes, Homeobox. RNA, Messenger. Molecular Sequence Data. Archival Collection:. ... Start Over You searched for: Subjects Amino Acid Sequence ✖Remove constraint Subjects: ...
Sequence data analysis, molecular species hypotheses[edit]. Sequences were aligned with ClustalW (reference), and maximum ... Cox1sequencing for community ecology[edit]. In Trigonopterus, it is possible to merely rely on cox1 sequence data to arrive at ... Maximum likelihood analyses of cox1 data included 1,002 Trigonopterus cox1 sequences and seven outgroups. The resulting cox1 ... Sequencing delivers objective data on taxa of incredible diversity but mostly without a solid taxonomic foundation and should ...
... 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 ...
... 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 ...
... an appropriate set of non-O-glycosylatable sequences is hard to find. Three sequences from similar post-translational ... In particular, if a binary response is used to distinguish between O-glycosylated and non-O-glycosylated sequences, ... Thus, predicting the likelihood of O-glycosylation with sequence and structural information using classical regression analysis ... 4 , BMC Molecular and Cell Biology. Fig. 4. From: Ridge regression estimated linear probability model predictions of O- ...
The model is used to analyze a genetic data set collected from a pain genetics project. We find that DNA haplotype GAC from ... The model provides a general procedure for identifying the number and types of optimal DNA sequence variants that are expressed ... model for the haplotype analysis of SNPs to estimate the effects of genetic imprinting expressed at the DNA sequence level. ... genetic markers for revealing the genetic architecture of complex traits in terms of nucleotide combination and sequence. Here ...
Paired CMA and WES data were acquired for 45 samples. A total of 219 CNVs (size ranged from 2.3 kb - 35 mb) identified on three ... Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and ... CNVs were called from WES data using XHMM, CoNIFER, and CNVnator with modified settings. All three software packages detected ... has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. ...
  • Accurate genotyping of a human papilloma virus (HPV) isolated from clinical specimens depends on molecular identification of the unique and exclusive nucleotide base sequence in the hypervariable region of a highly conserved segment of the HPV L1 gene. (
  • Molecular anthropology uses the tools and techniques of molecular genetics to answer anthropological questions, especially those concerning the origins and spread of humans across the globe. (
  • This is an interdisciplinary course, and the goal is to involve students who have either a strong computer science background or a strong background in molecular biology (such as students in the genetics graduate program), but not necessarily both. (
  • 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. (
  • Gfeller K, Roth M, Meile L, Teuber M. Sequence and genetic organization of the 19.3-kb erythromycin- and dalfopristin-resistance plasmid pLME300 from Lactobacillus fermentum ROT1. (
  • The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) apparatuses which, in essence, read billions of nucleotides per reaction. (
  • These genetic results, sharpened by ORIEN's clinical data and the significant size of the sample set, accurately elucidate known drivers of cancer, identify new genetic alterations, and reveal novel potential therapeutic targets. (
  • Whole exome sequencing (WES) has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. (
  • However, it was impossible to identify the population of blue whales the individuals belonged to, due to the lack of strong population genetic signals in the mitochondrial control region sequences. (
  • 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. (
  • Incorporating genetic variant data into the electronic health record (EHR) in discrete computable fashion has vexed the informatics community for years. (
  • Genetic sequence test results are typically communicated by the molecular laboratory and stored in the EHR as textual documents. (
  • Rasmus Nielsen is certainly one of these researchers, and his work so far has merged many population genetic and phylogenetic aspects of biological research under the umbrella of molecular evolution. (
  • In severe early-onset epilepsy, precise clinical and molecular genetic diagnosis is complex, as many metabolic and electro-physiological processes have been implicated in disease causation. (
  • It also uncovers unexpected genetic mechanisms and emphasizes the power of WGS as a clinical tool for making molecular diagnoses, particularly for highly heterogeneous disorders. (
  • To assess the genetic diversity and relationships between the isolates, we sequenced two housekeeping genes ( glmM and hspA ). (
  • This web-based application performed pairwise comparisons of HIV-1 protease and partial reverse transcriptase to measure sequence relatedness and identify sequences that were highly genetically similar at a genetic distance of ≤0.015 substitutions per site ( 6 , 7 ). (
  • Among other options, a heminested (nested) polymerase chain reaction (PCR) technology using two consecutive PCR replications of the target DNA in tandem with three consensus general primers may be used to detect a minute quantity of HPV DNA in crude proteinase K digestate of cervicovaginal cells, and to prepare the template for genotyping by automated direct DNA sequencing. (
  • Sequence comparisons suggest that tap is most closely related to two bHLH genes identified in several vertebrate species, neurogenin and neuroD, which are involved respectively in neural determination and in neuronal differentiation. (
  • Examines a selection of methods involving the generation and organization of data, including sequence data, RNA and protein structures, microarray expression data and functional annotations, methods for discovering the functional components of genomes, whether they be genes, alternative splice sites, non-coding RNAs or regulatory motifs, and several of the most interesting methods in phylogenetics and evolution. (
  • Techniques developed by computer scientists have enabled researchers at Celera Genomics, the Human Genome Project consortium, and other laboratories around the world to sequence the nearly 3 billion base pairs of the roughly 40,000 genes of the human genome. (
  • Here, we compared the evolution of MHC class I and class II genes in three sister clades of common passerine birds, finches (Fringillinae and Carduelinae) and buntings (Emberizidae) using a uniform methodological (genotyping and data processing) approach and uniform sample sizes. (
  • Balasubramaniam S, Bray RD, Mulder RA, Sunnucks P, Pavlova A, Melville J (2016) New data from basal Australian songbird lineages show that complex structure of MHC class II β genes has early evolutionary origins within passerines. (
  • Clinical whole-genome sequencing in severe early-onset epilepsy reveals new genes and improves molecular diagnosis. (
  • Molecular diagnosis has historically been confined to sequential testing of candidate genes known to be associated with specific sub-phenotypes, but the diagnostic yield of this approach can be low. (
  • a molecular analysis of ribosomal genes and histone H3 sequence data. (
  • We compared the sequences of two housekeeping genes ( hspA and glmM ) from these clones with those of 131 unrelated strains from patients living in different geographic regions. (
  • Clonal descent has been demonstrated by comparing alleles of genes such as vacA , flaA , and flaB of isolates infecting members of the same family ( 10 - 12 ) and by sequencing three housekeeping genes ( ureI , atpA , and ahpC ) ( 13 ). (
  • Analysis of the sequences of housekeeping genes ( atpD , scoB , glnA and recA ) showed that strains cluster according to their geographic origins ( 15 , 20 ). (
  • Analysis of the sequences the sequences of two housekeeping genes ( hspA and of housekeeping genes ( atpD , scoB , glnA and recA ) glmM ) from these clones with those of 131 unrelated showed that strains cluster according to their geographic strains from patients living in different geographic regions. (
  • Several mechanisms, such as point mutations, intragenic recombination, and introduction of foreign (African) alleles, sequenced two housekeeping genes ( glmM and hspA ). (
  • The data output of such high-throughput experiments typically becomes overwhelmingly large, and some statistical analyses must be performed to focus on the genes that are related to the experiment being conducted. (
  • As a partner in the ORIEN Avatar program, Discovery Life Sciences' sequencing and bioinformatics laboratory, HudsonAlpha Discovery, has conducted high-yield, high-quality dual RNA/DNA isolation from formalin-fixed, paraffin-embedded (FFPE) specimens as well as whole-exome sequencing and RNA sequencing services on more than 30,000 tumor and non-tumor samples. (
  • This Symposium will cover real-world use cases across many areas, including drug discovery and design, R&D, molecular modeling, next-generation sequencing, and bioinformatics. (
  • Bioinformatics: Volume 1: Data, Sequence Analysis and Evolution. (
  • Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecular structures, genome sequences, and gene expression data. (
  • With the availability of genomic data from multiple related species, molecular evolution has become one of the most active and fastest growing fields of study in genomics and bioinformatics. (
  • Bioinformatics involves the application of computational methods in order to address problems in molecular biology. (
  • Molecular phylogeny of Entomobrya (Collembola: Entomobryidae) from China: Color pattern groups and multiple origins. (
  • Marsupials (metatherians), with their position in vertebrate phylogeny and their unique biological features, have been studied for many years by a dedicated group of researchers, but it has only been since the sequencing of the first marsupial genome that their value has been more widely recognised. (
  • Traditionally, the practice has been to use one or more fossils as 'node calibrations' by associating their geologically derived age to a particular divergence in a molecular phylogeny. (
  • The difficulty lies in determining the appropriate ancestral divergence in the molecular phylogeny to associate the fossil with and the details of how this should be achieved within a full statistical inference framework [ 6 - 8 ]. (
  • Computomics to provide analysis for the winners of the PacBio sequencing raffle at PAG 2019. (
  • In WHO-convened Global Study of Origins of SARS-CoV-2: China Part released by the World Health Organization (WHO), SARS-CoV-2 surveillance data and virus cases reported in China are analyzed as far back as late 2019. (
  • 2019) based on molecular sequence data. (
  • 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. (
  • Based upon the strong monophyly of Serruria, DNA sequence data were collected for 53 of the 55 species from the plastid (rps16 intron, atpB-rbcL intergenic spacer, trnL-F region and psbA-trnH intergenic spacer) and nuclear (internal transcribed spacer region or ITS) genomes in order to investigate evolutionary relationships within the genus. (
  • Apart from this case, there was widespread agreement between the trees reconstructed using data from the two genomes. (
  • 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. (
  • However, generating full scaffolds of N. gonorrhoeae genomes from short reads, and the assignment of molecular epidemiological information (NG-MLST, NG-MAST, and NG-STAR) to multiple assembled samples, is challenging due to required manual tasks such as annotating antimicrobial resistance determinants with standard nomenclature for a large number of genomes. (
  • We present Gen2Epi, a pipeline that assembles short reads into full scaffolds and automatically assigns molecular epidemiological and AMR information to the assembled genomes. (
  • For its evaluation, the Gen2Epi pipeline successfully assembled the WGS short reads from 1484 N. gonorrhoeae samples into full-length genomes for both chromosomes and plasmids and was able to assign in silico molecular determinant information to each dataset automatically. (
  • Gen2Epi can be used to assemble short reads into full-length genomes and assign accurate molecular marker and AMR information automatically from NG-STAR, NG-MAST, and NG-MLST. (
  • In order to manage and analyze the large amount of data generated from sequencing techniques, initiatives to develop appropriate tools and software have been undertaken by the N. gonorrhoeae scientific community worldwide [ 3 ] with a number of methods developed to assemble genomes, predict antimicrobial resistance (AMR), and investigate strain transmission through analysis of genomic molecular determinants. (
  • We utilize DNA sequence data from the nuclear, chloroplast, and mitochondrial genomes to infer historical processes of biodiversification. (
  • We now have genome sequences for three distantly related marsupial species (the grey short-tailed opossum, the tammar wallaby, and Tasmanian devil), with the promise of many more genomes to be sequenced in the near future, making this a particularly exciting time in marsupial genomics. (
  • However, rapid progress has been made since the sequencing of the first and subsequent marsupial genomes. (
  • Human pathology due to a deficient alpha-oxidation is mostly linked to mutations in the gene coding for the second enzyme of the sequence, phytanoyl-CoA hydroxylase. (
  • 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. (
  • DAMBE (data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. (
  • DAMBE5: A comprehensive software package for data analysis in molecular biology and evolution. (
  • Several studies have focused on the evolution of HIV-1, but there is little information to link sequence similarities and evolutionary histories of HIV-1 to the epidemiological information of the infected individual. (
  • In the field of molecular evolution, inferences about past evolutionary events are made using molecular data from currently living species. (
  • Most studies in molecular evolution rely heavily on statistical procedures based on stochastic process modelling and advanced computational methods including high-dimensional numerical optimization and Markov Chain Monte Carlo. (
  • This book provides an overview of the statistical theory and methods used in studies of molecular evolution. (
  • This book is suitable for statisticians seeking to learn more about applications in molecular evolution and molecular evolutionary biologists with an interest in learning more about the theory behind the statistical methods applied in the field. (
  • Most relevant statistical concepts are introduced in the book in the context of their application in molecular evolution, and the book should be accessible for most biology graduate students with an interest in quantitative methods and theory. (
  • His is an associate editor of the Journal of Molecular Evolution and has published more than fifty original papers in peer-reviewed journals on the topic of this book. (
  • I find Statistical Methods in Molecular Evolution very interesting and useful. (
  • This book gives an overview of his interests and current achievements in molecular evolution. (
  • In addition, these genome sequences have facilitated studies aimed at answering questions regarding gene and genome evolution and provided insight into the evolution of epigenetic mechanisms. (
  • Here I highlight the major advances in our understanding of evolution and disease, facilitated by marsupial genome projects, and speculate on the future contributions to be made by such sequences. (
  • The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. (
  • It may be less widely appreciated by molecular evolutionary biologists that the statistical phylogenetic revolution in molecular evolution has also been mirrored in the increasing application of statistical phylogenetic reasoning in macroevolutionary and systematic studies of the fossil record [ 14 - 17 ]. (
  • Multiple sequence alignment with hierarchical clustering. (
  • Exome targets were captured using the Agilent SureSelect Human All Exon V4 or V5 kit (Agilent Technologies, Santa Clara, CA). Raw sequencing data (FASTQ format) were generated via the Illumina HiSeq 2000 platform (Illumina, Inc., San Diego, CA). The Burrows Wheeler Alignment tool (BWA) v0.2.10 [ 17 ] was employed for sequencing data alignment to the Human Reference Genome (NCBI build 37, hg 19). (
  • Sequencing of RNA-Seq libraries, processing and alignment to reference genome RNA was sequenced on the Illumina HiSeq 2000 sequencer (Illumina, USA) with a single-ended, 51-bp run producing raw fastq files. (
  • Topics in molecular biology that will motivate the algorithmic content of the course include: sequence alignment, phylogenetic tree reconstruction, prediction of RNA and protein structure, gene finding and sequence annotation, gene expression, and biomolecular computing. (
  • Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and software programs that utilize read-depth as the main information. (
  • Class assignments will familiarize students with biological data and tools for understanding this data and will help students gain a solid understanding of principles for design and analysis of algorithms. (
  • Jolly and Maiden initially developed BIGSdb (Bacterial Isolate Genome Sequence Database) [ 4 ] to store and investigate Multilocus Sequence Typing (MLST) profiles of sequences generated from multiple sources, such as multiple single amplicons or assembled contigs from sequencing technologies. (
  • Strain relationships within the family were determined by analyzing allelic variation at both loci and building phylogenetic trees and by using multilocus sequence typing. (
  • America, and Europe differ from those that are predomi- netic trees and by using multilocus sequence typing. (
  • Although standard variable typing regions (emm subtype, tee type, sof type, and multilocus sequence typing [MLST]) remained unchanged, uniquely the emergent clade had undergone six distinct regions of homologous recombination across the genome compared to the rest of the sequenced emm89 population. (
  • Analysis of sub-type specific mutation data from the BC cohort demonstrates an increased mutational load in ECM-related proteins, particularly the myosins, along with increased TP53 clonality in the non-LAR subtypes. (
  • Such predictions of demographic epidemiology based on sequence information may become valuable in assigning different treatment regimens to infected individuals. (
  • The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens. (
  • We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools. (
  • Recent adva1nces in whole genome sequencing (WGS) based technologies have facilitated multi-step applications for predicting antimicrobial resistance (AMR) and investigating the molecular epidemiology of Neisseria gonorrhoeae . (
  • The Homeland Security Digital Library (HSDL) maintains a collection of the Centers for Disease Control's (CDC) Morbidity and Mortality Weekly Report (MMWR), which collects and analyzes data from the United States Department of Health and Human Services (HHS) on epidemiology and public health. (
  • The NH-alpha CH coupling constants of turkey lysozyme are compared to torsion-angle data from three crystal structures of the protein and the results are interpreted in terms of crystal-structure resolution and refinement. (
  • Vanderhaeghen R, De Clercq R, Karimi M, Van Montagu M, Hilson P, Van Lijsebettens M. Leader sequence of a plant ribosomal protein gene with complementarity to the 18S rRNA triggers in vitro cap-independent translation. (
  • SEView is a Java applet that represents known or predicted elements of a protein or nucleotide sequence. (
  • We have designed, synthesized, and characterized a 216 amino acid residue sequence encoding a putative idealized α/β-barrel protein. (
  • A synthetic gene coding for the designed sequence was constructed and the recombinant artificial protein was expressed in bacteria, purified and characterized. (
  • These encouraging results show that de novo design of an idealized protein structure of more than 200 amino acid residues is now possible, from construction of a particular backbone conformation to determination of an amino acid sequence with an automated sequence selection algorithm. (
  • Our data base presently includes nucleotide sequences from multiple loci representing some 500-600 accessions of peatmosses. (
  • Analysis of sequences of the mitochondrial control region from baleen whales confirmed that the samples belonged to blue whales ( Balaenoptera musculus ). (
  • We apply the method to mitochondrial data from several different species. (
  • In a search for the HIV-1 reservoir, we have now sequenced the genome of a new SIVcpzstrain (SIVcpzUS) and have determined, by mitochondrial DNA analysis, the subspecies identity of all known SIVcpz-infected chimpanzees. (
  • Figure 1 illustrates an example of sequence classification on a dataset of DNA sequences. (
  • The resultant phylogenetic reconstruction thus supports palynological data of this subsection, and indicates the urgent need for a revision of the current morphological classification of Salter (1944). (
  • 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. (
  • Using standard phylogenetic and phenetic techniques on 100 HIV-1 subtype B sequences, we were able to show some correlation between the viral sequences and the geographic area of infection and the risk of men who engage in sex with men. (
  • To help identify more subtle relationships between the viral sequences, the method of multidimensional scaling (MDS) was performed. (
  • 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. (
  • Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. (
  • Prevention recommendations generated from national data (e.g., targeting preexposure prophylaxis for HIV-negative persons at high risk and implementing measures to maintain viral suppression among persons with HIV infection) also are relevant in a lower HIV-morbidity state. (
  • Molecular systematics of the Western Cape genus Serruria Salisb. (
  • Moreover, we find that HIV-1 group N is a mosaic of SIVcpzUS- and HIV-1-related sequences, indicating an ancestral recombination event in a chimpanzee host. (
  • The continual improvement of models and methods for statistical phylogenetic inference from molecular sequence data is well documented [ 4 , 5 ], and in recent years, it is arguably the case that molecular phylogenetics has taken primacy over the fossil record in providing a timescale for evolutionary history [ 1 ]. (
  • 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. (
  • An overview of the changes of our diagnostic approach before and after the transition to next-generation sequencing is also reported. (
  • Due to the rapid development of "-omics" technology, such as DNA microarrays [ 1 ] and next-generation sequencing (NGS) [ 2 , 3 ], scientists are now able to quantify large numbers of transcripts from organisms simultaneously. (
  • A recent study on sequence polymorphism of four FLC paralogs in B. oleracea indicated that they are not candidate in flowering time variation [ 22 ]. (
  • H. pylori is one of the most genetically diverse bacterial species, displaying from 2.7% to 8.0% of DNA sequence polymorphism ( 14 - 16 ). (
  • To look for evidence of intrafamilial infection, we isolat- sequence polymorphism (14-16). (
  • However, microarray technology is dependent on probe-target specificity and the 7 subtypes have yet to be validated using RNA sequencing data, and the presences of recurrent genomic alterations in the 7 subtypes are unknown. (
  • The reconstruction of phylogenetic trees from molecular sequences presents unusual problems for statistical inference. (
  • The plastid and nuclear data were therefore combined in order to analyse the data sets together. (
  • and related genera (Orchidaceae: Oncidiinae) were evaluated using parsimony analyses of data from the internal transcribed spacers of nuclear ribosomal (nrITS DNA) and three plastid regions (matK, trnL-F, and the atpB-rbcL intergenic spacer region). (
  • If a collaborating data producer has created an abstract, it will appear in the Other Abstract (OAB) field. (
  • of MLP, as well as ensemble methods based on resampling techniques, such as bagging and boosting, have been applied to the analysis of DNA microarray data [192, 158, 54, 178, 185]. (
  • We used DNA microarray data available on-line. (
  • Based on microarray data from Stanford Microarray Database, two hNAT pairs were found to display significant inverse expression patterns before and after insulin injection. (
  • No amino acid sequence difference was found between the two strains. (
  • An automated sequence selection algorithm, based on the dead-end elimination theorem, was used to find the optimal amino acid sequence fitting the target structure. (
  • Graph generated 15 March 2017 using data from PubMed using criteria . (
  • HIV-1 sequence data reported in Wisconsin during 2014-2017 for persons with HIV infection diagnosed through August 15, 2017, were analyzed using Secure HIV-TRACE (Secure HIV TRAnsmission Cluster Engine). (
  • Previous molecular and morphological analyses performed on the South African subfamily Proteoideae have shown Serruria, a CFR endemic, to form a well-supported monophyletic group. (
  • The molecular data does not support most of the groupings proposed by previous authors based on morphological data. (
  • Pollen data "sensu" Dreyer (1996) supports the clades retrieved in this study, whereas very few morphological characters could be plotted as potential synapomorphies for these clades. (
  • Current projects in the lab include molecular phylogenetic analyses of familial and ordinal level relationships in the arthrodontous mosses, studies of hybridization using molecular and morphological markers, and investigations of cryptic speciation within geographically widespread species. (
  • Morphological and molecular information is being used to explore geographic patterns in phylogenetic diversity within the peatmosses. (
  • As you'll know if you've been keeping up with the results of the various big molecular and morphological analyses - and who hasn't - the avian cladogram is gradually coming together, though areas of debate and disagreement remain. (
  • Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. (
  • We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses. (
  • The breadth and scope of the ORIEN Avatar clinical and molecular data enables the discovery of a wide array of DNA and RNA biomarkers, including those biomarkers associated with response to immuno-oncology agents. (
  • In a previous study, we presented the clinical and molecular findings in 140 FCCM individuals. (
  • A short target sequence of 40-60 bases excised from the computer-generated electropherogram is sufficient for BLAST determination of all clinically relevant HPV genotypes, based on the database stored in the GenBank. (
  • All sequences generated and used in this study have been deposited in GenBank (Nos: MW740435-MW741429). (
  • Phylogenetic analyses were conducted using the combined ITS-1 and ITS-2 data sets from the present study and using reference sequences from the GenBank database. (
  • Sequencing delivers objective data on taxa of incredible diversity but mostly without a solid taxonomic foundation and should help pave the road for the eventual formal naming of new species. (
  • Our results provide an estimate of the distribution of fitness effects of weakly selected mutations and provide a possible explanation for why the molecular clock is fairly constant across taxa and time. (
  • The Genomics & Sequencing Data Integration, Analysis and Visualization Symposium is a part of the Molecular Medicine Tri-Conference. (
  • Please join us for a talk by Ravi Madduri on the subject "Integrated Research Data Management and Analysis in NGS Using Globus Genomics. (
  • Globus Genomics is a robust, scale on-demand solution that provides end-to-end research data management for Next-Gen Sequencing Analysis using Galaxy, Globus Online and Amazon Web Services. (
  • Here, we evaluated three representative and popular read-depth based CNV detection programs: the eXome-Hidden Markov Model (XHMM), the Copy Number Inference From Exome Reads (CoNIFER), and CNVnator using clinical grade WES data. (
  • 1 Laboratory for Molecular Development and Tumor Biology, Centre for Molecular Medicine (CMM), Stockholm, S-171 76, Sweden. (
  • Third, the molecular laboratory is challenged to monitor its sequencing processes for nonrandom process variation and other quality metrics. (
  • Both parsimony and Bayesian analyses were carried out on each of these data sets. (
  • Although molecular data in higher HIV-morbidity states have been analyzed ( 1 - 3 ), few analyses exist for lower morbidity states ( 4 ), such as Wisconsin, which reported 4.6 HIV diagnoses per 100,000 persons aged ≥13 years in 2016 ( 5 ). (
  • This chapter discusses the principle and the essential technical elements in performing nested PCR DNA amplification for the detection of HPV from clinical specimens and short target sequence genotyping for HPV, using standard molecular biology laboratory equipment and commercially available reagents. (
  • The authors use standard Health Level 7 laboratory result message formats in conjunction with international standards, Systematized Nomenclature of Medicine Clinical Terms and Human Genome Variant Society nomenclature, to represent, communicate, and store discrete gene sequence data within the EHR in a scalable fashion. (
  • The Operating Innovative Networks (OIN) workshop series is designed to equip university and laboratory network engineers with the knowledge and training needed to build next-gen campus networks that are optimized for data-intensive science. (
  • Important Note: As of October 2016, the publisher of the original article has the capability to edit the citation data in the PubMed record using the PubMed Data Management system, with the exception of MeSH data . (
  • Items related to Deep Sequencing Data Analysis (Methods in Molecular. (
  • Effectively, when carefully planned, any experimental question which can be translated into reading nucleic acids can be applied.In Deep Sequencing Data Analysis , expert researchers in the field detail methods which are now commonly used to study the multi-facet deep sequencing data field. (
  • 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. (
  • When sequenced on the Illumina platform, the resulting libraries yielded NGS sequence data indistinguishable from the labor-intensive methods previously employed by the facility. (
  • 2008. (Methods in Molecular Biology, Volume 452). (
  • 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. (
  • It includes an introductory section suitable for readers that are new to the field, a section discussing practical methods for data analysis, and more specialized sections discussing specific models and addressing statistical issues relating to estimation and model choice. (
  • It is my hope that it will also help the 'wet lab' molecular evolutionist to better understand mathematical and statistical methods. (
  • 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. (
  • Because of the ongoing advancements of molecular based oncology, this trial allows a detailed focus on molecular testing as part of any cohort. (
  • Thought leaders will discuss the convergence of cloud computing and big data to support life sciences research. (