• genomic
  • And, until recently, all was in place: intuition, formal theory, and experimental observations all supported the proposition that although higher rates of mutation can appear occasionally, mutation rates in bacterial populations would remain low and mutator alleles (alleles elevating the genomic mutation rate) would not be selected. (genetics.org)
  • Relative quantification of DNA copy number data from the genomic regions 1 Mb apart from the candidate fusion genes is shown. (aacrjournals.org)
  • In plants, relative copy number of recombination-derived subgenomic DNA molecules within mitochondria is controlled by nuclear genes, and a genomic shifting process can result in their differential copy number suppression to nearly undetectable levels. (pnas.org)
  • Identifying proteins selectively associated with a genomic locus provides an important entry point toward understanding how a specific gene is regulated. (pnas.org)
  • Next, we targeted a different genomic locus, the Drosophila melanogaster histone cluster, and identified several regulators of the essential histone locus and validated their functional association with genes within the locus. (pnas.org)
  • To comprehensively survey the proteome directing gene expression at a specific genomic locus of interest, we developed an in vitro nuclease-deficient Cas9 (dCas9)-targeted chromatin-based purification strategy, called "CLASP" (Cas9 locus-associated proteome), to identify and functionally test associated gene-regulatory factors. (pnas.org)
  • Our CLASP method, coupled to mass spectrometry and functional screens, can be efficiently adapted for isolating associated regulatory factors in an unbiased manner targeting multiple genomic loci across different cell types. (pnas.org)
  • Given the importance of the ULBPs in antiviral immunity in other species, our goal was to determine the copy number and genomic organization of the ULBP genes in the cattle genome. (biomedcentral.com)
  • The purpose of the present study was to identify the number of ULBP genes in cattle and describe their genomic organization. (biomedcentral.com)
  • These gene models were predicted using a different algorithm and provide additional support to some Joint Genome Institute (JGI) gene models as well as indicate regions of the genomic sequence that need focused attention. (usda.gov)
  • quantitative trai
  • This topic involves the identification of quantitative trait loci (QTL) and genes underlying 16 target traits associated with resistance to disease and pests such as blast, bacterial blight and brown planthopper, as well as tolerance to environmental stresses such as drought, flood and salinity. (biotec.or.th)
  • genome
  • Genome change in wheat observed through the structure and expression of α/β-gliadin genes. (nih.gov)
  • Duplication of genome segments containing α/β-gliadin genes and retrotransposons were brought about through unequal crossing-over or saltatory replication and α/β-gliadin genes per se were duplicated without any recombination events. (nih.gov)
  • The ULBP loci in the cattle genome apparently arose by gene duplication and subsequent sequence divergence. (biomedcentral.com)
  • Southern blot analysis revealed the existence of a high copy number of ULBP genes in the cattle genome and seven other ruminant genomes. (biomedcentral.com)
  • one is to use the transgenic approach and RNAi for overexpression or co-suppression of the candidate genes and the other is using whole-genome mutagenesis called TILLING. (biotec.or.th)
  • RiceGeneThresher provides full access to an integrated multiplatform relational database of heterogeneous rice genome resources for decision-making and candidate gene selection, as well as tools from microarray analysis. (biotec.or.th)
  • A web-based application for mining genes underlying QTL in the rice genome. (biotec.or.th)
  • The locus was given the official name "SPCH1" (for speech-and-language-disorder-1) by the Human Genome Nomenclature committee. (wikipedia.org)
  • The olfactory receptor gene family is the largest in the genome. (wikipedia.org)
  • The Physical Mapping Problem is to reconstruct the relative position of fragments (clones) of DNA along the genome from information on their pairwise overlaps. (psu.edu)
  • The SoyBase genome viewer was updated with newly annotated soybean genes. (usda.gov)
  • SoyBase staff also added 50,574 National Center for Biotechnology Information (NCBI) RefSeq gene models to the SoyBase genome viewer. (usda.gov)
  • SoyBase and Legume Information System (LIS) personnel worked with Department of Energy-Joint Genome Institute (DOE-JGI) to revise the soybean gene annotations. (usda.gov)
  • EcoRI fragments of the P1 Bacteriophage genome were generated and cloned into lambda vectors. (wikipedia.org)
  • On the other hand, a variable number of repeats of entire genes is less commonly identified in the genome. (wikipedia.org)
  • molecular
  • In soybean [ Glycine max (L.) Merrill], several associations between photosensitivity and maturity loci are known, but only limited information at the molecular level is available. (genetics.org)
  • To fully understand the molecular mechanisms governing multiple steps in gene expression, including transcription and posttranscriptional regulation for a given gene, one must first identify the various protein factors involved in the process. (pnas.org)
  • This topic involves the study of genes controlling plant, flower and seed development to increase rice yield, as well as molecular mechanisms controlling plant growth and plant response to different environments. (biotec.or.th)
  • Restriction digest is most commonly used as part of the process of the molecular cloning of DNA fragment into a vector (such as a cloning vector or an expression vector). (wikipedia.org)
  • The development of molecular ecology is also closely related to the use of DNA microarrays, which allows for the simultaneous analysis of the expression of thousands of different genes. (wikipedia.org)
  • Molecular ecological techniques have recently been used to study in situ questions of bacterial diversity. (wikipedia.org)
  • sequences
  • Out of twelve intact α/β-gliadin genes detected from their sequences, nine were expressed, although their patterns of expression were distinct. (nih.gov)
  • Structures for the UBE2L3 and KRAS genes have their basis in the Genbank reference sequences. (aacrjournals.org)
  • We show that a clone containing Myf5 and 140 kb of upstream sequences is sufficient to recapitulate the known expression patterns of both genes. (biologists.org)
  • Restriction enzymes specific to hundreds of distinct sequences have been identified and synthesized for sale to laboratories, and as a result, several potential "restriction sites" appear in almost any gene or locus of interest on any chromosome. (wikipedia.org)
  • proteins
  • Eukaryotic gene regulation is a complex process, often coordinated by the action of tens to hundreds of proteins. (pnas.org)
  • These include the locus of enterocyte effacement (LEE)-encoded type III secretion system (T3SS), various T3-secreted effector proteins, H7 flagellin, and a number of specific adhesins, including F9 fimbriae and autotransporters. (frontiersin.org)
  • The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. (wikipedia.org)
  • The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. (wikipedia.org)
  • Despite their abundance and role in bacterial pathogenesis, most AT proteins have not been structurally characterized, and there is a paucity of detailed information with regard to their mode of action. (pnas.org)
  • We isolated the TAN gene and showed that the predicted polypeptide has seven WD repeat motifs, suggesting that TAN forms complexes with other proteins. (plantphysiol.org)
  • The mechanism of these recombination events was known to be unique as they occurred in the absence of bacterial RecA and RecBCD proteins. (wikipedia.org)
  • P. syringae pathogenesis is dependent on effector proteins secreted into the plant cell by the bacterial type III secretion system. (wikipedia.org)
  • bacteria
  • What happens when bacteria are faced with novel or fluctuating environmental conditions and no external sources of beneficial genes are available? (genetics.org)
  • A broad but not mechanistic answer from the classical theory is simply that those populations probably faced environments that fluctuated rapidly enough to favor mutator genes and that such fluctuations may be very common for bacteria. (genetics.org)
  • Notable contributions include the discovery of the bacterial virus λ, the transfer of genes between bacteria by specialized transduction, the development of replica plating, and the discovery of the bacterial fertility factor F (F plasmid). (wikipedia.org)
  • MazEF, a toxin-antitoxin locus found in E. coli and other bacteria, induces programmed cell death in response to starvation, specifically a lack of amino acids. (wikipedia.org)
  • rice
  • The Rice Gene Discovery Laboratory was established in 2001 through close collaboration between BIOTEC and Kasetsart University. (biotec.or.th)
  • Discovery of genes responsible for producing aroma in rice (Patent obtained in the US, Australia, Japan, Vietnam, France and Europe. (biotec.or.th)
  • Ronald's group subsequently mapped, sequenced, and cloned the Xa21 gene from this rice strain. (wikipedia.org)
  • In response, UC Davis allowed noncommercial use of the gene and released the gene to IRRI for the development of rice strains to be grown in developing nations. (wikipedia.org)
  • traits
  • This increases the resolution of QTL regions facilitating the discovery of genes responsible for agronomically important traits. (usda.gov)
  • functional
  • functional studies of the gene in mice and in songbirds indicate that it is important for modulating plasticity of neural circuits. (wikipedia.org)
  • The majority of fungal ecology research leveraging next-generation sequencing approaches involves sequencing of PCR amplicons of conserved regions of DNA (i.e. marker genes) to identify and describe the distribution of taxonomic groups in the fungal community in question, though more recent research has focused on sequencing functional gene amplicons (e.g. (wikipedia.org)
  • respectively
  • To establish consistency with the human nomenclature, the cattle MHCLA1 and MHCLA2 genes are renamed ULBP1 and ULBP2 , respectively, in this study. (biomedcentral.com)
  • Humans express two types of intelectins encoded by ITLN1 and ITLN2 genes respectively. (wikipedia.org)
  • immunity
  • The large number of ULBPs in cattle, their extensive diversification, and the high prevalence of bovine herpesvirus infections make this gene family a compelling target for studies of antiviral immunity. (biomedcentral.com)
  • The second tier, primarily governed by R gene products, is often termed effector-triggered immunity (ETI). (wikipedia.org)
  • amplification
  • A , left, amplification breakpoint analysis and ConSig scoring (yellow line) of 3′ amplified genes from a panel of advanced prostate cancer cell lines nominating KRAS as a fusion gene candidate with 3′ amplification (red columns) in the DU145 prostate cancer cell line. (aacrjournals.org)
  • Right, matching the amplification level of 5′ amplified genes in DU145 cells nominates SOX5, C14orf166 , and UBE2L3 as 5′ fusion partner candidates for KRAS . (aacrjournals.org)
  • transcription
  • For genes, the direction of transcription is indicated by arrows and exons, by bars. (aacrjournals.org)
  • The FOXP2 protein contains a forkhead-box DNA-binding domain, making it a member of the FOX group of transcription factors, involved in regulation of gene expression. (wikipedia.org)
  • Using a combination of bioinformatics and RNA analyses, they discovered that the gene codes for a novel protein belonging to the forkhead-box (FOX) group of transcription factors. (wikipedia.org)
  • Studies on the control of these alternative cycles have been very important for our understanding of the regulation of gene transcription. (wikipedia.org)
  • insertion
  • We calculated time since duplication of each set of α/β-gliadin genes and insertion of retrotransposons. (nih.gov)
  • distinct
  • Since they have similar cis-elements and promoter structures, the mechanisms underlying their distinct gene expression and possible applications are discussed. (nih.gov)
  • Passage through a unicellular bottleneck assures that each representative of the next generation of organisms represents a distinct clone. (wikipedia.org)
  • mechanism
  • Although the specific mechanism that allows the AMY1 gene to increase or decrease its copy number is still a topic of debate, some hypotheses suggest that the non-homologous end joining or the microhomology-mediated end joining is likely responsible for these whole gene repeats. (wikipedia.org)
  • 2001
  • In 2001, the team identified in CS that the mutation is in the middle of a protein-coding gene. (wikipedia.org)
  • encodes
  • Our data indicate that the tangerine gene, designated CRTISO, encodes an authentic carotenoid isomerase that is required during carotenoid desaturation. (mendeley.com)
  • One example of a whole gene repeat is the alpha-amylase 1 gene (AMY1) that encodes alpha-amylase which has a significant copy number variation between different populations with different diets. (wikipedia.org)
  • mutation
  • Remarkably, the inheritance of the disorder from one generation to the next was consistent with autosomal dominant inheritance, i.e., mutation of only a single gene on an autosome (non-sex chromosome) acting in a dominant fashion. (wikipedia.org)
  • When the researchers sequenced the FOXP2 gene in the KE family, they found a heterozygous point mutation shared by all the affected individuals, but not in unaffected members of the family and other people. (wikipedia.org)
  • In tangerine(mic), loss of function is attributable to a deletion mutation in CRTISO, and in tangerine(3183), expression of this gene is impaired. (mendeley.com)
  • hybridization
  • To verify the library, clones containing a complete locus of enterocyte effacement (LEE) were identified by DNA hybridization. (frontiersin.org)
  • Methods frequently include using microsatellites to determine gene flow and hybridization between populations. (wikipedia.org)
  • interactions
  • This work provides insight into the structure-function mechanisms that facilitate bacterial interactions during infection. (pnas.org)
  • As a graduate student at UC Berkeley, she began to study plant-bacterial interactions in the laboratory of Brian Staskawicz, working with peppers and tomatoes. (wikipedia.org)
  • regulation
  • Although previous biochemical studies have identified many components of the basal machinery and various ancillary factors involved in gene regulation, numerous gene-specific regulators remain undiscovered. (pnas.org)
  • In addition, if these tri-nucleotide repeats are in the same reading frame in the coding portion of a gene, it may lead to a long chain of the same amino acid, possibly creating protein aggregates in the cell, and if these short repeats fall into the non-coding portion of the gene, it may affect gene expression and regulation. (wikipedia.org)
  • forkhead box
  • Forkhead box protein P2 (FOXP2) is a protein that, in humans, is encoded by the FOXP2 gene, also known as CAGH44, SPCH1 or TNRC10, and is required for proper development of speech and language. (wikipedia.org)
  • transposons
  • In total, twelve α/β-gliadin intact genes and four pseudogenes were found, and retrotransposons or other transposons existed in each BAC clone. (nih.gov)
  • expression
  • Mrf4 expression requires at least four elements, one of which may be shared with Myf5, providing a possible explanation for the linkage of these genes throughout vertebrate phylogeny. (biologists.org)
  • Several recent studies have determined that a high percentage of AA patients show a T→A single nucleotide polymorphism at position +874 of intron 1 in the IFN-γ gene compared with normal controls, resulting in higher levels of IFN-γ expression. (bloodjournal.org)
  • Quantitative PCR may also be used to analyze gene expression as a result of changes in environmental conditions or different response by differently adapted individuals. (wikipedia.org)
  • DNA microarray technology was rapidly adopted for A. thaliana research and led to the development of "atlases" of gene expression in different tissues and under different conditions. (wikipedia.org)
  • Repeats of entire genes has immediate effects on expression of that particular gene, and the fact that the copy number variation of the AMY1 gene has been related to diet is a remarkable example of recent human evolutionary adaptation. (wikipedia.org)
  • FOXP2
  • FOXP2 is popularly dubbed the "language gene", but this is only partly correct since there are other genes involved in language development. (wikipedia.org)
  • FOXP2 and its gene were discovered as a result of investigations on an English family known as the KE family, half of whom (fifteen individuals across three generations) suffered from a speech and language disorder called developmental verbal dyspraxia. (wikipedia.org)
  • cattle
  • It was thus hypothesized that the cattle ULBP genes evolved rapidly by duplication and sequence divergence in response to selective pressure exerted by a viral pathogen(s). (biomedcentral.com)
  • abundance
  • This report shows that deletion of Gpr107 leads to an embryonic lethal phenotype that is characterized by a reduction in cubilin transcript abundance and a decrease in the representation of multiple genes implicated in the cubilin-megalin endocytic receptor complex (megalin is also known as LRP2). (biologists.org)
  • restriction
  • Based on their restriction fragment patterns, we selected five BAC clones, namely, two clones for Gli-A2, two clones for Gli-B2, and one clone for Gli-D2, to fully sequence. (nih.gov)
  • The vector typically contains a multiple cloning site where many restriction site may be found, and a foreign piece of DNA may be inserted into the vector by first cutting the restriction sites in the vector as well the DNA fragment, followed by ligation of the DNA fragment into the vector. (wikipedia.org)
  • infections
  • Many persistent and chronic bacterial infections are associated with the formation of large cell aggregates and biofilms that are difficult to treat. (pnas.org)
  • bovine
  • one involved three rounds of adherence assays to bovine primary rectal epithelial cells while the other competed the clones over three rounds of growth in bovine rectal mucus. (frontiersin.org)
  • representation
  • 2012). The locus of choice for description of the taxonomic structure of fungal communities has traditionally been the internal transcribed spacer (ITS) region of ribosomal RNA genes due to its utility in identifying fungi to genus or species taxonomic levels, and its high representation in public sequence databases. (wikipedia.org)
  • cluster
  • The major family of T3SS effectors in P. syringae is the hrp gene cluster, coding for the Hrp secretion apparatus. (wikipedia.org)
  • classification
  • 2013), the D1-D3 region of 28S ribosomal RNA genes, may not allow the low taxonomic level classification of the ITS, but demonstrates superior performance in sequence alignment and phylogenetics. (wikipedia.org)
  • However, there are no clear boundaries between the two groups and the classification depends on the nature of the loci of interest. (wikipedia.org)
  • studies
  • Similar to exploration of bacterial diversity, these techniques have allowed high-resolution studies of fundamental questions in fungal ecology such as phylogeography, fungal diversity in forest soils, stratification of fungal communities in soil horizons, and fungal succession on decomposing plant litter. (wikipedia.org)
  • The rationale for this project was to combine new high-throughput technologies with systematic gene-family-wide studies and community resources to accelerate progress beyond what was possible via piecemeal single-laboratory studies. (wikipedia.org)