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At least 1,063 records · Page 59Linked to original sources
PubMed2026

Genome sequence data of the chitinase-producing bacterium Paenibacillus mucilaginosus YWY-5.1.

Paenibacillus mucilaginosus is a beneficial bacterium widely applied as a biofertilizer in agriculture. To date, genomic information on this species remains limited; however, no genome assemblies from Vietnam have been reported. This work presented the draft genome of P. mucilaginosus YWY-5.1, a promising strain with strong chitin-degrading capability and agricultural potential, isolated from Yok Don National Park, Vietnam, using Illumina technology. Results showed that the assembled genome comprised 48 contigs with 4,076,146 bp and 73.8% GC-content. Genome annotation identified 3,611 protein-coding genes, 2 rRNA genes, and 53 tRNA genes. A total of 150 carbohydrate-active enzyme-related genes were predicted from the genome; among them, seven putative chitinolytic genes were identified, including 4 genes related to family 18 chitinase, 2 genes to family 20 β-N-acetylglucosaminidase, and one gene to auxiliary activity family 10. In addition, at least 32 genes related to plant growth-promoting functions were identified, including those associated with indole-3-acetic acid production, phosphate and potassium solubilization, siderophore biosynthesis, iron uptake, ACC metabolism, and nitrate transport and reduction. Furthermore, genome mining identified 4 biosynthetic gene clusters probably involved in secondary metabolite production, of which 3 displayed no similarity to previously reported clusters, indicating potential for novel bioactive compounds. These genomic data improved our understanding of the biodegradation capacity and agricultural potential of P. mucilaginosus YWY-5.1 isolated from Vietnam, and provided a valuable genomic resource for future functional and biotechnological investigations toward crop production and related fields.

Chitinases↗
PubMed2003

ESEfinder: A web resource to identify exonic splicing enhancers.

Point mutations frequently cause genetic diseases by disrupting the correct pattern of pre-mRNA splicing. The effect of a point mutation within a coding sequence is traditionally attributed to the deduced change in the corresponding amino acid. However, some point mutations can have much more severe effects on the structure of the encoded protein, for example when they inactivate an exonic splicing enhancer (ESE), thereby resulting in exon skipping. ESEs also appear to be especially important in exons that normally undergo alternative splicing. Different classes of ESE consensus motifs have been described, but they are not always easily identified. ESEfinder (http://exon.cshl.edu/ESE/) is a web-based resource that facilitates rapid analysis of exon sequences to identify putative ESEs responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.

Base Sequence↗
PubMed2006

Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs.

BACKGROUND: High-throughput genotyping technologies represent a highly efficient way to accelerate genetic mapping and enable association studies. As a first step toward this goal, we aimed to develop a resource of candidate Single Nucleotide Polymorphisms (SNP) in white spruce (Picea glauca [Moench] Voss), a softwood tree of major economic importance. RESULTS: A white spruce SNP resource encompassing 12,264 SNPs was constructed from a set of 6,459 contigs derived from Expressed Sequence Tags (EST) and by using the bayesian-based statistical software PolyBayes. Several parameters influencing the SNP prediction were analysed including the a priori expected polymorphism, the probability score (PSNP), and the contig depth and length. SNP detection in 3' and 5' reads from the same clones revealed a level of inconsistency between overlapping sequences as low as 1%. A subset of 245 predicted SNPs were verified through the independent resequencing of genomic DNA of a genotype also used to prepare cDNA libraries. The validation rate reached a maximum of 85% for SNPs predicted with either PSNP > or = 0.95 or > or = 0.99. A total of 9,310 SNPs were detected by using PSNP > or = 0.95 as a criterion. The SNPs were distributed among 3,590 contigs encompassing an array of broad functional categories, with an overall frequency of 1 SNP per 700 nucleotide sites. Experimental and statistical approaches were used to evaluate the proportion of paralogous SNPs, with estimates in the range of 8 to 12%. The 3,789 coding SNPs identified through coding region annotation and ORF prediction, were distributed into 39% nonsynonymous and 61% synonymous substitutions. Overall, there were 0.9 SNP per 1,000 nonsynonymous sites and 5.2 SNPs per 1,000 synonymous sites, for a genome-wide nonsynonymous to synonymous substitution rate ratio (Ka/Ks) of 0.17. CONCLUSION: We integrated the SNP data in the ForestTreeDB database along with functional annotations to provide a tool facilitating the choice of candidate genes for mapping purposes or association studies.

Algorithms↗
PubMed2006

MEME: discovering and analyzing DNA and protein sequence motifs.

MEME (Multiple EM for Motif Elicitation) is one of the most widely used tools for searching for novel 'signals' in sets of biological sequences. Applications include the discovery of new transcription factor binding sites and protein domains. MEME works by searching for repeated, ungapped sequence patterns that occur in the DNA or protein sequences provided by the user. Users can perform MEME searches via the web server hosted by the National Biomedical Computation Resource (http://meme.nbcr.net) and several mirror sites. Through the same web server, users can also access the Motif Alignment and Search Tool to search sequence databases for matches to motifs encoded in several popular formats. By clicking on buttons in the MEME output, users can compare the motifs discovered in their input sequences with databases of known motifs, search sequence databases for matches to the motifs and display the motifs in various formats. This article describes the freely accessible web server and its architecture, and discusses ways to use MEME effectively to find new sequence patterns in biological sequences and analyze their significance.

Amino Acid Motifs↗
PubMedDate not supplied

Expressed sequence tags for the chicken genome from a normalized 10-day-old White Leghorn whole embryo cDNA library: 1. DNA sequence characterization and linkage analysis.

Expressed sequence tags (ESTs) provide a rapid and reliable method for gene discovery as well as a resource for the large-scale analysis of gene expression of known and unknown genes. Here we describe a normalized cDNA library developed from a 10-day-old White Leghorn chicken whole embryo. The utility of the library was evaluated by partial sequencing of 99 randomly selected insert-containing clones and the analysis of EST-targeted genomic regions for single nucleotide polymorphisms (SNPs) in the East Lansing chicken reference DNA mapping panel. Using stringent match criteria of percent identity of 80 or higher across a length of 50 or more bases, 46 ESTs matched database sequences including previously reported Gallus gallus genes. Thirty-seven of the 50 primer pairs developed from 50 unique ESTs amplified a single fragment. The size of the 37 amplicons ranged from 276 to 693 bp for a total of 17,508 and an average of 473. About 70% of the SNPs detected were either G-->A or C-->T transition. The number of SNPs detected within the amplicons from EST-targeted genomic regions ranged from 0 to 4 for a total of 65 and a frequency of about 1 every 470 bases. About 35% of the amplicons contained only 1 SNP, while 19% had 4 SNPs. Using the SNPs that were informative in the East Lansing reference panel, 17 ESTs were mapped on the East Lansing chicken genetic map. The ESTs described, as well as the nucleotide variants identified within the EST-targeted genomic regions, represent significant resources for genome analysis in the chicken.

Animals↗
PubMed1996

The structural organization of the human skeletal muscle ryanodine receptor (RYR1) gene.

The RYR1 gene encoding the Ca2+ release channel of human skeletal muscle sarcoplasmic reticulum has been cloned and exon/intron boundaries have been determined, together with a minimum of 30 bp of intron sequence flanking each splice junction. The gene contains 106 exons, of which two are alternatively spliced. The length of the gene, determined by the alignment of 16 genomic phage clones, a cosmid clone, and several long polymerase chain reaction products, is approximately 160 kb. Exons range from 15 to 813 bp, while introns range from 85 to about 16,000 bp. Analysis of the gene has confirmed published errors in the human RYR1 cDNA and confirmed the structure of two alternatively spliced exons. The numbering of the nucleotides comprising the RYR1 cDNA and the numbering of amino acids encoded by them were corrected to account for these earlier errors and omissions. Analysis of 2.4 kb of the 5' upstream sequence indicated the presence of a CCAAT box and several Sp1 binding sites between nucleotides -200 and -60 bp, flanking the proposed transcription start site at -130 bp. Several other potential transcription factor binding sites were identified throughout the 5' sequence. Knowledge of the structure of the RYR1 gene will provide an invaluable resource for the discovery of mutations in the gene that are causal of human malignant hyperthermia and central core disease.

Amino Acid Sequence↗
PubMed2006

Molecular signatures (unique proteins and conserved indels) that are specific for the epsilon proteobacteria (Campylobacterales).

BACKGROUND: The epsilon proteobacteria, which include many important human pathogens, are presently recognized solely on the basis of their branching in rRNA trees. No unique molecular or biochemical characteristics specific for this group are known. RESULTS: Comparative analyses of proteins in the genomes of Wolinella succinogenes DSM 1740 and Campylobacter jejuni RM1221 against all available sequences have identified a large number of proteins that are unique to various epsilon proteobacteria (Campylobacterales), but whose homologs are not detected in other organisms. Of these proteins, 49 are uniquely found in nearly all sequenced epsilon-proteobacteria (viz. Helicobacter pylori (26695 and J99), H. hepaticus, C. jejuni (NCTC 11168, RM1221, HB93-13, 84-25, CF93-6, 260.94, 11168 and 81-176), C. lari, C. coli, C. upsaliensis, C. fetus, W. succinogenes DSM 1740 and Thiomicrospira denitrificans ATCC 33889), 11 are unique for the Wolinella and Helicobacter species (i.e. Helicobacteraceae family) and many others are specific for either some or all of the species within the Campylobacter genus. The primary sequences of many of these proteins are highly conserved and provide novel resources for diagnostics and therapeutics. We also report four conserved indels (i.e. inserts or deletions) in widely distributed proteins (viz. B subunit of exinuclease ABC, phenylalanyl-tRNA synthetase, RNA polymerase beta '-subunit and FtsH protein) that are specific for either all epsilon proteobacteria or different subgroups. In addition, a rare genetic event that caused fusion of the genes for the largest subunits of RNA polymerase (rpoB and rpoC) in Wolinella and Helicobacter is also described. The inter-relationships amongst Campylobacterales as deduced from these molecular signatures are in accordance with the phylogenetic trees based on the 16S rRNA and concatenated sequences for nine conserved proteins. CONCLUSION: These molecular signatures provide novel tools for identifying and circumscribing species from the Campylobacterales order and its subgroups in molecular terms. Although sequence information for these signatures is presently limited to Campylobacterales species, it is likely that many of them will also be found in other epsilon proteobacteria. Functional studies on these proteins and conserved indels should reveal novel biochemical or physiological characteristics that are unique to these groups of epsilon proteobacteria.

Bacterial Proteins↗
PubMed2000

Resources at EBI.

Explore the source record for details and available documents.

Amino Acid Sequence↗
PubMed2004

SSR marker and ITS cleaved amplified polymorphic sequence analysis of soybean x Glycine tomentella intersubgeneric derived lines.

Wild perennial Glycine species are an invaluable gene resource for the cultivated soybean [ Glycine max (L.) Merr., 2 n=40]. However, these wild species have been largely unexplored in soybean breeding programs because of their extremely low crossability with soybean and the need to employ in vitro embryo rescue methods to produce F(1) hybrids. The objective of this study was to develop molecular markers to identify gene introgression from G. tomentella, a wild perennial Glycine species, to soybean. A selection of 96 soybean simple sequence repeat (SSR) markers was evaluated for cross-specific amplification and polymorphism in G. tomentella. Thirty-two SSR markers (33%) revealed specific alleles for G. tomentella PI 483218 (2 n=78). These SSR markers were further examined with an amphidiploid line (2 n=118) and monosomic alien addition lines (MAALs), each with 2 n=40 chromosomes from soybean and one from G. tomentella. The results show that the use of SSR markers is a rapid and reliable method to detect G. tomentella chromosomes in MAALs. We also developed a cleaved amplification polymorphism sequence (CAPS) marker according to the sequences of internal transcribed spacer (ITS) regions in soybean and G. tomentella. Four MAALs that carry the ITS (rDNA) locus from G. tomentella were identified. The SSR and ITS-CAPS markers will greatly facilitate the introgression and characterization of gene transfer from G. tomentella to soybean.

Base Sequence↗
PubMed1996

Maintaining the integrity of human immunodeficiency virus sequence databases.

Human immunodeficiency virus type 1 (HIV-1) sequences are accumulating in the literature at a rapid pace. For this ever-expanding resource to be maximally useful, it is critical that researchers strive to maintain a high level of quality assurance, both in experimental design and conduct and in analyses. Here we present detailed analyses of problematic sets of HIV-1 sequences in the database that include sequence anomalies suggestive of mislabeling or sample contamination problems. These data are examined in the context of currently available HIV-1 sequence information to provide an example of how to identify potentially flawed data. Indicators of potential problems with sequences are (i) sequences that are nearly identical that are supposed to be derived from unlinked individuals and that are markedly distinct from other sequences from the putative source or (ii) sequences that are nearly identical to those of laboratory strains. We provide an outline of methods that researchers can use to perform preliminary laboratory and computational analyses that could help identify problematic data and thus help ensure the integrity of sequence databases.

Base Sequence↗
PubMed2005

Diversity of methanotrophic bacteria in tropical upland soils under different land uses.

Three upland soils from Thailand, a natural forest, a 16-year-old reforested site, and an agricultural field, were studied with regard to methane uptake and the community composition of methanotrophic bacteria (MB). The methane uptake rates were similar to rates described previously for forest and farmland soils of the temperate zone. The rates were lower at the agricultural site than at the native forest and reforested sites. The sites also differed in the MB community composition, which was characterized by denaturing gradient gel electrophoresis (DGGE) of pmoA gene fragments (coding for a subunit of particulate methane monooxygenase) that were PCR amplified from total soil DNA extracts. Cluster analysis based on the DGGE banding patterns indicated that the MB communities at the forested and reforested sites were similar to each other but different from that at the farmland site. Sequence analysis of excised DGGE bands indicated that Methylobacter spp. and Methylocystis spp. were present. Sequences of the "forest soil cluster" or "upland soil cluster alpha," which is postulated to represent organisms involved in atmospheric methane consumption in diverse soils, were detected only in samples from the native forest and reforested sites. Additional sequences that may represent uncultivated groups of MB in the Gammaproteobacteria were also detected.

Agriculture↗
PubMed1999

Developmental expression of specific genes detected in high-quality cDNA libraries from single human preimplantation embryos.

We describe an improved highly sensitive method for generating cDNA libraries containing a high proportion of cDNAs enriched with 5'-coding sequences from single human preimplantation embryos and a 10 week old whole foetus. The embryonic mRNA was isolated using oligo-(dT) linked to magnetic beads. First-strand cDNA synthesis was carried out directly on the bound mRNA, followed by PCR designed to amplify the cDNA molecules synthesized in their entirety. The complexities of the libraries are between 10(5) and 10(6) independent clones. The average cDNA size is 1.0 kb, and the size range is 0.5-3.0 kb. PCR analysis of the embryonic libraries for specific genes has revealed transcripts for genes known to be transcribed in preimplantation stages, such as the imprinted gene SNRPN, developmental genes WNT11, HOX, OCT-1 and the embryonic OCT-4, cytoskeletal genes keratin-18 and beta-actin, the cell cycle gene C-MOS, and housekeeping genes GAPDH and HPRT. Sequencing of random clones showed the presence of a variety of sequences, such as human chorionic gonadotrophin, ubiquitin, TFIIA, guanine nucleotide-binding protein (beta-subunit), annexin I, a gene encoding a kinesin-like protein, and TWIST, which encodes a basic helix-loop-helix (bHLH) transcription factor implicated in Saethre-Chotzen syndrome (characterized by craniofacial and limb anomalies). Approximately 40% of these randomly analysed clones were full length. In addition to cDNAs matching known ESTs (Expressed Sequence Tags) in the GenBank and dbEST databases, novel sequences were detected at a frequency of 16% of randomly picked clones. The libraries are a valuable resource, providing longer cDNAs representing genes expressed during human preimplantation development.

Actins↗
PubMed2005

Floral gene resources from basal angiosperms for comparative genomics research.

BACKGROUND: The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST) sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants. RESULTS: Random sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04) generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i) proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii) many known floral gene homologues have been captured, and (iii) phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms. CONCLUSION: Initial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and functional divergence, and analyses of adaptive molecular evolution. Since not all genes in the floral transcriptome will be associated with flowering, these EST resources will also be of interest to plant scientists working on other functions, such as photosynthesis, signal transduction, and metabolic pathways.

Biodiversity↗
PubMed2004

Genetic divergence, population structure and historical demography of rare springsnails (Pyrgulopsis) in the lower Colorado River basin.

Springsnails of the genus Pyrgulopsis are the most diverse group of freshwater gastropods in North America and current estimates show that Pyrgulopsis contains ~120 different species, many of which are at risk of extinction. Some factors contributing to their exceptional diversity include poor dispersal ability and extreme habitat specificity based on water availability, chemistry and depth. Most taxa exhibit high degrees of endemism, with many species occurring only in a single spring or seep, making springsnails ideal for studies of speciation and population structure. Here I present data from a survey of genetic variation at the mitochondrial gene cytochrome oxidase I from 37 populations and over 1000 individuals belonging to 16 species of Pyrgulopsis distributed throughout the lower Colorado River basin. High levels of interspecific sequence divergence indicate that Pyrgulopsis may have colonized this region multiple times beginning in the late Miocene (~6 Ma); earlier than previous estimates based on fossil evidence. Estimates of nucleotide diversity differ greatly among species and may reflect differences in demographic processes. These results are used to identify factors contributing to radiation of species in this region. The implications of this evolutionary history and genetic variation are discussed in relation to future management and conservation.

Animals↗
PubMed2004

HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development.

Hematopoiesis describes the process of the normal formation and development of blood cells, involving both proliferation and differentiation from stem cells. Abnormalities in this developmental program yield blood cell diseases, such as leukemia. Although, in recent years, extensive molecular research in normal hematopoietic development has characterized transcription factors and their binding sites in the target gene promoters, the information generated is highly fragmented. In order to integrate this important regulatory information with the corresponding genomic sequences, we have developed a new database called Hematopoiesis Promoter Database (HemoPDB). HemoPDB is a comprehensive resource focused on transcriptional regulation during hematopoietic development and associated aberrances that result in malignancy. HemoPDB (version 1.0) contains 246 promoter sequences and 604 experimentally known cis-regulatory elements of 187 different transcription factors, with links to published references. Orthologous promoters from different species are linked with each other and displayed in the same database record, accompanied by a visual image of the promoters and corresponding annotations of cis-regulatory elements. HemoPDB may be searched for the promoter of a specific gene, transcription factors and target genes, and genes that are expressed in a certain cell type or lineage, through a user-friendly web interface at http://bioinformatics.med.ohio-state.edu/HemoPDB. Links to the documentation and other technical details are provided on this website.

Animals↗
PubMed2005

Molecular identification of lizard by RAPD & FINS of mitochondrial 16s rRNA gene.

In the present study, we identified the structure-less skeleton suspected to be of house lizard present in jaggery, consumption of which caused mass food poisoning using, RAPD (Random Amplification of Polymorphic DNA) with random primers and FINS (Forensically Informative Nucleotide Sequencing) with mitochondrial 16s rRNA gene. The NJ tree dendogram based on distance calculated from RAPD bands clearly identified the structure-less as Calotes versicolor (Garden Lizard). In FINS analysis of the mitochondrial 16s rRNA gene the NJ tree based on Kimura-2-parameter distance matrices clearly reveal that the unknown sample clustered with Agmidae family and closest to Calotes versicolor (Garden Lizard) with 100% bootstrap support, whereas all other species belong to Gekkonida family form a single distinct cluster including Hemidactylus fluviviridis (House Lizard). This is the first successful typing of mitochondrial 16s rRNA with FINS approach to identify the biological origin of a structure-less skeleton. Our analysis also sustained successful identification of unknown samples using RAPD method with optimized conditions in a laboratory setup with low resources.

Animals↗
PubMed2005

Ciona intestinalis: chordate development made simple.

Thanks to their transparent and rapidly developing mosaic embryos, ascidians (or sea squirts) have been a model system for embryological studies for over a century. Recently, ascidians have entered the postgenomic era, with the sequencing of the Ciona intestinalis genome and the accumulation of molecular resources that rival those available for fruit flies and mice. One strength of ascidians as a model system is their close similarity to vertebrates. Literature reporting molecular homologies between vertebrate and ascidian tissues has flourished over the past 15 years, since the first ascidian genes were cloned. However, it should not be forgotten that ascidians diverged from the lineage leading to vertebrates over 500 million years ago. Here, we review the main similarities and differences so far identified, at the molecular level, between ascidian and vertebrate tissues and discuss the evolution of the compact ascidian genome.

Animals↗
PubMed1996

Assembly of a 1-Mb restriction-mapped cosmid contig spanning the candidate region for Finnish congenital nephrosis (NPHS1) in 19q13.1.

We describe the assembly of a 1-Mb cosmid contig and restriction map spanning the candidate region for Finnish congenital nephrosis (NPHS1) in 19q13.1. The map was constructed from 16 smaller contigs assembled by fingerprinting, a BAC and a PAC clone, and 42 previously unmapped cosmids. In most cases, single-step cosmid walks were sufficient to join two previously assembled contigs, and all but one gap was filled from this cosmid contig library. The remaining gap of about 19 kb was spanned with a single BAC and a single PAC clone. EcoRI mapping of a dense set of overlapping clones validated the assembly of the map and indicated a length of 1040 kb for the contig. This high-resolution clone map provides an ideal resource for gene identification through cDNA selection, exon trapping, and DNA sequencing.

Chromosome Mapping↗