Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Sequencing Resource”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,117 records · Page 62Linked to original sources
PubMed2004

Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing.

The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of approximately 30,000 nonredundant human mRNA sequences with identified coding regions representing 17,000 distinct loci. These high-quality mRNA sequences allow for the identification of transcribed regions in the human genome sequence, and many researchers accept them as the correct representation of each defined gene sequence. Computational comparison of these mRNA sequences and the recently published essentially finished human genome sequence reveals several thousand undocumented nonsynonymous substitution and frame shift discrepancies between the two resources. Additional analysis is undertaken to verify that the euchromatic human genome is sufficiently complete--containing nearly the whole mRNA collection, thus allowing for a comprehensive analysis to be undertaken. Many of the discrepancies will prove to be genuine polymorphisms in the human population, somatic cell genomic variants, or examples of RNA editing. It is observed that the genome sequence variant has significant additional support from other mRNAs and ESTs, almost four times more often than does the mRNA variant, suggesting that the genome sequence is more accurate. In approximately 15% of these cases, there is substantial support for both variants, suggestive of an undocumented polymorphism. An initial screening against a 24-individual genomic DNA diversity panel verified 60% of a small set of potential single nucleotide polymorphisms from which successful results could be obtained. We also find statistical evidence that a few of these discrepancies are due to RNA editing. Overall, these results suggest that the mRNA collections may contain a substantial number of errors. For current and future mRNA collections, it may be prudent to fully reconcile each genome sequence discrepancy, classifying each as a polymorphism, site of RNA editing or somatic cell variation, or genome sequence error.

Computational Biology↗
PubMed2003

Chlamydomonas reinhardtii genome project. A guide to the generation and use of the cDNA information.

The National Science Foundation-funded Chlamydomonas reinhardtii genome project involves (a) construction and sequencing of cDNAs isolated from cells exposed to various environmental conditions, (b) construction of a high-density cDNA microarray, (c) generation of genomic contigs that are nucleated around specific physical and genetic markers, (d) generation of a complete chloroplast genome sequence and analyses of chloroplast gene expression, and (e) the creation of a Web-based resource that allows for easy access of the information in a format that can be readily queried. Phases of the project performed by the groups at the Carnegie Institution and Duke University involve the generation of normalized cDNA libraries, sequencing of cDNAs, analysis and assembly of these sequences to generate contigs and a set of predicted unique genes, and the use of this information to construct a high-density DNA microarray. In this paper, we discuss techniques involved in obtaining cDNA end-sequence information and the ways in which this information is assembled and analyzed. Descriptions of protocols for preparing cDNA libraries, assembling cDNA sequences and annotating the sequence information are provided (the reader is directed to Web sites for more detailed descriptions of these methods). We also discuss preliminary results in which the different cDNA libraries are used to identify genes that are potentially differentially expressed.

Animals↗
PubMed2003

Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters.

Together with the hemichordates, sea urchins represent basal groups of nonchordate invertebrate deuterostomes that occupy a key position in bilaterian evolution. Because sea urchin embryos are also amenable to functional studies, the sea urchin system has emerged as one of the leading models for the analysis of the function of genomic regulatory networks that control development. We have analyzed a total of 107,283 cDNA clones of libraries that span the development of the sea urchin Strongylocentrotus purpuratus. Normalization by oligonucleotide fingerprinting, EST sequencing and sequence clustering resulted in an EST catalog comprised of 20,000 unique genes or gene fragments. Around 7000 of the unique EST consensus sequences were associated with molecular and developmental functions. Phylogenetic comparison of the identified genes to the genome of the urochordate Ciona intestinalis indicate that at least one quarter of the genes thought to be chordate specific were already present at the base of deuterostome evolution. Comparison of the number of gene copies in sea urchins to those in chordates and vertebrates indicates that the sea urchin genome has not undergone extensive gene or complete genome duplications. The established unique gene set represents an essential tool for the annotation and assembly of the forthcoming sea urchin genome sequence. All cDNA clones and filters of all analyzed libraries are available from the resource center of the German genome project at http://www.rzpd.de.

Animals↗
PubMed2005

Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity.

The Poales (which include the grasses) and Asparagales [which include onion (Allium cepa L.) and other Allium species] are the two most economically important monocot orders. Enormous genomic resources have been developed for the grasses; however, their applicability to other major monocot groups, such as the Asparagales, is unclear. Expressed sequence tags (ESTs) from onion that showed significant similarities (80% similarity over at least 70% of the sequence) to single positions in the rice genome were selected. One hundred new genetic markers developed from these ESTs were added to the intraspecific map derived from the BYG15-23xAC43 segregating family, producing 14 linkage groups encompassing 1,907 cM at LOD 4. Onion linkage groups were assigned to chromosomes using alien addition lines of Allium fistulosum L. carrying single onion chromosomes. Visual comparisons of genetic linkage in onion with physical linkage in rice revealed scant colinearity; however, short regions of colinearity could be identified. Our results demonstrate that the grasses may not be appropriate genomic models for other major monocot groups such as the Asparagales; this will make it necessary to develop genomic resources for these important plants.

Base Sequence↗
PubMedDate not supplied

Zebrafish as a neurotoxicological model.

At a time when common regulatory pathways are being identified in several different species and genomics is beginning to allow comparisons of genes, how they are arranged on chromosomes and how they are regulated, zebrafish has emerged as a valuable and complementary vertebrate model. Some of the characteristics that prove of value are described and illustrated. Fluorescent transgenic lines of zebrafish embryos are presented for time-line studies with neurotoxicants. While genetic knockout technology has yet to be developed for the model, the anti-sense, morpholino approach allows for knockdown of expression of genes for the 3 day, embryonic period. This can provide for phenocopies of mutant genes for those genes essential to embryonic development or it can provide for a limited inhibition of gene expression that allows subsequent development of the fish. With the zebrafish genomic sequencing effort, microarray technology is now developing for the model system. These resources and technologies allow one to challenge the system with toxicants, and to view the immediate effects of the toxicants with transgenic embryos that fluoresce in part or all of the nervous system. Behavioral and learning protocols have been developed for the organism so that early exposures can be assayed for effects upon adult fish. Microarray technology should allow for one to identify specific genes and pathways affected by a neurotoxicant. In the future, these approaches should provide a working protocol for exploring molecular mechanisms of neurotoxicants. This type of complementary approach should then allow for more efficient examination and testing of mechanisms in mammalian models.

Animals↗
PubMed2005

Organization and evolution of resistance gene analogs in peanut.

The scarcity of genetic polymorphism in Arachis hypogaea (peanut), as in other monophyletic polyploid species, makes it especially vulnerable to nematode, bacterial, fungal, and viral pathogens. Although no disease resistance genes have been cloned from peanut itself, the conserved motifs in cloned resistance genes from other plant species provide a means to isolate and analyze similar genes from peanut. To survey the number, diversity, evolutionary history, and genomic organization of resistance gene-like sequences in peanut, we isolated 234 resistance gene analogs (RGAs) by using primers designed from conserved regions of different classes of resistance genes including NBS-LRR, and LRR-TM classes. Phylogenetic and sequence analyses were performed to explore evolutionary relationships both among peanut RGAs and with orthologous genes from other plant taxa. Fifty-six overgos designed from the RGA sequences on the basis of their phyletic association were applied to a peanut BAC library; 736 hybridizing BAC clones were fingerprinted and contigs were formed in order to gain insights into the genomic organization of these genes. All the fingerprinting gels were blotted and screened with the respective overgos in order to verify the authenticity of the hits from initial screens, and to explore the physical organization of these genes in terms of both copy number and distribution in the genome. As a result, we identified 250 putative resistance gene loci. A correlation was found between the phyletic positions of the sequences and their physical locations. The BACs isolated here will serve as a valuable resource for future applications, such as map-based cloning, and will help improve our understanding of the evolution and organization of these genes in the peanut genome.

Amino Acid Sequence↗
PubMed2004

Phylogeography of a game species: the red-crested pochard (Netta rufina) and consequences for its management.

Western European populations of red-crested pochard (Netta rufina) are characterized by low size and high fragmentation, which accentuate their sensitivity to hunting. Uncertainties regarding the demographic trends of these populations highlight the need for pertinent hunting regulations. This requires identification of the limits of the populations under exploitation, i.e. delimiting a management unit. We used the left domain of the mitochondrial control region and seven nuclear loci (four microsatellites and three introns) to assess the level of genetic structure and demographic independence between the fragmented Western European and the large Central Asian populations. The second objective was to investigate the colonization history of the Western European populations. This study demonstrated that the Western European populations of red-crested pochard constitute a separate demographic conservation unit relative to the Asian population as a result of very low female dispersal (mitochondrial DNA: PhiST = 0.152). A morphometric analysis further suggested that Central Asian and Western European specimens of both sexes originate from different pools of individuals. Male dispersal seems higher than female dispersal, as suggested by the lack of clear genetic structure for the nuclear markers at this continental scale. Genetic data, in conjunction with historical demographic data, indicate that the current Western European populations probably originate from a recent colonization from Central Asia. As numbers of red-crested pochards in Western Europe cannot be efficiently supplemented by immigration from the larger Asian populations, a management plan regulating the harvest in Western Europe is required.

Animals↗
PubMed1997

[Effect of preload of working memory on components of evoked potentials during encoding of sequentially presented letter sequences].

In recent experiments with a pseudo-random sequence of 7 consonants to recall after trial (stimulus onset asynchrony 1000 ms) a reverse relationship between P300 amplitude of the event-related potential (ERP) and letter presentation position was shown (Grune et al., 1996). It was assumed that this relationship reflects competition between encoding and retention processes in this time regime. In order to find evidence for the resource competition hypothesis in working memory a 4 x 4 grid containing 4 digits preceded a sequence of 6 consonants. In the first block subjects were instructed to ignore the grid, in two remaining blocks they were asked to remember the digits or their position in the grid and to recognize them after the letter recall. In the ignore condition the expected effect of P300 decrease with letter position was found, especially at posterior electrode sites. When subjects had to process the preceding digit grid there was no position effect of P300 caused by small P300 amplitudes in the ERPs that were elicited by the first letters of the sequence. This effect was not specific to the modality of the interfering with the letter task information from the digit grid. We conclude that the grid information occupies working memory resources that are not available for the event-related processing of consonants to recall.

Adult↗
PubMed2005

Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles).

Expressed sequence tag (EST) sequences can provide a wealth of data for phylogenetic and genomic studies, but the utility of these resources is restricted by poor taxonomic sampling. Here, we use small EST libraries (<1,000 clones) to generate phylogenetic markers across a broad sample of insects, focusing on the species-rich Coleoptera (beetles). We sequenced over 23,000 ESTs from 34 taxa, which produced 8,728 unique sequences after clustering nonredundant sequences. Between taxa, the sequences could be grouped into 731 gene clusters, with the largest corresponding to mitochondrial DNA transcripts and gene families chymotrypsin, actin, troponin, and tubulin. While levels of paralogy were high in most gene clusters, several midsized clusters including many ribosomal protein (RP) genes appeared to be free of expressed paralogs. To evaluate the utility of EST data for molecular systematics, we curated available transcripts for 66 RP genes from representatives of the major groups of Coleoptera. Using supertree and supermatrix approaches for phylogenetic analysis, the results were consistent with the emerging phylogenetic conclusions about basal relationships in Coleoptera. Numerous small EST libraries from a taxonomically densely sampled lineage can provide a core set of genes that together act as a scaffold in phylogenetic reconstruction, comparative genomics, and studies of gene evolution.

Animals↗
PubMed2005

DED: Database of Evolutionary Distances.

A large database of homologous sequence alignments with good estimates of evolutionary distances can be a valuable resource for molecular evolutionary studies and phylogenetic research in particular. We recently created a database containing 159,921 transcripts from human, mouse, rat, zebrafish and fugu species. Approximately 1,000 homology groups were identified with the help of Ensembl homology evidence. At the macro-level, the database allows us to answer queries of the form: 1. What is the average k-distance between 5' untranslated regions of human and mouse? 2. List the 10 groups with the highest K(a)/K(s) ratio between mouse and rat. 3. List all identical proteins between human and rat. Researchers interested in specific proteins can use a simple web interface to retrieve the homology groups of interest, examine all pairwise distances between members of the group and study the conservation of exon-intron gene structures using a graphical interface. The database is available at http://warta.bio.psu.edu/DED/.

5' Untranslated Regions↗
PubMed1997

Purification and partial amino acid sequence of brevicin 27, a bacteriocin produced by Lactobacillus brevis SB27.

Brevicin 27, a bacteriocin produced by Lacto bacillus brevis SB27, is inhibitory mainly against closely related Lactobacillus brevis and Lactobacillus büchneri strains. It was purified from the culture supernatant by a four-step purification procedure including ammonium sulfate precipitation, cation exchange, hydrophobic interaction, and reverse-phase, high performance liquid chromatographies. The purified bacteriocin was subjected to mass spectrometry, amino acid composition analysis, and sequencing by Edman degradation. It was shown to be an about 5200-Da basic protein containing a high proportion of lysine and of hydrophobic amino acids. The partial N-terminal amino acid sequence (25 residues) was unique when compared with the Protein Data Bank (PDB), Swiss Prot, and Protein Information Resource(PIR) data banks and to the translated Gen Bank.

Amino Acid Sequence↗
PubMed2007

Developing a simplified river landscape assessment model: examples from the Chungkang and Touchien rivers, Taiwan.

Currently, river landscape evaluations cannot be conducted by the general public, due to their lack of professional training. However, consulting professionals is time consuming and costly. The research conducted addresses both problems by (1) developing suitable criteria for assessing river environments, and (2) formulating a strategy for using the proposed criteria, thereby creating an effective method for river management by non-professionals. This research was carried out, in accordance with Visual Resource Management theory, at 12 survey sites along the ChungKang River. The landscape quality sequences acquired were then evaluated using a revised and simplified assessment model. The same process was repeated on the Touchien River to verify its feasibility. This research developed both specific criteria as well a method for evaluating river landscapes, which can be employed by non-professional river project managers. Ultimately, the aim of this research is to develop and promote sustainable river resource management.

Environmental Health↗
PubMed2005

EDGE: a centralized resource for the comparison, analysis, and distribution of toxicogenomic information.

Transcriptional profiling via microarrays holds great promise for toxicant classification and hazard prediction. Unfortunately, the use of different microarray platforms, protocols, and informatics often hinders the meaningful comparison of transcriptional profiling data across laboratories. One solution to this problem is to provide a low-cost and centralized resource that enables researchers to share toxicogenomic data that has been generated on a common platform. In an effort to create such a resource, we developed a standardized set of microarray reagents and reproducible protocols to simplify the analysis of liver gene expression in the mouse model. This resource, referred to as EDGE, was then used to generate a training set of 117 publicly accessible transcriptional profiles that can be accessed at http://edge.oncology.wisc.edu/. The Web-accessible database was also linked to an informatics suite that allows on-line clustering and K-means analyses as well as Boolean and sequence-based searches of the data. We propose that EDGE can serve as a prototype resource for the sharing of toxicogenomics information and be used to develop algorithms for efficient chemical classification and hazard prediction.

Animals↗
PubMed2003

Steroid regulation of terminal protein glycosyltransferase genes: molecular and functional homologies within sialyltransferase and fucosyltransferase families.

OBJECTIVE: Terminal glycosylations such as fucosylation and especially sialylation are crucial in maturation of proteins for their particular function. In cells and tissues where their function is under hormonal control, often terminal processes including glycosylations are tightly regulated by hormones. Therefore, it is not surprising that two key enzyme families involved in these steps, fucosyltransferases and sialyltransferases, are directly controlled by steroid hormones. METHODS: Gene structure and protein sequences have been analyzed by set of Unix-based complex sequence analysis programs of the Wisconsin GCG package, and from some other resources. Protein secondary structure predictions were based on several independent programs and applications complementing each other depending on the algorithm used, all running on Unix platforms. RESULTS: Comparison of these two types of enzymes from organisms where they are known to be under direct hormonal regulation has revealed that although sialyltransferases are broad family of proteins, the only known enzymes to be under hormonal control are alpha-2,6-sialyltransferases and in the case of fucosyl moieties transferring enzymes these are alpha-1,2/6-fucosyltransferases. Interestingly, hormonally regulated sialyltransferases from as evolutionary distant organisms as human and fruitfly share several important features including secondary structure characteristics encompassing sialyl L and S motifs in which they differ from other sialyltransferases. Analogous organizational and structural similarities were found also in hormonally regulated fucosyltransferases. CONCLUSIONS: Data indicate that hormonal control of these classes of enzymes as a regulatory mechanism could be attained relatively early during the evolution in order to obtain selective control over specific protein modification process which plays an important role during ontogenic development.

Amino Acid Sequence↗
PubMed2006

The Histone Database: a comprehensive resource for histones and histone fold-containing proteins.

The Histone Database is a curated and searchable collection of full-length sequences and structures of histones and nonhistone proteins containing histone-like folds, compiled from major public databases. Several new histone fold-containing proteins have been identified, including the huntingtin-interacting protein HYPM. Additionally, based on the recent crystal structure of the Son of Sevenless protein, an interpretation of the sequence analysis of the histone fold domain is presented. The database contains an updated collection of multiple sequence alignments for the four core histones (H2A, H2B, H3, and H4) and the linker histones (H1/H5) from a total of 975 organisms. The database also contains information on the human histone gene complement and provides links to three-dimensional structures of histone and histone fold-containing proteins. The Histone Database is a comprehensive bioinformatics resource for the study of structure and function of histones and histone fold-containing proteins. The database is available at http://research.nhgri.nih.gov/histones/.

Amino Acid Sequence↗
PubMed2026

Chromosome-level genome assembly of the hemiparasitic Taxillus sutchuenensis (Loranthaceae).

Taxillus sutchuenensis, an ecologically and medicinally important hemiparasitic plant that parasitizes diverse woody hosts, was sequenced to generate a high-quality chromosome-level genome assembly. PacBio HiFi long reads, RNA-seq transcriptome data, and Hi-C data were used to assemble a 406.32&#x2009;Mb genome anchored onto nine pseudo-chromosomes, with a scaffold N50 of 45.59&#x2009;Mb. The assembly showed high completeness and accuracy, supported by BUSCO (93.6%) and Merqury QV (70.6) assessments. The LTR Assembly Index (LAI) of 13.98 indicated excellent continuity. A total of 21,795 protein-coding genes were predicted, with 94.46% functionally annotated. Repetitive sequences accounted for 50.05% of the genome, primarily LTR retrotransposons. This genome provides a valuable resource for investigating the evolution, functional genomics, and parasitic mechanisms of hemiparasitic plants.

Genome, Plant↗
PubMed2007

Appraisal of the consequences of the DDT-induced bottleneck on the level and geographic distribution of neutral genetic variation in Canadian peregrine falcons, Falco peregrinus.

Peregrine falcon populations underwent devastating declines in the mid-20th century due to the bioaccumulation of organochlorine contaminants, becoming essentially extirpated east of the Great Plains and significantly reduced elsewhere in North America. Extensive re-introduction programs and restrictions on pesticide use in Canada and the United States have returned many populations to predecline sizes. A proper population genetic appraisal of the consequences of this decline requires an appropriate context defined by (i) meaningful demographic entities; and (ii) suitable reference populations. Here we explore the validity of currently recognized subspecies designations using data from the mitochondrial control region and 11 polymorphic microsatellite loci taken from 184 contemporary individuals from across the breeding range, and compare patterns of population genetic structure with historical patterns inferred from 95 museum specimens. Of the three North American subspecies, the west coast marine subspecies Falco peregrinus pealei is well differentiated genetically in both time periods using nuclear loci. In contrast, the partitioning of continental Falco peregrinus anatum and arctic Falco peregrinus tundrius subspecies is not substantiated, as individuals from these subspecies are historically indistinguishable genetically. Bayesian clustering analyses demonstrate that contemporary genetic differentiation between these two subspecies is mainly due to changes within F. p. anatum (specifically the southern F. p. anatum populations). Despite expectations and a variety of tests, no genetic bottleneck signature is found in the identified populations; in fact, many contemporary indices of diversity are higher than historical values. These results are rationalized by the promptness of the recovery and the possible introduction of new genetic material.

Animals↗
PubMed2004

Application of comparative genomics to narrow-leafed lupin (Lupinus angustifolius L.) using sequence information from soybean and Arabidopsis.

The completion of genome-sequencing initiatives for model plants and EST databases for major crop species provides a large resource for gaining fundamental knowledge of complex gene interactions and the functional significance of proteins. There are increasingly numerous opportunities to transfer this information to other plant species with uncharacterized genomes and make advances in genome analysis, gene expression, and predicted protein function. In this study, we have used DNA sequences from soybean and Arabidopsis to determine the feasibility of applying comparative genomics to narrow-leafed lupin. We have used transcribed sequences from soybean and showed that a high proportion cross hybridize to lupin DNA, identifying similar genes and providing landmarks for estimating the degree of chromosomal synteny between species. To further investigate comparative relationships in this study, a detailed analysis of three lupin genes and comparison of orthologs from soybean and Arabidopsis shows that, in some cases, gene structure and expression are highly conserved and their proteins may have similar function. In other cases, genes show variation in expression profiles indicating alternative functions across species. The advantages and limitation of using soybean and Arabidopsis sequences for comparative genomics in lupins are discussed.

Amino Acid Sequence↗