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PubMed2006

A hexapod nuclear SSU rRNA secondary-structure model and catalog of taxon-specific structural variation.

RNA molecules and in particular the nuclear SSU RNA play an important role in molecular systematics. With the advent of increasingly parameterized substitution models in systematic research, the incorporation of secondary-structure information became a realistic option compensating interdependence of character variation. As a prerequisite, consensus structures of eukaryotic SSU RNA molecules have become available through extensive comparative analyses and crystallographic studies. Despite extensive research in hexapod phylogenetics, consensus SSU RNA secondary structures focusing on hexapods have not yet been explored. In this study, we compiled a representative hexapod SSU data set of 261 sequences and inferred a specific consensus SSU secondary-structure model. Our search for conserved structural motives relied on a combined approach of thermodynamic and covariation analyses. The hexapod consensus-structure model deviates from the canonical eukaryotic model in a number of helices. Additionally, in several helices the hexapod sequences did not support a single consensus structure. We provide consensus structures of these sections of single less-inclusive taxa, thus facilitating the adaptation of the consensus hexapod model to less-inclusive phylogenetic questions. The secondary-structure catalog will foster the application of RNA structure models in phylogenetic analyses using the SSU rRNA molecule, and it will improve the realism of substitution models and the reliability of reconstructions based on rRNA sequences.

Animals↗

PubMed2001

PicSNP: a browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome.

Recent progress in identification and mapping of single nucleotide polymorphisms (SNPs) in the human genome generates an unprecedented opportunity to explore cause-effect relationships between genetic variations and susceptibility to common diseases. For this purpose, one promising strategy would be to select a set of SNPs that potentially alter the function of proteins involved in the pathogenesis of the diseases and compare their frequencies in the affected individuals and the healthy population. In this respect, SNPs that change amino acid sequences (nonsynonymous SNPs; nsSNPs) are of particular interest, since they are more likely to affect protein functions. In this study, we have constructed a catalog of nsSNPs (PicSNP), whose unique features are (i) nsSNPs are classified according to the functions of the affected genes and are searchable under the guidance of hierarchical lists of protein functions and (ii) nsSNPs that lead to amino acid changes in the known functional sites and domains of proteins are highlighted. Out of 1,190,295 SNPs extracted from public database, we identified 3793 nsSNPs and classified them in 1247 categories of protein functions. 495 sites and domains annotated in the Swiss-Prot database were found to include nsSNPs, including 2 nsSNPs in disulfide-binding sites and 38 nsSNPs in transmembrane regions. PicSNP is available via the World Wide Web (http://picsnp.org) and would support research questing for SNPs involved in common diseases.

Databases, Factual↗

PubMed1987

Identification of shiitake genotypes by multilocus enzyme electrophoresis: catalog of lines.

Starch gel electrophoresis of allozymes extracted from mycelium grown in submerged culture was used to identify and catalog lines of Lentinula edodes. Variability at 11 multiallelic loci was used to separate 91 lines collected from worldwide sources into 35 genotypic classes. Genotypic class 2 was the largest, with 18 lines; 18 other genotypic classes contained more than one line; and 16 genotypic classes contained only one line each. Three hybrids, with potential commercial value, were produced by crossing single-spore-derived monokaryons of different genotypes. Each of the three hybrids could be differentiated from the above 35 classes based on their multilocus allelic combinations. Multilocus enzyme analysis should aid the description, registration, and licensing of improved shiitake cultivars.

Basidiomycota↗

PubMed2005

A catalog of nonsynonymous polymorphism on mouse chromosome 16.

Numerous phenotypic traits differ among inbred mice, and the genetic diversity of inbred strains has been exploited in studies of quantitative trait loci (QTL). Sequencing the mouse genome has resulted in improved tools for the study of QTL, but a comprehensive catalog of sequence variants between strains would be of great value in identifying and testing potentially causative alleles. A/J DNA was included in the Celera shotgun sequence of the mouse genome and C57BL/6 DNA was sequenced by an international consortium. We have resequenced A/J and B6 DNA to cover nearly all of the protein-coding portions of mouse Chromosome 16, revealing that there are 106 nonsynonymous substitutions in 74 of the 779 genes on the chromosome. The pattern of substitution is more similar to the spectrum of benign polymorphism in the human population than it is to human disease-causing mutations. In mouse, polymorphic variants tend to be associated with one another on large haplotypes; this pattern also holds true for nonsynonymous polymorphism. However, sufficient fragmentation of haplotypes is present to suggest that only a very-high-resolution haplotype map will enable effective inference of alleles in additional strains.

Analysis of Variance↗

PubMed2005

Identification of keratins and analysis of their expression in carp and goldfish: comparison with the zebrafish and trout keratin catalog.

With more than 50 genes in human, keratins make up a large gene family, but the evolutionary pressure leading to their diversity remains largely unclear. Nevertheless, this diversity offers a means to examine the evolutionary relationships among organisms that express keratins. Here, we report the analysis of keratins expressed in two cyprinid fishes, goldfish and carp, by two-dimensional polyacrylamide gel electrophoresis, complementary keratin blot binding assay, and immunoblotting. We further explore the expression of keratins by immunofluorescence microscopy. Comparison is made with the keratin expression and catalogs of zebrafish and rainbow trout. The keratins among these fishes exhibit a similar range of molecular weights and isoelectric points, with a similar overall pattern on two-dimensional gels. In addition, immunofluorescence microscopy studies of goldfish and carp tissues have revealed the expression of keratins in both epithelial and mesenchymally derived tissues, as reported previously for zebrafish and trout. We conclude that keratin expression is qualitatively similar among these fishes, with goldfish and carp patterns being more similar to each other than to zebrafish, and the cyprinid fishes being more similar to each other than to the salmonid trout. Because of the detected similarity of keratin expression among the cyprinid fishes, we propose that, for certain experiments, they are interchangeable. Although the zebrafish distinguishes itself as being a developmental and genetic/genomic model organism, we have found that the goldfish, in particular, is a more suitable model for both biochemical and histological studies of the cytoskeleton, especially since goldfish cytoskeletal preparations seem to be more resistant to degradation than those from carp or zebrafish.

Amino Acid Sequence↗

PubMed1978

Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates.

The amount of 140 individual proteins of E. coli B/r was measured during balanced growth in five different media. The abundance of each protein was determined from its absolute amount in 14C-glucose-minimal medium and a measurement of its relative amount at each growth rate using a double labeling technique. Separation of the proteins was carried out by two-dimensional gel electrophoresis. This catalog of proteins, combined with 50 additional ribosomal proteins already studied, comprises about 5% of the coding capacity of the genome, but accounts for two thirds of the cell's protein mass. The behavior of most of these proteins could be described by a relatively small number of patterns. 102 of the 140 proteins exhibited nearly linear variations with growth rate. The remaining 38 proteins exhibited levels which seemed to depend more on the chemical nature of the medium than on growth rate. Proteins, including the ribosomal proteins, that increase in amount with increasing growth rate account for 20% of total cell protein by weight during growth on acetate, 32% on glucose-minimal medium and 55% on glucose-rich medium. Proteins with invariant levels in the various media comprise about 4% of the cell's total protein.

Bacterial Proteins↗

PubMed1983

Australopithecus and the origin of the genus Homo: aspects of biometry and systematics with accompanying catalog of tooth metric data.

Having compiled a new comprehensive catalog of length and breadth measurements of hominid teeth, descriptive and range statistics for the six widely accepted extinct hominid species have been calculated. The analysis supports the Gingerich and Schoeninger hypothesis about tooth variability. There is as least as much differentiation in tooth metrics between A. africanus and A. afarensis as between other hominid taxa commonly accorded distinct species status. A strong biometrical argument emerges for considering A. afarensis a distinct species and more closely related to the genus Homo than A. africanus. Differentiation between taxa inhabiting different geographic regions is indicated and support is provided for Wright's population genetic model for semi-isolated groups.

Animals↗

PubMed2006

A catalog for transcripts in the venom gland of the Agkistrodon acutus: identification of the toxins potentially involved in coagulopathy.

Agkistrodon acutus is a special agkistrodon halys, only distributed in Southern China, with a few exceptions in Vietnam. It is a cherished element used in traditional Chinese medicine. In order to produce a global panorama of gene expression in the Agkistrodon acutus venom gland, a non-normalized cDNA library was constructed, and 8696 high quality 5' end expressed sequenced tags (ESTs) were sequenced and analyzed. The initial sequences were assembled into 2855 clusters. Of these clusters, only 45.60% clusters matched known sequence and 54.40% had no match to any known sequence in GenBank. Except for putative cellular proteins (1184 clusters), the remaining 118 clusters (40.16% of all ESTs) corresponded to sequences associated with diverse toxin function. According to expression abundance, the major toxin components were metalloproteinases (32.08%) and C-type lectin (5.22%), and other components including bradykinin-potentiating peptide (0.90%), serine proteases (0.51%), nucleotidase and nuclease (0.41%), phospholipase A2 (0.30%), disintegrin (0.05%), cytokine-like molecules (0.06%), and other proteins (0.63%). The majority of these components are thought to be responsible for coagulopathy after A. acutus bites. We have therefore generated a comprehensive catalog of the A. acutus venom gland described so far. Gene expression from the very specialized secretory tissue, especially for those involved in coagulopathy, can be surveyed and provide important information in finding novel toxins.

Agkistrodon↗

PubMed2004

Bitis gabonica (Gaboon viper) snake venom gland: toward a catalog for the full-length transcripts (cDNA) and proteins.

The venom gland of the snake Bitis gabonica (Gaboon viper) was used for the first time to construct a unidirectional cDNA phage library followed by high-throughput sequencing and bioinformatic analysis. Hundreds of cDNAs were obtained and clustered into contigs. We found mostly novel full-length cDNA coding for metalloproteases (P-II and P-III classes), Lys49-phospholipase A2, serine proteases with essential mutations in the active site, Kunitz protease inhibitors, several C-type lectins, bradykinin-potentiating peptide, vascular endothelial growth factor, nucleotidases and nucleases, nerve growth factor, and L-amino acid oxidases. Two new members of the recently described short coding region family of disintegrin, displaying RGD and MLD motifs are reported. In addition, we have identified for the first time a cytokine-like molecule and a multi-Kunitz protease inhibitor in snake venoms. The CLUSTAL alignment and the unrooted cladograms for selected families of B. gabonica venom proteins are also presented. A significant number of sequences were devoid of database matches, suggesting that their biologic function remains to be identified. This paper also reports the N-terminus of the 15 most abundant venom proteins and the sequences matching their corresponding transcripts. The electronic version of this manuscript, available on request, contains spreadsheets with hyperlinks to FASTA-formatted files for each contig and the best match to the GenBank and Conserved Domain Databases, in addition to CLUSTAL alignments of each contig. We have thus generated a comprehensive catalog of the B. gabonica venom gland, containing for each secreted protein: (i) the predicted molecular weight, (ii) the predicted isoelectric point, (iii) the accession number, and (iv) the putative function. The role of these molecules is discussed in the context of the envenomation caused by the Gaboon viper.

Amino Acid Oxidoreductases↗

PubMed2005

A catalog for the transcripts from the venomous structures of the caterpillar Lonomia obliqua: identification of the proteins potentially involved in the coagulation disorder and hemorrhagic syndrome.

Accidents with the caterpillar Lonomia obliqua are often associated with a coagulation disorder and hemorrhagic syndrome in humans. In the present study, we have constructed cDNA libraries from two venomous structures of the caterpillar, namely the tegument and the bristle. High-throughput sequencing and bioinformatics analyses were performed in parallel. Over one thousand cDNAs were obtained and clustered to produce a database of 538 contigs and singletons (clusters) for the tegument library and 368 for the bristle library. We have thus identified dozens of full-length cDNAs coding for proteins with sequence homology to snake venom prothrombin activator, trypsin-like enzymes, blood coagulation factors and prophenoloxidase cascade activators. We also report cDNA coding for cysteine proteases, Group III phospholipase A2, C-type lectins, lipocalins, in addition to protease inhibitors including serpins, Kazal-type inhibitors, cystatins and trypsin inhibitor-like molecules. Antibacterial proteins and housekeeping genes are also described. A significant number of sequences were devoid of database matches, suggesting that their biologic function remains to be defined. We also report the N-terminus of the most abundant proteins present in the bristle, tegument, hemolymph, and "cryosecretion". Thus, we have created a catalog that contains the predicted molecular weight, isoelectric point, accession number, and putative function for each selected molecule from the venomous structures of L. obliqua. The role of these molecules in the coagulation disorder and hemorrhagic syndrome caused by envenomation with this caterpillar is discussed. All sequence information and the , including figures and tables with hyperlinks to FASTA-formatted files for each contig and the best match to the databases, are available at http://www.ncbi.nih.gov/projects/omes.

Amino Acid Sequence↗

PubMed2006

Endodontics and implants, a catalog of therapeutic contrasts.

Dentists may be faced with the choice to retain a tooth by performing endodontic therapy and restoration or to extract the tooth and replace it with an implant and restoration. The purpose of this study was to catalog areas where implant and endodontic therapies differ so as to assist dentists in making treatment decisions and in identifying areas deserving of future research. Differences in diagnostic procedures and prognostic indicators were listed. With respect to treatment outcomes, study designs, success criteria, treatment results, systematic reviews, complications, clinician expertise, and the use of patient-based measures were discussed. The need for clinically applicable consensus statements and treatment protocols was noted. It was concluded that at this time, choices between implant and endodontic therapies cannot be solely based on outcomes measurement evidence; that different modes of outcome measure frustrate direct comparison; that endodontic and implant therapies profoundly differ in many ways; that although rigorous and clearly defined outcome measures have been proposed for use in endodontic and implant outcomes studies, they are very rarely used; that long-term, large, clearly defined studies, with simple and clear outcome measures, for example survival in combination with defined treatment protocols, are needed to measure the clinical performance of endodontic and implant therapies; and it was recognized that broad outcomes data may not be sufficiently specific to directly impact clinical decision making.

Consensus↗

PubMed1998

Cataloging altered gene expression during rat hippocampal long-term potentiation by means of differential display.

We have employed mRNA differential display (DD) to generate a catalog of cDNAs whose expression in the hippocampus was regulated during long-term potentiation (LTP) in dentate gyrus of anesthetized rats. DD with 459 combinations of primer pairs revealed that 80 out of approximately 70000 bands displayed showed a reproducible change in their expression level. These cDNAs were categorized into seven groups according to changes in their temporal expression pattern. Some of these cDNAs were induced rapidly, but transiently, after the LTP induction, some induced rapidly and persistently, some induced slowly, and some down-regulated following LTP. This suggests that a complex molecular hierarchy underlies the maintenance of hippocampal LTP.

Animals↗

PubMed2004

A catalog of dermatology utilities: a measure of the burden of skin diseases.

Utilities are measures of quality of life that reflect the strength of individuals' preferences or values for a particular health outcome. As such, utilities represent a measure of disease burden. The aim of this article is to introduce the concept of utilities to the dermatology community and to present a catalog of dermatology utilities obtained from direct patient interviews. Our data are based on 236 total subjects from Grady Hospital (Atlanta, GA), Stanford Medical Center (Palo Alto, CA), and Parkland Hospital (Dallas, TX). The mean time trade-off utilities ranged from 0.640 for blistering disorders to 1.000 for alopecia, cosmetic, and urticaria. The mean utility across all diagnoses was 0.943. We present utilities for 17 diagnostic categories and discuss the underlying reasons for the significant disease burden that these utilities represent. We also present these dermatology categories relative to noncutaneous diseases to place the cutaneous utilities in perspective and to compare the burden of disease. We have demonstrated that skin diseases have considerable burden of disease and provided a preliminary repository of utility data for future researchers and policy makers.

Cost of Illness↗

PubMed1998

Computerized polymorphic marker identification: experimental validation and a predicted human polymorphism catalog.

A computational system for the prediction of polymorphic loci directly and efficiently from human genomic sequence was developed and verified. A suite of programs, collectively called POMPOUS (polymorphic marker prediction of ubiquitous simple sequences) detects tandem repeats ranging from dinucleotides up to 250 mers, scores them according to predicted level of polymorphism, and designs appropriate flanking primers for PCR amplification. This approach was validated on an approximately 750-kilobase region of human chromosome 3p21.3, involved in lung and breast carcinoma homozygous deletions. Target DNA from 36 paired B lymphoblastoid and lung cancer lines was amplified and allelotyped for 33 loci predicted by POMPOUS to be variable in repeat size. We found that among those 36 predominately Caucasian individuals 22 of the 33 (67%) predicted loci were polymorphic with an average heterozygosity of 0.42. Allele loss in this region was found in 27/36 (75%) of the tumor lines using these markers. POMPOUS provides the genetic researcher with an additional tool for the rapid and efficient identification of polymorphic markers, and through a World Wide Web site, investigators can use POMPOUS to identify polymorphic markers for their research. A catalog of 13,261 potential polymorphic markers and associated primer sets has been created from the analysis of 141,779,504 base pairs of human genomic sequence in GenBank. This data is available on our Web site (pompous.swmed.edu) and will be updated periodically as GenBank is expanded and algorithm accuracy is improved.

Computer Communication Networks↗

PubMed1995

Cataloging altered gene expression in young and senescent cells using enhanced differential display.

Recently, a novel PCR-based technique, differential display (DD), has facilitated the study of differentially expressed genes at the mRNA level. We report here an improved version of DD, which we call Enhanced Differential Display (EDD). We have modified the technique to enhance reproducibility and to facilitate sequencing and cloning. Using EDD, we have generated and verified a catalog of genes that are differentially expressed between young and senescent human diploid fibroblasts (HDF). From 168 genetags that were identified initially, 84 could be sequenced directly from PCR amplified bands. These sequences represent 27 known genes and 37 novel genes. By Northern blot analysis we have confirmed the differential expression of a total of 23 genes (12 known, 11 novel), while 19 (seven known, 12 novel) did not show differential expression. Several of the known genes were previously observed by others to be differentially expressed between young and senescent fibroblasts, thereby validating the technique.

Base Sequence↗

PubMed2000

DBcat: a catalog of 500 biological databases.

The DBcat (http://www.infobiogen.fr/services/dbcat ) is a comprehensive catalog of biological databases, maintained and curated at Infobiogen. It contains 500 databases classified by application domains. The DBcat is a structured flat-file library, that can be searched by means of an SRS server or a dedicated Web interface. The files are available for download from Infobiogen anonymous ftp server.

Biology↗

PubMed1980

Codon catalog usage and the genome hypothesis.

Frequencies for each of the 61 amino acid codons have been determined in every published mRNA sequence of 50 or more codons. The frequencies are shown for each kind of genome and for each individual gene. A surprising consistency of choices exists among genes of the same or similar genomes. Thus each genome, or kind of genome, appears to possess a "system" for choosing between codons. Frameshift genes, however, have widely different choice strategies from normal genes. Our work indicates that the main factors distinguishing between mRNA sequences relate to choices among degenerate bases. These systematic third base choices can therefore be used to establish a new kind of genetic distance, which reflects differences in coding strategy. The choice patterns we find seem compatible with the idea that the genome and not the individual gene is the unit of selection. Each gene in a genome tends to conform to its species' usage of the codon catalog; this is our genome hypothesis.

Animals↗

PubMed1991

Catalog of risks extended and updated.

A large variety of risks are quantified in terms of the loss of life expectancy they cause in the United States. Risks considered include the following: diseases; accidents of various types at home, at work, in public, and in motor vehicles; unemployment; poor social connections; use of small cars; smoking; air pollution; other environmental pollutants leading to cancer and non-cancer effects; purposely ingested substances; sports participation; geography; medical care; epidemics; natural hazards; socioeconomic factors; Rn and other radiation; and energy conservation. A few suggestions for applications of this catalog of risks are offered.

Humans↗