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PubMed1995

An expression-independent catalog of genes from human chromosome 22.

To accomplish large-scale identification of genes from a single human chromosome, exon amplification was applied to large pools of clones from a flow-sorted human chromosome 22 cosmid library. Sequence analysis of more than one-third of the 6400 cloned products identified 35% of the known genes previously localized to this chromosome, as well as several unmapped genes and randomly sequenced cDNAs. Among the more interesting sequence similarities are those that represent novel human genes that are related to others with known or putative functions, such as one exon from a gene that may represent the human homolog of Drosophila Polycomb. It is anticipated that sequences from at least half of the genes residing on chromosome 22 are contained within this exon library. This approach is expected to facilitate fine-structure physical and transcription mapping of human chromosomes, and accelerate the process of disease gene identification.

Amino Acid Sequence↗
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↗
PubMed1966

Topics in library technology: copying techniques.

Photocopying applications in the library include the combining of previously separate material, the separation of a single item into two or more of its parts, and the selection of parts of existent material by the use of overlays. The production of catalog cards, the creation of sheet material (new book lists, reference bibliographies) from card-form materials, an Index Medicus-derived alerting service, and overdue notices copied from charge cards are among the applications exemplifying these general types. Larger-scale operations employing microfilm are noted. The distinction between copying and printing, in the light of equipment advances, is discussed.

Copying Processes↗
PubMed2000

Genome-wide analysis of oral cancer--early results from the Cancer Genome Anatomy Project.

The Cancer Genome Anatomy Project (CGAP) is a large cooperative effort sponsored by the US National Institutes of Health designed to find, catalog and annotate genes that are expressed during cancer development. In the past 2 years, the CGAP has sequenced over 700,000 clones from approximately 140 cDNA libraries, resulting in the identification of over 30,000 new human genes. As a first step in applying this project to oral cancer we entered four cell lines--two from oral cancer, one from primary oral keratinocytes, and one from oral keratinocytes which had been immortalized by human papillomavirus. Libraries of cDNA were made and sequenced and the data were deposited in GenBank. The expressed genes were then identified where possible. The cell lines, and the total number of expressed genes that were cloned from each were: HN3 (oral cancer), 263 genes; HN4 (oral cancer), 550 genes; HN5 (primary keratinocytes), 237 genes; HN6 (immortalized keratinocytes), 408 genes. The total number of different genes that were found was 1160. A total of 38 new genes, of unknown function, were discovered. The data presented here represent a beginning of the application of the CGAP technology to oral cancer. Even though the data are still quite incomplete, they already represent a large quantity of new information and clones of potential utility to the oral cancer community, and provide a glimpse of the data sets to be forthcoming from the Project. It must therefore be expected that there will soon be a large expansion in the volume of data regarding the genetics of oral cancer. Those who study this disease must be prepared to develop new methods of analysis and storage for handling the oncoming volumes of information.

Clone Cells↗
PubMed2004

Generation of a total of 6483 expressed sequence tags from 60 day-old bovine whole fetus and fetal placenta.

Expressed sequence tags (ESTs) generated based on characterization of clones isolated randomly from cDNA libraries are used to study gene expression profiles in specific tissues and to provide useful information for characterizing tissue physiology. In this study, two directionally cloned cDNA libraries were constructed from 60 day-old bovine whole fetus and fetal placenta. We have characterized 5357 and 1126 clones, and then identified 3464 and 795 unique sequences for the fetus and placenta cDNA libraries: 1851 and 504 showed homology to already identified genes, and 1613 and 291 showed no significant matches to any of the sequences in DNA databases, respectively. Further, we found 94 unique sequences overlapping in both the fetus and the placenta, leading to a catalog of 4165 genes expressed in 60 day-old fetus and placenta. The catalog is used to examine expression profile of genes in 60 day-old bovine fetus and placenta.

Animals↗
PubMed1991

Downloading from MEDLINE: a comparison of personal database software.

The compatibility of downloaded MEDLINE references with software packages designed for maintenance of personal bibliographic databases is considered. The nine packages reviewed enable one to import batches of records downloaded from one or more presentations of the MEDLINE database, online or CD-ROM; and enable the user to re-format records into the various styles required by journal editors. Some basic features of the packages are tabulated, and details of record-importing facilities are described. Details of suppliers and prices are given.

Catalogs, Commercial as Topic↗
PubMed2000

The prostate expression database (PEDB): status and enhancements in 2000.

The Prostate Expression Database (PEDB) is an online resource designed to access and analyze gene expression information derived from the human prostate. PEDB archives >55 000 expressed sequence tags (ESTs) from 43 cDNA libraries in a curated relational database that provides detailed library information including tissue source, library construction methods, sequence diversity and sequence abundance. The differential expression of each EST species can be viewed across all libraries using a Virtual Expression Analysis Tool (VEAT), a graphical user interface written in Java for intra- and inter-library species comparisons. Recent enhancements to PEDB include: (i) the functional categorization of annotated EST assemblies using a classification scheme developed at The Institute for Genome Research; (ii) catalogs of expressed genes in specific prostate tissue sources designated as transcriptomes; and (iii) the addition of prostate proteome information derived from two-dimensional electrophoreses and mass spectrometry of prostate cancer cell lines. PEDB may be accessed via the WWW at http://www.mbt.washington.edu/PEDB/

Databases, Factual↗
PubMed1994

Service providers and users discover the Internet.

Although the Internet has evolved over more than twenty years, resources useful to health information professionals have become available on the Internet only recently. A survey conducted by the Regional Medical Libraries of the National Network of Libraries of Medicine in the fall of 1993 indicates that libraries at academic institutions are much more likely to have access to the Internet (72%) than are libraries in hospital environments (24%). Health information professionals who take on the challenge and exploit the Internet's resources find rewards for themselves and their clients. The basic electronic mail capability of the Internet allows colleagues to collaborate, communicate, and participate in daily continuing education. Internet terminal and file-transfer capabilities provide improved access to traditional resources and first-time access to new electronic resources. Through the Internet, online catalogs are available worldwide, and document delivery is faster, cheaper, and more reliable than ever before. Institutions can make organizational, full-text, online, and publication information available through Internet tools such as direct file-transfer protocol (FTP), menu-based Gopher, and hypertext-based Mosaic. The National Library of Medicine (NLM) is among organizations finding new ways to provide service through the Internet. NLM now uses electronic mail to communicate with users, FTP service to distribute publications, and tools such as Gopher and Mosaic to distribute publications and graphics and connect users to online services. The Internet allows service providers and health sciences information professionals to work in a rich, new medium whose potential is just beginning to be explored. At the same time, its characteristics--including lack of formal organization, standards, quality control, and permanence--pose a challenge.

Computer Communication Networks↗
PubMed1990

Addressing the issue of cataloging and making chiropractic literature accessible: Part I: Defining the problem.

Health science journals are a principle source of new knowledge for chiropractors, chiropractic faculty and students. Regrettably, clinically or educationally relevant articles (appearing in the nearly 20,000 journals annually) are often overlooked due to access difficulties. Innovations are needed to assist the reader to select articles relevant to chiropractic and reduce the time spent sorting through the volumes of literature. A review of the literature shows there is a trend toward database management for cataloging and accessibility of other, nonchiropractic, literature. Most notable of these is an endeavor by National Technical Information Service, commonly referred to as MEDLARS (Medline). It is interesting to note that a computer-assisted library database program does not exist on any chiropractic campus. This is in contrast with the trend on campuses of other health care fields. Manual search strategies within the chiropractic literature are time consuming, subject to a high failure rate, and even if the search produces citations, there is no assurance the journal can be accessed unless a chiropractic campus is nearby. Furthermore, difficulties exist when a chiropractic literature search is attempted in any computerized database, e.g., MEDLARS (Medline). Journals/articles that are unique to chiropractic (national, international or on the state level) are not specifically included in these computerized databases. Aside from these difficulties, there exists the problem of finding those articles that contain valid and relevant information from among those that are less valid or informative.

Cataloging↗
PubMed2004

Gene cataloging and expression profiling in human gastric cancer cells by expressed sequence tags.

To understand the molecular mechanism associated with gastric carcinogenesis, we identified genes expressed in gastric cancer cell lines and tissues. Of 97,609 high-quality ESTs sequenced from 36 cDNA libraries, 92,545 were coalesced into 10,418 human Unigene clusters (Build 151). The gene expression profile was produced by counting the cluster frequencies in each library. Although the profiles of highly expressed genes varied greatly from library to library, those genes related to cell structure formation, heat shock proteins, the glycolysis pathway, and the signaling pathway were highly represented in human gastric cancer cell lines and in primary tumors. Conversely, the genes encoding immunoglobulins, ribosomal proteins, and digestive proteins were down-regulated in gastric cancer cell lines and tissues compared to normal tissues. The transcription levels of some of these genes were confirmed by RT-PCR. We found that genes related to cell adhesion, apoptosis, and cytoskeleton formation were particularly up-regulated in the gastric cancer cell lines established from malignant ascites compared to those from primary tumors. This comprehensive molecular profiling of human gastric cancer should be useful for elucidating the genetic events associated with human gastric cancer.

Base Sequence↗
PubMed2004

In silico screening of a saturated mutation library of tomato.

A comprehensive mutant population is a basic resource for exploring gene function. We developed an isogenic tomato 'mutation library' in the genetic background of the inbred variety M82. A total of 13 000 M(2) families, derived from EMS (ethyl methane sulfonate) and fast-neutron mutagenesis, were visually phenotyped in the field and categorized into a morphological catalog that includes 15 primary and 48 secondary categories. Currently, 3417 mutations have been cataloged; among them are most of the previously described phenotypes from the monogenic mutant collection of The Tomato Genetics Resource Center, and over a thousand new mutants, with multiple alleles per locus. The phenotypic database indicates that most mutations fall into more than a single category (pleiotropic), with some organs such as leaves more prone to alterations than others. All data and images can be searched and accessed in the Solanaceae Genome Network (SGN) on a site called 'The Genes That Make Tomatoes' (http://zamir.sgn.cornell.edu/mutants/).

Crosses, Genetic↗
PubMed1996

Multiplex selection technique (MuST): an approach to clone transcription factor binding sites.

We have used a multiplex selection approach to construct a library of DNA-protein interaction sites recognized by many of the DNA-binding proteins present in a cell type. An estimated minimum of two-thirds of the binding sites present in a library prepared from activated Jurkat T cells represent authentic transcription factor binding sites. We used the library for isolation of "optimal" binding site probes that facilitated cloning of a factor and to identify binding activities induced within 2 hr of activation of Jurkat cells. Since a large fraction of the oligonucleotides obtained appear to represent "optimal" binding sites for sequence-specific DNA-binding proteins, it is feasible to construct a catalog of consensus binding sites for DNA-binding proteins in a given cell type. Qualitative and quantitative comparisons of the catalogs of binding site sequences from various cell types could provide valuable insights into the process of differentiation acting at the level of transcriptional control.

Amino Acid Sequence↗
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↗
PubMed2001

Genome and genetic resources from the Cancer Genome Anatomy Project.

The Cancer Genome Anatomy Project (CGAP) is a collaborative network of cancer researchers with a common goal: to decipher the genetic changes that occur during cancer formation and progression. The project brings together several recent technologies capable of high-throughput analysis to help achieve this goal. Automated sequencing of cDNA libraries is a primary focus and is geared towards providing a comprehensive and annotated set of human and mouse transcribed sequences. This effort includes full-length transcript sequence generated by CGAP's new Mammalian Gene Collection initiative. Single nucleotide polymorphisms (SNPs) within human gene sequences (Genetic Annotation Initiative) and chromosomal rearrangements within cancer cells (Cancer Chromosome Aberration Project) are also being cataloged as part of CGAP. Finally, to help determine gene expression patterns related to cancer, CGAP provides a quantitative catalog of data through its SAGEmap initiative. The genome and genetic analysis tools listed in this review are all freely distributed by CGAP (http://cgap.nci.nih.gov/) without restriction.

Animals↗
PubMed1999

Interactive web-based radiology teaching file.

This multimedia radiology teaching file was developed for medical students, residents, physicians, and researchers to present teaching components related to clinical studies. Patient studies are used to create teaching cases, user can also create lecture series and custom presentations (catalogs) by linking related text and images. The user is able to make and preserve his/her own notes related to reviewed information. From the computer workstation, the user can perform search our case library by American College of Radiology (ACR) codes, keywords, modalities, or text. Results are presented in custom pages and include text lists, thumbnails lists, rescaled images, and full-size images. Text can be easily printed in custom format or exported to an ASCI file. To preserve the privacy of the student, access to our database is granted to the web browser by log-in panel. Image and text can be imported from Digital Imaging and Communications in Medicine (DICOM)-compatible devices or entered by using web forms. In conclusion, we developed a multifunctional interactive teaching environment accessible for multiplatform internet users.

Computer Security↗