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PubMed2002

Identification of Zfp393, a germ cell-specific gene encoding a novel zinc finger protein.

Using the digital differential display program of the National Center for Biotechnology Information, we identified a contig of expression sequence tags (ESTs) which were unique to ovary, testis, and egg libraries. The full-length cDNA of this transcript was deduced and further confirmed by reverse transcriptase polymerase chain reaction (RT-PCR). The cDNA encodes a novel protein of 341 amino acids with a nuclear localization signal. The carboxyl-terminus of the protein contains three C2H2 zinc fingers, and the NH(2)-terminus is proline and serine-rich. Based on the conserved zinc finger motifs, we have termed this novel protein as zinc finger protein 393 (ZFP393). Northern blot and RT-PCR analyses revealed that Zfp393 mRNA was exclusively expressed in testis and ovary. The expression sites were further localized by in situ hybridization to step 3-8 spermatids in testis and growing oocytes in ovary. The Zfp393 gene consists of three exons spanning approximately 8 kb on the distal part of mouse chromosome 4. The carboxyl-terminal zinc finger region is highly homologous to several zinc finger-containing proteins, but no proteins were found to share sequence similarity with the NH(2)-terminal region of ZFP393. Genomic database mining and Southern blot analysis indicate that Zfp393 is a single copy gene. We hypothesize that ZFP393 functions as a germ cell-specific transcription factor that plays important roles in spermatid differentiation and oocyte development.

Amino Acid Sequence↗
PubMed2004

Characterization of new transcripts enriched in the mouse retina and identification of candidate retinal disease genes.

PURPOSE: Most retinal disease genes are preferentially expressed in photoreceptors, the light-sensitive cells involved in phototransduction. In addition, some of the genes linked to retinal diseases are essential for normal retinal development. The goal of this study was to identify new transcripts enriched in photoreceptors involved in retinal development or diseases. METHODS: To isolate uncharacterized retinal transcripts, the bioinformatic method Digital Differential Display (DDD) was used. RNA in situ hybridization was used to characterize gene-expression patterns. RESULTS: Twenty-seven mouse ESTs highly represented in retinal libraries were identified. Eight ESTs were predominantly expressed in photoreceptors and/or in the retinal pigment epithelium (RPE), whereas transcripts for other ESTs were detected more ubiquitously in the retinal cells or abundantly in ganglion cells and/or the inner nuclear layer. Mapping of the corresponding human orthologues of the photoreceptor/RPE-enriched genes revealed that two of them are candidate disease genes for retinitis pigmentosa, loci RP22 and RP28. Both of these are predominantly expressed in rod photoreceptors. The candidate RP22 gene codes for a putative transmembrane protein showing homology to Cln8 (ceroid lipofuscinosis, neuronal 8), in which gene mutations are associated with photoreceptors degeneration in mice. Also identified were two genes expressed in photoreceptors that are candidate disease genes for recessive Bardet-Biedl syndrome type 3 (BBS3) and recessive ataxia with RP (AXPC1). CONCLUSIONS: This study demonstrates how bioinformatic analysis can be used to identify novel tissue-specific genes relevant to development and diseases.

Animals↗
PubMed2003

Programmed database system at the Chang Gung Craniofacial Center: part I.

BACKGROUND: A database is a system for the management of information. Databases of different forms are widely used in everyday life from telephone books to online library catalogs. The Craniofacial Center at Chang Gung Memorial Hospital has seen over 20,000 patients during the past 20 years. All of the patient records need to digitally input into a computer database. METHODS: A database was custom designed using Paradox 8. The ACDSee Photo browser and DOS linked them to the original program. The Paradox 8 was programmed to a standard mode for the diagnosis and treatment data input to prevent typographical errors. RESULTS: We collected the records of 25,200 patients from 1987 to 2002, of which 24,331 underwent operations. The data for 14,828 patients were registered as complete and/or incomplete cleft and the proportions of unilateral to bilateral and female to male are presented in Table 1. CONCLUSION: This new database system was designed to ensure the accuracy of data input using a standard model that is capable of correct data programming using the custom designed coding system for the Craniofacial Center. The system also provides easy and reliable data retrieval when using the powerful search tools.

Cleft Lip↗
PubMed2002

Consumer Health Information for Asians (CHIA): a collaborative project.

According to the 2000 United States Census, the Asian population in Houston, Texas, has increased more than 67% in the last ten years. To supplement an already active consumer health information program, the staff of the Houston Academy of Medicine-Texas Medical Center Library worked with community partners to bring health information to predominantly Asian neighborhoods. Brochures on health topics of concern to the Asian community were translated and placed in eight informational kiosks in Asian centers such as temples and an Asian grocery store. A press conference and a ribbon cutting ceremony were held to debut the kiosks and to introduce the Consumer Health Information for Asians (CHIA) program. Project goals for the future include digitizing the translated brochures, mounting them on the Houston HealthWays Website, and developing touch-screen kiosks. The CHIA group is investigating adding health resources in other Asian languages, as well as Spanish. Funding for this project has come from outside sources rather than from the regular library budget.

Academic Medical Centers↗
PubMed2005

Grouped congenital hypertrophy of the retinal pigment epithelium follows developmental patterns of pigmentary mosaicism.

PURPOSE: To determine whether sectorial-oriented grouped pigmentations of the retina follow developmental patterns of pigmentary mosaicism. DESIGN: Systematic literature review. PARTICIPANTS: Fundus images from patients with grouped congenital hypertrophy of the retinal pigment epithelium (CHRPE). METHODS: An extensive Internet and library search was performed to obtain articles dealing with grouped CHRPE. Each article was carefully screened for fundus images and inclusion criteria. Fundus images of sufficient quality were scanned, digitized, and matched in size using Adobe Photo Shop to compare the pattern location and extension of the pigmented lesion. These obtained patterns of grouped CHRPE were than mapped and superimposed. RESULTS: Forty-five images were retrieved from 32 articles with grouped CHRPE. The lesions extended from the margin of the optic disc and radiated in sectors to the fundus periphery. The stream of growth did not follow the pattern of the retinal nerve fiber layer, because the clusters of pigmented cells crossed the midline raphe not sparing the macular area. Smaller lesion clusters were mainly located near the optic disc, whereas larger lesions were found in the periphery. CONCLUSIONS: The growth pattern of grouped CHRPE is similar to cutaneous sectorial pigmentations. We speculate that pigmentary mosaicisms may be a modified wild-type allele in a somatic cell clone during early embryogenesis following developmental lines analogous to the cutaneous lines of Blaschko. The sectorial pigmentations on the ocular fundus may reflect the stream, outgrowth, and migration of retinal pigment epithelium cells during embryogenesis.

Humans↗
PubMed2005

Cloning and characterization of full length of a novel zebrafish gene Zsrg abundantly expressed in the germline stem cells.

Using the digital differential display program of the National Center for Biotechnology Information, we identified a contig of expression sequence tags (ESTs) (Accession No. BM316936), which came from zebrafish ovary and testis libraries. The full-length cDNA of this transcript was cloned and further confirmed by polymerase chain reaction and sequencing. The full-length cDNA of the novel gene is 807bp and encodes a novel protein of 187 amino acids, which shares no significant homology with any other known proteins. Characterization of genomic sequences of the gene revealed that it spans 6kb on the linkage group 3 and is composed of five exons and four introns. RT-PCR analysis showed that it was expressed in mature oocytes and one-cell stage, and persisted until 24h of development. RT-PCR also revealed that it is expressed in gonad and kidney, with the highest level of expression in the testis. The expression sites of the novel gene in adult gonad were further localized by in situ hybridization to oogonia and growing oocytes in ovary and to spermatogonia, spermatocytes but not to spermatids in testis. Based on its abundance in testis and the germline stem cell-spermatogonia and oogonia, we hypothesize that it may function as a testicular development and gametogenesis related gene that plays important roles in spermatogenesis, and named it Zsrg (zebrafish testis spermatogenesis related gene, Zsrg).

Amino Acid Sequence↗
PubMed1994

Top-down construction of an ordered Schizosaccharomyces pombe cosmid library.

A very rapid and efficient method for sorting and ordering large numbers of clones is presented. This top-down mapping approach divides the entire ordering problem into many smaller tasks and analyzes in parallel a gridded membrane array of clones by hybridization with probe pools. The strategy was tested on a 15-fold-coverage Schizosaccharomyces pombe cosmid library. About 1600 clones were assigned to chromosomes and to regions defined by the Not I and Sfi I restriction maps. Then, the clones were ordered into 20 contigs, which is consistent with statistical expectations for the degree of genome coverage used. The parallel ordering of clones and the computer-based analysis of digitized images make this approach very efficient; it is about 8-fold faster than existing methods. Only 61 hybridizations were needed to order 1600 clones.

Base Sequence↗
PubMed1998

Digital cloning: identification of human cDNAs homologous to novel kinases through expressed sequence tag database searching.

Identification of novel kinases based on their sequence conservation within kinase catalytic domain has relied so far on two major approaches, low-stringency hybridization of cDNA libraries, and PCR method using degenerate primers. Both of these approaches at times are technically difficult and time-consuming. We have developed a procedure that can significantly reduce the time and effort involved in searching for novel kinases and increase the sensitivity of the analysis. This procedure exploits the computer analysis of a vast resource of human cDNA sequences represented in the expressed sequence tag (EST) database. Seventeen novel human cDNA clones showing significant homology to serine/threonine kinases, including STE-20, CDK- and YAK-related family kinases, were identified by searching EST database. Further sequence analysis of these novel kinases obtained either directly from EST clones or from PCR-RACE products confirmed their identity as protein kinases. Given the rapid accumulation of the EST database and the advent of powerful computer analysis software, this approach provides a fast, sensitive, and economical way to identify novel kinases as well as other genes from EST database.

Amino Acid Sequence↗
PubMed1996

The modern library: lost and found.

The modern library, a term that was heard frequently in the mid-twentieth century, has fallen into disuse. The over-promotion of computers and all that their enthusiasts promised probably hastened its demise. Today, networking is transforming how libraries provide--and users seek--information. Although the Internet is the natural environment for the health sciences librarian, it is going through growing pains as we face issues of censorship and standards. Today's "modern librarian" must not only be adept at using the Internet but must become familiar with digital information in all its forms--images, full text, and factual data banks. Most important, to stay "modern," today's librarians must embark on a program of lifelong learning that will enable them to make optimum use of the advantages offered by modern technology.

Computer Communication Networks↗
PubMed2000

Software development for registration of digital subtraction angiography (DSA) images in uterine fibroid embolization.

The ISIS Center at Georgetown University Medical Center has developed a comprehensive program for image-guided procedures in the spine. As part of this program, ISIS has developed a software application known as I-SPINE (ISIS's Spine Procedure Imaging Navigation Engine). I-SPINE is a Windows NT application, which is based on the Analyze/AVM libraries. The software architecture follows the Microsoft Foundation Classes (MFC) single document, multiple view paradigm. This has allowed the developers to add new visualization modules to I-SPINE that aid physicians in procedures outside the spine. One such procedure I-SPINE has been expanded for is uterine fibroid embolization. The idea is that by registering and subtracting post-embolization angiographic images from pre-treatment images the resulting image can be used to quantify the embolization effect on the fibroid circulation and predict the treatment response. The I-SPINE digital subtraction angiography (DSA) module allows the interventional radiologist to open a series of pre and post-embolization DSA images that shows the vascular structures of the uterus and the fibroid or fibroids. From these images, the radiologist selects an appropriate image from each series. The selected images are then hand registered using pixel shifting. Once the images are registered, the pixels are subtracted resulting in an image that shows the embolized arteries that were supplying the fibroids.

Angiography, Digital Subtraction↗
PubMed2006

The role of National Library of Medicine web sites in newborn screening education.

Expanded newborn screening programs and subsequent detection of rare genetic disorders challenge parents and their medical providers to learn about the treatment and management of these disorders. Many people seek medical information on the Internet but may encounter requests for registration or fees, or find that resources are out of date, difficult to understand, or buried in advertisements. The U.S. National Library of Medicine (NLM), a component of the National Institutes of Health, provides web-based resources that address the challenges of newborn screening education. These resources include MedlinePlus, Genetics Home Reference, ClinicalTrials.gov, and PubMed. NLM websites are not commercial, do not require registration or fees, and provide varied levels of information for a continuum of audiences from low-literacy consumers to health professionals. Using phenylketonuria as an example, this study describes the information that parents and their medical providers can find through NLM resources. NLM has embraced the digital age and provides the public with reliable, accurate, and up-to-date educational materials.

Genetic Testing↗
PubMedDate not supplied

In-silico analysis of kallikrein gene expression in pancreatic and colon cancers.

Human kallikreins are a cluster of 15 serine protease genes located in the chromosomal band 19q13.4, a non-randomly rearranged region in many solid tumors, including pancreatic cancer. We utilized the SAGE and EST databases of the Cancer Genome Anatomy Project to perform in-silico analysis of kallikrein gene expression in normal and cancerous pancreatic and colon tissues and cell lines using virtual Northern blotting (VNB), digital differential display (DDD) and X-profiler. At least two kallikreins, KLK6 and KLK10, are significantly up-regulated in pancreatic cancer. We probed 2 normal and 6 pancreatic cancer SAGE libraries with gene-specific tags for each of these kallikreins. KLK6 was found to be expressed in 5/6 cancer libraries and showed the most marked (5-fold) increase in average expression levels in cancer vs. normal. These data were verified by screening the EST databases, where all mRNA clones isolated were from cancerous libraries, with no clones detected in normal pancreatic tissues or cell lines. X-profiler comparison of two pools of normal and cancerous pancreatic libraries further verified the significant increase of KLK6 expression levels in pancreatic cancer. DDD data showed a 13-fold increase in KLK10 expression in pancreatic cancer. Three kallikrein genes, KLK6, 8 and 10 are overexpressed in colon cancer compared to normal colon, while one kallikrein, KLK1, is down-regulated. While no expression of KLK6 was detected in normal colon, KLK6-specific tags were detectable in 2 cancer libraries. Similar results were obtained by EST screening; no KLK6 clones were detected in any of the 28 normal libraries examined, while 10 KLK6 EST clones were found in colon adenocarcinoma. KLK10 was not detectable in normal colon. Gene-specific tags were, however, detectable with high density in colon cancer and 7 EST clones were found to be expressed in colon Adenocarcinoma.

Adenocarcinoma↗
PubMedDate not supplied

[Inequities in access to information and inequities in health].

This piece presents evidence that inequities in information are an important determinant of health inequities and that eliminating these inequities in access to information, especially by using new information and communication technologies (ICTs), could represent a significant advance in terms of guaranteeing the right to health for all. The piece reviews the most important international scientific research findings on the determinants of the health of populations, emphasizing the role of socioeconomic inequities and of deteriorating social capital as factors that worsen health conditions. It is noteworthy that Latin America has both socioeconomic inequities and major sectors of the population living in poverty. Among the fundamental strategies for overcoming the inequalities and the poverty are greater participation by the poor in civic life and the strengthening of social capital. The contribution that the new ICTs could make to these strategies is analyzed, and the Virtual Health Library (VHL) is discussed. Coordinated by the Latin American and Caribbean Center on Health Sciences Information (BIREME), the VHL is a contribution by the Pan American Health Organization that takes advantage of the potential of ICTs to democratize information and knowledge and consequently promote equity in health. The "digital gap" is discussed as something that can produce inequity itself and also increase other inequities, including ones in health. Prospects are discussed for overcoming this gap, emphasizing the role that governments and international organizations should play in order to expand access to the global public good that information for social development is.

Caribbean Region↗
PubMed2004

Kallikrein gene downregulation in breast cancer.

Recent evidence suggests that many members of the human kallikrein gene family are differentially regulated in breast cancer and other endocrine-related malignancies. In this study, we utilised the serial analysis of gene expression (SAGE) and expressed sequence tag (EST) databases of the Cancer Genome Anatomy Project (CGAP) to perform in silico analyses of the expression pattern of the 15 human kallikrein genes in normal and cancerous breast tissues and cell lines using different analytical tools such as Virtual Northern blotting, Digital Differential Display and X-profiler. Our results indicate that at least four kallikrein genes (KLK5, 6, 8, 10) are downregulated in breast cancer. Probing eight normal and 24 breast cancer SAGE libraries with gene-specific tags for each of the above kallikreins indicated moderate-to-high expression densities in normal breast (27-319 tags per million; tpm, in two to five out of eight libraries), compared to no or low expression (0 - 34 tpm in zero to two libraries out of 24) in breast cancer. These data were verified by screening the EST databases, where all mRNA clones isolated for these genes, except for one in each, were from normal breast libraries, with no clones detected from breast cancer tissues or cell lines (with the exception of KLK8). X-profiler comparison of two pools of normal and breast cancer libraries further verified the presence of significant downregulation of expression levels of 4 of the kallikreins genes (KLK5, 6, 10, 12). We experimentally verified the downregulation of these four kallikreins (KLK5, 6, 8, 10 and 12) by RT - PCR analysis.

Blotting, Northern↗
PubMed1999

Optical mapping of Plasmodium falciparum chromosome 2.

Detailed restriction maps of microbial genomes are a valuable resource in genome sequencing studies but are toilsome to construct by contig construction of maps derived from cloned DNA. Analysis of genomic DNA enables large stretches of the genome to be mapped and circumvents library construction and associated cloning artifacts. We used pulsed-field gel electrophoresis purified Plasmodium falciparum chromosome 2 DNA as the starting material for optical mapping, a system for making ordered restriction maps from ensembles of individual DNA molecules. DNA molecules were bound to derivatized glass surfaces, cleaved with NheI or BamHI, and imaged by digital fluorescence microscopy. Large pieces of the chromosome containing ordered DNA restriction fragments were mapped. Maps were assembled from 50 molecules producing an average contig depth of 15 molecules and high-resolution restriction maps covering the entire chromosome. Chromosome 2 was found to be 976 kb by optical mapping with NheI, and 946 kb with BamHI, which compares closely to the published size of 947 kb from large-scale sequencing. The maps were used to further verify assemblies from the plasmid library used for sequencing. Maps generated in silico from the sequence data were compared to the optical mapping data, and good correspondence was found. Such high-resolution restriction maps may become an indispensable resource for large-scale genome sequencing projects.

Animals↗
PubMed2003

PhysioNet: an NIH research resource for complex signals.

The Research Resource for Complex Physiologic Signals, supported by the National Institutes of Health (NIH), is intended to promote and facilitate investigations in the study of cardiovascular and other complex biomedical signals. The resource website (www.physionet.org) has 3 interdependent components: 1) PhysioBank is an archive of well-characterized digital recordings of physiologic signals and related data, including databases of electrocardiogram and heart rate time series from patients with heart failure, coronary disease, sleep apnea syndromes, and cardiac arrhythmias; 2) PhysioToolkit is a library of open-source software for physiologic signal processing and analysis; and 3) PhysioNet, for which the resource is named, is an on-line forum for dissemination and exchange of recorded biomedical signals and open-source software for analyzing them. PhysioNet, in cooperation with the annual Computers in Cardiology conference, hosts a series of challenges inviting participants to tackle clinically interesting problems that are either unsolved or not well solved. PhysioNet invites contributions of databases and software from the biomedical community.

Atrial Fibrillation↗
PubMed2006

Design, synthesis, and biological evaluation of the combinatorial library with a new spirodiketopiperazine scaffold. Discovery of novel potent and selective low-molecular-weight CCR5 antagonists.

We previously reported the discovery of several spirodiketopiperazine derivatives as potent CCR5 antagonists with anti-HIV activity. Herein, we describe in detail the identification of these lead compounds using a combinatorial chemistry approach. A novel spirodiketopiperazine scaffold was designed on the basis of the concept of the privileged structure of G-protein-coupled receptors (GPCRs). This new framework was obtained in acceptable yield with high purity from the readily prepared isonitrile resin through the Ugi reaction, sequential transformations, and cyclative cleavage. By measuring the inhibitory activity of each compound in the initial library against the intracellular calcium mobilization stimulated by MIP-1alpha, several compounds were found to show modest but selective CCR5 antagonistic activity. After the rapid evaluation of these hit compounds, several single-digit nanomolar, low-molecular-weight CCR5 antagonists that can potently block the infectivity and replication of laboratory and clinical strains of HIV as well as those of highly drug-resistant HIV variants with minimal cytotoxicity have been identified.

Animals↗