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PubMed1987

Interdisciplinary andrology. STDs. AIDS research.

Multidisciplinary andrology deals with clinical application and modern technology for the evaluation and differential diagnosis of male infertility with emphasis on morphological, anatomical, biochemical, immunological, hereditary, and microbiological parameters. Little is known about the effects of diet, disease, stress, environmental, and drugs on male-related unexplained infertility of couples. Regional, national, and international centers of multidisciplinary andrology should provide (1) extensive and unique clinical services; (2) a computerized "patient referral center," (3) self-learning packages (slides/tape programs) for patients; and (4) a computer link to the National Library of Medicine and the Drug Information Center. Specialized laboratories and clinics can be served by expert consultants, visiting professors, bilingual and well-trained clinicians, nurses, laboratory technologists, computer operators, and related allied health personnel. Patient education pamphlets, updated every few years, can be distributed during training workshops when an extensive network of remote teleprinters can be utilized. Qualified client location may install a printer to allow on-site printing of reports in the shortest possible time. Special mailing containers are provided to clients who wish to mail their laboratory specimens. Other clinical services may include the following: 1. Central source of communication and information in andrology; 2. International roster of multidisciplinary andrology centers; 3. Patient referral to centers and consultations for developing countries; 4. Screening of husbands and wives for in vitro fertilization/embryo transfer (IVF/ET); 5. Screening of couples with unexplained infertility for sexually transmitted diseases (STDs) including AIDS; 6. Exchange of research material and methodology; 7. Coordination of multicenter research; 8. Organizing training workshops for clinicians, nurses, and laboratory technicians; 9. Establishing a repository of films, video tapes, slides, catalogs, instrumentation, books, SEM photos, and atlases; 10. Publication and editorial assistance; 11. Consultation for the appropriate selection, purchase, and quality control of instrumentation (all on one computer system); 12. Evaluation of new diagnostic tools for idiopathic infertility and fertility regulation; 13.(ABSTRACT TRUNCATED AT 400 WORDS)

Acquired Immunodeficiency Syndrome↗
PubMed2005

The rat blood-brain barrier transcriptome.

The blood-brain barrier (BBB) is the cellular interface between the circulating blood and neural environment, and is created by apposed endothelial cells and their intercellular tight junctions. Many aspects of how the BBB functions at the molecular level remain unresolved; therefore, we report for the first time a comprehensive gene expression profile of rat brain microvessels using serial analysis of gene expression (SAGE). We assembled a full and quantitative SAGE catalog containing 101,364 tags, of which 33% of the tags matched known genes, 51% matched expressed sequence tags (ESTs) in the Unigene database, and 16% of the tags were unassigned. The transcriptome catalog contains many new and novel transcripts among known BBB genes. A large compliment of junctional proteins and an extensive assortment of facilitated carrier and ATP-dependent transporters are included. To identify microvessel-enriched transcripts, we compared the microvessel SAGE catalog to cortex and hippocampus SAGE catalogs. This resulted in identification of 864 genes, including several known for their abundant expression at the BBB, such as the transferrin receptor (TrnR). Sorting enriched genes based on function revealed groups that encode transporters (11%), receptors (5%), proteins involved in vesicle trafficking (4%), structural proteins (10%), and components of signal transduction pathways (17%). This genomic repertoire emphasizes the unique cellular phenotype existing within the brain and further implicates the BBB as a mediator between the brain and periphery. These results may provide a useful resource and reference point from which to determine the effects of different physiological, developmental, and disease processes on BBB gene expression.

Animals↗
PubMed2006

Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera).

Aphids are the leading pests in agricultural crops. A large-scale sequencing of 40,904 ESTs from the pea aphid Acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. A strong AT bias was found, indicating a compositional shift between Drosophila melanogaster and A. pisum. An in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect.

Animals↗
PubMed2001

dbSNP: the NCBI database of genetic variation.

In response to a need for a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, the National Center for Biotechnology Information (NCBI) has established the dbSNP database [S.T.Sherry, M.Ward and K. Sirotkin (1999) Genome Res., 9, 677-679]. Submissions to dbSNP will be integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data. The complete contents of dbSNP are available to the public at website: http://www.ncbi.nlm.nih.gov/SNP. The complete contents of dbSNP can also be downloaded in multiple formats via anonymous FTP at ftp://ncbi.nlm.nih.gov/snp/.

Animals↗
PubMed2005

Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii.

The beet cyst nematode Heterodera schachtii is an important pathogen worldwide, but its molecular characterization has been limited to studying individual genes of interest. We undertook a high-throughput genomic approach and drastically increased the number of available sequences for this parasite. A total of 2,662 expressed sequence tags were grouped into 1,212 clusters representing a nonredundant catalog of H. schachtii genes. Implementing a bioinformatic workflow, we identified 50 sequences coding for candidate secreted proteins. All of these contain a putative signal peptide required for entry into the secretory pathway and lack any transmembrane domain. Included are previously postulated cell-wall-degrading enzymes and other parasitism-related genes. Moreover, we provide the first report of an arabinogalactan endo-1,4-beta-galactosidase enzyme (EC 3.2.1.89) in animals. As sequence data increase at a rapid rate, developing high-throughput genomic screening is a necessity. The in silico approach described here is an effective way to identify putative secreted proteins and prioritize candidates for further studies.

Animals↗
PubMed1995

An interactive histology image-barcode manual for a videodisc image library.

UNLABELLED: Cell Biology and HISTOLOGY (alias Microanatomy, alias Microscopic Anatomy) is a required course for first-year medical and dental students in most health science centers. The traditional approach used in teaching this discipline is to present photomicrographic images of structures to students in lecture using 35 mm slides of fields seen through the microscope. The students then spend many hours viewing and studying specimens of tissues using a light microscope in a laboratory setting. Students in traditional courses of histology spend an inordinate amount of time learning the component structures by attempting to find and identify them in tissue sections using a microscope, where the structure being sought is surrounded by a multitude of other structures with which they are also not familiar. With the recent availability of videodisc stored image libraries of histological samples, it is now possible to study histological principles without the use of the microscope as the primary learning tool. A videodisc entitled " HISTOLOGY: A Photographic Atlas" by S. Downing (published by Image Premastering Services Limited, Minneapolis, MN, 1991) has been incorporated into our histology course. Fifteen videodisc player stations are provided for 150 students. Images are retrieved by students using a bar code scanner attached to a videodisc player (Pioneer CLD-2400). Using this kind of image library, students can now learn basic histological structure, such as cell and tissue types, without the use of a microscope or as a tool for facilitating microscopy. The use of a videodisc library of randomly accessible images simplifies learning the basic components which all organs are composed of by presenting the learner with clear-cut examples to avoid confusion with other structures. However, videodisc players and TV monitors are still not appropriately priced for every student to own. This presents a problem in that the same images studied in class are not available to study and review outside of class. There is a need for resources for additional study outside of the institutional setting, for students to have and interact with to reinforce the learning experience in the teaching laboratory. A hard copy manual was created and is being used in our course; it incorporates photos captured from the videodisc. The images displayed in the manual are chosen to give the student one example of each histological component. Additional labeling is added to the images, and each image is accompanied by a bar code that may be used at a videodisc player with a bar code reader to retrieve the same color image from the disc displayed in larger format on a TV monitor. Each topic in the manual is accompanied by learning objectives and a statement of clinical relevance. Following the presentation of the images in each section of the manual, the students are encouraged to practice by viewing multiple examples of each structural component presented in the lesson. They can do this by using the bar-coded catalog supplied with each disc. The presentation of each topic concludes with a quiz composed of questions about images that the student can retrieve from the videodisc using barcodes in the text of the manual. Some of the images on the quiz are printed in miniature in the manual to provide the student with an opportunity for personal review at home when hardware to obtain and display images from a video disc is not available. This manual provides an answer to the dilemma faced by the learner when access to hardware is not available; reinforcement is therefore facilitated outside the teaching laboratory. This allows learning to continue outside of the classroom, using the same materials. (abstract truncated)

Computer-Assisted Instruction↗
PubMed2001

MicroSAGE analysis of 2,353 expressed genes in a single cell-derived colony of undifferentiated human mesenchymal stem cells reveals mRNAs of multiple cell lineages.

Mesenchymal stem cells (MSCs) isolated from the bone marrow of adult organisms are capable of differentiating into adipocytes, chondrocytes, myoblasts, osteoblasts, and hematopoiesis-supporting stroma. We recently demonstrated that MSCs also adopt glial cell fates when transplanted into the developing central nervous system and hence can produce tissue elements derived from a separate embryonic layer. Despite these remarkable properties, it has been difficult to establish specific criteria to characterize MSCs. Using a modified protocol for micro-serial analysis of gene expression, we cataloged 2,353 unique genes expressed by a single cell-derived colony of undifferentiated human MSCs. This analysis revealed that the MSC colony simultaneously expressed transcripts characteristic of various mesenchymal cell lineages including chondrocytes, myoblasts, osteoblasts, and hematopoiesis-supporting stroma. Therefore, the profile of expressed transcripts reflects the developmental potential of the cells. Additionally, the MSC colony expressed mRNAs characteristic of endothelial, epithelial and neuronal cell lineages, a combination that provides a unique molecular signature for the cells. Other expressed transcripts included various products involved in wound repair as well as several neurotrophic factors. A total of 268 novel transcripts were also identified, one of which is the most abundantly expressed mRNA in MSCs. This study represents the first extensive gene expression analysis of MSCs and as such reveals new insight into the biology, ontogeny, and in vivo function of the cells.

Base Sequence↗
PubMed1998

Bioinformatics: searching the Net.

During the past 30 years, there has been an explosion in the volume of published medical information. As this volume has increased, so has the need for efficient methods for searching the data. MEDLINE, the primary medical database, is currently limited to abstracts of the medical literature. MEDLINE searches use AND/OR/NOT logical searching for keywords that have been assigned to each article and for textwords included in article abstracts. Recently, the complete text of some scientific journals, including figures and tables, has become accessible electronically. Keyword and textword searches can provide an overwhelming number of results. Search engines that use phrase searching, or searches that limit the number of words between two finds, improve the precision of search engines. The development of the Internet as a vehicle for worldwide communication, and the emergence of the World Wide Web (WWW) as a common vehicle for communication have made instantaneous access to much of the entire body of medical information an exciting possibility. There is more than one way to search the WWW for information. At the present time, two broad strategies have emerged for cataloging the WWW: directories and search engines. These allow more efficient searching of the WWW. Directories catalog WWW information by creating categories and subcategories of information and then publishing pointers to information within the category listings. Directories are analogous to yellow pages of the phone book. Search engines make no attempt to categorize information. They automatically scour the WWW looking for words and then automatically create an index of those words. When a specific search engine is used, its index is searched for a particular word. Usually, search engines are nonspecific and produce voluminous results. Use of AND/OR/NOT and "near" and "adjacent" search refinements greatly improve the results of a search. Search engines that limit their scope to specific sites, and metasearch sites that use multiple search engines optimized for specific types of searches have recently emerged. The distinctions between search engines and directory searches have blurred. Eventually, conceptual searching in which the computer searches for related ideas, without having to be given all the related keywords, may become a reality. This will free the user from having to learn specific rules about searching, allowing energies to be focused on results of the search, not the search itself.

Computational Biology↗
PubMed2004

Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line.

BACKGROUND: The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames (ORFs) and flanking untranslated regions. The best currently available chicken transcript catalog is the Ensembl build based on the mappings of a relatively small number of full length cDNAs and ESTs to the genome as well as genome sequence derived in silico gene predictions. RESULTS: We use Long Serial Analysis of Gene Expression (LongSAGE) in bursal lymphocytes and the DT40 cell line to verify the quality and completeness of the annotated transcripts. 53.6% of the more than 38,000 unique SAGE tags (unitags) match to full length bursal cDNAs, the Ensembl transcript build or the genome sequence. The majority of all matching unitags show single matches to the genome, but no matches to the genome derived Ensembl transcript build. Nevertheless, most of these tags map close to the 3' boundaries of annotated Ensembl transcripts. CONCLUSIONS: These results suggests that rather few genes are missing in the current Ensembl chicken transcript build, but that the 3' ends of many transcripts may not have been accurately predicted. The tags with no match in the transcript sequences can now be used to improve gene predictions, pinpoint the genomic location of entirely missed transcripts and optimize the accuracy of gene finder software.

Animals↗
PubMed2005

Specificity and overlap in gene segment-defined antibody repertoires.

BACKGROUND: To date several studies have sought to catalog the full suite of antibodies that humans naturally produce against single antigens or other specificities (repertoire). Here we analyze the properties of all sequenced repertoires in order to better understand the specificity of antibody responses. Specifically, we ask whether the large-scale sequencing of antibody repertoires might provide a diagnostic tool for detecting antigen exposure. We do this by examining the overlap in VH-, D-, and JH- segment usage among sequenced repertoires. RESULTS: We find that repertoire overlap in VH-, D-, and JH-segment use is least for VH segments and greatest for JH segments, consistent with there being more VH than JH segments in the human genome. We find that for any two antigens chosen at random, chances are 90 percent that their repertoires' VH segments will overlap by less than half, and 98 percent that their VDJH combinations will overlap by < or =10 percent. We ran computer simulations to test whether enrichment for specific VDJH combinations could be detected in "antigen-exposed" populations, and found that enrichment is detectable with moderate-to-high sensitivity and high specificity, even when some VDJH combinations are not represented at all in some test sets. CONCLUSION: Thus, as large-scale sequencing becomes cost-effective for clinical testing, we suggest that sequencing an individual's expressed antibody repertoire has the potential to become a useful diagnostic modality.

Algorithms↗
PubMed2005

Biological activities encoded by the murine mesenchymal stem cell transcriptome provide a basis for their developmental potential and broad therapeutic efficacy.

We used serial analysis of gene expression to catalog the transcriptome of murine mesenchymal stem cells (MSCs) enriched from bone marrow by immunodepletion. Interrogation of this database, results of which are delineated in the appended databases, revealed that immunodepleted murine MSCs (IDmMSCs) highly express transcripts encoding connective tissue proteins and factors modulating T-cell proliferation, inflammation, and bone turnover. Categorizing the transcriptome based on gene ontologies revealed the cells also expressed mRNAs encoding proteins that regulate mesoderm development or that are characteristic of determined mesenchymal cell lineages, thereby reflecting both their stem cell nature and differentiation potential. Additionally, IDmMSCs also expressed transcripts encoding proteins regulating angiogenesis, cell motility and communication, hematopoiesis, immunity and defense as well as neural activities. Immunostaining and fluorescence-activated cell sorting analysis revealed that expression of various regulatory proteins was restricted to distinct subpopulations of IDmMSCs. Moreover, in some cases, these proteins were absent or expressed at reduced levels in other murine MSC preparations or cell lines. Lastly, by comparing their transcriptome to that of 17 other murine cell types, we also identified 43 IDmMSC-specific transcripts, the nature of which reflects their varied functions in bone and marrow. Collectively, these results demonstrate that IDmMSC express a diverse repertoire of regulatory proteins, which likely accounts for their demonstrated efficacy in treating a wide variety of diseases. The restricted expression pattern of these proteins within populations suggests that the cellular composition of marrow stroma and its associated functions are more complex than previously envisioned.

Animals↗
PubMed2003

Dupuytren's disease or Cooper's contracture?: Kenneth Fitzpatrick Russell Memorial Lecture.

In his position as curator of the Cowlishaw collection of historical medical books in the Library of the College, Kenneth Russell prepared the definitive catalogue of the collection. This catalogue is comprehensive and for almost all entries there is an annotation that demonstrates his meticulous attention to detail and the love of the book collection that he managed to secure for the College. It is from this catalogue that I have chosen two books in particular that bring together two great surgeons of the turn of the 19th century. Although he was a pupil of the great John Hunter, the young Astley Cooper possessed good manners and a gift of oratory of which the Scot, his teacher, was devoid. After his apprenticeship with Henry Cline senior, Cooper came to share the podium with Cline at Guy's and St Thomas' hospitals and the two dominated surgical teaching in London for some 22 years, until Cline's retirement in 1811. It was the latter who was first to recognize the true nature of the condition now known as Dupuytren's disease. Later, in 1822, Cooper wrote a detailed description of the contracture of the palmar aponeurosis and recommended fasciotomy as being curative. His book A Treatise on Dislocations and Fractures of the Joints, which contains this description of Dupuytren's contracture, is held in the Cowlishaw Collection. On the other side of the English Channel, M. le Baron Dupuytren repeatedly misquoted Cooper and stated that Cooper believed that the disease was incurable. In his famous lecture given to the staff of the Hôtel Dieu in Paris on 5th December 1931, he admitted to having seen 30 or 40 cases over 20 years of practice. It seems likely that he was not aware of the true cause of the condition before 1831 when he treated his first case. This lecture, along with others, are recorded in his Leçons Orales de Clinique Chirurgicale, a copy of which is also to be found in the Cowlishaw Collection.

Catalogs as Topic↗