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At least 487 records · Page 27Linked to original sources
PubMed1995

A handy database for culture collections worldwide: CCINFO-PC.

Culture collections are reservoirs of cultivable microbes, cell lines and gene libraries. Their role and duty are to supply biological resources to biomedical communities; nevertheless, their visibility from the public is low because most culture collections still have poor accesses via the Internet. Therefore the WFCC World Data Center on Micro-organisms (WDCM) developed a database that runs on IBM PCs and compatibles, which are the most popular computer and will be as powerful as workstations. The database includes various information: activities of 484 culture collections from 58 countries; an integrated list of their holdings of bacteria, fungi and yeast; and data entry system for culture collections.

Bacteria↗
PubMed1986

Information needs of practicing dentists.

Dentists, as health professionals, need access to information. As in other health sciences, the increase in the rate and volume of published information has made it more difficult for them to keep up with new developments. Five hundred randomly selected dentists in Louisiana were surveyed to determine what information dentists seek and what sources they prefer. Responses indicated that dentists need information on new techniques in dentistry and that preferred sources are professional colleagues and personal journal collections. Libraries were found to be used only infrequently as sources for information. Implications for planning libraries for applications- and technique-oriented professions are discussed.

Dentists↗
PubMedDate not supplied

Evaluation of the effectiveness of a Web-based graduate epidemiology course.

An online epidemiology course was developed, implemented, and evaluated for graduate nursing students through the collaborative efforts of nursing faculty and information, education, and instructional design staff of the library at a health sciences university. This epidemiology course is a core curriculum course for graduate nursing students. The course was piloted with 14 students (one student in Romania); the initial online offering ran concurrently with a traditional classroom section. Extensive evaluation data were collected and analyzed to compare the effectiveness of the classroom and distance-learning formats. Areas of evaluation included objective measures, such as midterm and final examination scores and content analysis comparisons, as well as subjective ratings by the students of time commitments, course objectives, technical aspects of the web-based course, areas of satisfaction or dissatisfaction, and self-confidence regarding epidemiology and computer skills. Recommendations for course development, implementation, and evaluation for similar distance-learning courses will be included.

Computer-Assisted Instruction↗
PubMed2006

A screening method for DNA aptamers that bind to a specific, unidentified protein in tissue samples.

Aptamers are oligonucleotide ligands with a high affinity to, and specificity for, various target molecules and they are expected to be powerful tools for proteomic analysis. To select aptamers that bind to a specific unidentified protein in tissues for protein analysis, a screening method was developed using chicken skeletal muscle as a model. Target proteins in the target mixture were separated by electrophoresis and transferred to a membrane, and a DNA library was added onto it. The aptamers that bound to the target protein were visualized by chemiluminescence and collected by cutting out the visualized band. The specific aptamers to the target protein were selected by only one round of selection using this screening, suggesting this screening method might be useful for selecting aptamers for proteome analysis.

Animals↗
PubMed2001

Initiation of a Sarcocystis neurona expressed sequence tag (EST) sequencing project: a preliminary report.

To accelerate genetic and molecular characterization of Sarcocystis neurona, the primary causative agent of equine protozoal myeloencephalitis (EPM), a sequencing project has been initiated that will generate approximately 7000-8000 expressed sequence tags (ESTs) from this apicomplexan parasite. Poly(A)(+) RNA was isolated from culture-derived S. neurona merozoites, and a cDNA library was constructed in a unidirectional lambda phage cloning vector. Sixty phage clones were randomly picked from the library, and the cDNA inserts were amplified from these clones using the T3 and T7 primers that flank the multi-cloning site of the lambda vector. This analysis demonstrated that 100% (60/60) of the clones selected from this library contained recombinant cDNA inserts ranging in size from 0.4 to 4.0 kilobases (kb) with an average size of 1.23kb. Single-pass sequencing from the 5' end of the 60 amplified cDNAs produced high-quality nucleotide sequence from 53 of the clones. Comparison of these ESTs to the current gene databases revealed significant matches for 10 of the ESTs, six of which are similar to sequences from other Apicomplexa (i.e., Toxoplasma gondii). Importantly, none of the ESTs were of obvious mammalian origin, thus indicating that the cDNAs in this library were derived primarily from parasite mRNA and not from mRNA of the bovine turbinate host cells. Collectively, these data indicate that the described cDNA library will provide an excellent substrate for generating a portion of the ESTs that are planned from S. neurona. This sequencing project will greatly hasten gene discovery for this protozoan pathogen thereby enhancing efforts towards the development of improved diagnostics, treatments, and preventatives for EPM. In addition, the S. neurona ESTs will represent a significant contribution to the extensive database of sequences from the Apicomplexa. Comparative analyses of these apicomplexan sequences will likely offer a multitude of important information about the biology and evolutionary history of this phylogenetic grouping of parasites.

Animals↗
PubMed2005

Metabolomics in human nutrition: opportunities and challenges.

Metabolomics has been widely adopted in pharmacology and toxicology but is relatively new in human nutrition. The ultimate goal, to understand the effects of exogenous compounds on human metabolic regulation, is similar in all 3 fields. However, the application of metabolomics to nutritional research will be met with unique challenges. Little is known of the extent to which changes in the nutrient content of the human diet elicit changes in metabolic profiles. Moreover, the metabolomic signal from nutrients absorbed from the diet must compete with the myriad of nonnutrient signals that are absorbed, metabolized, and secreted in both urine and saliva. The large-bowel microflora also produces significant metabolic signals that can contribute to and alter the metabolome of biofluids in human nutrition. Notwithstanding these possible confounding effects, every reason exists to be optimistic about the potential of metabolomics for the assessment of various biofluids in nutrition research. This potential lies both in metabolic profiling through the use of pattern-recognition statistics on assigned and unassigned metabolite signals and in the collection of comprehensive data sets of identified metabolites; both objectives have the potential to distinguish between different dietary treatments, which would not have been targeted with conventional techniques. The latter objective sets out a well-recognized challenge to modern biology: the development of libraries of small molecules to aid in metabolite identification. The purpose of the present review was to highlight some early challenges that need to be addressed if metabolomics is to realize its great potential in human nutrition.

Diet↗
PubMed2006

Analyses of expressed sequence tags from apple.

The domestic apple (Malus domestica; also known as Malus pumila Mill.) has become a model fruit crop in which to study commercial traits such as disease and pest resistance, grafting, and flavor and health compound biosynthesis. To speed the discovery of genes involved in these traits, develop markers to map genes, and breed new cultivars, we have produced a substantial expressed sequence tag collection from various tissues of apple, focusing on fruit tissues of the cultivar Royal Gala. Over 150,000 expressed sequence tags have been collected from 43 different cDNA libraries representing 34 different tissues and treatments. Clustering of these sequences results in a set of 42,938 nonredundant sequences comprising 17,460 tentative contigs and 25,478 singletons, together representing what we predict are approximately one-half the expressed genes from apple. Many potential molecular markers are abundant in the apple transcripts. Dinucleotide repeats are found in 4,018 nonredundant sequences, mainly in the 5'-untranslated region of the gene, with a bias toward one repeat type (containing AG, 88%) and against another (repeats containing CG, 0.1%). Trinucleotide repeats are most common in the predicted coding regions and do not show a similar degree of sequence bias in their representation. Bi-allelic single-nucleotide polymorphisms are highly abundant with one found, on average, every 706 bp of transcribed DNA. Predictions of the numbers of representatives from protein families indicate the presence of many genes involved in disease resistance and the biosynthesis of flavor and health-associated compounds. Comparisons of some of these gene families with Arabidopsis (Arabidopsis thaliana) suggest instances where there have been duplications in the lineages leading to apple of biosynthetic and regulatory genes that are expressed in fruit. This resource paves the way for a concerted functional genomics effort in this important temperate fruit crop.

Arabidopsis↗
PubMed1999

The mammalian gene collection.

The Mammalian Gene Collection (MGC) project is a new effort by the NIH to generate full-length complementary DNA (cDNA) resources. This project will provide publicly accessible resources to the full research community. The MGC project entails the production of libraries, sequencing, and database and repository development, as well as the support of library construction, sequencing, and analytic technologies dedicated to the goal of obtaining a full set of human and other mammalian full-length (open reading frame) sequences and clones of expressed genes.

Animals↗
PubMed2004

Natural sound archives: past, present and future.

Recordings of wild animals were first made in the Palearctic in 1900, in the Nearctic in 1929, in Antarctica in 1934, in Asia in 1937, and in the Neotropics in the 1940s. However, systematic collecting did not begin until the 1950s. Collections of animal sound recordings serve many uses in education, entertainment, science and nature conservation. In recent years, technological developments have transformed the ways in which sounds can be sampled, stored and accessed. Now the largest collections between them hold altogether around 0.5 million recordings with their associated data. The functioning of a major archive will be described with reference to the British Library Sound Archive. Preserving large collections for the long term is a primary concern in the digital age. While digitization and digital preservation has many advantages over analogue methods, the rate of technology change and lack of standardization are a serious problem for the world's major audio archives. Another challenge is to make collections more easily and widely accessible via electronic networks. On-line catalogues and access to the actual sounds via the internet are already available for some collections. Case studies describing the establishment and functioning of sound libraries in Mexico, Colombia and Brazil are given in individually authored sections in an Appendix.

Analog-Digital Conversion↗
PubMed1999

PC-based telerehabilitation system with force feedback.

A PC-based orthopedic rehabilitation system was developed for use at home, while allowing for remote monitoring from the clinic. The home rehabilitation station has a Pentium II PC with graphics accelerator, Polhemus tracker, and a novel Multipurpose Haptic Control Interface with its own Pentium board. This interface is used to sample patient's hand positions and to provide resistive forces using the Rutgers Master II (RMII) glove. A library of virtual rehabilitation routines was developed using WorldToolKit software. At the present time, it consists of two physical therapy exercises (DigiKey and Ball) and two functional rehabilitation exercises (Peg Board test and Ball game). All VR exercises allow automatic and transparent patient data collection into an Oracle database. A remote Pentium II PC is connected with the home-based PC over the Internet and an additional video-conferencing connection. The remote computer running Oracle server is used to maintain the patient database, monitor progress and change exercise level of difficulty. This allows for timely patient progress monitoring and repeat evaluations over time from the Clinic. The system will soon start clinical trails at Stanford Medical School, with progress being monitored remotely from Rutgers University. Other rehabilitation haptic interfaces under development include devices for elbow, and knee rehabilitation connected to the Multipurpose Haptic Control Interface.

Computer Graphics↗
PubMed2005

Selection of information resources for education in medical pharmacology.

Pharmacology is the foundation science of medical pharmacotherapy. Education in medical pharmacology (EP) requires the use of information resources (IR) to meet the challenge of the continuous introduction of new drugs and new educational, didactic and pedagogical theories to enhance knowledge. Hence criteria for selecting bibliographic material for EP should be clearly outlined and implemented. In this work we present a method to select IR for EP based on systems theory and focusing on the factors determining: (a) the integration of a list of recommended IR for EP; (b) the design of the acquisition list for faculty and students work; (c) the overall organization of the resources available for its optimal use and benefit in the educational process; and (d) a general strategy for assessing the impact of the bibliographic infrastructure. The proposal is based on information from: (i) lists of recommended readings in the academic program of the Pharmacology course given at the School of Medicine of UNAM in the last 30 years; (ii) the extent of discipline development measured by two indexes derived from the contents of Goodman and Gilman's "Pharmacological Basis of Therapeutics" (G & G); (iii) the number of texts currently found in the collection of FM-UNAM which are classified in the section of Pharmacology using the Library of Congress Classification System (LCCS); and (iv) the comparison of academic versus standardized classification of pharmacology topics, such as Medical Subject Heading (MESH) and LCCS The importance of this proposal relates to its usefulness for EP and for other medical disciplines.

Books↗
PubMed1989

Estimates of mRNA abundance in the mouse blastocyst based on cDNA library analysis.

Studies of gene expression during blastocyst formation in mouse preimplantation development have been limited by the amount of RNA available per embryo. Our present approach to this problem has been to construct a large, representative, blastocyst cDNA library in lambda gt11. Random hexadeoxynucleotides were used as primers with total blastocyst RNA serving as template. RNA collected from 4,100 32-64 cell embryos was used to generate a library with an initial size of 30 X 10(6) recombinants. By using clone frequency as a measure of relative mRNA abundance, our data support previous work on the relative and absolute amounts of actin, histone H2a, and intracisternal A particle. Furthermore, we provide estimates for the abundance of cytokeratin endo A, cytokeratin endo B, and beta-tubulin from clone frequency data. Insert sizes for isolated clones range from 200 bp to 3.6 kb with full-length or near-full-length insert sizes for selected clones, indicating that random primer methods generate cDNAs which can represent a significant portion of the mRNA. We have so far characterized products whose abundance is equal to or greater than 0.002% of total RNA. This library offers the potential for the analyses of presumptive regulatory gene products in the mouse preimplantation embryo which are represented as low abundance (less than 1% of mRNA) RNAs.

Actins↗
PubMed2004

Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L.

Large-insert bacterial artificial chromosome (BAC) libraries, plant-transformation-competent binary BAC (BIBAC) libraries, and simple sequence repeat (SSR) markers are essential for many aspects of genomics research. We constructed a BAC library and a BIBAC library from the nuclear DNA of chickpea, Cicer arietinum L., cv. Hadas, partially digested with HindIII and BamHI, respectively. The BAC library has 14,976 clones, with an average insert size of 121 kb, and the BIBAC library consists of 23,040 clones, with an average insert size of 145 kb. The combined libraries collectively cover ca. 7.0 x genomes of chickpea. We screened the BAC library with eight synthetic SSR oligos, (GA)10, (GAA)7, (AT)10, (TAA)7, (TGA)7, (CA)10, (CAA)7, and (CCA)7. Positive BACs were selected, subcloned, and sequenced for SSR marker development. Two hundred and thirty-three new chickpea SSR markers were developed and characterized by PCR, using chickpea DNA as template. These results have demonstrated that BACs are an excellent source for SSR marker development in chickpea. We also estimated the distribution of the SSR loci in the chickpea genome. The SSR motifs (TAA)n and (GA)n were much more abundant than the others, and the distribution of the SSR loci appeared non-random. The BAC and BIBAC libraries and new SSR markers will provide valuable resources for chickpea genomics research and breeding (the libraries and their filters are available to the public at http://hbz.tamu.edu).

Base Sequence↗
PubMed2006

Analysis of mercuric reductase (merA) gene diversity in an anaerobic mercury-contaminated sediment enrichment.

The reduction of ionic mercury to elemental mercury by the mercuric reductase (MerA) enzyme plays an important role in the biogeochemical cycling of mercury in contaminated environments by partitioning mercury to the atmosphere. This activity, common in aerobic environments, has rarely been examined in anoxic sediments where production of highly toxic methylmercury occurs. Novel degenerate PCR primers were developed which span the known diversity of merA genes in Gram-negative bacteria and amplify a 285 bp fragment at the 3' end of merA. These primers were used to create a clone library and to analyse merA diversity in an anaerobic sediment enrichment collected from a mercury-contaminated site in the Meadowlands, New Jersey. A total of 174 sequences were analysed, representing 71 merA phylotypes and four novel MerA clades. This first examination of merA diversity in anoxic environments suggests an untapped resource for novel merA sequences.

Anaerobiosis↗
PubMed2001

ADAM-HCV, a new-concept diagnostic assay for antibodies to hepatitis C virus in serum.

We screened phage libraries using sera from noninfected individuals and patients infected by hepatitis C virus (HCV). By applying different selection and maturation strategies, we identified a wide collection of efficient phage-borne ligands for HCV-specific antibodies. The selected ligands retained their antigenic properties when expressed as multimeric synthetic peptides. Peptides that mimic several immunodominant epitopes of the virus were used to develop a novel type of diagnostic assay which efficiently detects antibodies to HCV in serum. This type of analysis provides a conclusive diagnosis for many patients identified as indeterminate according to presently available serological assays.

Amino Acid Sequence↗
PubMedDate not supplied

Role and functions of Poisons Information Centre.

The Poisons Information Centre (PIC) is a specialized unit providing information on prevention, early diagnosis and treatment of poisoning and hazard management. Most of the developed and many developing countries have well established poison control centres with poisons information service, patient management facility and analytical laboratory. In India, the National Poisons Information Centre (NPIC) was established in February, 1995 in the Department of Pharmacology at the All India Institute of Medical Sciences, New Delhi. The centre provides toxicological information and advice on the management of poisoned patients adopted to the level of the enquirer. The basis of this service are the databases on poisoning, drug reactions and also the continuous and systematic collection of data from the library. This information service is available round the clock. The PIC has the training responsibility extending to medical and other health professionals and community. The NPIC organized two successive training courses for medical professionals and para professionals at all health levels. Further, NPIC is a participant of INTOX project of IPCS/WHO, receiving regular yearly training on the use of INTOX database. Laboratory service is an essential component of a poisons control programme, providing analytical services on emergency basis to help in diagnosis and management. The NPIC is developing facilities for quick diagnosis of poisoning cases. Toxicovigilance and prevention of poisoning is another major function of PIC. The Centre has prepared manuals and leaflets on prevention and management cards on treatment of various poisonings. Thus the Centre provides a service with considerable health benefits, reducing morbidity and mortality from poisoning and gives significant financial savings to the community.

Child↗
PubMed1997

De novo heme proteins from designed combinatorial libraries.

We previously reported the design of a library of de novo amino acid sequences targeted to fold into four-helix bundles. The design of these sequences was based on a "binary code" strategy, in which the patterning of polar and nonpolar amino acids is specified explicitly, but the exact identities of the side chains is varied extensively (Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH, 1993, Science 262:1680-1685). Because of this variability, the resulting collection of amino acid sequences may include de novo proteins capable of binding biologically important cofactors. To probe for such binding, the de novo sequences were screened for their ability to bind the heme cofactor. Among an initial collection of 30 binary code sequences, 15 are shown to bind heme and form bright red complexes. Characterization of several of these de novo heme proteins demonstrated that their absorption spectra and resonance Raman spectra resemble those of natural cytochromes. Because the design of these sequences is based on global features of polar/ nonpolar patterning, the finding that half of them bind heme highlights the power of the binary code strategy, and demonstrates that isolating de novo heme proteins does not require explicit design of the cofactor binding site. Because bound heme plays a key role in the functions of many natural proteins, these results suggest that binary code sequences may serve as initial prototypes for the development of large collections of functionally active de novo proteins.

Amino Acid Sequence↗
PubMed2005

Large-scale analysis of 73 329 physcomitrella plants transformed with different gene disruption libraries: production parameters and mutant phenotypes.

Gene targeting in the moss Physcomitrella patens has created a new platform for plant functional genomics. We produced a mutant collection of 73 329 Physcomitrella plants and evaluated the phenotype of each transformant in comparison to wild type Physcomitrella. Production parameters and morphological changes in 16 categories, such as plant structure, colour, coverage with gametophores, cell shape, etc., were listed and all data were compiled in a database (mossDB). Our mutant collection consists of at least 1804 auxotrophic mutants which showed growth defects on minimal Knop medium but were rescued on supplemented medium. 8129 haploid and 11 068 polyploid transformants had morphological alterations. 9 % of the haploid transformants had deviations in the leaf shape, 7 % developed less gametophores or had a different leaf cell shape. Other morphological deviations in plant structure, colour, and uniformity of leaves on a moss colony were less frequently observed. Preculture conditions of the plant material and the cDNA library (representing genes from either protonema, gametophore or sporophyte tissue) used to transform Physcomitrella had an effect on the number of transformants per transformation. We found correlations between ploidy level and plant morphology and growth rate on Knop medium. In haploid transformants correlations between the percentage of plants with specific phenotypes and the cDNA library used for transformation were detected. The number of different cDNAs present during transformation had no effect on the number of transformants per transformation, but it had an effect on the overall percentage of plants with phenotypic deviations. We conclude that by linking incoming molecular, proteome, and metabolome data of the transformants in the future, the database mossDB will be a valuable biological resource for systems biology.

Bryopsida↗