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At least 685 records · Page 38Linked to original sources
PubMed2000

A molecular analysis of NKT cells: identification of a class-I restricted T cell-associated molecule (CRTAM).

cDNA library subtraction techniques were used to identify transcripts expressed by activated mouse alphabetaTCR+ CD4-CD8- (double-negative; DN) T cells, a subset of natural killer T (NKT) cells. The most frequent cDNAs identified included the chemokines TCA3, macrophage inflammatory protein-1alpha (MIP-1alpha), MIP-1beta, and lymphotactin (LPTN), the cytokines interleukin-4 (IL-4) and interferon-gamma (IFN-gamma), and a granzyme. We also identified a new member of the immunoglobulin superfamily (Ig-SF). This molecule was designated class I-restricted T cell-associated molecule (CRTAM) as a result of its restricted expression pattern in T cells. Human CRTAM was also identified, and shares the same expression pattern as the mouse molecule. LPTN and CRTAM exhibit the same expression pattern in T cells, suggesting the existence of a gene expression program common to class I-MHC-restricted T cells.

Amino Acid Sequence↗
PubMed2004

Highly diverse heparan sulfate analogue libraries: providing access to expanded areas of sequence space for bioactivity screening.

Structurally diverse heparan sulfate analogue libraries were produced chemicoenzymatically from heparin. They possess vastly more heterogeneity than tissue heparan sulfates, expand the sequence space available for screening, and can help identify minimal structural features associated with activity. Library components are likely to exhibit fewer nonspecific interactions and side-effects than heparin or simple chemically modified heparin. A strategy for their use is illustrated for the fibroblast growth factor-receptor tyrosine kinase signaling system.

Cell Line↗
PubMed2006

Subtractive cDNA libraries identify differentially expressed genes in dormant and growing buds of leafy spurge (Euphorbia esula).

Two subtractive cDNA libraries were developed to study genes associated with bud dormancy (reverse library) and initiation of shoot growth (forward library) in leafy spurge. To identify unique sequences represented in each library, 15744 clones were screened to reduce the level of redundancy within both libraries. A total of 516 unique sequences were obtained from 2304 minimally redundant clones. Radioactive probes developed from RNAs extracted from crown buds of either intact (para-dormant control) or a series of growth-induced (2 h, 2, and 4 d after decapitation) plants were used to identify differentially expressed genes by macroarray analysis. Semi-quantitative RT-PCR was used to confirm results obtained by macroarray analysis and to determine the expression profiles for other transcripts identified within the subtractive libraries. Selected clones were also used to examine gene expression in crown buds after growth induction and/or during normal seasonal growth. In this study, four distinct patterns of gene expression were observed during the transition from para-dormancy to growth-induction. Many of the differentially regulated genes identified have unknown or hypothetical functions while others are known to play important roles in molecular functions. Gene ontology analysis identified a greater proportion of genes involved with catalytic activity in the forward library while the reverse library had a greater proportion of genes involved in DNA/RNA binding.

Cluster Analysis↗
PubMed2000

Approaches to detecting false positives in yeast two-hybrid systems.

While many novel associations predicted by two-hybrid library screens reflect actual biological associations of two proteins in vivo, at times the functional co-relevance of two proteins scored as interacting in the two-hybrid system is unlikely. The reason for this positive score remains obscure, which leads to designating such clones as false positives. After investigating the effect of over-expressing a series of putative false positives in yeast, we determined that expression of some of these clones induces an array of biological effects in yeast, including altered growth rate and cell permeability, that bias perceived activity of LacZ reporters. Based on these observations, we identify four simple strategies that can assist in determining whether a protein is likely to have been selected in a two-hybrid screen because of indirect metabolic effects.

Biotechnology↗
PubMed2004

ESTIMA, a tool for EST management in a multi-project environment.

BACKGROUND: Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users. RESULTS: A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA), has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for the management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. CONCLUSIONS: The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from http://titan.biotec.uiuc.edu/ESTIMA/. The entity-relationship (E-R) diagrams and the programs used to generate the Oracle database tables are also available. We have also provided detailed installation instructions and a tutorial at the same website. Presently the chromatograms, EST databases and their annotations have been made available for cattle and honeybee brain EST projects. Non-academic users need to contact the W.M. Keck Center for Functional and Comparative Genomics, University of Illinois at Urbana-Champaign, Urbana, IL, for licensing information.

Animals↗
PubMed1998

Octamer-primed cycle sequencing using dye-terminator chemistry.

Octamer Sequencing Technology, OST, is a method of DNA sequencing using single octamer oligonucleotides to prime cycle sequencing reactions. This sequencing strategy is faster than a traditional primer-walking strategy, since access to this optimized octamer library eliminates delays associated with designing and synthesizing gene specific primers. In this report, OST has been optimized for fluorescent, dye-terminator cycle sequencing reactions to facilitate parallel processing of samples. The successful adaptation of OST to an automated sequencing platform and the design of and access to an octamer library are critical steps towards developing an efficient 'closed-loop' DNA sequencing system.

Animals↗
PubMed2005

Identification and characterization of regions of the rice genome associated with broad-spectrum, quantitative disease resistance.

Much research has been devoted to understanding the biology of plant-pathogen interactions. The extensive genetic analysis of disease resistance in rice, coupled with the sequenced genome and genomic resources, provides the opportunity to seek convergent evidence implicating specific chromosomal segments and genes in the control of resistance. Published data on quantitative and qualitative disease resistance in rice were synthesized to evaluate the distributions of and associations among resistance loci. Quantitative trait loci (QTL) for resistance to multiple diseases and qualitative resistance loci (R genes) were clustered in the rice genome. R genes and their analogs of the nucleotide binding site-leucine-rich repeat class and genes identified on the basis of differential representation in disease-related EST libraries were significantly associated with QTL. Chromosomal segments associated with broad-spectrum quantitative disease resistance (BS-QDR) were identified. These segments contained numerous positional candidate genes identified on the basis of a range of criteria, and groups of genes belonging to two defense-associated biochemical pathways were found to underlie one BS-QDR region. Genetic dissection of disease QTL confidence intervals is needed to reduce the number of positional candidate genes for further functional analysis. This study provides a framework for future investigations of disease resistance in rice and related crop species.

Blotting, Northern↗
PubMed2004

Wide range of socioeconomic factors associated with mortality among cities in Japan.

The aim of this study was to identify socioeconomic factors associated with mortality among cities in Japan. Sex-specific and age-adjusted mortality rates for 1990 and 1995 were calculated by 779 local administrative units across the nation. One hundred indicators related to socioeconomic factors were compiled and divided into eight categories: economy, education, living conditions, vegetation and open space, transport, preventive activities, medical care and demography. Composite socioeconomic indices were formulated using factor analysis of the socioeconomic indicators by category, and the association between the indices and mortality rates was examined by correlation analysis and multiple regression analysis. Nineteen composite socioeconomic indices were obtained from factor analysis, and all indices except educational expenditure-related index were significantly correlated with mortality rates. Unemployment, old housing, primary health resources and density were independently positively associated, and higher education, public library activity, health check-up participation and population growth were independently negatively associated with both 1990 and 1995 male mortality rates. For female mortality, higher income, unemployment, spacious dwelling, old housing, less vegetation, road facility, numbers of cars per population, primary health resources and density were independently positively associated, and higher education, public library activity and health check-up participation were independently negatively associated. The relationship between mortality and socioeconomic conditions was stronger in males than in females, and higher income and less vegetation were associated with higher mortality only for females. The present study demonstrated a close link between mortality and a wide range of socioeconomic conditions by using a number of indicators compiled from various data sources. The results promote a deeper understanding of socioeconomic health determinants and development of multi-sectoral health policy to improve population health.

Adult↗
PubMed2004

Transgenic mouse in vivo library of human Down syndrome critical region 1: association between DYRK1A overexpression, brain development abnormalities, and cell cycle protein alteration.

Down syndrome is the most frequent genetic cause of mental retardation, having an incidence of 1 in 700 live births. In the present study we used a transgenic mouse in vivo library consisting of 4 yeast artificial chromosome (YAC) transgenic mouse lines, each bearing a different fragment of the Down syndrome critical region 1 (DCR-1), implicated in brain abnormalities characterizing this pathology. The 152F7 fragment, in addition to genes also located on the other DCR-1 fragments, bears the DYRK1A gene, encoding for a serine-threonine kinase. The neurobehavioral analysis of these mouse lines showed that DYRK1A overexpressing 152F7 mice but not the other lines display learning impairment and hyperactivity during development. Additionally, 152F7 mice display increased brain weight and neuronal size. At a biochemical level we found DYRK1A overexpression associated with a development-dependent increase in phosphorylation of the transcription factor FKHR and with high levels of cyclin B1, suggesting for the first time in vivo a correlation between DYRK1A overexpression and cell cycle protein alteration. In addition, we found an altered phosphorylation of transcription factors of CREB family. Our findings support a role of DYRK1A overexpression in the neuronal abnormalities seen in Down syndrome and suggest that this pathology is linked to altered levels of proteins involved in the regulation of cell cycle.

Animals↗
PubMed2000

Providing health information to the general public: a survey of current practices in academic health sciences libraries.

A questionnaire was mailed to 148 publicly and privately supported academic health sciences libraries affiliated with Association of American Medical Colleges (AAMC-accredited medical schools in the United States and Canada to determine level of access and services provided to the general public. For purposes of this study, "general public" was defined as nonaffiliated students or health care professionals, attorneys and other nonhealth-related professionals, patients from affiliated or other hospitals or clinics, and general consumers. One hundred five (71%) libraries responded. Results showed 98% of publicly supported libraries and 88% of privately supported libraries provided access to some or all of the general public. Publicly supported libraries saw greater numbers of public patrons, often provided more services, and were more likely to circulate materials from their collections than were privately supported libraries. A significant number of academic health sciences libraries housed a collection of consumer-oriented materials and many provided some level of document delivery service, usually for a fee. Most allowed the public to use some or all library computers. Results of this study indicated that academic health sciences libraries played a significant role in serving the information-seeking public and suggested a need to develop written policies or guidelines covering the services that will be provided to minimize the impact of this service on primary clientele.

Community Participation↗
PubMed2000

Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors.

Many attempts have been made to endow enzymes with new catalytic activities. One general strategy involves the creation of random combinatorial libraries of mutants associated with an efficient screening or selection scheme. Phage display has been shown to greatly facilitate the selection of polypeptides with desired properties by establishing a close link between the polypeptide and the gene that encodes it. Selection of phage displayed enzymes for new catalytic activities remains a challenge. The aim of this study was to display the serine protease subtilisin 309 (savinase) from Bacillus lentus on the surface of filamentous fd phage and to develop selection schemes that allow the extraction of subtilisin variants with a changed substrate specificity from libraries. Subtilisins are produced as secreted preproenzyme that mature in active enzyme autocatalytically. They have a broad substrate specificity but exhibit a significant preference for hydrophobic residues and very limited reactivity toward charged residues at the P4 site in the substrate. Here, we show that savinase can be functionally displayed on phage in the presence of the proteic inhibitor CI2. The free enzyme is released from its complex with CI2 upon addition of the anionic detergent LAS. The phage-enzyme can be panned on streptavidin beads after labelling by reaction with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-l-Ala-l-Ala-l-P ro-Phe(P)-diphenyl ester. Reactions of libraries, in which residues 104 and 107 forming part of the S4 pocket have been randomised, with (biotin-N-epsilon-aminocaproyl-cystamine-N'-glutaryl)-alpha-l-Lys-l-A la-l-Pro-Phe(P)-diphenylester allowed us to select enzymes with increased specific activity for a substrate containing a lysine in P4. Parameters influencing the selection as for instance the efficiency of maturation of mutant enzymes in libraries have been investigated.

Alkanesulfonic Acids↗
PubMed1998

A novel tumor-specific human single-chain Fv selected from an active specific immunotherapy phage display library.

A colon tumor-associated antigen, CTAA 28A32-32K (CTA # 2E), related to the annexin family of proteins, was initially identified by its reactivity with a low affinity human IgM monoclonal antibody (mAb), 28A32. Both in vitro lymphoproliferative assays with human peripheral blood lymphocytes and delayed type hypersensitivity responses in patients immunized with autologous colon tumor cells indicated that CTA # 2E elicits potent T cell mediated responses and may be an important antigen in the development of a generic colorectal vaccine (Pomato et al. Vaccine Res 1994;3:145-161). A CTA # 2E-specific, murine hybridoma-derived mAb, 5-11A, which recognizes the amino-terminus of the tumor-associated antigen, exhibited qualitative human colon tumor-specific immunohistochemical reactivity. To rapidly develop a human mAb with similar antigen specificity and tumor reactivity as the murine 5-11A mAb, antibody phage display technology was employed. Two human antibody phage display libraries with 3.1 x 10(7) and 2.3 x 10(8) members were prepared from the variable region genes expressed by circulating B cells of patients undergoing active specific immunotherapy (ASI) with autologous tumor cells, predominantly from the colon, admixed with Bacille Calmette-Guerin (BCG). A CTA # 2E-reactive human single-chain (sc)Fv was selected by panning the larger library on decreasing concentrations of biotinylated tumor-associated antigen in solution. It exhibited similar antigen specificity as the murine hybridoma-derived 5-11A scFv, requiring the presence of the CTA # 2E amino-terminus for reactivity. This human scFv exhibited qualitative human colon tumor-specific immunohistochemical reactivity when displayed as a gene III fusion protein on phage. When reconstructed and expressed as an intact human IgG1, K mAb, its qualitative colon tumor-specificity was unaltered. Two other CTA # 2E-reactive human scFvs were selected from the smaller library by panning initially on decreasing concentrations of CTA # 2E coated to polystyrene and then on biotinylated CTA # 2E in solution. These human scFvs, which exhibited modest reactivity with different epitopes on the CTA # 2E antigen, did not exhibit human colon tumor-specific immunohistochemical reactivity.

Animals↗
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↗
PubMed1995

Isolation of a cDNA encoding a growth-arrest associated gene and characterization of its regulation.

We are interested in understanding the molecular events associated with the growth-arrest of vascular SMCs. We constructed a subtracted cDNA library enriched in nucleotide sequences associated with quiescent SMCs. This library was screened with similarly subtracted 32P-labeled cDNAs to identify growth-arrest associated cDNA clones. Characterization of 19 of these cDNA clones revealed that 9 hybridized to mRNAs that exhibited a 2-3-fold increase in growth-arrested SMCs. In addition, two other cDNAs hybridized to a 5 Kb mRNA that was elevated approximately 10-fold in high density growth-arrested SMCs. Genomic Southern blot hybridization and DNA sequencing analysis indicated that these cDNAs encoded the same gene (LG7) and that this gene may be a member of a multigene family or that it may contain a sequence shared by other unrelated genes. Augmented expression of LG7 was associated with both high cell density and serum deprivation induced growth-arrest. LG7 mRNA expression was down-regulated when SMCs were incubated with FBS or with reagents that arrest cells in early S-phase. Additional analysis with cell cycle specific inhibitors indicated that LG7 mRNA levels were also low when cells were blocked at the G2 phase of the cell cycle but blockage at mitosis resulted in an elevated level of LG7 mRNA. We further demonstrated that the expression of LG7 was dependent on the presence of a relatively labile protein since protein synthesis inhibitors specifically blocked the expression of this mRNA but not the mRNA expression of alpha 1(III) collagen or ferritin H-chain. Finally, we demonstrated that Bt2cAMP was able to induce mRNA expression of LG7 within 2 h, suggesting that this gene may be directly regulated via the cyclic-AMP-dependent protein kinase pathway.

Animals↗
PubMed2002

Identification and characterization of a novel cancer/testis antigen gene CAGE.

We applied serological analysis of cDNA expression library technique to identify cancer-associated genes. We screened cDNA expression libraries of human testis and gastric cancer cell lines with sera of patients with gastric cancers. We identified a gene whose expression is testis-specific among normal tissues. We cloned and characterized this novel gene. It contains D-E-A-D box domain and encodes a putative protein of 630 amino acids with possible helicase activity. It showed wide expression in various cancer tissues and cancer cell lines. The corresponding gene was named cancer-associated gene (CAGE). PCR of human x hamster Radiation Hybrids showed localization of CAGE on the human chromosome Xp22. Transient transfection of CAGE showed predominantly nuclear localization. Both Western blot and plaque assay indicated seroreactivity of CAGE protein. We found that demethylation played a role in the activation of CAGE in some cancer cell lines that do not express it. Cell synchronization experiments showed that the expression of CAGE was related with cell cycle. This suggests that CAGE might play a role in cellular proliferation. Because CAGE is expressed in a variety of cancers but not in normal tissues except testis, this gene can be a target of antitumor immunotherapy.

Adenoma↗
PubMed1993

Cosmid library of the turkey herpesvirus genome constructed from nanogram quantities of viral DNA associated with an excess of cellular DNA.

A protocol was designed for the rapid and efficient construction of cosmid libraries from cell-associated viral genomes available in very low quantities. Purification of viral DNA from cellular DNA was unnecessary. The vast excess of cellular DNA compensated for the limited amount of available viral DNA, enabling titration of the restriction endonuclease partial digest. A cosmid library of the turkey herpesvirus DNA genome was constructed from 1.5 micrograms of cellular DNA containing approximately 6 nanograms of viral DNA.

Animals↗
PubMed1999

Empirical evidence of design-related bias in studies of diagnostic tests.

CONTEXT: The literature contains a large number of potential biases in the evaluation of diagnostic tests. Strict application of appropriate methodological criteria would invalidate the clinical application of most study results. OBJECTIVE: To empirically determine the quantitative effect of study design shortcomings on estimates of diagnostic accuracy. DESIGN AND SETTING: Observational study of the methodological features of 184 original studies evaluating 218 diagnostic tests. Meta-analyses on diagnostic tests were identified through a systematic search of the literature using MEDLINE, EMBASE, and DARE databases and the Cochrane Library (1996-1997). Associations between study characteristics and estimates of diagnostic accuracy were evaluated with a regression model. MAIN OUTCOME MEASURES: Relative diagnostic odds ratio (RDOR), which compared the diagnostic odds ratios of studies of a given test that lacked a particular methodological feature with those without the corresponding shortcomings in design. RESULTS: Fifteen (6.8%) of 218 evaluations met all 8 criteria; 64 (30%) met 6 or more. Studies evaluating tests in a diseased population and a separate control group overestimated the diagnostic performance compared with studies that used a clinical population (RDOR, 3.0; 95% confidence interval [CI], 2.0-4.5). Studies in which different reference tests were used for positive and negative results of the test under study overestimated the diagnostic performance compared with studies using a single reference test for all patients (RDOR, 2.2; 95% CI, 1.5-3.3). Diagnostic performance was also overestimated when the reference test was interpreted with knowledge of the test result (RDOR, 1.3; 95% CI, 1.0-1.9), when no criteria for the test were described (RDOR, 1.7; 95% CI, 1.1-2.5), and when no description of the population under study was provided (RDOR, 1.4; 95% CI, 1.1-1.7). CONCLUSION: These data provide empirical evidence that diagnostic studies with methodological shortcomings may overestimate the accuracy of a diagnostic test, particularly those including nonrepresentative patients or applying different reference standards.

Bias↗