New for SfE BES 2010 – Invitation for basic science cases

For SfE BES 2010, the Society is introducing a number of Basic Science Meet the Expert sessions. These will be relatively informal sessions with discussion based around new basic science technologies. If you would like to submit a specific issue to be discussed by the experts, please send a synopsis of the issue in a Word document (max. 300 words) to: conferences@endocrinology.org. The Basic Science Meet the Expert sessions will include: Metabolomics:challenges and rewards of deciphering the metabolome in diabetes and obesity; Resources in bioinformatics-How can it help your research?; and Mutagenesis resources – How to get your knock out mouse cheap and quick. The deadline for submissions is 18 January 2010.

Invitation for Clinic…

Androgen withdrawal can prolong life in men with advanced prostate cancer, but these remissions are temporary because the surviving cells progress as hormone-refractory cancer. The mechanisms that are involved in the transition of androgen-dependent prostate cancer into androgen-independent prostate cancer (AIPC) are not fully understood.To identify globally differentially expressed phosphoproteins in the androgen-independent prostate, to elucidate the molecular mechanisms that underlie the formation of AIPC and to identify new molecular targets that can be used to develop treatments for the disease.An androgen-independent LNCaP cell line, LNCaP-AI, was established using androgen ablation. Differentially expressed phosphoproteins in LNCaP cells and LNCaP-AI cells were enriched by immunopre…

The nuclear protein FOG-1 binds transcription factor GATA-1 to facilitate erythroid and megakaryocytic maturation. However, little is known about the function of FOG-1 during myeloid and lymphoid development or how FOG-1 expression is regulated in any tissue. We used in situ hybridization, gain- and loss-of-function studies in zebrafish to address these problems. Zebrafish FOG-1 is expressed in early hematopoietic cells, as well as heart, viscera, and paraspinal neurons, suggesting that it has multifaceted functions in organogenesis. We found that FOG-1 is dispensable for endoderm specification but is required for endoderm patterning affecting the expression of late-stage T-cell markers, independent of GATA-1. The suppression of FOG-1, in the presence of normal GATA-1 levels, induces sever…

We describe methodology and software to automatically identify cell populations in flow cytometry data. Our approach advances the paradigm of manually gating sequential two-dimensional projections of the data to a procedure that automatically produces gates based on statistical theory. Our approach is nonparametric and can reproduce nonconvex subpopulations that are known to occur in flow cytometry samples, but which cannot be produced with current parametric model-based approaches. We illustrate the methodology with a sample of mouse spleen and peritoneal cavity cells. (Source: Advances in Bioinformatics)

Conclusions:
Our results demonstrate that the proposed method can achieve near perfect peak detection performance while maintaining very small false alarm probabilities in case of gas chromatograms. Given the fact that biological signals appear in the form of peaks in various experimental data and that the propose method can easily be extended to such data, our approach will be a useful and robust tool that can help researchers highlight valid signals in their noisy measurements. (Source: BMC Bioinformatics – Latest articles)

Conclusions:
Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications. (Source: BMC Bioinformatics – Latest articles)div id=medwormpbiMedWorm Message:/i/b Get the very latest Swine Flu news via the MedWorm ba href=http://www.medworm.com/rss/search.php?qu=%2Bswine+%2B%28influenza+flu%29t=Swine+Fluf=infectiousdiseasesr=Anyo=d target =_selfSwine Flu RSS news feed/a/b – updated hourly from thousands of authoritative health and news sources./p/div

Conclusions:
SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at www.manchester.ac.uk/bioinformatics/sitesidentify/ (Source: BMC Bioinformatics – Latest articles)

Conclusionnbsp;nbsp;If urogynaecologists omitted pre-operative urodynamics in women in the low probability group, in our population, pre-operative
urodynamics would be reduced by 29%.

Content Type Journal ArticleCategory Original ArticleDOI 10.1007/s00192-009-1035-2Authors
R. Marijn Houwert, St. Elisabeth Hospital Tilburg Department of Obstetrics and Gynecology Rooseveltlaan 35 III 1079 AC Amsterdam The NetherlandsJan Paul W. R. Roovers, Academic Medical Centre Amsterdam Department of Obstetrics and Gynecology Amsterdam The NetherlandsPieter L. Venema, Haga Ziekenhuizen Department of Urology The Hague The NetherlandsHein W. Bruinse, University Medical Centre Utrecht Department of Obstetrics and Gynecology Utrecht The NetherlandsMarcel G. W. Dijkgraaf, Academic Medical Centre Am…

A next step to interpret the findings generated by genome-wide association studies is to associate molecular quantitative traits with disease-associated alleles. To this end, researchers are linking disease
risk alleles with gene expression quantitative trait loci (eQTL). However, gene expression at the
mRNA level is only an intermediate trait and flow cytometry analysis can provide more downstream
and biologically valuable protein level information in multiple cell subsets simultaneously using freshly
obtained samples. Because the throughput of flow cytometry is currently limited, experiments may
need to span over several weeks or months to obtain a sufficient sample size to demonstrate genetic
association. Therefore, normalisation methods are needed to control for technical variability a…

MicroRNAs (miRNAs) are a class of short endogenously expressed RNA molecules that regulate gene expression by binding directly to the messenger RNA of protein coding genes. They have been found to confer a novel layer of genetic regulation in a wide range of biological processes. Computational miRNA target prediction remains one of the key means used to decipher the role of miRNAs in development and disease. Here we introduce the basic idea behind the experimental identification of miRNA targets and present some of the most widely used computational miRNA target identification programs. The review includes an assessment of the prediction quality of these programs and their combinations.
Contact: p.alexiou@fleming.gr
Supplementary information: Supplementary data are available at Bioinformat…