Bioinformatics approaches in the discovery and understanding of reproduction-related biomarkers

The emerging field of bioinformatics in proteomics is introducing new algorithms in order to handle large and heterogeneous datasets and improve the knowledge-discovery process. Management systems, software construction and application, database population and leverage, as well as computed prediction, have crafted bioinformatics into a valuable tool for basic research. Human reproduction is one of many fields proteomics has been extensively studying over the last decade, accumulating complex experimental data at a rate far exceeding the ability to assimilate them. Transformation of the rapidly proliferating quantities of experimental information into a usable form in order to facilitate their analysis is a challenging task. On this track, bioinformatics, an essential part of proteomics research, aspires to amend inquiries into a better manipulated, a better handled and a better understood form so as to enhance existing knowledge expansion.     

A compendium of mouse knockouts with inner ear defects

Genetically engineered strains of mice, modified by gene targeting (knockouts), are increasingly being employed as alternative effective research tools in elucidating the genetic basis of human deafness. An impressive array of auditory and vestibular mouse knockouts is already available as a valuable resource for studying the ontogenesis, morphogenesis and function of the mammalian inner ear. This article provides a current catalog of mouse knockouts with inner ear morphogenetic malformations and hearing or balance deficits resulting from ablation of genes that are regionally expressed in the inner ear and/or within surrounding tissues, such as the hindbrain, neural crest and mesenchyme.     

Multiclass cancer classification using semisupervised ellipsoid ARTMAP and particle swarm optimization with gene expression data

It is crucial for cancer diagnosis and treatment to accurately identify the site of origin of a tumor. With the emergence and rapid advancement of DNA microarray technologies, constructing gene expression profiles for different cancer types has already become a promising means for cancer classification. In addition to research on binary classification such as normal versus tumor samples, which attracts numerous efforts from a variety of disciplines, the discrimination of multiple tumor types is also important. Meanwhile, the selection of genes which are relevant to a certain cancer type not only improves the performance of the classifiers, but also provides molecular insights for treatment and drug development. Here, we use semisupervised ellipsoid ARTMAP (ssEAM) for multiclass cancer discrimination and particle swarm optimization for informative gene selection. ssEAM is a neural network architecture rooted in adaptive resonance theory and suitable for classification tasks. ssEAM features fast, stable, and finite learning and creates hyperellipsoidal clusters, inducing complex nonlinear decision boundaries. PSO is an evolutionary algorithm-based technique for global optimization. A discrete binary version of PSO is employed to indicate whether genes are chosen or not. The effectiveness of ssEAM/PSO for multiclass cancer diagnosis is demonstrated by testing it on three publicly available multiple-class cancer data sets. ssEAM/PSO achieves competitive performance on all these data sets, with results comparable to or better than those obtained by other classifiers     

High plasma concentrations of acyl‐coenzyme A binding protein (ACBP) predispose to cardiovascular disease: Evidence for a phylogenetically conserved proaging function of ACBP

Autophagy defects accelerate aging, while stimulation of autophagy decelerates aging. Acyl‐coenzyme A binding protein (ACBP), which is encoded by a diazepam‐binding inhibitor (DBI), acts as an extracellular feedback regulator of autophagy. As shown here, knockout of the gene coding for the yeast orthologue of ACBP/DBI (ACB1) improves chronological aging, and this effect is reversed by knockout of essential autophagy genes (ATG5, ATG7) but less so by knockout of an essential mitophagy gene (ATG32). In humans, ACBP/DBI levels independently correlate with body mass index (BMI) as well as with chronological age. In still‐healthy individuals, we find that high ACBP/DBI levels correlate with future cardiovascular events (such as heart surgery, myocardial infarction, and stroke), an association that is independent of BMI and chronological age, suggesting that ACBP/DBI is indeed a biomarker of “biological” aging. Concurringly, ACBP/DBI plasma concentrations correlate with established cardiovascular risk factors (fasting glucose levels, systolic blood pressure, total free cholesterol, triglycerides), but are inversely correlated with atheroprotective high‐density lipoprotein (HDL). In mice, neutralization of ACBP/DBI through a monoclonal antibody attenuates anthracycline‐induced cardiotoxicity, which is a model of accelerated heart aging. In conclusion, plasma elevation of ACBP/DBI constitutes a novel biomarker of chronological aging and facets of biological aging with a prognostic value in cardiovascular disease.     

Effects of acyl-coenzyme A binding protein (ACBP)/diazepam-binding inhibitor (DBI) on body mass index

In mice, the plasma concentrations of the appetite-stimulatory and autophagy-inhibitory factor acyl-coenzyme A binding protein (ACBP, also called diazepam-binding inhibitor, DBI) acutely increase in response to starvation, but also do so upon chronic overnutrition leading to obesity. Here, we show that knockout of Acbp/Dbi in adipose tissue is sufficient to prevent high-fat diet-induced weight gain in mice. We investigated ACBP/DBI plasma concentrations in several patient cohorts to discover a similar dual pattern of regulation. In relatively healthy subjects, ACBP/DBI concentrations independently correlated with body mass index (BMI) and age. The association between ACBP/DBI and BMI was lost in subjects that underwent major weight gain in the subsequent 3–9 years, as well as in advanced cancer patients. Voluntary fasting, undernutrition in the context of advanced cancer, as well as chemotherapy were associated with an increase in circulating ACBP/DBI levels. Altogether, these results support the conclusion that ACBP/DBI may play an important role in body mass homeostasis as well as in its failure.Subject terms: Obesity, Diagnostic markers     

Molecular dissection of regulated secretory pathways in human gastric enterochromaffin-like cells: an immunohistochemical analysis

Enterochromaffin-like (ECL) cells regulate gastric acid secretion through vesicular release of histamine. Until now, the molecular machinery of human ECL cells involved in the formation and release of vesicles is largely unknown. We analyzed tissue samples obtained from normal human gastric mucosa (n=4) and ECLomas (n=5) immunohistochemically using the APAAP method or double immunofluorescence confocal laser microscopy. Human pheochromocytomas (n=5) were investigated in parallel and compared to ECL cells. Secretory pathways were characterized using antibodies specific for marker proteins of large dense-core vesicles (LDCVs; islet cell antigen 512, chromogranin A, pancreastatin, and vesicular monoamine transporter 2) and small synaptic vesicle (SSV) analogues (synaptophysin). Tissues were also analyzed for expression of the peptide hormone processing enzymes, carboxypeptidase E and prohormone convertase 1, as well as the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins, 25-kDa synaptosome-associated protein (SNAP25), syntaxin, and synaptobrevin. Immunoreactivity for markers of LDCVs and SSV analogues were detected in normal ECL cells and ECLomas. Both tissues also showed expression of carboxypeptidase E and prohormone convertase 1. Analysis of vesicular SNARE (v-SNARE) and target membrane SNARE (t-SNARE) proteins revealed the presence of SNAP25, syntaxin, and synaptobrevin in normal and neoplastic ECL cells. Our data suggest that ECL cells possess the two vesicle types of regulated neuroendocrine secretory pathways, LDCVs and SSV analogues. Since ECL cells also contain typical SNARE proteins, the molecular machinery underlying secretory processes in this cell type appears to be identical to the secretory apparatus of neuroendocrine cells and neurons. In addition, our findings suggest that the secretory apparatus of ECL cells is maintained during neoplastic transformation. Accepted: 10 June 1999     

Combined Effects of Water Activity, pH and Temperature on the Growth and Spoilage Potential of Fungi

S ummary . An arbitrary parameter 'rejection time', i.e. the time required for a fungal inoculum to form a 2 mm diam. colony, was used to express the shelf life of jam after unsealing and exposure of the contents to airborne contamination. Individual and combined effects of water activity ( a_w ), pH value and temperature on rejection time of low sugar jam were estimated from the radial growth on agar of colonies of 9 fungi. The decreases in a_w (0·94–0·90) and temperature (25–15°) practicable for low sugar jam were more effective in increasing rejection time than the feasible decrease in pH value (3·7–2·9). The interaction between a_w and temperature was significant. The effect of the changes in a_w , temperature and pH on rejection time was broadly similar for media adjusted by either sucrose or glycerol. At a given a_w , moulds were slightly more tolerant of glycerol than sucrose but yeasts, except for the osmophile Saccharomyces rouxii , were markedly more tolerant of glycerol than sucrose.     

Differences in the genetic structure of Bacillus subitilis strains carrying the trpE26 mutation and strain 168.

It was previously shown that in strains of Bacillus subtilis bearing the trpE26 mutation a chromosome segment (from trpD to ilvA) is translocated to a position near the thr region. Further PBS1-mediated transduction data have now revealed that these strains also possess an inversion of part of the chromosome from the origin of replication, down to the tre locus on one side and the cysB locus on the other. These data concern evidence of linkage of tre-12- to markers in the translocation (hisH2, tyrA1, and metB3) as well as linkage of the cysB3 marker to thi-86, gly-133, and catA. They explain the previously observed absence of linkage of markers in the translocated segment to cysB3. The model proposed for the formation of merodiploids in trpE26 strains, which calls for the fusion of two genetic elements, is not incompatible with this new finding.