FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps

Fault Tolerant Contact Map Reconstruction (FT-COMAR) is a heuristic algorithm for the reconstruction of the protein three-dimensional structure from (possibly) incomplete (i.e. containing unknown entries) and noisy contact maps. FT-COMAR runs within minutes, allowing its application to a large-scale number of predictions. AVAILABILITY: http://bioinformatics.cs.unibo.it/FT-COMAR     

Post mortem findings in sows and gilts euthanised or found dead in a large Swedish herd

Background  

The aim of this study was to get information on post mortem diagnoses of sows found dead or euthanised and to understand the diagnoses aetiology (causative background). Moreover, the study was to evaluate the association between the clinical symptoms observed on farm and post mortem findings.     

Transforming growth factor-beta1, transforming growth factor-beta2, and transforming growth factor-beta3 enhance ovarian cancer metastatic potential by inducing a Smad3-dependent epithelial-to-mesenchymal transition

Transforming growth factor-beta (TGF-beta) is thought to play a role in the pathobiological progression of ovarian cancer because this peptide hormone is overexpressed in cancer tissue, plasma, and peritoneal fluid. In the current study, we investigated the role of the TGF-beta/Smad3 pathway in ovarian cancer metastasis by regulation of an epithelial-to-mesenchymal transition. When cancer cells were cultured on plastic, TGF-beta1, TGF-beta2, and TGF-beta3 induced pro-matrix metalloproteinase (MMP) secretion, loss of cell-cell junctions, down-regulation of E-cadherin, up-regulation of N-cadherin, and acquisition of a fibroblastoid phenotype, consistent with an epithelial-to-mesenchymal transition. Furthermore, Smad3 small interfering RNA transfection inhibited TGF-beta-mediated changes to a fibroblastic morphology, but not MMP secretion. When cancer cells were cultured on a three-dimensional collagen matrix, TGF-beta1, TGF-beta2, and TGF-beta3 stimulated both pro-MMP and active MMP secretion and invasion. Smad3 small interfering RNA transfection of cells cultured on a collagen matrix abrogated TGF-beta-stimulated invasion and MMP secretion. Analysis of Smad3 nuclear expression in microarrays of serous benign tumors, borderline tumors, and cystadenocarcinoma revealed that Smad3 expression could be used to distinguish benign and borderline tumors from carcinoma (P = 0.006). Higher Smad3 expression also correlated with poor survival (P = 0.031). Furthermore, a direct relationship exists between Smad3 nuclear expression and expression of the mesenchymal marker N-cadherin in cancer patients (P = 0.0057). Collectively, these results implicate an important role for the TGF-beta/Smad3 pathway in mediating ovarian oncogenesis by enhancing metastatic potential.     

A proteomics approach to the study of absorption, distribution, metabolism, excretion, and toxicity.

A proteomics approach was used to identify liver proteins that displayed altered levels in mice following treatment with a candidate drug. Samples from livers of mice treated with candidate drug or untreated were prepared, quantified, labeled with CyDye DIGE Fluors, and subjected to two-dimensional electrophoresis. Following scanning and imaging of gels from three different isoelectric focusing intervals (3-10, 7-11, 6.2-7.5), automated spot handling was performed on a large number of gel spots including those found to differ more than 20% between the treated and untreated condition. Subsequently, differentially regulated proteins were subjected to a three-step approach of mass spectrometry using (a) matrix-assisted laser desorption/ionization time-of-flight mass spectrometry peptide mass fingerprinting, (b) post-source decay utilizing chemically assisted fragmentation, and (c) liquid chromatography-tandem mass spectrometry. Using this approach we have so far resolved 121 differentially regulated proteins following treatment of mice with the candidate drug and identified 110 of these using mass spectrometry. Such data can potentially give improved molecular insight into the metabolism of drugs as well as the proteins involved in potential toxicity following the treatment. The differentially regulated proteins could be used as targets for metabolic studies or as markers for toxicity.     

Are Sexual Dissatisfaction and Sexual Abuse Associated with Obesity? A Population‐Based Study

Objective: To investigate whether there is any association between obesity and sexual satisfaction and sexual abuse in a normal population. Research Methods and Procedures: A representative sample of 2810 subjects from a population study was interviewed about sexual satisfaction, sexual abuse, and life satisfaction. The answers from normal weight, overweight, and obese participants were compared. Univariate and multivariate analyses were performed. Results: Data were presented separately for two age groups, 18 to 49 and 50 to 74 years, and gender. The older group of obese men reported a greater decrease of sexual desire compared with 5 years prior than normal weight men [odds ratios (OR), 2.44; 95% confidence interval (CI), 1.4 to 4.3]. The older group of overweight men reported involuntary participation in sexual activities more often than normal weight men (OR, 2.06; 95% CI, 1.1 to 3.8). Although older overweight and obese women were diagnosed with a lingering disease (defined as >1 month) more often than normal weight women (overweight: OR, 2.41; 95% CI, 1.3 to 4.4; obese: OR, 4.45; 95% CI, 1.7 to 11.5), there was no difference between BMI groups in satisfaction with physical health. Discussion: Overweight and obese groups seem to be heterogeneous with respect to sexual satisfaction and experiences of sexual abuse. No significant differences were detected between BMI groups, which does not exclude the possibility of significant differences between BMI groups among patients seeking medical attention.     

The use of circular dichroism spectroscopy for studying the chiral molecular self-assembly: an overview

Self-assembly plays an important role in the formation of many chiral biological structures and in the preparation of chiral functional materials. Therefore the control of chirality in synthetic or biological self-assembled systems is important either for the comprehension of recognition phenomena or to obtain materials with predictable and controllable properties. Circular dichroism was developed to study molecular chirality, however, because of its outstanding sensitivity to chiral perturbations of the system under investigation; it has been extended more recently to supramolecular chemistry. In particular, self-assembly processes leading to the formation of chiral supramolecular architectures (and eventually to gels or liquid crystal phases) can be monitored by CD. Furthermore, CD spectroscopy often allows one to obtain structural information on the assembled structures. This review deals with representative contributions to the study of supramolecular chirality by means of circular dichroism.     

Apoptotic neutrophils containing Staphylococcus epidermidis stimulate macrophages to release the proinflammatory cytokines tumor necrosis factor-alpha and interleukin-6.

Staphylococcus epidermidis infections are usually nosocomial and involve colonization of biomaterials. The immune defense system cannot efficiently control the bacteria during these infections, which often results in protracted chronic inflammation, in which a key event is disturbed removal of neutrophils by tissue macrophages. While ingesting uninfected apoptotic neutrophils, macrophages release anti-inflammatory cytokines that lead to resolution of inflammation. In clinical studies, we have previously found elevated levels of the proinflammatory cytokines tumor necrosis factor-alpha (TNF-alpha) and interleukin-6 in synovial fluid from prostheses infected with coagulase negative staphylococci. We show that macrophages phagocytosing apoptotic neutrophils containing S. epidermidis released TNF-alpha and interleukin-6, whereas macrophages phagocytosing spontaneously apoptotic neutrophils did not. This difference was not due to dissimilar phagocytic capacities, because macrophages ingested both types of neutrophils to the same extent. The activation was induced mainly by the apoptotic neutrophils themselves, not by the few remaining extracellular bacteria. Macrophages were not activated by apoptotic neutrophils that contained paraformaldehyde-killed S. epidermidis. Proinflammatory reactions induced by clearance of apoptotic neutrophils containing S. epidermidis might represent an important mechanism to combat the infective agent. This activation of macrophages may contribute to the development of chronic inflammation instead of inflammation resolution.     

Metal retention on pine bark and blast furnace slag--on-site experiment for treatment of low strength landfill leachate

Treatment of landfill leachate using blast furnace slag and pine bark as reactive sorbents was studied in an in situ column experiment at the Lilla Nyby landfill site in Eskilstuna, Sweden. The columns were filled with approximately 101 of each sorbent and leachate was supplied at three different flow rates during a period of 4 months. Samples of inflow and outflow were collected three times a week and were analyzed for physical and chemical parameters, including concentrations of some metals, and toxicity. It was found that pine bark removed metals more efficiently than did the blast furnace slags; that Zn was most efficiently retained in the filters and that both retention time and initial concentration played an important role in the sorption process. It was also observed that the pine bark column did not release COD. No toxicity of the untreated or the treated leachate was found with the test organisms and test responses used.     

Active beta-catenin signaling is an inhibitory pathway for human immunodeficiency virus replication in peripheral blood mononuclear cells

The Wnt/β-catenin pathway is involved in cell functions governing development and disease. In modeling postentry restriction of human immunodeficiency virus (HIV) replication in astrocytes, we reported that part of this natural resistance to productive replication of HIV in astrocytes involved expression of proteins of the Wnt/β-catenin signaling pathway. We determined here whether induction of β-catenin signaling in peripheral blood mononuclear cells (PBMCs) can modulate HIV replication. Given that lithium is an inducer of β-catenin signaling, we used it as a tool to determine the impact of β-catenin signaling on HIV replication in PBMCs. We demonstrated that lithium inhibited the replication of T-tropic and primary isolates of HIV by >90% and did so in noncytotoxic/noncytostatic concentrations and in a β-catenin-dependent manner. Specifically, inhibiting β-catenin signaling by transfection of dominant-negative mutant constructs to either T-cell factor 4, the downstream effector of Wnt signaling, or β-catenin, the central mediator of this pathway, abrogated the ability of lithium to inhibit HIV replication. Moreover, when Wnt/β-catenin signaling was inhibited, the level of HIV replication was enhanced by fourfold. To confirm the in vivo relevance of the β-catenin pathway in repressing HIV replication, we evaluated HIV-positive antiretroviral therapy-naive patients who were on lithium therapy. These patients demonstrated a reduction in viral load, which increased as the dose of lithium was reduced. Collectively, these data indicate that β-catenin signaling is an intrinsic molecular pathway restricting HIV replication in PBMCs.