GeneSyn: a tool for detecting conserved gene order across genomes

SUMMARY: GeneSyn is a software tool that allows automatic detection of conserved gene order from annotated genomes. AVAILABILITY: Available free of charge for Unix/Linux/Cygwin platforms at ftp://159.149.110.11/pub/GeneSyn_1.0/ SUPPLEMENTARY INFORMATION: ftp://159.149.110.11/pub/GeneSyn_1.0/     

Influence of beta-carotene on lysosomal hydrolases and their natural substrates in major salivary glands of hamsters treated with 7,12-dimethylbenzanthracene (DMBA)

We evaluated the effects of beta-carotene, a precursor of vitamin A, on the activity of some lysosomal hydrolases and on the levels of their natural substrates in hamster major salivary glands during experimental oral 7,12-dimethylbenzanthracene (DMBA) carcinogenesis. Sixty-four hamsters (Cricetus auratus) were divided into four groups--group 1: untreated control; group 2: DMBA was painted three times a week in the left buccal pouch; group 3: beta-carotene was painted three times a week in the left buccal pouch; group 4: DMBA and beta-carotene were painted alternatively in the left buccal pouch. After 16 weeks, the animals were sacrificed and the activities of some lysosomal hydrolases and their natural substrates in the major salivary glands were measured. beta-Carotene when administered topically in DMBA treated animals (group 4) reduced the levels of the majority of enzymes and substrates closer to those of the untreated control group, thus outlining a mild protective effect of beta-carotene towards the DMBA carcinogenic stress. Nevertheless, the presence of some enzymes which responded negatively to the combined administration of DMBA and beta-carotene suggests the necessity for future studies on the effect of beta-carotene at different concentrations, the systemic administration and the possibility to combine the topical beta-carotene administration with other chemopreventive drugs.     

Calcitriol downregulates TNF-α and IL-6 expression in cultured placental cells from preeclamptic women

Placenta is an important source and target of hormones that contribute to immunological tolerance and maintenance of pregnancy. In preeclampsia (PE), placental calcitriol synthesis is low; whereas pro-inflammatory cytokines levels are increased, threatening pregnancy outcome. Previously, we showed that calcitriol inhibits Th-1 cytokines under experimental inflammatory conditions in normal trophoblasts. However, a study of the regulation of inflammatory cytokines by calcitriol in trophoblasts from a natural inflammatory condition, such as PE, is still lacking. Therefore, the aim of the present study was to investigate calcitriol effects upon TNF-α, IFN-γ, IL-6 and IL-1β in cultured placental cells from preeclamptic women by using qPCR and ELISA. Placentas were collected after cesarean section from preeclamptic women and enriched trophoblastic preparations were cultured in the absence or presence of different calcitriol concentrations during 24 h. In these cell cultures, pro-inflammatory cytokines TNF-α and IL-6 secretion and mRNA expression were downregulated by calcitriol (P < 0.05). No significant effects of calcitriol upon IFN-γ and IL-1β were observed. In addition, basal expression of TNF-α, IL-6 and IL-1β decreased as the cells formed syncytia. Our study supports an important autocrine/paracrine role of placental calcitriol in controlling adverse immunological responses at the feto–maternal interface, particularly in gestational pathologies associated with exacerbated inflammatory responses such as preeclampsia.     

Integration of mRNA Expression Profile,Copy Number Alterations,and microRNA Expression Levels in Breast Cancer to Improve Grade Definition

Defining the aggressiveness and growth rate of a malignant cell population is a key step in the clinical approach to treating tumor disease. The correct grading of breast cancer (BC) is a fundamental part in determining the appropriate treatment. Biological variables can make it difficult to elucidate the mechanisms underlying BC development. To identify potential markers that can be used for BC classification, we analyzed mRNAs expression profiles, gene copy numbers, microRNAs expression and their association with tumor grade in BC microarray-derived datasets. From mRNA expression results, we found that grade 2 BC is most likely a mixture of grade 1 and grade 3 that have been misclassified, being described by the gene signature of either grade 1 or grade 3. We assessed the potential of the new approach of integrating mRNA expression profile, copy number alterations, and microRNA expression levels to select a limited number of genomic BC biomarkers. The combination of mRNA profile analysis and copy number data with microRNA expression levels led to the identification of two gene signatures of 42 and 4 altered genes (FOXM1, KPNA4, H2AFV and DDX19A) respectively, the latter obtained through a meta-analytical procedure. The 42-based gene signature identifies 4 classes of up- or down-regulated microRNAs (17 microRNAs) and of their 17 target mRNA, and the 4-based genes signature identified 4 microRNAs (Hsa-miR-320d, Hsa-miR-139-5p, Hsa-miR-567 and Hsa-let-7c). These results are discussed from a biological point of view with respect to pathological features of BC. Our identified mRNAs and microRNAs were validated as prognostic factors of BC disease progression, and could potentially facilitate the implementation of assays for laboratory validation, due to their reduced number.     

Muscle loading and activation of the shoulder joint during humeral external rotation by pulley and variable resistance

BackgroundThe aim of the study was to evaluate differences in the loading of glenohumeral joint muscles between a cable pulley machine (CP) and variable resistance machine (VR) during axial humeral external rotation.MethodsEleven healthy male subjects took part in the study. Intramuscular electromyography from five muscles of the shoulder (medial deltoid, supraspinatus, infraspinatus and upper part of the trapezius), torque and power output was measured at different rotation angles and with different loads (10%, 50% and 100% of 1RM). Also the compressive and shear force in the glenohumeral joint was analyzed at the horizontal level at angles of rotation. External rotation was performed with a self-selected velocity on the scapular plane.FindingsIn the CP the range of movement became narrower than in the VR with increasing workload (P < 0.05). The activity of the infraspinatus did not grow in the CP after 50% load, while it did in the VR (P < 0.01). The upper part of the trapezius was activated less in the CP than in the VR (P < 0.01) machine when using 50% and 100% loads. In comparison with the CP, the shear forces that pull the head of the humerus in a posterior direction were more evenly distributed in the VR than in the CP at different angles of rotation (P < 0.001).InterpretationThe VR seems to make a broader range of motion possible, lager activation the primary external rotators and evenly distributed shear forces than the CP. However, performing the exercise with VR and high load also activates the upper part of the trapezius.RelevanceThese findings can be used in the development of exercise designs, methods and equipment for shoulder injury rehabilitation.     

Rhenium(III) and rhenium(V) complexes stabilized by the potentially tetradentate ligand tris(2-diphenylphosphinoethyl)amine

The reaction of the rhenium(V) nitrido complex [Re(N)Cl₂(PPh₃)₂] with the tripodal ligand N(CH₂CH₂PPh₂)₃ (NP₃) in THF gave [Re(N)Cl₂(η²-P,P-NP₃)] (1) in which NP₃ acts as a tridentate ligand using the nitrogen and two phosphorus donors for coordination. Refluxing 1 in a polar solvent such as ethanol produced [(η⁴-NP₃)Re(N)Cl]Cl (2) in which NP₃ acts as a tetradentate ligand. Treatment of complex [Re(O)Cl₃(AsPh₃)₂] containing the [ReO]³⁺ core with NP₃ in THF yielded [ReCl₃{η³-N,P,P-(N{CH₂CH₂Ph₂}₂{CH₂CH₂P(O)Ph₂})}] (3). Complexes 1 and 3 have been characterized by single-crystal X-ray analyses.     

Changes in the distribution of ZO-1, occludin,and claudins in the rat uterine epithelium during the estrous cycle

During the estrous cycle, the endometrium epithelium experiences marked cellular structural changes. For fertilization to proceed, maintenance of an adequate uterine environment by ovarian hormones is essential. Epithelial cells lining the uterine lumen are associated with each other by tight junctions (TJs), which regulate the passage of ions and molecules through the paracellular pathway. The aim of the present study was to assess by confocal immunofluorescence the distribution pattern of the TJ proteins ZO-1, occludin, and claudins 1–7 in the rat uterus during the estrous cycle. Our results reveal that on proestrus, the day when mating takes place, ZO-1, occludin, and claudins 1 and 5 are located in the TJs, while claudins 3 and 7 display a basolateral distribution. In contrast, on metestrus day, when no sexual mating occurs and the uterine lumen is devoid of secretions, none of these proteins were detected in the TJ region, and only a diffuse cytosolic staining was observed for some of the proteins. On estrus and diestrus days, an intermediate situation was encountered, since ZO-1 localized in the TJs, whereas occludin was no longer detectable in the TJs. The distribution of claudins during these stages varied from the lowermost portion of the basolateral membrane to its apex. In conclusion, the results show that the protein composition of TJs present in the luminal epithelial cells of the uterus changes during the different days of the estrous cycle, and suggest that the expression of TJ proteins participates in providing an adequate environment for a successful fertilization.This work was supported by grants PAPIIT (IN210902, IX228504) and PAIP (6190-08) from the National Autonomous University of Mexico (UNAM), and by grants G34511-M and 37846-N from the Mexican National Council on Science and Technology (CONACYT).     

The integrative role of cryo electron microscopy in molecular and cellular structural biology

After gradually moving away from preparation methods prone to artefacts such as plastic embedding and negative staining for cell sections and single particles, the field of cryo electron microscopy (cryo‐EM) is now heading off at unprecedented speed towards high‐resolution analysis of biological objects of various sizes. This ‘revolution in resolution’ is happening largely thanks to new developments of new‐generation cameras used for recording the images in the cryo electron microscope which have much increased sensitivity being based on complementary metal oxide semiconductor devices. Combined with advanced image processing and 3D reconstruction, the cryo‐EM analysis of nucleoprotein complexes can provide unprecedented insights at molecular and atomic levels and address regulatory mechanisms in the cell. These advances reinforce the integrative role of cryo‐EM in synergy with other methods such as X‐ray crystallography, fluorescence imaging or focussed‐ion beam milling as exemplified here by some recent studies from our laboratory on ribosomes, viruses, chromatin and nuclear receptors. Such multi‐scale and multi‐resolution approaches allow integrating molecular and cellular levels when applied to purified or in situ macromolecular complexes, thus illustrating the trend of the field towards cellular structural biology.