Mining Genomic Patterns in Mycobacterium tuberculosis H37Rv Using a Web Server Tuber-Gene

Mycobacterium tuberculosis (MTB), causative agent of tuberculosis, is one of the most dreaded diseases of the century. It has long been studied by researchers throughout the world using various wet-lab and dry-lab techniques. In this study, we focus on mining useful patterns at genomic level that can be applied for in silico functional characterization of genes from the MTB complex. The model developed on the basis of the patterns found in this study can correctly identify 99.77% of the input genes from the genome of MTB strain H37Rv. The model was tested against four other MTB strains and the homologue M. bovis to further evaluate its generalization capability. The mean prediction accuracy was 85.76%. It was also observed that the GC content remained fairly constant throughout the genome, implicating the absence of any pathogenicity island transferred from other organisms. This study reveals that dinucleotide composition is an efficient functional class discriminator for MTB complex. To facilitate the application of this model, a web server Tuber-Gene has been developed, which can be freely ac- cessed at http://www.bifmanit.org/tb2/.     

Sex and gender in medical education: a national student survey

Background

Gender- and sex-specific medicine is defined as the practice of medicine based on the understanding that biology (dictated by sex chromosomes) and social roles (gender) are important in and have implications for prevention, screening, diagnosis, and treatment in men and women. In light of the many ways that sex and gender influence disease presentation and patient management, there have been various initiatives to improve the integration of these topics into medical education curriculum. Although certain schools may include the topics, their impact on the student body’s knowledge has not been as fully studied. By studying the opinions of US allopathic and osteopathic-enrolled students on the extent to which their schools address these topics and their understanding of these topics, this study examined the role of gender specific medicine in the US medical school curriculum.

Methods

An email solicitation with link to an anonymous survey was sent to approximately 35,876 student members of five US medical student organizations. The survey instrument consisted of yes/no, multiple choice, and attitude awareness questions. Data was analyzed as a complete data set to evaluate national trends and via subset analysis using chi-square, paired t test, and one-way anova.

Results

A total of 1097 students responded. The majority of respondents strongly agreed that sex and gender medicine (SGBM) improves patient management (96.0 %) and should be included as a part of the medical school curriculum (94.4 %). Only 2.4 % of participants agreed that SGBM is the same as Women’s Health. When asked specifically about inclusion of an identified sex and gender-based medicine curriculum at their institution, students answered not sure at 40.8, 25.1, 19.1, and 20.3 % from first year to fourth year, respectively. Males reported a higher rate of exposure to SGBM content areas (in medical history taking, domestic violence) than women.

Conclusions

Medical students recognize the differentiation between SGBM principles and women’s health, and understand the translational value of sex and gender-specific principles in the clinical setting. However, current curricular offerings fall short of providing students with adequate coverage of specific evidence-based health differences.

     

An integrated process for the production of 1,3-propanediol,lactate and 3-hydroxypropionic acid by an engineered Lactobacillus reuteri

The process economy of food grade 1,3-propanediol (1,3-PD) production by GRAS organisms like Lactobacillus reuteri (L. reuteri), is negatively impacted by the low yield and use of expensive feedstocks. In order to improve the process economy, we have developed a multiproduct process involving the production of three commercially important chemicals, namely, 1,3-PD, lactate and 3-Hydroxypropionic acid (3-HP), by engineered L. reuteri. The maximum 1,3-PD and lactate titer of 41 g/L and 31 g/L, with a volumetric productivity of 1.69 g/L/h and 0.67 g/L/h were achieved, respectively. The maximum 3-HP titer of 5.2 g/L with a volumetric productivity of 1.3 g/L/h, was obtained by biotransformation using cells recovered from the repeated fed-batch process. The volumetric productivity of 1,3-PD obtained in this study is the highest ever reported for this organism. Further cost reduction can be achieved by using waste feedstocks like milk whey, biomass hydrolysate, and crude glycerol.     

Carvacrol modulates instability of xenobiotic metabolizing enzymes and downregulates the expressions of PCNA,MMP-2, and MMP-9 during diethylnitrosamine-induced hepatocarcinogenesis in rats

Vascular calcification (VC) is highly associated with increased morbidity and mortality in patients with advanced chronic kidney disease. Paracrine/autocrine factors such as vasoactive peptides are involved in VC development. Here, we investigated the expression of the novel peptide C-type natriuretic peptide (CNP) in the vasculature, tested its ability to prevent VC in vivo and in vitro, and examined the mechanism involved. Rat aortic VC was induced by vitamin D3 plus nicotine (VDN). CNP (500 ng/kg/h) was administered by mini-osmotic pump. Calcification was examined by von Kossa staining; CNP and cyclic guanosine monophosphate (cGMP) contents were detected by radioimmunoassay, and mRNA and protein levels were examined by real-time PCR and Western blot analysis in aortas and calcified vascular smooth muscle cells (VSMCs). VDN-treated rat aortas showed higher CNP content and decreased expression of its receptor natriuretic peptide receptor B, along with increased vascular calcium deposition and alkaline phosphatase (ALP) activity. Low CNP levels were accompanied by increased vascular calcium deposition and ALP activity in VDN-treated rats when compared to vehicle treatment, which was further confirmed in cultured VSMCs. Administration of CNP greatly reduced VC in VDN-treated aortas compared with controls, which was confirmed in calcified VSMCs. The decrease in alpha-actin expression was ameliorated by CNP in vitro. Moreover, protein expression levels of osteopontin (OPN) were significantly up-regulated in calcified aortas, and CNP increased OPN expression in calcified aortas. Furthermore, CNP downregulated OPN and bone morphogenic protein 2 (BMP-2) expression in calcified aortas and VSMCs. Modulation of OPN and BMP-2 expression by CNP and the beneficial effects of CNP on calcified VSMCs were blocked significantly by protein kinase G inhibitor H7. Impaired local endogenous CNP and its receptor system may be associated with increased mineralization in vivo in rat aortas with VC, and administration of CNP inhibits VC development in vivo and in vitro, at least in part, via a cGMP/PKG pathway.     

Insulin regulates menin expression, cytoplasmic localization, and interaction with FOXO1

Menin is the ubiquitously expressed nuclear protein product of the MEN1 gene, which interacts with PKB/Akt in the cytoplasm to inhibit its activity. This study describes a novel insulin-dependent mechanism of menin regulation and interaction with other metabolic proteins. We show that insulin downregulated menin in a time-dependent manner via the human insulin receptor. Inhibition analysis indicated a critical role for the protein kinase Akt in regulation of menin expression and localization. Insulin-mediated decrease in menin expression was abrogated by the PI3K/Akt inhibitor LY-294002 at early time points, from 2 to 7 h. Furthermore, exposure to insulin resulted in the cytoplasmic localization of menin and increased interaction with FOXO1. Fasting followed by refeeding modulates serum insulin levels, which corresponded to an increase in menin interaction with FOXO1 in the liver. Liver-specific hemizygous deletion of menin resulted in increased expression of FOXO1 target genes, namely IGFBP-1, PGC-1α, insulin receptor, Akt, and G-6-Pase. This study provides evidence that menin expression and localization are regulated by insulin signaling and that this regulation triggers an increase in its interaction with FOXO1 via Akt with metabolic consequences.     

Deepithelialized turnover flaps in burns

Acute and chronic burns leave behind a full-thickness defect that always requires a flap cover. Such defects are common in electrical burn injuries of the limbs. This paper deals with 35 patients with full-thickness defects following burns in whom deepithelialized turnover dermis flaps and deepithelialized turnover flaps with deep fascia have been used. This flap is an extension of Hynes's reversed dermis graft and Smahel's deepithelialized turnover flap where there is a larger area of blood supply on the deeper aspect of the dermis. If a good hinge is provided for safe blood supply, such a flap settles well in the defect, and cumbersome multistaged procedures can be avoided. If there is less fatty tissue in the area of flap used, then reversed dermis flaps are ideal because split-skin graft take is good. When there is a lot of fatty tissue on the undersurface of dermis, the fascia is also included to make it a reversed fasciocutaneous flap to augment the blood supply and for better split-skin graft survival. Advantages of the procedure and complications are elaborated.     

Calcium-dependent Binding of HCN1 Channel Protein to Hair Cell Stereociliary Tip Link Protein Protocadherin 15 CD3

The cytoplasmic amino terminus of HCN1, the primary full-length HCN isoform expressed in trout saccular hair cells, was found by yeast two-hybrid protocols to bind the cytoplasmic carboxyl-terminal domain of a protocadherin 15a-like protein. HCN1 was immunolocalized to discrete sites on saccular hair cell stereocilia, consistent with gradated distribution expected for tip link sites of protocadherin 15a. HCN1 message was also detected in cDNA libraries of rat cochlear inner and outer hair cells, and HCN1 protein was immunolocalized to cochlear hair cell stereocilia. As predicted by the trout hair cell model, the amino terminus of rat organ of Corti HCN1 was found by yeast two-hybrid analysis to bind the carboxyl terminus of protocadherin 15 CD3, a tip link protein implicated in mechanosensory transduction. Specific binding between HCN1 and protocadherin 15 CD3 was confirmed with pull-down assays and surface plasmon resonance analysis, both predicting dependence on Ca²⁺. In the presence of calcium chelators, binding between HCN1 and protocadherin 15 CD3 was characterized by a K_D = 2.39 × 10^-7 m. Ca²⁺ at 26.5-68.0 μm promoted binding, with K_D = 5.26 × 10^-8 m (at 61 μm Ca²⁺). Binding by deletion mutants of protocadherin 15 CD3 pointed to amino acids 158-179 (GenBank™ accession number {"type":"entrez-protein","attrs":{"text":"XP_238200","term_id":"293356762","term_text":"XP_238200"}}XP_238200), with homology to the comparable region in trout hair cell protocadherin 15a-like protein, as necessary for binding to HCN1. Amino terminus binding of HCN1 to HCN1, hypothesized to underlie HCN1 channel formation, was also found to be Ca²⁺-dependent, although the binding was skewed toward a lower effective maximum [Ca²⁺] than for the HCN1 interaction with protocadherin 15 CD3. Competition may therefore exist in vivo between the two binding sites for HCN1, with binding of HCN1 to protocadherin 15 CD3 favored between 26.5 and 68 μm Ca²⁺. Taken together, the evidence supports a role for HCN1 in mechanosensory transduction of inner ear hair cells.HCN1² is the primary full-length HCN isoform underlying I_h (hyperpolarization-activated, cyclic nucleotide-gated, nonselective cation channel current) in a model hair cell preparation from the trout sacccule (1). cAMP-gated I_h, possibly in addition to the mechanosensory-transduction current, sets the membrane potential for a subpopulation of saccular hair cells (2, 3). The membrane potential in the saccular hair cell subpopulation is sufficiently depolarized to activate voltage-gated calcium channels, permitting influx of calcium and secretion of hair cell transmitter (2). Given that saccular hair cells expressing I_K1 in addition to I_h are more hyperpolarized, not supporting activation of the voltage-gated calcium channels, we predicted that spontaneous release of transmitter from the subpopulation of hair cells would constitute hair cell-generated spontaneous activity for the saccule (1). However, little has been previously reported on the morphological localization of the HCN1 isoform in hair cells or possible links to structural proteins that mechanistically would localize HCN1 in hair cells (for preliminary report, see Ref. 4). In general, little is known about protein-protein interactions for the HCN isoforms that would modulate I_h and/or the associated instantaneous current (5).Protocadherin 15 is a proposed tip link protein involved in connecting shorter stereocilia to adjacent taller stereocilia in the stereociliary array of inner ear hair cells, facilitating the opening of the mechanosensory transduction channel in response to auditory and vestibular stimuli. The active tip link protein in Danio rerio is protocadherin 15a (6), characterized by splice variants in its carboxyl terminus. In the mammal, protocadherin 15 CD3 is hypothesized to be a tip link protein at insertion sites in the tips of the shorter stereocilia of the stereociliary array (7, 8).     

Linkage and association of phospholipid transfer protein activity to LASS4

Phospholipid transfer protein activity (PLTPa) is associated with insulin levels and has been implicated in atherosclerotic disease in both mice and humans. Variation at the PLTP structural locus on chromosome 20 explains some, but not all, heritable variation in PLTPa. In order to detect quantitative trait loci (QTLs) elsewhere in the genome that affect PLTPa, we performed both oligogenic and single QTL linkage analysis on four large families (n = 227 with phenotype, n = 330 with genotype, n = 462 total), ascertained for familial combined hyperlipidemia. We detected evidence of linkage between PLTPa and chromosome 19p (lod = 3.2) for a single family and chromosome 2q (lod = 2.8) for all families. Inclusion of additional marker and exome sequence data in the analysis refined the linkage signal on chromosome 19 and implicated coding variation in LASS4, a gene regulated by leptin that is involved in ceramide synthesis. Association between PLTPa and LASS4 variation was replicated in the other three families (P = 0.02), adjusting for pedigree structure. To our knowledge, this is the first example for which exome data was used in families to identify a complex QTL that is not the structural locus.