Down-regulation of circulating microRNA let-7a in Egyptian smokers

Altered miRNAs were associated with cigarette smoking. The study aimed to examine the gene expression level of plasma let-7a among healthy smokers and compared it with the non-smokers. Forty subjects were recruited for the present study and classified into 21 smokers and 19 non-smokers, age, and sex were matched. The software that used to design functional primers was MIRprimer. Quantitative real-time PCR was employed to compare the relative expression of plasma let-7a. Results showed that the level of let-7a was down-regulated in smokers to 0.34fold (p?=?0.006) that of the non-smokers. Plasma let-7a showed an area under curve (AUC) of 0.749 with sensitivity 43% and specificity 100%. In conclusion, plasma let-7a was significantly down-regulated in the smokers, and it might be considered a candidate biomarker to discriminate between smokers and non-smokers.     

Historical and ecological influence in the evolutionary diversification of external morphology of neotropical spiny rats (Echimyidae,Rodentia)

The radiation of neotropical echimyid rodents resulted in the diversification of spiny rats, hutias, and the coypu, grouped into four major clades. Different echimyid lineages specialized for terrestrial, semifossorial, semiaquatic, and arboreal locomotion, and for living in bamboo thickets. Comparative phylogenetic methods were herein used for evaluating the relative effect of historical and ecological factors in shaping morphometric traits of external morphology (length of head and body, tail, ear, and hindfeet). Additionally, we investigated whether the adoption of different locomotory habits was associated with changes in their macroevolutionary dynamics. Our findings showed that variation of all traits was phylogenetically structured, although size was less structured than other traits. Tail, ear, and mainly hindfeet were allometrically correlated with head and body length, indicating the occurrence of evolutionary structural constraints. In addition to phylogenetic and allometric components, morphometric variation was strongly associated with locomotory specializations, except for body size. Disparification of body size and tail length took place gradually, fitting the Brownian motion model albeit with some punctual shifts in evolutionary rates. Some of these shifts were associated with changes in locomotory habits, notably with adoption of a semiaquatic habit by the large‐sized Myocastor lineage, which occurred with an accelerated rate of size evolution. Evolutionary changes in ear and hindfeet length were concentrated during early echimyid diversification, concomitantly with the emergence of most locomotory habits, with subsequent deceleration of evolutionary rates. These findings indicated a complex interaction between phylogenetic, structural, and ecological effects gradually shaping echimyid external morphology.     

Plastid phylogenomics and molecular evolution of Alismatales

Past phylogenetic studies of the monocot order Alismatales left several higher‐order relationships unresolved. We addressed these uncertainties using a nearly complete genus‐level sampling of whole plastid genomes (gene sets representing 83 protein‐coding and ribosomal genes) from members of the core alismatid families, Tofieldiaceae and additional taxa (Araceae and other angiosperms). Parsimony and likelihood analyses inferred generally highly congruent phylogenetic relationships within the order, and several alternative likelihood partitioning schemes had little impact on patterns of clade support. All families with multiple genera were resolved as monophyletic, and we inferred strong bootstrap support for most inter‐ and intrafamilial relationships. The precise placement of Tofieldiaceae in the order was not well supported. Although most analyses inferred Tofieldiaceae to be the sister‐group of the rest of the order, one likelihood analysis indicated a contrasting Araceae‐sister arrangement. Acorus (Acorales) was not supported as a member of the order. We also investigated the molecular evolution of plastid NADH dehydrogenase, a large enzymatic complex that may play a role in photooxidative stress responses. Ancestral‐state reconstructions support four convergent losses of a functional NADH dehydrogenase complex in Alismatales, including a single loss in Tofieldiaceae.     

Pretreatment Predictors of Response to PegIFN-RBV Therapy in Egyptian Patients with HCV Genotype 4

BackgroundEgypt has the highest prevalence of a difficult to treat chronic hepatitis C virus (HCV), genotype 4. Pretreatment factors could guide individualization of therapy which aids in treatment optimization and interleukin IL28B gene polymorphism has been shown to closely relate to HCV treatment response. Polymorphisms in genes encoding inhibitors of T-cell response, which have role in disease progression as Programmed Cell Death 1 (PD-1), and Cytotoxic T-Lymphocytes Antigen-4 (CTLA-4), could be candidate markers predicting treatment response.MethodsThis cohort study consisted of 200 chronic HCV genotype 4 infected patients treated with PegIFN α-2a and RBV in 2 hepatology centers. Genotyping of the polymorphisms in the IL28B gene region (rs12979860), PD1.3 (rs11568821) and CTLA-4 (rs231775) was performed on DNA collected from each patient using TaqMan^® genotyping assay. Groups were classified according to response into sustained virological responders (SVR), or non-responders (NR). A multivariate logistic regression analysis was used to identify potential markers, host pretreatment clinical and viral predictive factors including viral load, insulin resistance, and alpha fetoprotein (AFP) related to treatment response.ResultsOur results showed that in a multivariate analyses IL28B C/C genotype was the most significant predictor for SVR (OR = 10.86; p<0.0001) followed by AFP (OR = 0.915; p = 0.001) then CTLA-4/G genotypes (OR = 1.948; p = 0.022). However, PD-1.3/A genotypes and platelets count were significantly related to response in univariate analysis only (OR = 1.973; p = 0.023; OR = 1.007; p = 0.009 respectively).ConclusionIL28B SNP, AFP level, and CTLA-4 SNP could be used in conjunction to predict treatment response in HCV genotype 4 infected Egyptian patients.     

Bacterial Sulphate Reduction and the Development of Alkalinity. III. Experiments under Natural Conditions in the Wadi Natrûn

Evidence that microbial sulphate reduction is mainly responsible for the formation of the natron (hydrated Na₂CO₃) deposits in Wadi Natrûn is presented. The sulphate in the infiltrating water is reduced during passage through the surrounding waterlogged soil and the bicarbonate formed is later concentrated by evaporation in the lakes.     

Skin calcium-binding protein: effect of vitamin D deficiency and vitamin D treatment

The amount of skin calcium-binding protein, evaluated using a sensitive radioimmunoassay and indirect immunofluorescence, was decreased in vitamin-D deficient rats and increased after one week vitamin D3 or 1 alpha-hydroxyvitamin D3 treatment. In vitamin D replete and in vitamin D-deficient animals, skin calcium-binding protein was not sensitive to changes in dietary and/or serum calcium concentrations. These results indicate that this protein is different from other calcium-binding proteins such as parvalbumin and calmodulin which are not vitamin D-dependent, and also different from intestinal calcium-binding protein which, in D replete animals, is sensitive to changes in dietary and serum calcium concentrations. Skin calcium-binding protein may, therefore, represent a new class of vitamin D-dependent protein.     

Scale‐dependent strategies for coexistence of mesocarnivores in human‐dominated landscapes

Identifying factors influencing the distribution of and interactions within carnivore communities is important for understanding how they are affected by human activities. Species differ in their ability to adapt to humans depending on their degree of specialization in habitat use and feeding habits. This results in asymmetric changes in the ecology of co‐occurring species that can influence their interactions. We investigated whether human infrastructures and free‐ranging domestic dogs (a species typically associated with humans) influenced the co‐occurrence and habitat use of mesocarnivores in a landscape of high human population density in Maharashtra, India. We used 40 camera trap locations during 233 trapping nights and used Bayesian co‐occurrence occupancy models to investigate the habitat use and coexistence of species at different spatial scales. Additionally, we investigated their temporal overlap in space use. Indian foxes altered their habitat use both spatially and temporally in order to avoid free‐ranging domestic dogs and other larger competitors. The use of human infrastructure by jackals and jungle cats was limited by the presence of dogs. Our results illustrate how habitat use of smaller carnivore species changes both spatially and temporally in order to avoid larger competitors. We also show that the presence of species associated with humans mediates the influence of human infrastructures on the habitat use of mesocarnivores. We highlight the importance of acknowledging the potential impact of urbanization not only on single species, but also on the interactions within the community.     

Differential segregation of protective immunity by encoded antigen in DNA vaccine against pseudorabies virus

A murine model immunized with plasmid DNA vaccine expressing three glycoproteins pCIgB, pCIgC and pCIgD were used to examine the relative potency of major glycoproteins as well as the contribution of immunological parameters in providing protective immunity against the pseudorabies virus (PrV). Among the three glycoprotein-encoded plasmid DNA vaccines, pCIgB produced the strongest response of PrV-specific IgG in the sera. pCIgB and pCIgD also induced a contrast pattern of immunity that was biased to the Th1 and Th2 types, respectively. pCIgC showed the potent inducer of CD8+ T-cell-mediated CTL activity against PrV. In addition, a cocktail vaccination of all three glycoprotein-encoded plasmid DNA vaccines induced the production of both cytokine types, Th1 and Th2 with levels that were the same as that of each immunogen. With regard to protective efficacy, pCIgB induced the most effective protection against a virulent virus challenge and a cocktail vaccination appeared to offer complete protection against a 5 LD50 challenge, but not a 10 LD50 one. pCIgD induced protection that was same as pCIgB, but pCIgC offered no effective protection. These results show the relative potency of the three glycoprotein-encoded PrV DNA vaccines in inducing protective immunity against PrV infection. The results in this study support previous results showing the importance of Th1-type CD4+ T cells and their antibodies in conferring protection.     

Ensemble Modeling for Aromatic Production in Escherichia coli

Ensemble Modeling (EM) is a recently developed method for metabolic modeling, particularly for utilizing the effect of enzyme tuning data on the production of a specific compound to refine the model. This approach is used here to investigate the production of aromatic products in Escherichia coli. Instead of using dynamic metabolite data to fit a model, the EM approach uses phenotypic data (effects of enzyme overexpression or knockouts on the steady state production rate) to screen possible models. These data are routinely generated during strain design. An ensemble of models is constructed that all reach the same steady state and are based on the same mechanistic framework at the elementary reaction level. The behavior of the models spans the kinetics allowable by thermodynamics. Then by using existing data from the literature for the overexpression of genes coding for transketolase (Tkt), transaldolase (Tal), and phosphoenolpyruvate synthase (Pps) to screen the ensemble, we arrive at a set of models that properly describes the known enzyme overexpression phenotypes. This subset of models becomes more predictive as additional data are used to refine the models. The final ensemble of models demonstrates the characteristic of the cell that Tkt is the first rate controlling step, and correctly predicts that only after Tkt is overexpressed does an increase in Pps increase the production rate of aromatics. This work demonstrates that EM is able to capture the result of enzyme overexpression on aromatic producing bacteria by successfully utilizing routinely generated enzyme tuning data to guide model learning.