Age-related macular degeneration and genetic polymorphisms of glutathione <Emphasis Type="Italic">S</Emphasis>-transferases M1 (<Emphasis Type="Italic">GSTM1</Emphasis>) and T1 (<Emphasis Type="Italic">GSTT1</Emphasis>)

The aim of this study is to understand the multifactorial causes of age-related macular degeneration (ARMD), and, therefore, it is reasonable to investigate whether genetic polymorphisms of antioxidant enzymes (GSTM1 and GSTT1) contribute to the development of ARMD. This study consisted of 112 subjects (44 females, 68 males) with exudative ARMD, who were recruited from Khalili Hospital ophthalmic clinic in Shiraz (southern Iran), referred by vitreoretinal surgeon. Also 112 sex-matched controls (44 females, 68 males) were randomly selected from unrelated volunteers in the same clinic. We excluded patients and controls with cataract or past history of cataract surgery, asthma, past history of malignancy, cardiovascular disease that on medication and known cases of glaucoma, because these traits were associated with GSTM1 and/or GSTT1 polymorphisms. There was no association between polymorphisms of neither GSTM1 nor GSTT1 and risk of ARMD. The combination genotypes of GSTM1 and GSTT1 were not associated with the risk of ARMD. We considered the time of deterioration of vision as the time of onset of exudative ARMD. The Kaplan–Meier analysis revealed that there was significant difference between genotypes of GSTM1 (log rank statistic = 7.03, df = 1, P = 0.008). The age at onset among GSTM1 null genotype was lower than the active genotype of GSTM1. Our results support the hypothesis that the protein encoded by the GSTM1 gene might have a protective function against oxidative stress in retina. Since the age at onset is influenced by the GSTM1 polymorphism, this implies that GSTM1 is a modifier gene.     

Retrospective dosimetry using OSL of tooth enamel and dental repair materials irradiated under wet and dry conditions

Following a radiological or nuclear emergency event, there is a need for quick and reliable dose estimations of potentially exposed people. In situations where dosimeters are not readily available, the dose estimations must be carried out using alternative methods. In the present study, the optically stimulated luminescence (OSL) properties of tooth enamel and different dental repair materials have been examined. Specimens of the materials were exposed to gamma and beta radiation in different types of liquid environments to mimic the actual irradiation situation in the mouth. Measurements were taken using a Ris? TL/OSL reader, and irradiations were made using a ⁹⁰Sr/⁹⁰Y source and a linear accelerator (6 MV photons). Results show that the OSL signal from tooth enamel decreases substantially when the enamel is kept in a wet environment. Thus, tooth enamel is not reliable for retrospective dose assessment without further studies of the phenomenon. Dental repair materials, on the other hand, do not exhibit the same effect when exposed to liquids. In addition, dose–response and fading measurements of the dental repair materials show promising results, making these materials highly interesting for retrospective dosimetry. The minimum detectable dose for the dental repair materials has been estimated to be 20–185?mGy.     

Evolutionary genetics of the human Rh blood group system

The evolutionary history of variation in the human Rh blood group system, determined by variants in the RHD and RHCE genes, has long been an unresolved puzzle in human genetics. Prior to medical treatments and interventions developed in the last century, the D-positive (RhD positive) children of D-negative (RhD negative) women were at risk for hemolytic disease of the newborn, if the mother produced anti-D antibodies following sensitization to the blood of a previous D-positive child. Given the deleterious fitness consequences of this disease, the appreciable frequencies in European populations of the responsible RHD gene deletion variant (for example, 0.43 in our study) seem surprising. In this study, we used new molecular and genomic data generated from four HapMap population samples to test the idea that positive selection for an as-of-yet unknown fitness benefit of the RHD deletion may have offset the otherwise negative fitness effects of hemolytic disease of the newborn. We found no evidence that positive natural selection affected the frequency of the RHD deletion. Thus, the initial rise to intermediate frequency of the RHD deletion in European populations may simply be explained by genetic drift/founder effect, or by an older or more complex sweep that we are insufficiently powered to detect. However, our simulations recapitulate previous findings that selection on the RHD deletion is frequency dependent and weak or absent near 0.5. Therefore, once such a frequency was achieved, it could have been maintained by a relatively small amount of genetic drift. We unexpectedly observed evidence for positive selection on the C allele of RHCE in non-African populations (on chromosomes with intact copies of the RHD gene) in the form of an unusually high F( ST ) value and the high frequency of a single haplotype carrying the C allele. RhCE function is not well understood, but the C/c antigenic variant is clinically relevant and can result in hemolytic disease of the newborn, albeit much less commonly and severely than that related to the D-negative blood type. Therefore, the potential fitness benefits of the RHCE C allele are currently unknown but merit further exploration.     

Vasoactive intestinal peptide suppresses ovarian granulosa cell apoptosis in vitro by up-regulating Bcl-2 gene expression

Vasoactive intestinal peptide (VIP) is an endogenous peptide showing a rich profile of biological activities. Within ovaries, VIP directly regulates the ovarian functions, including granulosa cells (GCs) development. In the present study, the effects of VIP on proliferation and apoptosis in goose granulosa cells were demonstrated and its underlying mechanism investigated. A strategy of RNAi-mediated "gene silencing" of Bcl-2 (RV-Bcl-2), over-expression of Bcl-2 (JLV-Bcl-2) synthesis, and exogenous VIP was used to treat goose GCs. The results showed the amounts of Bcl-2 protein were negatively correlated with apoptosis of goose GCs in all experimental groups. Compared with other control groups, apoptosis was decreased in goose GCs following treatment of 100 nM VIP, and the amount of Bcl-2 protein was increased (P < 0.05) increased. However, VIP failed to exert an effect on cell proliferation (P > 0.05). In conclusion, the exogenous VIP plays an important role in inhibiting apoptosis of goose GCs via inducing Bcl-2 gene expression.     

Molecular Events Initiating Exit of a Copper-transporting ATPase ATP7B from the Trans-Golgi Network

The copper-transporting ATPase ATP7B has a dual intracellular localization: the trans-Golgi network (TGN) and cytosolic vesicles. Changes in copper levels, kinase-mediated phosphorylation, and mutations associated with Wilson disease alter the steady-state distribution of ATP7B between these compartments. To identify a primary molecular event that triggers ATP7B exit from the TGN, we characterized the folding, activity, and trafficking of the ATP7B variants with mutations within the regulatory N-terminal domain (N-ATP7B). We found that structural changes disrupting the inter-domain contacts facilitate ATP7B exit from the TGN. Mutating Ser-340/341 in the N-ATP7B individually or together to Ala, Gly, Thr, or Asp produced active protein and shifted the steady-state localization of ATP7B to vesicles, independently of copper levels. The Ser340/341G mutant had a lower kinase-mediated phosphorylation under basal conditions and no copper-dependent phosphorylation. Thus, negative charges introduced by copper-dependent phosphorylation are not obligatory for ATP7B trafficking from the TGN. The Ser340/341A mutation did not alter the overall fold of N-ATP7B, but significantly decreased interactions with the nucleotide-binding domain, mimicking consequences of copper binding to N-ATP7B. We propose that structural changes that specifically alter the inter-domain contacts initiate exit of ATP7B from the TGN, whereas increased phosphorylation may be needed to maintain an open interface between the domains.     

Regulation of mammalian mitochondrial translation by post-translational modifications

Mitochondria are responsible for the production of over 90% of the energy in eukaryotes through oxidative phosphorylation performed by electron transfer and ATP synthase complexes. Mitochondrial translation machinery is responsible for the synthesis of 13 essential proteins of these complexes encoded by the mitochondrial genome. Emerging data suggest that acetyl-CoA, NAD(+), and ATP are involved in regulation of this machinery through post-translational modifications of its protein components. Recent high-throughput proteomics analyses and mapping studies have provided further evidence for phosphorylation and acetylation of ribosomal proteins and translation factors. Here, we will review our current knowledge related to these modifications and their possible role(s) in the regulation of mitochondrial protein synthesis using the homology between mitochondrial and bacterial translation machineries. However, we have yet to determine the effects of phosphorylation and acetylation of translation components in mammalian mitochondrial biogenesis. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.     

Genomic analysis of ICEVchBan8: An atypical genetic element in Vibrio cholerae

Genomic islands (GIs) and integrative conjugative elements (ICEs) are major players in bacterial evolution since they encode genes involved in adaptive functions of medical or environmental importance. Here we performed the genomic analysis of ICEVchBan8, an unusual ICE found in the genome of a clinical non-toxigenic Vibrio cholerae O37 isolate. ICEVchBan8 shares most of its genetic structure with SXT/R391 ICEs. However, this ICE codes for a different integration/excision module is located at a different insertion site, and part of its genetic cargo shows homology to other pathogenicity islands of V. cholerae.     

Swift block-updating EM and pseudo-EM procedures for Bayesian shrinkage analysis of quantitative trait loci

Introduction

Virtually all existing expectation-maximization (EM) algorithms for quantitative trait locus (QTL) mapping overlook the covariance structure of genetic effects, even though this information can help enhance the robustness of model-based inferences.

Results

Here, we propose fast EM and pseudo-EM-based procedures for Bayesian shrinkage analysis of QTLs, designed to accommodate the posterior covariance structure of genetic effects through a block-updating scheme. That is, updating all genetic effects simultaneously through many cycles of iterations.

Conclusion

Simulation results based on computer-generated and real-world marker data demonstrated the ability of our method to swiftly produce sensible results regarding the phenotype-to-genotype association. Our new method provides a robust and remarkably fast alternative to full Bayesian estimation in high-dimensional models where the computational burden associated with Markov chain Monte Carlo simulation is often unwieldy. The R code used to fit the model to the data is provided in the online supplementary material.