Genetic Variants in Nuclear-Encoded Mitochondrial Genes Influence AIDS Progression

Background

The human mitochondrial genome includes only 13 coding genes while nuclear-encoded genes account for 99% of proteins responsible for mitochondrial morphology, redox regulation, and energetics. Mitochondrial pathogenesis occurs in HIV patients and genetically, mitochondrial DNA haplogroups with presumed functional differences have been associated with differential AIDS progression.

Methodology/Principal Findings

Here we explore whether single nucleotide polymorphisms (SNPs) within 904 of the estimated 1,500 genes that specify nuclear-encoded mitochondrial proteins (NEMPs) influence AIDS progression among HIV-1 infected patients. We examined NEMPs for association with the rate of AIDS progression using genotypes generated by an Affymetrix 6.0 genotyping array of 1,455 European American patients from five US AIDS cohorts. Successfully genotyped SNPs gave 50% or better haplotype coverage for 679 of known NEMP genes. With a Bonferroni adjustment for the number of genes and tests examined, multiple SNPs within two NEMP genes showed significant association with AIDS progression: acyl-CoA synthetase medium-chain family member 4 (ACSM4) on chromosome 12 and peroxisomal D3,D2-enoyl-CoA isomerase (PECI) on chromosome 6.

Conclusions

Our previous studies on mitochondrial DNA showed that European haplogroups with presumed functional differences were associated with AIDS progression and HAART mediated adverse events. The modest influences of nuclear-encoded mitochondrial genes found in the current study add support to the idea that mitochondrial function plays a role in AIDS pathogenesis.     

Alpha Lipoic Acid Application Promotes Water-Deficit Tolerance by Modulating Osmoprotectant Metabolism-Related Genes in Maize

Russian Journal of Plant Physiology - Alpha lipoic acid (ALA) is a potent antioxidant molecule that has positive effects on plant growth and the adaptation of plants to environmental stresses....     

Candida rugosa lipase encapsulated with magnetic sporopollenin: design and enantioselective hydrolysis of racemic arylpropanoic acid esters

Abstract

The aim of this study was to prepare the encapsulation of Candida rugosa lipase (CRL) with magnetic sporopollenin. The sporopollenin was covalent immobilized onto magnetic nanoparticles (Fe₃O₄), grafted amino (APTES), or epoxy groups (EPPTMS). CRL was sol-gel encapsulated in the presence of magnetic sporopollenin/Fe₃O₄ nanoparticles. The influence of activation agents ([3-(2,3-epoxypropoxy) propyl] trimethoxysilane (EPPTMS), (3-Aminopropyl)triethoxysilane (APTES) and pH and thermal stabilities of the biocatalyst were assessed. Experimental data showed the improved catalytic activity at different pH and temperature values. At 60?°C, free lipase lost its initial activity within 80?min of time, although the encapsulated lipases retained their initial activities of about 65% by APTES and 60% by EPPTMS after 120?min of heat treatment at 60?°C. The catalytic properties of the encapsulated lipases were utilized to hydrolysis of racemic aromatic carboxylic acid methyl esters (Naproxen and 2-phenoxypropionic acid). The results show that the sporopollenin-based encapsulated lipase (Fe-A-Spo-E) has greater enantioselectivity and conversion in comparison with the encapsulated lipase without supports (lipase-enc).     

Higher titer hyaluronic acid production in recombinant Lactococcus lactis

Abstract

Hyaluronic acid (HA) is a natural biopolymer and has long been attracting the attention of biotechnology industry due to its various biological functions. HA production with natural producer Streptococcus equi subsp. zooepidemicus has not been preferred because it has many drawbacks due to its pathogenicity. Therefore, in the present study, Streptococcal hyaluronan synthase gene (hasA) was introduced and expressed in Lactococcus lactis, through the auto inducible NICE system and the effect of nisin amount on the production of HA was examined. Newly constructed plasmid was transformed into L. lactis CES15, produced 6.09 g/l HA in static flask culture after three hours of induction period with initial 7.5 ng/ml nisin concentration within total six hours of incubation. The highest HA titer value ever was reported for recombinant HA-producing L. lactis by examining the effect of initial nisin concentration. We have shown that initial nisin concentration, which used to initiate the auto-inducing mechanism of NICE system and consequently hyaluronan synthase expression, has a direct and significant effect on the produced HA amount. Recently constructed recombinant L. lactis CES15 strain provide significant advantages for industrial HA production than those in literature in terms of production time, energy demand, carbon usage, and safety status.     

Effects of Chronic Boron Exposure on Semen Profile

The possible changes in semen quality were studied in men living in a boron mining area. The subjects in the boron group had exposure to boron at an average level of 6.5 mg/day, as determined by urinary analysis. The results obtained by the boron group were compared to those obtained for the control group whose subjects were living in the same geographical area but away from the boron region; average exposure level was 1.4 mg/day for this group. The semen samples were analyzed according to the recommendations of the World Health Organization. Boron levels were established in the water samples obtained from various locations in the study region. In the boron mining fields where the subjects in the boron group live, water samples contained boron in the range of 1.4–6.5 mg/L, while the values were <0.01 mg/L for the water samples obtained from the region where the subjects of the control group reside. No negative effects were found in the sperm samples obtained from the subjects of the boron group.     

The Kaposi's sarcoma-associated herpesvirus ORF6 DNA binding protein forms long DNA-free helical protein filaments

The Kaposi's sarcoma-associated herpesvirus ORF6 has a 41% sequence identity with Balf2 protein of Epstein-Barr virus and 23% with ICP8 protein of Herpes Simplex type I. Balf2 and ICP8 are multi-functional DNA binding proteins with roles central to viral DNA replication and recombination. In this study, we cloned the KSHV ORF6 gene, expressed the full length ORF6 protein in insect cells and purified it to homogeneity. Gel filtration revealed the protein to be present in a broad spectrum of sizes ranging from monomers to high molecular weight oligomers. Transmission electron microscopy (TEM) using negative staining under conditions favoring monomers and small oligomers revealed fields of globular particles measuring 11nm in diameter consistent with the size of a protein monomer. Incubation of ORF6 protein at room temperature for extended periods of time resulted in the bulk of the protein forming very long helical filaments. Measurements from negative staining revealed that the filaments were up to 2600nm in length, with a width of 13.7nm and a long gentle helical periodicity of 42.9nm along the filament axis. Using rapid freezing and freeze-drying, it was possible to show that the filaments consist of two protein chains wrapped around each other. The possibility that these protein filaments generate a scaffold upon which viral DNA replication, recombination, and encapsidation occur in the infected cell nucleus is discussed.     

Combining Soil Databases for Topsoil Organic Carbon Mapping in Europe

Accuracy in assessing the distribution of soil organic carbon (SOC) is an important issue because of playing key roles in the functions of both natural ecosystems and agricultural systems. There are several studies in the literature with the aim of finding the best method to assess and map the distribution of SOC content for Europe. Therefore this study aims searching for another aspect of this issue by looking to the performances of using aggregated soil samples coming from different studies and land-uses. The total number of the soil samples in this study was 23,835 and they’re collected from the “Land Use/Cover Area frame Statistical Survey” (LUCAS) Project (samples from agricultural soil), BioSoil Project (samples from forest soil), and “Soil Transformations in European Catchments” (SoilTrEC) Project (samples from local soil data coming from six different critical zone observatories (CZOs) in Europe). Moreover, 15 spatial indicators (slope, aspect, elevation, compound topographic index (CTI), CORINE land-cover classification, parent material, texture, world reference base (WRB) soil classification, geological formations, annual average temperature, min-max temperature, total precipitation and average precipitation (for years 1960–1990 and 2000–2010)) were used as auxiliary variables in this prediction. One of the most popular geostatistical techniques, Regression-Kriging (RK), was applied to build the model and assess the distribution of SOC. This study showed that, even though RK method was appropriate for successful SOC mapping, using combined databases was not helpful to increase the statistical significance of the method results for assessing the SOC distribution. According to our results; SOC variation was mainly affected by elevation, slope, CTI, average temperature, average and total precipitation, texture, WRB and CORINE variables for Europe scale in our model. Moreover, the highest average SOC contents were found in the wetland areas; agricultural areas have much lower soil organic carbon content than forest and semi natural areas; Ireland, Sweden and Finland has the highest SOC, on the contrary, Portugal, Poland, Hungary, Spain, Italy have the lowest values with the average 3%.     

Zoobenthos-inhabiting Sarcotragus muscarum (Porifera: Demospongiae) from the Aegean Sea

The cavities and outer surfaces of 20 individuals of the sponge Sarcotragus muscarum collected from the Turkish Aegean coast during July–September 1993 contained a total of 148 zoobenthic species with 5299 individuals belonging to seven taxonomic groups. Among these, Polychaeta accounted for 60% of the total number of species, while Crustacea comprised 71% of the total number of individuals and 40% of the wet weight of biomass. The amphipod and decapod crustaceans Tritaeta gibbosa and Synalpheus gambarelloides, and the bivalve Hiatella arctica, were the most abundant species on the sponge samples both in terms of number of individuals and biomass values. The community structure inside the sponges was greatly influenced by the nature of the substratum around the sponge, and by the overwhelming population of the Lessepsian echinoderm Ophiactis savignyi. Number of species, biomass and diversity index values were found to be positively related to the sponge volume. Mean density and biomass of the associated taxa are 0.22 ind cm^–3 and 11.63 mg cm^–3, respectively.     

Polymorphisms in the aurora-A gene is not associated with lung cancer in the Turkish population

Lung cancer, a complex neoplasm of lung tissue, is influenced by several environmental and genetic factors which could be changed in each individual. Aurora-A gene is related to mitotic events such as: chromosome instability, cell cycle regulation, spindle formation, and kinetechore-microtubule connections. This centrosomic serine/threonine kinase provides a strong connection between mitotic errors and carcinogenesis. The genomic alterations such as single nucleotide polymorphisms (SNPs) can exist in molecular pathways of lung cancer. Therefore, we evaluated the role of genetic polymorphisms of Aurora-A gene in the lung cancer in the Turkish population. Genotypes of five Aurora-A polymorphisms (F31I, V57I, 6328G/A, P50L, and S104L) were determined in 102 healty controls and 102 new diagnosed lung cancer cases. All samples were genotyped with DNA sequence technique. There were not any genotype variations in P50L, S104L, and 6328G/A polymorphisms. The frequencies of both genotypes F31I and V57I in lung cancer patients were not significantly different from those in controls (p > 0.05). A multivariable logistic regression analysis including patient characteristics, such as age and gender, did not change the results.