Scoring the collective effects of SNPs: association of minor alleles with complex traits in model organisms

It has long been assumed that most parts of a genome and most genetic variations or SNPs are non-functional with regard to reproductive fitness.However,the collective effects of SNPs have yet to be examined by experimental science.We here developed a novel approach to examine the relationship between traits and the total amount of SNPs in panels of genetic reference populations.We identified the minor alleles(MAs)in each panel and the MA content(MAC)that each inbred strain carried for a set of SNPs with genotypes determined in these panels.MAC was nearly linearly linked to quantitative variations in numerous traits in model organisms,including life span,tumor susceptibility,learning and memory,sensitivity to alcohol and anti-psychotic drugs,and two correlated traits poor reproductive fitness and strong immunity.These results suggest that the collective effects of SNPs are functional and do affect reproductive fitness.     

Evolutionary engineering of a glycerol‐3‐phosphate dehydrogenase‐negative,acetate‐reducing Saccharomyces cerevisiae strain enables anaerobic growth at high glucose concentrations

Glycerol production by Saccharomyces cerevisiae, which is required for redox-cofactor balancing in anaerobic cultures, causes yield reduction in industrial bioethanol production. Recently, glycerol formation in anaerobic S. cerevisiae cultures was eliminated by expressing Escherichia coli (acetylating) acetaldehyde dehydrogenase (encoded by mhpF) and simultaneously deleting the GPD1 and GPD2 genes encoding glycerol-3-phosphate dehydrogenase, thus coupling NADH reoxidation to reduction of acetate to ethanol. Gpd^– strains are, however, sensitive to high sugar concentrations, which complicates industrial implementation of this metabolic engineering concept. In this study, laboratory evolution was used to improve osmotolerance of a Gpd^– mhpF-expressing S. cerevisiae strain. Serial batch cultivation at increasing osmotic pressure enabled isolation of an evolved strain that grew anaerobically at 1 M glucose, at a specific growth rate of 0.12 h⁻¹. The evolved strain produced glycerol at low concentrations (0.64 ± 0.33 g l⁻¹). However, these glycerol concentrations were below 10% of those observed with a Gpd⁺ reference strain. Consequently, the ethanol yield on sugar increased from 79% of the theoretical maximum in the reference strain to 92% for the evolved strains. Genetic analysis indicated that osmotolerance under aerobic conditions required a single dominant chromosomal mutation, and one further mutation in the plasmid-borne mhpF gene for anaerobic growth.     

Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons

Full-length Del elements from ten angiosperm genomes, 5 monocot and 5 dicot, were retrieved and putative attachment (att) sites were identified. In the 2432 Del elements, two types of U5 att sites and a single conserved type of U3 att site were identified. Retroviral att sites confer specificity to the integration process, different att sites types therefore implies lineage specificity. While some features are common to all Del elements, CpG island patterns within the LTRs were particular to lineage specific clusters. All eudicot copies grouped into one single clade while the monocots harbour a more diverse collection of elements. Furthermore, full-length Del elements and truncated copies were unevenly distributed amongst chromosomes. Elements of Del lineage are organized in plants into three clusters and each cluster is composed of elements with distinct LTR features. Our results suggest that the Del lineage efficiently amplified in the monocots and that one branch is probably a newly emerging sub-lineage. Finally, sequences in all groups are under purifying selection. These results show the LTR region is dynamic and important in the evolution of LTR-retrotransposons, we speculate that it is a trigger for retrotransposon diversification.     

Hepatitis B and Delta Virus Are Prevalent but Often Subclinical Co-Infections among HIV Infected Patients in Guinea-Bissau,West Africa: A Cross-Sectional Study

BackgroundCo-infection with human immunodeficiency virus (HIV) and hepatitis B virus (HBV) may lead to accelerated hepatic disease progression with higher rates of liver cirrhosis and liver-related mortality compared with HBV mono-infection. Co or super-infection with hepatitis Delta virus (HDV) may worsen the liver disease and complicate treatment possibilities.MethodsIn this cross-sectional study we included HIV-infected individuals who had a routine blood analysis performed at an HIV clinic in Bissau, Guinea-Bissau between the 28^th of April and 30^th of September 2011. All patients were interviewed, had a clinical exam performed and had a blood sample stored. The patients'' samples were tested for HBV and HDV serology, and HBV/HDV viral loads were analyzed using in-house real-time PCR methods.ResultsIn total, 576 patients (417 HIV-1, 104 HIV-2 and 55 HIV-1/2) were included in this study. Ninety-four (16.3%) patients were HBsAg positive of whom 16 (17.0%) were HBeAg positive. In multivariable logistic regression analysis, CD4 cell count <200 cells/ µl and animist religion were significantly associated with HBsAg positivity. Due to scarcity of available plasma, virological analyses were not performed for eight patients. HBV DNA was detected in 42 of 86 samples (48.8%) positive for HBsAg and genotyping was performed in 26 patients; 25 of whom had genotype E and one genotype D. Among 9 patients on antiretroviral treatment (ART), one patient had the [L180M, M204V] mutation associated with lamivudine resistance. Among the HBsAg positive patients 25.0% were also positive for anti-HDV and 4/9 (44.4%) had detectable HDV RNA.ConclusionHBV and HDV were frequent co-infections among HIV positive patients in Guinea-Bissau and chronic infection was associated with severe immunosuppression. Lamivudine was widely used among HBsAg positive patients with the risk of developing resistant HBV.     

Role of critical charged residues in reduction potential modulation of ferredoxin-NADP+ reductase.

Reduction potential determinations of K75E, E139K and E301A ferredoxin-NADP+ reductases provide valuable information concerning the factors that contribute to tune the flavin reduction potential. Thus, while E139 is not involved in such modulation, the K75 side-chain tunes the flavin potential by creating a defined environment that modulates the FAD conformation. Finally, the E301 side-chain influences not only the flavin reduction potential, but also the electron transfer mechanism, as suggested from the values determined for the E301A mutant, where E(ox/rd) and E(sq/rd) shifted +41 and +102 mV, respectively, with regard to wild-type. Reduction potentials allowed estimation of binding energies differences of the FAD cofactor upon reduction.     

SEM observations of some noteworthy diatoms from the Ikpoba reservoir,Nigeria

ABSTRACT

Eighteen taxa of diatoms from the Ikpoba reservoir, southern Nigeria are listed in this report. They belong to the genera Cymbella, Stenopterobia, Eunotia, Brachysira, Frustulia, Navicula, Pinnularia, Stauroneis and Surirella. The occurrences and distribution of the algae are indicated. Two of these taxa occurred very frequently, six frequently and four occasionally. Five taxa had rare occurrences while one was very rare. They were compared with national as well as regional records.     

Calf thymus high mobility group proteins are nonenzymatically glycated but not significantly glycosylated

Over the past decade, there have been many reports suggesting the presence of complex carbohydrates on nuclear and cytoplasmic proteins in mammalian cells. Some of the most often cited of these reports deal with the glycosylation of the high mobility group (HMG) proteins. These are relatively abundant chromosomal proteins that are known to be associated with nucleosomes and actively transcribed regions of chromatin. The original report describing HMG protein glycosylation presented several lines of evidence suggesting that these proteins are glycosylated, including carbohydrate compositional analysis and periodic-acid Schiff staining. We have attempted to repeat these observations with more highly purified protein than was utilized in the original study. Using carbohydrate compositional analysis performed by high pH anion exchange chromatography coupled to pulsed-amperometric detection, we saw no evidence for significant glycosylation of these proteins. In addition, we found no evidence for the presence of O- GlcNAc, a well known form of nuclear glycosylation. The HMG proteins did react with periodate, suggesting the presence of a modification containing cis-diols on the protein. Several tryptic peptides isolated from HMG 14 and 17 which retained the periodate reactivity had in common lysine residues, suggesting a potential modification of the straightepsilon-amino groups of lysines such as nonenzymatic glycation. Western blot analysis of the HMG proteins using anti-advanced glycation endproducts (AGE) antibodies confirmed the presence of glycation products on the HMG proteins.      

Effects of plant growth promoting bacteria and mycorrhizal on Capsicum annuum L. var. aviculare ([Dierbach] D’Arcy and Eshbaugh) germination under stressing abiotic conditions

Capsicum annuum var. aviculare to Tarahumara and Papago Indians and farmers of Sonora desert is a promising biological and commercial value as a natural resource from arid and semiarid coastal zones. Traditionally, apply synthetic fertilizers to compensate for soil nitrogen deficiency. However, indiscriminate use of these fertilizers might increase salinity. The inoculation by plant growth promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) represents an alternative as potential bio fertilizer resources for salty areas. Seeds ecotypes from four areas of Sonora desert (Mazocahui, Baviacora, Arizpe, La Tortuga), in order to inoculate them with one species of PGPB and AMF. Two germination tests were carried out to study the effect of salinity, temperature regime (night/day) and inoculation with PGPB and AMF growth factors measured on germination (percentage and rate), plant height, root length, and produced biomass (fresh and dry matter). The results indicated that from four studied ecotypes, Mazocahui was the most outstanding of all, showing the highest germination under saline and non-saline conditions. However, the PGPB and AMF influenced the others variables evaluated. This study is the first step to obtain an ideal ecotype of C. a. var. aviculare, which grows in the northwest of México and promoting this type of microorganisms as an efficient and reliable biological product. Studies of the association of PGPB and AMF with the C. a. var. aviculare-Mazocahui ecotype are recommended to determine the extent to which these observations can be reproduced under field conditions.