Visualization of viral DNA assembly using nonfluorescent staining

ABSTRACT

We present an easy test for rapid visualization of viral DNA assemblies in infected cell cytoplasm. We selected the best stains for nuclear staining: Nile blue A, Bismarck brown, gallocyanin chrome alum, methyl green pyronin and azure II. None of the staining techniques is fluorescent, which facilitates their use in everyday experiments. Methyl green is most promising for routine detection of viral DNA assemblies in the cytoplasm; the procedure enables ready detection of viral DNA accumulation in the cytoplasm.     

Antiviral Activity of Nanocomplexes of Antisense Oligonucleotides Targeting VP72 Protein in Vero Cells Infected by African Swine Fever Virus

Russian Journal of Bioorganic Chemistry - Antiviral activity of antisense oligodeoxyribonucleotides with phosphorothioate or mesyl phosphoramidate internucleotidic groups targeting the main capsid...     

The environmental fate and behaviour of antifouling paint booster biocides: A review

Antifouling paint booster biocides are a group of organic compounds added to antifouling paints to improve their efficacy. They have become prevalent since the requirement for alternative antifouling paints formulations for small boats (< 25 m). This need followed a ban on the use of triorganotin biocides in antifouling paints for small boats, in the late 1980's. Worldwide, around eighteen compounds are currently used as antifouling biocides, viz. benzmethylamide, chlorothalonil, copper pyrithione, dichlofluanid, diuron, fluorofolpet, Irgarol 1051, Sea‐Nine 211, Mancozeb, Polyphase, pyridine‐triphenyl‐borane, TCMS (2,3,5,6‐tetrachloro‐4‐methylsulfonyl) pyridine, TCMTB [2‐(thiocyanomethylthio)benzothia‐zole], Thiram, tolyfluanid, zinc pyrithione (ZPT), ziram and Zineb. Any booster biocide released into the environment is subjected to a complex set of processes. These processes include transport mechanisms, transformation, degradation, cross media partitioning, and bioaccumulation. This paper reviews the fate and behaviour data currently available in the public domain concerning antifouling paint booster biocides.     

Morphometry of nuclear and nucleolar structures in a CaCo-2 cell line

The number of the nucleoli in a CaCo-2 cell nucleus does not generally depend on the quantity of DNA in the nucleus, but nucleolar DNA content is directly proportional to total nuclear DNA. However, in multinucleolar cells (three or more nucleoli), the nucleolar DNA content increases after 96 h incubation in culture without concomitant quantitative changes in nuclear DNA. The percentage of multinucleolar cells and the average number of nucleoli per nucleus increase with increasing incubation time. After 72 and 96 h in culture, multinucleolar cells show distinctive morphologies. The ratio of the sum of nucleolar perimeters to the nuclear perimeter increases linearly when the number of nucleoli in a nucleus increases, but there is no concomitant increase in total nucleolar area or DNA content, except in the 72 and 96 h populations. When the number of nucleoli in CaCo-2 cells increases after 48 and 60 h in culture, the amount of DNA per nucleolus decreases.     

Functional evolution of two subtly different (similar) folds

Background

The function of proteins is a direct consequence of their three-dimensional structure. The structural classification of proteins describes the ways of folding patterns all proteins could adopt. Although, the protein folds were described in many ways the functional properties of individual folds were not studied.

Results

We have analyzed two β-barrel folds generally adopted by small proteins to be looking similar but have different topology. On the basis of the topology they could be divided into two different folds named SH3-fold and OB-fold. There was no sequence homology between any of the proteins considered. The sequence diversity and loop variability was found to be important for various binding functions.

Conclusions

The function of Oligonucleotide/oligosaccharide-binding (OB) fold proteins was restricted to either DNA/RNA binding or sugar binding whereas the Src homology 3 (SH3) domain like proteins bind to a variety of ligands through loop modulations. A question was raised whether the evolution of these two folds was through DNA shuffling.     

Evaluating the Impact of Zimbabwe’s Prevention of Mother-to-Child HIV Transmission Program: Population-Level Estimates of HIV-Free Infant Survival Pre-Option A

Objective

We estimated HIV-free infant survival and mother-to-child HIV transmission (MTCT) rates in Zimbabwe, some of the first community-based estimates from a UNAIDS priority country.

Methods

In 2012 we surveyed mother-infant pairs residing in the catchment areas of 157 health facilities randomly selected from 5 of 10 provinces in Zimbabwe. Enrolled infants were born 9–18 months before the survey. We collected questionnaires, blood samples for HIV testing, and verbal autopsies for deceased mothers/infants. Estimates were assessed among i) all HIV-exposed infants, as part of an impact evaluation of Option A of the 2010 WHO guidelines (rolled out in Zimbabwe in 2011), and ii) the subgroup of infants unexposed to Option A. We compared province-level MTCT rates measured among women in the community with MTCT rates measured using program monitoring data from facilities serving those communities.

Findings

Among 8568 women with known HIV serostatus, 1107 (12.9%) were HIV-infected. Among all HIV-exposed infants, HIV-free infant survival was 90.9% (95% confidence interval (CI): 88.7–92.7) and MTCT was 8.8% (95% CI: 6.9–11.1). Sixty-six percent of HIV-exposed infants were still breastfeeding. Among the 762 infants born before Option A was implemented, 90.5% (95% CI: 88.1–92.5) were alive and HIV-uninfected at 9–18 months of age, and 9.1% (95%CI: 7.1–11.7) were HIV-infected. In four provinces, the community-based MTCT rate was higher than the facility-based MTCT rate. In Harare, the community and facility-based rates were 6.0% and 9.1%, respectively.

Conclusion

By 2012 Zimbabwe had made substantial progress towards the elimination of MTCT. Our HIV-free infant survival and MTCT estimates capture HIV transmissions during pregnancy, delivery and breastfeeding regardless of whether or not mothers accessed health services. These estimates also provide a baseline against which to measure the impact of Option A guidelines (and subsequently Option B+).     

Proton translocation coupled to formate oxidation in anaerobically grown fermenting Escherichia coli

Proton translocation, coupled to formate oxidation and hydrogen evolution, was studied in anaerobically grown fermenting Escherichia coli JW136 carrying hydrogenase 1 (hya) and hydrogenase 2 (hyb) double deletions. Rapid acidification of the medium by EDTA-treated anaerobic suspension of the whole cells or its alkalization by inverted membranes was observed in response to application of formate. The formate-dependent proton translocation and 2H(+)-K(+) exchange coupled to H(2) evolution were sensitive to the uncoupler, carbonylcyanide-m-chlorophenylhydrazone, and to copper ions, inhibitors of hydrogenases. No pH changes were observed in a suspension of formate-pulsed aerobically grown ("respiring") cells. The apparent H(+)/formate ratio of 1.3 was obtained in cells oxidizing formate. The 2H(+)-K(+) exchange of the ATP synthase inhibitor N,N'-dicyclohexylcarbodiimide-sensitive ion fluxes does take place in JW136 cell suspension. Hydrogen formation from formate by cell suspensions of E. coli JW136 resulted in the formation of a membrane potential (Deltapsi) across the cytoplasmic membrane of -130 mV (inside negative). This was abolished in the presence of copper ions, although they had little effect on the value of Deltapsi generated by E. coli under respiration. We conclude that the hydrogen production by hydrogenase 3 is coupled to formate-dependent proton pumping that regulates 2H(+)-K(+) exchange in fermenting bacteria.     

Comparison of impact of EMCV replication on the nuclear apparatus of NIH 3T3 and HEp-2 cells

We have investigated differences between the actions of encephalomyocarditis virus (EMCV) on cytometric indices in cultured NIH 3T3 and HEp-2 cells, which are characterized by different levels of transformation. HEp-2 cells surviving 48 h after EMCV infection showed lower nuclear ploidy, reduced nuclear area, fewer nucleoli and a higher percentage of euploid cells. There was a significant increase of nucleolar/nuclear DNA 6-24 h after EMCV infection. However, EMCV had markedly different effects on NIH 3T3 cells: there was a consistent increase in population ploidy, but the average number of nucleoli and the number of euploid cells in the population remained constant. The nucleolar/nuclear DNA ratio was almost unchanged. These different viral effects might be explained by the contrasting levels of differentiation of the cultured cell lines. The number of nucleoli does not depend on the amount of nuclear DNA in either viral-infected or intact cells but on the euploidy-to-aneuploidy ratio. The ratio of the sums of the nucleolar perimeters to the nuclear perimeter increases linearly with the number of nucleoli per nucleus in both intact and virus-infected cells. In both cell lines, the amount of DNA per nucleolus decreases as the number of nucleoli increases.     

Infant mortality in Armenia, 1992–2003

Health system reforms have been taken in Armenia during a time of dramatic economic and fiscal distress. It is important to assess trends in health indicators and ascertain if the changes in socio-economic systems affected the health status of infants as the most vulnerable part of the population. We find that infant mortality has fallen during the period c. 1992-2003 in spite of the difficult economic circumstances because of health-care procedures that were introduced. Particular attention is paid to the underreporting of infants' death cases in the state registration system as well as to estimating the role of different factors influencing infant mortality in Armenia.     

Investigation of interaction between enolase and phosphoglycerate mutase using molecular dynamics simulation

Two glycolytic enzymes, phosphoglycerate mutase (PGM) and enolase from Saccharomyces cerevisiae have been chosen to detect complex formation between active centers (a/c), using molecular dynamics simulation. Enzymes have been separated by 10 A distance and placed in a water box of size 173 x 173 x 173 A. Three different orientations where a/c of PGM and enolase were positioned toward each other have been used for investigation. The two initial 3-phosphoglycerate substrates at near active centers of initial structure of PGM have been replaced with final 2-phosphoglycerate products. 150mM of NaCl have been added to the system to observe binding activity in the near physiological conditions. Analysis of interaction energies and conformation changes for 3ns simulation indicates that PGM and enolase do show binding affinity between their near active regions. Moreover the similarity between final conformations of the first two orientations with the initial conformation of the third orientation suggests that complex formation between a/c of enzymes is not confined only by discussed orientations. Clear interaction of enolase with C-terminal tail of PGM has been recorded. These results suggest that substrate direct transfer mechanism may exist between enzymes.