Intrapatient diversity and its correlation with viral setpoint in human immunodeficiency virus type 1 CRF02_A/G-IbNG infection

The human immunodeficiency virus type 1 (HIV-1) viral setpoint during the disease-free interval has been strongly associated with future risk of disease progression. An awareness of the correlation between viral setpoint and HIV-1 genetic evolution over time is important in the understanding of viral dynamics and infection. We examined genetic diversity in HIV-1 CRF02_A/G-IbNG-infected seroincident women in Dakar, Senegal; determined whether a viral setpoint kinetic pattern existed for CRF02_A/G-IbNG during the disease-free interval; and correlated viral load level and diversity. Samples were drawn during the disease-free interval from consenting CRF02_A/G-IbNG-infected, antiretroviral therapy-na?ve female commercial sex workers in Dakar, Senegal. Based on sequential plasma RNA values, low and high viral setpoint groups were established. Intrapatient diversity and divergence over time was determined from earlier and later time point DNA samples from each person. Most individuals followed the viral setpoint paradigm. For each 1/-/log(10) copy/ml of plasma increase in viral load, intrapatient diversity increased by 1.4% (P = 0.028). A greater diversification rate was observed in the high viral setpoint group than in the low viral setpoint group (P = 0.01). Greater nucleotide (P = 0.015) and amino acid (P = 0.048) divergences and a greater nucleotide divergence rate (P = 0.03) were found in the high viral setpoint group. There was no difference between the groups in the ratio of the number of nonsynonymous substitutions per nonsynonymous site to the number of synonymous substitutions per synonymous site. The greater intrapatient diversity, divergence, and diversification rates observed in the high viral setpoint group supports the notion that diversity is driven by cycles of viral replication resulting in accumulated mutations. Recognizing diversity potential based on viral load levels in individuals may inform the design of vaccines and therapies.     

Molecular mapping of QTLs for Karnal bunt resistance in two recombinant inbred populations of bread wheat

Karnal bunt (KB) of wheat, caused by the fungus Tilletia indica, is a challenge to the grain industry, owing not to direct yield loss but to quarantine regulations that may restrict international movement of affected grain. Several different sources of resistance to KB have been reported. Understanding the genetics of resistance will facilitate the introgression of resistance into new wheat cultivars. The objectives of this study were to identify quantitative trait loci (QTLs) associated with KB resistance and to identify DNA markers in two recombinant inbred line populations derived from crosses of the susceptible cultivar WH542 with resistant lines HD29 and W485. Populations were evaluated for resistance against the KB pathogen for 3 years at Punjab Agricultural University, Ludhiana, India. Two new QTLs (Qkb.ksu-5BL.1 and Qkb.ksu-6BS.1) with resistance alleles from HD29 were identified and mapped in the intervals Xgdm116–Xwmc235 on chromosome 5B (deletion bin 5BL9-0.76-0.79) and Xwmc105–Xgwm88 on chromosome 6B (C-6BS5-0.76). They explained up to 19 and 13% of phenotypic variance, respectively. Another QTL (Qkb.ksu-4BL.1) with a resistance allele from W485 mapped in the interval Xgwm6–Xwmc349 on chromosome 4B (4BL5-0.86-1.00) and explained up to 15% of phenotypic variance. Qkb.ksu-6BS.1 showed pairwise interactions with loci on chromosomes 3B and 6A. Markers suitable for marker-assisted selection are available for all three QTLs. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Ion channels and transporters in cancer. 6. Vascularizing the tumor: TRP channels as molecular targets

Tumor vascularization is a critical process that determines tumor growth and metastasis. In the last decade new experimental evidence obtained from in vitro and in vivo studies have challenged the classical angiogenesis model forcing us to consider new scenarios for tumor neovascularization. In particular, the genetic stability of tumor-derived endothelial cells (TECs) has been recently questioned in several studies, which show that TECs, as well as pericytes, differ significantly from their normal counterparts at genetic and functional levels. In addition to such an epigenetic action of tumor microenvironment on endothelial cells (ECs) commitment, the distinct characteristics of TECs could be due to differences in their origin compared with preexisting differentiated ECs. Intracellular Ca(2+) signals are involved at different critical phases in the regulation of the complex process of angiogenesis and tumor progression. These signals are generated by a wide variety of intrinsic and extrinsic factors. Several key components of Ca(2+) signaling including Ca(2+) channels in the plasma membrane, endoplasmic reticulum, calcium pumps, and mitochondria contribute to the generation, amplitude, and frequency of these Ca(2+) change. In particular, several members of the transient receptor potential (TRP) family of calcium-permeable channels have profound effects on the function of ECs. Because of its multifaceted role in the control of cell function, proliferation, and motility, TRP channels have been suggested as a potential molecular target for control of tumor neovascularization. Since plasma membrane Ca(2+) channels are easily and directly accessible via the bloodstream, they are potential targets for a number of pharmacological and antibody-targeted therapeutic strategies, with specificity being the main limitation. In this review we discuss recent advances in understanding the role of Ca(2+) channels, with specific reference to TRP channels, in tumor vascularization process.     

TRPC3 controls agonist-stimulated intracellular Ca2+ release by mediating the interaction between inositol 1,4,5-trisphosphate receptor and RACK1

Activation of TRPC3 channels is concurrent with inositol 1,4,5-trisphosphate (IP(3)) receptor (IP(3)R)-mediated intracellular Ca(2+) release and associated with phosphatidylinositol 4,5-bisphosphate hydrolysis and recruitment to the plasma membrane. Here we report that interaction of TRPC3 with receptor for activated C-kinase-1 (RACK1) not only determines plasma membrane localization of the channel but also the interaction of IP(3)R with RACK1 and IP(3)-dependent intracellular Ca(2+) release. We show that TRPC3 interacts with RACK1 via N-terminal residues Glu-232, Asp-233, Glu-240, and Glu-244. Carbachol (CCh) stimulation of HEK293 cells expressing wild type TRPC3 induced recruitment of a ternary TRPC3-RACK1-IP(3)R complex and increased surface expression of TRPC3 and Ca(2+) entry. Mutation of the putative RACK1 binding sequence in TRPC3 disrupted plasma membrane localization of the channel. CCh-stimulated recruitment of TRPC3-RACK1-IP(3)R complex as well as increased surface expression of TRPC3 and receptor-operated Ca(2+) entry were also attenuated. Importantly, CCh-induced intracellular Ca(2+) release was significantly reduced as was RACK1-IP(3)R association without any change in thapsigargin-stimulated Ca(2+) release and entry. Knockdown of endogenous TRPC3 also decreased RACK1-IP(3)R association and decreased CCh-stimulated Ca(2+) entry. Furthermore, an oscillatory pattern of CCh-stimulated intracellular Ca(2+) release was seen in these cells compared with the more sustained pattern seen in control cells. Similar oscillatory pattern of Ca(2+) release was seen after CCh stimulation of cells expressing the TRPC3 mutant. Together these data demonstrate a novel role for TRPC3 in regulation of IP(3)R function. We suggest TRPC3 controls agonist-stimulated intracellular Ca(2+) release by mediating interaction between IP(3)R and RACK1.     

Analysis of Aβ (1-40) and Aβ (1-42) monomer and fibrils by capillary electrophoresis

A method based on capillary electrophoresis (CE) with UV absorbance detection is presented to characterize synthetic amyloid beta (Aβ) peptide preparations at different aggregation states. Aggregation of Aβ (1-40) and Aβ (1-42) is closely linked to Alzheimer's disease (AD), and studying how Aβ peptides self-assemble to form aggregates is the focus of intense research. Developing methods capable of identifying, characterizing and quantifying a wide range of Aβ species from monomers to fully formed fibrils is critical for AD research and is a major analytical challenge. Monomer and fibril samples of Aβ (1-40) and Aβ (1-42) were prepared and characterized for this study. The monomer-equivalent concentration for each sample was determined by HPLC-UV, and aggregate formation was confirmed and characterized by transmission electron microscopy. The same samples were studied using CE with UV absorbance detection. Analysis by mass spectrometry of collected CE fractions was used to confirm the presence of Aβ for some CE-UV peaks. The CE-UV method reported here clearly indicates that monomeric and aggregated Aβ were electrophoretically separated, and substantial differences in the electrophoretic profiles between samples of Aβ (1-40) and Aβ (1-42) were observed. This CE-UV method can differentiate between Aβ monomer, oligomeric intermediates, and mature fibrils.     

Comparison of the immunological properties of mammalian (rodent), bird,fish, amphibian (toad), and invertebrate (crab) metallothioneins

Summary Immunoassays such as rocket immunoelectrophoresis, western dot blot hybridization, and competitive ELISA analysis were used to estimate and compare homology among fishes (several species), crab, toad, chicken and rodent metallothioneins. The relative abundance of tissue-specific metallothionein in catfish was highest in liver followed by kidney and pancreas like mammalian systems. Immunologically, considerable homology exists among fish metallothioneins, although the extent of homology differs to some extent. No homology was found between fish or chicken metallothioneins. The amphibian (toad) and invertebrate (crab) metallothioneins showed only partial homology with fish metallothioneins in antigenic determinants.Abbreviations MT Metallothionein - PBS Phosphate Buffered Saline - SDS Sodium Dodecyl Sulfate - PAGE Polyacrylamide Gel Electrophoresis - ELISA Enzyme Linked Immunosorbent Assay - ME 2-Mercaptoethanol - BSA Bovine Serum Albumim     

Biocontrol potential of two novel grapevine associated Bacillus strains for management of anthracnose disease caused by Colletotrichum gloeosporioides

A study was conducted to identify bacterial antagonists for biological control of anthracnose which is one of the economically important diseases of grapes. In India, it is caused by Colletotrichum gloeosporioides. Two hundred and ninety-three bacteria were isolated from the grape ecosystem of 43 spatially distant vineyards in peninsular India. Of these, 25 bacteria substantially inhibited the radial growth of C. gloeosporioides in in vitro studies and 18 bacteria significantly reduced infections in vivo. Of these 18 bacteria, 5 and 3 bacteria also significantly reduced percent disease index (PDI) of downy and powdery mildew diseases, respectively. These bacteria were labelled as strains, DR-38, DR-39, TL-171, DRo-198, TS-204, TS-205, and DR-219, and were identified as Bacillus species based on morphological and molecular characterisation. Aqueous suspensions of all these strains applied as foliar sprays at 1×10⁸ cfu/ml on field grown vines significantly lowered the PDI and the AUDPC (area under disease progress curve) of anthracnose when compared with the untreated control, except DRo-198. Strains TS-204 and TL-171 recorded lower PDIs and AUDPC when compared with the other five strains, and TS-204 could effectively suppress ripe rot of berries, too, in vivo. Strains TS-204 and TL-171 are identified for biocontrol of anthracnose in grapes.     

Enrichment, isolation and characterization of pentachlorophenol degrading bacterium Acinetobacter sp. ISTPCP-3 from effluent discharge site

Three pentachlorophenol (PCP) degrading bacterial strains were isolated from sediment core of pulp and paper mill effluent discharge site. The strains were continuously enriched in mineral salts medium supplemented with PCP as sole source of carbon and energy. One of the acclimated strains with relatively high PCP degradation capability was selected and characterized in this study. Based on morphology, biochemical tests, 16S rDNA sequence analysis and phylogenetic characteristics, the strains showed greatest similarity with Acinetobacter spp. The strain was identified as Acinetobacter sp. ISTPCP-3. The physiological characteristics and optimum growth conditions of the bacterial strain were investigated. The results of optimum growth temperature revealed that it was a mesophile. The optimum growth temperature for the strain was 30°C. The preferential initial pH for the strain was ranging at 6.5–7.5, the optimum pH was 7. The bacterium was able to tolerate and degrade PCP up to a concentration of 200 mg/l. Increase in PCP concentration had a negative effect on biodegradation rate and PCP concentration above 250 mg/l was inhibitory to its growth. Acinetobacter sp. ISTPCP-3 was able to utilize PCP through an oxidative route with ortho ring-cleavage with the formation of 2,3,5,6-tetrachlorohydroquinone and 2-chloro-1,4-benzenediol, identified using gas chromatograph–mass spectrometric (GC–MS) analysis. The degradation pathway followed by isolated bacterium is different from previously characterized pathway.