Genital tract sequestration of SIV following acute infection

We characterized the evolution of simian immunodeficiency virus (SIV) in the male genital tract by examining blood- and semen-associated virus from experimentally and sham vaccinated rhesus monkeys during primary infection. At the time of peak virus replication, SIV sequences were intermixed between the blood and semen supporting a scenario of high-level virus "spillover" into the male genital tract. However, at the time of virus set point, compartmentalization was apparent in 4 of 7 evaluated monkeys, likely as a consequence of restricted virus gene flow between anatomic compartments after the resolution of primary viremia. These findings suggest that SIV replication in the male genital tract evolves to compartmentalization after peak viremia resolves.     

Micropropagation of tea (Camellia sinensis (L.) O. Kuntze) using Thidiazuron

The effect of thidiazuron (TDZ) on the micropropagation of Camellia sinensis (China hybrid) was compared with that of benzylaminopurine (BAP) using nodal segments from in vitro raised seedlings. Extremely low concentrations of TDZ (1pM–100nM) alone were effective in inducing shoot bud proliferation and maintaining high rates of shoot multiplication on hormone-free media. On the other hand, higher concentrations of BAP (1–10M) and its continued presence were required to initiate and sustain shoot proliferation. While wider ranges of BAP combined favourably with auxins like NAA or IBA, only specific combinations of TDZ and NAA were effective for shoot proliferation. TDZ treated explants yielded healthy shoots, with sturdy leaves, even during the initial stages of growth, whereas, the effect of BAP was cumulative over subcultures in attaining a high proliferative rate.     

Primary Identification,Biochemical Characterization,and Immunologic Properties of the Allergenic Pollen Cyclophilin Cat r 1

Cyclophilin (Cyp) allergens are considered pan-allergens due to frequently reported cross-reactivity. In addition to well studied fungal Cyps, a number of plant Cyps were identified as allergens (e.g. Bet v 7 from birch pollen, Cat r 1 from periwinkle pollen). However, there are conflicting data regarding their antigenic/allergenic cross-reactivity, with no plant Cyp allergen structures available for comparison. Because amino acid residues are fairly conserved between plant and fungal Cyps, it is particularly interesting to check whether they can cross-react. Cat r 1 was identified by immunoblotting using allergic patients'' sera followed by N-terminal sequencing. Cat r 1 (∼91% sequence identity to Bet v 7) was cloned from a cDNA library and expressed in Escherichia coli. Recombinant Cat r 1 was utilized to confirm peptidyl-prolyl cis-trans-isomerase (PPIase) activity by a PPIase assay and the allergenic property by an IgE-specific immunoblotting and rat basophil leukemia cell (RBL-SX38) mediator release assay. Inhibition-ELISA showed cross-reactive binding of serum IgE from Cat r 1-allergic individuals to fungal allergenic Cyps Asp f 11 and Mala s 6. The molecular structure of Cat r 1 was determined by NMR spectroscopy. The antigenic surface was examined in relation to its plant, animal, and fungal homologues. The structure revealed a typical cyclophilin fold consisting of a compact β-barrel made up of seven anti-parallel β-strands along with two surrounding α-helices. This is the first structure of an allergenic plant Cyp revealing high conservation of the antigenic surface particularly near the PPIase active site, which supports the pronounced cross-reactivity among Cyps from various sources.     

Algal Biomass as Potential Biosorbent for Reduction of Organic Load in Gray Water and Subsequent Reuse: Effect on Seed Germination and Enzyme Activity

Biosorptive treatment using algal biomass of Rhizoclonium riparium was proposed for higher-loading gray water for its effective utilization. A batch sorption study was conducted using composite wastewater having a wide range of initial chemical oxygen demand (COD) values (2400–44,800 mg/L). The study showed an optimum dose of 5 g/L of biosorbent resulted in 96% reduction of COD for wastewater with an initial COD of 10,500 mg/L. The equilibrium isotherm data at different temperatures were fitted to linear and nonlinear isotherms. Biosorption kinetics was studied by various kinetic models. Chemical composition and surface morphology of the biosorbent were characterized by infrared, x-ray diffraction, and scanning electron microscopy techniques before and after biosorption. Applicability of the biosorbent-treated wastewater in agricultural uses was explored by studying the effect of untreated and treated wastewater on the germination of two seeds, i.e., Vigna radiata and Lens esculenta, and subsequently the activity of peroxidase (POD) enzymes were studied to understand the toxicity in plants. The study revealed that compared with seeds treated with different dilutions of untreated wastewater, germination (%) was significantly higher for biosorbent-treated wastewater, with a reduced level of POD activity, indicating positive response of the seeds towards the biosorptive treatment.     

EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes

Background

The genome of the pico-eukaryotic (bacterial-sized) prasinophyte green alga Ostreococcus lucimarinus has one of the highest gene densities known in eukaryotes, yet it contains many introns. Phylogenetic studies suggest this unusually compact genome (13.2 Mb) is an evolutionarily derived state among prasinophytes. The presence of introns in the highly reduced O. lucimarinus genome appears to be in opposition to simple explanations of genome evolution based on unidirectional tendencies, either neutral or selective. Therefore, patterns of intron retention in this species can potentially provide insights into the forces governing intron evolution.

Methodology/Principal Findings

Here we studied intron features and levels of expression in O. lucimarinus using expressed sequence tags (ESTs) to annotate the current genome assembly. ESTs were assembled into unigene clusters that were mapped back to the O. lucimarinus Build 2.0 assembly using BLAST and the level of gene expression was inferred from the number of ESTs in each cluster. We find a positive correlation between expression levels and both intron number (R = +0.0893, p = <0.0005) and intron density (number of introns/kb of CDS; R = +0.0753, p = <0.005).

Conclusions/Significance

In a species with a genome that has been recently subjected to a great reduction of non-coding DNA, these results imply the existence of selective/functional roles for introns that are principally detectable in highly expressed genes. In these cases, introns are likely maintained by balancing the selective forces favoring their maintenance with other mutational and/or selective forces acting on genome size.     

Polymorphism and natural selection of antigen B1 of <Emphasis Type="Italic">Echinococcus granulosus</Emphasis> isolated from different host assemblages in India

Antigen B (AgB) is an excretory–secretory product of larval stage of Echinococcus granulosus. This antigen is abundantly secreted by larval stage of the worm. AgB is encoded by a multigene family and is suggested to be involved in evasion of host immune system. During the present study a total of 110 animal isolates of E. granulosus has been screened by mutation scan screening. A total of 14 conformers were detected on the basis of single strand banding profile of 129 bp fragment of AgB1 subunit. Analysis of sequence information of 14 conformers could cluster the isolates into two different group viz. buffalo–cattle and sheep–goat cluster. Conceptual amino acid sequence information of two clusters could be differentiated in terms of MHCII binding propensity of agretope and B-cell epitope region. This type of analysis of clustering of animal isolates on the basis of binding propensity towards different MHC antigens and B-cell linear epitope is the example of its own kind. Positive Tajima’s D value indicated that, AgB1 is under balancing selection pressure which might be considered as heterogeneous selection pressure exerted by the host.     

Enhanced Biodegradation of Anthracene by Bacillus Cereus Strain JMG-01 Isolated from Hydrocarbon Contaminated Soils

The present study displays the biodegradation capacities of native bacteria toward polycyclic aromatic hydrocarbons with particular emphasis to anthracene. A total of 23 bacterial strains were isolated from hydrocarbon-contaminated sites of Guwahati city, using anthracene as the carbon source. Among all these isolates, one Gram-positive strain (JMG-01) was selected as an efficient anthracene degrader, based on its maximum growth ability in anthracene enriched medium (100 ppm–700 ppm). At 500 ppm concentration, strain JMG-01 showed the maximum growth rate with 98% of anthracene degradation within 21 days of observation. The strain also demonstrated its potentiality by utilizing naphthalene and higher molecular hydrocarbons like pyrene, and benzo(a)pyrene at 500 ppm. The morphological, biochemical and molecular characterization identified the strain as Bacillus cereus. Surface morphology of the biomass, captured by Atomic Force Microscope, showed a distinctive modification, during the process of degradation. Study revealed that the effect of hydrocarbon exhibited the alteration, which concurrently enhanced the metabolic activity. Further, Gas chromatography-mass spectrometer analysis elucidates the possible metabolic pathway of anthracene degradation, depending on the intermediate metabolites produced. The finding thus suggests the essence of Bacillus cereus strain JMG-01 in enhanced anthracene degradation along the utilization of other hydrocarbons.     

Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium

Long-chain n-3 polyunsaturated fatty acids (PUFAs) can derive from diet or from α-linolenic acid (ALA) by elongation and desaturation. We investigated the association of common genetic variation with plasma phospholipid levels of the four major n-3 PUFAs by performing genome-wide association studies in five population-based cohorts comprising 8,866 subjects of European ancestry. Minor alleles of SNPs in FADS1 and FADS2 (desaturases) were associated with higher levels of ALA (p = 3×10⁻⁶⁴) and lower levels of eicosapentaenoic acid (EPA, p = 5×10⁻⁵⁸) and docosapentaenoic acid (DPA, p = 4×10⁻¹⁵⁴). Minor alleles of SNPs in ELOVL2 (elongase) were associated with higher EPA (p = 2×10⁻¹²) and DPA (p = 1×10⁻⁴³) and lower docosahexaenoic acid (DHA, p = 1×10⁻¹⁵). In addition to genes in the n-3 pathway, we identified a novel association of DPA with several SNPs in GCKR (glucokinase regulator, p = 1×10⁻⁸). We observed a weaker association between ALA and EPA among carriers of the minor allele of a representative SNP in FADS2 (rs1535), suggesting a lower rate of ALA-to-EPA conversion in these subjects. In samples of African, Chinese, and Hispanic ancestry, associations of n-3 PUFAs were similar with a representative SNP in FADS1 but less consistent with a representative SNP in ELOVL2. Our findings show that common variation in n-3 metabolic pathway genes and in GCKR influences plasma phospholipid levels of n-3 PUFAs in populations of European ancestry and, for FADS1, in other ancestries.     

Multiple Shoot Regeneration from Immature Embryo Explants of Papaya

A simple and rapid method for multiple shoot formation in vitro from immature embryo axis explants of Carica papaya L. cvs. Honey Dew, Washington and Co2 is described. Multiple shoot regeneration was achieved by culture of the explants on modified Murashige and Skoog (MS) medium supplemented either with thidiazuron (TDZ; 0.45–22.7 μM) or a combination of benzylaminopurine (BAP; 0.2 – 8.84 μM) and naphthalene acetic acid (NAA; 0.5 – 2.64 μM). Highest frequency of shoot regeneration occurred on medium supplemented either with 2.25 μM TDZ or a combination of BAP (4.4 μM) and NAA (0.5 μM). Composition of the basal media influenced the frequency of multiple shoot initiation. Stunted shoots regenerated at 4.5 μM and higher concentrations of TDZ. Such shoots could, however, be elongated by transfer to medium containing 5.7 μM GA₃. Rooting of the regenerated shoots was achieved in presence of indolebutyric acid (IBA; 4.92 – 19.68 μM), however, least response was in presence of 14.7 μM IBA. Rooted plants were hardened and transferred to pots. This revised version was published online in July 2006 with corrections to the Cover Date.