Waterbirds and substrate quality of the Pichavaram wetlands,southern India

The water and mud characteristics of the six types of wetlands in Pichavaram were compared in order to determine whether the habitat of waterbird species was characterized by them. Waterbird species richness was most influenced by mud phosphorus levels. Variation in water pH was the principal factor that determined waterbird diversity. The water level mainly determined the density of waterbirds. Levels of pH and nitrites in the water also appeared to influence significant variations in waterbird diversity and density, respectively. Bottom substrate variables, viz. pH and phosphorus levels, were also significantly correlated with the density and richness of waterbirds, respectively. Water quality factors, viz. pH and nitrite and mud pH and phosphorus, were correlated with the abundance, while water depth was correlated with the accessibility of prey to the birds.     

Extraction of RNA from Ca-alginate-encapsulated yeast for transcriptional profiling

We have developed a method for preparing high-quality total RNA from Ca-alginate-encapsulated Saccharomyces cerevisiae that is suitable for microarray analysis. Encapsulated cells were harvested from immobilized cell reactors and flash-frozen in liquid nitrogen. Following low-temperature mechanical disruption, cells were freed from Ca-alginate by reverse ionotropic gelation and purified by centrifugation, and then total RNA was extracted using hot acid phenol. The yield and quality of the RNA were consistently high; the RNA was free of contaminating alginate, and in microarray analysis it performed as well as RNA isolated from planktonic cells.     

Growth optimization of an ectomycorrhizal fungus with respect to pH and temperature in vitro, using Design of Experiments

The effect of external factors like pH of the medium, temperature and incubation period on the growth of the ectomycorrhizal fungus, Pisolithus tinctorius was studied as a function of the total fungal biomass produced, extracellular protein content and residual pH of the medium. The effect of the three parameters on the three responses was found to be significant and interdependent. Therefore, an attempt was made to optimize the growth of the fungus under varying conditions of pH, temperature and incubation period using the Box-Behnken Design of Experiments which is a second order model involving Response Surface Methodology and a second order quadratic equation. With this design expert, the optimum conditions of the three parameters that favoured the maximum growth of the fungus in vitro were found. The experimental values corroborated with the predicted values got from the model with the correlation coefficients 0.9349 for biomass, 0.9913 for protein and 0.9959 for final pH.     

A genetically selected cyclic peptide inhibitor of BCL6 homodimerization

We report an inhibitor of the homodimeric protein-protein interaction of the BCL6 oncoprotein, identified from a genetically encoded SICLOPPS library of 3.2 million cyclic hexapeptides in combination with a bacterial reverse two-hybrid system. This cyclic peptide is shown to bind the BTB domain of BCL6, disrupts its homodimerization, and subsequent binding of the SMRT2 corepressor peptide.     

Marker-assisted improvement of bacterial blight resistance in parental lines of Pusa RH10, a superfine grain aromatic rice hybrid

Pusa RH10, the widely cultivated superfine grain aromatic rice hybrid, and its parental lines Pusa6B and PRR78 are susceptible to bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae. Pusa1460, a Basmati rice variety, was utilized as the donor for introgressing BB resistance genes xa13 and Xa21 into Pusa6B and PRR78 using a marker-assisted backcross breeding program. The markers RG136 and pTA248 linked to BB resistance genes xa13 and Xa21, respectively, were used for foreground selection. Seventy-four STMS markers polymorphic between Pusa6B and Pusa1460, and 54 STMS markers polymorphic between PRR78 and Pusa1460, were utilized for background selection to recover the recurrent parent genome ranging from 85.14 to 97.30% and 87.04 to 92.81% in the 10 best BC₂F₅ families of Pusa6B and PRR78, respectively. RM6100, an STMS marker linked to fertility restorer gene (Rf), was used for marker-assisted selection of Rf gene in an improved version of PRR78. The extent of donor segments in the improved version of Pusa6B was estimated to be <0.97 and <2.15 Mb in the genomic regions flanking xa13 and Xa21, respectively, whereas in improved PRR78, it was estimated to be <2.07 and <3.45 Mb in the corresponding genomic regions. Improved lines of Pusa6B and PRR78 showed yield advantages of up to 8.24 and 5.23%, respectively. The performance of the BB-resistant version of Pusa RH10 produced by intercrossing the improved parental lines was on a par with or superior to the original Pusa RH10.     

Synonymous codon usage in chloroplast genome of Coffea arabica

Synonymous codon usage of 53 protein coding genes in chloroplast genome of Coffea arabica was analyzed for the first time to find out the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons as chloroplast genomes are rich in AT. No difference in preference for preferred codons was observed in any of the two strands, viz., leading and lagging strands. Complex correlations between total base compositions (A, T, G, C, GC) and silent base contents (A₃, T₃, G₃, C₃, GC₃) revealed that compositional constraints played crucial role in shaping the codon usage pattern of C. arabica chloroplast genome. ENC Vs GC₃ plot grouped majority of the analyzed genes on or just below the left side of the expected GC₃ curve indicating the influence of base compositional constraints in regulating codon usage. But some of the genes lie distantly below the continuous curve confirmed the influence of some other factors on the codon usage across those genes. Influence of compositional constraints was further confirmed by correspondence analysis as axis 1 and 3 had significant correlations with silent base contents. Correlation of ENC with axis 1, 4 and CAI with 1, 2 prognosticated the minor influence of selection in nature but exact separation of highly and lowly expressed genes could not be seen. From the present study, we concluded that mutational pressure combined with weak selection influenced the pattern of synonymous codon usage across the genes in the chloroplast genomes of C. arabica.     

Conformational studies of proteoglycans: theoretical studies on the conformation of heparin.

Various models proposed for heparin have been examined by a stereochemical approach involving contact distance criteria and potential energy calculations. The present study suggests that the model favored by Atkins and coworkers [Biochem. J. (1973) 135 , 729–733 and (1974) 143 , 251–252] is not stereochemically satisfactory. An alternative model has been proposed with N-acetyl-D -glucosamine and one of the uronides in the ⁴C₁ conformation and the other uronide (probably sulfated) in the ¹C₄ conformation. The observed variations in the tetrasaccharide periodicities (16.5–17.3 Å) in different crystalline modifications of heparin have been attributed to possible changes in the rotational angles about the interunit glycosidic bonds rather than a change in the pyranose ring conformation. The proposed model is also independent of the observed variation in the relative composition of uronic acid residues in heparin. These conclusions are in disagreement with those of earlier workers.     

Expression and characterization of glycolipid-anchored B7-1 (CD80) from baculovirus-infected insect cells: protein transfer onto tumor cells.

Tumor cells can be modified to express immunostimulatory molecules such as B7-1 by protein transfer using purified glycosylphosphatidylinositol-anchored B7-1 (GPI-B7-1). In this study recombinant baculovirus encoding GPI-B7-1 (vBacB7-1(GPI)) was established to obtain large quantities of purified GPI-B7-1 to modify tumor cells by protein transfer. vBacB7-1(GPI)-infected insect cells showed high-level cell surface expression of GPI-B7-1 that was susceptible to PIPLC treatment. GPI-B7-1 expressed in insect cells (Bac-GPI-B7-1) mediated T cell proliferation, indicating that the GPI-B7-1 retains costimulatory activity. Moreover, Bac-GPI-B7-1 was completely solubilized in Triton X-100 at 4 degrees C compared to 22% solubilization of GPI-B7-1 expressed in CHOK1 cells, suggesting that GPI-anchored proteins expressed in insect cells may not be clustered into the detergent-insoluble fraction. SDS-PAGE analysis of Bac-GPI-B7-1 showed faster mobility (45 kDa) compared to GPI-B7-1 from CHOK1 (68 kDa) and this difference may be due to a difference in glycosylation. Cell binding assays showed that immunoaffinity-purified Bac-GPI-B7-1 retained its functional ability to bind CD28(+) cells. Moreover, when human tumor cells were incubated with this functionally active purified GPI-B7-1, an efficient transfer of B7-1 onto tumor cells was observed. These results demonstrate that GPI-B7-1 can be expressed in insect cells in a functionally active form and can be used to modify tumor cells for immunotherapeutic applications.     

Influence of low irradiance on chloroplast proteins and photosystem activities in rice cultivars

In six rice cultivars the relative amounts of 55, 26–28 and 15 kDa polypeptides were mostly lower in plants grown for 15 d under low irradiance than in plants grown under saturating irradiance. This decline in the polypeptides, especially in those related to light-harvesting chlorophyll proteins, was accompanied with a decrease in the whole chain electron transport and the photosystem 2 activity.