Association analysis of TNFRSF1B polymorphisms with type 2 diabetes and its related traits in North India

Inflammation plays a crucial role in the pathogenesis of type 2 diabetes and various lines of evidences suggest an important contribution of type 2 receptor for TNFα (TNFR2), a mediator of inflammatory responses. Though genetic association of TNFRSF1B (encoding TNFR2) polymorphisms have been investigated in various studies, their involvement is not clear because of inconsistent findings. Because of high susceptibility of Indian population to type 2 diabetes and its complications, we evaluated the association of TNFRSF1B polymorphisms-rs1061622 (M196R; exon6) and rs3397 (3′UTR) and (CA) _n repeat (intron 4) in 1,852 subjects including 1,040 cases and 812 controls with type 2 diabetes and its associated peripheral neuropathy and hypertension in North Indians of Indo-European ethnicity. The allelic and genotypic distributions of these polymorphisms were comparable among healthy control vs. type 2 diabetes, peripheral neuropathy vs. non-neuropathy and hypertensive vs. normotensive groups. (CA) _n polymorphism has been shown to be associated with diabetic neuropathy in Caucasians, however, this could not be replicated in our study (P = 0.27). None of the polymorphisms were found to influence the 14 anthropometric and biochemical traits related to type 2 diabetes studied here. Thus, we conclude that TNFRSF1B is not a major contributing factor to the genetic risk of type 2 diabetes, its associated peripheral neuropathy and hypertension and related metabolic traits in North Indians.     

Geometry dependent two-dimensional heteronuclear multiplet effects in paramagnetic proteins

We report experimental observation and numerical simulation of a two-dimensional multiplet effect in the heteronuclear correlation spectrum of a paramagnetic protein that depends on molecular geometry. This effect arises as a consequence of cross-correlated relaxation involving the Curie spin relaxation and internuclear dipolar relaxation mechanisms. It also manifests itself in resolution and sensitivity improvement in transverse relaxation optimised spectroscopy (TROSY) kind of experiments. Characteristic multiplet patterns in heteronuclear coupled two-dimensional NMR spectra encode directional information for the heteronuclear bond with respect to the paramagnetic center. These patterns, which are simulated here using Redfield's relaxation theory, can be used to obtain a new type of geometry restriction for structure determination and refinement of paramagnetic macromolecular systems.     

Molecular Characterization of Primary Gene Pool of Chickpea Based on ISSR Markers

Genetic diversity and relationships within and among members of the primary gene pool of chickpea, including 38 accessions of Cicer arietinum, six of C. reticulatum,, and four of C. echinospermum, were investigated using 31 ISSR markers. The study revealed moderate diversity, detecting 141 fragments, of which 79 (56%) were polymorphic. Averages were 0.125 for polymorphic information content, 0.350 for marker index, and 0.715 for resolving power. The UPGMA dendrogram and the principal coordinate analysis revealed a clear differentiation between wild and cultivated accessions. The clustering pattern did not strictly follow the grouping of accessions by geographic origin but was in good agreement with the pedigree data and the seed type. The study demonstrates that ISSRs provide promising marker tools in revealing genetic diversity and relationships in chickpea and can contribute to efficient identification, conservation, and utilization of germplasm for plant improvement through conventional as well as molecular breeding approaches.     

Phosphorylation of p36 in vitro by protein kinase C

The 36kDa subunit of protein I (p36) is a major substrate of several tyrosine protein kinases. Here we demonstrate that protein kinase C catalyzes the incorporation of 1.7 moles of phosphate per mole of protein I. Phosphorylation is absolutely dependent on the presence of both calcium and phospholipid, and is specific for serine and threonine residues. Phosphorylation of protein I by the c-AMP dependent protein kinase, phosphorylase kinase, casein kinase I, and casein kinase II was not observed. The in vivo significance of protein kinase C dependent phosphorylation of p36 is discussed.     

Effect of copy number on the expression levels of hepatitis B surface antigen in the methylotrophic yeast Pichia pastoris

High-level expression and efficient assembly of hepatitis B surface Antigen (HBsAg) has been reported in Pichia pastoris by integrating a single copy of the HBsAg gene under control of the AOX1 promoter. To fully utilize the expression potential of the P. pastoris expression system, we investigated the influence of gene copy number on the expression of HBsAg in this yeast. A panel of Pichia clones carrying progressively increasing copies of the heterologous gene expression cassette was created using an in vitro multimerization approach. Using this strategy, constructs containing up to a maximum of eight direct repeats of the HBsAg-expressing cassettes could be created. These expression cassettes were targeted for integration into the genome of the host strain GS115 with simultaneous elimination of the resident AOX1 gene. Deletion of the AOX1 gene was intended to create Mut(s) (methanol utilization slow) transformants that are known to have an increased ability to generate HBsAg in particulate form. A systematic investigation of the resultant clones demonstrated that the increase in copy number results in a proportional elevation in the steady-state levels of the HBsAg-specific mRNA, which in turn is closely paralleled by a corresponding increase in the total levels of the HBsAg protein. Virtually all the recombinant protein in the soluble fraction was present in the particulate form based on particle-specific ELISA and sedimentation behavior. Further, our studies also revealed the continued physical and functional integrity of the HBsAg-expressing cassettes during the course of an extended induction phase spanning 6 days.     

Recognition of immunologically important antigens in Bacteroides fragilis infection —an experimental study in mice

When the outer membrane proteins (OMP) of Bacteroides fragilis ATCC 23745 grown under seven different culture conditions were analysed by SDS-PAGE, five of the seven preparations showed similar protein profiles. When the three different OMP preparations were subsequently analysed by Western blotting, that from B. fragilis grown in brain heart infusion broth supplemented with haemin and menadione alone showed more immunodominant bands than those grown with additional cholesterol and methionine or cholesterol and cysteine. Only the former showed immunodominant proteins around 45.6 kDa and 66.2 kDa throughout the course of infection in mice. A protein corresponding to 97.4 kDa was found under all culture conditions. The results emphasise the importance of culture conditions in the expression of immunologically reactive antigens and also the possible use of such antigens in the serodiagnosis of B. fragilis infection.T. Khanna is and D. Panigrahi was with the Department of Medical Microbiology and N.K. Ganguly and S. Majumdar are with the Department of Experimental Medicine, at the Postgraduate Institute of Medical Education and Research, Chandigarh, India. D. Panigrahi is now with Kuwait University, Faculty of Alled Health Science, P.O. Box 31470 Sulaibikhat, 90805, Kuwait     

Differential prioritization between relevance and redundancy in correlation-based feature selection techniques for multiclass gene expression data

Background  

Due to the large number of genes in a typical microarray dataset, feature selection looks set to play an important role in reducing noise and computational cost in gene expression-based tissue classification while improving accuracy at the same time. Surprisingly, this does not appear to be the case for all multiclass microarray datasets. The reason is that many feature selection techniques applied on microarray datasets are either rank-based and hence do not take into account correlations between genes, or are wrapper-based, which require high computational cost, and often yield difficult-to-reproduce results. In studies where correlations between genes are considered, attempts to establish the merit of the proposed techniques are hampered by evaluation procedures which are less than meticulous, resulting in overly optimistic estimates of accuracy.     

Expression and purification of Dengue virus type 2 envelope protein as a fusion with hepatitis B surface antigen in Pichia pastoris

The methylotrophic yeast, Pichia pastoris, has been used as a host to express the envelope protein (Den2E) of dengue type 2 virus (NGC strain) as a chimera with hepatitis B surface antigen (HBsAg): a protein known to self assemble into virus-like particles (VLPs) and to be efficiently expressed in P. pastoris. The Den2E gene used in this study is a truncated version encoding the first 395 amino acid (aa) residues of the mature Den2E protein; the HBsAg gene encodes the full length 226 aa HBsAg protein. Two in-frame gene fusions were constructed for intracellular expression in P. pastoris. The first one contains the HBsAg gene as the 5' partner and the Den2E gene as the 3'partner (HBsAg-Den2E). In the second one, the relative positions of the two partners of the gene fusion were reversed to create the hybrid Den2E-HBsAg gene. These fusion genes were integrated into the genome of P. pastoris under the control of the methanol-inducible alcohol oxidase (AOX1) promoter. Of the two fusions, the Den2E-HBsAg gene was expressed at higher levels in P. pastoris based on Northern analysis. The hybrid protein ( approximately 68 kDa) expressed by this clone was purified to near homogeneity using a combination of acid precipitation, hydrophobic interaction, and immunoaffinity chromatographic steps. Final purification achieved was approximately 1400-fold with a yield of approximately 26%. The chimeric protein was found to possess the ability to assemble into high molecular weight aggregates (akin to HBsAg particles). The recombinant fusion protein eluted close to the void volume of a Sepharose CL-4B column indicating its macromolecular nature. On a CsCl density gradient the recombinant fusion protein sedimented to a position very similar to that of HBsAg VLPs. The hybrid protein is recognized by the two neutralizing monoclonals against the two components of the chimeric protein.     

hSK4/hIK1, a calmodulin-binding KCa channel in human T lymphocytes. Roles in proliferation and volume regulation.

Human T lymphocytes express a Ca2+-activated K+ current (IK), whose roles and regulation are poorly understood. We amplified hSK4 cDNA from human T lymphoblasts, and we showed that its biophysical and pharmacological properties when stably expressed in Chinese hamster ovary cells were essentially identical to the native IK current. In activated lymphoblasts, hSK4 mRNA increased 14.6-fold (Kv1.3 mRNA increased 1.3-fold), with functional consequences. Proliferation was inhibited when Kv1.3 and IK were blocked in naive T cells, but IK block alone inhibited re-stimulated lymphoblasts. IK and Kv1.3 were involved in volume regulation, but IK was more important, particularly in lymphoblasts. hSK4 lacks known Ca2+-binding sites; however, we mapped a Ca2+-dependent calmodulin (CaM)-binding site to the proximal C terminus (Ct1) of hSK4. Full-length hSK4 produced a highly negative membrane potential (Vm) in Chinese hamster ovary cells, whereas the channels did not function when either Ct1 or the distal C terminus was deleted (Vm approximately 0 mV). Native IK (but not expressed hSK4) current was inhibited by CaM and CaM kinase antagonists at physiological Vm values, suggesting modulation by an accessory molecule in native cells. Our results provide evidence for increased roles for IK/hSK4 in activated T cell functions; thus hSK4 may be a promising therapeutic target for disorders involving the secondary immune response.     

Regulation and manipulation of the gene clusters encoding type-I PKSs

Modular polyketide synthases are large, multifunctional enzyme complexes that are involved in the biosynthesis of important polyketides. Recent studies have revolutionized our understanding of the linear organization of polyketide-synthase-gene clusters. They have provided crucial information on the initiation, elongation and termination of polyketide chains, and thus a rational basis for the generation of novel compounds. Combinatorial libraries have helped this field to move from a random approach to a more empirical phase. The large number of diverse analogs of antibiotics that are presently produced demonstrate the enormous potential of combinatorial biosynthesis.