Farnesyl pyrophosphate is a novel transcriptional activator for a subset of nuclear hormone receptors

In silico docking of a chemical library with the ligand-binding domain of thyroid hormone nuclear receptor-beta (TRbeta) suggested that farnesyl pyrophosphate (FPP), a key intermediate in cholesterol synthesis and protein farnesylation, might function as an agonist. Surprisingly, addition of FPP to cells activated TR as well as the classical steroid hormone receptors but not peroxisome proliferative-activating receptors, farnesoid X receptor, liver X receptor, or several orphan nuclear receptors the ligands of which are unknown. FPP enhanced receptor-coactivator binding in vitro and in vivo, and elevation of FPP levels in cells by squalene synthetase or farnesyl transferase inhibitors leads to activation. The FPP effect was blocked by selective receptor antagonists, and in silico docking with 143 nuclear receptor ligand-binding domain structures revealed that FPP only docked with the agonist conformation of those receptors activated by FPP. Our results suggest that certain nuclear receptors maintain a common structural feature that may reflect an action of FPP on an ancient nuclear receptor or that FPP could function as a ligand for one of the many orphan nuclear receptors the ligands of which have not yet been identified. This finding also has potential interesting implications that may, in part, explain the pleotropic effects of statins as well as certain actions of farnesylation inhibitors in cells.     

Siglec-7 undergoes a major conformational change when complexed with the alpha(2,8)-disialylganglioside GT1b

The siglecs are a group of mammalian sialic acid binding receptors expressed predominantly in the immune system. The CD33-related siglecs show complex recognition patterns for sialylated glycans. Siglec-7 shows a preference for alpha(2,8)-disialylated ligands and provides a structural template for studying the key interactions that drive this selectivity. We have co-crystallized Siglec-7 with a synthetic oligosaccharide corresponding to the alpha(2,8)-disialylated ganglioside GT1b. The crystal structure of the complex offers a first glimpse into how this important family of lectins binds the structurally diverse gangliosides. The structure reveals that the C-C' loop, a region implicated in previous studies as driving siglec specificity, undergoes a dramatic conformational shift, allowing it to interact with the underlying neutral glycan core of the ganglioside. The structural data in combination with mutagenesis studies show that binding of the ganglioside is driven by extensive hydrophobic contacts together with key polar interactions and that the binding site structure is complementary to preferred solution conformations of GT1b.     

New species of Phaeoramularia, Pseudocercospora and Stenella from Western Ghats of India

Four new species of the hyphomycete genera Phaeoramularia viz. Ph. caesalpinae, Pseudocercospora viz., Ps. tiliacearum, Stenella, viz. S. argyreiae and S. grewiae occurring on Caesalpinia bonducella Fleming (Caesalpiniaceae), Grewia sp. (Tiliaceae), Argyrea sp. Lour (Convolvulaceae) and Grewia sp. L. (Tiliaceae), respectively are described and illustrated here. All these fungi were collected from Western Ghats of India.     

Moving from Rabies Research to Rabies Control: Lessons from India

BACKGROUND: Despite the availability of effective interventions and public recognition of the severity of the problem, rabies continues to suffer neglect by programme planners in India and other low and middle income countries. We investigate whether this state of 'policy impasse' is due to, at least in part, the research community not catering to the information needs of the policy makers. METHODS #ENTITYSTARTX00026; FINDINGS: Our objective was to review the research output on rabies from India and examine its alignment with national policy priorities. A systematic literature review of all rabies research articles published from India between 2001 and 2011 was conducted. The distribution of conducted research was compared to the findings of an earlier research prioritization exercise. It was found that a total of 93 research articles were published from India since 2001, out of which 61% consisted of laboratory based studies focussing on rabies virus. Animals were the least studied group, comprising only 8% of the research output. One third of the articles were published in three journals focussing on vaccines and infectious disease epidemiology and the top 4 institutions (2 each from the animal and human health sectors) collectively produced 49% of the national research output. Biomedical research related to development of new interventions dominated the total output as opposed to the identified priority domains of socio-politic-economic research, basic epidemiological research and research to improve existing interventions. CONCLUSION: The paper highlights the gaps between rabies research and policy needs, and makes the case for developing a strategic research agenda that focusses on rabies control as an expected outcome.     

Design and synthesis of substituted pyridine derivatives as HIF-1alpha prolyl hydroxylase inhibitors

Structure-guided de novo drug design led to the identification of a novel series of substituted pyridine derivatives as HIF-1alpha prolyl hydroxylase inhibitors. Pyridine carboxyamide derivatives bearing a substituted aryl group at the 5-position of the pyridine ring show appreciable activity, while constraining the side chain by placing a pyrazole carboxylic acid generated a potent lead series with consistent activity against EGLN-1.     

Development of novel economical methodologies for zymographic analysis of purified xylano–pectinolytic enzymes using agrowaste-based substrates

In this study, zymographic analysis for xylanase and pectinase enzymes has been carried out using agrowaste residues, wheat bran and citrus peel as well as their extracts. Isozymic forms of xylanase as well as pectinase enzyme displayed comparable zymographic bands onto agar petriplates containing either commercial substrates (xylan and pectin), agrowaste-based substrates (wheat bran and citrus peel), or polysaccharides extracted from these agrowastes (crude xylan and pectin extracted from wheat bran and citrus peel, respectively), indicating the fact that agro residues and their extracts can be utilized as a substitute of cost-intensive commercial substrates, xylan and pectin for zymographic analysis. This is the first report revealing the zymographic analysis of xylano–pectinolytic enzymes using agro-based solid residues particles or polysaccharides extracted from agro-based residues.     

Japanese encephalitis virus: from genome to infectome

Japanese encephalitis virus (JEV) is an arbovirus belonging to the family Flaviviridae. It is maintained in a zoonotic cycle involving pigs, ardeid birds and Culex species of mosquitoes. Humans are accidental/dead end hosts of JEV infection because they cannot sustain high viral titers. Factors affecting the clinical manifestations and pathogenesis of JEV infection are not well understood. Though, vaccines are currently available against JEV, it has to be further improved. Here we review the literature on the JEV life cycle, pathogenesis and host immune responses to JEV infection.     

Network constrained clustering for gene microarray data

Many bioinformatics problems can be tackled from a fresh angle offered by the network perspective. Directly inspired by metabolic network structural studies, we propose an improved gene clustering approach for inferring gene signaling pathways from gene microarray data. Based on the construction of co-expression networks that consists of both significantly linear and non-linear gene associations together with controlled biological and statistical significance, our approach tends to group functionally related genes into tight clusters despite their expression dissimilarities. We illustrate our approach and compare it to the traditional clustering approaches on a yeast galactose metabolism dataset and a retinal gene expression dataset. Our approach greatly outperforms the traditional approach in rediscovering the relatively well known galactose metabolism pathway in yeast and in clustering genes of the photoreceptor differentiation pathway. AVAILABILITY: The clustering method has been implemented in an R package "GeneNT" that is freely available from: http://www.cran.org.     

Paenibacillus lentimorbus Enhanced Abiotic Stress Tolerance Through Lateral Root Formation and Phytohormone Regulation

Under the stressed conditions plant growth-promoting rhizobacteria (PGPR) are able to stimulate plant growth through several mechanisms, including antioxidants alleviation, regulation of stress responsive genes and phytohormones etc. Present study is conducted to investigate the impact of Paenibacillus lentimorbus B-30488 inoculation on salinity and drought stress mitigation in Arabidopsis thaliana through modulation in defense enzymes, phyto-hormones and root system architecture associated gene expression profiling. In vitro experiments clearly demonstrated the role of B-30488 in stimulating the root length, branches, lateral root formation and biomass under salinity and drought stress. The inoculation of B-30488 modulated the phytohormones levels to protect the plants from salinity and drought stress. Similarly, defence enzymes were also activated under the stressed conditions, but B-30488 inoculation reduced the antioxidants content during salinity and drought stress as compared to their respective controls. Microscopy results showed decrease in lateral roots hair formation under both stresses and B-30488 inoculation not only mitigate but also enhanced the lateral root formation. Gene expression analysis through real time polymerase chain reaction (RT-PCR) showed modulated expression of several genes related to root development, stress and lateral root formation in B-30488 inoculated seedlings. Results based on the present study, B-30488 is also involved in alteration root architecture, its growth regulation via modulation in phytohormones and genes expression and overall significant improvement in plant growth under stress conditions.

     

High‐performance liquid chromatography separation of enantiomers of mandelic acid and its analogs on a chiral stationary phase

The enantiomers of mandelic acid and its analogs have been chromatographically separated on a chiral stationary phase (CSP) derived from 4‐(3,5‐dinitrobenzamido) tetrahydrophenanthrene. The rationale of separations of these compounds is discussed with respect to the method development for determining enantiomeric purity and possibility of obtaining enantiomerically pure materials by high‐pressure liquid chromatography. The relationship of analyte structure to the extent of enantiomeric separation has been examined and separation factors (α) are presented for various groups of structurally related compounds. Chiral recognition models have been suggested to account for the observed separations. These models provide mechanistic insights into the chiral recognition process. Chirality 2010. © 2009 Wiley‐Liss, Inc.