Current status of Potyvirus in India

Potyvirus particles are flexuous rods of 700–900?nm in length and contain one positive sense single-stranded genomic RNA molecule of approximately 10?kb, which is encapsidated by a single type of coat protein. According to available NCBI database, Potyvirus infection is prominently present in Solanaceae, Leguminosae and Cucurbitaceae families in India. Potyviruses can induce a wide range of different symptoms in infected host plants including mosaic, stripe, mottling, vein clearing, vein banding, ringspots, necrotic or chlorotic lesions, flower breaking, stunting, wilting, and most commonly lead tostunting and yield losses. PCR-based methods for the detection and identification of potyviruses rely on degenerate primers designed for conserved regions. Potyvirus infection requires the interaction of host factors with viral proteins and RNA for its replication and systemic spread, i.e interaction between VPg and eIF4E is required for Potyvirus genome translation. Mutations in host translational initiation factor eIF4E cause the conformational shift in encoded proteins which are unable to bind with viral protein (VPg), resulting in broad-spectrum Potyvirus resistance.     

Pathogenic and molecular characterisations of pigeonpea wilt pathogen Fusarium udum

Thirty two pathogenic isolates of Fusarium udum from different pigeonpea growing areas in India were studied for pathogenic and molecular variability. Pathogenic variability was tested on 12 pigeonpea differential genotypes, which revealed prevalence of five variants in F. udum. The amount of genetic variation was evaluated by Polymerase Chain Reaction (PCR) amplification with 20 random amplified polymorphic DNA (RAPD) markers and nine microsatellite markers. All amplifications revealed scorable polymorphisms among the isolates, and a total of 137 polymorphic fragments were scored for the RAPD markers and 16 alleles for the simple sequence repeat (SSR) markers. RAPD primers showed 86% polymorphism. Genetic similarity was calculated using Jaccard's similarity coefficient and cluster analysis was used to generate a dendrogram showing relationships between them. Isolates could be grouped into three subpopulations based on molecular analysis. Results indicated that there is high genetic variability among a subpopulation of F. udum as identified by RAPD and SSR markers and pathogenicity on differential genotypes.     

Effect of root exudates of mycorrhizal tomato plants on microconidia germination of Fusarium oxysporum f. sp. lycopersici

The effect of root exudates from mycorrhizal and non-mycorrhizal tomato plants on microconidia germination of the tomato pathogen Fusarium oxysporum f. sp. lycopersici was tested. Microconidia germination was enhanced in the presence of root exudates from mycorrhizal tomato plants. Tomato plants were colonised by the arbuscular mycorrhizal fungus Glomus fasciculatum, indicating that alterations of the exudation pattern depended on the degree of root AM colonisation. Testing the exudates from plants with a high and a low P level revealed that the alterations of the root exudates from mycorrhizal plants, resulting in a changed effect on microconidia germination, are not due to an improved P status of mycorrhizal plants.     

Synthesis of hexyl α-glucoside and α-polyglucosides by a novel Microbacterium isolate

Alkyl-glucosides and alkyl-polyglucosides are the new-generation biodegradable surfactants with good emulsifying and wetting properties. The α-forms of these glucosides occur in antibiotics and also stimulate nasal absorption of many drugs. In this paper, we report the synthesis of hexyl α-glucoside and α-polyglucosides using cell-bound α-glucosidase activity of a novel strain of Microbacterium paraoxydans. A number of cell-bound glycosyl hydrolase activities were detected in the isolate with the maximum hydrolytic activity of 180 IU g^?1 dry wt cells on p-nitrophenyl-α-d-glucopyranoside. In a micro-aqueous system, at a water activity of 0.69, 1.8 g l^?1 of hexyl α-glucoside (corresponding to about 25 % yield) was synthesized by whole cells with maltose and hexanol as substrates. The concentration was enhanced to 11 g l^?1 (~60 % yield) in a biphasic system at a water content of 60 %. ¹H and ¹³C NMR spectra of the purified compound confirmed the synthesized product to be hexyl-α-d-glucopyranoside, while the presence of hexyl di- and tri-glucosides was confirmed by electrospray ionization mass spectrometry. The cell-driven synthesis makes this an extremely attractive alternative for synthesis of such compounds.     

Carcass traits of different marketable sizes of rohu,Labeo rohita (Hamilton, 1822)

The present study was carried out to investigate the carcass traits of farmed freshwater Labeo rohita in relation to body size as important information to calculate yield and/or support for machine/manual processing. For this purpose ninety specimens were collected for nine weight groups from 600 to 1100 g, each group with a 100 g increment. Specimens were collected from grow‐out culture ponds of the Central Institute of Freshwater Aquaculture (CIFA), Bhubaneswar. The carcass evaluation technique was followed to evaluate carcass yield, offal yield and carcass cutability. Head size percentage of rohu increased as the body mass increased, which in turn increased the processing yield. Dry matter and ether extract percentage also increased with the body mass; however, moisture percentage showed a decreasing trend. The fore cut showed a distinctly higher ether extract percentage followed by the middle and posterior cuts. There was a good correlation development to describe the relationship between yield traits and body weight.     

Binding of ibuprofen to human hemoglobin: elucidation of their molecular recognition by spectroscopy,calorimetry, and molecular modeling techniques

Ibuprofen, used for the treatment of acute and chronic pain, osteoarthritis, rheumatoid arthritis, and related conditions has ample affinity to globular proteins. Here we have explored this fundamental study pertaining to the interaction of ibuprofen with human hemoglobin (HHb), using multispectroscopic, calorimetric, and molecular modeling techniques to gain insights into molecular aspects of binding mechanism. Ibuprofen-induced graded decrease in absorption spectra indicates protein disruption along with sedimentation of HHb particle. Red shifting of absorption peak at 195 nm indicates alteration in the secondary structure of HHb upon interaction with ibuprofen. Flouremetric and isothermal titration calorimetric (ITC) studies suggested one binding site in HHb for ibuprofen at 298.15 K. However, with increase in temperature, ITC revealed increasing number of binding sites. The negative values of Gibbs energy change (ΔG⁰) and enthalpy change (ΔH⁰) along with positive value of entropy change (ΔS⁰) strongly suggest that it is entropy-driven spontaneous exothermic reaction. Moreover, hydrophobic interaction, hydrogen bonding, and π–π interaction play major role in this binding process as evidenced from ANS (8-anilino-1-napthalenesulphonic acid), sucrose binding, and molecular modeling studies. The interaction impacts on structural integrity and functional aspects of HHb as confirmed by CD spectroscopy, increased free iron release, increased rate of co-oxidation and decreased rate of esterase activity. These findings suggest us to conclude that ibuprofen upon interaction perturbs both structural and functional aspects of HHb.     

Protein Quality Control System in Neurodegeneration: A Healing Company Hard to Beat but Failure is Fatal

A common feature in most neurodegenerative diseases and aging is the progressive accumulation of damaged proteins. Proteins are essential for all crucial biological functions. Under some notorious conditions, proteins loss their three dimensional native conformations and are converted into disordered aggregated structures. Such changes rise into pathological conditions and eventually cause serious protein conformation disorders. Protein aggregation and inclusion bodies formation mediated multifactorial proteotoxic stress has been reported in the progression of Parkinson’s disease (PD), Huntington’s disease (HD), Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS) and Prion disease. Ongoing studies have been remarkably informative in providing a systematic outlook for better understanding the concept and fundamentals of protein misfolding and aggregations. However, the precise role of protein quality control system and precursors of this mechanism remains elusive. In this review, we highlight recent insights and discuss emerging cytoprotective strategies of cellular protein quality control system implicated in protein deposition diseases. Our current review provides a clear, understandable framework of protein quality control system that may offer the more suitable therapeutic strategies for protein-associated diseases.     

Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member

MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase from the bacterial menaquinone biosynthesis pathway, catalyzes an intramolecular Claisen condensation (Dieckmann reaction) in which the electrophile is an unactivated carboxylic acid. Mechanistic studies on this crotonase family member have been hindered by partial active site disorder in existing MenB X-ray structures. In the current work the 2.0 ? structure of O-succinylbenzoyl-aminoCoA (OSB-NCoA) bound to the MenB from Escherichia coli provides important insight into the catalytic mechanism by revealing the position of all active site residues. This has been accomplished by the use of a stable analogue of the O-succinylbenzoyl-CoA (OSB-CoA) substrate in which the CoA thiol has been replaced by an amine. The resulting OSB-NCoA is stable, and the X-ray structure of this molecule bound to MenB reveals the structure of the enzyme-substrate complex poised for carbon-carbon bond formation. The structural data support a mechanism in which two conserved active site Tyr residues, Y97 and Y258, participate directly in the intramolecular transfer of the substrate α-proton to the benzylic carboxylate of the substrate, leading to protonation of the electrophile and formation of the required carbanion. Y97 and Y258 are also ideally positioned to function as the second oxyanion hole required for stabilization of the tetrahedral intermediate formed during carbon-carbon bond formation. In contrast, D163, which is structurally homologous to the acid-base catalyst E144 in crotonase (enoyl-CoA hydratase), is not directly involved in carbanion formation and may instead play a structural role by stabilizing the loop that carries Y97. When similar studies were performed on the MenB from Mycobacterium tuberculosis, a twisted hexamer was unexpectedly observed, demonstrating the flexibility of the interfacial loops that are involved in the generation of the novel tertiary and quaternary structures found in the crotonase superfamily. This work reinforces the utility of using a stable substrate analogue as a mechanistic probe in which only one atom has been altered leading to a decrease in α-proton acidity.     

Structure and lipid interactions of an anti-inflammatory and anti-atherogenic 10-residue class G(*) apolipoprotein J peptide using solution NMR

The surprising observation that a 10-residue class G(?) peptide from apolipoprotein J, [113-122]apoJ, possesses anti-inflammatory and anti-atherogenic properties prompted us to delineate its structural characteristics in the presence of normal and oxidized lipid. Towards this, we have determined high-resolution structure of [113-122]apoJ in solution using nuclear magnetic resonance (NMR) spectroscopy and studied its interaction with lipids, including oxidized lipids, using a number of biophysical methods. Circular dichroism and NMR studies established that in the presence of dodecylphosphocholine (DPC) micelle, this peptide adopts amphipathic α-helical structure. The observed Nuclear Overhauser effects indicate that the amphipathic helical structure of the peptide is stabilized by the N-terminal acetyl and C-terminal amide blocking groups. We used isothermal titration calorimetry to measure binding enthalpy of the peptide with DPC micelle, an oxidized lipid, 1-(palmitoyl)-2-(5-keto-6-octene-dioyl) phosphatidylcholine (KOdiA-PC), and the mixture of these two lipids (5mol% KOdiA-PC in DPC micelle). We find that the peptide binding with DPC micelle is associated with an enthalpy change (-16.75±0.16 Kcal/mol) much larger than that resulting from the binding with KodiA-PC (-3.67±0.13 Kcal/mol). Incorporation of a small amount of KOdiA-PC (5mol%) in DPC micelle also results in the lowering of peptide binding enthalpy (-13.43±0.18 Kcal/mol). These results are consistent with overall negative charge and altered conformational properties of oxidized sn-2 chain of KOdiA-PC. Our results have unambiguously established the amphipathic α-helical structure of [113-122]apoJ peptide in the presence of DPC micelle as well as its ability to bind oxidized lipid. These in vitro results help explain the previously observed anti-inflammatory and anti-atherosclerotic properties of this peptide.