Bio-efficacy of pumpkin phloem lectin on red spider mite, Oligonychus coffeae (Nietner) infesting tea

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Photo-antagonism of the GABAA receptor

Neurotransmitter receptor trafficking is fundamentally important for synaptic transmission and neural network activity. GABAA receptors and inhibitory synapses are vital components of brain function, yet much of our knowledge regarding receptor mobility and function at inhibitory synapses is derived indirectly from using recombinant receptors, antibody-tagged native receptors and pharmacological treatments. Here we describe the use of a set of research tools that can irreversibly bind to and affect the function of recombinant and neuronal GABAA receptors following ultraviolet photoactivation. These compounds are based on the competitive antagonist gabazine and incorporate a variety of photoactive groups. By using site-directed mutagenesis and ligand-docking studies, they reveal new areas of the GABA binding site at the interface between receptor β and α subunits. These compounds enable the selected inactivation of native GABAA receptor populations providing new insight into the function of inhibitory synapses and extrasynaptic receptors in controlling neuronal excitation

Inference of Co-Evolving Site Pairs: an Excellent Predictor of Contact Residue Pairs in Protein 3D structures

Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints on each residue site. Selective constraints on residue sites are recorded in amino acid orders in homologous sequences and also in the evolutionary trace of amino acid substitutions. A challenge is to extract direct dependences between residue sites by removing indirect dependences through other residues within a protein or even through other molecules. Recent attempts of disentangling direct from indirect dependences of amino acid types between residue positions in multiple sequence alignments have revealed that the strength of inferred residue pair couplings is an excellent predictor of residue-residue proximity in folded structures. Here, we report an alternative attempt of inferring co-evolving site pairs from concurrent and compensatory substitutions between sites in each branch of a phylogenetic tree. First, branch lengths of a phylogenetic tree inferred by the neighbor-joining method are optimized as well as other parameters by maximizing a likelihood of the tree in a mechanistic codon substitution model. Mean changes of quantities, which are characteristic of concurrent and compensatory substitutions, accompanied by substitutions at each site in each branch of the tree are estimated with the likelihood of each substitution. Partial correlation coefficients of the characteristic changes along branches between sites are calculated and used to rank co-evolving site pairs. Accuracy of contact prediction based on the present co-evolution score is comparable to that achieved by a maximum entropy model of protein sequences for 15 protein families taken from the Pfam release 26.0. Besides, this excellent accuracy indicates that compensatory substitutions are significant in protein evolution.Comment: 17 pages, 4 figures, and 4 tables with supplementary information of 5 figure

The concept of RNA-assisted protein folding: the role of tRNA

We suggest that tRNA actively participates in the transfer of 3D information from mRNA to peptides - in addition to its well-known, "classical" role of translating the 3-letter RNA codes into the one letter protein code. The tRNA molecule displays a series of thermodynamically favored configurations during translation, a movement which places the codon and coded amino acids in proximity to each other and make physical contact between some amino acids and their codons possible. This specific codon-amino acid interaction of some selected amino acids is necessary for the transfer of spatial information from mRNA to coded proteins, and is known as RNA-assisted protein folding

Protein 3D Structure Computed from Evolutionary Sequence Variation

The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing

Geotechnical Investigation and Microanalysis of Black Cotton Soil Amended with Guar Gum and Polyethylene Terephlate Fibre

Polymer-based soil stabilization has fascinated substantial interest in the field of research intending to gain a better knowledge of the anticipated soil characteristics after polymer treatment. Intricate research on the engineering performance of expansive soil which is highly challenging due to its swell and shrink nature based on variations in water regime, treated with guar gum, a biopolymer made from gum along with polyethylene terephthalate fibre, one of the most generated plastics, resulting in massive waste, is accomplished through this entire experimental investigation. Comprehensive geotechnical tests and microstructural examinations have been performed to optimize the guar gum for enhancement of soil properties and to comprehend the interactive mechanism with the soil. The biopolymer at dosages 0.5%, 1%, 1.5%, and 2% was added to the soil. Polyethylene terephthalate Fibre with an aspect ratio of 28 is used with the soil at an increment of 0.4% up to 1.6%. The optimum dosage of biopolymer was mixed with polyethylene terephthalate fibres, and its effect on geotechnical properties was carried out separately. From the experimental investigations, it is comprehended that there is a reduction of 27% and 40% in plasticity index and swelling, respectively, at an optimum dosage of 0.5% GG when compared to untreated soil. Furthermore, there is a marginal decrease of 24% in dry density, 310% increase in CBR value, and 33% reduction in compressibility of the soil treated with 0.5% GG with 1.6% PET fibre, when compared to virgin soil. The present study was conducted to improve the subgrade soil strength beneath the pavements. The usage of biopolymer and its combination with polyethylene terephthalate fibres shows that there is a considerable improvement in modifying the geotechnical properties, and its coupling effect contributes to higher California bearing ratio values. According to the outcomes of this investigation, it is proven that biopolymer and polyethylene terephthalate fibre is definitely an alternate to conventional materials. The present study was conducted to improve the subgrade soil strength beneath the pavements

Characterization of ginger rhizome lectin and its efficacy in controlling red spider mite in tea

Methodology was developed to isolate and characterize the ginger rhizome lectin and its applied aspects in integrated pest management in tea. Lectin, a defense protein with mannose specificity was purified from fresh rhizomes of ginger (Zingiber officinale Roscoe) by affinity chromatography. Purified fractions of lectin showed agglutination with rabbit erythrocytes. SDS PAGE analysis revealed the presence of 15 KDa ginger rhizome lectin. Bio-efficacy of purified ginger rhizome lectin was experimented on red spider mite (Oligonychus coffeae Nietner) under in-vitro conditions. It was observed that 100 µg ml–1 of purified lectin caused in toto mortality of adult red spider mite. Identical results were observed in terms of ovipositional deterrence of red spider mite at 100 µg ml–1 of ginger rhizome lectin. Results suggest that ginger rhizome could be used as an alternative plant source for lectin isolation and it can be used as an acaricide in the IPM schedule or organic tea fields

Optimal contact definition for reconstruction of Contact Maps

<p>Abstract</p> <p>Background</p> <p>Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure.</p> <p>Results</p> <p>We use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a) to what accuracy does a contact map represent its corresponding 3D structure, b) what is the best contact map representation with regard to reconstructability and c) what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11Å around the <it>C</it>_{<it>β </it>}atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2Å RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity.</p> <p>Conclusions</p> <p>Thus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through contacts and structural alignments based on maximum contact map overlap.</p