Luffa acutangula agglutinin: Primary structure determination and identification of a tryptophan residue involved in its carbohydrate-binding activity using mass spectrometry

A lectin from phloem exudates of Luffa acutangula (ridge gourd) was purified on chitin affinity chromatography and characterized for its amino acid sequence and to study the role of tryptophan in its activity. The purified lectin was subjected to various proteolytic digestions, and the resulting peptides were analyzed by liquid chromatography coupled electrospray ionization ion trap mass spectrometer. The peptide precursor ions were fragmented by collision-induced dissociation or electron transfer dissociation experiments, and a manual interpretation of MS/MS was performed to deduce amino acid sequence. This gave rise to almost complete sequence coverage of the lectin which showed high-sequence similarity with deduced sequences of phloem lectins present in the database. Chemical modification of lysine, tyrosine, histidine, arginine, aspartic acid, and glutamic acid residues did not inhibit the hemagglutinating activity. However, the modification of tryptophan residues using N-bromosuccinimide showed the loss of hemagglutinating activity. Additionally, the mapping of tryptophan residues was performed to determine the extent and number of residues modified, which revealed that six residues per molecule were oxidized suggesting their accessibility. The retention of the lectin activity was seen when the modifications were performed in the presence of chitooligosaccharides due to protection of a tryptophan residue (W-102) in the protein. These studies taken together have led to the identification of a particular tryptophan residue (W-102) in the activity of the lectin. (c) 2015 IUBMB Life, 67(12):943-953, 2015

Ischaemic concentrations of lactate increase TREK1 channel activity by interacting with a single histidine residue in the carboxy terminal domain

Key points The physiological metabolite, lactate and the two-pore domain leak potassium channel, TREK1 are known neuroprotectants against cerebral ischaemia. However, it is not known whether lactate interacts with TREK1 channel to provide neuroprotection. In this study we show that lactate increases TREK1 channel activity and hyperpolarizes CA1 stratum radiatum astrocytes in hippocampal slices. Lactate increases open probability and decreases longer close time of the human (h)TREK1 channel in a concentration dependent manner. Lactate interacts with histidine 328 (H328) in the carboxy terminal domain of hTREK1 channel to decrease its dwell time in the longer closed state. This interaction was dependent on the charge on H328. Lactate-insensitive mutant H328A hTREK1 showed pH sensitivity similar to wild-type hTREK1, indicating that the effect of lactate on hTREK1 is independent of pH change. AbstractA rise in lactate concentration and the leak potassium channel TREK1 have been independently associated with cerebral ischaemia. Recent literature suggests lactate to be neuroprotective and TREK1 knockout mice show an increased sensitivity to brain and spinal cord ischaemia; however, the connecting link between the two is missing. Therefore we hypothesized that lactate might interact with TREK1 channels. In the present study, we show that lactate at ischaemic concentrations (15-30mm) at pH7.4 increases TREK1 current in CA1 stratum radiatum astrocytes and causes membrane hyperpolarization. We confirm the intracellular action of lactate on TREK1 in hippocampal slices using monocarboxylate transporter blockers and at single channel level in cell-free inside-out membrane patches. The intracellular effect of lactate on TREK1 is specific since other monocarboxylates such as pyruvate and acetate at pH7.4 failed to increase TREK1 current. Deletion and point mutation experiments suggest that lactate decreases the longer close dwell time incrementally with increase in lactate concentration by interacting with the histidine residue at position 328 (H328) in the carboxy terminal domain of the TREK1 channel. The interaction of lactate with H328 is dependent on the charge on the histidine residue since isosteric mutation of H328 to glutamine did not show an increase in TREK1 channel activity with lactate. This is the first demonstration of a direct effect of lactate on ion channel activity. The action of lactate on the TREK1 channel signifies a separate neuroprotective mechanism in ischaemia since it was found to be independent of the effect of acidic pH on channel activity. Key points The physiological metabolite, lactate and the two-pore domain leak potassium channel, TREK1 are known neuroprotectants against cerebral ischaemia. However, it is not known whether lactate interacts with TREK1 channel to provide neuroprotection. In this study we show that lactate increases TREK1 channel activity and hyperpolarizes CA1 stratum radiatum astrocytes in hippocampal slices. Lactate increases open probability and decreases longer close time of the human (h)TREK1 channel in a concentration dependent manner. Lactate interacts with histidine 328 (H328) in the carboxy terminal domain of hTREK1 channel to decrease its dwell time in the longer closed state. This interaction was dependent on the charge on H328. Lactate-insensitive mutant H328A hTREK1 showed pH sensitivity similar to wild-type hTREK1, indicating that the effect of lactate on hTREK1 is independent of pH change.

Biomineralization and Biobeneficiation of Bauxite

Role of indigenous microbes in the formation and conversion of bauxite minerals is illustrated. Many types of microorganisms such as fungi, heterotrophic and autotrophic bacteria and yeasts inhabit bauxite ore deposits bringing about biogenesis and biomineraliztion. Organisms capable of iron oxidation and reduction and solubilising calcium carbonate and silica can be isolated from bauxite deposits and are used to bring about selective mineral beneficiation to remove iron, calcium and silica. Use of Paenibacillus polymyxa in the efficient removal of calcium from low grade bauxites is demonstrated through bioreactor technology. Similarly, for iron removal from bauxite, iron-reducing bacteria can be used. Silicate bacteria aid in selective silica solubilisation to control alumina: silica ratios. Microorganisms can also be used to bring about environmental control with respect to red mud disposal through bioremediation technology.

Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis

Identification of residue-residue contacts from primary sequence can be used to guide protein structure prediction. Using Escherichia coli CcdB as the test case, we describe an experimental method termed saturation-suppressor mutagenesis to acquire residue contact information. In this methodology, for each of five inactive CcdB mutants, exhaustive screens for suppressors were performed. Proximal suppressors were accurately discriminated from distal suppressors based on their phenotypes when present as single mutants. Experimentally identified putative proximal pairs formed spatial constraints to recover >98% of native-like models of CcdB from a decoy dataset. Suppressor methodology was also applied to the integral membrane protein, diacylglycerol kinase A where the structures determined by X-ray crystallography and NMR were significantly different. Suppressor as well as sequence co-variation data clearly point to the Xray structure being the functional one adopted in vivo. The methodology is applicable to any macromolecular system for which a convenient phenotypic assay exists.

Spatial determination of gold catalyst residue used in the production of ZnO nanowires by SIMS depth profiling analysis

In this paper we demonstrate how secondary ion mass spectrometry (SIMS) can be applied to ZnO nanowire structures for gold catalyst residue determination. Gold plays a significant role in determining the structural properties of such nanowires, with the location of the gold after growth being a strong indicator of the growth mechanism. For the material investigated here, we find that the gold remains at the substrate-nanowire interface. This was not anticipated as the usual growth mechanism associated with catalyst growth is of a vapour-liquid-solid (VLS) type. The results presented here favour a vapour-solid (VS) growth mechanism instead. Copyright © 2007 John Wiley & Sons, Ltd.

Significant Residue Features Revealed By Eigenvalue Decomposition Analysis Of Blosum Matrices

Here we attempt to characterize protein evolution by residue features which dominate residue substitution in homologous proteins. Evolutionary information contained in residue substitution matrix is abstracted with the method of eigenvalue decomposition. Top eigenvectors in the eigenvalue spectrums are analyzed as function of the level of similarity, i.e. sequence identity (SI) between homologous proteins. It is found that hydrophobicity and volume are two significant residue features conserved in protein evolution. There is a transition point at SI approximate to 45%. Residue hydrophobicity is a feature governing residue substitution as SI >= 45%. Whereas below this SI level, residue volume is a dominant feature. (C) 2007 Elsevier B.V. All rights reserved.

Efficacy and Residue Comparisons between Two Slow-release Formulations of Fluridone

Residue profiles and efficacy of Avast and Sonar, two slow release pellet formulations of fluridone {1-methyl-3-phenyl-5- [3-(trifluoromethyl)phenly]-4(1H)-pyridinone}, were compared in outdoor tanks. Hydrilla (Hydrilla verticillata (L.f.) Royle) and southern naiad (Najas guadalupensis (Sprengel) Magnus) were treated with a split application of 6, 12, 18 and 24 μg/l a.i. fluridone and the concentrations of both formulations compared over a 134-day period. Both pellet formulations exhibited very similar residues over time for each respective treatment, resulted in peak concentrations of fluridone 40 to 50 days after application, and effectively and similarly controlled southern naiad and hydrilla at all rates tested by 92 days after initial application. (PDF contains 3 pages.)

Preparação, caracterização e avaliação de nanocompósitos de PBAT/amido de milho e vermiculita organofilizada

Nos últimos 20-30 anos polímeros biodegradáveis vêm sendo estudados e desenvolvidos e atualmente já são comercializados. Contudo, o custo, a processabilidade e algumas propriedades ainda dificultam a penetração desses polímeros no mercado e a competição com as chamadas commodities. Não são poucos os autores que se dedicam a desenvolver aditivos e formulações para superar essas limitações. Desta forma, esta Tese se dedicou ao desenvolvimento de compósitos de Ecobras, fabricado pela Basf e comercializado pela Corn Products, utilizando como carga mineral resíduo da extração da bauxita, no município de Santa Luzia/PB, o qual consiste em sua totalidade de vermiculita. Esta vermiculita foi quimicamente modificada com sais de alquil fosfônio para melhorar a compatibilidade com a matriz polimérica e também espaçar as camadas de aluminossilicato. De fato, a modificação com o brometo de hexadecil tributil fosfônio resultou na esfoliação da vermiculita tornando-a potencialmente apropriada para a obtenção de nanocompósitos. A preparação dos compósitos foi realizada pelo método de intercalação no estado fundido e foram comparadas a utilização da câmara interna de mistura e da mini extrusora de dupla rosca, sendo esta última mais eficaz na dispersão da vermiculita, conforme revelado pela microscopia eletrônica de varredura, difração de raios-X e reometria de placas. O grau de dispersão também foi influenciado pela estrutura química do modificador da vermiculita e pelo teor dessa carga incorporada à matriz. Teores mais elevados levaram a formação de aglomerados, enquanto a modificação da carga implicou na formação de micro e nanocompósitos. Ainda houve alterações das propriedades térmicas com aumento dos valores da temperatura de transição vítrea, de cristalização e fusão, embora o grau de cristalinidade tenha sido mantido. Nitidamente, foram obtidos materiais mais rígidos, com maior módulo e menor capacidade de deformação. Cerca de 58% de perda de massa foi observada para os micro e nanocompósitos obtidos após 17 semanas de enterro em solo simulado para avaliação da biodegradabilidade, valor bem próximo ao Ecobras puro. De modo geral, a incorporação das diferentes vermiculitas retardou nas primeiras semanas a biodegradação, provavelmente em função de modificações na estrutura cristalina, conforme sugerido pelos maiores valores de temperatura de fusão observados durante o acompanhamento do processo de biodegradação. No entanto, após 7 semanas os perfis de biodegradação dos micro e nanocompósitos se aproximaram bastante do Ecobras puro. Desta forma, foi possível nesta Tese obter um nanocompósito de Ecobras com vermiculita modificada com brometo de hexadecil fosfônio utilizando ferramentas comuns de processamento no estado fundido com biodegradabilidade próxima ao polímero de partida, porém mais rígido e menos deformável

Studies on shark liver oil and its residue

Seasonal variation in oil and moisture contents and vitamin A potency of oil in livers from different species of sharks landed at Veraval coast were studied. Values of moisture, protein, ash and vitamins in defatted liver residue were determined.

The residue measurment of pesticide in water and biota of the Sorkhrood River in the south of the Caspian Sea

Pesticide residue is considered as a crucial factor in the fresh water ecosystem pollution of north Iran (Esp. Gillan and Mazandaran provinces). It is also regarded dangerous to the health of human being and animals. In this research , pesticide residue in 3 species of fish was gauged in stations of the Haraz river , the Sorkhrood river , and the Caspian sea. The sampeles were taken during 27 mounths (started in April 97 and ended to June 99). The maximum level of pesticide in water was found in July 98 for lindine at 12.4 ppb. The level of chlorinated pesticide residue recorded at 63 ppb in April 98. The level of. organophosphorus pesticides residue in water was at 1.75 ppb in Aug 97. The toxicity of the mentioned pesticide and bioaccomulation were taken into account in conducting this researched.