Crystal structure of dimeric FabZ of Plasmodium falciparum reveals conformational switching to active hexamers by peptide flips

The crystal structure of beta-hydroxyacyl acyl carrier protein dehydratase of Plasmodium falciparum (PfFabZ) has been determined at a resolution of 2.4 angstrom. PfFabZ has been found to exist as a homodimer (d-PfFabZ) in the crystals of the present study in contrast to the reported hexameric form (h-PfFabZ) which is a trimer of dimers crystallized in a different condition. The catalytic sites of this enzyme are located in deep narrow tunnel-shaped pockets formed at the dimer interface. A histidine residue from one subunit of the dimer and a glutamate residue from the other subunit lining the tunnel form the catalytic dyad in the reported crystal structures. While the position of glutamate remains unaltered in the crystal structure of d-PffabZ compared to that in b-PfFabZ, the histidine residue takes up an entirely different conformation and moves away from the tunnel leading to a His-Phe cis-trans peptide flip at the histidine residue. In addition, a loop in the vicinity has been observed to undergo a similar flip at a Tyr-Pro peptide bond. These alterations not only prevent the formation of a hexamer but also distort the active site geometry resulting in a dimeric form of FabZ that is incapable of substrate binding. The dimeric state and an altered catalytic site architecture make d-PfFabZ distinctly different from the FabZ structures described so far. Dynamic light scattering and size exclusion chromatographic studies clearly indicate a pH-related switching of the dimers to active hexamers. (c) 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserv.

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

Novel Algorithm for estimation of Swell Pressure of Fine Grained Soils Based on Diffuse Double Layer (DDL) Theory

Use of engineered landfills for the disposal of industrial wastes is currently a common practice. Bentonite is attracting a greater attention not only as capping and lining materials in landfills but also as buffer and backfill materials for repositories of high-level nuclear waste around the world. In the design of buffer and backfill materials, it is important to know the swelling pressures of compacted bentonite with different electrolyte solutions. The theoretical studies on swell pressure behaviour are all based on Diffuse Double Layer (DDL) theory. To establish a relation between the swell pressure and void ratio of the soil, it is necessary to calculate the mid-plane potential in the diffuse part of the interacting ionic double layers. The difficulty in these calculations is the elliptic integral involved in the relation between half space distance and mid plane potential. Several investigators circumvented this problem using indirect methods or by using cumbersome numerical techniques. In this work, a novel approach is proposed for theoretical estimations of swell pressures of fine-grained soil from the DDL theory. The proposed approach circumvents the complex computations in establishing the relationship between mid-plane potential and diffused plates’ distances in other words, between swell pressure and void ratio.

Design enhancement of the underwater noise control linings through a parsimonious parametric study

Control of sound transmission through the structure and reflection from the structure immersed in fluid media impose highly conflicting requirements on the design of the carpeted noise control linings. These requirements become even more stringent if the structure is expected to be moving with considerable speed particularly under intense hydrostatic pressure. Numerous configurations are possible for designing these linings. Therefore, in this paper, a few lining configurations are identified from the literature for parametric study so that the designer is provided with an environment to analyze and design the lining. A scheme of finite element analysis is used to analyze these linings for their acoustic performance. Commercial finite element software, NISA®, is used as a platform to develop a customized environment wherein design parameters of different configurations can be varied with consistency checks and generate the finite element meshes using the 8-noded hexahedral element. Four types of designs proposed and analysed here address the parameters of interest such as the echo reduction and the transmission loss. Study of the effect of different surface distributions of the cavities is carried out. Effect of static pressure on different designs is reported.

Influence of nano-fillers on electrical treeing in epoxy insulation

This paper presents the results of a study on the effect of alumina nano-fillers on electrical tree growth in epoxy insulation. Treeing experiments were conducted at a fixed ac voltage of 15 kV, 50 Hz on unfilled epoxy samples as well as epoxy nanocomposites with different loadings of alumina nano-fillers. Time for tree inception as well as tree growth patterns were studied. The results show that there is a significant improvement in tree initiation time with the increase in nano-filler loading. Different tree growth patterns as well as slower tree growth with increasing filler loadings were observed in epoxy nanocomposites. The nature of the tree channel and the elemental composition of the material on the inner lining of the tree channels have been studied using SEM imaging and EDAX analysis respectively of the cut section of the tree channels. It has been shown that the type of bonding at the interface has an influence on the electrical tree growth pattern. The nature of the bonding at the interface between the epoxy and the nano-filler has been studied using FTIR spectrometry. Finally the influence of the interface on tree growth phenomena in nanocomposites has been explained by a physical model.

Stability of a circular tunnel in presence of pseudostatic seismic body forces

The stability of a long circular tunnel in a cohesive frictional soil medium has been determined in the presence of horizontal pseudo-static seismic body forces. The tunnel is supported by means of lining and anchorage system which is assumed to exert uniform internal compressive normal pressure on its periphery. The upper bound finite element limit analysis has been performed to compute the magnitude of the internal compressive pressure required to support the tunnel. The results have been presented in terms of normalized compressive normal stress, defined in terms of sigma(i)/c; where sigma(i) is the magnitude of the compressive normal pressure on the periphery of the tunnel and c refers to soil cohesion. The variation of sigma(i)/c with horizontal earthquake acceleration coefficient (alpha(h)) has been established for different combinations of H/D, gamma D/c and phi where (i) H and D refers to tunnel cover and diameter, respectively, and (ii) gamma and phi correspond to unit weight and internal friction angle of soil mass, respectively. Nodal velocity patterns have also been plotted for assessing the zones of significant plastic deformation. The analysis clearly reveals that an increase in the magnitude of the earthquake acceleration leads to a significant increment in the magnitude of internal compressive pressure. (C) 2014 Elsevier Ltd. All rights reserved.

Phytomedicinal importance of Saraca asoca (Ashoka): an exciting past, an emerging present and a promising future

Since the dawn of civilization, natural resources have remained the mainstay of various remedial approaches of humans vis-a-vis a large number of illnesses. Saraca asoca (Roxb.) de Wilde (Saraca indica L.) belonging to the family Caesalpiniaceae has been regarded as a universal panacea in old Indian Ayurvedic texts and has especially been used to manage gynaecological complications and infections besides treating haemmorhagic dysentery, uterine pain, bacterial infections, skin problems, tumours, worm infestations, cardiac and circulatory problems. Almost all parts of the plant are considered pharmacologically valuable. Extensive folkloric practices and ethnobotanical applications of this plant have even lead to the availability of several commercial S. asoca formulations recommended for different indications though adulteration of these remains a pressing concern. Though a wealth of knowledge on this plant is available in both the classical and modern literature, extensive research on its phytomedicinal worth using state-of-the-art tools and methodologies is lacking. Recent reports on bioprospecting of S. asoca endophytic fungi for industrial bioproducts and useful pharmacologically relevant metabolites provide a silver lining to uncover single molecular bio-effectors from its endophytes. Here, we describe socio-ethnobotanical usage, present the current pharmacological status and discuss potential bottlenecks in harnessing the proclaimed phytomedicinal worth of this prescribed Ayurvedic medicinal plant. Finally, we also look into the possible future of the drug discovery and pharmaceutical R&D efforts directed at exploring its pharma legacy.

Surface-waves, stability, and scattering for a lined duct with flow

We consider a straight cylindrical duct with a steady subsonic axial flow and a reacting boundary (e.g. an acoustic lining). The wave modes are separated into ordinary acoustic duct modes, and surface modes confined to a small neighbourhood of the boundary. Many researchers have used a mass-spring-damper boundary model, for which one surface mode has previously been identified as a convective instability; however, we show the stability analysis used in such cases to be questionable. We investigate instead the stability of the surface modes using the Briggs-Bers criterion for a Flügge thin-shell boundary model. For modest frequencies and wavenumbers the thin-shell has an impedance which is effectively that of a mass-spring-damper, although for the large wavenumbers needed for the stability analysis the thin-shell and mass-spring-damper impedances diverge, owing to the thin shell's bending stiffness. The thin shell model may therefore be viewed as a regularization of the mass-spring-damper model which accounts for nonlocally-reacting effects. We find all modes to be stable for realistic thin-shell parameters, while absolute instabilities are demonstrated for extremely thin boundary thicknesses. The limit of vanishing bending stiffness is found to be a singular limit, yielding absolute instabilities of arbitrarily large temporal growth rate. We propose that the problems with previous stability analyses are due to the neglect of something akin to bending stiffness in the boundary model. Our conclusion is that the surface mode previously identified as a convective instability may well be stable in reality. Finally, inspired by Rienstra's recent analysis, we investigate the scattering of an acoustic mode as it encounters a sudden change from a hard-wall to a thin-shell boundary, using a Wiener-Hopf technique. The thin-shell is considered to be clamped to the hard-wall. The acoustic mode is found to scatter into transmitted and reflected acoustic modes, and surface modes strongly linked to the solid waves in the boundary, although no longitudinal or transverse waves within the boundary are excited. Examples are provided that demonstrate total transmission, total reflection, and a combination of the two. This thin-shell scattering problem is preferable to the mass-spring-damper scattering problem presented by Rienstra, since the thin-shell problem is fully determined and does not need to appeal to a Kutta-like condition or the inclusion of an instability in order to avoid a surface-streamline cusp at the boundary change.

Sound transmission in strongly-curved slowly-varying cylindrical and annular lined ducts with flow

In this paper we consider the propagation of acoustic waves along a curved hollow or annular duct with lined walls. The curvature of the duct centreline and the wall radii vary slowly along the duct, allowing application of an asymptotic multiple scales analysis. This generalises Rienstra's analysis of a straight duct of varying cross-sectional radius. The result of the analysis is that the modal wavenumbers and mode shapes are determined locally as modes of a torus with the same local curvature, while the amplitude of the modes evolves as the mode propagates along the duct. The duct modes are found numerically at each axial location using a pseudo-spectral method. Unlike the case of a straight duct, there is a fundamental asymmetry between upstream and downstream propagating modes, with some mode shapes tending to be concentrated on either the inside or outside of the bend depending on the direction of propagation. The interaction between the presence of wall lining and curvature is investigated in particular; for instance, in a representative case it is found that the curvature causes the first few acoustic modes to be more heavily damped by the duct boundary than would be expected for a straight duct. Analytical progress can be made in the limit of very high mode order, in which case well-known 'whispering gallery' modes, localised close to the wall, can be identified.

Structural and mechanistic motifs in membrane proteins: the three-dimensional modelling of rhodopsin, band 3, and the nicotinic acetylcholine receptor

Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, β-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.

Specific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and β-adrenergic receptors.

The nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.

Band 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.

Etxebizitzetako barne hormen diseinu berritzailea eraikuntzako kode teknikoaren arabera

[EU]Proiektu honen helburua etxebizitzetako barne hormen dimentsionamendu berritzailearen azterketa bat egitea da, orain arte erabilitako horma klasikoen ezaugarriak mantenduz, diseinu optimoagoa lortzeko asmoa izanda, material kantitatearen murrizketa bat bilatuz. Hau burutzeko diseinatua dagoen igeltsuzko horma bat hartuko da oinarri modura eta honen moldeaketa bat eginez, eta isolatzaile industrial biren arteko konparaketa bat aurrera eroanez, berregite optimo bat sortuko da, beharrezko suaren kontrako ezaugarri mekaniko eta termikoak betetzen dituena.

The Regulation of Sleep and Circadian Rhythms: The Role of Melatonin and Adenosine in Zebrafish

Sleep is a highly conserved behavioral state whose regulation is still unclear. In this thesis I initially briefly introduce the known sleep circuitry and regulation in vertebrates, and why zebrafish is seen as a good model to study sleep-regulation. I describe the existing two-process model of sleep regulation, which posits that the two processes C (circadian) and S (homeostatic) control timing of sleep-wake behavior. I then study the role melatonin plays in the circadian regulation of sleep using zebrafish. Firstly, we find that the absence of melatonin results in a reduction of sleep at night, establishing that endogenous melatonin is required for sleep at night. Secondly, melatonin mutants show a reduction in sleep in animals with no functional behavioral rhythms suggesting that melatonin does not require intact circadian rhythms for its effect on sleep. Thirdly, melatonin mutants do not exhibit any changes in circadian rhythms, suggesting that the circadian clock does not require melatonin for its function. Fourthly, we find that in the absence of melatonin, there is no rhythmic expression of sleep, suggesting that melatonin is the output molecule of process C. Lastly, we describe a connection between adenosine signaling (output molecules of process S), and melatonin. Following this we proceed to study the role adenosine signaling plays in sleep-wake behavior. We find that firstly, adenosine receptor A1 and A2 are involved in sleep- wake behavior in zebrafish, based on agonist/antagonist behavioral results. Secondly, we find that several brain regions such as PACAP cells in the rostral midbrain, GABAergic cells in the forebrain and hindbrain, Dopamine and serotonin cells in the caudal hypothalamus and sox2 cells lining the hindbrain ventricle are activated in response to the A1 antagonist and VMAT positive cells are activated in response to the A2A agonist, suggesting these areas are involved in adenosine signaling in zebrafish. Thirdly, we find that knocking out the zebrafish adenosine receptors has no effect on sleep architecture. Lastly, we find that while the A1 agonist phenotype requires the zfAdora1a receptor, the antagonist and the A2A agonist behavioral phenotypes are not mediated by the zfAdora1a, zfAdora1b and zfAdoraA2Aa, zfAdora2Ab receptors respectively.

The ecology of the Gussage, a lined winterbourne

The Gussage, a Dorset winterhourne (intermittent chalk stream), has been used to convey water from a compensation borehole to the River Allen to supplement its flow to meet demand for water. Sections of the Gussage have been lined with chalk, butyl sheeting or polythene sheeting to prevent water loss through the porous bed. The effects of this major environmental modification associated with these abstraction practices in the winterbourne catchments have been studied in the Gussage system since 1973. To compensate for the lack of adequate pre-lining data, comparative studies have been made on 3 small unlined chalk streams of varying flow regimes, ie. the Crichel (a winterbourne), the North Winterbourne and the Tarrant (permanent discharge in the reaches studies). The distribution of macrophytes and invertebrates in winterbournes are compared with that in natural and artificial permanent streams. Statistical analysis showed samples from the winterbourne sites and the unmodified permanent stream sites are quite distinct, despite the fact that no samples were taken from winterbourne sites during the dry phase. This emphasizes the differences between the fauna of an intermittent and a permanent stream and suggests that alteration of the flow regime could be a significant factor. Where flow regime has been altered, as in the Gussage downstream of the borehole, the samples occupy an intermediate position. Within this group of modified sites there is no apparent gross difference between the invertebrates of lined or unlined reaches.

Efeito da 1,10-fenantrolina e seus derivados complexados em metal na atividade proteolítica de Leishmania braziliensis

Leishmanioses são um grupo de doenças com um largo espectro de manifestações clínicas, as quais variam desde lesões cutâneas até o envolvimento visceral severo, podendo levar ao óbito. A leishmaniose é, ainda hoje, uma doença negligenciada, estando entre os agravos prioritários do programa de pesquisa sobre doenças da pobreza da Organização Mundial da Saúde (OMS). Além de não haver vacinas disponíveis, a terapia é baseada em medicamentos injetáveis que causam sérios efeitos colaterais, tornando o tratamento inviável para muitos países endêmicos. Drogas derivadas de metal representam um novo arsenal terapêutico antimicrobiano e anti-câncer. Os inibidores de peptidase/agentes quelantes tais como 1,10-fenantrolina e seus derivados, no estado livre de metal ou como ligantes com metais de transição, interferem com a função de vários sistemas biológicos. Em trabalhos anteriores, nosso grupo descreveu que o parasito L. braziliensis produziu moléculas gp63 sensíveis a 1,10-fenantrolina. No presente trabalho, demonstramos a distribuição celular da molécula gp63 em uma cepa virulenta de L. braziliensis por meio de análises bioquímicas e imuno-histoquímica. Depois disso, relatamos os efeitos inibitórios de três compostos derivados da 1,10-fenantrolina, 1,10-fenantrolina-5,6-diona (phendio), [Cu(phendio)2] e [Ag(phendio)2], nas atividades metalopeptidases celulares e extracelulares produzidas por promastigotas de L. braziliensis, bem como as suas ações sobre a viabilidade do parasita e na interação com as células de macrófagos murinos. As moléculas gp63 foram detectadas em compartimentos de parasitos, incluindo membrana citoplasmatica e bolsa flagelar. O tratamento de promastigotas de L. braziliensis durante 1 hora com 1,10-fenantrolina e seus derivados resultou numa inibição significativa da viabilidade celular e mostrou um mecanismo de ação irreversível. Estes inibidores de metalopeptidases induziram apoptose em promastigotas de L. braziliensis, demonstrada através da marcação com anexina/iodeto de propídio e ensaio TUNEL. O pré-tratamento de promastigotas com os inibidores de metalopeptidases induziram uma diminuição na expressão de moléculas de superfície gp63, assim como uma redução significativa no índice de associação com macrófagos. Em paralelo, macrófagos infectados com L. braziliensis e tratados com 1,10-fenantrolina e seus derivados promoveram uma potente redução sobre o número de amastigotas intracelulares. O tratamento de macrófagos com 1,10-fenantrolina e seus derivados não induziram o aumento de óxido nítrico. A ação combinatória sobre a capacidade de crescimento entre os compostos derivados da 1,10-fenantrolina e Glucantime, quando ambos foram utilizados em concentracões sub-inibidoras, também foi observada. In vivo os compostos derivados da 1,10-fenantrolina e seus drivados foram capazes de controlar o tamanho das lesões a partir da terceira semana de tratamento em relação ao controle não tratado em hamsters infectados quando administrado por via intraperitoneal. Os animais tratados com os compostos apresentaram maior resposta intradérmica (DTH) aos antígenos de L. braziliensis. Coletivamente, a 1,10-fenantrolina e seus derivados metálicos apresentam uma nova perspectiva de estudos para o desenvolvimento de novos fármacos anti-L. braziliensis

Percepção socioambiental aplicada em instituição de ensino no âmbito da racionalização do uso da água a partir de aproveitamento de águas pluviais.

Devido à falta de água em algumas regiões, o tema aproveitamento de águas pluviais vem se desenvolvendo ultimamente. Fica evidente a importância de sensibilizar as pessoas para que ajam de modo responsável e com consciência. A escola é um espaço de sensibilidade e conscientização que pode educar os alunos junto ao meio escolar e à comunidade local sobre o meio ambiente. O objetivo do presente trabalho foi o de realizar no Instituto de Aplicação Fernando Rodrigues da Silveira (CAp-UERJ) uma pesquisa de percepção ambiental com os alunos do 2 e 5 ano dos anos iniciais do Ensino Fundamental, a partir da conscientização pautada na educação ambiental após instalado o sistema de captação de águas pluviais, desenvolvida no projeto de Manejo de Águas Pluviais - MAPLU aprovado pelo FINEP, cujo objetivo é o desenvolvimento de soluções urbanísticas e ambientalmente adequadas de manejo de águas pluviais. Foram realizadas as oficinas com cada grupo focal e aplicados questionários para avaliar os resultados gerados. As oficinas demonstraram um avanço no conhecimento, pois a partir de uma abordagem participativa, os alunos puderam expressar os seus interesses e conhecimentos. Para quantificar o consumo de água no Instituto, foram levantadas informações relativas aos usuários, medições de vazões e faturas de consumos de água disponibilizados pela Companhia Estadual de Águas e Esgoto - CEDAE. Por meio de entrevistas com amostras de população, verificou-se a frequência e o tempo médio de utilização dos aparelhos, bem como as principais atividades que consomem água. Estimou-se o consumo médio diário de água no CAp-UERJ em 13 L/dia por aluno.