Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure

High conservation of glycyl residues in homologous proteins is fairly frequent. It is commonly understood that glycine tends to be highly conserved either because of its unique Ramachandran angles or to avoid steric clash that would arise with a larger side chain. Using a database of aligned 3D structures of homologous proteins we identified conserved Gly in 288 alignment positions from 85 families. Ninety-six of these alignment positions correspond to conserved Gly residue with (phi, ) values allowed for non-glycyl residues. Reasons for this observation were investigated by in-silico mutation of these glycyl residues to Ala. We found in 94% of the cases a short contact exists between the C atom of the introduced Ala with the atoms which are often distant in the primary structure. This suggests the lack of space even for a short side chain thereby explaining high conservation of glycyl residues even when they adopt (phi, ) values allowed for Ala. In 189 alignment positions, the conserved glycyl residues adopt (phi, ) values which are disallowed for Ala. In-silico mutation of these Gly residues to Ala almost always results in steric hindrance involving C atom of Ala as one would expect by comparing Ramachandran maps for Ala and Gly. Rare occurrence of the disallowed glycyl conformations even in ultrahigh resolution protein structures are accompanied by short contacts in the crystal structures and such disallowed conformations are not conserved in the homologues. These observations raise the doubt on the accuracy of such glycyl conformations in proteins.

Avoiding acidic region streaking in two-dimensional gel electrophoresis: Case study with two bacterial whole cell protein extracts

Acidic region streaking (ARS) is one of the lacunae in two-dimensional gel electrophoresis (2DE) of bacterial proteome. This streaking is primarily caused by nucleic acid (NuA) contamination and poses major problem in the downstream processes like image analysis and protein identification. Although cleanup and nuclease digestion are practiced as remedial options, these strategies may incur loss in protein recovery and perform incomplete removal of NuA. As a result, ARS has remained a common observation across publications, including the recent ones. In this work, we demonstrate how ultrasound wave can be used to shear NuA in plain ice-cooled water, facilitating the elimination of ARS in the 2DE gels without the need for any additional sample cleanup tasks. In combination with a suitable buffer recipe, IEF program and frequent paper-wick changing approach, we are able to reproducibly demonstrate the production of clean 2DE gels with improved protein recovery and negligible or no ARS. We illustrate our procedure using whole cell protein extracts from two diverse organisms, Escherichia coli and Mycobacterium smegmatis. Our designed protocols are straightforward and expected to provide good 2DE gels without ARS, with comparable times and significantly lower cost.

Statistical significance of episodes with general partial orders

Frequent episode discovery is one of the methods used for temporal pattern discovery in sequential data. An episode is a partially ordered set of nodes with each node associated with an event type. For more than a decade, algorithms existed for episode discovery only when the associated partial order is total (serial episode) or trivial (parallel episode). Recently, the literature has seen algorithms for discovering episodes with general partial orders. In frequent pattern mining, the threshold beyond which a pattern is inferred to be interesting is typically user-defined and arbitrary. One way of addressing this issue in the pattern mining literature has been based on the framework of statistical hypothesis testing. This paper presents a method of assessing statistical significance of episode patterns with general partial orders. A method is proposed to calculate thresholds, on the non-overlapped frequency, beyond which an episode pattern would be inferred to be statistically significant. The method is first explained for the case of injective episodes with general partial orders. An injective episode is one where event-types are not allowed to repeat. Later it is pointed out how the method can be extended to the class of all episodes. The significance threshold calculations for general partial order episodes proposed here also generalize the existing significance results for serial episodes. Through simulations studies, the usefulness of these statistical thresholds in pruning uninteresting patterns is illustrated. (C) 2014 Elsevier Inc. All rights reserved.

Probable maximum precipitation estimation for catchments in Mahanadi river basin

Probable maximum precipitation (PMP) is a theoretical concept that is widely used by hydrologists to arrive at estimates for probable maximum flood (PMF) that find use in planning, design and risk assessment of high-hazard hydrological structures such as flood control dams upstream of populated areas. The PMP represents the greatest depth of precipitation for a given duration that is meteorologically possible for a watershed or an area at a particular time of year, with no allowance made for long-term climatic trends. Various methods are in use for estimation of PMP over a target location corresponding to different durations. Moisture maximization method and Hershfield method are two widely used methods. The former method maximizes the observed storms assuming that the atmospheric moisture would rise up to a very high value estimated based on the maximum daily dew point temperature. On the other hand, the latter method is a statistical method based on a general frequency equation given by Chow. The present study provides one-day PMP estimates and PMP maps for Mahanadi river basin based on the aforementioned methods. There is a need for such estimates and maps, as the river basin is prone to frequent floods. Utility of the constructed PMP maps in computing PMP for various catchments in the river basin is demonstrated. The PMP estimates can eventually be used to arrive at PMF estimates for those catchments. (C) 2015 The Authors. Published by Elsevier B.V.

Evolution of texture and its influence on the failure of components in some aluminium alloys

This paper describes the evolution of crystallographic texture in three of the most important high strength aluminium alloys, viz., AA2219, AA7075 and AFNOR7020 in the cold rolled and artificially aged condition. Bulk texture results were obtained by plotting pole figures from X-ray diffraction results followed by Orientation Distribution Function (ODF) analysis and micro-textures were measured using EBSD. The results indicate that the deformation texture components Cu, Bs and S, which were also present in the starting materials, strengthen with increase in amount of deformation. On the other hand, recrystallization texture components Goss and Cube weaken. The Bs component is stronger in the deformation texture. This is attributed to the shear banding. In-service applications indicate that the as-processed AFNOR7020 alloy fails more frequently compared to the other high strength Al alloys used in the aerospace industry. Detailed study of deformation texture revealed that strong Brass (Bs) component could be associated to shear banding, which in turn could explain the frequent failures in AFNOR7020 alloy. The alloying elements in this alloy that could possibly influence the stacking fault energy of the material could be accounted for the strong Bs component in the texture.

BLOC-2 targets recycling endosomal tubules to melanosomes for cargo delivery

Hermansky-Pudlak syndrome (HPS) is a group of disorders characterized by the malformation of lysosome-related organelles, such as pigment cell melanosomes. Three of nine characterized HPS subtypes result from mutations in subunits of BLOC-2, a protein complex with no known molecular function. In this paper, we exploit melanocytes from mouse HPS models to place BLOC-2 within a cargo transport pathway from recycling endosomal domains to maturing melanosomes. In BLOC-2-deficient melanocytes, the melanosomal protein TYRP1 was largely depleted from pigment granules and underwent accelerated recycling from endosomes to the plasma membrane and to the Golgi. By live-cell imaging, recycling endosomal tubules of wild-type melanocytes made frequent and prolonged contacts with maturing melanosomes; in contrast, tubules from BLOC-2-deficient cells were shorter in length and made fewer, more transient contacts with melanosomes. These results support a model in which BLOC-2 functions to direct recycling endosomal tubular transport intermediates to maturing melanosomes and thereby promote cargo delivery and optimal pigmentation.

QoS Performance Analysis of Routing Protocols in Vehicular Ad-hoc Networks

Vehicular Ad-hoc Networks (VANET), is a type of wireless ad-hoc network that aims to provide communication among vehicles. A key characteristic of VANETs is the very high mobility of nodes that result in a frequently changing topology along with the frequent breakage and linkage of the paths among the nodes involved. These characteristics make the Quality of Service (QoS) requirements in VANET a challenging issue. In this paper we characterize the performance available to applications in infrastructureless VANETs in terms of path holding time, path breakage probability and per session throughput as a function of various vehicle densities on road, data traffic rate and number of connections formed among vehicles by making use of table-driven and on-demand routing algorithms. Several QoS constraints in the applications of infrastructureless VANETs are observed in the results obtained.

Emergent Intelligence Based QoS Routing in MANET

Mobile Ad hoc Networks (MANETs) are self-organized, infrastructureless, decentralized wireless networks consist of a group of heterogeneous mobile devices. Due to the inherent characteristics of MANE -Ts, such as frequent change of topology, nodes mobility, resource scarcity, lack of central control, etc., makes QoS routing is the hardest task. QoS routing is the task of routing data packets from source to destination depending upon the QoS resource constraints, such as bandwidth, delay, packet loss rate, cost, etc. In this paper, we proposed a novel scheme of providing QoS routing in MANETs by using Emergent Intelligence (El). The El is a group intelligence, which is derived from the periodical interaction among a group of agents and nodes. We logically divide MANET into clusters by centrally located static agent, and in each cluster a mobile agent is deployed. The mobile agent interacts with the nodes, neighboring mobile agents and static agent for collection of QoS resource information, negotiations, finding secure and reliable nodes and finding an optimal QoS path from source to destination. Simulation and analytical results show that the effectiveness of the scheme. (C) 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.ore/licenscs/by-nc-nd/4.0/). Peer-review under responsibility of the Conference Program Chairs

Limited-view light sheet fluorescence microscopy for three dimensional volume imaging

We propose and demonstrate a limited-view light sheet microscopy (LV-LSM) for three dimensional (3D) volume imaging. Realizing that longer and frequent image acquisition results in significant photo-bleaching, we have taken limited angular views (18 views) of the macroscopic specimen and integrated with maximum likelihood (ML) technique for reconstructing high quality 3D volume images. Existing variants of light-sheet microscopy require both rotation and translation with a total of approximately 10-fold more views to render a 3D volume image. Comparatively, LV-LSM technique reduces data acquisition time and consequently minimizes light-exposure by many-folds. Since ML is a post-processing technique and highly parallelizable, this does not cost precious imaging time. Results show noise-free and high contrast volume images when compared to the state-of-the-art selective plane illumination microscopy. (C) 2015 AIP Publishing LLC.

Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

Discovering compressing serial episodes from event sequences

Most pattern mining methods yield a large number of frequent patterns, and isolating a small relevant subset of patterns is a challenging problem of current interest. In this paper, we address this problem in the context of discovering frequent episodes from symbolic time-series data. Motivated by the Minimum Description Length principle, we formulate the problem of selecting relevant subset of patterns as one of searching for a subset of patterns that achieves best data compression. We present algorithms for discovering small sets of relevant non-redundant episodes that achieve good data compression. The algorithms employ a novel encoding scheme and use serial episodes with inter-event constraints as the patterns. We present extensive simulation studies with both synthetic and real data, comparing our method with the existing schemes such as GoKrimp and SQS. We also demonstrate the effectiveness of these algorithms on event sequences from a composable conveyor system; this system represents a new application area where use of frequent patterns for compressing the event sequence is likely to be important for decision support and control.

Mechanism Analysis of Landslide of a Layered Slope Induced by Drawdown of Water Level

The frequent drawdown of water level of Yangtze River will greatly influence the stability of the widely existing slopes in the Three Gorges reservoir zone, especially those layered ones. Apart from the fluctuating speed of water level, the different geological materials will also play important roles in the failure of slopes. Thus, it must be first to study the mechanism of such a landslide caused by drawdown of water level.A new experimental setup is designed to study the performance of a layered slope under the drawdown of water level. The pattern of landslide of a layered slope induced by drawdown of water level has been explored by means of simulating experiments. The influence of fluctuating speed of water level on the stability of the layered slope is probed,especially the whole process of deformation and development of landslide of the slope versus time. The experimental results show that the slope is stable during the water level rising, and the sliding body occurs in the upper layer of the slope under a certain drawdown speed of water level. In the process of slope failure, some new small sliding body will develop on the main sliding body, and the result is that they speed up the disassembly of the whole slope.Based on the simulating experiment on landslide of a layered slope induced by drawdown of water level, the stress and displacement field of the slope are calculated.The seepage velocity, the pore water pressure, and the gradient of pore water head are also calculated for the whole process of drawdown of water level. The computing results are in good agreement with the experimental results. Accordingly, the mechanism of deformation and landslide of the layered slope induced by drawdown of water level is analyzed. It may provide basis for treating this kind of layered slopes in practical engineering.

La Celestina en escenarios argentinos : observaciones comparatistas sobre las adaptaciones de Jorge Goldenberg (1993) y Daniel Suárez Marzal (2007)

Integran este número de la revista ponencias presentadas en Studia Hispanica Medievalia VIII: Actas de las IX Jornadas Internacionales de Literatura Española Medieval, 2008, y de Homenaje al Quinto Centenario de Amadis de Gaula.

La souffrance émotionnelle des personnels d’intervention : résultats préliminaires de l’étude sur la santé et la qualité de vie au travail dans les métiers du secteur de l’aide et du soin à domicile

Resumen: La prolongación de la edad y el aumento de la expectativa de vida han hecho surgir nuevas necesidades de atención para las personas ancianas y ello ha inducido a la ampliación de las prestaciones de servicios a domicilio. En este sentido, el trabajo de estos profesionales de intervención a domicilio, así como sus misiones, están en plena mutación. Es un sector con dificultades, debido a la dificultad de reclutar un personal especializado y al absentismo inquietante. Después de un análisis sobre el estado de este sector de la profesión en el que se establece la diferencia entre el enfoque físico y el psicológico sobre la salud, nuestra reflexión se centra en los riesgos psicosociales de esta población de profesionales. Se presentan los resultados preliminares de la investigación realizada con una muestra de 38 personas que ejercían laboralmente en este sector. Emerge la expresión de un sufrimiento emocional, en la que el aislamiento de los participantes es uno de los factores que caracterizan los oficios identificados con una fuerte dimensión relacional con personas vulnerables. La dimensión asistencial del trabajo se presenta como fuente de satisfacción del oficio pero, a su vez, puede conducir a una dificultad de gestionar acontecimientos no previstos