Identification of Proteins Secreted by Malaria Parasite into Erythrocyte using SVM and PSSM profiles

Background  

Malaria parasite secretes various proteins in infected RBC for its growth and survival. Thus identification of these secretory proteins is important for developing vaccine/drug against malaria. The existing motif-based methods have got limited success due to lack of universal motif in all secretory proteins of malaria parasite.     

Wnt/��-catenin signaling in hepatic organogenesis

Wnt/β-catenin signaling has come to the forefront of liver biology in recent years. This pathway regulates key pathophysiological events inherent to the liver including development, regeneration and cancer, by dictating several biological processes such as proliferation, apoptosis, differentiation, adhesion, zonation and metabolism in various cells of the liver. This review will examine the studies that have uncovered the relevant roles of Wnt/β-catenin signaling during the process of liver development. We will discuss the potential roles of Wnt/β-catenin signaling during the phases of development, including competence, hepatic induction, expansion and morphogenesis. In addition, we will discuss the role of negative and positive regulation of this pathway and how the temporal expression of Wnt/β-catenin can direct key processes during hepatic development. We will also identify some of the major deficits in the current understanding of the role of Wnt/β-catenin signaling in liver development in order to provide a perspective for future studies. Thus, this review will provide a contextual overview of the role of Wnt/β-catenin signaling during hepatic organogenesis.Key words: liver development, liver cancer, liver regeneration, Wnt signaling, proliferation, differentiationThe Wnt/β-catenin pathway is an evolutionarily well-conserved pathway that has proven to be essential to normal cellular processes such as development, growth, survival, regeneration and self-renewal.^1–5 Its diverse functions also include the initiation and progression of cancer.⁶ In fact, one area in which this pathway has been extensively studied is in liver cancer.Mutations of Wnt/β-catenin pathway members in hepatocarcinogenesis are common. For example, 90–100% of hepatoblastomas contain mutations in adenomatous polyposis coli (APC), CTNNB1 and/or Axin1/2, which causes cytoplasmic and nuclear localization of β-catenin.^7–9 Axin1 and β-catenin mutations have also been identified in approximately 25% of hepatocellular carcinomas,^10–12 while overexpression of the frizzled-7 receptor¹³ and glycogen synthase kinase-3 (GSK-3) inactivation¹⁴ can also lead to aberrant β-catenin pathway activation. The dysregulation of this pathway in hepatic cancers makes it an attractive target for potential therapies, and experimental treatment in vivo has shown promising results. For example, inhibiting β-catenin expression by siRNA or R-Etodolac decreases proliferation and survival of human hepatoma cell lines.^15,16 Since cancer recapitulates development, determining the timing of β-catenin activation during hepatogenesis will help us to better understand the inappropriate activation of this pathway in hepatocarcinogenesis.Recent work has elucidated the role of β-catenin signaling in the liver, and has highlighted its essential role in liver health and disease.¹⁷ In addition, emerging evidence suggests that this pathway plays a key role in liver organogenesis.     

Identification of ATP binding residues of a protein from its primary sequence

Background  

One of the major challenges in post-genomic era is to provide functional annotations for large number of proteins arising from genome sequencing projects. The function of many proteins depends on their interaction with small molecules or ligands. ATP is one such important ligand that plays critical role as a coenzyme in the functionality of many proteins. There is a need to develop method for identifying ATP interacting residues in a ATP binding proteins (ABPs), in order to understand mechanism of protein-ligands interaction.     

Production of scleroglucan from Sclerotium rolfsii MTCC 2156

Scleroglucan, a neutral homopolysaccaride consisting of a linear chain of beta-D-(1-3)-glucopyranosyl and beta-D-(1-6)-glucopyranosyl groups, was produced by pure culture fermentation from Sclerotium rolfsii MTCC 2156 by submerged culture. Fermentation process was optimized in two steps. In the first step, one-factor-at-a-time method was used to investigate the effects of medium constituents such as carbon and nitrogen sources. In the second step, concentration of medium components was optimized using an L16-orthogonal array method. In all, 10 different carbon sources and eight different nitrogen sources were evaluated. Maximum yield of 16.58 g/l was obtained in a medium containing sucrose as a carbon source and sodium nitrate and yeast extract as nitrogen source.     

Physiological methods to study biofilm disinfection

This report reviews the development of a rapidin situ approach to study the physiological responses of bacteria within biofilms to disinfectants. One method utilized direct viable counts (DVC) to assess the disinfection efficacy when thin biofilms were exposed to chlorine or monochloramine. Results obtained using the DVC method were one log higher than plate count (PC) estimates of the surviving population after disinfection. Other methods incorporated the use of fluorogenic stains, a cryotomy technique to yield thin (5-m) sections of biofilm communities and examination by fluorescence microscopy. The fluorogenic stains used in this approach included 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), which indicates cellular electron transport activity and Rhodamine 123, which responds specifically to proton motive force. The use of these stains allowed the microscopic discrimination of physiologically active bacteria as well as heterogeneities of active cells within thicker biofilms. The results of experiments using these techniques with pure culture and binary population biofilms on stainless steel coupons indicated biocidal activity of chlorine-based disinfectants occurred initially at the bulk-fluid interface of the communities and progressed toward the substratum. This approach provided a unique opportunity to describe the spatial response of bacteria within biofilms to antimicrobial agents and address mechanisms explaining their comparative resistance to disinfection in a way that has not been possible using traditional approaches. Results obtained using this alternative approach were also consistently higher than PC data following disinfection. These observations suggest that traditional methods involving biofilm removal and bacterial enumeration by colony formation overestimate biocide efficacy. Hence the alternative approach described here more accurately indicates the ability of bacteria surviving disinfection to recover and grow as well as demonstrate spatial heterogeneities in cellular physiological activities within biofilms.     

Myosin light-chain expression during avian muscle development

Monoclonal antibodies to adult chicken myosin light chains were generated and used to quantitate the types of myosin light-chain (MLC) isoforms expressed during development of the pectoralis major (PM), anterior latissimus dorsi (ALD), and medial adductor (MA) muscles of the chicken. These are muscles which, in the adult, are composed predominantly of fast, slow, and a mixture of fiber types, respectively. Three distinct phases of MLC expression characterized the development of the PM and MA muscles. The first identifiable pase occurred during the period of 5-7 d of incubation in ovo. Extracts of muscles from the pectoral region (which included the presumptive PM muscle) contained only fast MLC isoforms. This period of exclusive fast light-chain synthesis was followed by a phase (8- 12 d of incubation in ovo) in which coexpression of both fast and slow MLC isoforms was apparent in both PM and MA muscles. During the period, the composition of both fast and slow MLC isoforms in the PM and MA muscles was identical. Beginning at day 12 in ovo, the ALD was also subjected to immunochemical analyses. The proportion of fast and slow MLCs in this muscle at day 12 was similar to that present in the other muscles studied. The third development phase of MLC expression began at approximately 12 d of incubation in ovo and encompassed the transition in MLC composition to the isoform patterns incubation in ovo and encompassed the transition in MLC composition to the isoform patterns typical of adult muscle. During this period, the relative proportion of slow MLC rose in both the MA and ALD and fell in the PM. By day 16, the third fast light chain, LC(3f), was apparent in extracts of both the PM and MA. These results show that there is a developmental progression in the expression of MLC in the two avian muscles studied from day 5 in ovo; first, only fast MLCs are accumulated, then both fast and slow MLC isoforms are expressed. Only during the latter third of development in ovo is the final MLC isoform pattern characteristic of a particular muscle type expressed.     

Last‐century changes of alpine grassland water‐use efficiency: a reconstruction through carbon isotope analysis of a time‐series of Capra ibex horns

The ecophysiological response of an alpine grassland to recent climate change and increasing atmospheric CO₂ concentration was investigated with a new strategy to go back in time: using a time‐series of Capra ibex horns as archives of the alpine grasslands' carbon isotope discrimination (¹³Δ). From the collection of the Natural History Museum of Bern, horns of 24 males from the population of the Augstmatthorn–Brienzer Rothorn mountains, Switzerland, were sampled covering the period from 1938 to 2006. Samples were taken from the beginning of each year‐ring of the horns, representing the beginning of the horn growth period, the spring. The horns' carbon ¹³C content (Δ¹³C) declined together with that of atmospheric CO₂ over the 69‐year period, but ¹³Δ increased slightly (+0.4‰), though significantly (P<0.05), over the observation period. Estimated intercellular CO₂ concentration increased (+56 μmol mol^?1) less than the atmospheric CO₂ concentration (+81 μmol mol^?1), so that intrinsic water‐use efficiency increased by 17.8% during the 69‐year period. However, the atmospheric evaporative demand at the site increased by approximately 0.1 kPa between 1955 and 2006, thus counteracting the improvement of intrinsic water‐use efficiency. As a result, instantaneous water‐use efficiency did not change. The observed changes in intrinsic water‐use efficiency were in the same range as those of trees (as reported by others), indicating that leaf‐level control of water‐use efficiency of grassland and forests followed the same principles. This is the first reconstruction of the water‐use efficiency response of a natural grassland ecosystem to last century CO₂ and climatic changes. The results indicate that the alpine grassland community has responded to climate change by improving the physiological control of carbon gain to water loss, following the increases in atmospheric CO₂ and evaporative demand. But, effective leaf‐level water‐use efficiency has remained unchanged.     

Machine learning techniques in disease forecasting: a case study on rice blast prediction

Background  

Diverse modeling approaches viz. neural networks and multiple regression have been followed to date for disease prediction in plant populations. However, due to their inability to predict value of unknown data points and longer training times, there is need for exploiting new prediction softwares for better understanding of plant-pathogen-environment relationships. Further, there is no online tool available which can help the plant researchers or farmers in timely application of control measures. This paper introduces a new prediction approach based on support vector machines for developing weather-based prediction models of plant diseases.