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The 1st japan-india bilateral symposium on bioinformatics

P06 Koki Tsukamoto
Molecular Function Team, CBRC, E-mail: @aist.go.jp
Title: The development of an affinity evaluation and prediction system by using protein-protein
docking simulations and parameter tuning
A system was developed to evaluate and predict the interaction between protein pairs by using the widely used shape complementarity search method as the algorithm for docking simulations between the proteins. We used this system, which we call the affinity evaluation and prediction (AEP) system, to evaluate the interaction between 20 protein pairs. The system first executes a “round robin” shape complementarity search of the target protein group, and evaluates the interaction between the complex structures obtained by the search. These complex structures are selected by using a statistical procedure that we developed called grouping. At a low prevalence of 5.0%, our AEP system predicted protein-protein interactions with a 45.0% recall, 47.4% precision, 94.8% accuracy and an F-measure of 0.462. By optimizing the grouping process, our AEP system successfully predicted 9 protein pairs (among 20 pairs) that were biologically significant combinations. Our ultimate goal is to construct an affinity database that will provide cell biologists and drug designers with crucial information obtained
P07 Kana Shimizu
Molecular Function Team, CBRC, E-mail: shimizu-kana@aist.go.jp
Title: Analysis of intrinsic protein disorder in a human protein-protein interaction network
Intrinsic protein disorder is a widespread phenomenon, in which there is a lack of a stable three-dimensional structure. This flexible region is considered to play an important role in protein-protein interaction (PPI) networks, because dynamic conformation may allow proteins to interact with several structurally different targets. In this work, we investigate what kind of molecular recognition is preferred in PPI, by analyzing a human PPI network and large-scale predictive results of protein disorder. We defined three protein interaction types with regard to protein disorder, as order-order interaction: interaction between folded proteins, order-disorder: interaction between a mostly disordered protein and a folded protein, and disorder-disorder interaction: interaction between mostly disordered proteins. To estimate numbers of interactions for each interaction type, we predicted disorder by using POODLE for all proteins which are included in a human PPI network, and classified those proteins into mostly folded proteins or mostly disordered proteins. The result shows that larger number of disorder-disorder interactions are estimated in human PPI network comparing to those in a random network, which indicates that molecular recognition without stable 3D structures are preferred. Also, functional analysis gives the results that large number of disorder-disorder interactions is found in several cancer-associated pathways and neurodegenerative diseases-associated pathway. P08 Shinsuke Yamada
Molecular Function Team, CBRC, E-mail: yamada-shinsuke@aist.go.jp
Title: Improvement in speed of multiple sequence alignment program PRIME
Multiple sequence alignment (MSA) provides a fundamental tool in bioinformatics. Although many programs have been developed, there is room for improvement in accuracy and speed. Until now, we have developed an MSA program, PRIME, which employs a doubly nested randomized iterative refinement strategy optimizing a weighted sum-of-pairs score. The major feature of PRIME is to use a group-to-group sequence alignment algorithm with a piecewise linear function as a gap cost. Although PRIME can construct accurate alignments comparable to the most accurate programs, its computational The 1st Japan-India Bilateral Symposium on Bioinformatics speed is somewhat slower than these programs. In order to improve calculation speed of PRIME, we incorporated two heuristics into PRIME: anchoring and grouping methods. An anchoring method is to locate well-conserved regions in a given MSA that act as anchor points to reduce the region of DP matrix to be examined, while a grouping method detects conserved subfamily alignments in a given MSA to reduce the number of DP computations. In addition to these heuristics, we introduced a progressive method, which parallelizes not only distance calculation but also alignment construction process. This poster will discuss the effects of these heuristics and the performance improvement of the parallelized
P09 Masayuki Kimura
Molecular Function Team, CBRC, E-mail: masayuki.kimura@aist.go.jp
Department of Applied Biological Science, Faculty of Science & Technology, Tokyo University of Science
Title: A study of mannose-6-phosphate binding poses on lectin by using GOLD
Carbohydrates have a variety of structural diversities and functions in biosystems. They take place in nature as simple or complex carbohydrates, either by themselves or linked to proteins and lipids. In the endoplasmic reticulum, it is known that N-linked carbohydrates are only high mannose type. We are interested in recognizing mechanism between carbohydrates and lectins. Phosphorylated carbohydrate was chosen as a ligand and mannose-6-phosphate (M6P) receptor was chosen as a lectin for docking simulation. M6P is a phosphorylated mannose and a precursor of the glycosylation. We study interactions between M6P receptor and phosphorylated carbohydrates by docking simulation using the program GOLD (Genetic Optimization for Ligand Docking). A genetic algorithm is used for protein-ligand docking calculation. The GOLD evaluates the scoring of docking simulations. In this presentation we report the binding poses of various carbohydrates with M6P receptor.
P10 Hiroaki Suzuki
Molecular Function Team, CBRC, E-mail: hiroaki.suzuki@aist.go.jp
Department of Chemistry, School of Science, The University of Tokyo
Title: Fragmentation of Lewis-Type Trisaccharides in the Gas Phase: Experimental and
Theoretical Studies
Oligosaccharides have been the targets of intense study because they play essential roles in various biochemical processes: they act as media for cell–cell recognition, aid in the processes of fertilization and inflammation, and add functionality to proteins by post-translational modification. In particular, the structural study of oligosaccharides has become an essential part of glycobiology, because oligosaccharide structure has a close relationship with receptor molecular recognition, and carbohydrates structure directly affects carbohydrate function. As an analytical method for the structural analysis of oligosaccharides, mass spectrometry has widely been applied to obtain fragment ion spectra of various oligosaccharides. The advantage of applying mass spectrometry to such structural analyses is that fragment ion spectra that yield various structural information can be obtained by decomposition via collision-induced dissociation (CID) or postsource decay (PSD). We can obtain a variety of structural information of oligosaccharides by using mass spectrometry, including information on sequence, isomeric configuration, and stereochemistry, such as anomeric configuration and linkage type. A study of the fragmentation mechanism is indispensable to any discussion of the theoretical aspects of why each oligosaccharide produces a characteristic pattern in mass spectra. In this study, fragmentation mechanism of negatively charged Lewis-type trisaccharides in the gas phase was studied using mass
spectrometry and theoretical calculations. P11 Shuichi Hirose
Molecular Function Team, CBRC, E-mail: hirose-shuichi@aist.go.jp
Title: Prediction of protein structural flexibility from an amino acid sequence
A protein structural flexibility is often associated with protein function. Thus, the identification of a flexible region can provide valuable information for inferring functionally important residues in a protein sequence. The movement of a polypeptide segment can be classified conceptually into two forms: internal motion and external motion. The former is a deformation of segment itself, conversely the latter involves only rotational and translational motions as a rigid body. Normal Mode Analysis (NMA) can derive these motions, but its application remains limited because it requires full structural information. Here, we present a novel method for predicting these two protein motions solely from amino acid sequence information. We prepared a dataset by calculating internal and external motions using NMA. Then, we developed a prediction method based on the Random Forest algorithm using information on the adjacent paired amino acid residues and the predicted secondary structure. Our method exhibited higher prediction accuracy when compared to results of the predictions using the naïve P12 Jihoon Ryu, Tomoko Yaguchi, Il-Kyu Choi, Chae-Ok Yun and Sunil C. Kaul and Renu Wadhwa 1. Research Institute for Cell Engineering (RICE) 2. Institute for Cancer Research, Yonsei University College of Medicine, 134 Shinchon-Dong, Title: BST-2: a novel mediator of drug resistance of cancer cells
We performed a retrovirus driven expression screening for identification of drug resistance mediating cellular factors. A large variety of cancer cell lines and the drugs including DNA toxins and topoisomerase inhibitors (doxorubicin, etoposide and camptothecin), anti-metabolite (fluorouracil), microtubule poisons and(nocodazol and taxol and withaferin A) were used to select drug resistant cells and cloning of candidate cDNAs mediating the drug resistance phenotype. We have identified bone marrow stromal cell antigen 2 (BST-2) as the most common factor that was upregulated in drug resistant cells. BST-2 was first cloned as an enriched protein in multiple myelomas and has been predicted to be involved in carcinogenesis, angiogenesis and chromosomal instability. We have validated the involvement of BST-2 in drug resistant phenotype of cancer cells by enforced overexpression and silencing. Furthermore, BST-2 was seen to increase the invasiveness of cancer cells. The study has demonstrated a novel function of BST-2 and suggested it as a target for cancer
P13 Caroline Cheung, Md. Kamrul Hasan, Renu Wadhwa and Sunil Kaul
Research Institute for Cell Engineering (RICE), AIST
Title: CARF plays a vital role in replicative and stress-induced senescence of human cells
We had previously cloned a novel protein, CARF (Collaborator of ARF) that enhanced ARF- dependent and -independent wild type p53 function, central to the control of cellular senescence and stress response of human cells. It was further shown that the CARF interacts with ARF, p53 and HDM2 proteins, and in turn gets regulated by HDM2-mediated degradation. Since CARF also acts as a transcriptional repressor of HDM2, it causes its own regulation by feedback loops. In an attempt to discern the function of CARF, we utilized an in silico approach to identify its functional domains. Motif scan using the protein sequence predicted sites for N-glycosylation, protein kinase C The 1st Japan-India Bilateral Symposium on Bioinformatics phosphorylation, tyrosine kinase phosphorylation, double-stranded RNA-binding domain and bipartite . Based on these predictions, CARF appeared to have structural characteristics of a regulatory protein. We then undertook a study on the functional significance of CARF during replicative and stress-induced senescence of human cells. We found that the CARF is upregulated during replicative senescence and its overexpression induces premature senescence that is mediated by the upregulation of p53 and p21 proteins. Furthermore, an induction of senescence in cancer cells by DNA damaging reagents was accompanied by increased level of CARF protein and its downstream effectors p53 and p21. Taken together, we demonstrate a vital role of CARF during senescence of human cells and propose it as a new reliable bio-marker for detection of senescence and cancer therapeutics.
P14 Navjot Shah,1,2 Gurcharan Kaur,2 Renu Wadhwa,1 and Sunil Kaul1
1. Research Institute for Cell Engineering (RICE), AIST
2. Department of Biotechnology, Guru Nanak Dev University, Amritsar - 143005, India
Title: Neuroprotective potential of Ashwagandha leaf extract
Ashwagandha (Withania somnifera) roots have been in use for thousands of year in Ayurvedic medicine (Indian traditional system of medicine) to promote physical and mental health. However, their potentials are yet to be known globally. Many recent studies have provided evidence to its anti-stress, anti-oxidant, adaptogenic and immuno-stimulant activities. We have recently demonstrated that the leaf extract of Ashwagandha (LASH) has selective killing activity for cancer cells and it functions through selective activation of tumor suppressor protein p53. We also showed that the leaf extract is rich in withaferin A, withanone and withanolides of which withanone functions to kill the cancer cells selectively. Besides, we have also detected (i) anti-aging activity in LASH by using replicative senescence of human cells as a model and (ii) neuro-regenerative activity by using induced Parkinson‟s disease (PD) in mouse as a model. In the present study, we considered that the herb has traditionally been popular for improving memory, brain functions and nervous exhaustion. Indeed, Ashwagandha root extract was shown to possess gamma amino-butyric acid (GABA, a calming neurotransmitter in the brain)-like activity that appears to explain, at least in part, its positive effects for insomnia, behavioral disturbances, anti-depressant and anti-anxiety. The molecular mechanism of such activity and the active components are yet to be defined. In view of these, we anticipated the possibility of identification of neuronally active components that might be recruited in neurodegenerative diseases including Alzheimer‟s disease (AD), Parkinson‟s disease (PD) and dementia that still remain a challenge to modern medicine. We tested the effects of Ashwagandha leaf extract and its components in neuronal plasticity by using human neuroblastoma differentiation as a model system and molecular markers of differentiation. LASH and its components were investigated for induction of neuronal differentiation in a variety of neuroblastomas and the effects were evaluated in comparison to retinoic acid, a standard differentiation inducer. We also investigated if Ashwagandha-derived compounds have any protective role against (i) b-Amyloid induced toxicity and (ii) oxidation damage, the two leading pathologies of AD brain. The results may have implications in neuro-degenerative therapeutics.

Source: http://jst-dst.cbrc.jp/poster.pdf

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