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| M Shankaracharya; Suchitra Kumari; Ambarish S. Vidyarthi. |
| Hepatitis is deadly, and the fifth leading cause of death after heart disease, stroke, chest disease and cancer. Worldwide, 1.5 million deaths per year have been estimated. Detection of hepatitis is a big problem for general practitioners. An expert doctor commonly makes decisions by evaluating the current test results of a patient or by comparing the patient with others with the same condition with reference to the previous decisions. Many machine learning and data mining techniques have been designed for the automatic diagnosis of hepatitis. However, no one tool is available to the general population for the diagnosis of Hepatitis. Hence, a graphical user interface-enabled tool needs to be developed, through which medical practitioners can feed patient... |
| Tipo: Poster |
Palavras-chave: Biotechnology; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7093/version/1 |
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| Stephan Kraemer; Jonathon D. Vaught; Christopher Bock; Larry Gold; Evaldas Katilius; Tracy R. Keeney; Nancy Kim; Nicholas A. Saccomano; Sheri K. Wilcox; Dom Zichi; Glenn M. Sanders. |
| Recently, we reported an aptamer-based, highly multiplexed assay for the purpose of biomarker identification. To enable seamless transition from highly multiplexed biomarker discovery assays to a format suitable and convenient for diagnostic and life-science applications, we developed a streamlined, plate-based version of the assay. The plate-based version of the assay is robust, sensitive (sub-picomolar), rapid, can be highly multiplexed (upwards of 60 analytes), and fully automated. We demonstrate that quantification by microarray-based hybridization, Luminex bead-based methods, and qPCR are each compatible with our platform, further expanding the breadth of proteomic applications for a wide user community. |
| Tipo: Manuscript |
Palavras-chave: Biotechnology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4642/version/1 |
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| Dharmendra Kumar Yadav; Feroz Khan; Arvind Singh Negi. |
| Immuno-modulation is the process of alteration in immune response due to foreign intrusion of molecules inside the body. In the present communication QSAR and molecular docking studies for immuno-modulatory activity of derivatives of gallic acid were performed. Molecular docking studies showed higher binding affinity with INFα-2, IL-6, and IL-4 receptors. Binding site residues indicate hydrogen bonds formation with gallic acid derivative compounds G-3, G-4, G-5, G-6, G-7 and G-10. Further screening through quantitative structure activity relationship model establishes the immuno-modulatory activity of the compounds G-4, G-7, G-9, G-10, G-12 and G-13. Activity was predicted through a robust statistical model, developed by forward feed multiple... |
| Tipo: Presentation |
Palavras-chave: Biotechnology; Cancer; Chemistry; Pharmacology; Bioinformatics; Plant Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6620/version/1 |
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| Swapnil G. Sanmukh; Waman N. Paunikar. |
| The structure and function prediction for the Microsystin synthetases from Microsystis aerogenosa (LNSAMB) were carried out for verifying the authenticity of the sequenced genes. The genes for Microsystin synthetases (mcyA, mcyB, mcyD and mcyE,), were predicted by the application of computational methods and Bioinformatics web tools. The probable function prediction for the proteins was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching protein databases for the presence of conserved domains. While tertiary structures were constructed using PS2 Server- Protein Structure Prediction server. This study revealed structural and functional validation of sequenced genes. |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6835/version/1 |
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| Marie Loh; Adrian Mondry. |
| Countless statistical methods have been described for the analysis of DNA microarrays, and each yields distinct results. This raises the question whether DNA microarrays are robust diagnostic tools.

In order to address this issue, we compared five formally similar statistical tests for gene selection on a single data set derived from acute leukemia patients. Inter-test agreement of gene selection, of sample classification and with standard clinical diagnosis was calculated using Cohen's κ-score.

The inter-test agreement scores were 0.15 < κ < 0.68 for gene selection, and 0.60 < κ < 0.89 for sample classification.... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Cancer; Genetics & Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1056/version/1 |
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| Zhidong Zhou; Tit Meng Lim. |
| In this study we demonstrate for the first time that GSH could rapidly conjugate with dopamine (DA)-derived DA-o-quinones without enzymatic catalysis to form short-lived intermediate GSH-conjugates (2-S-GSH-DA-o-quinone and 5-S-GSH-DA-o-quinone). These intermediate GSH-conjugates are unstable and would finally form reactive or non-reactive GSH-conjugates dependent on ambient reductive forces. Under insufficient reductive forces, the intermediate GSH-conjugates could cyclize spontaneously to form reactive 7-S-GSH-aminochrome (7-S-GSH-AM). The 7-S-GSH-AM is so reactive that it could further react with another GSH to form 4,7-bi-GSH-5,6-dihydroindole. Its reactivity could also abrogate tyrosinase activity in solutions. In addition, the 7-S-GSH-AM could... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Chemistry; Neuroscience; Pharmacology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/2963/version/1 |
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| Pradeep Sharma1,2; J. Sakata2; Y. Shibuya2; Masato Ikegami2. |
| Begomoviruses are currently emerging as a major threat to vegetable production in many tropical and subtropical regions worldwide. Pepper yellow leaf curl disease (PepYLCD) has been noticed in many Capsicum annum L. producing regions from East Asia especially from Indonesia and causes devastating damage to pepper crop production since 2000. In this study we have cloned and sequenced complete nucleotide of begomoviruses from pepper exhibiting leaf curling and bright yellowing symptoms. Besides, we also determined the occurrence of disease on tomato evoking leaf curl symptoms and ageratum with yellow vein type of symptoms. On the basis of genome organization and sequence homology, these viruses were designated as Pepper yellow leaf curl Indonesia virus... |
| Tipo: Poster |
Palavras-chave: Biotechnology; Genetics & Genomics; Plant Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4162/version/1 |
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| Subhrangsu Chatterjee; Wimal Pathmasiri; Jyoti Chattopadhyaya. |
| The role of the sequence-context in the self-organization of four single-stranded (ss) isosequential pairs of DNAs (1 – 4) and RNAs (5 – 8), [d/r-(5'C^1^A^2^X^3^G^4^Y^5^A^6^C^7^): X^3^ = A or C, Y^5^ = A or C; sequence variations: 2^2^ = 4], has been elucidated by NMR-constrained Molecular Dynamics (MD) simulations (2 ns). Following sequence-specific observations have been made from the solution NMR and the NMR constrained MD simulation study: (i) Analysis of the NOESY footprints, mainly (H8/H6)~n~ to (H1' and H3')~n-1~ contacts, of ssDNAs (1 - 4) and ssRNAs (5 – 8) in the aqueous medium have shown that all ssDNAs (1 - 4) and ssRNAs (5 - 8) adopt right handed stacked helical structures in the NMR... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Chemistry; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1685/version/1 |
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| Shaheed SM; Rohit JP; Madhan R; Selvakumar K. |
| Ethanol derived from non-edible biomass is renewable and a clean source of energy. It is independent of the food industry and it is economically feasible. The first generation biofuel or bioethanol is still not a very convenient source of energy as it prominently depends on the availability of grains. The main objective of this work is to develop an industrious efficient process to produce ethanol from lignocellulosic biomasses like wood and leaf in a lab scale. Two processes were compared. The first process involved an alkaline pre-treatment of the powdered biomass followed by dilute acid hydrolysis. The second process involved an alkaline treatment followed by direct hydrolysis of the biomass by use of a fungal species obtained from rotting wood.... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6579/version/1 |
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| Tristan Giesa; Melis Arslan; Nicola Pugno; Markus J. Buehler. |
| Silk is an exceptionally strong, extensible and tough material made from simple protein building blocks. The molecular structure of dragline spider silk repeat units consists of semi-amorphous and nanocrystalline beta-sheet protein domains. Here we show by a series of computational experiments how the nanoscale properties of silk repeat units are scaled up to create macroscopic silk fibers with outstanding mechanical properties despite the presence of cavities, tears and cracks. We demonstrate that the geometric confinement of silk fibrils to diameters of 50±30 nm width is critical to facilitate a powerful mechanism by which hundreds of thousands of protein domains synergistically resist deformation and failure to provide enhanced strength,... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Chemistry; Bioinformatics; Earth & Environment. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5916/version/2 |
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| Zohar Gavish; Amir Arav; Menahem Ben-Haim. |
| Preservation of vascularized organs such as the liver is limited to 24hrs. before destructive processes disqualify it for transplantation. This narrow time window prevents surgeons from performing optimal pathogen screening and matching tests which often lead to re-transplantation. Numerous problems are associated with viably freezing and thawing a whole liver: complicated geometry, poor heat transfer, release of latent heat and the difficulty of generating a uniform cooling rate. Our past success led us to apply our novel freezing technique to a larger solid organ, the liver. Whole livers were frozen/thawed using a directional solidification apparatuses; viability was tested by means of integrity and functionality in vitro and in auxiliary liver... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1352/version/1 |
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| C. M. Anuradha; B. Babajan; M. Chaitanaya; C. Rajasekhar; Suresh Kumar Chitta. |
| Worldwide, tuberculosis (TB) remains the most frequent and important infectious disease causing morbidity and death. One-third of the world's population is infected with Mycobacterium tuberculosis (Mtb), the etiologic agent of TB. In this context, TB is in the top three, with malaria and HIV being the leading causes of death from a single infectious agent, and about two million deaths are attributable to TB annually. The bacterial enzyme MurA catalyzes the transfer of enolpyruvate from phosphoenolpyruvate (PEP) to uridine diphospho-N-acetylglucosamine (UNAG), which is the first committed step of bacterial cell wall biosynthesis. In this work, 3D structural model of Mtb-MurA enzyme has been developed, for the first time, by homology modeling and... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Microbiology; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3731/version/1 |
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| Abhishek Kumar. |
| Computational and statistical analysis has formed a large component of the biophysical efforts put forth to understand protein structure and function, due to the diversity and complexity of their structure. Outer membrane proteins form a diverse and complex set of proteins. Of these, porins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective. The objective of this study is to analyze the structural organization of porins using atomic temperature factor as a parameter. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. As good crystal structures have fewer possibilities of errors... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Microbiology; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7016/version/1 |
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| Amelia G. White; Avi Ma'ayan. |
| Multivariate experiments and genomics studies applied to mammalian cells often produce lists of genes or proteins altered under treatment/disease vs. control/normal conditions. Such lists can be identified in known protein-protein interaction networks to produce subnetworks that “connect” the genes or proteins from the lists. Such subnetworks are valuable for biologists since they can suggest regulatory mechanisms that are altered under different conditions. Often such subnetworks are overloaded with links and nodes resulting in connectivity diagrams that are illegible due to edge overlap. In this study, we attempt to address this problem by implementing an approximation to the Steiner Tree problem to connect seed lists of mammalian... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1768/version/1 |
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| Alfonso Gautieri; Simone Vesentini; Alberto Redaelli; Markus J. Buehler. |
| Collagen constitutes one third of the human proteome, providing mechanical stability, elasticity and strength to connective tissues. Collagen is also the dominating material in the extracellular matrix (ECM) and is thus crucial for cell differentiation, growth and pathology. However, fundamental questions remain with respect to the origin of the unique mechanical properties of collagenous tissues, and in particular its stiffness, extensibility and nonlinear mechanical response. By using x-ray diffraction data of a collagen fibril reported by Orgel et al. (Proceedings of the National Academy of Sciences USA, 2006) in combination with protein structure identification methods, here we present an experimentally validated model of the nanomechanics of a... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Chemistry; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4995/version/1 |
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