Nature Precedings
Not a member yet
3446 research outputs found
Sort by
Towards a web-based simulation experiment description repository
No full textModellers are producing more and more complex models. Unless these models are sufficiently characterised and made available to the research community their reuse will be minimal, and reproducing simulation experiments incorporating them will prove problematic. Consensus on the content and form of experiment recipes that combine models and simulations will encourage model sharing and facilitate reuse.

A set of guidelines specifying the 'Minimum Information About a Simulation Experiment'(MIASE) proposes a common set of information necessary to reproduce simulation experiments that incorporate quantitative models.

We have instantiated these guidelines in a web-based content management system. With our system you can create Simulation and Experiment Descriptions, enrich them with experimental data and annotate them with domain meta-information to facilitate classification, searching and cross referencing - all with the goal of reusing your models and reproducing your experimental results
Betaine aldehyde dehydrogenase (BADH) from Hordeum vulgare- an in-silico study
Get PDFGlycine Betaine is a quaternary amino compound that accumulates in stress conditions, mainly abiotic stresses like drought and salinity & synthesized by the two-step oxidation of choline via the intermediate betaine aldehyde, catalyzed by Choline monooxygenase and Betaine aldehyde dehydrogenase (BADH).
The sequence analysis of key enzymes of Glycine betaine biosynthesis i.e. BADH was carried out using various online proteomic tools available on Expasy and EBL, and then homologous modeling of this enzyme was performed using automated mode SWISS-MODEL & GENO 3D and models were analyzed on QMEAN. This was an attempt to find the possible model of BADH, because no physical model of BADH is yet available on PDB
Distribution of ABO blood groups and Rh(D) factor among the Brahmin and Kushwaha populations of Jhansi District(U.P)
Get PDFThe distribution of ABO blood groups and Rh(D) factor has been studied among the Brahmin and Kushwaha populations of Jhansi Uttar Pradesh. The A,B,O and AB blood group percentage in Brahmins was recorded as 20.88%, 36.64%, 37.02% and 10.44% .The Rh(D) positive percentage was 96.20% and Rh(d) negative 3.79%. In Kushwaha population the percentage of A,B,O and AB was recorded as 25.65%, 30.26%, 31.25% and 12.82% respectively. The Rh (D) positive was recorded as 97.36% and Rh(d) negative as 2.63%. The allele frequency of ABO among Brahmins was 0.198, 0.266, 0.536 and in Kushwaha the allele frequency of ABO was recorded as 0.251, 0.278, and 0.471 respectively. So the prevalence of the ABO from the area under study can be shown with a general formula as O>B>A>AB
SBFC - The Systems Biology Format Converter Framework
Get PDFThe System Biology Format Converter (SBFC) aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biology. Although there are various tools available to convert models from one format to another, most of them have been independently developed and cannot easily be combined, specially to provide support for more formats. The framework is written in Java and can be used as a standalone executable. Recently a prototype has been developed with OSGi to achieve a more modular framework structure. This is a collaborative project and we hope that developers will provide support for more formats by creating new modules. SBFC allows anyone to easily add new converters and to integrate existing converters with a minimum of changes. We will also allow to combine several existing converters
Pachydermoperiostosis-Like Disease In Captive Red Ruffled Lemurs (Varecia Variegatus Rubra)
Get PDFPachydermatoperiostosis, a rare form of hypertrophic osteoarthropathy, is of unknown etiology and previously thought limited to humans. The only periosteal reaction previously reported in prosimians is related to renal disease. Notation of hypertrophic osteoarthritis in three prosimians led to recognition that this was the first non-human documentation of the disease. Three related red ruffed lemurs (Varecia variegatus rubra) had diaphyseal periosteal reaction classic for hypertrophic osteoarthropathy. Workup was negative for known underlying causes and for the secondary hyperparathyroidism which produces bone alterations in black Eulemur macao, black and white Varecia variegatatus varigatus and ringtail Lemur catta lemurs. Recognition of facial coarsening allows identification of the primary form of hypertrophic osteoarthropathy, categorized in humans as primary hypertrophic osteoarthropathy. This is the first recognition of the phenomenon in the order primates, exclusive of humans, and represents a new model for this rare disease
Some thoughts about the future of SBML
Get PDFSBML was designed in 2000, merely 2 years after the first official specification of XML. 11 years afterward, the current structure of the language is largely unchanged. Since then, its user base evolved much, as did the whole field of modeling in biology. 
If one wants SBML to evolve in the next decade, it is time to start discussing the basics now. The presentation covers a series of fundamental issues such as SBML coverage, unity of the language, use of elements and attributes etc
Towards a Modelling Ecosystem for Libraries of Modular, Reusable Components
No full textCellML 1.1 [1] is an XML-based model exchange protocol with inherent support for modularity.
To assist in answering complex biomedical research questions, we are developing libraries of modular model components that facilitate mathematical model construction. 
Stored in the online, publicly accessible CellML Repository [2], the libraries vary from genetic and associated regulatory components for Synthetic Biology [3] to quantifying the Systems Biology of cardiovascular wall mal-adaptation [4,5].
 

Currently however, using the libraries is not as easy as it should be. Here I describe progress towards a modelling ecosystem to encompasses component search and retrieval, composition, visualization and analysis services [6], building upon research in semantic annotation [7,8], graphical rendering [9], collaborative model storage [10] and large-scale parallel model simulation environments [11,12]. 
 
Development of this ecosystem provides ample motivation to explore the applicability of emerging community standards as well as iteratively refine their efficacy in real biomedical problem scenarios.

[1] Cuellar A. A., et al. (2003) Sim.
[2] http://models.cellml.org
[3] Cooling M. T., et al. (2010) Bioinf.
[4] Ho H., et al. (2010) IFMBE Proc.
[5] Ho H., et al. (2011) in press.
[6] Cooling M. T., et al. (2010) IWBDA Proc.
[7] Cooling M. T. (2011) ISMB Proc.
[8] Misirli G., et al. (2011) Bioinf.
[9] Wimalaratne, S. M., et al. (2009) Bioinf.
[10] Yu, T., et al. (2011) Bioinf.
[11] Sher, A. A. et al. (2010) IEEE EMBS Proc.
[12] Cooling M. T., et al. (2010) NZ eResearch Symp
Circulating Neutrophils from Trauma Patients Induce Apoptosis Through Dephosphorylation of Epithelial Cell Caspase-8
Get PDFActivated neutrophils can cause oxidant-mediated bystander injury to host cells. This injury has previously been ascribed to the direct effects of oxidants on membrane phospholipids. We show here that oxidants released by neutrophils activated in vivo in survivors of multiple trauma or in vitro by exposure to bacterial lipopolysaccharide (LPS) can also promote the apoptotic death of epithelial cells, through the SHP-1-mediated dephosphorylation of epithelial cell caspase-8. Neutrophils from a cohort of patients who sustained serious injury induced the apoptotic death of cultured epithelial cells in a manner that was dependent on the activity of the NADPH oxidase and the generation of neutrophil-derived reactive oxygen intermediates. Caspase-8 is constitutively tyrosine phosphorylated in a panel of resting epithelial cells, but undergoes dephosphorylation in response to hydrogen peroxide (H2O2), activated neutrophils, or inhibition of Src kinases. Mutation of either of 2 key caspase-8 tyrosine residues, Y397 and Y465 to a non-phosphorylatable phenylalanine accelerates the apoptosis of epithelial cells transfected with caspase-8, while mutation of the same tyrosine residues to the phosphomimetic glutamic acid, or transfection with the Src kinases Lyn or c-Src inhibits H2O2-induced apoptosis. Exposure to either H2O2 or LPS-stimulated neutrophils, increases the phosphorylation and activity of the phosphatase SHP-1, increases the activity of caspases-8 and -3, and accelerates epithelial cell apoptosis. Together these data reveal a novel mechanism for neutrophil-mediated tissue injury through oxidant-dependent SHP-1-mediated dephosphorylation of caspase-8 resulting in enhanced epithelial cell apoptosis
Purification and physicochemical studies of metalloprotease, cotinifolin from Euphorbia cotinifolia
No full textA detailed procedure for the purification of cotinifolin from the latex of Euphorbia cotinifolia using ion exchange chromatography and hydrophobic interaction chromatography is described.
Various biochemical characteristics of cotinifolin and other enzymatic properties along with spectroscopic parameters like circular dichorism and fluorescence have been reported. Cotinifolin is stable over a wide range of pH and under extreme conditions of chaotrops and organic solvents where most proteins lost their functions. Further studies on the identification of physiological substrates, biophysical and structural studies will give insight into the utility of the enzyme in the biotechnological industries and protein engineering