Últimos itens adicionados do Acervo: Proceedings Nature

Nature é uma das mais prestigiosas e antigas revistas científicas do mundo: sua primeira edição é de 4 de novembro de 1869. Entre as inúmeras descobertas científicas publicadas na Nature estão a dos raios X, da estrutura em dupla hélice do ADN e o buraco na camada de ozônio.

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‣ Prospect and importance of green mulching on the soil status of tropical tasar plantation fields in India

Rangareddygari Manohar Reddy; Ramkumar -
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
The soils of tropical tasar plantation fields in general are sloppy and are primarily deficient of nutrition due to top soil erosion and constant leaf productivity exploitation to rear tasar silk insect, Antheraea mylitta Drury. The rainfed field of Terminalia tomentosa (W&A) plantation has been evaluated for soil fortification with green mulching through legumes, Sun hemp (Crotalaria juncea), Daincha (Sesbania aculeata), Green gram (Vigna radiatus) and Black gram (Vigna mungo) during rainy season. The mulching has enhanced the water holding, moisture retention, electrical conductivity, organic carbon, nitrogen (N) and potassium (K) and reduced the bulk density and pore space of soil. Among the legumes, Sun hemp has shown higher improvement of water holding (56.9%), moisture content (68.5 & 37.9%) at 30 and 45 cm depth, electrical conductivity (0.30 mhos/cm), bulk density (1.12g/ cm³), pore space (50.4%), organic carbon (0.61%), nitrogen (109 kg/ha) and potassium (254 kg/ha) of the soil, and could augment the leaf yield of tasar food plant with 24.8 MT/ha. The study infers the prospect and importance of green mulching in tasar food plantation in improving the physico chemical nature and fertility status of soil to attain optimal leaf yield in the T. tomentosa food plant.

‣ A Modular Semantic Annotation Framework: CellML Metadata Specifications 2.0

Michael T. Cooling
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
In the last decade or so, model encoding efforts such as CellML and SBML have greatly facilitated model availability. But, as the complexity of models increases, the utility of these models can vary. The addition of semantic information is crucial to transforming mathematical models from esoteric to informative resources. We have developed a metadata specification framework to better enable the annotation of CellML models with metadata. The framework consists of a core specification describing, in general terms, how annotations should be attached using RDF/XML, and satellite specifications covering several domains of immediate interest, using elements from the Dublin Core, FOAF (Friend-Of-A-Friend), BIBO (Bibliographic Ontology), MIRIAM URNs and Biomodels Qualifiers. We also describe what we see as several emerging challenges in the field, uncovered during the application of this annotation scheme to mathematical models.

‣ Towards a Modelling Ecosystem for Libraries of Modular, Reusable Components

Michael T. Cooling
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
CellML 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....

‣ Circulating Neutrophils from Trauma Patients Induce Apoptosis Through Dephosphorylation of Epithelial Cell Caspase-8

Songhui Jia; Jean Parodo; Emmanuel Battisti-Charbonney; Jennifer Tsang; Sangyang Jia; Ori D. Rotstein; Andras Kapus; John C. Marshall
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Activated 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...

‣ libSBML Status update

Sarah M. Keating
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
Overview of current status of libSBML development.

‣ libSBML New conversion API

Sarah M. Keating; Frank T. Bergmann
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
Description of the new API for including converters within libSBML.

‣ Identifiers.org/MIRIAM Registry annotation and cross-referencing framework

Nick Juty; Camille Laibe; Nicolas Le Novere
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
We describe the MIRIAM Registry, which forms a foundation layer database upon which persistent, unambiguous and perennial identifiers of data can be built. We describe the existing MIRIAM URI identifiers, and the newly minted resolvable, parallel forms of these identifiers which use Identifiers.org URLs.

‣ Purification and physicochemical studies of metalloprotease, cotinifolin from Euphorbia cotinifolia

Reetesh Kumar
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
A 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.

‣ Targeted delivery of anti-inflammatory therapy to rheumatoid tissue by fusion proteins containing an IL-4-linked synovial targeting peptide

Sarah E. Wythe; Danielle DiCara; Taher E. I. Taher; Ciara M. Finucane; Rita Jones; Y. K. Stella Man; Michele Bombardieri; Ahuva Nissim; Stephen J. Mather; Yuti Chernajovsky; Costantino Pitzalis
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
We provide first-time evidence that the synovial endothelium-targeting peptide (SyETP) CKSTHDRLC successfully delivers conjugated IL-4 to human rheumatoid synovium transplanted into SCID mice. SyETP, previously isolated by in vivo phage display and shown to preferentially localize to synovial xenografts, was linked by recombinant technology to hIL-4 via an MMP-cleavable sequence. Both IL-4 and the MMP-cleavable sequence were shown to be functional. IL-4-SyETP augmented production of IL-1ra by synoviocytes stimulated with IL-1[beta] in a dose-dependent manner. In vivo imaging confirmed increased retention of SyETP-linked-IL-4 in synovial grafts which was enhanced by increasing number of copies (one to three) in the constructs. Strikingly, SyETP delivered bioactive IL-4 in vivo as demonstrated by increased pSTAT6 in synovial grafts. Thus, this study provides proof of concept for peptide-tissue-specific targeted immunotherapy in rheumatoid arthritis. This technology is potentially applicable to other biological therapies providing enhanced potency to inflammatory sites and reducing systemic toxicity.

‣ Identification and Evolution of Transcription Factors in Stramenopiles

Francisco Buitrago; Silvia Restrepo; Diego Riaño-Pachón
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
Background. Many transcriptional regulatory proteins have been identified and classified into several families on the basis of sequence similarity (Fukami, 2003), these families usually regulate important biological processes, such as development and responses to external stimuli. Transcription factors (TFs) regulate spatial and temporal gene expression by binding to DNA and either activating or repressing the action of RNA polymerases (Latchman, 2004); in addition to TFs, other Transcriptional regulators (TRs) participate in transcriptional modulation by e.g., chromatin remodeling. With the availability of genome sequences for several organisms and computational strategies for gene functional annotation, the entire set of Transcription factors (TFs) and Transcription regulators (TRs) can be identified, described, and compared between species and lineages. The diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they are present in freshwater, marine and terrestrial habitats and embrace many ecologically important algal (e.g. diatoms, brown algae, chrysophytes), and heterotrophic (e.g., Oomycetes) groups. Methods. In order to find TF and TR genes in the deduced proteomes of Stramenopile we followed the approach developed in Perez et al. 2010. Briefly...

‣ SBML Team facilities & software

Frank T. Bergmann; Sarah M. Keating
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
This presentation provides a brief overview of the new SBML online validator and the updates in the SBML Tool Matrix. This presentation ends with an update on the new version of the SBML Toolbox.

‣ Hierarchical Model Composition updates

Lucian Smith
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
A summary of the status of the hierarchical model composition package for SBML Level 3, and of its current implementation.

‣ SBML Editor’s Report: Principles for Package Development

Lucian Smith
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
In the last six months, the SBML Editors have developed several principles to guide the development of SBML Level 3 packages. An update on what those principles are, and some controversies that have arisen as a result.

‣ Update: MIRIAM Registry and SBO

Nick Juty
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
We describe the MIRIAM Registry, which forms a foundation layer database upon which persistent, unambiguous and perennial identifiers of data can be built. We also describe current status and planned improvements to this system, as well as providing an update on the Systems Biology ontology since the last COMBINE meeting in Edinburgh (2010).

‣ Predicting Prostate Cancer Aggressiveness through a Nanoparticle Test

Qun Huo; Shannon Sullivan; Hillari Hallquist; Sally Litherland; David Decker; Inoel Rivera-Ramirez
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Prostate cancer (PCa) is the most common malignancy and the second leading cause of cancer death in American men. Due to the lack of accurate tests to distinguish aggressive cancer from indolent tumor, prostate cancer is often over-treated. Post-surgery pathology analysis revealed that 30% of tumors removed by radical prostatectomy are deemed clinically insignificant and would not have required such invasive treatment.^1^ Over-diagnosis and treatment of low-risk prostate cancer has serious and long-lasting side effect: as high as 70% of the patients who receive radical prostatectomy treatment will suffer a loss of sexual potency that cannot be remedied by drugs such as sildenafil citrate.^2^ We herein report a simple nanoparticle-serum protein adsorption test that not only can distinguish prostate cancer from normal and benign conditions, but also is capable of predicting the aggressiveness of prostate cancer quantitatively. This new test could potentially deliver the long-expected and very much needed solution for better individualization of prostate cancer treatment.

‣ Copper induced peroxidase, CCPP form Caribbean copper plant

Reetesh Kumar
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
Plant peroxidase exhibit broad substrate specificity and is active in a wide range of pH and temperature, and in the presence of organic compounds as well as other additives. The peroxidase is known to be involved in many physiological and regulatory processes in plants. This ppt presents an introduction on plant peroxidase and their applications. A purification protocol has been developed and the purified protein, named as CCPP is biochemically and physiologically characterized. The physiochemical properties such as molecular weight, isoelectric point have been experimentally determined. The enzymatic efficiency has been evaluated through temperature optimum, pH optimum, Km and other enzymatic properties along with spectroscopic parameters like circular dichorism and fluorescence have been mentioned. The enzyme is stable under adverse conditions like pH, strong denaturants, temperature, and organic solvents which facilitate exploring the possibilities of utilization in industrial and biotechnological applications.

‣ Standardized Model for Repeated Social Defeat Stress vs. Sensory Contact Model: similarities and differences, strengths and weaknesses

Natalia N. Kudryavtseva
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Of all the models used by behavioral neuroscience the biosocial models are gaining in popularity among the scientists who study the consequences of chronic social conflicts and social stress in animals. One of such models, the Standardized Model for Repeated Social Defeat Stress (SMRSDS) (Golden et al., 2011) has been widely applied to produce important results on the molecular mechanisms of the social defeat stress (Berton et al., 2006). SMRSDS is a modified version of the Sensory Contact Model (SCM) (Kudryavtseva, 1991), which has been used by different laboratories in its original or modified forms for elucidating implications of chronic social conflicts. The basic design and justification of the SCM different stages are described in detail in the latest publication “Sensory contact model: Protocol, control, applications” (Kudryavtseva, 2011). Thus, it is now possible to compare similarities, differences and, as a consequence, strengths and weaknesses of these two behavioral

‣ The Proteomics World is Flat: Dependence of Regulation upon Abundance

David Good; Roman Zubarev
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
The long-standing assumption that proteins divide into house-keeping and cell-specific groups was recently struck down after discovering that the vast majority of expressed proteins are shared across cell lines. Here, we tested a related hypothesis that abundant proteins are less regulated than low-abundance ones. Meta-analysis of published data revealed that protein regulation is only weakly dependent upon the protein abundance, thus providing support to cell characterization by the "top" proteome.

‣ Multifunction moonlighting and intrinsically disordered proteins: Information catalysis, nonrigid molecule symmetries, and the 'logic gate' spectrum

Rodrick Wallace
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Intrinsically disordered proteins (IDP) appear far more likely to engage in functional moonlighting than well-structured proteins. The recent use of nonrigid molecule theory to address IDP structure and dynamics produces this result directly: Mirror image subgroup or subgroupoid tiling matching of the molecular fuzzy lock-and-key can be much richer for IDPs since the number of possible group or groupoid symmetries can grow exponentially with molecule length, while tiling matching for 3D structured proteins is relatively limited. A simple information catalysis model suggests how this mechanism can produce a vast spectrum of biological 'logic gates' having subtle properties far beyond familiar AND, OR, XOR, etc. behaviors. Inferring the general from the particular, the analysis adds weight to arguments that a fundamental defining characteristic of the living state is the operation of chemical or other cognitive processes at virtually every scale and level of organization.

‣ Novel developments in SBGN-ED and applications

Tobias Czauderna; Eva Grafahrend-Belau; Astrid Junker; Anja Hartmann; Matthias Klapperstück; Falk Schreiber
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
Systems Biology Graphical Notation (SBGN, http://sbgn.org) [1] is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology. Three different views (Process Description, Entity Relationship, and Activity Flow) cover several aspects of the represented processes in different levels of detail. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary. We present methods for these tasks and novel developments in SBGN-ED (www.sbgn-ed.org) [2], a tool which allows to create all three types of SBGN maps from scratch, to validate these maps for syntactical and semantical correctness, to translate maps from the KEGG database into SBGN, and to export SBGN maps into several file and image formats. SBGN-ED is based on VANTED (Visualization and Analysis of NeTworks containing Experimental Data, http://www.vanted.org) [3]. As applications of SBGN and SBGN-ED we present furthermore MetaCrop (http://metacrop.ipk-gatersleben.de) [4], a database that summarizes diverse information about metabolic pathways in crop plants...