455 research outputs found
Proceedings of the Fourth Annual Agricultural Marketing Conference "Government and Marketing"
Universal features of correlated bursty behaviour
Inhomogeneous temporal processes, like those appearing in human
communications, neuron spike trains, and seismic signals, consist of
high-activity bursty intervals alternating with long low-activity periods. In
recent studies such bursty behavior has been characterized by a fat-tailed
inter-event time distribution, while temporal correlations were measured by the
autocorrelation function. However, these characteristic functions are not
capable to fully characterize temporally correlated heterogenous behavior. Here
we show that the distribution of the number of events in a bursty period serves
as a good indicator of the dependencies, leading to the universal observation
of power-law distribution in a broad class of phenomena. We find that the
correlations in these quite different systems can be commonly interpreted by
memory effects and described by a simple phenomenological model, which displays
temporal behavior qualitatively similar to that in real systems
Lysosomes in iron metabolism, ageing and apoptosis
The lysosomal compartment is essential for a variety of cellular functions, including the normal turnover of most long-lived proteins and all organelles. The compartment consists of numerous acidic vesicles (pH ā¼4 to 5) that constantly fuse and divide. It receives a large number of hydrolases (ā¼50) from the trans-Golgi network, and substrates from both the cellsā outside (heterophagy) and inside (autophagy). Many macromolecules contain iron that gives rise to an iron-rich environment in lysosomes that recently have degraded such macromolecules. Iron-rich lysosomes are sensitive to oxidative stress, while ārestingā lysosomes, which have not recently participated in autophagic events, are not. The magnitude of oxidative stress determines the degree of lysosomal destabilization and, consequently, whether arrested growth, reparative autophagy, apoptosis, or necrosis will follow. Heterophagy is the first step in the process by which immunocompetent cells modify antigens and produce antibodies, while exocytosis of lysosomal enzymes may promote tumor invasion, angiogenesis, and metastasis. Apart from being an essential turnover process, autophagy is also a mechanism by which cells will be able to sustain temporary starvation and rid themselves of intracellular organisms that have invaded, although some pathogens have evolved mechanisms to prevent their destruction. Mutated lysosomal enzymes are the underlying cause of a number of lysosomal storage diseases involving the accumulation of materials that would be the substrate for the corresponding hydrolases, were they not defective. The normal, low-level diffusion of hydrogen peroxide into iron-rich lysosomes causes the slow formation of lipofuscin in long-lived postmitotic cells, where it occupies a substantial part of the lysosomal compartment at the end of the life span. This seems to result in the diversion of newly produced lysosomal enzymes away from autophagosomes, leading to the accumulation of malfunctioning mitochondria and proteins with consequent cellular dysfunction. If autophagy were a perfect turnover process, postmitotic ageing and several age-related neurodegenerative diseases would, perhaps, not take place
FungiDB: an integrated functional genomics database for fungi
FungiDB (http://FungiDB.org) is a functional genomic resource for pan-fungal genomes that was developed in partnership with the Eukaryotic Pathogen Bioinformatic resource center (http://EuPathDB.org). FungiDB uses the same infrastructure and user interface as EuPathDB, which allows for sophisticated and integrated searches to be performed using an intuitive graphical system. The current release of FungiDB contains genome sequence and annotation from 18 species spanning several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal āZygomyceteā lineage Mucormycotina. Additionally, FungiDB contains cell cycle microarray data, hyphal growth RNA-sequence data and yeast two hybrid interaction data. The underlying genomic sequence and annotation combined with functional data, additional data from the FungiDB standard analysis pipeline and the ability to leverage orthology provides a powerful resource for in silico experimentation
Ligand-Receptor Interactions
The formation and dissociation of specific noncovalent interactions between a
variety of macromolecules play a crucial role in the function of biological
systems. During the last few years, three main lines of research led to a
dramatic improvement of our understanding of these important phenomena. First,
combination of genetic engineering and X ray cristallography made available a
simultaneous knowledg of the precise structure and affinity of series or
related ligand-receptor systems differing by a few well-defined atoms. Second,
improvement of computer power and simulation techniques allowed extended
exploration of the interaction of realistic macromolecules. Third, simultaneous
development of a variety of techniques based on atomic force microscopy,
hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or
flexible transducers yielded direct experimental information of the behavior of
single ligand receptor bonds. At the same time, investigation of well defined
cellular models raised the interest of biologists to the kinetic and mechanical
properties of cell membrane receptors. The aim of this review is to give a
description of these advances that benefitted from a largely multidisciplinar
approach
GiardiaDB and TrichDB : integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis
Ā© 2008 The Authors. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License. The definitive version was published in Nucleic Acids Research 37 (2009): D526-D530, doi:10.1093/nar/gkn631.GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.Federal funds from the National Institute of Allergy and Infectious Diseases; Department of Health and Human Services, National Institutes of Health (HHSN266200400037C). Funding for open access charge: National Institutes of Health (HHSN266200400037C)
ToxoDB: an integrated Toxoplasma gondii database resource
ToxoDB (http://ToxoDB.org) is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. ToxoDB has matured significantly since its initial release. Here we outline the numerous updates with respect to the data and increased functionality available on the website
Global Research Alliance N2O chamber methodology guidelines: considerations for automated flux measurement
Nitrous oxide (N2O) emissions are highly episodic in response to nitrogen additions and changes in soil moisture. Automated gas sampling provides the necessary high temporal frequency to capture these emission events in real time, ensuring the development of accurate N2O inventories and effective mitigation strategies to reduce global warming. This paper outlines the design and operational considerations of automated chamber systems including chamber design and deployment, frequency of gas sampling, and options in terms of the analysis of gas samples. The basic hardware and software requirements for automated chambers are described, including the major challenges and obstacles in their implementation and operation in a wide range of environments. Detailed descriptions are provided of automated systems that have been deployed to assess the impacts of agronomy on the emissions of N2O and other significant greenhouse gases. This information will assist researchers across the world in the successful deployment and operation of automated N2O chamber systems
EuPathDB: the eukaryotic pathogen genomics database resource
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of hostāpathogen interactions
JNK mediates UVB-induced apoptosis upstream lysosomal membrane permeabilization and Bcl-2 family proteins
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