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Functional Equations and the Generalised Elliptic Genus  [PDF]
H. W. Braden,K. E. Feldman
Mathematics , 2005, DOI: 10.2991/jnmp.2005.12.s1.7
Abstract: We give a new derivation and characterisation of the generalised elliptic genus of Krichever-H\"ohn by means of a functional equation.
Identification of fungi of the genus Aspergillus section nigri using polyphasic taxonomy
Silva, Daiani M.;Batista, Luís R.;Rezende, Elisangela F.;Fungaro, Maria Helena P.;Sartori, Daniele;Alves, Eduardo;
Brazilian Journal of Microbiology , 2011, DOI: 10.1590/S1517-83822011000200044
Abstract: in spite of the taxonomy of the aspergillus species of the nigri section being regarded as troublesome, a number of methods have been proposed to aid in the classification of this section. this work aimed to distinguish aspergillus species of the nigri section from foods, grains and caves on the basis in polyphasic taxonomy by utilizing morphologic and physiologic characters, and sequencing of ?-tubulin and calmodulin genes. the morphologic identification proved useful for some species, such as a. carbonarius and aspergillus sp ufla dca 01, despite not having been totally effective in elucidating species related to a. niger. the isolation of the species of the nigri section on creatine sucrose agar (crea) enabled to distinguish the aspergillus sp species, which was characterized by the lack of sporulation and by the production of sclerotia. scanning electron microscopy (sem) allowed distinguishing the species into two distinct groups. the production of ochratoxin a (ota) was only found in the a. carbonarius and a. niger species. the sequencing of β-tubulin gene was efficient in differing most of the aspergillus species from the nigri section with the exception of aspergillus ufla dca 01, which could not be distinguished from a. costaricaensis. this species is morphologically similar to a. costaricaencis for its low sporulation capacity and high sclerotia production, but it differs morphologically from a. costaricaensis for its conidial ornamentation and size of vesicles. equally, based on partial calmodulin gene sequence data aspergillus ufla dca 01 differs from a. costaricaensis.
Functional analysis of OAT gene in Aspergillus Niger  [PDF]
Chuang Zhou, Xihong He, Hao Liu
Engineering (ENG) , 2012, DOI: 10.4236/eng.2012.410B036
Abstract:
Mitochondrial oxaloacetate transporter protein encoded by OAT gene transports oxaloacetate from cytoplasm into mitochondria. To investigate the primary effects of OAT gene on relative metabolism in Aspergillus niger, a oat-deleted mutant was derived from wild-type A. niger ATCC1015 using the double-crossover chromosome replacement technique. Then batch fermentation was performed to evaluate the mutant. Compared with the wild type, the mutant showed lower organic acids production, with the experimental data that the production of pyruvate and 2-ketoglutarate decreased by 31.6% and 35.7%, respectively, and by contrast, the mutant showed higher glycerol formation. The results suggest that OAT gene plays significant roles on metabolism in A. niger.
What can comparative genomics tell us about species concepts in the genus Aspergillus?
A. Rokas,G. Payne,N.D. Fedorova,S.E. Baker
Studies in Mycology , 2007,
Abstract: Understanding the nature of species" boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intraspecific comparisons, whereas the other two deal with interspecific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus – N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species.
An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer  [PDF]
Rod K. Nibbe ,Mehmet Koyutürk,Mark R. Chance
PLOS Computational Biology , 2010, DOI: 10.1371/journal.pcbi.1000639
Abstract: Emerging evidence indicates that gene products implicated in human cancers often cluster together in “hot spots” in protein-protein interaction (PPI) networks. Additionally, small sub-networks within PPI networks that demonstrate synergistic differential expression with respect to tumorigenic phenotypes were recently shown to be more accurate classifiers of disease progression when compared to single targets identified by traditional approaches. However, many of these studies rely exclusively on mRNA expression data, a useful but limited measure of cellular activity. Proteomic profiling experiments provide information at the post-translational level, yet they generally screen only a limited fraction of the proteome. Here, we demonstrate that integration of these complementary data sources with a “proteomics-first” approach can enhance the discovery of candidate sub-networks in cancer that are well-suited for mechanistic validation in disease. We propose that small changes in the mRNA expression of multiple genes in the neighborhood of a protein-hub can be synergistically associated with significant changes in the activity of that protein and its network neighbors. Further, we hypothesize that proteomic targets with significant fold change between phenotype and control may be used to “seed” a search for small PPI sub-networks that are functionally associated with these targets. To test this hypothesis, we select proteomic targets having significant expression changes in human colorectal cancer (CRC) from two independent 2-D gel-based screens. Then, we use random walk based models of network crosstalk and develop novel reference models to identify sub-networks that are statistically significant in terms of their functional association with these proteomic targets. Subsequently, using an information-theoretic measure, we evaluate synergistic changes in the activity of identified sub-networks based on genome-wide screens of mRNA expression in CRC. Cross-classification experiments to predict disease class show excellent performance using only a few sub-networks, underwriting the strength of the proposed approach in discovering relevant and reproducible sub-networks.
ECOMICS: A Web-Based Toolkit for Investigating the Biomolecular Web in Ecosystems Using a Trans-omics Approach  [PDF]
Yoshiyuki Ogata,Eisuke Chikayama,Yusuke Morioka,R. Craig Everroad,Amiu Shino,Akihiro Matsushima,Hideaki Haruna,Shigeharu Moriya,Tetsuro Toyoda,Jun Kikuchi
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0030263
Abstract: Ecosystems can be conceptually thought of as interconnected environmental and metabolic systems, in which small molecules to macro-molecules interact through diverse networks. State-of-the-art technologies in post-genomic science offer ways to inspect and analyze this biomolecular web using omics-based approaches. Exploring useful genes and enzymes, as well as biomass resources responsible for anabolism and catabolism within ecosystems will contribute to a better understanding of environmental functions and their application to biotechnology. Here we present ECOMICS, a suite of web-based tools for ECosystem trans-OMICS investigation that target metagenomic, metatranscriptomic, and meta-metabolomic systems, including biomacromolecular mixtures derived from biomass. ECOMICS is made of four integrated webtools. E-class allows for the sequence-based taxonomic classification of eukaryotic and prokaryotic ribosomal data and the functional classification of selected enzymes. FT2B allows for the digital processing of NMR spectra for downstream metabolic or chemical phenotyping. Bm-Char allows for statistical assignment of specific compounds found in lignocellulose-based biomass, and HetMap is a data matrix generator and correlation calculator that can be applied to trans-omics datasets as analyzed by these and other web tools. This web suite is unique in that it allows for the monitoring of biomass metabolism in a particular environment, i.e., from macromolecular complexes (FT2DB and Bm-Char) to microbial composition and degradation (E-class), and makes possible the understanding of relationships between molecular and microbial elements (HetMap). This website is available to the public domain at: https://database.riken.jp/ecomics/.
Improved protocols for functional analysis in the pathogenic fungus Aspergillus flavus
Zhu-Mei He, Michael S Price, Gregory R OBrian, D Ryan Georgianna, Gary A Payne
BMC Microbiology , 2007, DOI: 10.1186/1471-2180-7-104
Abstract: The efficiency of the genetic transformation system for A. flavus based on uracil auxotrophy was improved. In addition, A. flavus was shown to be sensitive to the antibiotic, phleomycin. Transformation of A. flavus with the ble gene for resistance to phleomycin resulted in stable transformants when selected on 100 μg/ml phleomycin. We also compared the phleomycin system with one based on complementation for uracil auxotrophy which was confirmed by uracil and 5-fluoroorotic acid selection and via transformation with the pyr4 gene from Neurospora crassa and pyrG gene from A. nidulans in A. flavus NRRL 3357. A transformation protocol using pyr4 as a selectable marker resulted in site specific disruption of a target gene. A rapid and convenient colony PCR method for screening genetically altered transformants was also developed in this study.We employed phleomycin resistance as a new positive selectable marker for genetic transformation of A. flavus. The experiments outlined herein constitute the first report of the use of the antibiotic phleomycin for transformation of A. flavus. Further, we demonstrated that this transformation protocol could be used for directed gene disruption in A. flavus. The significance of this is twofold. First, it allows strains to be transformed without having to generate an auxotrophic mutation, which is time consuming and may result in undesirable mutations. Second, this protocol allows for double gene knockouts when used in conjunction with existing strains with auxotrophic mutations.To further facilitate functional analysis in this strain we developed a colony PCR-based method that is a rapid and convenient method for screening genetically altered transformants. This work will be of interest to those working on molecular biology of aflatoxin metabolism in A. flavus, especially for functional analysis using gene deletion and gene expression.Aspergillus flavus is a ubiquitous fungus and a plant and animal health concern. It can colonize see
Techniques for integrating -omics data  [cached]
Siva Prasad Akula,Raghava Naidu Miriyala,Hanuman Thota,Allam Appa Rao
Bioinformation , 2009,
Abstract: The challenge for -omics research is to tackle the problem of fragmentation of knowledge by integrating several sources of heterogeneous information into a coherent entity. It is widely recognized that successful data integration is one of the keys to improve productivity for stored data. Through proper data integration tools and algorithms, researchers may correlate relationships that enable them to make better and faster decisions. The need for data integration is essential for present -omics community, because -omics data is currently spread world wide in wide variety of formats. These formats can be integrated and migrated across platforms through different techniques and one of the important techniques often used is XML. XML is used to provide a document markup language that is easier to learn, retrieve, store and transmit. It is semantically richer than HTML. Here, we describe bio warehousing, database federation, controlled vocabularies and highlighting the XML application to store, migrate and validate -omics data.
The functional equation for the twisted spinor L-series of genus 2  [PDF]
Aloys Krieg,Martin Raum
Mathematics , 2009,
Abstract: We prove the functional equation for the twisted spinor L-series of a cuspidal, holomorphic Siegel eigenform for the full modular group of genus 2. It follows from a more general functional equation, valid for Rankin convolutions of paramodular cuspforms. A non-vanishing result for Fourier-Jacabi coefficients of the eigenforms in question is the central pillar of the deduction of the former from the latter functional equation.
Wheat EST resources for functional genomics of abiotic stress
Mario Houde, Mahdi Belcaid, Fran?ois Ouellet, Jean Danyluk, Antonio F Monroy, Ani Dryanova, Patrick Gulick, Anne Bergeron, André Laroche, Matthew G Links, Luke MacCarthy, William L Crosby, Fathey Sarhan
BMC Genomics , 2006, DOI: 10.1186/1471-2164-7-149
Abstract: We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology.We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals.Cold acclimation (CA) allows hardy plants to develop the efficient freezing tolerance (FT) mechanisms needed for winter survival. During the period of exposure to low temperature (LT), numerous biochemical, physiological and metabolic functions are altered in plants, and these changes are regulated by LT mostly at the gene expression level. The identification of LT-responsive genes is therefore required to understand the molecular basis of CA. Cold-induc
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