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Biological Networks (biological + network)
Selected AbstractsPrediction of missing enzyme genes in a bacterial metabolic networkFEBS JOURNAL, Issue 9 2007Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa The metabolic network is an important biological network which consists of enzymes and chemical compounds. However, a large number of metabolic pathways remains unknown, and most organism-specific metabolic pathways contain many missing enzymes. We present a novel method to identify the genes coding for missing enzymes using available genomic and chemical information from bacterial genomes. The proposed method consists of two steps: (a) estimation of the functional association between the genes with respect to chromosomal proximity and evolutionary association, using supervised network inference; and (b) selection of gene candidates for missing enzymes based on the original candidate score and the chemical reaction information encoded in the EC number. We applied the proposed methods to infer the metabolic network for the bacteria Pseudomonas aeruginosa from two genomic datasets: gene position and phylogenetic profiles. Next, we predicted several missing enzyme genes to reconstruct the lysine-degradation pathway in P. aeruginosa using EC number information. As a result, we identified PA0266 as a putative 5-aminovalerate aminotransferase (EC 2.6.1.48) and PA0265 as a putative glutarate semialdehyde dehydrogenase (EC 1.2.1.20). To verify our prediction, we conducted biochemical assays and examined the activity of the products of the predicted genes, PA0265 and PA0266, in a coupled reaction. We observed that the predicted gene products catalyzed the expected reactions; no activity was seen when both gene products were omitted from the reaction. [source] Activation of an IL-6:STAT3-dependent transcriptome in pediatric-onset inflammatory bowel diseaseINFLAMMATORY BOWEL DISEASES, Issue 4 2008Rebecca Carey MD Abstract Background: While activation of the IL-6-dependent transcription factor signal transducer and activator of transcription 3 (STAT3) has been implicated in the pathogenesis of inflammatory bowel disease (IBD), a direct effect on mucosal gene expression and inflammation has not been shown. We hypothesized that a proinflammatory IL-6:STAT3-dependent biological network would be up regulated in pediatric-onset IBD patients, and would be associated with the severity of mucosal inflammation. Methods: Patients with pediatric-onset IBD were enrolled at diagnosis and during therapy. Serum cytokine analysis was performed using Bioplex. STAT3 phosphorylation (pSTAT3) in peripheral blood leukocytes (PBLs) was assessed by flow cytometry. Immunohistochemistry of colonic mucosa was used to localize pSTAT3 and STAT3 target genes. Microarray analysis was used to determine RNA expression profiles from colon biopsies. Results: Circulating IL-6 was upregulated in active IBD patients at diagnosis and during therapy. STAT3 activation was increased in PB granulocytes, IL-6-stimulated CD3+/CD4+ lymphocytes, and affected colon biopsies of IBD patients. The frequency of pSTAT3+ PB granulocytes and colon epithelial and lamina propria cells was highly correlated with the degree of mucosal inflammation. Microarray and Ingenuity Systems bioinformatics analysis identified IL-6:STAT3-dependent biological networks upregulated in IBD patients which control leukocyte recruitment, HLA expression, angiogenesis, and tissue remodeling. Conclusions: A proinflammatory IL6:STAT3 biologic network is upregulated in active pediatric IBD patients at diagnosis and during therapy. Specific targeting of this network may be effective in reducing mucosal inflammation. (Inflamm Bowel Dis 2007) [source] Multiple pathways in the FGF signaling network are frequently deregulated by gene amplification in oral dysplasiasINTERNATIONAL JOURNAL OF CANCER, Issue 9 2009Ivy F.L. Tsui Abstract Genetic alteration in oral premalignant lesions (OPLs), the precursors of oral squamous cell carcinomas (OSCCs), may represent key changes in disease initiation and development. We ask if DNA amplification occurs at this early stage of cancer development and which oncogenic pathways are disrupted in OPLs. Here, we evaluated 50 high-grade dysplasias and low-grade dysplasias that later progressed to cancer for gene dosage aberrations using tiling-path DNA microarrays. Early occurrences of DNA amplification and homozygous deletion were frequently detected, with 40% (20/50) of these early lesions exhibiting such features. Expression for 88 genes in 7 recurrent amplicons were evaluated in 5 independent head and neck cancer datasets, with 40 candidates found to be overexpressed relative to normal tissues. These genes were significantly enriched in the canonical ERK/MAPK, FGF, p53, PTEN and PI3K/AKT signaling pathways (p = 8.95 × 10,3 to 3.18 × 10,2). These identified pathways share interactions in one signaling network, and amplification-mediated deregulation of this network was found in 30.0% of these preinvasive lesions. No such alterations were found in 14 low-grade dysplasias that did not progress, whereas 43.5% (10/23) of OSCCs were found to have altered genes within the pathways with DNA amplification. Multitarget FISH showed that amplification of EGFR and CCND1 can coexist in single cells of an oral dysplasia, suggesting the dependence on multiple oncogenes for OPL progression. Taken together, these findings identify a critical biological network that is frequently disrupted in high-risk OPLs, with different specific genes disrupted in different individuals. © 2009 UICC [source] Identification of erythroid-enriched gene expression in the mouse embryonic yolk sac using microdissected cellsDEVELOPMENTAL DYNAMICS, Issue 2 2008Latasha C. Redmond Abstract Little is known about the genes that control the embryonic erythroid program. Laser capture microdissection was used to isolate primitive erythroid precursors and epithelial cells from frozen sections of the embryonic day 9.5 yolk sac. The RNA samples were amplified and labeled for hybridization to Affymetrix GeneChip Mouse Genome 430A 2.0 arrays. Ninety-one genes are expressed significantly higher in erythroid than in epithelial cells. Ingenuity pathway analysis indicates that many of these erythroid-enriched genes cluster in highly significant biological networks. One of these networks contains RBTN2/LMO2, SCL/TAL1, and EKLF/KLF1, three of the very few genes required for primitive erythropoiesis. Quantitative real-time polymerase chain reaction was used to verify that platelet factor 4, reelin, thrombospondin - 1, and muscleblind - like 1 mRNA is erythroid-enriched. These genes have established roles in development or differentiation in other systems, and are, therefore, good candidates for regulating primitive erythropoiesis. These results provide a catalog of genes expressed during primitive erythropoiesis. Developmental Dynamics 237:436,446, 2008. © 2008 Wiley-Liss, Inc. [source] Complex networks: two ways to be robust?ECOLOGY LETTERS, Issue 6 2002Carlos J. Melián Abstract Recent studies of biological networks have focused on the distribution of the number of links per node. However, the connectivity distribution does not uncover all the complexity of their topology. Here, we analyse the relation between the connectivity of a species and the average connectivity of its nearest neighbours in three of the most resolved community food webs. We compare the pattern arising with the one recently reported for protein networks and for a simple null model of a random network. Whereas two highly connected nodes are unlikely to be connected between each other in protein networks, the reverse happens in food webs. We discuss this difference in organization in relation to the robustness of biological networks to different types of perturbation. [source] Activation of an IL-6:STAT3-dependent transcriptome in pediatric-onset inflammatory bowel diseaseINFLAMMATORY BOWEL DISEASES, Issue 4 2008Rebecca Carey MD Abstract Background: While activation of the IL-6-dependent transcription factor signal transducer and activator of transcription 3 (STAT3) has been implicated in the pathogenesis of inflammatory bowel disease (IBD), a direct effect on mucosal gene expression and inflammation has not been shown. We hypothesized that a proinflammatory IL-6:STAT3-dependent biological network would be up regulated in pediatric-onset IBD patients, and would be associated with the severity of mucosal inflammation. Methods: Patients with pediatric-onset IBD were enrolled at diagnosis and during therapy. Serum cytokine analysis was performed using Bioplex. STAT3 phosphorylation (pSTAT3) in peripheral blood leukocytes (PBLs) was assessed by flow cytometry. Immunohistochemistry of colonic mucosa was used to localize pSTAT3 and STAT3 target genes. Microarray analysis was used to determine RNA expression profiles from colon biopsies. Results: Circulating IL-6 was upregulated in active IBD patients at diagnosis and during therapy. STAT3 activation was increased in PB granulocytes, IL-6-stimulated CD3+/CD4+ lymphocytes, and affected colon biopsies of IBD patients. The frequency of pSTAT3+ PB granulocytes and colon epithelial and lamina propria cells was highly correlated with the degree of mucosal inflammation. Microarray and Ingenuity Systems bioinformatics analysis identified IL-6:STAT3-dependent biological networks upregulated in IBD patients which control leukocyte recruitment, HLA expression, angiogenesis, and tissue remodeling. Conclusions: A proinflammatory IL6:STAT3 biologic network is upregulated in active pediatric IBD patients at diagnosis and during therapy. Specific targeting of this network may be effective in reducing mucosal inflammation. (Inflamm Bowel Dis 2007) [source] Analysis of biological networksJOURNAL OF ANATOMY, Issue 4 2009Jonathan Bard No abstract is available for this article. [source] Feeding trials in organic food quality and health researchJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 2 2010Alberta Velimirov Abstract Feeding experiments comparing organically and conventionally produced food are performed to assess the overall impact on the animals' health as a model for the effects experienced by the human consumers. These experiments are based on systems research and characterized by their focus on production methods, whole food testing and procedures in accordance with the terms of organic farming. A short review of such experiments shows that the majority of these tests revealed effects of the organically produced feed on health parameters such as reproductive performance and immune responses. Systems research is not just about simple cause,effect chains, but rather about the pluralism of interactions in biological networks; therefore, the interpretation of the outcome of whole food experiments is difficult. Furthermore, the test diets of organic and conventional origin can be constituted in different ways, compensating for or maintaining existing differences in nutrient and energy contents. The science-based results suggest positive influences from organic feeds, but there is still a need for confirmation in animals and, finally, in humans. For this purpose animal feeding trials with feed from different production systems should be conducted, with the aims to define health indicators and to establish biomarkers as a basis for future dietary intervention studies in humans. Copyright © 2009 Society of Chemical Industry [source] Discovering functions and revealing mechanisms at molecular level from biological networksPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 16 2007Shihua Zhang Abstract With the increasingly accumulated data from high-throughput technologies, study on biomolecular networks has become one of key focuses in systems biology and bioinformatics. In particular, various types of molecular networks (e.g., protein,protein interaction (PPI) network; gene regulatory network (GRN); metabolic network (MN); gene coexpression network (GCEN)) have been extensively investigated, and those studies demonstrate great potentials to discover basic functions and to reveal essential mechanisms for various biological phenomena, by understanding biological systems not at individual component level but at a system-wide level. Recent studies on networks have created very prolific researches on many aspects of living organisms. In this paper, we aim to review the recent developments on topics related to molecular networks in a comprehensive manner, with the special emphasis on the computational aspect. The contents of the survey cover global topological properties and local structural characteristics, network motifs, network comparison and query, detection of functional modules and network motifs, function prediction from network analysis, inferring molecular networks from biological data as well as representative databases and software tools. [source] Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large-scale organization and robustnessPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 2 2006Dong Li Abstract High-throughput screens have begun to reveal protein interaction networks in several organisms. To understand the general properties of these protein interaction networks, a systematic analysis of topological structure and robustness was performed on the protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. It shows that the three protein interaction networks have a scale-free and high-degree clustering nature as the consequence of their hierarchical organization. It also shows that they have the small-world property with similar diameter at 4,5. Evaluation of the consequences of random removal of both proteins and interactions from the protein interaction networks suggests their high degree of robustness. Simulation of a protein's removal shows that the protein interaction network's error tolerance is accompanied by attack vulnerability. These fundamental analyses of the networks might serve as a starting point for further exploring complex biological networks and the coming research of "systems biology". [source] Proteomic profiling reveals comprehensive insights into adrenergic receptor-mediated hypertrophy in neonatal rat cardiomyocytesPROTEOMICS - CLINICAL APPLICATIONS, Issue 12 2009Zijian Li Abstract Myocardial adrenergic receptors (ARs) play important roles in cardiac hypertrophy. However, the detailed molecular mechanism of AR-mediated cardiac hypertrophy remains elusive to date. To gain full insight into how ARs are involved in the regulation of cardiac hypertrophy, protein expression profiling was performed with comparative proteomics approach on neonatal rat cardiomyocytes. Forty-six proteins were identified as differentially expressed in hypertrophic cardiomyocytes induced by AR stimulation. To better understand the biological significance of the obtained proteomic data, we utilized the ingenuity pathway analysis tool to construct biological networks and analyze function and pathways that might associate with AR-mediated cardiac hypertrophy. Pathway analysis strongly suggested that ROS may be involved in the development of AR-mediated cardiac hypertrophy, which was then confirmed by further experimentation. The results showed that a marked increase in ROS production was detected in AR-mediated cardiac hypertrophy and blocking of ROS production significantly inhibited AR-mediated cardiac hypertrophy. We further proved that the ROS production was through NADPH oxidase or the mitochondrial electron transport chain and this ROS accumulation resulted in activation of extracellular signal-regulated kinase 1/2 leading to AR-mediated cardiac hypertrophy. These experimental results support the hypothesis, from the ingenuity pathway analysis, that AR-mediated cardiac hypertrophy is associated with the dysregulation of a complicated oxidative stress-regulatory network. In conclusion, our results provide a basis for understanding the detailed molecular mechanisms of AR-mediated cardiac hypertrophy. [source] Improved network performance via antagonism: From synthetic rescues to multi-drug combinationsBIOESSAYS, Issue 3 2010Adilson E. Motter Abstract Recent research shows that a faulty or sub-optimally operating metabolic network can often be rescued by the targeted removal of enzyme-coding genes , the exact opposite of what traditional gene therapy would suggest. Predictions go as far as to assert that certain gene knockouts can restore the growth of otherwise nonviable gene-deficient cells. Many questions follow from this discovery: What are the underlying mechanisms? How generalizable is this effect? What are the potential applications? Here, I approach these questions from the perspective of compensatory perturbations on networks. Relations are drawn between such synthetic rescues and naturally occurring cascades of reaction inactivation, as well as their analogs in physical and other biological networks. I specially discuss how rescue interactions can lead to the rational design of antagonistic drug combinations that select against resistance and how they can illuminate medical research on cancer, antibiotics, and metabolic diseases. , Editor's suggested further reading in BioEssays The evolutionary context of robust and redundant cell biological mechanismsAbstract Reprogramming cell fates: reconciling rarity with robustnessAbstract [source] Making the right connections: biological networks in the light of evolutionBIOESSAYS, Issue 10 2009Christopher G. Knight Abstract Our understanding of how evolution acts on biological networks remains patchy, as is our knowledge of how that action is best identified, modelled and understood. Starting with network structure and the evolution of protein,protein interaction networks, we briefly survey the ways in which network evolution is being addressed in the fields of systems biology, development and ecology. The approaches highlighted demonstrate a movement away from a focus on network topology towards a more integrated view, placing biological properties centre-stage. We argue that there remains great potential in a closer synergy between evolutionary biology and biological network analysis, although that may require the development of novel approaches and even different analogies for biological networks themselves. [source] Four correlates of complex behavioral networks: Differentiation, behavior, connectivity, and compartmentalization: Carving networks at their jointsCOMPLEXITY, Issue 6 2005Mark A. Changizi Abstract Some of the most complex networks are those that (i) have been engineered under selective pressure (either economic or evolutionary), and (ii) are capable of eliciting network-level behaviors. Some examples are nervous systems, ant colonies, electronic circuits and computer software. Here we provide evidence that many such selected, behavioral networks are similar in at least four respects. (1) Differentiation: Nodes of different types are used in a combinatorial fashion to build network structures through local connections, and networks accommodate more structure types via increasing the number of node types in the network (i.e., increasing differentiation), not via increasing the length of structures. (2) Behavior: Structures are themselves combined globally to implement behaviors, and networks accommodate a greater behavioral repertoire via increasing the number of lower-level behavior types (including structures), not via increasing the length of behaviors. (3) Connectivity: In order for structures in behavioral networks to combine with other structures within a fixed behavior length, the network must maintain an invariant network diameter, and this is accomplished via increasing network connectivity in larger networks. (4) Compartmentalization: Finally, for re sons of economical wiring, behavioral networks become increasingly parcellated. Special attention is given to nervous systems and computer software, but data from a variety of other behavioral selected networks are also provided, including ant colonies, electronic circuits, web sites and businesses. A general framework is introduced illuminating why behavioral selected networks share these four correlates. Because the four above features appear to apply to computer software as well as to biological networks, computer software provides a useful framework for comprehending the large-scale function and organization of biological networks. © 2005 Wiley Periodicals, Inc. Complexity 10: 13,40, 2005 [source] | ||||||||||||||||