Escherichia coli genome-wide promoter analysis: Identification of additional AtoC binding target elements

<p>Abstract</p> <p>Background</p> <p>Studies on bacterial signal transduction systems have revealed complex networks of functional interactions, where the response regulators play a pivotal role. The AtoSC system of <it>E. coli </it>activates the expression of <it>atoDAEB </it>operon genes, and the subsequent catabolism of short-chain fatty acids, upon acetoacetate induction. Transcriptome and phenotypic analyses suggested that <it>atoSC </it>is also involved in several other cellular activities, although we have recently reported a palindromic repeat within the <it>atoDAEB </it>promoter as the single, <it>cis</it>-regulatory binding site of the AtoC response regulator. In this work, we used a computational approach to explore the presence of yet unidentified AtoC binding sites within other parts of the <it>E. coli </it>genome.</p> <p>Results</p> <p>Through the implementation of a computational <it>de novo </it>motif detection workflow, a set of candidate motifs was generated, representing putative AtoC binding targets within the <it>E. coli </it>genome. In order to assess the biological relevance of the motifs and to select for experimental validation of those sequences related robustly with distinct cellular functions, we implemented a novel approach that applies Gene Ontology Term Analysis to the motif hits and selected those that were qualified through this procedure. The computational results were validated using Chromatin Immunoprecipitation assays to assess the <it>in vivo </it>binding of AtoC to the predicted sites. This process verified twenty-two additional AtoC binding sites, located not only within intergenic regions, but also within gene-encoding sequences.</p> <p>Conclusions</p> <p>This study, by tracing a number of putative AtoC binding sites, has indicated an AtoC-related cross-regulatory function. This highlights the significance of computational genome-wide approaches in elucidating complex patterns of bacterial cell regulation.</p

Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species

Serum screening with Down's syndrome markers to predict pre-eclampsia and small for gestational age: Systematic review and meta-analysis

<p>Abstract</p> <p>Background</p> <p>Reliable antenatal identification of pre-eclampsia and small for gestational age is crucial to judicious allocation of monitoring resources and use of preventative treatment with the prospect of improving maternal/perinatal outcome. The purpose of this systematic review was to determine the accuracy of five serum analytes used in Down's serum screening for prediction of pre-eclampsia and/or small for gestational age.</p> <p>Methods</p> <p>The data sources included Medline, Embase, Cochrane library, Medion (inception to February 2007), hand searching of relevant journals, reference list checking of included articles, contact with experts. Two reviewers independently selected the articles in which the accuracy of an analyte used in Downs's serum screening before the 25^thgestational week was associated with the occurrence of pre-eclampsia and/or small for gestational age without language restrictions. Two authors independently extracted data on study characteristics, quality and results.</p> <p>Results</p> <p>Five serum screening markers were evaluated. 44 studies, testing 169,637 pregnant women (4376 pre-eclampsia cases) and 86 studies, testing 382,005 women (20,339 fetal growth restriction cases) met the selection criteria. The results showed low predictive accuracy overall. For pre-eclampsia the best predictor was inhibin A>2.79MoM positive likelihood ratio 19.52 (8.33,45.79) and negative likelihood ratio 0.30 (0.13,0.68) (single study). For small for gestational age it was AFP>2.0MoM to predict birth weight < 10^thcentile with birth < 37 weeks positive likelihood ratio 27.96 (8.02,97.48) and negative likelihood ratio 0.78 (0.55,1.11) (single study). A potential clinical application using aspirin as a treatment is given as an example.</p> <p>There were methodological and reporting limitations in the included studies thus studies were heterogeneous giving pooled results with wide confidence intervals.</p> <p>Conclusion</p> <p>Down's serum screening analytes have low predictive accuracy for pre-eclampsia and small for gestational age. They may be a useful means of risk assessment or of use in prediction when combined with other tests.</p

Control of anterior GRadient 2 (AGR2) dimerization links endoplasmic reticulum proteostasis to inflammation

International audienceAnterior gradient 2 (AGR2) is a dimeric protein disulfide isomerase family member involved in the regulation of protein quality control in the endoplasmic reticulum (ER). Mouse AGR2 deletion increases intestinal inflammation and promotes the development of inflammatory bowel disease (IBD). Although these biological effects are well established, the underlying molecular mechanisms of AGR2 function toward inflammation remain poorly defined. Here, using a protein-protein interaction screen to identify cellular regulators of AGR2 dimerization, we unveiled specific enhancers, including TMED2, and inhibitors of AGR2 dimerization, that control AGR2 functions. We demonstrate that modulation of AGR2 dimer formation, whether enhancing or inhibiting the process, yields pro-inflammatory phenotypes, through either autophagy-dependent processes or secretion of AGR2, respectively. We also demonstrate that in IBD and specifically in Crohn's disease, the levels of AGR2 dimerization modulators are selectively deregulated, and this correlates with severity of disease. Our study demonstrates that AGR2 dimers act as sensors of ER homeostasis which are disrupted upon ER stress and promote the secretion of AGR2 monomers. The latter might represent systemic alarm signals for pro-inflammatory responses

Evaluation of a two-step ultrasound examination protocol for the detection of major fetal structural defects

Objective: To evaluate a two-step screening protocol of ultrasound examinations (1114 and 2024 weeks) for the detection of major fetal structural defects. Methods: Retrospective study in a private maternity hospital. Women with viable singleton pregnancies having both first trimester scan and anomaly scan at our department and subsequently delivered at our hospital were included. Major fetal structural defects were defined as those requiring medical or surgical treatment or those causing mental handicap. Results: A total of 3,902 pregnancies included 61 fetuses with structural defects (1.56%). Twenty-six (42.6%) were diagnosed in the first trimester and 29 (47.5%) in the second. Six anomalies were detected in the third trimester or after birth. Overall detection rate of the two-step program was 90.2%. Conclusions: Detailed examination of fetal anatomy at 1114 weeks resulted in the early diagnosis of about 40% of major structural defects © 2012 Informa UK, Ltd

E. coli genome-wide promoter analysis in search for potential AtoC target elements

Journal URL: http://www3.interscience.wiley.com/journal/119878145Abstract Poster PresentationThe AtoSC two-component system in E. coli activates atoDAEB operon genes to catabolize short-chain fatty acids, acetoacetate being the inducer. The AtoC response regulator was first described as the Antizyme of the polyamine biosynthetic ornithine decarboxylase. The AtoC binding site within the ato promoter was experimentally verified as an inverted 20 bp palindromic repeat. Transcriptome and phenotypic analyses however, indicated the involvement of atoSC to various other cellular activities, such as flagellar synthesis. Here we report a bioinformatic analysis for the localization of the AtoC binding motif within the E. coli genome that could indicate a putative implication, direct or indirect, of the AtoC in other operons regulation. A genome-wide promoter analysis was performed using a program for the de novo detection of overrepresented motifs within promoters. The motif sampling was initiated using the intergenic region where the AtoC binding site is located. By applying an iterative algorithm, including TCS regulated promoters, the program resulted to promoter sets comprising high-scoring putative cis-regulatory elements. The AtoC binding ability to these elements was tested by chromatin immunoprecipitation, using anti-AtoC polyclonal antibody. MotifScanner identified occurrences of different motifs connected to the ato palindromic sequence, and those related to established AtoC functions were singled out and used as templates for the design of primers, in order to analyse the immunoprecipitated chromatin in strains lacking or comprising atoSC, with or without acetoacetate induction. Experimental verification of predicted correlations could provide an insight to gene regulatory networks in bacteria, enabling us to foresee potential targets for response regulators

GRISSOM web based grid portal: Exploiting the power of grid infrastructure for the interpretation and storage of DNA microarray experiments

DNA Microarrays have dramatically reshaped modern biological research by deriving profiles of genome-wide expression of living organisms, and producing an unprecedented wealth of quantitative data. Given this characteristic, microarray experiments are considered high-throughput both in terms of data (data intensive) and processing (computationally intensive). GRISSOM enables exploitation of GRID resources for DNA microarray distributed processing. It provides experts with a complete web-based solution for managing, searching and disseminating biological knowledge in the context of gene expression patterns on a genomic scale. The platform is developed and deployed using open source software components. Through the use of web service technologies (WSDL language) GRISSOM can be encapsulated in other biomedical processing workflows, thus rendering access to its algorithms, transparent and generic. ©2009 IEEE