ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data

Metagenomic analysis of environmental samples provides deep insight into the enzymatic mixture of the corresponding niches, capable of revealing peptide sequences with novel functional properties exploiting the high performance of next-generation sequencing (NGS) technologies. At the same time due to their ever increasing complexity, there is a compelling need for ever larger computational configurations to ensure proper bioinformatic analysis, and fine annotation. With the aiming to address the challenges of such an endeavor, we have developed a novel web-based application named ANASTASIA (automated nucleotide aminoacid sequences translational plAtform for systemic interpretation and analysis). ANASTASIA provides a rich environment of bioinformatic tools, either publicly available or novel, proprietary algorithms, integrated within numerous automated algorithmic workflows, and which enables versatile data processing tasks for (meta)genomic sequence datasets. ANASTASIA was initially developed in the framework of the European FP7 project HotZyme, whose aim was to perform exhaustive analysis of metagenomes derived from thermal springs around the globe and to discover new enzymes of industrial interest. ANASTASIA has evolved to become a stable and extensible environment for diversified, metagenomic, functional analyses for a range of applications overarching industrial biotechnology to biomedicine, within the frames of the ELIXIR-GR project. As a showcase, we report the successful in silico mining of a novel thermostable esterase termed “EstDZ4” from a metagenomic sample collected from a hot spring located in Krisuvik, Iceland

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

Body stalk anomaly diagnosed in the 2nd trimester

We examined a 20-year-old primigravida by ultrasound at 21 weeks of gestation during routine anomaly scanning. Several fetal deformities were demonstrated: the upper part of the body was in the amniotic cavity, while the lower part was in the celomic cavity. A large abdominal wall defect was detected with herniation of the liver and the intestine. The limbs were deformed, the spine had severe kyphoscoliosis, and the umbilical cord was very short. These findings were suggestive of a body stalk anomaly. Termination of the pregnancy was offered and decided by the parents. The pathology report confirmed the ultrasonographic diagnosis. Copyright (C) 2003 S. Karger AG, Basel

Rupture of noncommunicating rudimentary uterine horn pregnancy

BACKGROUND: We present a rare case of pregnancy in a noncommunicating rudimentary horn that ruptured at 20 weeks. CASE: A 30-year-old woman presented with a history of two spontaneous abortions. An ultrasound scan showed a bicornuate uterus, with one normal and one hypoplastic horn. Hysterosalpingography revealed a single uterine cavity with only one tube, suggesting a unicornuate uterus. Hysteroscopy and laparoscopy were recommended but declined. She presented again 2 months later at 7 weeks’ gestation. A single intrauterine pregnancy in the hypoplastic right horn was diagnosed. A transvaginal scan showed a single cervical canal in continuity with the left uterine horn, which led to the suspicion of a pregnancy in a rudimentary horn. The option of pregnancy termination was offered. A laparoscopy was repeatedly suggested but declined. Excision of a ruptured noncommunicating rudimentary horn and ipsilateral salpingectomy were performed after an emergency laparotomy at 20 weeks because of the sudden onset of abdominal pain and signs of shock. CONCLUSION: Although a rudimentary horn pregnancy had been suspected before the laparotomy, the patient presented as a clinical emergency. This report, like others, indicates that prompt diagnosis and immediate removal of the rudimentary horn is lifesaving. (C) 2002 by The American College of Obstetricians and Gynecologists

Management of early viable cervical pregnancy

Objective To evaluate conservative management of early viable cervical pregnancy. Design Prospective study. Setting A tertiary teaching hospital. Population All cases of cervical pregnancies with fetal cardiac activity presenting to our hospital over six years. Methods All cases were managed with trans-abdominal intra-amniotic injection of 25 mg of methotrexate under ultrasound guidance. Follow up sonographic examinations and serum beta-hCG measurements were performed every three days. Cervical curettage was performed after two follow up ultrasound examinations had shown a dead fetus and a regressing gestational sac as well as declining beta-hCG levels. Patients were managed as outpatients. Main outcome measures Successful management and need for hospitalisation. Results Nine cases were encountered. Two required a second injection of methotrexate for persistent fetal cardiac activity and serum beta-hCG rise in the follow up examination. We did not observe any side effects and no patient required admission to the hospital. Conclusions Intra-amniotic methotrexate injection and subsequent cervical curettage after one week is a successful alternative for the management of cervical pregnancies

Screening for birth weight deviations by second and third trimester ultrasound scan

Objective: The aim of this article was to predict small for gestational age (SGA, at or less than the fifth birth weight percentile) and large for gestational age (LGA, at or greater than the 95th birth weight percentile) fetuses by using maternal and fetal parameters from the second and third trimester ultrasound examinations. Method: This article is a retrospective cohort study on 1979 singleton pregnancies that had a routine 20 to 24weeks anomaly and a 30 to 34weeks growth ultrasound scans. SGA delivered before 30 gestational weeks were excluded. Results: Second trimester estimated fetal weight (EFW2), uterine arteries pulsatility index (PI), and maternal pregnancy characteristics were predictive for SGA (SGA second trimester model: R2=0.225, area under the curve [AUC]=0.815) and LGA (LGA second trimester model: R2=0.203, AUC=0.793). Third trimester EFW (EFW3), EFW2, uterine arteries PI2, umbilical PI, and maternal pregnancy characteristics improved the prediction of SGA (SGA combined model: R2=0.423, AUC=0.896) and LGA (LGA combined model: R2=0.383, AUC=0.882). Contingent screening with risk stratification by the second trimester model performed equally well for SGA (AUC=0.882) and LGA (AUC=0.861) as the combined models. Conclusion: Second trimester model performs well in the prediction of SGA and LGA. The addition of third trimester scan offers substantial improvement. Contingency screening is feasible with similar effectiveness. © 2014 John Wiley &amp;amp; Sons, Ltd. What&apos;s already known about this topic? First trimester ultrasound scan in combination with maternal pregnancy characteristics and biochemical indices is predictive of small for gestational age and large for gestational age. Third trimester scan is the superior method to assess fetal growth. What does this study add? Second trimester scan has satisfactory performance in the prediction of small for gestational age and large for gestational age. Second and third trimester contingent screening for fetal growth deviations has similar performance to a routine second and third trimester screening. © 2014 John Wiley &amp;amp; Sons, Ltd