A Novel Optimization-Based Tool to Automate Infeasible Cycle-Free Gapfilling of Genome-Scale Metabolic Models, Schroeder and Saha
Contributors: Wheaton Schroeder, Rajib Saha
... Dataset related to the paper of the same title submitted for publication in the journal iScience. The abstract is as follows.
Contributors: Tetsuji Okada
... DSA files of human (N to Z, by gene name) : UniProt ID is used for a protein to which no gene name is assigned.
Reshaping commensal gut microbiota in early life with amoxicillin presents with lower blood pressure
Contributors: Saroj Chakraborty
... Pediatric hypertension is recognized as an emerging global health concern. While new guidelines are developed for facilitating clinical management, the reasons for the prevalence of hypertension in children remain unknown. Genetics and environmental factors do not fully account for the growing incidence of pediatric hypertension. Because stable bacterial flora in early life are linked with health outcomes later in life, we hypothesized that reshaping of gut microbiota in early developmental stages of life affects blood pressure (BP) of pediatric subjects. To test this hypothesis, we administered amoxicillin, the most commonly prescribed pediatric antibiotic, to alter gut microbiota of young, genetically hypertensive rats (study 1) and dams during gestation and lactation to reshape microbiota of offspring (study 2). Reshaping of microbiota, with reductions in Firmicutes/Bacteriodetes ratio observed in Amoxicillin treated young rats and in dams. Amoxicillin treated rats also had lower blood pressure compared to the untreated rats. In the young rats treated with amoxicillin, the lowering effect on blood pressure persisted even after the antibiotics were discontinued. Similarly, the offspring from the dams treated with amoxicillin also showed lower systolic blood pressure compared to the control rats. Remarkably, in all cases, a decrease in BP was associated with lowering of Veillonellaceae, which are succinate-producing bacteria. Elevated plasma succinate is reported in hypertension. Accordingly, serum succinate was measured and found lower in animals treated with amoxicillin. Our results demonstrate a direct correlation between succinate-producing gut microbiota and early development of hypertension, and indicate that reshaping gut microbiota, especially by depleting succinate-producing microbiota early in life may have long-term benefits for hypertension-prone individuals.
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A new method for analyzing sustainability performance of global supply chains and its application to material resources
Contributors: Livia Cabernard, Stephan Pfister, Stefanie Hellweg
... VERSION 2 Compared to version 1, version 2 runs without matlab. The file “Instructions.pdf” attached below explains how to install and use this application. The file “Explanation_method_examples.pptx” attached below illustrates the principle of the method and how to use the application with several examples. OVERALL DESCRIPTION (same as for version 1): We share here the data compiled to calculate the results presented in the study «A new method for analyzing sustainability performance of global supply chains and its application to material resources». In order to allow for the compilation of all results of interest, we provide an application. This application is based on the multi-regional-input output database EXIOBASE3 (version 3.4) and data to assess the potential environmental impacts of emissions and resource use. While the data for assessing the environmental impacts is provided here, the user must download the Exiobase data from the Exiobase website (due to copyright issues). The provided application allows to assess the cumulated upstream impacts of any sector or region on the globe without double-counting and to track these impacts upstream and downstream the global value chain. The application covers a broad set of environmental and socio-economic indicators and the timespan from 1995 to 2011. The methodology of this application is comprehensively explained in the study: «A new method for analyzing sustainability performance of global supply chains and its application to material resources» (e.g Section 2.1 gives a broad overview of the principle of the method). Link to the study: https://doi.org/10.1016/j.scitotenv.2019.04.434
Regional heterogeneity in gene expression, regulation and coherence in hippocampus and prefrontal cortex across development and in schizophrenia. Collado-Torres et al, Neuron, 2019.
Contributors: Leonardo Collado-Torres, Emily E Burke, Amy Peterson, Joo Heon Shin, Richard E Straub, Nina Rajpurohit, Stephen A Semick, William S Ulrich, BrainSeq Consortium, Amanda J Price
... This dataset contains the Supplementary Figures and Tables for the "Regional heterogeneity in gene expression, regulation and coherence in hippocampus and prefrontal cortex across development and in schizophrenia" article by Collado-Torres et al, Neuron, 2019. Please cite the original article as well as the data itself if appropriate. For clarifications about the figures or data, please contact us by creating an issue at https://github.com/LieberInstitute/brainseq_phase2/issues. Thank you!
The NAD-booster nicotinamide riboside potently stimulates hematopoiesis through increased mitochondrial clearance
Contributors: Olaia Naveiras
... It has been recently shown that increased oxidative phosphorylation, as reflected by increased mitochondrial activity, together with impairment of the mitochondrial stress response can severely compromise hematopoietic stem cell (HSC) regeneration. Here we show that the NAD+-boosting agent Nicotinamide Riboside (NR) reduces mitochondrial activity within HSCs through increased mitochondrial clearance, leading to increased asymmetric HSC divisions. NR dietary supplementation results in a significantly enlarged pool of progenitors, without concurrent HSC exhaustion, improves survival by 80%, and accelerates blood recovery after murine lethal irradiation and limiting-HSC transplantation. In immune-deficient mice, NR increased the production of human leucocytes from hCD34+ progenitors. Our work demonstrates for the first time a positive effect of NAD+ boosting strategies on the most primitive blood stem cells, establishes a novel link between HSC mitochondrial stress, mitophagy and stem cell fate decision, and unveils the potential of NR to improve recovery of patients suffering from hematological failure including post-chemo/radiotherapy.
Contributors: Philipp Keller
... Guide's software and data repository- compact version
Contributors: Philipp Keller
... Guide's software and data repository- full version
Contributors: Agnieszka Tudek
... A nuclear export block triggers the decay of newly synthesized polyadenylated RNA Agnieszka Tudek1, Manfred Schmid1, Marius Makaras1, J. David Barrass2, Jean D. Beggs2, Torben Heick Jensen1* 1Department of Molecular Biology and Genetics, Aarhus University, C. F. Møllers Allé 3, building 1130, 8000 Aarhus C, Denmark, 2Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK *corresponding author and lead contact: firstname.lastname@example.org Keywords: nuclear export of pA+ RNA, nuclear degradation of pA+ RNA, Mex67p, Nab2p, transcription. ABSTRACT Genomes are promiscuously transcribed necessitating mechanisms that facilitate the sorting of RNA for function or destruction. The polyA (pA) tail is one such distinguishing feature, which in the Saccharomyces cerevisiae nucleus is bound by the Nab2p protein, yielding transcript protection. As Nab2p also contacts the main nuclear export factor Mex67p, we asked whether transport kinetics contributes to RNA sorting. Indeed, 3’end sequencing of newly transcribed pA+ RNAs demonstrates that nuclear depletion of Mex67p elicits their instant and global decay. A similar phenotype is evident upon inactivation of other export factors and proportional to the amount of nuclear pA+ RNA. As RNA expression is partially rescued by Nab2p over-expression, we propose that an export-block out-titrates Nab2p onto nuclear retained pA+ RNA, reducing the pool of Nab2p available to protect new transcripts. More generally, we suggest that nuclear RNA decay, negotiated by Nab2p availability, aids in balancing cellular transcript supply with demand.