Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR 7156 CNRS, 67000 Strasbourg, France.
Published: June 2022
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Article Abstract
Dichloromethane (DCM, methylene chloride) is a toxic halogenated volatile organic compound massively used for industrial applications, and consequently often detected in the environment as a major pollutant. DCM biotransformation suggests a sustainable decontamination strategy of polluted sites. Among methylotrophic bacteria able to use DCM as a sole source of carbon and energy for growth, DM4 is a longstanding reference strain. Here, the primary 5'-ends of transcripts were obtained using a differential RNA-seq (dRNA-seq) approach to provide the first transcription start site (TSS) genome-wide landscape of a methylotroph using DCM or methanol. In total, 7231 putative TSSs were annotated and classified with respect to their localization to coding sequences (CDSs). TSSs on the opposite strand of CDS (antisense TSS) account for 31% of all identified TSSs. One-third of the detected TSSs were located at a distance to the start codon inferior to 250 nt (average of 84 nt) with 7% of leaderless mRNA. Taken together, the global TSS map for bacterial growth using DCM or methanol will facilitate future studies in which transcriptional regulation is crucial, and efficient DCM removal at polluted sites is limited by regulatory processes.
RNAs are increasingly recognized as promising therapeutic targets, susceptible to modulation by strategies that include targeting with small molecules, antisense oligonucleotides, deoxyribozymes (DNAzymes), or CRISPR/Cas13. However, while drug development for proteins follows well-established paths for rational design based on the accurate knowledge of their three-dimensional structure, RNA-targeting strategies are challenging since comprehensive RNA structures are yet scarce and challenging to acquire. Numerous methods have been developed to elucidate the secondary and three-dimensional structure of RNAs, including X-ray crystallography, cryo-electron microscopy, nuclear magnetic resonance, SHAPE, DMS, and bioinformatic methods, yet they have often revealed flexible transcripts and co-existing populations rather than single-defined structures.
Limiting the level of piglet losses before weaning is a growing demand from producers and society to improve the welfare and health of sows and piglets. In particular, perinatal mortality, which can be defined as the complete development allowing survival at birth, is mostly due to reduced piglet maturity that occurs at the end of gestation. Fetal growth and maturation depend on a fine balance between the nutrient requirements for optimal fetal growth and the maternal nutrient requirements.
Department of Physiology, University of Granada, Granada 18071, Spain; Instituto de Investigación Biosanitaria (ibs.Granada), Granada 18014, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Granada 18071, Spain.
Background: Mammalian cells possess molecular clocks, the adequate functioning of which is decisive for metabolic health. Exercise is known to modulate these clocks, potentially having distinct effects on metabolism depending on the time of day. This study aimed to investigate the impact of morning vs.
Amsterdam UMC, Department of Public and Occupational Health, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 7, NL-1081 BT, Amsterdam, The Netherlands.
Background: The Antarctic krill Euphausia superba is a keystone species in the Southern Ocean ecosystem. This crustacean has an ancestral clock whose main components have been identified and characterized in the past few years. However, the second feedback loop, modulating clock gene expression through two transcription factors, VRI and PDP1, has yet to be described.
