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91.
92.
Guangyi Fan Yaolei Zhang Xiaochuan Liu Jiahao Wang Zeguo Sun Shuai Sun He Zhang Jianwei Chen Meiqi Lv Kai Han Xiaoxuan Tan Jie Hu Rui Guan Yuanyuan Fu Shanshan Liu Xi Chen Qiwu Xu Yating Qin Longqi Liu Jie Bai Ou Wang Jingbo Tang Haorong Lu Zhouchun Shang Bo Wang Guohai Hu Xia Zhao Yan Zou Ao Chen Meihua Gong Wenwei Zhang Simon M.‐Y. Lee Songhai Li Junnian Liu Zhen Li Yishan Lu Jamal S. M. Sabir Mumdooh J. Sabir Muhummadh Khan Nahid H. Hajrah Ye Yin Karsten Kristiansen Huanming Yang Jian Wang Xun Xu Xin Liu 《Molecular ecology resources》2019,19(4):944-956
Marine mammals are important models for studying convergent evolution and aquatic adaption, and thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome‐level marine mammal genome assembly based on the data generated by the BGISEQ‐500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of the sperm whale, including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparing with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. We detected a high proportion of long interspersed nuclear elements and expanded gene families, and contraction of major histocompatibility complex region genes which were specific to sperm whale. Using comparisons with sheep and cattle, we analysed positively selected genes to identify gene pathways that may be related to adaptation to the marine environment. Further, we identified possible convergent evolution in aquatic mammals by testing for positively selected genes across three orders of marine mammals. In addition, we used publicly available resequencing data to confirm a rapid decline in global population size in the Pliocene to Pleistocene transition. This study sheds light on the chromosome evolution and genetic mechanisms underpinning sperm whale adaptations, providing valuable resources for future comparative genomics. 相似文献
93.
Hyunsoo Kang Byeonghyeok Park Nicole R. Bolo Duleepa Pathiraja Shinyoung Park Minseok Cha In‐G. Choi In S. Chang 《Biotechnology journal》2019,14(6)
Syngas fermentation is largely dependent on acetogens that occur in various anaerobic environmental samples including soil, sediment, and feces. Here the authors report the metagenomic isolation of acetogens for C2 chemical production from syngas. Screening acetogens for C2 chemical production typically involves detecting the presence of the Wood‐Ljungdahl Pathway for carbon monoxide conversion. The authors collect samples from river‐bed sediments potentially having conditions suitable for carbon monoxide‐converting anaerobes, and enrich the samples under carbon monoxide selection pressure. Changes in the microbial community during the experimental procedure are investigated using both amplicon and shotgun metagenome sequencing. Combined next‐generation sequencing techniques enabl in situ tracking of the major acetogenic bacterial group and lead to the discovery of a 16 kb of gene cluster for WLP. The authors isolat an acetogenic clostridial strain from the enrichment culture (strain H21‐9). The functional activity of H21‐9 is confirmed by its high level of production of C2 chemicals from carbon monoxide (77.4 mM acetate and 2.5 mM of ethanol). This approach of incorporating experimental enrichment with metagenomic analysis can facilitate the discovery of novel strains from environmental habitats by tracking target strains during the screening process, combined with validation of their functional activity. 相似文献
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95.
Cyanobacteria are of great importance to Earth's ecology. Due to their capability in photosynthesis and C1 metabolism, they are ideal microbial chassis that can be engineered for direct conversion of carbon dioxide and solar energy into biofuels and biochemicals. Facilitated by the elucidation of the basic biology of the photoautotrophic microbes and rapid advances in synthetic biology, genetic toolkits have been developed to enable implementation of nonnatural functionalities in engineered cyanobacteria. Hence, cyanobacteria are fast becoming an emerging platform in synthetic biology and metabolic engineering. Herein, the progress made in the synthetic biology toolkits for cyanobacteria and their utilization for transforming cyanobacteria into microbial cell factories for sustainable production of biofuels and biochemicals is outlined. Current techniques in heterologous gene expression, strategies in genome editing, and development of programmable regulatory parts and modules for engineering cyanobacteria towards biochemical production are discussed and prospected. As cyanobacteria synthetic biology is still in its infancy, apart from the achievements made, the difficulties and challenges in applying and developing genetic toolkits in cyanobacteria for biochemical production are also evaluated. 相似文献
96.
Giulia Schiroli Anastasia Conti Samuele Ferrari Lucrezia della Volpe Aurelien Jacob Luisa Albano Stefano Beretta Andrea Calabria Valentina Vavassori Patrizia Gasparini Eralda Salataj Delphine Ndiaye-Lobry Chiara Brombin Julie Chaumeil Eugenio Montini Ivan Merelli Pietro Genovese Luigi Naldini Raffaella Di Micco 《Cell Stem Cell》2019,24(4):551-565.e8
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98.
Benedetta Artegiani Lisa van Voorthuijsen Rik G.H. Lindeboom Daniëlle Seinstra Inha Heo Pablo Tapia Carmen López-Iglesias Daniel Postrach Talya Dayton Rurika Oka Huili Hu Ruben van Boxtel Johan H. van Es Johan Offerhaus Peter J. Peters Jacco van Rheenen Michiel Vermeulen Hans Clevers 《Cell Stem Cell》2019,24(6):927-943.e6
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100.
Edward R. Cruz Hung Nguyen Tin Nguyen Ian S. Wallace 《The Plant journal : for cell and molecular biology》2019,99(5):1003-1013
Post‐translational modifications (PTMs) are critical regulators of protein function, and nearly 200 different types of PTM have been identified. Advances in high‐resolution mass spectrometry have led to the identification of an unprecedented number of PTM sites in numerous organisms, potentially facilitating a more complete understanding of how PTMs regulate cellular behavior. While databases have been created to house the resulting data, most of these resources focus on individual types of PTM, do not consider quantitative PTM analyses or do not provide tools for the visualization and analysis of PTM data. Here, we describe the Functional Analysis Tools for Post‐Translational Modifications (FAT‐PTM) database ( https://bioinformatics.cse.unr.edu/fat-ptm/ ), which currently supports eight different types of PTM and over 49 000 PTM sites identified in large‐scale proteomic surveys of the model organism Arabidopsis thaliana. The FAT‐PTM database currently supports tools to visualize protein‐centric PTM networks, quantitative phosphorylation site data from over 10 different quantitative phosphoproteomic studies, PTM information displayed in protein‐centric metabolic pathways and groups of proteins that are co‐modified by multiple PTMs. Overall, the FAT‐PTM database provides users with a robust platform to share and visualize experimentally supported PTM data, develop hypotheses related to target proteins or identify emergent patterns in PTM data for signaling and metabolic pathways. 相似文献