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Spontaneous mutations and mutational responses to penicillin treatment in the bacterial pathogen Streptococcus pneumoniae D39

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Marine Life Science & Technology 2024年第3期6卷 198-211页

作者： Wanyue Jiang Tongtong Lin Jiao Pan Caitlyn ERivera Clayton Tincher Yaohai Wang Yu Zhang Xiang Gao Yan Wang Ho‑Ching T.Tsui Malcolm E.Winkler Michael Lynch hongan long Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China Laboratory for Marine Biology and Biotechnology Laoshan LaboratoryQingdao 266237China Department of Biology Indiana UniversityBloomingtonIN 47405USA School of Mathematics Science Ocean University of ChinaQingdao 266000China State Key Laboratory of Microbial Technology Microbial Technology InstituteSchool of Life ScienceShandong UniversityQingdao 266237China Biodesign Center for Mechanisms of Evolution Arizona State UniversityTempeAZ 85281USA

Bacteria with functional DNA repair systems are expected to have low mutation rates due to strong natural selection for genomic ***,our study of the wild-type Streptococcus pneumoniae D39,a pathogen responsible for many common diseases,revealed a high spontaneous mutation rate of 0.02 per genome per cell division in mutation-accumulation(MA)*** rate is orders of magnitude higher than that of other non-mutator bacteria and is characterized by a high mutation bias in the A/T *** high mutation rate may have resulted from a reduction in the overall efficiency of selection,conferred by the tiny effective population size in *** line with this,*** D39 also exhibited the lowest DNA mismatch-repair(MMR)efficiency among *** with the antibiotic penicillin did not elevate the mutation rate,as penicillin did not induce DNA damage and *** lacks a stress response *** findings suggested that the MA results are applicable to within-host scenarios and provide insights into pathogen evolution.

关键词： Neutral evolution Mutation spectrum Antibiotics DNA mismatch repair Oxidative damage repair

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Special topic on EvoDevo:emerging models and perspectives

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Marine Life Science & Technology 2023年第4期5卷 431-434页

作者： hongan long Bo Dong MoE Key Laboratory of Evolution and Marine Biodiversity Institute of Evolution and Marine BiodiversityOcean University of ChinaQingdao 266003China

Communication between developmental and evolutionary scientists has historically been a challenge,with their respective foci being molecular mechanisms during the development of an individual and long-term shifts in allele frequency in ***,uniting these perspectives provides a better understanding of biological *** Haeckel’s biogenetic argument that,“ontogeny recapitulates phylogeny,”offers us with an early glimpse at how useful such a synthesis of evolution and development(EvoDevo)can be.

关键词： functions. argument synthesis

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Marine life science and technology (MLST): a new journal highlighting all aspects of marine biology and biotechnology research

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Marine Life Science & Technology 2019年第1期1卷 1-3页

作者： hongan long Xiao-Hua Zhang Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China College of Marine Life Sciences Ocean University of China5 Yushan RoadQingdao 266003China Laboratory for Marine Ecology and Environmental Science Qingdao National Laboratory for Marine Science and TechnologyQingdao 266071China

The majestic nature of the oceans and their charismaticflora and fauna clearly justify the study of marine life, espe・cially to the general public. Consequently, the explorationof marine biota has provided both insights and highlightedchallenges, leading to the appreciation that marine biologyand its supporting technology must be at the forefront of 21stcentury science. Still, this field is not progressing as fast orin as much detail as might be expected, or needed. Possiblythe most notable gap is the lack of academic journals thatcover cross-disciplinary topics.

关键词： marine life Marine

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The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria

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Marine Life Science & Technology 2021年第1期3卷 20-27页

作者： Jiao Pan Emily Williams Way Sung Michael Lynch hongan long Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China Center for Mechanisms of Evolution The Biodesign InstituteArizona State UniversityTempeAZ 85281USA Department of Bioinformatics and Genomics University of North CarolinaCharlotteNC 28223USA

Mutation is a primary source of genetic variation that is used to power *** studies,however,have shown that most mutations are deleterious and,as a result,extremely low mutation rates might be benefcial for *** a mutation accumulation experiment,an unbiased method for mutation study,we found an extremely low base-substitution mutation rate of 5.94×10^(-11) per nucleotide site per cell division(95%Poisson confdence intervals:4.65×10^(-11),7.48×10^(-11))and indel mutation rate of 8.25×10^(-12) per site per cell division(95%confdence intervals:3.96×10^(-12),1.52×10^(-11))in the bacterium Photorhabdus luminescens *** mutations are strongly A/T-biased with a mutation bias of 10.28 in the A/T *** has been hypothesized that the ability for selection to lower mutation rates is inversely proportional to the efective population size(drift-barrier hypothesis)and we found that the efective population size of this bacterium is signifcantly greater than most other *** fnding further decreases the lower-bounds of bacterial mutation rates and provides evidence that extreme levels of replication fdelity can evolve within organisms that maintain large efective population sizes.

关键词： Neutral evolution Mutation accumulation Mutation spectrum Drift-barrier hypothesis Lower-limit of mutation rate

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Cost-reduction strategies in massive genomics experiments

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Marine Life Science & Technology 2019年第1期1卷 15-21页

作者： Haichao Li Kun Wu Chenchen Ruan Jiao Pan Yujin Wang hongan long Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China

Many modern biology studies require deep, whole-genome sequencing of hundreds to thousands of samples. Although persamplecosts have dramatically decreased, the total budget for such massive genome sequencing constitutes a significantbarrier for poorly funded labs. The costly lab tools required for genomics experiments further hinder such studies. Here, weshare two strategies for extensively reducing the costs of massive genomics experiments, including miniaturization of theNEBNext Ultra II FS DNA Library Prep Kit for Illumina (reducing the per-sample total costs to ~ 1/6 of that charged byservice providers) and in-lab 3D model-designing of genomics tools. These strategies not only dramatically release fundingpressure for labs, but also provide students with additional training in hands-on genomics and 3D-model-designing skills,demonstrating the high potential for their application in genomics experiments and science education.

关键词： 3D model designing and printing Genome sequencing Lab-made tools Library construction Miniaturization

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First Record and Redefinition of the Qingdao Population of Marine Ciliate Cardiostomatella vermiformis (Kahl, 1928) Corliss, 1960 (Protozoa, Ciliophora)

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Journal of Ocean University of China 2007年第4期6卷 387-392页

作者： WANG Yangang HU Xiaozhong long hongan SONG Weibo Laboratory of Protozoology Ocean University of China Qingdao 266003 P. R. China

The living morphology and infraciliature of a marine ciliate, Cardiostomatella vermiformis isolated from a sand beach of the Jiaozhou Bay near Qingdao, China, were investigated by live observation, protargol and silver carbonate impregnation methods. Both the morphological and morphometric data largely agree with former records. Based on the data obtained, an improved diagnosis for Cardiostomatella vermiformis is supplied: Large marine Cardiostomatella with cylindrical body shape and several prolonged caudal cilia; cells in vivo about (90–500) μm×(30–120) μm; macronucleus beaded; single contractile vacuole caudally positioned; buccal apparatus conspicuously small, genus typical; three to six postoral kineties; 96-130 somatic kineties. This species is recorded for the first time in China.

关键词： morphology infraciliature Cardiostomatella vermiformis

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Contribution of the SOS response and the DNA repair systems to norfloxacin induced mutations in ***

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Marine Life Science & Technology 2023年第4期5卷 538-550页

作者： Tongtong Lin Jiao Pan Colin Gregory Yaohai Wang Clayton Tincher Caitlyn Rivera Michael Lynch hongan long Yu Zhang Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China Laboratory for Marine Biology and Biotechnology Laoshan LaboratoryQingdao 266237China Department of Biology Indiana UniversityBloomington 47405USA Biodesign Center for Mechanisms of Evolution Arizona State UniversityTempe 85281USA School of Mathematics Science Ocean University of ChinaQingdao 266000China

Antibiotic-resistant bacteria severely threaten human *** spontaneous mutations generated by endogenous factors,the resistance might also originate from mutations induced by certain antibiotics,such as the *** antibiotics increase the genome-wide mutation rate by introducing replication errors from the SOS response pathway or decreasing the efficiency of the DNA repair ***,the relative contributions of these molecular mechanisms remain unclear,hindering understanding of the generation of resistant ***,using newly-accumulated mutations of wild-type and SOS-uninducible Escherichia coli strains,as well as those of the strains deficient for the mismatch repair(MMR)and the oxidative damage repair pathways,we find that the SOS response is the major mutagenesis contributor in mutation elevation,responsible for~30–50%of the total base-pair substitution(BPS)mutation-rate elevation upon treatment with sublethal levels of norfloxacin(0~50 ng/mL).We further estimate the significance of the effects on other mutational features of these mechanisms(i.e.,transversions,structural variations,and mutation spectrum)in *** using linear *** SOS response plays a positive role in all three mutational features(mutation rates of BPSs,transversions,structural variations)and affects the mutational *** repair systems significantly reduce the BPS mutation rate and the transversion rate,regardless of whether antibiotics are present,while significantly increasing the structural variation rate in *** results quantitatively disentangle the contributions of the SOS response and DNA repair systems in antibiotic-induced mutagenesis.

关键词： Stress response Antibiotic-induced mutagenesis Mutation spectrum Linear model

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An integrative protocol for one‑step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data

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Marine Life Science & Technology 2023年第4期5卷 564-572页

作者： Jiahao Ni Jiao Pan Yaohai Wang Tianhao Chen Xinshi Feng Yichen Li Tongtong Lin Michael Lynch hongan long Weiyi Li Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China Laboratory for Marine Biology and Biotechnology Laoshan LaboratoryQingdao 266237China Biodesign Center for Mechanisms of Evolution Arizona State UniversityTempeAZ 85281USA Department of Biology Indiana UniversityBloomingtonIN 47401USA Present Address:SLAC National Accelerator Laboratory Stanford UniversityStanford 94305USA

High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures,greatly promoting biological studies involving large amounts of complex samples,especially those involving environmental and pathogen-monitoring *** library preparation kits for amplicon sequencing,which generally require multiple steps,including adapter ligation and indexing,are expensive and time-consuming,especially for applications at a large *** overcome these limitations,a“one-step PCR approach”has been previously proposed for constructions of amplicon libraries using long fusion ***,efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be *** tackle these,we present an integrative protocol for one-step PCR amplicon library construction(OSPALC).High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental *** this protocol,the amplicon library is constructed through one regular PCR with long primers,and the total cost per DNA/cDNA sample decreases to just 7%of the typical cost via the multi-step PCR *** tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case *** to design primers targeting at any genomic regions are also *** principle,OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples,and will facilitate research in numerous fields.

关键词： Amplicon library preparation Lab-made protocol long-primer PCR Cost efficiency

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Biodiversity-based development and evolution:the emerging research systems in model and non-model organisms

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Science China(Life Sciences) 2021年第8期64卷 1236-1280页

作者： long Zhao Feng Gao Shan Gao Yujun Liang hongan long Zhiyi Lv Ying Su Naihao Ye Liusuo Zhang Chengtian Zhao Xiaoyu Wang Weibo Song Shicui Zhang Bo Dong Institute of Evolution and Marine Biodiversity(IEMB) Ocean University of ChinaQingdao 266003China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and TechnologyQingdao 266237China College of Fisheries Ocean University of ChinaQingdao 266003China College of Marine Life Sciences Ocean University of ChinaQingdao 266003China Yellow Sea Fisheries Research Institute Chinese Academy of Fishery SciencesQingdao 266071China CAS Key Laboratory of Experimental Marine Biology Institute of OceanologyChinese Academy of SciencesQingdao 266071China

Evolutionary developmental biology,or Evo-Devo for short,has become an established field that,broadly speaking,seeks to understand how changes in development drive major transitions and innovation in organismal *** does so via integrating the principles and methods of many subdisciplines of *** we have gained unprecedented knowledge from the studies on model organisms in the past decades,many fundamental and crucially essential processes remain a *** the tremendous biodiversity of our planet,the current model organisms seem insufficient for us to understand the evolutionary and physiological processes of life and its adaptation to exterior *** currently increasing genomic data and the recently available gene-editing tools make it possible to extend our studies to non-model *** this review,we review the recent work on the regulatory signaling of developmental and regeneration processes,environmental adaptation,and evolutionary mechanisms using both the existing model animals such as zebrafish and Drosophila,and the emerging nonstandard model organisms including amphioxus,ascidian,ciliates,single-celled phytoplankton,and marine *** addition,the challenging questions and new directions in these systems are outlined as well.

关键词： Biodiversity evolutionary planet

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Anchoring Ru clusters to highly defective N-doped carbon nanotubes via a thermal-shock strategy for stable industrial hydrogen evolution

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Nano Research 2024年第6期17卷 5261-5269页

作者： Zhiming Li Xinyu Li Haiqing Ma Chenliang Ye hongan Yu long Nie Meng Zheng Jin Wang College of Materials Science and Engineering Shenzhen UniversityShenzhen 518060China School of Chemistry and Materials Science Anhui Normal UniversityWuhu 241002China Department of Power Engineering North China Electric Power UniversityBaoding 071003China

Non-Pt or low-Pt catalysts capable for stable generation of hydrogen via water electrolysis at an industrial level of current density are highly *** of strong metal-support connection is beneficial to improve the performance stability of *** we employed highly defective N-doped carbon nanotubes(d-N-CNT)as the support to achieve uniform and firm anchoring of Ru clusters(~1.9 nm)via a thermal-shock *** as-prepared Ru/d-N-CNT catalyst shows excellent catalytic activity for hydrogen evolution reaction(HER)in alkaline media and requires an overpotential(ƞ)of 12 mV at 10 mA·cm^(−2)and 116 mV at 200 mA·cm^(−2)with a Ru loading of 0.025 mg·cm^(−2).Impressively,Ru/d-N-CNT presents robust stability for HER at both low current density(stable for at least 1000 h at 10 mA·cm^(−2))and the industrial level of current density(stable for at least 100 h at 1000 mA·cm^(−2)),remarkably outperforming commercial Pt/C and Ru/*** highly defective nature of the N-CNT support endowed the as-prepared Ru/d-N-CNT catalyst with strong metal-support adhesion that efficiently suppressed agglomeration as well as obscission of Ru ***,the rich defects increased the surface energy of the N-CNT support and resulted in improved hydrophilicity as evidenced by the liquid contact angle measurement and the bubble evolution process,which also played an important role in stabilizing the HER performance especially at large current density.

关键词： thermal-shock method hydrogen evolution reaction large-current-density Ru cluster

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