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| 1 | Biodiversity-based development and evolution:the emerging research systems in model and non-model organisms显示文摘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 evolution.It does so via integrating the principles and methods of many subdisciplines of biology.Although we have gained unprecedented knowledge from the studies on model organisms in the past decades,many fundamental and crucially essential processes remain a mystery.Considering 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 environments.The currently increasing genomic data and the recently available gene-editing tools make it possible to extend our studies to non-model organisms.In 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 nematode.In addition,the challenging questions and new directions in these systems are outlined as well. | 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 | 2021 | Science China(Life Sciences)2021，64，8： | 9 |
| 2 | The insect-killing bacterium Photorhabdus luminescens has the lowest mutation rate among bacteria显示文摘Mutation is a primary source of genetic variation that is used to power evolution.Many studies,however,have shown that most mutations are deleterious and,as a result,extremely low mutation rates might be benefcial for survival.Using 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 ATCC29999.The mutations are strongly A/T-biased with a mutation bias of 10.28 in the A/T direction.It 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 bacteria.This 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. | Jiao Pan Emily Williams Way Sung Michael Lynch Hongan Long | 2021 | Marine Life Science & Technology2021，3，1： | 2 |
| 3 | Cost-reduction strategies in massive genomics experiments显示文摘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. | Haichao Li Kun Wu Chenchen Ruan Jiao Pan Yujin Wang Hongan Long | 2019 | Marine Life Science & Technology2019，1，1： | 2 |
| 4 | Contribution of the SOS response and the DNA repair systems to norfloxacin induced mutations in E.coli显示文摘Antibiotic-resistant bacteria severely threaten human health.Besides spontaneous mutations generated by endogenous factors,the resistance might also originate from mutations induced by certain antibiotics,such as the fluoroquinolones.Such antibiotics increase the genome-wide mutation rate by introducing replication errors from the SOS response pathway or decreasing the efficiency of the DNA repair systems.However,the relative contributions of these molecular mechanisms remain unclear,hindering understanding of the generation of resistant pathogens.Here,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 E.coli using linear models.The SOS response plays a positive role in all three mutational features(mutation rates of BPSs,transversions,structural variations)and affects the mutational spectrum.The 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 E.coli.Our results quantitatively disentangle the contributions of the SOS response and DNA repair systems in antibiotic-induced mutagenesis. | Tongtong Lin Jiao Pan Colin Gregory Yaohai Wang Clayton Tincher Caitlyn Rivera Michael Lynch Hongan Long Yu Zhang | 2023 | Marine Life Science & Technology2023，5，4： | 1 |
| 5 | An integrative protocol for one‑step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data显示文摘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 ones.Commercial 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 scale.To overcome these limitations,a“one-step PCR approach”has been previously proposed for constructions of amplicon libraries using long fusion primers.However,efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed.To 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 samples.With 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 approach.Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study.Tools to design primers targeting at any genomic regions are also presented.In 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. | Jiahao Ni Jiao Pan Yaohai Wang Tianhao Chen Xinshi Feng Yichen Li Tongtong Lin Michael Lynch Hongan Long Weiyi Li | 2023 | Marine Life Science & Technology2023，5，4： | 1 |
| 6 | MomL inhibits bacterial antibiotic resistance through the starvation stringent response pathway显示文摘Antibiotic resistance in gram-negative pathogens has become one of the most serious global public health threats.The role of the N-acyl homoserine lactone(AHL)-mediated signaling pathway,which is widespread in gram-negative bacteria,in the bacterial resistance process should be studied in depth.Here,we report a degrading enzyme of AHLs,MomL,that inhibits the antibiotic resistance of Pseudomonas aeruginosa through a novel mechanism.The MomL-mediated reactivation of kanamycin is highly associated with the relA-mediated starvation stringent response.The degradation of AHLs by MomL results in the inability of LasR to activate relA,which,in turn,stops the activation of downstream rpoS.Further results show that rpoS directly regulates the type VI secretion system H2-T6SS.Under MomL treatment,inactivated RpoS fails to regulate H2-T6SS;therefore,the expression of effector phospholipase A is reduced,and the adaptability of bacteria to antibiotics is weakened.MomL in combination with kanamycin is effective against a wide range of gram-negative pathogenic bacteria.Therefore,this study reports a MomL-antibiotic treatment strategy on antibiotic-resistant bacteria and reveals its mechanism of action. | Qin Dou Jin Yuan Rilei Yu Jiahui Yang Jiayi Wang Yuxiang Zhu Jing Zhong Hongan Long Zhiqing Liu Xianghong Wang Yuying Li Yichen Xiao Jiazhen Liang Xiao-Hua Zhang Yan Wang | 2022 | mLife2022，1，4： | 0 |
| 7 | Marine life science and technology (MLST): a new journal highlighting all aspects of marine biology and biotechnology research显示文摘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. | Hongan Long Xiao-Hua Zhang | 2019 | Marine Life Science & Technology2019，1，1： | 0 |
| 8 | First Record and Redefinition of the Qingdao Population of Marine Ciliate Cardiostomatella vermiformis (Kahl, 1928) Corliss, 1960 (Protozoa, Ciliophora)显示文摘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. | WANG Yangang HU Xiaozhong LONG Hongan SONG Weibo | 2007 | Journal of Ocean University of China2007，6，4： | 0 |
| 9 | Special topic on EvoDevo:emerging models and perspectives显示文摘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 populations.Yet,uniting these perspectives provides a better understanding of biological functions.Ernst 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. | Hongan Long Bo Dong | 2023 | Marine Life Science & Technology2023，5，4： | 0 |
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