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Full-length transcriptome sequencing analysis reveals differential skin color regulation in snakeheads fish Channa argus

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Aquaculture and fisheries 2024年第4期9卷 590-596页

作者： Leigang Mao Yongan Zhu Jiaren Yan Longgang Zhang Shuren Zhu Li An Qinglei Meng Zhishan Zhang Xirong Wang College of fisheries and life science Shanghai Ocean UniversityShanghai201306China Shandong Freshwater fisheries Research Institute Jinan250017China

Albinism is a genetic disorder caused by a series of genetic abnormalities that result in a decrease in *** yellow snakehead fish(GCAS)has been discovered while the Channa argus(CAS)breeding,but the genetic mechanism that causes its albinism is not *** sequencing and comparison of CAS and GCAS skin using Oxford Nanopore Technologies(ONT)technology to elucidate the molecular mechanisms of snakehead albinism.27.1 G clean reads and 26,198 full-length non-redundant sequences were generated via ONT ***,8079 new transcripts and 7231 genes were identified by comparing and analyzing redundant removed transcripts and known reference genome *** results of DEGs analysis showed that a total of 59 transcripts were differentially expressed in the two groups,including 22 up-regulated transcripts and 37 down-regulated *** causative genes associated with albinism have been identified,including TYR(Tyrosinase)and SOX10(SRY-box transcription factor 10)(tyrosinase synthesis and metabolism),S-100(S100 calcium binding protein A1)(melanin production),NLRC3(NLR family CARD domain containing 3)(disease immunity)are significantly down-regulated in GCAS,while RhoGEFs expression(melanin synthesis)is *** interaction analysis revealed that GAPDH(Glyceraldehyde-3-phosphate dehydrogenase)is the top hub gene in the regulation of skin color in *** addition,the skin of snakehead fish is regulated by metabolic(GAPDH),immune[Tumor protein p53(TP53),C-X-C motif chemokine ligand 8(CXCL8),SRC proto-oncogene,non-receptor tyrosine kinase(SRC),CD274]and neural[Notch receptor 1(NOTCH1),C-X-C motif chemokine ligand 12(CXCL12)]related genes to achieve differences in skin *** findings in understanding the process by which albinism in fish develops.

关键词： Albinism Channa argus Nanopore-based RNA sequencing Melanin

Resolving the geometric structure of trastuzumab by mobility capillary electrophoresis and native mass spectrometry

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Chinese Chemical Letters 2024年第3期35卷 221-225页

作者： Wenjing Zhang Jie Hong Lei Yang Zuqiang Xu Yu Xiang Wei Xu school of life science Beijing Institute of TechnologyBeijing 100081China

Available online Immunoglobulins G(IgGs)are Y-shaped globular proteins,however,their high flexibility and heterogeneity pose great challenges to their structure and conformation *** structure of IgG closely correlates to its biofunctions,such as the antibody escape of human immunodeficiency virus(HIV)could attribute to the distance mismatch between the ends of two Fab arms(antigen-binding sites)and envelope glycoprotein spikes on virion ***,we report the first use of mobility capillary electrophoresis(MCE)and native mass spectrometry(nMS)to resolve the internal geometric structure and conformation of an IgG(trastuzumab)in solution *** proteolysis,the ellipsoid dimensions of IgG and its subunits were measured by MCE-nMS *** was then reconstructed,in which the sizes and relative positions of these three subunits in three-dimensional space were *** was found that the two Fab arms have an angle of~102.1°and a distance of~11.0 nm between the two antigen-binding sites under native condition,and the Fc arm was tilted~16.0°towards one of the Fab *** was not on the plane of Fab-Fab,but has an angle of no larger than 103.1°.Under acidic environment(pH 3.0),each subunit of the IgG would unfold into larger dimensions,and the angles between these subunits also *** great potential for tumor imaging and therapy,the structure of F(ab')_(2)fragments was also measured and validated by molecular dynamic *** was found that the electrostatic force among these three subunits and steric hindrance stemming from Fc help maintaining the angle between two Fab arms.

关键词： Native mass spectrometry Mobility capillary electrophoresis Trastuzumab Protein structure Geometric structure

Combined intestinal microbiota and transcriptomic analysis to investigate the effect of different stocking densities on the ability of Pacific white shrimp(Litopenaeus vannamei)to utilize Chlorella sorokiniana

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Animal Nutrition 2024年第3期18卷 203-219页

作者： Hang Yuan Minghua Xie Jian Chen Naijie Hu Honming Wang Beiping Tan Lili Shi Shuang Zhang College of fisheries Guangdong Ocean UniversityZhanjiangChina College of fisheries and life science Dalian Ocean UniversityDalianChina Zhanjiang Experimental Station Chinese Academy of Tropical Agricultural SciencesZhanjiangChina

Aiming to investigate the impact of different stocking densities on the ability of Pacific white shrimp(Litopenaeus vannamei)to utilize Chlorella sorokiniana(CHL),a 3×2 factorial design stocking experiment was used in this ***,shrimp was fed with two dietary protein sources(fishmeal[FM]and CHL)at low(LSD;100 per m^(3)),medium(MSD;200 per m^(3))and high(HSD;300 per m^(3))stocking densities for 8 *** growth performance and resistance to Vibrio parahaemolyticus(1.0×10^(7) CFU/mL)of shrimp decreased with the increase of stocking density,but dietary CHL improved this *** between the CHL and FM groups for *** resistance were significant only under high-density conditions(P<0.05).Significant interactions between stocking density and protein source were found on the activities of catalase(CAT),superoxide dismutase(SOD)and phenol oxidase(PO),and the contents of malondialdehyde(MDA)in the hepatopancreas and the activities of intestinal amylase,most of which were significantly different between CHL and FM groups only at high stocking density(P<0.05).Analysis of 16S rDNA sequencing showed that dietary CHL increased the alpha diversity of intestinal microbiota,inhibited the colonization of pathogenic bacteria and enhanced the abundance of beneficial *** results showed that at high stocking densities,differentially expressed genes(DEGs)in the FM vs CHL group were mostly upregulated and primarily enriched in immune and metabolic related pathways including Toll,immune deficiency(Imd)and glycolysis–gluconeogenesis *** correlation analysis revealed significant correlation between the top ten intestinal bacteria at the genus level and markedly enriched DEGs,also more were detected under high density *** conclusion,CHL has great potential as a novel protein source in the intensive farming of shrimp.

关键词： Chlorella sorokiniana Stocking density Microbiota structure Transcriptomic profile Litopenaeus vannamei

The autophagy protein Atg9 functions in glia and contributes to parkinsonian symptoms in a Drosophila model of Parkinson’s disease

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Neural Regeneration Research 2024年第5期19卷 1150-1155页

作者： Shuanglong Yi Linfang Wang Margaret S.Ho Shiping Zhang school of life science and Technology ShanghaiTech UniversityShanghaiChina College of life sciences University of Chinese Academy of SciencesBeijingChina

Parkinson’s disease is a progressive neurodegenerative disease characterized by motor deficits,dopaminergic neuron loss,and brain accumulation ofα-synuclein aggregates called Lewy *** in protein degradation pathways,such as autophagy,has been demonstrated in neurons as a critical mechanism for eliminating protein aggregates in Parkinson’s ***,it is less well understood how protein aggregates are eliminated in glia,the other cell type in the *** the present study,we show that autophagy-related gene 9(Atg9),the only transmembrane protein in the autophagy machinery,is highly expressed in Drosophila glia from adult *** from immunostaining and live cell imaging analysis reveal that a portion of Atg9 localizes to the trans-Golgi network,autophagosomes,and lysosomes in ***9 is persistently in contact with these *** glial atg9 reduces the number of omegasomes and autophagosomes,and impairs autophagic substrate *** suggests that glial Atg9 participates in the early steps of autophagy,and hence the control of autophagic ***,loss of glial atg9 induces parkinsonian symptoms in Drosophila including progressive loss of dopaminergic neurons,locomotion deficits,and glial *** findings identify a functional role of Atg9 in glial autophagy and establish a potential link between glial autophagy and Parkinson’s *** results may provide new insights on the underlying mechanism of Parkinson’s disease.

关键词： Atg9 autophagy glia Parkinson’s disease

Involvement of the ABA-and H_(2)O_(2)-Mediated Ascorbate-Glutathione Cycle in the Drought Stress Responses of Wheat Roots

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Phyton-International Journal of Experimental Botany 2024年第2期93卷 329-342页

作者： Mengyuan Li Zhongye Gao Lina Jiang Leishan Chen Jianhui Ma College of life science Henan Normal UniversityXinxiang453007China school of life science and Basic Medicine Xinxiang UniversityXinxiang453003China

Abscisic acid(ABA),hydrogen peroxide(H_(2)O_(2)) and ascorbate(AsA)–glutathione(GSH)cycle are widely known for their participation in various ***,the relationship between ABA and H_(2)O_(2) levels and the AsA–GSH cycle under drought stress in wheat has not been *** this study,a hydroponic experiment was conducted in wheat seedlings subjected to 15%polyethylene glycol(PEG)6000–induced *** stress caused the rapid accumulation of endogenous ABA and H_(2)O_(2) and significantly decreased the number of root tips compared with the *** application of ABA significantly increased the number of root tips,whereas the application of H_(2)O_(2) markedly reduced the number of root tips,compared with that under 15%*** addition,drought stress markedly increased the DHA,GSH and GSSG levels,but decreased the AsA levels,AsA/DHA and GSH/GSSG ratios compared with those in the *** activities of the four enzymes in the AsA–GSH cycle were also markedly increased under drought stress,including glutathione reductase(GR),ascorbate peroxidase(APX),monodehydroascorbate reductase(MDHAR)and dehydroascorbate reductase(DHAR),compared with those in the ***,the application of an ABA inhibitor significantly inhibited GR,DHAR and APX activities,whereas the application of an H_(2)O_(2) inhibitor significantly inhibited DHAR and MDHAR ***,the application of ABA inhibitor significantly promoted the increases of H_(2)O_(2) and the application of H_(2)O_(2) inhibitor significantly blocked the increases of ABA,compared with those under 15% *** together,the results indicated that ABA and H_(2)O_(2) probably interact under drought stress in wheat;and both of them can mediate drought stress by modulating the enzymes in AsA–GSH cycle,where ABA acts as the main regulator of GR,DHAR,and APX activities,and H_(2)O_(2) acts as the main regulator of DHAR and MDHAR activities.

关键词： ABA H_(2)O_(2) AsA-GSH cycle drought stress wheat roots

Inhibition mechanisms of CRISPR-Cas9 by AcrⅡA25.1 and AcrⅡA32

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science China(life sciences) 2024年第9期67卷 1781-1791页

作者： Jianlin Zheng Yuwei Zhu Tengjin Huang Wenbo Gao Jiale He Zhiwei Huang HIT Center for life sciences School of Life Science and TechnologyHarbin Institute of TechnologyHarbin 150080China Westlake Center for Genome Editing Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou 310024China

In the ongoing arms race between bacteria and bacteriophages,bacteriophages have evolved anti-CRISPR proteins to counteract bacterial CRISPR-Cas ***,AcrⅡA25.1 and AcrⅡA32 have been found to effectively inhibit the activity of Spy Cas9 both in bacterial and human ***,their molecular mechanisms remain ***,we report the cryo-electron microscopy structures of ternary complexes formed by AcrⅡA25.1 and AcrⅡA32 bound to Spy Cas9-sg *** structural analysis and biochemical experiments,we revealed that AcrⅡA25.1 and AcrⅡA32 recognize a novel,previously-unidentified anti-CRISPR binding site on Spy *** found that both AcrⅡA25.1 and AcrⅡA32 directly interact with the WED domain,where they spatially obstruct conformational changes of the WED and PI domains,thereby inhibiting Spy Cas9 from recognizing protospacer adjacent motif(PAM)and unwinding double-stranded *** addition,they may inhibit nuclease activity by blocking the dynamic conformational changes of the Spy Cas9 surveillance *** summary,our data elucidate the inhibition mechanisms of two new anti-CRISPR proteins,provide new strategies for the modulation of Spy Cas9 activity,and expand our understanding of the diversity of anti-CRISPR protein inhibition mechanisms.

关键词： anti-CRISPR cryo-EM Spy Cas9 AcrⅡA25.1 AcrⅡA32 inhibiton

Screening of morphology-related genes based on predatorinduced transcriptome sequencing and the functional analysis of Dagcut gene in Daphnia galeata

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Current Zoology 2024年第4期70卷 440-452页

作者： Ya-Qin Cao Ya-Jie Zhao Hui-Ying Qi Jin-Fei Huang Fu-Cheng Zhu Wen-Ping Wang Dao-Gui Deng school of life science Huaibei Normal UniversityHuaibei 235000AnhuiChina

High fish predation pressure can trigger"induced defense"in Daphnia species,resulting in phenotypic plasticity in morphology,behavior,or life-history *** molecular mechanisms of defense morphogenesis(e.g.,the tail spine and helmet)in Daphnia remain *** the pres-ent study,the tail spine,helmet,and body of Daphnia galeata under fish and non-fish kairomones conditions were collected for transcriptome analysis.A total of 24 candidate genes related to the morphological defense of *** were identified,including 2 trypsin,one cuticle protein,1 C1qDC protein,and 2 ferritin *** function of the Dagcut gene(*** cuticle protein gene)in relation to tail spine morphology was assessed using RNA interference(RNAi).Compared with the EGFP(Enhanced green fluorescent protein)treatment,after RNAi,the expression levels of the Dagcut gene(*** cuticle protein gene)showed a significant ***,the tail spines of the offspring pro-duced by *** after RNAi of the Dagcut gene appeared curved during the *** whole-mount in situ hybridization,a clear signal site was detected on the tail spine of *** before RNAi which disappeared after *** results suggest that the Dagcut gene may play an important role in tail spine formation of ***,and will provide a theoretical basis for studying the molecular mechanisms of the morpho-logical plasticityin cladocera inthefuture.

关键词： Dagcut Daphnia galeata fish kairomones RNAi tail spine transcriptome sequencing.

Molecular cloning and functional analysis of two calcium associated cuticular protein genes in Neocaridina denticulata sinensis

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Journal of Oceanology and Limnology 2024年第5期42卷 1659-1672页

作者： Xi GAO Mengmeng DUAN Yuying SUN Jiquan ZHANG school of life sciences/Hebei Basic science Center for Biotic Interaction Hebei UniversityBaoding 071002China Institute of life science and Green Development Hebei UniversityBaoding 071002China

The body surface of crustaceans is covered with a sturdy *** growth and development of crustaceans are realized through *** denticulata sinensis is a suitable candidate for crustacean scientific *** calcium-associated cuticular protein genes,named NdCAP-1 and NdCAP-2,were obtained from *** *** docking simulated the binding effect of both proteins and calcium ***-quantitative reverse transcription PCR results show that NdCAP-1 is expressed in D_(2-4) stage,NdCAP-2 expressed in D_(2-4) and A-B stages,and both were significantly expressed in the cephalothorax cuticle and ***,it was revealed that NdCAP-1 and NdCAP-2 are regulated by NdEcR-mediated 20 E signaling *** of NdCAP-1 and NdCAP-2 was observed to cause surface *** recombinant proteins(rNdCAP-1 and rNdCAP-2),obtained by prokaryotic expression,had calcium-binding and chitin-binding ability,inhibited formation of calcium carbonate *** results show that calcium-associated cuticular proteins play important roles in cuticle formation and calcification.

关键词： Neocaridina denticulata sinensis calcium-associated cuticular protein molting cycle RNAi calcium-binding ability

Defect engineering on constructing surface active sites in catalysts for environment and energy applications

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Frontiers of Chemical science and Engineering 2024年第7期18卷 11-32页

作者： Yawen Cai Baowei Hu Xiangke Wang school of life science Shaoxing UniversityShaoxing 312000China College of Environmental science and Engineering North China Electric Power UniversityBeijing 102206China

The precise engineering of surface active sites is deemed as an efficient protocol for regulating surfaces and catalytic properties of *** engineering is the most feasible option to modulate the surface active sites of *** specific active sites on the catalyst allows precise modulation of its electronic structure and physicochemical ***,we outlined the engineering of several types of defects,including vacancy defects,void defects,dopant-related defects,and defect-based single atomic *** overview of progress in fabricating structural defects on catalysts via de novo synthesis or post-synthetic modification was ***,the applications of the well-designed defective catalysts in energy conversion and environmental remediation were carefully ***,current challenges in the precise construction of active defect sites on the catalyst and future perspectives for the development directions of precisely controlled synthesis of defective catalysts were also proposed.

关键词： defect engineering vacancy void defects doping single atomic sites