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Dominance of transposable element‑related satDNAs results in great complexity of“satDNA library”and invokes the extension towards“repetitive DNA library”

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Marine Life Science & Technology 2024年第2期6卷 236-251页

作者： Monika Tunjić‑Cvitanić Daniel García‑Souto Juan J.Pasantes EvaŠatović‑Vukšić Division of molecular biology Ruđer BoškovićInstitute10000 ZagrebCroatia Genomes and Disease Centre for Research in Molecular Medicine and Chronic Diseases(CIMUS)Universidade de Santiago de Compostela15706 Santiago de CompostelaSpain department of Zoology Genetics and Physical AnthropologyUniversidade de Santiago de Compostela15706 Santiago de CompostelaSpain Centro de Investigación Mariña Dpto de BioquímicaXenética e InmunoloxíaUniversidade de Vigo36310 VigoSpain

Research on bivalves is fast-growing,including genome-wide analyses and genome *** characteristics qualify oysters as a valuable model to explore repetitive DNA sequences and their genome *** we char-acterize the satellitomes of five species in the family Ostreidae(Crassostrea angulata,***,***,***,Ostrea edulis),revealing a substantial number of satellite DNAs(satDNAs)per genome(ranging between 33 and 61)and peculiarities in the composition of their *** satDNAs were either associated to or derived from transposable elements,displaying a scarcity of transposable element-unrelated satDNAs in these *** to the non-conventional satellitome constitution and dominance of Helitron-associated satDNAs,comparative satellitomics demanded more in-depth analyses than standardly *** analyses(including ***,the first bivalve species with a defined satellitome)revealed that 13 satDNAs occur in all six oyster genomes,with Cg170/HindIII satDNA being the most abundant in all of *** the“satDNA library model”highlighted the necessity to adjust this term when studying tandem repeat evolution in organisms with such *** repetitive sequences with potential variation in the organizational form and repeat-type affiliation are examined across related species,the introduction of the terms“TE library”and“repetitive DNA library”becomes essential.

关键词： Satellitome Comparative satellitomics Helitron Bivalves “Dark matter of the genome”

Dysregulation of RNA modification systems in clinical populations with neurocognitive disorders

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Neural Regeneration Research 2024年第6期19卷 1256-1261页

作者： Helen M.Knight Merve DemirbugenÖz Adriana PerezGrovas-Saltijeral Division of Cells Organisms and Molecular GeneticsSchool of Life SciencesUniversity of NottinghamNottinghamUK department of Pharmaceutical Toxicology Faculty of PharmacyAnkara UniversityAnkaraTurkey

The study of modified RNA known as epitranscriptomics has become increasingly relevant in our understanding of disease-modifying *** of N6 adenosine(m^(6)A)and C5 cytosine(m^(5)C)bases occur on mRNAs,tRNA,mt-tRNA,and rRNA species as well as non-coding *** emerging knowledge of RNA binding proteins that act as writer,reader,and eraser effector proteins,comes a new understanding of physiological processes controlled by these *** processes when spatiotemporally disrupted within cellular nanodomains in highly specialized tissues such as the brain,give rise to different forms of *** this review,we discuss accumulating evidence that changes in the m^(6)A and m^(5)C methylation systems contribute to neurocognitive *** studies first identified mutations within FMR1 to cause intellectual disability Fragile X syndromes several years before FMR1 was identified as an m^(6)A RNA reader ***,familial mutations within the m^(6)A writer gene METTL5,m^(5)C writer genes NSUN2,NSUN3,NSUN5,and NSUN6,as well as THOC2 and THOC6 that form a protein complex with the m^(5)C reader protein ALYREF,were recognized to cause intellectual development ***,differences in expression of the m^(5)C writer and reader effector proteins,NSUN6,NSUN7,and ALYREF in brain tissue are indicated in individuals with Alzheimer's disease,individuals with a high neuropathological load or have suffered traumatic brain ***,an abundance of m^(6)A reader and anti-reader proteins are reported to change across brain regions in Lewy bodies diseases,Alzheimer's disease,and individuals with high cognitive reserve.m^(6)A-modified RNAs are also reported significantly more abundant in dementia with Lewy bodies brain tissue but significantly reduced in Parkinson's disease tissue,whilst modified RNAs are misplaced within diseased cells,particularly where synapses are *** parahippocampal brain tissue,m^(6)A modification is enri

关键词： 5-methylcytosine methylation Alzheimer's disease cognitive diseases epitranscriptomics intellectual disability Lewy body diseases N6 adenosine RNA modification

Emerging delivery systems based on aqueous two-phase systems:A review

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Acta Pharmaceutica Sinica B 2024年第1期14卷 110-132页

作者： Yaowen Zhang Yankun Luo Jingqi Zhao Wenzhuo Zheng Jun Zhan Huaping Zheng Feng Luo State Key Laboratory of Oral diseases National Clinical Research Center for Oral DiseasesWest China School of StomatologySichuan UniversityChengdu 610041China department of Obstetrics and Gynecology West China Second University HospitalSichuan UniversityChengdu 610041China Key Laboratory of Birth Defects and Related diseases of Women and Children(Sichuan University) Ministry of EducationChengdu 610041China department of Dermatology Rare Diseases CenterInstitutes for Systems GeneticsFrontiers Science Center for Disease-related Molecular NetworkWest China HospitalSichuan UniversityChengdu 610041China department of Prosthodontics West China School of StomatologySichuan UniversityChengdu 610041China

The aqueous two-phase system(ATPS)is an all-aqueous system fabricated from two immiscible aqueous *** is spontaneously assembled through physical liquid-liquid phase separation(LLPS)and can create suitable templates like the multicompartment of the intracellular *** structures containing multiple compartments make it possible to endow materials with advanced *** to the properties of ATPSs,ATPS-based drug delivery systems exhibit excellent biocompatibility,extraordinary loading efficiency,and intelligently controlled content release,which are particularly advantageous for delivering drugs in ***,we will systematically review and evaluate ATPSs as an ideal drug delivery *** on the basic mechanisms and influencing factors in forming ATPSs,the transformation of ATPSs into valuable biomaterials is ***,we concentrate on the most recent cutting-edge research on ATPS-based delivery ***,the potential for further collaborations between ATPS-based drug-carrying biomaterials and disease diagnosis and treatment is also explored.

关键词： Aqueous two-phase systems Drug delivery systems Biomaterials Microcapsules Microparticles Cell therapy Cancer treatment Organ regeneration

Mathematical Modeling of Cell Polarity Establishment of Budding Yeast

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Communications on Applied Mathematics and Computation 2024年第1期6卷 218-235页

作者： Yue Liu Jun Xie Hay-Oak Park Wing-Cheong Lo department of Mathematics City University of Hong KongTat Chee AvenueKowloonHong KongChina department of molecular genetics The Ohio State UniversityColumbusOHUSA

The budding yeast Saccharomyces cerevisiae is a powerful model system for studying the cell polarity *** cell polarization process is regulated by signaling molecules,which are initially distributed in the cytoplasm and then recruited to a proper location on the cell membrane in response to spatial cues or *** of these signaling molecules involves complex regulation,so the mathematical models become a useful tool to investigate the mechanism behind the *** this review,we discuss how mathematical modeling has shed light on different regulations in the cell *** also propose future applications for the mathematical modeling of cell polarization and morphogenesis.

关键词： Budding yeast Cdc42 Morphogenesis Septin Mathematical models

Mitigating growth-stress tradeoffs via elevated TOR signaling in rice

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molecular Plant 2024年第2期17卷 240-257页

作者： Wei Li Jiaqi Liu Zeqi Li Ruiqiang Ye Wenzhen Chen Yuqing Huang Yue Yuan Yi Zhang Huayi Hu Peng Zheng Zhongming Fang Zeng Tao Shiyong Song Ronghui Pan Jian Zhang Jumim Tu Jen Sheen Hao Du State Key Laboratory of Rice biology College of Agriculture and BiotechnologyZhejiang UniversityYu-Hang-Tang Road No.866Hangzhou 310058China ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang UniversityHangzhou 311215China Hainan Institute of Zhejiang University Sanya 572025China National Key Laboratory of Plant molecular genetics CASCenter for Excellence in Molecular Plant SciencesShanghai lnstitute of Plant Physiology and EcologyChineseAcademy of SciencesShanghai 200032China Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region(Ministry of Education) College of Agricultural SciencesGuizhouUniversityGuiyang 550025China State Key Laboratory of Rice biology and Breeding China National Rice Research InstituteHangzhou 311400China department of molecular biology and Center for Computational and Integrative biology Massachusetts General Hospitaland Department of GeneticsHarvard Medical SchoolBostonMA02114USA

Rice production accounts for approximately half of the freshwater resources utilized in agriculture,result-ing in greenhouse gas emissions such as methane(CH4)from flooded paddy *** address this chal-lenge,environmentally friendly and cost-effective water-saving techniques have become widely adopted in rice ***,the implementation of water-saving treatments(WsTs)in paddy-field rice has been associated with a substantial yield loss of up to 50%as well as a reduction in nitrogen use efficiency(NUE).In this study,we discovered that the target of rapamycin(TOR)signaling pathway is compromised in rice under *** profiling-coupled transcriptome sequencing(polysome-seq)analysis unveiled a substantial reduction in global translation in response to WST associated with the downregulation of TOR ***,biochemical,and genetic analyses revealed new insights into the impact of the positive TOR-S6K-RPS6 and negative TOR-MAF1 modules on translation repression under ***,ammonium exhibited a greater ability to alleviate growth constraints under WsT by enhancing TOR signaling,which simultaneously promoted uptake and utilization of ammonium and nitrogen *** further demonstrated that TOR modulates the ammonium transporter AMT1;1 as well as the amino acid permease APP1 and dipeptide transporter NPF7.3 at the translational level through the 5'untranslated ***,these findings reveal that enhancing TOR signaling could mitigate rice yield penalty due to WST by regulating the processes involved in protein synthesis and *** study will contribute to the breeding of new rice varieties with increased water and fertilizer utilization efficiency.

关键词： target of rapamycin TOR water-saving rice low-carbon agriculture drought nitrogen use efficiency NUE

Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences

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Asian Pacific Journal of Tropical Medicine 2024年第5期17卷 214-225,I0004-I0038页

作者： Lihini Sandaleka Muthukumarana Methsala Madurangi Wedage Samanthika Rathnayake Nissanka Kolitha De Silva department of Zoology Faculty of Applied SciencesUniversity of Sri JayewardenepuraGangodawilaNugegodaSri Lanka genetics and molecular biology Unit Faculty of Applied SciencesUniversity of Sri JayewardenepuraGangodawilaNugegodaSri Lanka Sri Lanka Institute of Biotechnology PitipanaHomagamaSri Lanka

Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2(ITS2)and cytochrome C oxidase I(COI)sequences deposited at the ***:Seventy-five ITS2,210 COI and 26 concatenated sequences available in the NCBI database were *** analysis was performed using Bayesian likelihood trees,whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic *** diversity indices and genetic differentiation were also ***:Two genetically divergent molecular forms of *** species complex corresponding to sibling species A and B are *** A evolved around 37-82 million years ago in Sri Lanka,India,and the Netherlands,and species B evolved around 22-79 million years ago in Sri Lanka,India,and ***,Thailand,and Cambodia have two molecular forms:one is phylogenetically similar to species *** forms differ from species A and B and evolved recently in the above mentioned countries,Indonesia and the *** subdivision among Sri Lanka,India,and the Netherlands is almost absent.A substantial genetic differentiation was obtained for some populations due to isolation by large geographical *** diversity indices reveal the presence of a long-established stable mosquito population,at mutation-drift equilibrium,regardless of population ***:*** species complex consists of more than two genetically divergent molecular *** A is highly divergent from the *** Lanka and India contain only species A and B.

关键词： molecular systematics ITS2 COI DNA sequences Phylogeny Phylogeography

A novel deep generative model for mRNA vaccine development: Designing 5′ UTRs with N1-methyl-pseudouridine modification

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Acta Pharmaceutica Sinica B 2024年第4期14卷 1814-1826页

作者： Xiaoshan Tang Miaozhe Huo Yuting Chen Hai Huang Shugang Qin Jiaqi Luo Zeyi Qin Xin Jiang Yongmei Liu Xing Duan Ruohan Wang Lingxi Chen Hao Li Na Fan Zhongshan He Xi He Bairong Shen Shuai Cheng Li Xiangrong Song Institute of Systems genetics Department of Critical Care MedicineFrontiers Science Center for Disease-related Molecular NetworkState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengdu 610000China department of Computer Science City University of Hong KongHong Kong 99907China department of biology Brandeis UniversityBostonMA 02453USA

Efficient translation mediated by the 5'untranslated region(5'UTR)is essential for the robust efficacy of mRNA ***,the N1-methyl-pseudouridine(m1)modification of mRNA can impact the translation efficiency of the 5'*** discovered that the optimal 5'UTR for m1y-modified mRNA(m1y-5'UTR)differs significantly from its unmodified counterpart,high-lighting the need for a specialized tool for designing mly-5'UTRs rather than directly utilizing high-expression endogenous gene 5'*** response,we developed a novel machine learning-based tool,Smart5UTR,which employs a deep generative model to identify superior m1y-5'UTRs in *** tailored loss function and network architecture enable Smart5UTR to overcome limitations inherent in existing *** a result,Smart5UTR can successfully design superior 5'UTRs,greatly benefiting mRNA vaccine ***,Smart5UTR-designed superior 5'UTRs significantly enhanced antibody titers induced by COVID-19 mRNA vaccines against the Delta and Omicron variants of SARS-CoV-2,surpassing the performance of vaccines using high-expression endogenous gene 5'UTRs.

关键词： mRNA vaccine Machine learning 5'UTR mRNA design Sequence design N1-Methyl-pseudouridine COVID-19 SARS-CoV-2

Inbreeding and genetic load in a pair of sibling grouse species:Tetrastes sewersowi and ***

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Avian Research 2024年第2期15卷 265-270页

作者： Kai Song Tom van der Valk Bin Gao Peter Halvarsson Yun Fang Wendong Xie Siegfried Klaus Zhiming Han Yue-Hua Sun Jacob Hoglund Key Laboratory of Animal Ecology and Conservation biology Institute of ZoologyChinese Academy of SciencesBeijing100101China Animal Ecology Department of Ecology and GeneticsUppsala UniversityNorbyvagen 18DUppsala75236Sweden department of Cell and molecular biology Uppsala75273Sweden Unit of Parasitology Department of Biomedicine and Veterinary Public HealthSwedish University of Agricultural SciencesPO Box 7036Uppsala75007Sweden Lindenhohe 5 JenaD-07749Germany The State Key Laboratory of Reproductive biology Institute of ZoologyChinese Academy of SciencesBeijing100101China

Genetic load and inbreeding are recognized as important factors to be considered in conservation *** levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals,including humans(inbreeding depression).Genomic tech-niques are increasingly used in measuring and understanding genetic load and inbreeding and their importance in evolution and *** used whole genome resequencing data from two sibling grouse species in subarctic Eurasia to quantify *** found a large range of inbreeding measured as FROH(fraction of runs of homozygosity)in individuals from different populations of Chinese Grouse(Tetrastes sewerzowi)and Hazel Grouse(***).FROH estimated from genome-wide runs of homozygosity(ROH)ranged from 0.02 to 0.24 among Chinese Grouse populations and from 0.01 to 0.44 in Hazel *** from a population of Chinese Grouse residing in the Qilian mountains and from the European populations of Hazel Grouse(including samples from Sweden,Germany and Northeast Poland)were the most inbred(FROH ranged from 0.10 to 0.23 and 0.11 to 0.44,respectively).These levels are comparable to other highly inbred populations of *** Grouse from northern China and Chinese Grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding *** of the ratio between deleterious missense mutations and synonymous mutations revealed higher levels in Chinese Grouse as compared to Hazel *** results are possibly explained by higher fixation rates,mutational melt down,in the range-restricted Chinese Grouse compared to the wide-ranging Hazel ***,when we compared the relatively more severe class of loss-of-function muta-tions,Hazel Grouse had slightly higher levels than Chinese Grouse,a result which may indicate that purifying selection(purging)has been more efficient in Chinese Grouse on this class of mutations.

关键词： Genetic load Inbreeding Purifying selection Qinghai-Tibetan Plateau ROH Tetrastes

CD36 promotes tubular ferroptosis by regulating the ubiquitination of FSP1 in acute kidney injury

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Genes & diseases 2024年第1期11卷 449-463页

作者： Yixin Ma Lili Huang Zheng Zhang Pengfei Yang Qingsong Chen Xujia Zeng Fangyan Tan Chunxia Wang Xiongzhong Ruan Xiaohui Liao department of Nephrology The Second Affiliated HospitalChongqing Medical UniversityChongqing 400010China department of Cell biology and genetics Chongqing Medical UniversityChongqing 400016China Centre for Nephrology Royal Free and University College Medical SchoolUniversity College LondonRoyal Free CampusRowland Hill StreetLondon NW32PFUnited Kingdom Centre for Lipid Research Key Laboratory of Molecular Biology on Infectious DiseasesMinistry of EducationChongqing Medical UniversityChongqing 400016China Kuanren Laboratory of Translational Lipidology Centre for Lipid ResearchSecond Affiliated Hospital of Chongqing Medical UniversityChongqing 400010China

Reactive oxidative species(ROos)production-driven ferroptosis plays a role in acute kidney injury(Akl).However,its exact molecular mechanism is poorly *** receptor CD36 has important roles in oxidizing lipids,lipid accumulation,metabolic syndrome,and insulin resistance in chronic kidney disease,but its roles remain unexplored in *** present study investigated the role and mechanism of CD36 in regulating proximal tubular cell ferroptosis and *** expression of CD36 was found to be significantly up-regulated in AKI renal tissues and correlated with renal function,which might serve as an independent biomarker for AKl ***,in adult mice subjected to AKl,deletion of CD36(CD36-/-)induced tubular cell Ros accumulation,ferroptosis activation,and renal ***,combining LC-MS/MS,co-IP,and ubiquitination analyses revealed that CD36 could specifically bind to ferroptosis suppressor protein 1(FSP1)and regulate its ubiquitination at sites K16 and K24,leading to FSP1 degradation and progression of ferroptosis in *** present results emphasize a novel mechanism of CD36 in cisplatin-induced *** discovery of the special CD36 roles in promoting ferroptosis and AKI development by regulating the ubiquitination of FSP1 in proximal tubular cells may be potential therapeutic targets for ***,CD36 may play a key role in the progression of ***,targeting CD36 may provide a promising treatment option for AKI.

关键词： Acute kidney injury CD36 Ferroptosis FSP1 Ubiquitin-dependent degradation