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Early results of the integrative epigenomic-transcriptomic landscape of colorectal adenoma and cancer

World Journal of Gastrointestinal Oncology 2024年第2期16卷 414-435页

作者： You-Wang Lu Zhao-Li Ding Rui Mao Gui-Gang Zhao Yu-Qi He Xiao-Lu Li Jiang Liu Department of Dermatology and Venereology The First Affiliated Hospital of Kunming Medical UniversityKunming 650032Yunnan ProvinceChina Kunming Biological Diversity Regional center of Large Apparatus and Equipments Public Technical Service CenterKunming Institute of ZoologyKunming 650223Yunnan ProvinceChina School of Stomatology Kunming Medical UniversityKunming 650500Yunnan ProvinceChina Genome center of biodiversity Kunming Institute of ZoologyChinese Academy of ScienceKunming 650223Yunnan ProvinceChina Department of Reproduction and Genetics The First Affiliated Hospital of Kunming Medical UniversityKunming 650032Yunnan ProvinceChina

BACKGROUND Aberrant methylation is common during the initiation and progression of colorectal cancer(CRC),and detecting these changes that occur during early adenoma(ADE)formation and CRC progression has clinical *** To identify potential DNA methylation markers specific to ADE and *** Here,we performed SeqCap targeted bisulfite sequencing and RNA-seq analysis of colorectal ADE and CRC samples to profile the epigenomic-transcriptomic *** Comparing 22 CRC and 25 ADE samples,global methylation was higher in the former,but both showed similar methylation patterns regarding differentially methylated gene positions,chromatin signatures,and repeated ***-grade CRC tended to exhibit elevated methylation levels in gene promoter regions compared to those in low-grade *** with RNA-seq gene expression data,we identified 14 methylation-regulated differentially expressed genes,of which only AGTR1 and NECAB1 methylation had prognostic *** Our results suggest that genome-wide alterations in DNA methylation occur during the early stages of CRC and demonstrate the methylation signatures associated with colorectal ADEs and CRC,suggesting prognostic biomarkers for CRC.

关键词： Colorectal cancer Epigenomic alteration Transcriptome Methylation-regulated differentially expressed genes

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Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 51-65页

作者： Binzhong Wang Bin Wu Xueqing Liu Yacheng Hu Yao Ming Mingzhou Bai Juanjuan Liu Kan Xiao Qingkai Zeng Jing Yang Hongqi Wang Baifu Guo Chun Tan Zixuan Hu Xun Zhao Yanhong Li Zhen Yue Junpu Mei Wei Jiang Yuanjin Yang Zhiyuan Li Yong Gao Lei Chen Jianbo Jian Hejun Du Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes Yichang 443100China Chinese Sturgeon Research Institute China Three Gorges CorporationYichang 443100China Yangtze River biodiversity Research center China Three Gorges CorporationWuhan 430014China BGI-Shenzhen Shenzhen 518083China BGI Genomics BGI-ShenzhenShenzhen 518083China Department of Biotechnology and Biomedicine Technical University of DenmarkLyngby 2800Denmark River Basin Complex Administration center China Three Gorges CorporationYichang 443100China BGI-Sanya BGI-ShenzhenSanya 572025China Yangtze Eco-Environment Engineering Research center China Three Gorges CorporationBeijing 100038China

The order Acipenseriformes,which includes sturgeons and paddlefishes,represents“living fossils”with complex genomes that are good models for understanding whole-genome duplication(WGD)and ploidy evolution in ***,we sequenced and assembled the first high-quality chromosome-level genome for the complex octoploid Acipenser sinensis(Chinese sturgeon),a critically endangered species that also represents a poorly understood ploidy group in *** results show that *** is a complex autooctoploid species containing four kinds of octovalents(8n),a hexavalent(6n),two tetravalents(4n),and a divalent(2n).An analysis taking into account delayed rediploidization reveals that the octoploid genome composition of Chinese sturgeon results from two rounds of homologous WGDs,and further provides insights into the timing of its ploidy *** study provides the first octoploid genome resource of Acipenseriformes for understanding ploidy compositions and evolutionary trajectories of polyploid fishes.

关键词： Chinese sturgeon Whole-genome sequencing Autooctoploid Polyploidization and diploidization Whole-genome duplication

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Potential and progress of studying mountain biodiversity by means of butterfly genetics and genomics

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Journal of Genetics and Genomics 2024年第3期51卷 292-301页

作者： Shuting Wang Marco Girardello Wei Zhang State Key Laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China Peking-Tsinghua center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China cE3c-Centre for Ecology Evolution and Environmental Changes/Azorean Biodiversity GroupFaculdade de Ciencias Agrarias e do AmbienteUniversidade dos Açores9700-042 Angra do HeroísmoTerceiraPortugal

Mountains are rich in biodiversity,and butterflies are species-rich and have a good ecological and evolutionary research *** review addresses the potential and progress of studying mountain biodiversity using butterflies as a *** discuss the uniqueness of mountain ecosystems,factors influencing the distribution of mountain butterflies,representative genetic and evolutionary models in butterfly research,and evolutionary studies of mountain biodiversity involving butterfly genetics and ***,we demonstrate the necessity of studying mountain butterflies and propose future *** review provides insights for studying the biodiversity of mountain butterflies as well as a summary of research methods for reference.

关键词： Mountain ecosystem Butterfly biodiversity Adaptation Genomics Genetics

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Giant panda(Ailuropoda melanoleuca)neonates use broadband calls to communicate with their mothers

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Integrative Zoology 2024年第2期19卷 277-287页

作者： Lin ZHAO Jianbin CHENG Wen ZENG Bo YANG Guiquan ZHANG Desheng LI Hemin ZHANG Christina DBUESCHING Dingzhen LIU Ministry of Education Key Laboratory of Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park China Conservation and Research Center for the Giant PandaDujiangyanSichuan611830China Department of Biology Irving K.Barber Faculty of ScienceUniversity of British ColumbiaOkanaganKelownaBritish ColumbiaCanada

Infant call structure should have evolved to elicit maximum maternal attention and *** of giant pandas produce three types of vocalizations reported to be vitally important in the context of mother–infant ***,how cubs,0–15 days old,communicate with their mothers to elicit maternal care remains *** analyzed 12 different call parameters of 3475 squawks,1355 squalls,and 491 croaks from 11 captive giant panda(Ailuropoda melanoleuca)neonates from age 0 to 15 *** playback experiments,we also tested whether mothers could detect *** results show that neonates use broadband calls with ultrasonic frequencies up to 65 kHz to convey information about their physiological needs and to attract maternal *** playback experiments,we tested if mothers reacted differently to broadband calls(BBC)than to artificially altered calls that included only frequencies20 kHz(USC).Playback confirmed that,although adult females responded significantly less often to USC,BBC than to or AUDC,they could detect USC,BBC and generally made appropriate behavioral responses,indicating a potential benefit for neonates to utilize ultrasonic and broadband *** findings provide a new insight into mother–infant communication in giant pandas and will be helpful for reducing the mortality of cubs,younger than 1 month old,in captivity.

关键词： acoustic communication broadband calls maternal care neonates ultrasonic frequencies

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Ecological Networks of Allometric Growth,Feeding Behavior and Gut Microbiota in Chinese Alligator Hatchlings

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Asian Herpetological Research 2024年第2期15卷 104-114页

作者： Ke SUN Wengang LI Guangwei FAN Liuyang YANG Huabin ZHANG Yilin SHU Yongkang ZHOU Genjun TU Song ZHANG Pingsi YI Maliha AYUB Xiaobing WU Tao PAN College of Life Sciences Anhui Normal UniversityWuhu 241000AnhuiChina The Anhui Provincial Key Laboratory of biodiversity Conservation and Ecological Security in the Yangtze River Basin Wuhu 241000AnhuiChina School of Wetland Yancheng Teachers UniversityYancheng 224007JiangsuChina National Long-term Scientific Research Base for Chinese Alligator Artificial Breeding and Protection in Anhui Anhui Research Center for Chinese Alligator ReproductionXuancheng 242034AnhuiChina

Chinese alligator hatchlings in captivity are fragile and have a high mortality rate within first *** body mass gain of reptile animals is closely related to their feeding behavior and gut *** study analyzed the intrinsic factors influencing the allometric growth of Chinese alligator hatchlings based on their body mass gain,feeding behavior,and gut *** information would enhance the health management of Chinese alligator *** was a significant correlation between the total distance moved,the average number of conspecifics nearby,and body mass *** alligator hatchlings with a greater growth rate showed greater activity and more independent behavior during feeding than those with a lower growth ***,after feeding started,some functions of the gut microbiota showed significant relationships with growth rate and feeding *** alligator hatchlings with a greater growth rate showed greater levels of heme biosynthesis than those with a lower growth rate,and feeding activity was inhibited by long-chain fatty acid *** results elucidate the relationships between health,feeding behavior,and the gut microbiota of Chinese alligator *** the intrinsic factors of their health and feeding behavior can improve the health management of Chinese alligator hatchlings in captivity for conservation.

关键词： allometric growth behavior Chinese alligator hatchlings gut microbiota

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Pseudomonas aeruginosa regulator PvrA binds simultaneously to multiple pseudo-palindromic sites for efficient transcription activation

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Science China(Life Sciences) 2024年第5期67卷 900-912页

作者： Yibo Zhu Bingnan Luo Xingyu Mou Yingjie Song Yonghong Zhou Yongbo Luo Bo Sun Youfu Luo Hong Tang Zhaoming Su Rui Bao center of Infectious Diseases Division of Infectious Diseases in State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu 610041China Department of Geriatrics and National Clinical Research center for Geriatrics West China HospitalSichuan UniversityChengdu 610041China Key Laboratory of biodiversity and Environment on the Qinghai-Tibetan Plateau Ministry of EducationSchool of Ecology and EnvironmentTibet UniversityLhasa 850000China Shanghai Advanced Research Institute Chinese Academy of SciencesShanghai 201210China College of Life Science Sichuan Normal UniversityChengdu 610101China Accurate Biotechnology(Hunan)Co. LtdChangsha 410006China

Tetracycline repressor(TetR)family regulators(TFRs)are the largest group of DNA-binding transcription factors and are widely distributed in bacteria and *** play vital roles in controlling the expression of various genes and regulating diverse physiological ***,a TFR protein Pseudomonas virulence regulator A(PvrA),was identified from Pseudomonas aeruginosa as the transcriptional activator of genes involved in fatty acid utilization and bacterial ***,we show that PvrA can simultaneously bind to multiple pseudo-palindromic sites and upregulate the expression levels of target ***-electron microscopy(cryo-EM)analysis indicates the simultaneous DNA recognition mechanism of PvrA and suggests that the bound DNA fragments consist of a distorted B-DNA double *** crystal structure and functional analysis of PvrA reveal a hinge region that secures the correct domain motion for recognition of the promiscuous ***,our results showed that mutations disrupting the regulatory hinge region have differential effects on biofilm formation and pyocyanin biosynthesis,resulting in attenuated bacterial ***,these findings will improve the understanding of the relationship between the structure and function of the TetR family and provide new insights into the mechanism of regulation of *** virulence.

关键词： Pseudomonas aeruginosa transcription regulator TetR protein-structure virulence

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Poleward increase in feeding efficiency of leafminer Stigmella lapponica(Lepidoptera:Nepticulidae)in a latitudinal gradient crossing a boreal forest zone

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Insect Science 2023年第3期30卷 857-866页

作者： Mikhail V.Kozlov Vitali Zverev Tobias M.Sandner Erik J.van Nieukerken Elena L.Zvereva Department of Biology University of TurkuTurkuFinland Department of Biology Philipps-Universitat MarburgMarburgGermany naturalis biodiversity center Leidenthe Netherlands

Damage to plant communities imposed by insect herbivores generally decreases from low to high *** decrease is routinely attributed to declines in herbivore abundance and/or diversity,whereas latitudinal changes in per capita food consumption remain virtually ***,we tested the hypothesis that the lifetime food consumption by a herbivore individual decreases from low to high latitudes due to a temperature-driven decrease in metabolic *** 2016 to 2019,we explored latitudinal changes in multiple characteristics of linear(gallery)mines made by larvae of the pygmy moth,Stigmella lapponica,in leaves of downy birch,Betula *** mined leaves were larger than intact leaves at the southern end of our latitudinal gradient(at 60°N)but smaller than intact leaves at its northern end(at 69°N),suggesting that female oviposition preference changes with *** latitudinal changes were observed in larval size,mine length or area,and in per capita food consumption,but the larval feeding efficiency(quantified as the ratio between larval size and mine size)increased with ***,*** larvae consumed less foliar biomass at higher latitudes than at lower latitudes to reach the same *** on space-for-time substitution,we suggest that climate warming will increase metabolic expenses of insect herbivores with uncertain consequences for plant-herbivore interactions.

关键词： Betula pubescens climate change food quality insect herbivory metabolic expenses oviposition preference

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Diverse foraging strategies of breeding Swinhoe's Storm-petrel in the productive marginal sea of the Northwest Pacific

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Avian Research 2024年第1期15卷 27-34页

作者： Yachang Cheng Lei Zhu Lin Xue Shisheng Ma Nan Jia Shaoping Zang Zhihai Cao Jing Yuan Yang Liu State Key Laboratory of Biocontrol School of EcologySun Yat-sen UniversityShenzhen 518107China Guangxi Mangrove Research center Guangxi Marine Academy of SciencesNanning 530021China Qingdao Bird Watch Society Qingdao 266121China Jiangsu Provincial Environmental Monitoring center Nanjing 210019China Marine Science and Engineering Qingdao Agricultural UniversityQingdao 266109China Ministry of Education Key Laboratory for biodiversity Science and Ecological Engineering Fudan UniversityShanghai 200433China Qingdao Marine Management and Support Centre Qingdao 266555China Management Committee of Lingshan Island Provincial Nature Reserve Qingdao 266428China

Understanding the foraging behavior is essential for investigating seabird ecology and conservation,as well as monitoring the well-being of the marine *** seabirds adopt diverse foraging strategies to maximize energy gains and cope with the intensified challenges of parenting and *** tradeoff may stem from the heterogeneity of food resources and the constraints of central place ***,abundant marine productivity could alleviate the energy limitation for seabirds,resulting in a consistent foraging ***,we investigated the foraging strategy during the breeding season of a cryptic small-sized seabird,Swinhoe’s Storm-petrel(Hydrobates monorhis),in the Yellow Sea,a productive marginal sea of the Northwest *** GPS tracking,we evaluated habitat preference,quantified the foraging strategy,and tested if environmental conditions and individual traits influence foraging *** found that Swinhoe’s Storm-petrels preferred nearshore areas with shallow water and engaged in primarily short foraging *** southeastward and southwestward strategies emerged when combining trip metrics,including foraging direction,duration,and maximum *** bathymetry,proximity to the coastline,and sea surface temperature differed in two foraging *** strategies exhibited flexibility between individuals,potentially explained by wing morphology,in which longer-winged birds are more likely to embark on longer-distance foraging *** findings highlight the impact of environmental factors and individual traits on seabirds’foraging decisions in productive marginal sea *** study also provides valuable insights into the foraging ecology of this Asian endemic storm-petrel.

关键词： Behavioral strategy Biologging Central place foraging Marine primary productivity Seabird Sea surface temperature

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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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Antidiabetic Properties of Bidens pilosa and Its Polyacetylenic Compounds for Management of Diabetes: Systematic Review

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Journal of Biosciences and Medicines 2024年第2期12卷 164-179页

作者： Kenneth Waititu Caroline Mugo Daisy Nyawira Peter Mwethera Animal Sciences Department Kenya Institute of Primate Research Nairobi Kenya center for biodiversity National Museums of Kenya Nairobi Kenya Department of Reproductive Health and Biology Kenya Institute of Primate Research Nairobi Kenya

Bidens pilosa is a member of the Asteraceae family that is widely distributed across the tropics. It has been utilized by different communities both as food and medicinal herb. This plant and its polyacetylenic compounds hold potential as a natural antidiabetic intervention that can be used to combat this global public health problem. Bioactive compounds found in this plant constitute promising interventions for combating obesity which is a major risk factor for the development of type 2 diabetes. These phytocompounds can work independently or synergistically to modulate appetite, lipase activity, adipogenesis and adipocyte apoptosis. However, the efficacy, mode of action and scope of management of diabetes by these compounds remains elusive. The current review aims to summarize data on efficacy in the management of diabetes, an antidiabetic candidate polyacetylenic compound and possible biological activities as an antidiabetic agent from the available literature. Much emphasis has been directed to cytopiloyne as a representative of polyacetylenic compounds extracted from Bidens pilosa and its activity on diabetic animal models. The majority of the studies conducted on animal models described antidiabetic mechanisms that range from hypoglycemic to secretagogue activity of cytopiloyne in a dose-dependent manner. A clinical trial pilot indicated improved glycemic control of Bidens pilosa formulation among diabetic patients in the study. Bidens pilosa and its compounds are highly potent antidiabetic agent(s) that should be graduated to an intervention for management of diabetes through pre-clinical and clinical trials to elucidate its efficacy and safety.

关键词： Antidiabetic Cytopiloyne Bidens pilosa Polyacetylenic Compounds

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