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The genome-wide meiotic recombination landscape in ciliates and its implications for crossover regulation and genome evolution

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Journal of Genetics and Genomics 2024年第3期51卷 302-312页

作者： Lu Fu Chen Gu Kazufumi Mochizuki Jie Xiong Wei Miao Guangying Wang key laboratory of aquatic biodiversity and conservation Institute of HydrobiologyChinese Academy of SciencesWuhanHubei 430072China University of chinese academy of sciences Beijing 100049China Institute of Human Genetics(IGH) CNRSUniversity of Montpellier34396 MontpellierFrance key laboratory of Breeding Biotechnology and Sustainable Aquaculture Chinese Academy of SciencesWuhanHubei 430072China key laboratory of Lake and Watershed Science for Water Security Chinese Academy of SciencesNanjingJiangsu 210008China

Meiotic recombination is essential for sexual reproduction and its regulation has been extensively studied in many taxa.However,genome-wide recombination landscape has not been reported in ciliates and it remains unknown how it is affected by the unique features of ciliates:the synaptonemal complex(SC)-independent meiosis and the nuclear dimorphism.Here,we show the recombination landscape in the model ciliate Tetrahymena thermophila by analyzing single-nucleotide polymorphism datasets from 38 hybrid progeny.We detect 1021 crossover(CO)events(35.8 per meiosis),corresponding to an overall CO rate of 9.9 cM/Mb.However,gene conversion by non-crossover is rare(1.03 per meiosis)and not biased towards G or C alleles.Consistent with the reported roles of SC in CO interference,we find no obvious sign of CO interference.CO tends to occur within germ-soma common genomic regions and many of the 44 identified CO hotspots localize at the centromeric or subtelomeric regions.Gene ontology analyses show that CO hotspots are strongly associated with genes responding to environmental changes.We discuss these results with respect to how nuclear dimorphism has potentially driven the formation of the observed recombination landscape to facilitate environmental adaptation and the sharing of machinery among meiotic and somatic recombination.

关键词： Meiotic recombination Hotspot Crossover interference Adaptive evolution

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Evaluation of water management on arsenic methylation and volatilization in arsenic-contaminated soils strengthened by bioaugmentation and biostimulation

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Journal of Environmental sciences 2024年第3期137卷 515-526页

作者： Peng Chen Yi Liu Guo-Xin Sun State key laboratory of Urban and Regional Ecology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China key laboratory of aquatic Botany and Watershed Ecology Wuhan Botanical GardenChinese Academy of SciencesWuhan 430074China University of chinese academy of sciences Beijing 100049China

Arsenic(As) fate in paddy fields has been one of the most significant current issues due to the strong As accumulation potential of rice plants under fooded conditions. However,no attempt was done to explore As methylation and volatilization under non-fooded conditions. Herein, we investigated the effects of water management on As methylation and volatilization in three arsenic-contaminated soils enhanced by biostimulation with strawderived organic matter and bioaugmentation with genetic engineered Pseudomonas putida KT2440(GE P. putida). Under fooded conditions, the application of biochar(BC), rice straw(RS)and their combination(BC+RS) increased total As in porewater. However, these effects were greatly attenuated under non-fooded conditions. Compared with RS amendment alone, the combination of GE P. putida and RS further promoted the As methylation and volatilization,and the promotion percentage under non-fooded conditions were significantly higher than that under fooded conditions. The combined GE P. putida and RS showed the highest efficiency in As methylation(88 μg/L) and volatilization(415.4 μg/(kg·year)) in the non-fooded soil with moderate As contamination. Finally, stepwise multiple linear regression analysis presented that methylated As, DOC and p H in porewater were the most important factors contributing to As volatilization. Overall, our findings suggest that combination of bioaugmentation with GE P. putida and biostimulation with RS/BC+RS is a potential strategy for bioremediation of arsenic-contaminated soils by enhancing As methylation and volatilization under non-fooded conditions.

关键词： Arsenic methylation Arsenic volatilization Water management Straw incorporation Bioaugmentation

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Geographical patterns and determinants of insect biodiversity in China

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Science China(Life sciences) 2024年第6期67卷 1255-1265页

作者： Huizhong Fan Tongyi Liu Youhua Chen Ziyan Liao Jun Chen Yibo Hu Gexia Qiao Fuwen Wei CAS key laboratory of Animal Ecology and conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China CAS key laboratory of Mountain Ecological Restoration and Bioresource Utilization&China-Croatia“Belt and Road”Joint laboratory on biodiversity and Ecosystem Services Chengdu Institute of BiologyChinese Academy of SciencesChengdu 610041China Jiangxi Provincial key laboratory of conservation Biology College of ForestryJiangxi Agricultural UniversityNanchang 330045China University of chinese academy of sciences Beijing 100049China

Insects play important roles in the maintenance of ecosystem functioning and the provision of livelihoods for millions of people.However,compared with terrestrial vertebrates and angiosperms,such as the giant panda,crested ibis,and the metasequoia,insect conservation has not attracted enough attention,and a basic understanding of the geographical biodiversity patterns for major components of insects in China is lacking.Herein,we investigated the geographical distribution of insect biodiversity across multiple dimensions(taxonomic,genetic,and phylogenetic diversity)based on the spatial distribution and molecular DNA sequencing data of insects.Our analysis included 18 orders,360 families,5,275 genera,and 14,115 species of insects.The results revealed that Southwestern and Southeastern China harbored higher insect biodiversity and numerous older lineages,representing a museum,whereas regions located in Northwestern China harbored lower insect biodiversity and younger lineages,serving as an evolutionary cradle.We also observed that mean annual temperature and precipitation had significantly positive effects,whereas altitude had significantly negative effects on insect biodiversity in most cases.Moreover,cultivated vegetation harbored the highest insect taxonomic and phylogenetic diversity,and needleleaf and broadleaf mixed forests harbored the highest insect genetic diversity.These results indicated that human activities may positively contribute to insect spatial diversity on a regional scale.Our study fills a knowledge gap in insect spatial diversity in China.These findings could help guide national-level conservation plans and the post-2020 biodiversity conservation framework.

关键词： insect spatial patterns multiple dimensions driving factors vegetation types

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Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini

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Zoological Research 2024年第1期45卷 160-175页

作者： Yu-Ran Li Zheng-Wei Wang Richard T.Corlett Wen-Bin Yu Yunnan key laboratory for the conservation of Tropical Rainforests and Asian Elephants&Center for Integrative conservation Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnan 666303China CAS key laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnan 666303China Southeast Asia biodiversity Research Institute Chinese Academy of SciencesMenglaYunnan 666303China University of chinese academy of sciences Shijingshan DistrictBeijing 100049China

The insect mitogenome is typically a compact circular molecule with highly conserved gene contents.Nonetheless,mitogenome structural variations have been reported in specific taxa,and gene rearrangements,usually the tRNAs,occur in different lineages.Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences,comparative analyses of mitogenomes have been given increasing attention.However,most studies use a very few species to represent the whole genus,tribe,family,or even order,overlooking potential variations at lower taxonomic levels,which might lead to some incorrect inferences.To provide new insights into mitogenome organizations and their implications for phylogenetic inference,this study conducted comparative analyses for mitogenomes of three social bee tribes(Meliponini,Bombini,and Apini)based on the phylogenetic framework with denser taxonomic sampling at the species and population levels.Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type,while those of Meliponini show diverse variations in mitogenome sizes and organizations.Large inverted repeats(IRs)cause significant gene rearrangements of protein coding genes(PCGs)and rRNAs in Indo-Malay/Australian stingless bee species.Molecular evolution analyses showed that the lineage with IRs have lower dN/dS ratios for PCGs than lineages without IRs,indicating potential effects of IRs on the evolution of mitochondrial genes.The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution.Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini,tRNA rearrangements are common across all three tribes of social bees,and are significant even at the species level,indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements,and their implications for phylogenetic inference.

关键词： Social bees Phylogeny Mitogenome structure Gene rearrangement Inverted repeats

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Diversity and ecological assembly process of aerobic anoxygenic phototrophic bacteria in a low irradiation area,Three Gorges Reservoir

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Journal of Environmental sciences 2024年第9期143卷 116-125页

作者： Lixin Huo Anran Ma Hong Liu Xingzu Wang Cheng Song Chongqing Institute of Green and Intelligent Technology Chinese Academy of SciencesChongqing 400714China Chongqing School University of Chinese Academy of SciencesCollege of Resources and EnvironmentChongqing 400714China key laboratory of Reservoir aquatic Environment Chinese Academy of SciencesChongqing 400714China University of chinese academy of sciences Beijing 100049China

Aerobic anoxygenic phototrophic bacteria(AAPB)are significant bacterial groups in aquatic ecosystems,known for their rapid growth and photoheterotrophic characteristics.However,the distribution and ecological assembly process of AAPB in low irradiation freshwater basins remain unclear,warranting further investigation.In this study,we present the diversity,abundance,spatial variations,ecological process,and community interaction of AAPB in sediment of Three Gorges Reservoir(TGR)under low irradiation.Our findings demonstrate the dominant genera of AAPB community that exist in the TGR area also are appeared in different waters,with some regional preference.Moreover,the concentration of pufM gene,an indicator for AAPB,maintains a consistently high numerical level ranging from(2.21±0.44)×10^(4)to(9.98±0.30)×10^(7)gene copies/g.Although solar irradiation is suggested as the major factor affecting AAPB,it remains unclear whether and how AAPB differ between regions due to varying solar irradiation levels.Our results show spatial differences between total bacteria and AAPB communities,with significant differences observed only in AAPB.Geographical and environmental factor contributed less than 10%to the spatial difference of community,with sediment type and environmental factors being the key factors influencing microbial community structure.The stochastic process plays a dominant role in the aggregation and replacement of AAPB communities,among which the most contribution is dispersal limitation.For AAPB network,Yoonia and Gemmobacter are the hubs for modules.Those results valuable insights into the AAPB communities in TGR with low irradiation.

关键词： Three Gorges Reservoir(TGR) Aerobic anoxygenic phototrophic bacteria(AAPB) Bacterial community Null model Community assembly

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VOC emitted by biopharmaceutical industries:Source profiles,health risks,and secondary pollution

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Journal of Environmental sciences 2024年第1期135卷 570-584页

作者： Jiawei Ma Lin Li State key laboratory of Environmental aquatic Chemistry Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China University of chinese academy of sciences Beijing 100049China National Engineering laboratory for VOCs Pollution Control Material&Technology University of Chinese Academy of SciencesBeijing 101408China

The biopharmaceutical industry contributes substantially to volatile organic compounds(VOCs)emissions,causing growing concerns and social developmental conflicts.This study conducted an on-site investigation of the process-based emission of VOCs from three biopharmaceutical enterprises.In the workshops of the three enterprises,26 VOCs were detected,which could be sorted into 4 classes:hydrocarbons,aromatic hydrocarbons,oxygen-containing compounds,and nitrogen-containing compounds.Ketones were the main components of waste gases,accounting for 44.13%-77.85%of the overall VOCs.Process-based source profiles were compiled for each process unit,with the fermentation and extraction units of tiamulin fumarate being the main source of VOC emissions.Dimethyl heptanone,vinyl acetate,diethylamine,propylene glycol methyl ether(PGME),and benzene were screened as priority pollutants through a fuzzy comprehensive evaluation system.Ground level concentration simulation results of the Gauss plume diffusion model demonstrated that the diffusivity of VOCs in the atmosphere was relatively high,indicating potential non-carcinogenic and carcinogenic risks 1.5-2 km downwind.Furthermore,the process-based formation potentials of ozone and secondary organic aerosols(SOAs)were determined and indicated that N-methyl-2-pyrrolidone,dimethyl heptanone,and PGME should be preferentially controlled to reduce the ozone formation potential,whereas the control of benzene and chlorobenzene should be prioritized to reduce the generation of SOAs.Our results provide a basis for understanding the characteristics of VOC emission by biopharmaceutical industries and their diffusion,potentially allowing the development of measures to reduce health risks and secondary pollution.

关键词： Biopharmaceutical Volatile organic compound Priority pollutant Exposure risk Secondary pollution

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Nano polystyrene microplastics could accumulate in Nile tilapia(Oreochromis niloticus):Negatively impacts on the intestinal and liver health through water exposure

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Journal of Environmental sciences 2024年第3期137卷 604-614页

作者： Di Wu Xing Lu Li-Xue Dong Juan Tian Jin Deng Lei Wei Hua Wen Shan Zhong Ming Jiang School of Basic Medical sciences Wuhan UniversityWuhan 430071China key laboratory of Freshwater biodiversity conservation Ministry of Agriculture and Rural AffairsYangtze River Fisheries Research InstituteChinese Academy of Fishery SciencesWuhan 430223China Hubei Province key laboratory of Allergy and Immunology Wuhan 430071China

Microplastics(MPs)have become a significant concern for their potential toxicity.However,the correlation between the size of plastic particles and their toxicity remains inconclusive.Here,we investigate the toxic effects of different sizes(80 nm,800 nm,8μm and 80μm)polystyrene MPs(PS-MPs)on the model organism Nile tilapia(Oreochromis niloticus).The results of bioluminescent imaging indicate that the 80 nm PS-MPs are more likely to invade the body.H&E staining shows severe damage on the intestinal villi and distinct hepatic steatosis in the 80 nm group.Ed U labeling shows that the proliferation activity of intestinal and liver cells reduces significantly in the 80 nm group.The gut microbiome analysis shows a severe imbalance of gut microbiota homeostasis in the 80 nm group.The analysis of liver transcriptomics and metabolomics shows that the liver lipid metabolism is disordered in the 80 nm group.In conclusion,this study confirms that the 80 nm PS-MPs are more likely to induce intestinal and liver toxicity.All the above lay the foundation for further study on the pathological damage of MPs to other organisms.

关键词： Microplastics(MPs) Intestinal toxicity Liver toxicity Gut microbiome Lipid metabolism

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A New Species of the Genus Scincella Mittleman,1950(Squamata:Scincidae)from Sichuan Province,Southwest China

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Asian Herpetological Research 2024年第2期15卷 115-129页

作者： Ruwan JIA Zongyuan GAO Dihao WU Jinlong REN Dechun JIANG Wei WU CAS key laboratory of Mountain Ecological Restoration and Bioresource Utilization&Ecological Restoration and biodiversity conservation key laboratory of Sichuan Province Chengdu Institute of BiologyChinese Academy of SciencesChengdu 610213SichuanChina University of chinese academy of sciences Beijing 100049China

The genus Scincella Mittleman,1950,within the family Scincidae,is a diverse group comprising 39 described species.The taxonomy of the genus is complex due to morphological similarities among species,which often obscures the true extent of biodiversity,resulting in several undescribed species requiring further exploration.In China,particularly within the unique ecosystems of the Hengduan Mountains,the diversity of Scincella is notably underestimated,with only 12 species currently recognized.In the present study,we describe a new species of the genus Scincella,Scincella liangshanensis sp.nov.,from Sichuan Province,Southwest China.Morphological characteristics and phylogenetic analyses revealed that the putative new species is distinct from all other known congeners.This discovery not only expands the known diversity of Scincella but also emphasizes the inadequacies in our current understanding of herpetological diversity in China.The addition of this species to the scientific record highlights the necessity for ongoing biodiversity assessments to uncover hidden species and enhance our understanding of the intricate web of life in one of the world’s biodiversity hotspots.

关键词： morphology phylogeny Scincella liangshanensis sp.nov. taxonomy the Hengduan Mountains

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Nutrient transport following water transfer through the world's largest water diversion channel

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Journal of Environmental sciences 2024年第1期135卷 703-714页

作者： Yuanhui Cheng Hong Zhang Wei Yin State key laboratory of Environmental aquatic Chemistry Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085 China Changjiang Water Resources Protection Institute Wuhan 430051China University of chinese academy of sciences Beijing 100049China

Nutrient levels in the artificial channel constructed for the Middle Route Project are significant indicators of water quality safety and aquatic ecological integrity for this large,interbasin scheme.However,the distribution and transport of nutrients along the channel were poorly understood.Based on a time-series dataset as well as mass balance and material flow analysis methods,the water and nutrient transport fluxes in the Middle Route of the South-to-North Water Diversion Project were identified in this study.The results indicate that the nutrient concentrations varied considerably with time,but there was no significant difference among the 30 stations of the main channel.Seasonal temperature difference was the major factor in the large fluctuations of water quality indicators over time.The nutrient loadings varied with the water volume outputs from the main channel to the waterreceiving cities.Atmospheric deposition was an important source of nutrients in the main channel,accounting for 9.13%,20.6%,and 0.635%of the nitrogen,phosphorus,and sulfur input from the Danjiangkou Reservoir,respectively.In 2021,a net accumulation of 988 tons of N,29 tons of P,and 2,540 tons of S,respectively,were present in the main channel.The increase of these external and internal nutrient loadings would cause water quality fluctuation and deterioration in some local sections of the main channel.Our study quantified the spatial and temporal patterns of nutrient transport in the Middle Route and revealed the ecological effects on the aquatic environment,assisting authorities on the project to develop effective water conservation strategies.

关键词： Nutrient transport Spatiotemporal patterns The Middle Route The South-to-North Diversion Project Hydro-ecological effects Water-receiving cities

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Bias distribution and regulation in photoelectrochemical overall water-splitting cells

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National Science Review 2024年第4期11卷 141-150页

作者： Kun Dang Siqin Liu Lei Wu Daojian Tang Jing Xue Jiaming Wang Hongwei Ji Chuncheng Chen Yuchao Zhang Jincai Zhao key laboratory of Photochemistry CAS ResearchEducation Center for Excellence in Molecular Sciences Institute of Chemistry Chinese Academy of Sciences University of chinese academy of sciences

The water oxidation half-reaction at anodes is always considered the rate-limiting step of overall water splitting（OWS）,but the actual bias distribution between photoanodes and cathodes of photoelectro chemical（PEC） OWS cells has not been investigated systematically.In this work,we find that,for PEC cells consisting of photoanodes（nickel-modified n-Si [Ni/n-Si] and α-Fe2O3） with low photovoltage(Vph 1V,the bias required for cathode activation can be significantly reduced,exhibiting a kinetics-controlled characteristic.Further investigations show that the bias distribution can be regulated by tuning the electrolyte pH and using alternative half-reaction couplings.Accordingly,a volcano plot is presented for the rational design of the overall reactions and unbiased PEC cells.Motivated by this,an unbiased PEC cell consisting of a simple Ni/n-Si photoanode and Pt cathode is assembled,delivering a photo current density of 5.3±0.2 mA cm-2.

关键词： photoelectrochemistry overall reaction cell bias distribution photoanode water splitting

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