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Identification and effective regulation of scarb1 gene involved in pigmentation change in autotetraploid Carassius auratus

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Zoological research 2024年第2期45卷 381-397页

作者： Xi-Dan Xu Yue Zhou Chong-Qing Wang Xu Huang Kun Zhang Xiao-Wei Xu Li-Wen He Xin-Yue Zhang Xin-Zhu Fu Ming Ma Qin-Bo Qin Shao-Jun Liu State Key Laboratory of Developmental Biology of Freshwater Fish Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education MinistryCollege of Life SciencesHunan Normal UniversityChangshaHunan 410081China Nansha-South China Agricultural University Fishery research Institute GuangzhouGuangdong 511458China Hunan Yuelu Mountain Science and Technology Co.Ltd.for Aquatic Breeding ChangshaHunan 410081China College of Chemistry and Chemical engineering Hunan Normal UniversityChangshaHunan 410081China

The autotetraploid Carassius auratus(4nRR,4n=200,RRRR)is derived from whole-genome duplication of Carassius auratus red var.(RCC,2n=100,RR).In the current study,we demonstrated that chromatophores and pigment changes directly caused the coloration and variation of 4nRR skin(red in RCC,brownish-yellow in4nRR).To further explore the molecular mechanisms underlying coloration formation and variation in 4nRR,we performed transcriptome profiling and molecular functional verification in RCC and *** revealed that scarb1,associated with carotenoid metabolism,underwent significant down-regulation in *** editing of this candidate pigment gene provided clear evidence of its significant role in RCC ***,we identified four divergent scarb1 homeologs in 4nRR:two original scarb1 homeologs from RCC and two duplicated ***,three of these homeologs possessed two highly conserved alleles,exhibiting biased and allelespecific expression in the ***,after precise editing of both the original and duplicated scarb1homeologs and/or alleles,4nRR individuals,whether singly or multiply mutated,displayed a transition from brownishyellow skin to a cyan-gray ***,the proportional areas of the cyan-gray regions displayed a gene-dose *** findings illustrate the subfunctionalization of duplicated scarb1,with all scarb1genes synergistically and equally contributing to the pigmentation of *** is the first report concerning the functional differentiation of duplicated homeologs in an autopolyploidfish,substantiallyenrichingour understanding of coloration formation and change within this group of organisms.

关键词： Autopolyploidization Coloration change scarb1 Functional differentiation genetic changes

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New perspectives on the genetic structure of dotted gizzard shad(Konosirus punctatus)based on RAD-seq

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Marine Life Science & Technology 2024年第1期6卷 50-67页

作者： Ying Peng Yifan Liu Jiasheng Li Kun Zhang Xun Jin Sixu Zheng Yunpeng Wang Zhenming Lu Liqin Liu Li Gong Bingjian Liu National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization Zhejiang Ocean UniversityZhoushan 316022China National engineering research center for Facilitated Marine Aquaculture Marine Science and Technology CollegeZhejiang Ocean UniversityZhoushan 316022China

To maintain,develop and rationally utilize marine organisms,understanding their genetic structure and habitat adaptation pattern is *** punctatus,which is a commercial fish species inhabiting the Indo-west Pacific Ocean,has shown an obvious annual global capture and aquaculture production decline due to climate changes and human *** the present study,restriction-site associated DNA sequencing(RAD-seq)was used to describe its genome-wide single nucleotide polymorphisms panel(SNPs).Among 146 individuals collected at nine locations scattered in China,Korea and Japan,a set of 632,090 SNPs were *** genetic analysis showed that *** individuals were divided into two significant genetic ***,potential genetic differentiation between northern and southern population of *** was *** results indicated that gene flow existed among sampling locations of ***,especially from southern Japan to ***,candidate genes associated with habitat adaptations of *** were identified,which are involved in diverse physiological processes of *** including growth and development(e.g.,KIDINS220,PAN3),substance metabolism(e.g.,PGM5)and immune response(e.g.,VAV3,CCT7,HSPA12B).Our findings may aid in understanding the possible mechanisms for the population genetic structure and local adaptation of ***,which is beneficial to establish the management and conservation units of ***,guiding the rational use of resources,with reference significance for a profound understanding of the adaptative mechanisms of other marine organisms to the environment.

关键词： Population structure Konosirus punctatus SNP RAD-seq Local adaptation

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Knowledge-embedded spatio-temporal analysis for euploidy embryos identification in couples with chromosomal rearrangements

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Chinese Medical Journal 2024年第6期137卷 694-703页

作者： Fangying Chen Xiang Xie Du Cai Pengxiang Yan Chenhui Ding Yangxing Wen Yanwen Xu Feng Gao Canquan Zhou Guanbin Li Qingyun Mai Reproductive Medicine center The First Affiliated Hospital of Sun Yat-sen UniversityGuangzhouGuangdong 510080China guangdong Provincial Key Laboratory of Reproductive Medicine GuangzhouGuangdong 510080China School of Computer Science and engineering Sun Yat-sen UniversityGuangzhouGuangdong 510006China Department of General Surgery(Colorectal Surgery) The Sixth Affiliated Hospital of Sun Yat-sen UniversityGuangzhouGuangdong 510655China guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases The Sixth Affiliated HospitalSun Yat-sen UniversityGuangzhouGuangdong 510655China Biomedical Innovation center The Sixth Affiliated HospitalSun Yat-sen UniversityGuangzhouGuangdong 510655China Shanghai Artificial Intelligence Laboratory Shanghai 200232China

Background:The goal of the assisted reproductive treatment is to transfer one euploid blastocyst and to help infertile women giving birth one healthy *** algorithms have been used to assess the ploidy status of embryos derived from couples with normal chromosome,who subjected to preimplantation genetic testing for aneuploidy(PGT-A)***,it is currently unknown whether artificial intelligence model can be used to assess the euploidy status of blastocyst derived from populations with chromosomal ***:From February 2020 to May 2021,we collected the whole raw time-lapse videos at multiple focal planes from in vitro cultured embryos,the clinical information of couples,and the comprehensive chromosome screening results of those blastocysts that had received PGT ***,we developed a novel deep learning model called the Attentive Multi-Focus Selection Network(AMSNet)to analyze time-lapse videos in real time and predict blastocyst *** upon AMSNet,we integrated additional clinically predictive variables and created a second deep learning model,the Attentive Multi-Focus Video and Clinical Information Fusion Network(AMCFNet),to assess the euploidy status of *** efficacy of the AMCFNet was further tested in embryos with parental chromosomal *** receiver operating characteristic curve(ROC)was used to evaluate the superiority of the ***:A total of 4112 embryos with complete time-lapse videos were enrolled for the blastocyst formation prediction task,and 1422 qualified blastocysts received PGT-A(n=589)or PGT for chromosomal structural rearrangement(PGT-SR,n=833)were enrolled for the euploidy assessment task in this *** AMSNet model using seven focal raw time-lapse videos has the best real-time *** real-time accuracy for AMSNet to predict blastocyst formation reached above 70%on the day 2 of embryo culture,and then increased to 80%on the day 4 of embryo ***

关键词： Euploidy status Embryo Time-lapse imaging Deep learning Spatio-temporal analysis Preimplantation genetic testing for chromosomal structural rearrangement

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Aptamers targeting SARS-CoV-2 nucleocapsid protein exhibit potential ant1ip1 an-coronavirus activity

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Signal Transduction and Targeted Therapy 2024年第3期9卷 1186-1198页

作者： Minghui Yang Chunhui Li Guoguo Ye Chenguang Shen Huiping Shi Liping Zhong Yuxin Tian Mengyuan Zhao Pengfei Wu Abid Hussain Tian Zhang Haiyin Yang Jun Yang Yuhua Weng Xinyue Liu Zhimin Wang Lu Gan Qianyu Zhang Yingxia Liu Ge Yang Yuanyu Huang Yongxiang Zhao School of Life Science Advanced Research Institute of Multidisciplinary ScienceKey Laboratory of Molecular Medicine and BiotherapyBeijing Institute of TechnologyBeijing 100081China National Clinical research center for infectious disease Shenzhen Third People’s HospitalSecond Hospital Affiliated to Southern University of Science and TechnologyShenzhen 518112China guangdong Provincial Key Laboratory of Tropical Disease research School of Public HealthSouthern Medical UniversityGuangzhou 510515China State Key Laboratory of Targeting Oncology National Center for International Research of Biotargeting TheranosticsGuangxi Key Laboratory of Biotargeting TheranosticsCollaborative Innovation Center for Targeting Tumor Diagnosis and TherapyGuangxi Medical UniversityNanning 530021China CAMS Key Laboratory of Antiviral Drug research Beijing Key Laboratory of Antimicrobial AgentsInstitute of Medicinal BiotechnologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China

Emerging and recurrent infectious diseases caused by human coronaviruses(HCoVs)continue to pose a significant threat to global public health *** light of this ongoing threat,the development of a broad-spectrum drug to combat HCoVs is an urgently ***,we report a series of anti-pan-coronavirus ssDNA aptamers screened using Systematic Evolution of Ligands by Exponential Enrichment(SELEX).These aptamers have nanomolar affinity with the nucleocapsid protein(NP)of Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)and also show excellent binding efficiency to the N proteins of both SARS,MERS,HCoV-OC43 and-NL63 with affinity KD values of 1.31 to 135.36 *** aptamer-based therapeutics exhibited potent antiviral activity against both the authentic SARS-CoV-2 prototype strain and the Omicron variant(BA.5)with EC50 values at 2.00 nM and 41.08 nM,*** protein docking analysis also evidenced that these aptamers exhibit strong affinities for N proteins of pan-coronavirus and other HCoVs(−229E and-HKU1).In conclusion,we have identified six aptamers with a high pan-coronavirus antiviral activity,which could potentially serve as an effective strategy for preventing infections by unknown coronaviruses and addressing the ongoing global health threat.

关键词： acute threat conclusion

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Multi-omic Analyses Shed Light on The genetic Control of High-altitude Adaptation in Sheep

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 43-56页

作者： Chao Li Bingchun Chen Suo Langda Peng Pu Xiaojia Zhu Shiwei Zhou Peter Kalds Ke Zhang Meenu Bhati Alexander Leonard Shuhong Huang Ran Li Awang Cuoji Xiran Wang Haolin Zhu Yujiang Wu Renqin Cuomu Ba Gui Ming Li Yutao Wang Yan Li Wenwen Fang Ting Jia Tianchun Pu Xiangyu Pan Yudong Cai Chong He Liming Wang Yu Jiang Jian-Lin Han Yulin Chen Ping Zhou Hubert Pausch Xiaolong Wang International Joint Agriculture research center for Animal Bio-Breeding Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal GeneticsBreeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China Animal Genomics ETH ZürichZürich 8092Switzerland Institute of Animal Science Tibet Academy of Agricultural and Animal Husbandry SciencesLhasa 850009China School of Biological and Pharmaceutical engineering Lanzhou Jiaotong UniversityLanzhou 730070China College of Life Sciences Shaanxi Normal UniversityXi’an 710119China Zoology and Evolutionary Biology Department of BiologyUniversity of Konstanz78457 KonstanzGermany College of Life and Geographic Sciences Kashi UniversityKashi 844000China Beijing Key Laboratory of Captive Wildlife Technologies Beijing ZooBeijing 100044China Department of Medical research Guangdong Provincial People’s HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China Key Laboratory of Agricultural Internet of Things Ministry of Agriculture and Rural Affairs/Shaanxi Key Laboratory of Agricultural Information Perception and Intelligent ServiceCollege of Information EngineeringNorthwest A&F UniversityYangling 712100China Institute of Animal Husbandry and Veterinary Medicine Xinjiang Academy of Agricultural and Reclamation SciencesShihezi 832000China State Key Laboratory of Sheep genetic Improvement and Healthy Production Xinjiang Academy of Agricultural and Reclamation SciencesShihezi 832000China CAAS-ILRI Joint Laboratory on Livestock and Forage genetic Resources Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China Livestock genetics Program International Livestock Research InstituteNairobi 00100Kenya

Sheep were domesticated in the Fertile Crescent and then spread globally,where they have been encountering various environmental *** Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 *** explore genomic variants associated with high-altitude adaptation in Tibetan sheep,we analyzed Illumina short-reads of 994 whole genomes representing∼60 sheep breeds/populations at varied altitudes,PacBio High fidelity(HiFi)reads of 13 breeds,and 96 transcriptomes from 12 sheep *** testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude *** accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associatedβ-globin locus and to validate the presence of two haplotypes A and B among 13 sheep *** haplotype A carried two homologous gene clusters:(1)HBE1,HBE2,HBB-like,and HBBC,and(2)HBE1-like,HBE2-like,HBB-like,and HBB;while the haplotype B lacked the first *** high-altitude sheep showed highly frequent or nearly fixed haplotype A,while the low-altitude sheep dominated by haplotype *** further demonstrated that sheep with haplotype A had an increased hemoglobin–O2 affinity compared with those carrying haplotype *** highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude *** results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.

关键词： Environmental adaptation High altitude Hypoxia Selection signature Sheep

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Carbon Emission Factors Prediction of Power Grid by Using Graph Attention Network

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Energy engineering 2024年第7期121卷 1945-1961页

作者： Xin Shen Jiahao Li YujunYin Jianlin Tang Weibin Lin Mi Zhou Measurement center Yunnan Power Grid Co.Ltd.Kunming650000China Electric Power research Institute China Southern Power Grid Co.Ltd.Guangzhou510530China guangdong Provincial Key Laboratory of Intelligent Measurement and Advanced Metering of Power Grid Guangzhou510530China

Advanced carbon emission factors of a power grid can provide users with effective carbon reduction advice,which is of immense importance in mobilizing the entire society to reduce carbon *** method of calculating node carbon emission factors based on the carbon emissions flow theory requires real-time parameters of a power ***,it cannot provide carbon factor information *** address this issue,a prediction model based on the graph attention network is *** model uses a graph structure that is suitable for the topology of the power grid and designs a supervised network using the loads of the grid nodes and the corresponding carbon factor *** network extracts features and transmits information more suitable for the power system and can flexibly adjust the equivalent topology,thereby increasing the diversity of the *** input and output data are simple,without the power grid *** demonstrated its effect by testing IEEE-39 bus and IEEE-118 bus systems with average error rates of 2.46%and 2.51%.

关键词： Predict carbon factors graph attention network prediction algorithm power grid operating parameters

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Functional predictability of universal gene circuits in diverse microbial hosts

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Quantitative Biology 2024年第2期12卷 129-140页

作者： Chenrui Qin Tong Xu Xuejin Zhao Yeqing Zong Haoqian M.Zhang Chunbo Lou Qi Ouyang Long Qian Peking-Tsinghua Joint center for Life Sciences Peking UniversityBeijingChina CAS Key Laboratory of Microbial Physiological and Metabolic engineering Institute of MicrobiologyChinese Academy of SciencesBeijingChina Bluepha Co. LtdBeijingChina center for Cell and Gene Circuit Design CAS Key Laboratory of Quantitative Engineering BiologyGuangdong Provincial Key Laboratory of Synthetic GenomicsShenzhen Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina center for Quantitative Biology Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina

Although the principles of synthetic biology were initially established in model bacteria,microbial producers,extremophiles and gut microbes have now emerged as valuable prokaryotic chassis for biological *** the host range in which designed circuits can function reliably and predictably presents a major challenge for the concept of synthetic biology to *** this work,we systematically characterized the cross-species universality of two transcriptional regulatory modules—the T7 RNA polymerase activator module and the repressors module—in three non-model *** found striking linear relationships in circuit activities among different organisms for both *** model fitting revealed host non-specific parameters defining the universality of both ***,a genetic NOT gate and a band-pass filter circuit were constructed from these modules and tested in non-model *** models employing host non-specific parameters were successful in quantitatively predicting circuit behaviors,underscoring the potential of universal biological parts and predictive modeling in synthetic bioengineering.

关键词： circuit predictability host-independent genetic circuits host-nonspecific parameters parts characterization transcriptional regulatory modules

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Recent Progress in Optical Sensors Based on MXenes Quantum Dots and MXenes Nanosheets

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Journal of Analysis and testing 2024年第1期8卷 95-113页

作者： Chunxiao Lin Xinhong Song Weilan Ye Ting Liu Mingcong Rong Li Niu Guangzhou Key Laboratory of Sensing Materials and Devices/center for Advanced Analytical Science/School of Chemistry and Chemical engineering Guangzhou UniversityGuangzhou 510006China College of Ocean Science and engineering Shanghai Maritime UniversityShanghai 201306China

In recent years,MXenes,as a new promising two-dimensional material,have received extensive attentions in the fields of environmental remediation,catalysts,sensors,and energy *** broaden the applications of MXenes in sensing,MXenes nanosheets(MNSs) and MXenes quantum dots(MQDs) are prepared by physical etching or chemical *** are monolayered or multilayered MXenes nanosheets within several nanometers in height,and can serve as the perfect reaction substrate and fluorescence *** are spherical,fluorescent MXenes QDs within several nanometers in size,which possess favorable stability and photo *** the distinct features such as high conductivity,favorable hydrophilicity,biocompatibility,abundant surface functional groups,and easy functionalization,MNSs and MQDs show potential applications in the fields of anti-counterfeiting,environmental monitoring,biosensing and *** review focuses on the research of MNS s/MQDs-based optical sensors,including colorimetric sensors,fluorescence sensors,electrochemiluminescence sensors,surface plasmon resonance sensors,and surface-enhanced Raman scattering ***,the current challenges and prospects concerning MNSs/MQDs-based optical sensing techniques are discussed.

关键词： MXenes quantum dots Fluorescence Colorimetry Electrochemiluminescence Surface plasmon resonance

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Jet Characteristics and Optimization of a Cavitation Nozzle for Hydraulic Fracturing Applications

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Fluid Dynamics & Materials Processing 2024年第1期20卷 179-192页

作者： Yu Gao Zhenqiang Xu Kaixiang Shen Shenzhen South China Sea Oil Economic Development Co. Ltd.Shenzhen518000China Guangzhou Marine Geological Survey China Geological SurveyGuangzhou511458China National engineering research center of Gas Hydrate Exploration and Development Guangzhou511458China

Hydraulic jetting is a form of fracturing that involves using a high-pressure jet of water to create fractures in the reservoir rock with a nozzle serving as the central component of the hydraulic sandblasting perforation *** this study,the flow behavior of the nozzle is simulated numerically in the framework of a SST k-ωturbulence *** results show that the nozzle structure can significantly influence the jet performance and related cavitation *** orthogonal experiments,the nozzle geometric parameters are optimized,and the following configuration is found accordingly:contraction angle 20°,contraction segment length 6 mm,cylindrical segment diameter 6 mm,cylindrical segment length 12 mm,spread segment length 10 mm,and spread angle 55°.

关键词： Cavitation jet angle nozzle hydraulic characteristics nozzle parameters

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Deamidation enables pathogenic SMAD6 variants to activate the BMP signaling pathway

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Science China(Life Sciences) 2024年第9期67卷 1915-1927页

作者： Ling Li Lei Lu Ziqi Xiao Jingyi Lv Hefeng Huang Bo Wu Tongjin Zhao Chengtao Li Weimin Wang Hongyan Wang Obstetrics and Gynecology Hospital State Key Laboratory of Genetic EngineeringInstitute of Reproduction and Developmentand Children’s HospitalFudan UniversityShanghai 200090China Shanghai Key Laboratory of Metabolic Remodeling and Health Institute of Metabolism and Integrative BiologyFudan UniversityShanghai 200438China Prenatal Diagnosis center of Shenzhen Maternity&Child Healthcare Hospital Shenzhen 518028China Shanghai Medical College Fudan UniversityShanghai 200032China Department of Pharmacy College of Life SciencesChina Jiliang UniversityHangzhou 310018China

The BMP signaling pathway plays a crucial role in regulating early embryonic development and tissue ***6 encodes a negative regulator of BMP,and rare variants of SMAD6 are recurrently found in individuals with birth ***,we observed that a subset of rare pathogenic variants of SMAD6 consistently exhibited positive regulatory effects instead of the initial negative effects on the BMP signaling *** sought to determine whether these SMAD6 variants have common pathogenic ***,we showed that pathogenic SMAD6 variants accompanying this functional reversal exhibit similar increases in ***,increased deamidation of SMAD6 variants promotes the accumulation of the BMP receptor BMPR1A and the formation of new complexes,both of which lead to BMP signaling pathway ***,two residues,N262 and N404,in SMAD6 were identified as the crucial sites of deamidation,which was catalyzed primarily by glutamine-fructose-6-phosphate transaminase 2(GFPT2).Additionally,treatment of cells harboring SMAD6 variants with a deamidase inhibitor restored the inhibitory effect of SMAD6 on the BMP signaling ***,when wild-type SMAD6 was manually simulated to mimic the deamidated state,the reversed function of activating BMP signaling was *** together,these findings show that deamidation of SMAD6 plays a crucial role in the functional reversal of BMP signaling activity,which can be induced by a subset of various SMAD6 *** study reveals a common pathogenic mechanism shared by these variants and provides a potential strategy for preventing birth defects through deamidation regulation,which might prevent the off-target effects of gene editing.

关键词： SMAD6 deamidation BMP signaling pathway GFPT2

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