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A computational model to identify fertility-related proteins using sequence information

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Frontiers of Computer science 2024年第1期18卷 229-237页

作者： Yan LIN Jiashu WANG Xiaowei LIU Xueqin XIE De WU Junjie ZHANG Hui DING Key laboratory for Animal Disease-Resistance Nutrition of the Ministry of Agriculture Animal Nutrition InstituteSichuan Agricultural UniversityChengdu 611130China School of life science and Technology and Center for Informational Biology University of Electronic Science and Technology of ChinaChengdu 610054China

Fertility is the most crucial step in the development process,which is controlled by many fertility-related proteins,including spermatogenesis-,oogenesis-and embryogenesis-related *** identification of fertility-related proteins can provide important clues for studying the role of these proteins in ***,in this study,we constructed a two-layer classifier to identify fertility-related *** this classifier,we first used the composition of amino acids(AA)and their physical and chemical properties to code these three fertility-related ***,the feature set is optimized by analysis of variance(ANOVA)and incremental feature selection(IFS)to obtain the optimal feature *** five-fold cross-validation(CV)and independent data tests,the performance of models constructed by different machine learning(ML)methods is evaluated and ***,based on support vector machine(SVM),we obtained a two-layer model to classify three fertility-related *** the independent test data set,the accuracy(ACC)and the area under the receiver operating characteristic curve(AUC)of the first layer classifier are 81.95%and 0.89,respectively,and them of the second layer classifier are 84.74%and 0.90,*** results show that the proposed model has stable performance and satisfactory prediction accuracy,and can become a powerful model to identify more fertility related proteins.

关键词： sfertility-related proteins machine1 learning sequence information feature selection

Sulfur doped iron-nitrogen-hard carbon nanosheets as efficient and robust noble metal-free catalysts for oxygen reduction reaction in PEMFC

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Journal of Energy Chemistry 2024年第2期89卷 422-433,I0010页

作者： Bin Liu Jiawang Li Bowen Yan Qi Wei Xingyu Wen Huarui Xie Huan He Pei Kang Shen Zhi Qun Tian Collaborative Innovation Center of Sustainable Energy Materials School of Physical Science and TechnologyGuangxi UniversityGuangxi Key Laboratory of Electrochemical Energy MaterialsState Key Laboratory of Featured Metal Materials and Life-cycle Safety for Composite StructuresNanning 530004GuangxiChina

Transition metal-nitrogen-carbon(M-N-C)as a promising substitute for the conventional noble metalbased catalyst still suffers from low activity and durability for oxygen reduction reaction(ORR)in proton exchange membrane fuel cells(PEMFCs).To tackle the issue,herein,a new type of sulfur-doped ironnitrogen-hard carbon(S-Fe-N-HC)nanosheets with high activity and durability in acid media were developed by using a newly synthesized precursor of amide-based polymer with Fe ions based on copolymerizing two monomers of 2,5-thiophene dicarboxylic acid(TDA)as S source and 1,8-diaminonaphthalene(DAN)as N source via an amination *** as-synthesized S-Fe-N-HC features highly dispersed atomic Fe Nxmoieties embedded into rich thiophene-S doped hard carbon nanosheets filled with highly twisted graphite-like microcrystals,which is distinguished from the majority of M-N-C with soft or graphitic carbon *** unique characteristics endow S-Fe-N-HC with high ORR activity and outstanding durability in 0.5 M H_(2)SO_(4).Its initial half-wave potential is 0.80 V and the corresponding loss is only 21 m V after 30,000 ***,its practical PEMFC performance is a maximum power output of 628.0 mW cm^(-2)and a slight power density loss is 83.0 m W cm^(-2)after 200-cycle practical ***,theoretical calculation shows that the activity of Fe Nxmoieties on ORR can be further enhanced by sulfur doping at meta-site near FeN_(4)*** results evidently demonstrate that the dual effect of hard carbon substrate and S doping derived from the precursor platform of amid-polymers can effectively enhance the activity and durability of Fe-N-C catalysts,providing a new guidance for developing advanced M-N-C catalysts for ORR.

关键词： Transition metal-nitrogen-carbon Oxygen reduction reaction Hard carbon Amide based polymer reaction Proton exchange membrane cells

Osteoarthritis versus psoriasis arthritis: Physiopathology, cellular signaling, and therapeutic strategies

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Genes & Diseases 2024年第3期11卷 232-247页

作者： Salma Nassor Juma Junguang Liao Yuping Huang Rexhina Vlashi Qingwan Wang Bocong Wu Dan Wang Mengrui Wu Guiqian Chen College of life science and Medicine Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and BiomedicineZhejiang Sci-Tech UniversityHangzhouZhejiang 310018China Department of Cell and Developmental Biology College of Life SciencesZhejiang UniversityHangzhouZhejiang 310058China

Osteoarthritis and psoriasis arthritis are two degenerative forms of arthritis that share similar yet also different manifestations at the histological,cellular,and clinical *** have marked them as two entirely distinct *** recent dis-coveries in disease initiation and progression,potential mechanisms,cellular signaling path-ways,and ongoing clinical therapeutics,there are now more opportunities for discovering osteoarthritis *** review summarized the osteoarthritis and psoriasis arthritis signaling pathways,crosstalk between BMP,WNT,TGF-β,VEGF,TLR,and FGF signaling pathways,bio-markers,and anatomical *** bench research,we demonstrated that regen-erative medicine is a promising alternative for treating osteoarthritis by highlighting significant scientific discoveries on entheses,multiple signaling blockers,and novel molecules such as immunoglobulin new antigen receptors targeted for potential drug ***,we offered valuable therapeutic approaches with a multidisciplinary strategy to treat patients with osteoarthritis or psoriasis arthritis in the coming future in the clinic.

关键词： Newantigen receptor Osteoarthritis Physiopathology Psoriasisarthritis Signaling pathway

STING signaling in islet macrophages impairs insulin secretion in obesity

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science China(life sciences) 2024年第2期67卷 345-359页

作者： Ze Hong Saihua Chen Jing Sun Dan Cheng Hanli Guo Jiahao Mei Xiang Zhang Munire Maimaiti Haiping Hao Peng Cao Haiyang Hu Chen Wang School of Pharmacy Nanjing University of Chinese MedicineNanjing 210023China State Key laboratory of Natural Medicines Department of Life Science and TechnologyChina Pharmaceutical UniversityNanjing 211198China School of life sciences Westlake UniversityHangzhou 310012China

The innate immune regulator stimulator of interferon genes(STING)mediates self-DNA sensing and leads to the induction of type I interferons and inflammatory cytokines,which promotes the progression of various inflammatory and autoimmune *** immune system plays a critical role in regulating obesity-induced islet dysfunction,whereas the potential effect of STING signaling is not fully ***,we demonstrate that STING is mainly expressed and activated in islet macrophages upon high-fat diet(HFD)***^(-/-)alleviates HFD-induced islet inflammation by inhibiting the expression of pro-inflammatory cytokines and the infiltration of ***,palmitic acid incubation promotes mitochondrial DNA leakage into the cytosol and subsequently activates STING pathway in ***,STING activation in macrophages impairs glucose-stimulated insulin secretion by mediating the engulfment ofβcell insulin secretory *** inhibiting STING activation enhances insulin secretion to control ***,our results reveal a regulatory mechanism in controlling the islet inflammation and insulin secretion in dietinduced obesity and suggest that selective blocking of the STING activation may be a promising strategy for treating type 2 diabetes.

关键词： STING obesity type 2 diabetes insulin macrophages islet

Ca^(2+)-independent ZmCPK2 is inhibited by Ca^(2+)-dependent ZmCPK17 during drought response in maize

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Journal of Integrative Plant Biology 2024年第7期66卷 1313-1333页

作者： Xiaoying Hu Jinkui Cheng Minmin Lu Tingting Fang Yujuan Zhu Zhen Li Xiqing Wang Yu Wang Yan Guo Shuhua Yang Zhizhong Gong State Key laboratory of Plant Environmental Resilience Frontiers Science Center for Molecular Design BreedingCenter for Crop Functional Genomics and Molecular BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing 100193China College of life sciences Institute of Life Science and Green DevelopmentHebei UniversityBaoding 071002China

Calcium oscillations are induced by different ***-dependent protein kinases(CDPKs/CPKs)are one major group of the plant calcium decoders that are involved in various processes including drought *** CPKs are ***,we identified ZmCPK2 as a negative regulator of drought resistance by screening an overexpression transgenic maize *** found that ZmCPK2 does not bind calcium,and its activity is mainly inhibited during short term abscisic acid(ABA)treatment,and dynamically changed in prolonged ***,ZmCPK2 interacts with and is inhibited by calcium-dependent ZmCPK17,a positive regulator of drought resistance,which is activated by ***17 could prevent the nuclear localization of ZmCPK2 through phosphorylation of ***2 interacts with and phosphorylates and activates ZmYAB15,a negative transcriptional factor for drought *** results suggest that drought stress-induced Ca^(2+)can be decoded directly by ZmCPK17 that inhibits ZmCPK2,thereby promoting plant adaptation to water deficit.

关键词： CDPK drought response phosphorylation stomatal movement transcriptional regulation

Allotetraploidization event of Coptis chinensis shared by all Ranunculales

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Horticultural Plant Journal 2024年第1期10卷 288-303页

作者： Yan Zhang Weina Ge Jia Teng Yanmei Yang Jianyu Wang Zijian Yu Jiaqi Wang Qimeng Xiao Junxin Zhao Shaoqi Shen Yishan Feng Shoutong Bao Yu Li Yuxian Li Tianyu Lei Yuxin Pan Lan Zhang Jinpeng Wang Department of Bioinformatics School of Life SciencesNorth China University of Science and TechnologyTangshanHebei 063000China School of life sciences North China University of Science and TechnologyTangshanHebei 063000China State Key laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of sciences Beijing 100049China

Coptis chinensis Franch.,also named Chinese goldthread is a member of Ranunculaceae in the order Ranunculales and represents an important lineage of early eudicots with traditional medicinal *** our study,by using syntenic analysis combined with phylogenomic analysis of *** and four other representative genomes from basal and core eudicots,we confirmed that the WGD event in *** was shared by Aquilegia coerulea and Papaver somniferum *** quickly occurred after Ranunculales diverged from other eudicots,likely a Ranunculales common tetraploidization(RCT).The synonymous nucleotide substitutions at synonymous sites distribution of syntenic blocks across these genomes showed that the evolutionary rate of the *** genome is faster than that of the *** genome by approximately 13.7%,possibly due to Papaveraceaes having an additional special tetraploidization event(PST).After Ks correction,the RCT dated to 115—130 million years ago(MYA),which was close to the divergence of Ranunculaceaes and Papaveraceaes approximately115.45—130.51 ***,we identified homologous genes related to polyploidization and speciation and constructed multiple sequence alignments with different reference ***,the event-related subgenomes in the basal genomes all showed genomic fractionation bias,suggesting a likely allopolyploid nature of the RCT,PST and T-Alpha and T-Beta events in Tetracentron *** addition,we detected that the sixteen P450 subfamilies were markedly expanded in the genomes of Ranunculales,and most of them were related to the RCT and PST *** constructed a new platform for Early Eudicot Comparative Genomic Research(http://***/***)to store more *** summary,our findings support the WGD of *** shared by Ranunculales,which is likely an allotetraploidization *** present effort offered new insights into the evolution of key polyploidization events and the genes related to second

关键词： Coptis chinensis Ranunculales Polyploidization Genomic fractionation P450 genes

High-efficiency gene editing in Anopheles sinensis using ReMOT control

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Insect science 2024年第1期31卷 307-312页

作者： Xiao-lin Yang Xia Ling Quan Sun Pin-pin Qiu Kai Xiang Jun-feng Hong Shu-lin He Jie Chen Xin Ding Hai Hu Zheng-bo He Cao Zhou Bin Chen Liang Qiao Chongqing Key laboratory of Vector Insects Institute of Entomology and Molecular BiologyCollege of Life SciencesChongqing Normal UniversityChongqingChina Xunjian life science&Technology Co.Ltd. ChongqingChina State Key laboratory of Resource Insects Southwest UniversityChongqingChina

Dear editor,Functional genomics studies of mosquito vectors are crucial for understanding their physiological behavior,pathogen transmission,and evolution,and for providing essential molecular targets for genetic control(Severson&Behura,201l;Alphey,2014;Ruzzante et al.,2019;Hong et al.,2022).The main methods involve clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)gene editing via embryo microinjection(Criscione et al.,2015;Kistler et al.,2015).

关键词： editor editing injection

An artificial interphase enables stable PVDF-based solid-state Li metal batteries

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Nano Research 2024年第3期17卷 1482-1490页

作者： Mengjun Wu Jiangping Song Jiaheng Lei Haolin Tang State Key laboratory of Advanced Technology for Materials Synthesis and Processing Wuhan University of TechnologyWuhan 430070China Department of Chemistry School of ChemistryChemical Engineering and Life SciencesWuhan University of TechnologyWuhan 430070China Foshan Xianhu laboratory of the Advanced Energy science and Technology Guangdong laboratory Foshan 528200China

Composite polymer electrolytes(CPEs)have attracted much attention for high energy density solid-state lithium-metal batteries owing to their flexibility,low cost,and easy ***,the unstable Li/CPE interface is always challengeable for the practical utilization of ***,a polymer interlayer containing K+prepared by ultraviolet(UV)-curing precursor solution is coated on Li surface to stabilize the interface between poly(vinylidene difluoride)(PVDF)composite electrolytes and Li *** from the physical barrier of the interlayer,the continuous decomposition of PVDF is restrained and the intimate contact between electrode and electrolyte is also achieved to reduce the interface ***,the added K+is utilized to further regulate smooth Li *** a consequence,the symmetric Li|Li cell with coated Li demonstrates steady cycling at 0.4 mAh·cm^(-2) and a high critical current density of 1 mA·cm^(-2).The assembled Li|lifePO_(4) cell presents outstanding cycling stability(capacity retention of 90%after 400 cycles at 1 C)and good rate *** associated pouch cell performs impressive flexibility and *** work provides a convenient strategy to achieve stable Li/PVDF interface for high-performance PVDF-based solid state Li metal batteries.

关键词： interfacial modification solid-state batteries composite polymer electrolytes interfacial compatibility lithium dendrite

Taxonomy of Two New Peritrich Ciliates(Protozoa:Ciliophora)from Inland Saltwaters of China

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Journal of Ocean University of China 2024年第3期23卷 811-821页

作者： YU Ying ZHANG Yong LIANG Ziyao LI Jiqiu LIN Xiaofeng Key laboratory of Ministry of Education for Coastal and Wetland Ecosystems Fujian Provincial Key Laboratory of Coastal Ecology and Environmental StudiesCollege of the Environment and EcologyXiamen UniversityXiamen 361102China School of life science South China Normal UniversityGuangzhou 510631China State Key laboratory of Marine Environmental science Xiamen UniversityXiamen 361102China

The inland saltwater lakes harbor exceptional ***,two new species of solitary sessile peritrich ciliates were isolated from Qinghai Lake,the largest inland saltwater lake in *** morphology,ciliature,silverline system,and molecular phylogeny were investigated based on live observation,silver staining,and analysis of the small subunit ribosomal DNA(SSU rDNA).Vorticella paraglobosa *** characterized mainly by its obconical or elongate bell-shaped zooid,C-shaped macronucleus,single ventrally located contractile vacuole,two-rowed infundibular polykinety 3,and 28-38 silverlines between peristome and aboral tro-chal band and 10-15 between aboral trochal band and *** cotyliformis *** from its congeners mainly by its double-layered peristomial lip,cup-shaped zooid,J-shaped macronucleus,single ventrally positioned contractile vacuole,three-rowed infundibular polykinety 3,and 70-85 silverlines between peristome and aboral trochal band and 21-25 between aboral trochal band and *** SSU rDNA sequences of the two new species were obtained,and the subsequent molecular phylogenetic analysis supported their taxonomic classification.

关键词： molecular phylogeny morphology new species Qinghai Lake taxonomy