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Quantitative prediction and evaluation of geothermal resource areas in the southwest section of the Mid-Spine Belt of Beautiful China

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International Journal of Digital Earth 2022年第1期15卷 748-769页

作者： Zhe Chen Ruichun Chang Wenbo Zhao sijia Li Huadong Guo Keyan Xiao lin Wu Dong Hou Lu Zou College of Mathematics and Physics Chengdu University of TechnologyChengduPeople’s Republic of China Digital Hu line Research Institute Chengdu University of TechnologyChengduPeople’s Republic of China Geomathematics Key Laboratory of Sichuan Province ChengduPeople’s Republic of China Key Laboratory of Digital Earth Science Chinese Academy of SciencesAerospace Information Research InstituteBeijingPeople’s Republic of China University of Chinese Academy of Sciences BeijingPeople’s Republic of China International Research Centre of Big Data for Sustainable Development Goals (CBAS) BeijingPeople’s Republic of China MNR Key Laboratory of Metallogeny and Mineral Assessment Institute of Mineral ResourcesChinese Academy of Geological SciencesBeijingPeople’s Republic of China

The geothermal resources in the southwest section of the Mid-Spine Belt of Beautiful China are abundant,but the quantitative prediction and evaluation of geothermal resources are very difficult. Based on geographic information system (GIS) and remote sensing (RS) platforms,six impact factors,namely land surface temperature,fault density,Gutenberg–Liszt B value,formation combination entropy,distance to river and aeromagnetic anomaly were selected. Through the establishment of the certainty factor model (CF),weights of the information entropy certainty factor model (ICF) and weights of the evidence certainty factor model (ECF),the geothermal potential in the study area were predicted quantitatively. Based on the ECF results,the six main geothermal resource areas were delineated. The results show that (1) ECF had high prediction accuracy (success index is 0.00405%,area ratio is 0.867);(2) The geothermal resource areas obtained were Ganzi–Ya’an–Liangshan,Panzhihua–Liangshan,Dali–Chuxiong,Nujiang–Baoshan,Diqing–Dali,and Lijiang–Diqing. The results provide a basis for the effective development and utilization of geothermal resources in the southwest section of the mid-ridge belt.

关键词： Mid-Spine Belt of Beautiful China certainty factor geothermal resource area weights of evidence

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Genome wide association analysis identifies candidate genes for fruit quality and yield in Actinidia eriantha

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Journal of Integrative Agriculture 2024年第6期23卷 1929-1939页

作者： Yingzhen Wang Ying Wu Xinlei Wang Wangmei Ren Qinyao Chen sijia Zhang Feng Zhang Yunzhi lin Junyang Yue Yongsheng Liu School of Horticulture Anhui Agricultural UniversityHefei 230036China School of Forestry Science and Technology Lishui Vocational and Technical CollegeLishui 323000China College of Life Science Sichuan UniversityChengdu 610064China

Quality and yield are the primary concerns in kiwifruit breeding,but research on the genetic mechanisms of fruit size,shape,and ascorbic acid(ASA)content is currently very limited,which restricts the development of kiwifruit molecular *** this study,we obtained a total of 8.88 million highly reliable single nucleotide polymorphism(SNP)markers from 140 individuals from the natural hybrid offspring of Actinidia eriantha cv.‘White’using whole genome resequencing technology.A genome-wide association study was conducted on eight key agronomic traits,including single fruit weight,fruit shape,ASA content,and the number of inflorescences per branch.A total of 59 genetic loci containing potential functional genes were located,and candidate genes related to single fruit weight,fruit length,ASA content,number of inflorescences per branch and other traits were identified within the candidate interval,such as AeWUSCHEL,AeCDK1(cell cycle dependent kinase),AeAO1(ascorbic oxidase)and AeCO1(CONSTANS-like 4).After constructing an RNAi vector for AeAO1 and injecting it into the fruit of cv.‘Midao 31’to interfere with the expression of the AeAO1 gene,the results showed that the activity of ascorbic oxidase in the fruit of‘Midao 31’significantly decreased,while the content of ASA significantly *** study provides valuable insights into the genetic basis of variation in *** fruit traits,which may benefit molecular marker-assisted breeding efforts.

关键词： Actinidia eriantha GWAS SNP QTLs fruit quality

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Large-scale translatome profiling annotates the functional genome and reveals the key role of genic 30 untranslated regions in translatomic variation in plants

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Plant Communications 2021年第4期2卷 38-51页

作者： Wanchao Zhu Jing Xu sijia Chen Jian Chen Yan Liang Cuijie Zhang Qing Li Jinsheng Lai lin Li National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China State Key Laboratory of Agrobiotechnology and National Maize Improvement Center Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China Novogene Co. Ltd.Beijing100015China

The translatome,a profile of the translational status of genetic information within cells,provides a new perspective on gene *** many plant genomes have been sequenced,comprehensive translatomic annotations are not available for plants due to a lack of efficient translatome profiling ***,we developed a new technique termed 30 ribosome-profiling sequencing(30Ribo-seq)for reliable,robust translatomic profiling.30Ribo-seq combines polysome profiling and 30 selection with a barcoding and pooling *** translatome profiling of different tissues of Arabidopsis,rice,and maize using conventional ribosome profiling(Ribo-seq)and 30Ribo-seq revealed many novel translational genomic loci,thereby complementing functional genome annotation in *** the low-cost,efficient 30Ribo-seq technique and genome-wide association mapping of translatome expression(eGWAS),we performed a population-level dissection of the translatomes of 159 diverse maize inbred lines and identified 1,777 translational expression quantitative trait loci(eQTLs).Notably,local eQTLs are significantly enriched in the 30 untranslated regions of *** eQTL analysis suggested that sequence variation around the polyadenylation(polyA)signal motif plays a key role in translatomic *** study provides a comprehensive translatome annotation of plant functional genomes and introduces 30Ribo-seq,which paves the way for deep translatomic analysis at the population level.

关键词： translatome Ribo-seq 30Ribo-seq translational eGWAS functional genomics

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Current Status and Analysis of Machine Learning in Hepatocellular Carcinoma

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Journal of Clinical and Translational Hepatology 2023年第5期11卷 1184-1191页

作者： sijia Feng Jianhua Wang Liheng Wang Qixuan Qiu Dongdong Chen Huo Su Xiaoli Li Yao Xiao Chiayen lin General Surgery Central South University Xiangya HospitalChangshaHunanChina

Hepatocellular carcinoma(HCC)is a common *** the diagnosis and treatment of HCC have made great progress,the overall prognosis remains *** the core component of artificial intelligence,machine learning(ML)has developed rapidly in the past *** particular,ML has become widely used in the medical field,and it has helped in the diagnosis and treatment of *** algorithms of ML have different roles in diagnosis,treatment,and *** article reviews recent research,explains the application of different ML models in HCC,and provides suggestions for follow-up research.

关键词： Machine learning Hepatocellular carcinoma Artificial intelligence Prognosis

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TCM practitioners’ attitudes and perceptions regarding the use of Ephedra sinica Stapf: An observational study

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Journal of Traditional Chinese Medical Sciences 2024年第4期11卷 435-442页

作者： Chang, Aiwen Zhao, Xiaopeng Zhang, lin Zhao, sijia Pan, Zhongyi Song, Chenxi Fu, Yanling School of Traditional Chinese Medicine Beijing University of Chinese Medicine Postdoctoral Station Beijing University of Chinese Medicine Postdoctoral Workstation China Beijing Tongrentang (Group) Co. Ltd. Continuing Education College Beijing University of Chinese Medicine

Objective: To understand the attitudes and perceptions of traditional Chinese medicine (TCM) practitioners in Beijing TCM hospitals regarding the use of Ephedra sinica Stapf (E. sinica, Ma Huang). Methods: A two-stage cross-sectional study was conducted using a questionnaire survey of TCM practitioners in Beijing TCM hospitals between April 2023 and March 2024. The questionnaire included demographic information, the clinical background of TCM practitioners, and the clinical application of E. sinica. Logistic regression analysis was used to analyze the relevant influencing factors when using E. sinica. Results: Of the 465 questionnaires collected, 441 were valid. Among these, 84.81% (374/441) reported having used E. sinica in clinical practice at least once. The commonly used doses of E. sinica—excluding the pediatric department—were 10 g for high doses, 6 g for medium, and 3 g for low. The three most frequently used formulas for E. sinica included Maxing Shigan decoction, Mahuang decoction, and Xiao Qing Long decoction. The most common TCM patterns treated with a high dose of E. sinica were wind-cold fettering the exterior, wind-cold invading the lung, and cold congealing in the meridian. The top three Western medical diagnoses when using E. sinica for treatment were common cold, pneumonia, and upper respiratory tract infections. Nearly half of the respondents reported experiencing adverse reactions from the oral administration of E. sinica, with the most common being palpitations, insomnia, and restlessness. Starting with a low dose and gradually increasing it as appropriate was identified as an effective approach. According to the respondents, the most important factor affecting the efficacy of E. sinica is the dose used. Conclusion: This study investigated the attitudes and perceptions of TCM practitioners in Beijing TCM hospitals regarding the dose–efficacy–adverse reaction relationship of E. sinica, providing a reference for the safe and effective clinical use

关键词： Dose-efficacy-adverse reaction relationship Ephedra sinica Stapf Questionnaire Traditional Chinese medicine

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PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders

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Genomics, Proteomics & Bioinformatics 2019年第4期17卷 453-464页

作者： Guan Ning lin sijia Guo Xian Tan Weidi Wang Wei Qian Weichen Song Jingru Wang Shunying Yu Zhen Wang Donghong Cui Han Wang Shanghai Mental Health Center Shanghai Jiao Tong University School of MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai 200030China Shanghai Key Laboratory of Psychotic Disorders Shanghai 200030China Brain Science and Technology Research Center Shanghai Jiao Tong UniversityShanghai 200030China College of Information Science and Technology Northeast Normal UniversityChangchun 130117China Institution of Computational Biology Northeast Normal UniversityChangchun 130117China

De novo variants(DNVs)are one of the most significant contributors to severe earlyonset genetic disorders such as autism spectrum disorder,intellectual disability,and other developmental and neuropsychiatric(DNP)***,a plethora of DNVs have been identified using next-generation sequencing,and many efforts have been made to understand their impact at the gene ***,there has been little exploration of the effects at the isoform *** brain contains a high level of alternative splicing and regulation,and exhibits a more divergent splicing program than other ***,it is crucial to explore variants at the transcriptional regulation level to better interpret the mechanisms underlying DNP *** facilitate a better usage and improve the isoform-level interpretation of variants,we developed NeuroPsychiatric Mutation Knowledge Base(PsyMuKB).It contains a comprehensive,carefully curated list of DNVs with transcriptional and translational annotations to enable identification of isoformspecific *** allows a flexible search of genes or variants and provides both table-based descriptions and associated visualizations,such as expression,transcript genomic structures,protein interactions,and the mutation sites mapped on the protein *** also provides an easy-to-use web interface,allowing users to rapidly visualize the locations and characteristics of mutations and the expression patterns of the impacted genes and *** thus constitutes a valuable resource for identifying tissue-specific DNVs for further functional studies of related *** is freely accessible at http://***.

关键词： De novo mutation Developmental and neuropsychiatric disorders Database Isoforms Tissue specificity

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Telomere‑to‑telomere and haplotype‑resolved genome of the kiwifruit Actinidia eriantha

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Molecular Horticulture 2023年第1期3卷 361-371页

作者： Yingzhen Wang Minhui Dong Ying Wu Feng Zhang Wangmei Ren Yunzhi lin Qinyao Chen sijia Zhang Junyang Yue Yongsheng Liu School of Horticulture Anhui Agricultural UniversityHefei 230036China School of Forestry Science and Technology Lishui Vocational and Technical CollegeLishui 323000China Ministry of Education Key Laboratory for Bio‑Resource and Eco‑Environment College of Life ScienceState Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengdu 610064China

Actinidia eriantha is a characteristic fruit tree featuring with great potential for its abundant vitamin C and strong disease *** has been used in a wide range of breeding programs and functional genomics *** published genome assemblies of *** are quite fragmented and not highly *** multiple sequencing strategies,we get the haplotype-resolved and gap-free genomes of an elite breeding line“Midao 31”(MD),termed MDHAPA and *** new assemblies anchored to 29 pseudochromosome pairs with a length of 619.3 Mb and 611.7 Mb,as well as resolved 27 and 28 gap-close chromosomes in a telomere-to-telomere(T2T)*** on the haplotype-resolved genome,we found that most alleles experienced purifying selection and coordinately *** to the high continuity of assemblies,we defined the centromeric regions of ***,and identified the major repeating monomer,which is designated as *** resource lays a solid foundation for further functional genomics study and horticultural traits improvement in kiwifruit.

关键词： Kiwifruit Actinidia eriantha Genome Telomere-to-telomere Haplotype Centromeric

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Transcriptome and metabolome analysis reveal that oral secretions from Helicoverpa armigera and Spodoptera litura influence wound-induced host response in cotton

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The Crop Journal 2020年第6期8卷 929-942页

作者： Huan Si Hongling Liu Yiwen Sun Zhongping Xu sijia Liang Bo Li Xiao Ding Jianying Li Qiongqiong Wang lin Sun Xianlong Zhang Shuangxia Jin National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070HubeiChina

Cotton(Gossypium hirsutum)is an important fiber crop *** attack causes cotton yield and quality ***,little is known about the mechanism of cotton response to insect *** simulated insect feeding by applying insect oral secretions(OS)to wounds,and combined transcriptome and metabolome analysis to investigate how OS from two major pest species(Helicoverpa armigera and Spodoptera litura)affect cotton defense *** found that respectively 12,668 and 13,379 genes were differentially expressed in comparison with wounding *** addition of OS,the jasmonic acid signaling pathway was rapidly and strongly induced,whereas genes involved in salicylic acid biosynthesis were *** constructing a coexpression gene network,we identified a hub gene encoding a leucine-rich repeat receptor kinase that may play an important role in early signal recognition and *** from the two insect species altered the abundance of flavonoid-related compounds in different *** remained in lower concentration after OS application than after wounding alone,suggesting a suppressive effect of OS on cotton defense *** study illustrated transcriptional and metabolic changes of cotton in responding to OS from two chewing insect species,identified potential key response genes,and revealed evidence for OS inhibition of wounding-induced cotton defense response.

关键词： Oral secretions Helicoverpa armigera Spodoptera litura Cotton Host plant defense

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Two soybean homologues of TERMINAL FLOWER 1 control flowering time under long day conditions

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The Crop Journal 2023年第3期11卷 704-712页

作者： lingshuang Wang Chun lin Bohui Li Tong Su Shichen Li Haiyang Li Fanglei He Chuanjie Gou Zheng Chen Yanan Wang Jun Qin Baohui Liu Fanjiang Kong lin Yue sijia Lu Chao Fang Guangdong Key Laboratory of Plant Adaptation and Molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510006GuangdongChina College of Agriculture and Biotechnology Yunnan Agricultural UniversityKunming 650201YunnanChina National Key Laboratory of Crop Genetics and Germplasm Enhancement National Center for Soybean ImprovementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjing 210095JiangsuChina Institute of Cereal&Oil Crop Hebei Academy of Agricultural and Forestry SciencesKey Laboratory of Crop Genetics and Breeding of HebeiShijiazhuang 050035HebeiChina

Flowering time is a key agronomic trait that directly affect the adaptation and yield of *** whole genome duplications,about 75%of genes being represented by multiple copies in *** are four TERMINAL FLOWER 1(TFL1)genes in soybean,and the TFL1b(Dt1)has been characterized as the determinant of stem growth *** function of other TFL1 homologs in soybean is still ***,we generated knockout mutants by CRISPR/Cas9 genome editing technology and found that the tfl1c/tfl1d double mutants flowered significantly earlier than wild-type *** investigated that TFL1c and TFL1d could physically interact with the b ZIP transcription factor FDc1 and bind to the promoter of APETALA1a(AP1a).RNA-seq and q RT-PCR analyses indicated that TFL1c and TFL1d repressed the expressions of the four AP1 homologs and delayed the flowering time in *** two genes play important roles in the regulation of flowering time in soybean and mainly act as the flowering inhibitors under long-day *** results identify novel components in the flowering-time regulation network of soybean and will be invaluable for molecular breeding of improved soybean yield.

关键词： Soybean TFL1c TFL1d Flowering time

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Soybean AP1 homologs control flowering time and plant height

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Journal of Integrative Plant Biology 2020年第12期62卷 1868-1879页

作者： Liyu Chen Haiyang Nan lingping Kong lin Yue Hui Yang Qingsong Zhao Chao Fang Haiyang Li Qun Cheng sijia Lu Fanjiang Kong Baohui Liu Lidong Dong Innovative Center of Molecular Genetics and Evolution School of Life SciencesGuangzhou UniversityGuangzhou 510006China The Key Laboratory of Crop Genetics and Breeding of Hebei Institute of Cereal and Oil CropsHebei Academy of Agricultural and ForestrySciencesShijiazhuang 050000China National Key Laboratory of Crop Genetics and Germplasm Enhancement Jiangsu Collaborative Innovation Center for Modern CropProductionNanjing Agricultural UniversityNanjing 210000China The Innovative Academy of Seed Design Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography andAgroecologythe Chinese Academy of SciencesHarbin 150000China

Flowering time and plant height are key agronomic traits that directly affect soybean(Glycine max)***1(AP1)functions as a class A gene in the ABCE model for floral organ development,helping to specify carpel,stamen,petal,and sepal *** are four AP1 homologs in soybean,all of which are mainly expressed in the shoot ***,we used clustered regularly interspaced short palindromic repeats(CRISPR)–CRISPR-associated protein 9 technology to generate a homozygous quadruple mutant,gmap1,with loss-of-function mutations in all four GmAP1 *** short-day(SD)conditions,the gmap1 quadruple mutant exhibited delayed flowering,changes in flower morphology,and increased node number and internode length,resulting in plants that were taller than the wild ***,overexpression of GmAP1a resulted in early flowering and reduced plant height compared to the wild type under SD *** gmap1 mutant and the overexpression lines also exhibited altered expression of several genes related to flowering and gibberellic acid metabolism,thereby providing insight into the role of GmAP1 in the regulatory networks controlling flowering time and plant height in *** node number is the trait with the most promise for enhancing soybean pod number and grain ***,the mutant alleles of the four AP1 homologs described here will be invaluable for molecular breeding of improved soybean yield.

关键词： soybean breeding height

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