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Whole-genome sequencing in medicinal plants:current progress and prospect

Science China(Life Sciences) 2024年第2期67卷 258-273页

作者： Yifei Pei Liang leng Wei Sun Baocai Liu Xue Feng Xiwen Li Shilin Chen Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China Innovative Institute of Chinese Medicine and Pharmacy Chengdu University of Traditional Chinese MedicineChengdu 611137China Institute of Agricultural Bioresource Fujian Academy of Agricultural SciencesFuzhou 350003China

Advancements in genomics have dramatically accelerated the research on medicinal plants,and the development of herbgenomics has promoted the“Project of 1K Medicinal Plant Genome”to decipher their genetic ***,it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic *** genomes of 123 medicinal plants were published until September *** published genome sequences were investigated in this review,covering their classification,research teams,ploidy,medicinal functions,and sequencing *** than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant *** species account for a majority of sequenced medicinal *** whole genomes of plants in the Poaceae family are the most *** 40%of the published papers studied species with tonifying,replenishing,and heat-cleaning medicinal *** plants are still in the process of domestication as compared with crops,thereby resulting in unclear genetic backgrounds and the lack of pure lines,thus making their genomes more difficult to *** addition,there is still no clear routine framework for a medicinal plant to obtain a high-quality whole ***,a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal ***,whole genome-based biological studies of medicinal plants,including breeding and biosynthesis,were *** also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.

关键词： herbgenomics whole genome high throughput sequencing research strategy model species application

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Single nucleus/cell RNA-seq of the chicken hypothalamicpituitaryovarian axis offers new insights into the molecular regulatory mechanisms of ovarian development

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Zoological Research 2024年第5期45卷 1088-1107页

作者： Dong leng Bo Zeng Tao Wang Bin-Long Chen Di-Yan Li Zhuan-Jian Li School of Pharmacy Chengdu UniversityChengduSichuan 610106China College of Animal Science and Technology Sichuan Agricultural UniversityChengduSichuan 611130China College of Animal Science Xichang UniversityXichangSichuan 615000China College of Animal Science and Technology Henan Agricultural UniversityZhengzhouHenan 450046China

The hypothalamic-pituitary-ovarian(HPO)axis represents a central neuroendocrine network essential for reproductive *** its critical role,the intrinsic heterogeneity within the HPO axis across vertebrates and the complex intercellular interactions remain poorly *** study provides the first comprehensive,unbiased,cell type-specific molecular profiling of all three components of the HPO axis in adult Lohmann layers and Liangshan Yanying *** the hypothalamus,pituitary,and ovary,seven,12,and 13 distinct cell types were identified,*** indicated that the pituitary adenylate cyclase activating polypeptide(PACAP),follicle-stimulating hormone(FSH),and prolactin(PRL)signaling pathways may modulate the synthesis and secretion of gonadotropin-releasing hormone(GnRH),FSH,and luteinizing hormone(LH)within the hypothalamus and *** the ovary,interactions between granulosa cells and oocytes involved the KIT,CD99,LIFR,FN1,and ANGPTL signaling pathways,which collectively regulate follicular *** SEMA4 signaling pathway emerged as a critical mediator across all three tissues of the HPO ***,gene expression analysis revealed that relaxin 3(RLN3),gastrin-releasing peptide(GRP),and cocaine-and amphetamine regulated transcripts(CART,also known as CARTPT)may function as novel endocrine hormones,influencing the HPO axis through autocrine,paracrine,and endocrine *** analyses between Lohmann layers and Liangshan Yanying chickens demonstrated higher expression levels of GRP,RLN3,CARTPT,LHCGR,FSHR,and GRPR in the ovaries of Lohmann layers,potentially contributing to their superior reproductive *** conclusion,this study provides a detailed molecular characterization of the HPO axis,offering novel insights into the regulatory mechanisms underlying reproductive biology.

关键词： Chickens Single nucleus/cell transcriptome Hypothalamic-pituitary-ovarian axis Signal crosstalk Hormones

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Effectiveness of urban distributed runoff model for discharge and water depth calculation in urban drainage pipe networks

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Journal of Hydrodynamics 2024年第3期36卷 582-591页

作者： Yang Zhou Yi-ling leng Peng-yu Wang Shang-hong Zhang Yu-long Zhu Yu-jun Yi School of Water Resources and Hydropower Engineering North China Electric Power UniversityBeijing102206China State Key Laboratory of Water Environment Simulation School of EnvironmentBeijing Normal UniversityBeijing100875China

Effective urban land-use re-planning and the strategic arrangement of drainage pipe networks can significantly enhance urban flood defense *** at reducing the potential risks of urban flooding,this paper presents a straightforward and efficient approach to an urban distributed runoff model(UDRM).The model is developed to quantify the discharge and water depth within urban drainage pipe networks under varying rainfall intensities and land-use *** Nash efficiency coefficient of UDRM exceeds 0.9,which indicates its high computational efficiency and potential benefit in predicting urban *** prediction of drainage conditions under both current and re-planned land-use types is achieved by adopting different flood recurrence *** findings reveal that the re-planned land-use strategies could effectively diminish flood risk upstream of the drainage pipe network across 20-year and 50-year flood recurrence ***,in the case of extreme rainfall events(a 100-year flood recurrence),the re-planned land-use approach fell short of fulfilling the requirements necessary for flood disaster *** these instances,the adoption of larger-diameter drainage pipes becomes an essential requisite to satisfy drainage ***,the proposed UDRM effectively combines land-use information with pipeline data to give practical suggestions for pipeline modification and land-use optimization to combat urban ***,this methodology warrants further promotion in the field of urban re-planning.

关键词： Stormwater runoff water depth urban distributed runoff model urban drainage pipe networks urban land-use re-planning

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Anti-vascular endothelial growth factor drugs combined with laser photocoagulation maintain retinal ganglion cell integrity in patients with diabetic macular edema: study protocol for a prospective, non-randomized, controlled clinical trial

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Neural Regeneration Research 2024年第4期19卷 923-928页

作者： Xiangjun Li Chunyan Li Hai Huang Dan Bai Jingyi Wang Anqi Chen Yu Gong Ying leng Department of Ophthalmology Affiliated Hospital of Beihua University Department of Endocrinology Affiliated Hospital of Beihua University

The integrity of retinal ganglion cells is tightly associated with diabetic macular degeneration that leads to damage and death of retinal ganglion cells,affecting *** major clinical treatments for diabetic macular edema are anti-vascular endothelial growth factor drugs and laser ***,although the macular thickness can be normalized with each of these two therapies used alone,the vision does not improve in many *** might result from the incomplete recovery of retinal ganglion cell ***,a prospective,non-randomized,controlled clinical trial was designed to investigate the effect of anti-vascular endothelial growth factor drugs combined with laser photocoagulation on the integrity of retinal ganglion cells in patients with diabetic macular edema and its relationship with vision *** this trial,150 patients with diabetic macular edema will be equally divided into three groups according to therapeutic methods,followed by treatment with anti-vascular endothelial growth factor drugs,laser photocoagulation therapy,and their *** patients will be followed up for 12 *** primary outcome measure is retinal ganglion cell-inner plexiform layer thickness at 12 months after *** secondary outcome measures include retinal ganglion cell-inner plexiform layer thickness before and 1,3,6,and 9 months after treatment,retinal nerve fiber layer thickness,best-corrected visual acuity,macular area thickness,and choroidal thickness before and 1,3,6,9,and 12 months after *** measure is the incidence of adverse events at 1,3,6,9,and 12 months after *** study protocol hopes to validate the better efficacy and safety of the combined treatment in patients with diabetic macula compared with the other two monotherapies alone during the 12-month follow-up *** trial is designed to focus on clarifying the time-effect relationship between imaging measures related to the integrity of retinal

关键词： choroidal thickness diabetic macular edema laser photocoagulation retinal ganglion cell-inner plexiform layer thickness retinal ganglion cells retinal nerve fiber layer thickness thickness of the macular area vascular endothelial growth factor visual acuity

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Functional analysis of the novel mitochondrial tRNA^(Trp)and tRNA^(Ser(AGY))variants associated with type 2 diabetes mellitus

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World Journal of Diabetes 2024年第8期15卷 1753-1763页

作者： Yu Ding Xue-Jiao Yu Qin-Xian Guo Jian-Hang leng Central Laboratory Hangzhou First People’s HospitalHangzhou 310006Zhejiang ProvinceChina Clinical Laboratory Quzhou People’s HospitalQuzhou 324000Zhejiang ProvinceChina

BACKGROUND Mutations in mitochondrial tRNA(mt-tRNA)genes that result in mitochondrial dysfunction play important roles in type 2 diabetes mellitus(T2DM).We previously reported a large Chinese pedigree with maternally inherited T2DM that harbors novel mt-tRNA^(Trp)A5514G and tRNA^(Ser(AGY))C12237T variants,however,the effects of these mt-tRNA variants on T2DM progression are largely *** To assess the potential pathogenicity of T2DM-associated m.A5514G and m.C12237T variants at genetic,molecular,and biochemical *** Cytoplasmic hybrid(cybrid)cells carrying both m.A5514G and m.C12237T variants,and healthy control cells without these mitochondrial DNA(mtDNA)variants were generated using trans-mitochondrial *** features,including mt-tRNA steady-state level,levels of adenosine triphosphate(ATP),mitochondrial membrane potential(MMP),reactive oxygen species(ROS),mtDNA copy number,nicotinamide adenine dinucleotide(NAD+)/NADH ratio,enzymatic activities of respiratory chain complexes(RCCs),8-hydroxy-deoxyguanine(8-OhdG),malondialdehyde(MDA),and superoxide dismutase(SOD)were examined in cell lines with and without these mt-tRNA *** Compared with control cells,the m.A5514G variant caused an approximately 35%reduction in the steady-state level of mt-tRNA^(Trp)(P<0.0001);however,the m.C12237T variant did not affect the mt-tRNA^(Ser(AGY))steady-state level(P=0.5849).Biochemical analysis revealed that cells with both m.A5514G and m.C12237T variants exhibited more severe mitochondrial dysfunctions and elevated oxidative stress than control cells:ATP,MMP,NAD+/NADH ratio,enzyme activities of RCCs and SOD levels were markedly decreased in mutant cells(P<0.05 for all measures).By contrast,the levels of ROS,8-OhdG and MDA were significantly increased(P<0.05 for all measures),but mtDNA copy number was not affected by m.A5514G and m.C12237T variants(P=0.5942).CONCLUSION The m.A5514G variant impaired mt-tRNA^(Trp)metabolism,which subsequent

关键词： Type 2 diabetes mellitus Mitochondrial tRNA genes Novel variants Oxidative stress Mitochondrial dysfunctions

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Meta-device:advanced manufacturing

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Light(Advanced Manufacturing) 2024年第1期5卷 115-130页

作者： Borui leng Yao Zhang Din Ping Tsai Shumin Xiao Department of Electrical Engineering City University of Hong KongHong Kong999077China Centre for Biosystems Neuroscience and NanotechnologyCity University of Hong KongHong Kong999077China The State Key Laboratory of Terahertz and Millimeter Waves City University of Hong KongHong Kong999077China Ministry of Industry and Information Technology Key Lab of Micro-Nano Optoelectronic Information System Guangdong Provincial Key Laboratory of Semiconductor Optoelectronic Materials and Intelligent Photonic SystemsHarbin Institute of TechnologyShenzhen 518055China Pengcheng Laboratory Shenzhen 518055China

Metasurfaces are one of the most promising devices to break through the limitations of bulky optical *** offering a new method of light manipulation based on the light-matter interaction in subwavelength nanostructures,metasurfaces enable the efficient manipulation of the amplitude,phase,polarization,and frequency of light and derive a series of possibilities for important ***,one key challenge for the realization of applications for meta-devices is how to fabricate large-scale,uniform nanostructures with high *** this review,we review the state-of-the-art nanofabrication techniques compatible with the manufacture of *** lithography,masked lithography,and other nanofabrication techniques are highlighted in *** also delve into the constraints and limitations of the current fabrication methods while providing some insights on solutions to overcome these challenges for advanced nanophotonic applications.

关键词： Meta-device Metasurface Nanofabrication COMS-compatible fabrication

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Exploration for the Priority of HIV Intervention:Modelling Health Impact and Cost-Effectiveness—Six Cities,Eastern China,2019-2028

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China CDC weekly 2024年第20期6卷 463-468,I0008-I0014页

作者： Youran Zhang Lili Wang Zhen Jiang Hongjing Yan Xiaoxia Liu Jing Gu Guoyong Wang Xiaosong Cheng Qiyan leng Qisui Long Zimian Liang Jing Wang Liang Liang Yanchao Qiu lin Chen Hang Hong School of Health Service Management Anhui Medical UniversityHefei CityAnhui ProvinceChina Division of Prevention and intervention National Center for AIDS and STD Control and PreventionChinese Center for Disease Control and PreventionBeijingChina Jiangsu Provincial Center for Disease Control and Prevention Nanjing CityJiangsu ProvinceChina Zhenjiang Center for Disease Control and Prevention Zhenjiang CityJiangsu ProvinceChina Wuxi Center for Disease Control and Prevention Wuxi CityJiangsu ProvinceChina Shandong Provincial Center for Disease Control and Prevention Jinan CityShandong ProvinceChina Yantai Center for Disease Control and Prevention Yantai CityShandong ProvinceChina Guangdong Provincial Center for Disease Control and Prevention Guangzhou CityGuangdong ProvinceChina Foshan Center for Disease Control and Prevention Foshan CityGuangdong ProvinceChina Hebei Provincial Center for Disease Control and Prevention Shijiazhuang CityHebei ProvinceChina Shijiazhuang Center for Disease Control and Prevention Shijiazhuang CityChina Zhejiang Provincial Center for Disease Control and Prevention Hangzhou CityZhejiang ProvinceChina Ningbo Center for Disease Control and Prevention Ningbo CityZhejiang ProvinceChina

Introduction:In order to enhance the effectiveness of resource allocation,regions must tailor their responses to their specific epidemiological and economic ***:Utilizing Spectrum software,we projected the cost-effectiveness of 10 chosen HIV interventions in six cities in eastern China from 2019 to *** assessed three scenarios—Base,Achievable,and Idealized—for each *** analysis included the projected number of HIV infections and deaths averted,as well as the incremental costeffectiveness ratios for each intervention in the six ***:In Shijiazhuang,Wuxi,Yantai,and Zhenjiang,cities with initially low antiretroviral therapy(ART)coverage,ART showed significant effectiveness,especially for ***,in Foshan and Ningbo,where ART coverage was notably high,oral pre-exposure prophylaxis(PrEP)for men who have sex with men(MSM)proved effective in the Idealized *** outreach,ART for males,and ART for females demonstrated cost-effectiveness across all six cities in both Achievable and Idealized scenarios at the predefined thresholds for each ***:Maintaining an appropriate coverage rate for outreach to MSM can lead to *** cities with low ART coverage,scaling up ART remains a crucial *** regions with high ART coverage,consideration may be given to the utilization of oral PrEP for MSM individuals,requiring budget allocation.

关键词： Eastern Ningbo Impact

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Thermal pretreatment of willow branches impacts yield and pore development of activated carbon in subsequent activation with ZnCl_(2) via modifying cellulose structure

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Chinese Journal of Chemical Engineering 2024年第5期69卷 227-237页

作者： linghui Kong Chao Li Runxing Sun Shu Zhang Yi Wang Jun Xiang Song Hu Dong Wang Chuanjun leng Xun Hu School of Material Science and Engineering University of JinanJinan 250022China Joint International Research Laboratory of Biomass Energy and Materials College of Materials Science and EngineeringNanjing Forestry UniversityNanjing 210037China State Key Laboratory of Coal Combustion Huazhong University of Science and TechnologyWuhan 430074China Shandong BASAN Graphite New Material Plant Zibo 255311China

Development of pore structures of activated carbon(AC)from activation of biomass with ZnCl_(2) relies on content and structure of cellulose/hemicellulose in the *** pretreatment of biomass could induce dehydration and/or aromatization to change the structure of cellulose/*** might interfere with evolution of structures of AC,which was investigated herein via thermal pretreatment of willow branch(WB)from 200 to 360℃and the subsequent activation with ZnCl_(2) at 550℃.The results showed that thermal pretreatment at 360℃(WB-360)could lead to substantial pyrolysis to form biochar,with a yield of 31.9%,accompanying with nearly complete destruction of cellulose crystals and remarkably enhanced aromatic ***,cellulose residual in WB-360 could still be activated to form AC-360 with specific surface area of 1837.9 m~2·g^(-1),which was lower than that in AC from activation of untreated WB(AC-blank,2077.8 m~2·g^(-1)).Nonetheless,the AC-200 from activation of WB-200 had more developed pores(2113.9 m~2·g^(-1))and superior capability for adsorption of phenol,due to increased permeability of ZnCl_(2) to the largely intact cellulose structure in *** thermal pretreatment did increase diameters of micropores of AC but reduced the overall yield of AC(26.8%for AC-blank versus 18.0%for AC-360),resulting from accelerated cracking but reduced intensity of ***-situ infrared characterization of the activation showed that ZnCl_(2) mainly catalyzed dehydration,dehydrogenation,condensation,and aromatization but not cracking,suppressing the formation of derivatives of cellulose and lignin in *** thermal pretreatment formed phenolic-OH and C=O with higher chemical innerness,which changed the reaction network in activation,shifting morphology of fibrous structures in AC-blank to“melting surface”in AC-200 or AC-280.

关键词： Thermal pretreatment Activation with ZnCl_(2) Willow branch Activated carbon Biochar

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Maternal weight and its association with risk of overweight in offspring:a trajectory analysis from a birth cohort in China

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World Journal of Pediatrics 2024年第5期20卷 496-505页

作者： Rui Deng Wei-Qin Li Xing-Xiu Li Liu-Mei Wei Jie Hu Jun-Hong leng Bin Dong Institute of Child and Adolescent Health School of Public HealthPeking University Health Science CenterNo.38 Xueyuan RdHaidian DistrictBeijing100191China Tianjin Women and Children’s Health Center No.96 Guizhou RdHeping DistrictTianjin300070China Menzies Health Institute Queensland Griffith UniversityNathanQLD4111Australia

Background Most studies on the association of maternal pregnancy weight with offspring weight trajectory have a short follow-up *** study aimed to explore the associations of maternal prepregnancy body mass index(BMI)and gestational weight gain(GWG)with childhood weight trajectories in a 7-year birth *** A total of 946 mother–child pairs(467 boys and 479 girls)from a longitudinal birth cohort in Tianjin City,China,were included in this study,ranging from pregnancy to offspring at 7 *** outcome variable was defined as overweight or not overweight in offspring at the last round.A group-based trajectory model was applied to identify childhood BMI trajectory *** Five discrete BMI trajectory groups were identified and characterized as constant underweight(25.2%),constant normal weight(42.8%),and high or increasing trajectory[at risk of overweight(16.9%),progressive overweight(11.0%)and progressive obesity(4.1%)].Maternal prepregnancy overweight was associated with 1.72(95%CI 1.14–2.60,P=0.01)to 4.02(95%CI 1.94–8.36,P<0.001)times the risk of all high or increasing trajectory groups,and excessive GWG was related to groups at risk of overweight[relative risk ratio(RRR)2.09,95%CI 1.27–3.46,P=0.004]and progressive obesity(RRR 3.33,95%CI 1.13–9.79,P=0.029).Children in all high or increasing trajectory groups were associated with greater overweight risk at the last round[risk ratios(RRs)ranged from 3.54(95%CI 2.53–4.95,P<0.001)to 6.18(95%CI 4.05–9.42,P<0.001)].Conclusion Maternal prepregnancy overweight and excessive gestational weight gain were associated with increasing or high-level childhood body mass index trajectories as well as a greater risk of overweight at 7 years.

关键词： Body-weight trajectory Child Gestational weight gain Overweight Pregnancy

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Porous-DeepONet:Learning the Solution Operators of Parametric Reactive Transport Equations in Porous Media

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Engineering 2024年第8期39卷 94-103页

作者： Pan Huang Yifei leng Cheng Lian Honglai Liu State Key Laboratory of Chemical Engineering&Shanghai Engineering Research Center of Hierarchical Structure Nanomaterials School of Chemical EngineeringEast China University of Science and TechnologyShanghai 200237China School of Chemistry and Molecular Engineering East China University of Science and TechnologyShanghai 200237China Product Planning and New Auto Technologies Research Institute BYD Auto Industry Company LimitedShenzhen 518118China

Reactive transport equations in porous media are critical in various scientific and engineering disciplines,but solving these equations can be computationally expensive when exploring different scenarios,such as varying porous structures and initial or boundary *** deep operator network(DeepONet)has emerged as a popular deep learning framework for solving parametric partial differential ***,applying the DeepONet to porous media presents significant challenges due to its limited capability to extract representative features from intricate *** address this issue,we propose the Porous-DeepONet,a simple yet highly effective extension of the DeepONet framework that leverages convolutional neural networks(CNNs)to learn the solution operators of parametric reactive transport equations in porous *** incorporating CNNs,we can effectively capture the intricate features of porous media,enabling accurate and efficient learning of the solution *** demonstrate the effectiveness of the Porous-DeepONet in accurately and rapidly learning the solution operators of parametric reactive transport equations with various boundary conditions,multiple phases,and multiphysical fields through five *** approach offers significant computational savings,potentially reducing the computation time by 50–1000 times compared with the finite-element *** work may provide a robust alternative for solving parametric reactive transport equations in porous media,paving the way for exploring complex phenomena in porous media.

关键词： Porous media Reactive transport Solution operator DeepONet Neural network

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