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Exploring noncoding variants in genetic diseases:from detection to functional insights

Journal of Genetics and Genomics 2024年第2期51卷 111-132页

作者： Ke Wu Fengxiao Bu Yang Wu Gen Zhang Xin Wang Shunmin He mo-fang liu Runsheng Chen Huijun Yuan Institute of Rare Diseases West China Hospital of Sichuan UniversityChengduSichuan 610041China Key Laboratory of Systems Health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouZhejiang 310024China Key Laboratory of RNA Biology Center for Big Data Research in HealthInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory of molecular Biology State Key Laboratory of Cell BiologyShanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai 200031China

Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.

关键词： Noncoding variation Genetic disease Research approach Challenge

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精子发生中小非编码RNA的新见解

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Science Bulletin 2024年第11期69卷 1581-1585页

作者：王鑫张振翼赵爽刘默芳 Key Laboratory of Systems Health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China New Cornerstone Science Laboratory State Key Laboratory of Molecular BiologyState Key Laboratory of Cell BiologyShanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai 200031China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China

Spermatogenesis is one of the most complicated cell differentiation processes in animals, which consists of mitosis, meiosis, and the post-meiotic phase of male germ cell development, i.e.,spermiogenesis. Mitosis is responsible for germline maintenance,while meiosis reduces the chromosome number by half and creates genetic diversity in the sperm.

关键词：精子发生 maintenance mitosis

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Small RNAs:An expanding world with therapeutic promises

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Fundamental Research 2023年第5期3卷 676-682页

作者： Lan-Tao Gou Qifan Zhu mo-fang liu State Key Laboratory of molecular Biology Shanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai 200031China School of Life Science Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China School of Life Science and Technology Shanghai Tech UniversityShanghai 201210China

Small non-coding RNAs(sncRNAs),such as microRNAs(miRNAs),small interfering RNAs(siRNAs),PIWIinteracting RNAs(piRNAs),and transfer RNA(tRNA)-derived small RNAs(tsRNAs),play essential roles in regulating various cellular and developmental *** the past three decades,researchers have identified novel sncRNA species from various *** molecules demonstrate dynamic expression and diverse functions,and they are subject to intricate regulation through RNA modifications in both healthy and diseased ***,certain sncRNAs in gametes,particularly sperm,respond to environmental stimuli and facilitate epigenetic ***,the in-depth understanding of sncRNA functions and mechanisms has accelerated the development of small RNA-based *** this review,we present the recent advances in the field,including new sncRNA species and the regulatory influences of RNA *** also discuss the current limitations and challenges associated with using small RNAs as either biomarkers or therapeutic drugs.

关键词： Small non-coding RNAs RNA modifications Human diseases RNA therapeutics Biomarkers

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A dual role of the PIWI/pi RNA machinery in regulating mRNAs during mouse spermiogenesis

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Science China(Life Sciences) 2020年第3期63卷 447-449页

作者： Peng Dai Xin Wang mo-fang liu State Key Laboratory'of molecular Biology、Shanghai Key Laboratory of molecular Andrology CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of Sciences-University of Chinese Academy of SciencesShanghai 200031China

The post-meiotic phase of male germ cell development in mammals undergoes a series of dramatic morphological changes,including acrosome and flagellum formation,nuclear condensation,and cytoplasmic exclusion,which is driven by a highly regulated sequence of biochemical reactions(Meistrich and Hess,2013).Such differentiation process called spermiogenesis consists of at least 16 sequential transition steps in mice,including steps I to 8 for round spermatids,steps 9 to 11 for elongating spermatids,steps 12 to 14 for elongated or condensed spermatids,and final steps 15 to 16 for spermatozoa(Meistrich and Hess,2013).

关键词： steps condensed condensation

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Removal of Cr(Ⅵ)by glutaraldehyde-crosslinked chitosan encapsulating microscale zero-valent iron:Synthesis,mechanism,and longevity

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Journal of Environmental Sciences 2024年第8期142卷 115-128页

作者： Yijun Duan fang liu Xiang liu Miao Li School of Environment Tsinghua UniversityBeijing 100084China Transportation Institute of Inner mongolia University Hohhot 010070China

Microscale zero-valent iron(mZVI)has shown great potential for groundwater Cr(Ⅵ)***,low Cr(Ⅵ)removal capacity caused by passivation restricted the wide use of *** prepared mZVI/GCS by encapsulating mZVI in a porous glutaraldehydecrosslinked chitosan matrix,and the formation of the passivation layer was alleviated by reducing the contact between zero-valent iron *** average pore diameter of mZVI/GCS was 8.775 nm,which confirmed the mesoporous characteristic of this *** of batch experiments demonstrated that mZVI/GCS exhibited high Cr(Ⅵ)removal efficiency in a wide range of pH(2-10)and temperature(5-35℃).Common groundwater coexisting ions slightly affected m ZVI/*** material showed great reusability,and the average Cr(Ⅵ)removal efficiency was 90.41%during eight *** this study,we also conducted kinetics and isotherms ***-second-order model was the most matched kinetics *** Cr(Ⅵ)adsorption process was fitted by both Langmuir and Freundlich isotherms models,and the maximum Langmuir adsorption capacity of m ZVI/GCS reached243.63 mg/g,which is higher than the adsorption capacities of materials reported in most of the previous ***,the column capacity for Cr(Ⅵ)removal of a mZVI/GCS-packed column was 6.4 times higher than that of a mZVI-packed column in a 50-day ***,mZVI/GCS with a porous structure effectively relieved passivation problems of mZVI and showed practical application prospects as groundwater Cr(Ⅵ)remediation material with practical application prospects.

关键词： Chitosan Glutaraldehyde mZVI Cr(Ⅵ) Groundwater

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Exploring battery material failure mechanisms through synchrotron X-ray characterization techniques

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Journal of Energy Chemistry 2024年第7期94卷 128-135页

作者： Lingzhe fang Xiaozhao liu Tao Li Department of Chemistry and Biochemistry Northern Illinois UniversityDeKalbIL 60115USA X-ray Science Division and Joint Center forEnergy Storage Research Argonne National LaboratoryLemontIL6439UA

Rechargeable battery cycling performance and related safety have been persistent *** is crucial to decipher the capacity fading induced by electrode material failure via a range of *** these,synchrotron-based X-ray techniques with high flux and brightness play a key role in understanding degradation *** this comprehensive review,we summarize recent advancements in degra-dation modes and mechanisms that were revealed by synchrotron X-ray ***,an overview of X-ray absorption spectroscopy and X-ray scattering techniques is introduced for charac-terizing failure phenomena at local coordination atomic environment and long-range order crystal struc-ture scale,*** last,we envision the future of exploring material failure mechanism.

关键词： Battery failure Synchrotron-based techniques X-ray scattering X-ray absorption spectroscopy

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Giant low-field reversible magnetocaloric effect at liquid helium temperature of niobium and iron co-substituted EuTiO_(3) compounds

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Journal of Rare Earths 2024年第4期42卷 710-715页

作者： Zhihong Hao Quanyi liu Huicai Xie Yan Zhang Zhaojun mo School of Rare Earth and New Materials Engineering Ganzhou Innovation Center of Rare Earth Permanent Magnet Material Advanced Manufacturing and Intelligent Equipment TechnologyGannan University of Science and TechnologyGanzhou341000China Ganjiang Innovation Academy Chinese Academy of SciencesGanzhou34119China School of Materials Science and Engineering Taiyuan University of Science and TechnologyTaiyuan030024China

Giant magnetocaloric effect(MCE)materials in the liquid helium temperature region have attracted a lot of attention in the field of low-temperature magnetic refrigeration(MR).In this study,a series of niobium(Nb)and iron(Fe)co-substituted EuTiO_(3) perovskites with cubic structure(space group pm3m)was successfully fabricated,and their magnetic properties as well as cryogenic magnetocaloric effects were investigated in *** expected,the introduction of Nb and Fe can significantly modulate the magnetic phase transition and magnetocaloric effect of the EuTiO_(3) *** increasing Fe concentration,two local minima corresponding to the AFM-FM magnetic phase transition near 5.0 K and FM-PM transition near 10 K with no hysteresis in the thermomagnetic curves are observed,which is attributed to an enhancement of FM *** the same time,the gradually widened-ΔSM-T curves and the two peaks with a broad shoulder lead to considerable refrigeration capacity(RC).With the field change ofΔH=2 T,the calculated values of-ΔS_(M)^(max) for the EuTi_(0.9375-x)Nb_(0.0625)Fe_(x)O_(3)(x=0.075,0.1,0.125,0.15)compounds are 24.2,17.6,14.5 and 14.0 J/(kg·K),*** corresponding RC values were calculated to be 144.6,138.3,151.2 and 159 J/kg,***,the values of-ΔS_(M)^(max) for EuTi_(0.8625)Nb_(0.0625)Fe_(0.075)O_(3) are 8.6 and 15.1 J/(kg·K)under low field changes of 0.5 and 1 T,*** giant low-field reversible magnetocaloric effect makes them attractive candidates for magnetic refrigeration in the liquid helium temperature region.

关键词： Magnetocaloric effect Refrigeration capacity Magnetic entropy change Rareearths

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modelling analysis embodies drastic transition among global potential natural vegetations in face of changing climate

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Forest Ecosystems 2024年第2期11卷 184-192页

作者： Zhengchao Ren Lei liu fang Yin Xiaoni liu School of Earth Science and Resources Chang’an UniversityXi’an710054China Research Center of Ecological Construction and Environmental Conservation in Gansu Province Gansu Agricultural UniversityLanzhou730070China State Key Laboratory of Tibetan Plateau Earth System Environment and Resources(TPESER)Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing100101China School of Land Engineering Chang’an UniversityXi’an710054China College of Pratacultural Science Gansu Agricultural UniversityLanzhou730070China

Potential natural vegetation(PNV)is a valuable reference for ecosystem renovation and has garnered increasing attention ***,there is limited knowledge on the spatio-temporal distributions,transitional processes,and underlying mechanisms of global natural vegetation,particularly in the case of ongoing climate *** this study,we visualize the spatio-temporal pattern and inter-transition procedure of global PNV,analyse the shifting distances and directions of global PNV under the influence of climatic disturbance,and explore the mechanisms of global PNV in response to temperature and precipitation *** achieve this,we utilize meteorological data,mainly temperature and precipitation,from six phases:the Last Inter-Glacial(LIG),the Last Glacial Maximum(LGM),the Mid Holocene(MH),the Present Day(PD),2030(20212040)and 2090(2081–2100),and employ a widely-accepted comprehensive and sequential classification sy–stem(CSCS)for global PNV *** find that the spatial patterns of five PNV groups(forest,shrubland,savanna,grassland and tundra)generally align with their respective ecotopes,although their distributions have shifted due to fluctuating temperature and ***,we observe an unexpected transition between tundra and savanna despite their geographical *** shifts in distance and direction of five PNV groups are mainly driven by temperature and precipitation,although there is heterogeneity among these shifts for each ***,the heterogeneity observed among different global PNV groups suggests that they may possess varying capacities to adjust to and withstand the impacts of changing *** spatio-temporal distributions,mutual transitions and shift tendencies of global PNV and its underlying mechanism in face of changing climate,as revealed in this study,can significantly contribute to the development of strategies for mitigating warming and promoting re-vegetation in degraded regions worldwide.

关键词： Potential natural vegetation Global warming Vegetation classification Predicted model CSCS

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Thermo-hydro-mechanical (THM) coupled simulation of the land subsidence due to aquifer thermal energy storage (ATES) system in soft soils

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第6期16卷 1952-1966页

作者： Yang Wang Fengshou Zhang fang liu Department of Geotechnical Engineering College of Civil EngineeringTongji UniversityShanghai200092China Key Laboratory of Geotechnical and Underground Engineering of Ministry of Education Tongji UniversityShanghai200092China Shanghai Engineering and Technology Research Center of Shallow Geothermal Energy Shanghai200072China

Aquifer thermal energy storage(ATES)system has received attention for heating or cooling ***,it is well known that land subsidence becomes a major environmental concern for ATES ***,the effect of temperature on land subsidence has received practically no attention in the *** paper presents a thermo-hydro-mechanical(THM)coupled numerical study on an ATES system in Shanghai,*** water wells were installed for seasonal heating and cooling of an agriculture *** target aquifer at a depth of 74e104.5 m consisted of alternating layers of sand and silty sand and was covered with *** level,temperature,and land subsidence data from 2015 to 2017 were collected using field monitoring *** by data,we constructed a field scale three-dimensional(3D)model using TOUGH(Transport of Unsaturated Groundwater and Heat)and FLAC3D(Fast Lagrangian Analysis of Continua)equipped with a thermo-elastoplastic constitutive *** effectiveness of the numerical model was validated by field *** model was used to reproduce groundwater flow,heat transfer,and mechanical responses in porous media over three years and capture the thermo-and pressure-induced land *** results show that the maximum thermoinduced land subsidence accounts for about 60%of the total *** thermo-induced subsidence is slightly greater in winter than that in summer,and more pronounced near the cold well area than the hot well *** study provides some valuable guidelines for controlling land subsidence caused by ATES systems installed in soft soils.

关键词： Aquifer thermal energy storage(ATES) Land subsidence TOUGH-FLAC3D Thermo-elastoplastic constitutive model

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Transplantation of fibrin-thrombin encapsulated human induced neural stem cells promotes functional recovery of spinal cord injury rats through modulation of the microenvironment

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Neural Regeneration Research 2024年第2期19卷 440-446页

作者： Sumei liu Baoguo liu Qian Li Tianqi Zheng Bochao liu mo Li Zhiguo Chen Cell Therapy Center Beijing Institute of GeriatricsXuanwu HospitalCapital Medical UniversityNational Clinical Research Center for Geriatric Diseasesand Key Laboratory of Neurodegenerative DiseasesMinistry of EducationBeijingChina Center of Neural Injury and Repair Beijing Institute for Brain DisordersBeijingChina Center of Parkinson’s Disease Beijing Institute for Brain DisordersBeijingChina

Recent studies have mostly focused on engraftment of cells at the lesioned spinal cord,with the expectation that differentiated neurons facilitate *** a few studies have attempted to use transplanted cells and/or biomaterials as major modulators of the spinal cord injury ***,we aimed to investigate the role of microenvironment modulation by cell graft on functional recovery after spinal cord *** neural stem cells reprogrammed from human peripheral blood mononuclear cells,and/or thrombin plus fibrinogen,were transplanted into the lesion site of an immunosuppressed rat spinal cord injury ***,Beattie and Bresnahan score,electrophysiological function,and immunofluorescence/histological analyses showed that transplantation facilitates motor and electrophysiological function,reduces lesion volume,and promotes axonal neurofilament expression at the lesion *** of the graft and niche components revealed that although the graft only survived for a relatively short period(up to 15 days),it still had a crucial impact on the ***,induced neural stem cells and human fibrin reduced the number of infiltrated immune cells,biased microglia towards a regenerative M2 phenotype,and changed the cytokine expression profile at the lesion ***-induced changes of the microenvironment during the acute and subacute stages might have disrupted the inflammatory cascade chain reactions,which may have exerted a long-term impact on the functional recovery of spinal cord injury rats.

关键词： biomaterial fibrinogen functional recovery induced neural stem cell transplantation microenvironment microglia spinal cord injury thrombin

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