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Panoramic variation analysis of a family with neurodevelopmental disorders caused by biallelic loss-of-function variants in TMEM141,DDHD2,and LHFPL5

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Frontiers of Medicine 2024年第1期18卷 81-97页

作者： Liwei Sun xueting Yang Amjad Khan xue Yu Han zhang Shirui Han Xiaerbati Habulieti Yang Sun Rongrong Wang xue zhang McKusick-zhang Center for Genetic Medicine State Key Laboratory for Complex Severe and Rare DiseasesInstitute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijing100005China Chongqing Key Laboratory of Human Embryo Engineering Center for Reproductive MedicineNational Key Clinical Speciality Construction Project(Obstetrics and Gynecology)Chongqing Health Center for Women and ChildrenChongqing400013China Chongqing Clinical Research Center for Reproductive Medicine Women and Children’s Hospital of Chongqing Medical UniversityChongqing400013China Faculty of Biological Sciences Department of ZoologyUniversity of Lakki MarwatKhyber Pakhtunkhwa28420Pakistan Institute for Medical Genetics and Applied Genomics University of TübingenTübingen72076Germany Alexander von Humboldt fellowship Foundation Berlin10117Germany Department of Pediatrics The First Affiliated Hospital of Guangxi Medical UniversityNanning530000China Department of Laboratory Medicine State Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Science and Peking Union Medical CollegeBeijing100730China

Highly clinical and genetic heterogeneity of neurodevelopmental disorders presents a major challenge in clinical genetics and medicine.Panoramic variation analysis is imperative to analyze the disease phenotypes resulting from multilocus genomic variation.Here,a Pakistani family with parental consanguinity was presented,characterized with severe intellectual disability(ID),spastic paraplegia,and deafness.Homozygosity mapping,integrated single nucleotide polymorphism(SNP)array,whole-exome sequencing,and whole-genome sequencing were performed,and homozygous variants in TMEM141(c.270G>A,p.Trp90^(*)),DDHD2(c.411+767_c.1249-327del),and LHFPL5(c.250delC,p.Leu84^(*))were identified.A Tmem141^(p.Trp90^(*)/p.Trp90^(*))mouse model was generated.Behavioral studies showed impairments in learning ability and motor coordination.Brain slice electrophysiology and Golgi staining demonstrated deficient synaptic plasticity in hippocampal neurons and abnormal dendritic branching in cerebellar Purkinje cells.Transmission electron microscopy showed abnormal mitochondrial morphology.Furthermore,studies on a human in vitro neuronal model(SH-SY5Y cells)with stable shRNA-mediated knockdown of TMEM141 showed deleterious effect on bioenergetic function,possibly explaining the pathogenesis of replicated phenotypes in the cross-species mouse model.Conclusively,panoramic variation analysis revealed that multilocus genomic variations of TMEM141,DDHD2,and LHFPL5 together caused variable phenotypes in patient.Notably,the biallelic loss-of-function variants of TMEM141 were responsible for syndromic ID.

关键词： neurodevelopmental disorder autosomal recessive intellectual disability consanguinity spastic paraplegia hearing loss TMEM141

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A stable implicit nodal integration-based particle finite element method(N-PFEM)for modelling saturated soil dynamics

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第6期16卷 2172-2183页

作者： Liang Wang xue zhang Jingjing Meng Qinghua Lei Department of Earth Sciences ETH ZürichZürich8092Switzerland Department of Civil Engineering and Industrial Design University of LiverpoolLiverpoolL693BXUK Department of Civil Environmental and Natural Resources EngineeringLuleåUniversity of TechnologyLuleå97187Sweden Department of Earth Sciences Uppsala UniversityUppsala75105Sweden

In this study,we present a novel nodal integration-based particle finite element method(N-PFEM)designed for the dynamic analysis of saturated soils.Our approach incorporates the nodal integration technique into a generalised Hellinger-Reissner(HR)variational principle,creating an implicit PFEM formulation.To mitigate the volumetric locking issue in low-order elements,we employ a node-based strain smoothing technique.By discretising field variables at the centre of smoothing cells,we achieve nodal integration over cells,eliminating the need for sophisticated mapping operations after re-meshing in the PFEM.We express the discretised governing equations as a min-max optimisation problem,which is further reformulated as a standard second-order cone programming(SOCP)problem.Stresses,pore water pressure,and displacements are simultaneously determined using the advanced primal-dual interior point method.Consequently,our numerical model offers improved accuracy for stresses and pore water pressure compared to the displacement-based PFEM formulation.Numerical experiments demonstrate that the N-PFEM efficiently captures both transient and long-term hydro-mechanical behaviour of saturated soils with high accuracy,obviating the need for stabilisation or regularisation techniques commonly employed in other nodal integration-based PFEM approaches.This work holds significant implications for the development of robust and accurate numerical tools for studying saturated soil dynamics.

关键词： Particle finite element method Nodal integration Dynamic saturated media Second-order cone programming(SOCP)

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From germline genome to highly fragmented somatic genome:genome-wide DNA rearrangement during the sexual process in ciliated protists

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Marine Life Science & Technology 2024年第1期6卷 31-49页

作者： Liping Lyu xue zhang Yunyi Gao Tengteng zhang Jinyu Fu Naomi A.Stover Feng Gao Key Laboratory of Evolution&Marine Biodiversity(Ministry of Education) and Institute of Evolution&Marine BiodiversityOcean University of ChinaQingdao 266003China Department of Biology Bradley UniversityPeoriaIL 61625USA Laoshan Laboratory Qingdao 266237China

Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements(PGR)play important roles in generating genomic diversity.However,genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of PGR.To expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements,we focus on ciliated protists(ciliates).Ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline genomes.PGR in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome dur-ing development of the somatic genome.We report the partial germline genomes of two spirotrich ciliate species,namely Strombidium cf.sulcatum and Halteria grandinella,along with the most compact and highly fragmented somatic genome for S.cf.sulcatum.We provide the first insights into the genome rearrangements of these two species and compare these features with those of other ciliates.Our analyses reveal:(1)DNA sequence loss through evolution and during PGR in S.cf.sulcatum has combined to produce the most compact and efficient nanochromosomes observed to date;(2)the compact,transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences;(3)long chromosome breakage site motifs are duplicated and retained in the somatic genome,revealing a complex model of chromosome fragmentation in spirotrichs;(4)gene scrambling and alternative pro-cessing are found throughout the core spirotrichs,offering unique opportunities to increase genetic diversity and regulation in this group.

关键词： Alternative processing Ciliates Gene scrambling Genome rearrangement Germline genome Somatic genome

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Tipping Point Detection Using Reservoir Computing

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Research 2024年第1期6卷 779-790页

作者： Xin Li Qunxi Zhu Chengli Zhao Xuzhe Qian xue zhang Xiaojun Duan Wei Lin College of Science National University of Defense TechnologyChangshaHunan 410073China Research Institute of Intelligent Complex Systems and MOE Frontiers Center for Brain Science Fudan UniversityShanghai 200433China Shanghai Artificial Intelligence Laboratory Shanghai 200232China School of Mathematical Sciences SCMSSCAMand CCSBFudan UniversityShanghai 200433China

Detection in high fidelity of tipping points,the emergence of which is often induced by invisible changes in internal structures or/and external interferences,is paramountly beneficial to understanding and predicting complex dynamical systems(CDSs).Detection approaches,which have been fruitfully developed from several perspectives(e.g.,statistics,dynamics,and machine learning),have their own advantages but still encounter difficulties in the face of high-dimensional,fluctuating datasets.Here,using the reservoir computing(RC),a recently notable,resource-conserving machine learning method for reconstructing and predicting CDSs,we articulate a model-free framework to accomplish the detection only using the time series observationally recorded from the underlying unknown CDSs.

关键词： computing record ping

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Tendencies of alloyed engineering in BiOX-based photocatalysts:a state-of-the-art review

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Rare Metals 2024年第4期43卷 1488-1512页

作者： Yan-Dong Sun Chao Zeng xue zhang Zi-Qi zhang Bo Yang Sheng-Qi Guo Tianjin Key Laboratory of Clean Energy and Pollutant Control School of Energy and Environmental EngineeringHebei University of Technology State-Province Joint Engineering Laboratory of Zeolite Membrane Materials Institute of Advanced MaterialsCollege of Chemistry and Chemical EngineeringJiangxi Normal University Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation School of Physics and Electronic InformationAnhui Province Industrial Generic Technology Research Center for Alumics MaterialsHuaibei Normal University

Energy-saving and environmentally friendly photocatalysis has emerged as a popular research area in response to issues with energy scarcity and environmental degradation.Due to the unique layer-like structure,BiOX（Cl,Br,I） is frequently used in photocatalysis.However,inherent flaws in BiOX,such as an inappropriate band gap and low carrier separation efficiency,restrict its capacity for photocatalysis.Owing to the tunable grouping layer,alloying engineering is employed to optimize the intrinsic properties of BiOX and alloyed BiOX becomes a promising photocatalytic material.This review describes the structure of BiOX,where tunable halogen layers provide favorable conditions for the implementation of alloying engineering to improve intrinsic properties.The article compares the effects and mechanisms of alloying engineering on the optimization of the energy band structure and carrier behavior of BiOX,and lists various modification methods used to improve the optimization of the intrinsic properties by alloying engineering,including defect engineering,morphology control as well as the synergy between alloying and other modification methods（bismuth-rich strategies,cation doping,construction of heterojunctions and plasma resonance effects）.Subsequently,applications of alloyed BiOX in energy and environmental fields are summarized,including contaminant degradation,antibacterial,CO2reduction,nitrogen fixation and organic synthesis.Finally,we summarize the current challenges and future directions of alloyed BiOX.It is expected that this work will provide guidance and assistance for an in-depth study and understanding of the mechanisms of alloying engineering to optimize intrinsic properties and design alloyed BiOX with higher photocatalytic activity.

关键词： Bismuth oxyhalide Photocatalytic Alloyed engineering Microstructural regulation Application

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Atorvastatin, etanercept and the nephrogenic cardiac sympathetic remodeling in chronic renal failure rats

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Journal of Geriatric Cardiology 2024年第4期21卷 443-457页

作者： Jing-Yue XU Zheng-Kai xue Ya-Ru zhang Xing LIU xue zhang Xi YANG Tong LIU Kang-Yin CHEN Tianjin Key Laboratory of Ionic-Molecular Function of Cardiovascular Disease Department of CardiologyTianjin Institute of Cardiologythe Second Hospital of Tianjin Medical UniversityTianjinChina

BACKGROUND Chronic renal failure(CRF) patients are predisposed to arrhythmias, while the detailed mechanisms are unclear. We hypothesized the chronic inflammatory state of CRF patients may lead to cardiac sympathetic remodeling, increasing the incidence of ventricular arrhythmia(VA) and sudden cardiac death. And explored the role of atorvastatin and etanercept in this process.METHODS A total of 48 rats were randomly divided into sham operation group(Sham group), CRF group, CRF + atorvastatin group(CRF + statin group), and CRF + etanercept group(CRF + rhTNFR-Fcgroup). Sympathetic nerve remodeling was assessed by immunofluorescence of growth-associated protein 43(GAP-43) and tyrosine hydroxylase positive area fraction. Electrophysiological testing was performed to assess the incidence of VA by assessing the ventricular effective refractory period and ventricular fibrillation threshold. The levels of tumor necrosis factor-alpha(TNF-α) and interleukin-1beta were determined by Western blotting and enzyme-linked immunosorbent assay.RESULTS Echocardiogram showed that compared with the Sham group, left ventricular end-systolic diameter and ventricular weight/body weight ratio were significantly higher in the CRF group. Hematoxylin-eosin and Masson staining indicated that myocardial fibers were broken, disordered, and fibrotic in the CRF group. Western blotting, enzyme-linked immunosorbent assay,immunofluorescence and electrophysiological examination suggested that compared with the Sham group, GAP-43 and TNF-α proteins were significantly upregulated, GAP-43 and tyrosine hydroxylase positive nerve fiber area was increased, and ventricular fibrillation threshold was significantly decreased in the CRF group. The above effects were inhibited in the CRF + statin group and the CRF + rhTNFR-Fcgroup.CONCLUSIONS In CRF rats, TNF-α was upregulated, cardiac sympathetic remodeling was more severe, and the nephrogenic cardiac sympathetic remodeling existed. Atorvastatin and etanercept could downregulate the expression of TNF-α or inh

关键词： remodeling cardiac inhibited

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Nitrogen‑Doped Magnetic‑Dielectric‑Carbon Aerogel for High‑Efficiency Electromagnetic Wave Absorption

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Nano-Micro Letters 2024年第1期16卷 313-327页

作者： Shijie Wang xue zhang Shuyan Hao Jing Qiao Zhou Wang Lili Wu Jiurong Liu Fenglong Wang Key Laboratory for Liquid‑Solid Structural Evolution and Processing of Materials Ministry of Education Shandong UniversityJinan 250061People’s Republic of China School of Mechanical Engineering Shandong UniversityJinan 250061People’s Republic of China Shenzhen Research Institute of Shandong University Shenzhen 518057GuangdongPeople’s Republic of China

Carbonbased aerogels derived from biomass chitosan are encountering a flourishing moment in electromagnetic protection on account of lightweight,controllable fabrication and versatility.Nevertheless,developing a facile construction method of component design with carbon-based aerogels for high-efficiency electromagnetic wave absorption(EWA)materials with a broad effective absorption bandwidth(EAB)and strong absorption yet hits some snags.Herein,the nitrogen-doped magnetic-dielectric-carbon aerogel was obtained via ice template method followed by carbonization treatment,homogeneous and abundant nickel(Ni)and manganese oxide(MnO)particles in situ grew on the carbon aerogels.Thanks to the optimization of impedance matching of dielectric/magnetic components to carbon aerogels,the nitrogen-doped magnetic-dielectric-carbon aerogel(Ni/MnO-CA)suggests a praiseworthy EWA performance,with an ultra-wide EAB of 7.36 GHz and a minimum reflection loss(RLmin)of−64.09 dB,while achieving a specific reflection loss of−253.32 dB mm−1.Furthermore,the aerogel reveals excellent radar stealth,infrared stealth,and thermal management capabilities.Hence,the high-performance,easy fabricated and multifunctional nickel/manganese oxide/carbon aerogels have broad application aspects for electromagnetic protection,electronic devices and aerospace.

关键词： Electromagnetic wave absorption Wide bandwidth Dielectric-magnetic synergy Multifunction

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Ferroptosis inhibitors reduce celastrol toxicity and preserve its insulin sensitizing effects in insulin resistant HepG2 cells

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Journal of Integrative Medicine 2024年第3期22卷 286-294页

作者： Jia-jia Liu xue zhang Bang-lan Cai Man-man Qi Yong-bin Chi Bin Peng Deng-hai zhang School of Medicine Shanghai UniversityShanghai 200444China Shanghai Health Commission Key Lab of Artificial Intelligence-Based Management of Inflammation and Chronic Diseases Shanghai Pudong Gongli HospitalSecondary Military Medical UniversityShanghai 200135China School of Basic Medicine Ningxia Medical UniversityYinchuan 750004Ningxia Hui Autonomous RegionChina

Objective:Research has shown that celastrol can effectively treat a variety of diseases,yet when passing a certain dosage threshold,celastrol becomes toxic,causing complications such as liver and kidney damage and erythrocytopenia,among others.With this dichotomy in mind,it is extremely important to find ways to preserve celastrol’s efficacy while reducing or preventing its toxicity.Methods:In this study,insulin-resistant Hep G2(IR-Hep G2)cells were prepared using palmitic acid and used for in vitro experiments.IR-Hep G2 cells were treated with celastrol alone or in combination with Nacetylcysteine(NAC)or ferrostatin-1(Fer-1)for 12,24 or 48 h,at a range of doses.Cell counting kit-8assay,Western blotting,quantitative reverse transcription-polymerase chain reaction,glucose consumption assessment,and flow cytometry were performed to measure celastrol’s cytotoxicity and whether the cell death was linked to ferroptosis.Results:Celastrol treatment increased lipid oxidation and decreased expression of anti-ferroptosis proteins in IR-Hep G2 cells.Celastrol downregulated glutathione peroxidase 4(GPX4)m RNA.Molecular docking models predicted that solute carrier family 7 member 11(SLC7A11)and GPX4 were covalently bound by celastrol.Importantly,we found for the first time that the application of ferroptosis inhibitors(especially NAC)was able to reduce celastrol’s toxicity while preserving its ability to improve insulin sensitivity in IR-Hep G2 cells.Conclusion:One potential mechanism of celastrol’s cytotoxicity is the induction of ferroptosis,which can be alleviated by treatment with ferroptosis inhibitors.These findings provide a new strategy to block celastrol’s toxicity while preserving its therapeutic effects.

关键词： Celastrol Insulin resistance Ferroptosis N-Acetylcysteine Palmitic acid Molecular docking

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Identification of TP53 mutation-associated prognostic genes and investigation of the immune cell infiltration in patients with hepatocellular carcinoma

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Genes & Diseases 2024年第2期11卷 520-523页

作者： Qijun Yang Lianke Gao Yuhan Xu Gaoquan Cao Yingcheng He Wenyige zhang xue zhang Chengfeng Wu Kaili Liao Xiaozhong Wang Department of Clinical Laboratory The Second Affiliated Hospital of Nanchang UniversityNanchangJiangxi 330006China Queen Mary College of Nanchang University NanchangJiangxi 330031China Advanced Manufacturing College of Nanchang University NanchangJiangxi 330031China The Forth Clinical School of Nanchang University The South Road of Bayi SquareNanchangJiangxi 330031China Department of Vascular Surgery The Second Affiliated Hospital of Nanchang UniversityNanchangJiangxi 330006China

Primary liver cancer,which is mainly composed of hepatocellular carcinoma(HcC),is the sixth most common type of cancer worldwide and the thirdmost common cause of cancer mortality.1 The total number of mutations present in tumor specimens is called tumor mutation burden(TMB)and it is an emerging biomarker of immunotherapy response.2 TMB can predict clinical responses to immunotherapy such as ICl(immune checkpoint inhibitor)treatments and higher TMB is related to better survival.3 TP53,a gene encoding a tumor suppressor protein that triggers apoptosis and cell cycle arrest,is one of the most prevalent mutations in 25%-30%of HCC patients.4 Research shows that TP53 mutations in HCC patients are associated with advanced tumor grade and poor prognosis.5 To identify the TP53 mutation-related genes which can predict HCC patients'prognosis and explore the immune cell infiltration,we constructed a risk model based on six TP53 mutation-related genes which can accurately predict patients'prognosis.Besides,six immune cells with a similar expression pattern were identified in The Cancer Genome Atlas(TCGA)and International Cancer Genome Consortium(ICGC)databases.

关键词： TP53 patients hepatocellular

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Dysregulated N6-methyladenosine modification in peripheral immune cells contributes to the pathogenesis of amyotrophic lateral sclerosis

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Frontiers of Medicine 2024年第2期18卷 285-302页

作者： Di He Xunzhe Yang Liyang Liu Dongchao Shen Qing Liu Mingsheng Liu xue zhang Liying Cui Department of Neurology Peking Union Medical College Hospital(PUMCH)Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100730China Medical Doctor Program Chinese Academy of Medical Science and Peking Union Medical CollegeBeijing100730China McKusick-zhang Center for Genetic Medicine State Key Laboratory of Medical Molecular BiologyInstitute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic MedicinePeking Union Medical CollegeBeijing100730China Neuroscience Center Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100730China

Amyotrophic lateral sclerosis(ALS)is a progressive neurogenerative disorder with uncertain origins.Emerging evidence implicates N6-methyladenosine(m6A)modification in ALS pathogenesis.Methylated RNA immunoprecipitation sequencing(MeRIP-seq)and liquid chromatography–mass spectrometry were utilized for m6A profiling in peripheral immune cells and serum proteome analysis,respectively,in patients with ALS(n=16)and controls(n=6).The single-cell transcriptomic dataset(GSE174332)of primary motor cortex was further analyzed to illuminate the biological implications of differentially methylated genes and cell communication changes.Analysis of peripheral immune cells revealed extensive RNA hypermethylation,highlighting candidate genes with differential m6A modification and expression,including C-X3-C motif chemokine receptor 1(CX3CR1).In RAW264.7 macrophages,disrupted CX3CR1 signaling affected chemotaxis,potentially influencing immune cell migration in ALS.Serum proteome analysis demonstrated the role of dysregulated immune cell migration in ALS.Cell type-specific expression variations of these genes in the central nervous system(CNS),particularly microglia,were observed.Intercellular communication between neurons and glial cells was selectively altered in ALS CNS.This integrated approach underscores m6A dysregulation in immune cells as a potential ALS contributor.

关键词： amyotrophic lateral sclerosis N^(6)-methyladenosine epi-transcriptome proteome single cell RNA sequencing analysis CX3CR1

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