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Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism

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Plant Communications 2024年第8期5卷 32-49页

作者： Ershang Han Zhenxing Geng Yue Qin Yuewei Wang Shisong Ma MOE Key Laboratory for Cellular Dynamics School of Life SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaInnovation Academy for Seed DesignChinese Academy of SciencesHefei 230027China School of Data Science University of Science and Technology of ChinaHefei 230027China

Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated,but related comprehensive gene co-expression network analyses are *** conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM *** analysis identified 149 gene co-expression modules,which we considered to be gene expression programs(GEPs).By examining their spatiotemporal expression,we identified GEPs specifically expressed in major root cell types along their developmental *** GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental *** examples,a GEP specific for the quiescent center(QC)contains 20 genes regulating QC and stem cell niche homeostasis,and four GEPs are expressed in sieve elements(SEs)from early to late developmental stages,with the early-stage GEP containing 17 known SE developmental *** also identified GEPs for metabolic pathways with cell-type-specific expression,suggesting the existence of cell-type-specific metabolism in *** the GEPs,we discovered and verified a columellaspecific gene,NRL27,as a regulator of the auxin-related root gravitropism *** analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.

关键词： single-cell RNA sequencing single-cell gene co-expression network analysis gene expression program Arabidopsis root development NRL27 gravitropism

TIP60 acetylation of Bub1 regulates centromeric H2AT120 phosphorylation for faithful chromosome segregation

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Science China(life sciences) 2024年第9期67卷 1957-1969页

作者： Mengjie Sun Biying Yang Guangwei Xin Yao Wang Jia Luo Qing Jiang Chuanmao Zhang The Academy for Cell and life Health Faculty of Life Science and TechnologyKunming University of Science and TechnologyKunming 650500China The Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education College of Life SciencesPeking UniversityBeijing 100871China

Proper function of the centromeres ensures correct attachment of kinetochores to spindle microtubules and faithful chromosome segregation in *** in the integrity and function of centromeres can result in chromosome missegregation and genomic ***1 is essential for the mitotic centromere dynamics,yet the underlying molecular mechanisms remain largely ***,we demonstrate that TIP60 acetylates Bub1 at K424 and K431 on kinetochores in early *** acetylation increases the kinase activity of Bub1 to phosphorylate centromeric histone H2A at T120(H2Ap T120),which recruits Aurora B and Shugoshin 1(Sgo1)to regulate centromere integrity,protect centromeric cohesion,and ensure the subsequent faithful chromosome *** of the nonacetylated Bub1 mutant reduces its kinase activity,decreases the level of H2Ap T120,and disrupts the recruitment of centromere proteins and chromosome congression,leading to genomic instability of daughter *** cells exit mitosis,HDAC1-regulated deacetylation of Bub1 decreases H2Ap T120 levels and thereby promotes the departure of centromeric CPC and Sgo1,ensuring timely centromeres ***,our results reveal a molecular mechanism by which the acetylation and deacetylation cycle of Bub1 modulates the phosphorylation of H2A at T120 for recruitment of Aurora B and Sgo1 to the centromeres,ensuring faithful chromosome segregation during mitosis.

关键词： acetylation Bub1 TIP60 H2ApT120 chromosome segregation

OsPDR20 is an ABCG metal transporter regulating cadmium accumulation in rice

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Journal of Environmental sciences 2024年第2期136卷 21-34页

作者： He Li Chao Li Di Sun Zhi Min Yang department of Biochemistry and Molecular Biology College of Life SciencesNanjing Agricultural UniversityNanjing 210095China

Cadmium(Cd)is a non-essential toxic heavy metal,seriously posing high environmental risks to human *** genetic resources relevant to functional genes is important for understanding the metal absorption and accumulation in crops and bioremediation of Cd-polluted *** study investigated a functionally uncharacterized ATP binding cassette transporter G family(ABCG)gene encoding a Pleiotropic Drug Resistance 20(PDR20)type metal transporter which is localized to the plasma membrane of ***20 was transcriptionally expressed in almost all tissues and organs in lifespan and was strongly induced in roots and shoots of young rice under Cd *** expression of OsPDR20 in a yeast mutant ycf1 sensitive to Cd conferred cellular tolerance with less Cd *** of OsPDR20 by RNA interference(RNAi)moderately attenuated root/shoot elongation and biomass,with reduced chlorophylls in rice grown under hydroponic medium with 2 and 10μmol/L Cd,but led to more Cd accumulation.A field trial of rice grown in a realistic Cd-contaminated soil(0.40 mg/kg)showed that RNAi plants growth and development were also compromised compared to wild-type(WT),with smaller panicles and lower spikelet fertility but little effect on yield of ***,OsPDR20 suppression resulted in unexpectedly higher levels of Cd accumulation in rice straw including lower leaves and culm and *** results suggest that OsPDR20 is actively involved in Cd accumulation and homeostasis in rice *** increased Cd accumulation in the RNAi plants has the potential application in phytoremediation of Cd-polluted wetland soils.

关键词： Rice ABCG transporter Cadmium accumulation Phytoremediation

Therapeutic advances in neural regeneration for Huntington’s disease

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Neural Regeneration Research 2024年第9期19卷 1991-1997页

作者： Francesco D’Egidio Vanessa Castelli Giorgia Lombardozzi Fabrizio Ammannito Annamaria Cimini Michele d’Angelo department of life Health and Environmental SciencesUniversity of L’AquilaL’AquilaItaly

Huntington’s disease is a neurodegenerative disease caused by the expansion mutation of a cytosine-adenine-guanine triplet in the exon 1 of the HTT gene which is responsible for the production of the huntingtin (Htt) protein. In physiological conditions, Htt is involved in many cellular processes such as cell signaling, transcriptional regulation, energy metabolism regulation, DNA maintenance, axonal trafficking, and antiapoptotic activity. When the genetic alteration is present, the production of a mutant version of Htt (mHtt) occurs, which is characterized by a plethora of pathogenic activities that, finally, lead to cell death. Among all the cells in which mHtt exerts its dangerous activity, the GABAergic Medium Spiny Neurons seem to be the most affected by the mHtt-induced excitotoxicity both in the cortex and in the striatum. However, as the neurodegeneration proceeds ahead the neuronal loss grows also in other brain areas such as the cerebellum, hypothalamus, thalamus, subthalamic nucleus, globus pallidus, and substantia nigra, determining the variety of symptoms that characterize Huntington’s disease. From a clinical point of view, Huntington’s disease is characterized by a wide spectrum of symptoms spanning from motor impairment to cognitive disorders and dementia. Huntington’s disease shows a prevalence of around 3.92 cases every 100,000 worldwide and an incidence of 0.48 new cases every 100,000/year. To date, there is no available cure for Huntington’s disease. Several treatments have been developed so far, aiming to reduce the severity of one or more symptoms to slow down the inexorable decline caused by the disease. In this context, the search for reliable strategies to target the different aspects of Huntington’s disease become of the utmost interest. In recent years, a variety of studies demonstrated the detrimental role of neuronal loss in Huntington’s disease condition highlighting how the replacement of lost cells would be a reasonable strategy to o

关键词： cell therapy exosomes extracellular vesicles Huntingtin Huntington’s disease medium spiny neurons neurodegenerative disease neurogenesis neuronal loss stem cells

Solid-state atomic hydrogen as a broad-spectrum RONS scavenger for accelerated diabetic wound healing

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National Science Review 2024年第2期11卷 196-206页

作者： Man Luo Qin Wang Gang Zhao Wei Jiang Cici Zeng Qingao Zhang Ruyu Yang Wang Dong Yunxi Zhao Guozhen Zhang Jun Jiang Yucai Wang Qing Zhu Key Laboratory of Precision and Intelligent Chemistry School of Chemistry and Materials Science University of Science and Technology of China department of Radiology The First Affiliated Hospital of University of Science and Technology of China Division of Life Sciences and Medicine University of Science and Technology of China Shenzhen Senior High School Institute of Intelligent Innovation Henan Academy of Sciences

Hydrogen therapy shows great promise as a versatile treatment method for diseases associated with the overexpression of reactive oxygen and nitrogen species（RONS）. However, developing an advanced hydrogen therapy platform that integrates controllable hydrogen release, efficient RONS elimination, and biodegradability remains a giant technical challenge. In this study, we demonstrate for the first time that the tungsten bronze phase H0.53WO3（HWO） is an exceptionally ideal hydrogen carrier, with salient features including temperature-dependent highly-reductive atomic hydrogen release and broad-spectrum RONS scavenging capability distinct from that of molecular hydrogen. Moreover, its unique p H-responsive biodegradability ensures post-therapeutic clearance at pathological sites. Treatment with HWO of diabetic wounds in an animal model indicates that the solid-state atomic H promotes vascular formation by activating M2-type macrophage polarization and anti-inflammatory cytokine production, resulting in acceleration of chronic wound healing. Our findings significantly expand the basic categories of hydrogen therapeutic materials and pave the way for investigating more physical forms of hydrogen species as efficient RONS scavengers for clinical disease treatment.

关键词： atomic hydrogen RONS scavenger inflammatory regulation diabetic wound healing hydrogen therapy

Cav3.2 channel regulates cerebral ischemia/reperfusion injury:a promising target for intervention

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Neural Regeneration Research 2024年第11期19卷 2480-2487页

作者： Feibiao Dai Chengyun Hu Xue Li Zhetao Zhang Hongtao Wang Wanjun Zhou Jiawu Wang Qingtian Geng Yongfei Dong Chaoliang Tang Graduate School Wannan Medical CollegeWuhuAnhui ProvinceChina department of Anesthesiology The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui ProvinceChina Core Facility Center for Medical sciences The First Affiliated Hospital of USTC(Anhui Provincial Hospital)HefeiAnhui ProvinceChina department of Pharmacy The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui ProvinceChina department of Neurosurgery The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui ProvinceChina

Calcium influx into neurons triggers neuronal death during cerebral ischemia/reperfusion *** calcium channels are involved in cerebral ischemia/reperfusion ***3.2 channel is a main subtype of T-type calcium channels.T-type calcium channel blockers,such as pimozide and mibefradil,have been shown to prevent cerebral ischemia/reperfusion injury-induced brain ***,the role of Cav3.2 channels in cerebral ischemia/reperfusion injury remains ***,in vitro and in vivo models of cerebral ischemia/reperfusion injury were established using middle cerebral artery occlusion in mice and high glucose hypoxia/reoxygenation exposure in primary hippocampal *** results showed that Cav3.2 expression was significantly upregulated in injured hippocampal tissue and primary hippocampal *** further established a Cav3.2 gene-knockout mouse model of cerebral ischemia/reperfusion ***3.2 knockout markedly reduced infarct volume and brain water content,and alleviated neurological dysfunction after cerebral ischemia/reperfusion ***,Cav3.2 knockout attenuated cerebral ischemia/reperfusion injury-induced oxidative stress,inflammatory response,and neuronal *** the hippocampus of Cav3.2-knockout mice,calcineurin overexpression offset the beneficial effect of Cav3.2 knockout after cerebral ischemia/reperfusion *** findings suggest that the neuroprotective function of Cav3.2 knockout is mediated by calcineurin/nuclear factor of activated T cells 3 *** from this study suggest that Cav3.2 could be a promising target for treatment of cerebral ischemia/reperfusion injury.

关键词： calcineurin Cav3.2 channel cerebral ischemia/reperfusion hippocampus hypoxia/reoxygenation inflammatory response nuclear factor of activated T cells 3 oxidative stress primary hippocampal neurons stroke

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

Mechanism of Metabolic Dysfunction-associated Steatotic Liver Disease:Important role of lipid metabolism

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Journal of Clinical and Translational Hepatology 2024年第9期12卷 815-826页

作者： Xiaoxi Feng Rutong Zhang Zhenye Yang Kaiguang Zhang Jun Xing department of Digestive Disease The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina

Metabolic dysfunction-associated steatotic liver disease(MASLD),formerly known as non-alcoholic fatty liver disease,has a high global prevalence and can progress to metabolic dysfunction-associated steatohepatitis,cirrhosis,and hepatocellular *** pathogenesis of MASLD is primarily driven by disturbances in hepatic lipid metabolism,involving six key processes:increased hepatic fatty acid uptake,enhanced fatty acid synthesis,reduced oxidative degradation of fatty acids,increased cholesterol uptake,elevated cholesterol synthesis,and increased bile acid ***,maintaining hepatic lipid metabolic homeostasis is essential for effective MASLD *** novel molecules and Chinese proprietary medicines have demonstrated promising therapeutic potential in treating MASLD,primarily by inhibiting lipid synthesis and promoting lipid *** this review,we summarized recent research on MASLD,elucidated the molecular mechanisms by which lipid metabolism disorders contribute to MASLD pathogenesis,and discussed various lipid metabolism-targeted therapeutic approaches for MASLD.

关键词： MASLD Lipid metabolism Cholesterol metabolism Lipogenesis Lipolysis lipid metabolism-targeted drugs Chinese proprietary medicine

Density functional theory study of B- and Si-doped carbons and their adsorption interactions with sulfur compounds

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Carbon Energy 2024年第2期6卷 195-208页

作者： Peng Guo Hong Zhang Shuliang Dong Libao An College of Mechanical Engineering North China University of Science and TechnologyTangshanHebeiChina College of life sciences North China University of Science and TechnologyTangshanHebeiChina

Understanding the adsorption interactions between carbon materials and sulfur compounds has far-reaching impacts,in addition to their well-known important role in energy storage and conversion,such as lithium-ion *** this paper,properties of intrinsic B or Si single-atom doped,and B-Si codoped graphene(GR)and graphdiyne(GDY)were investigated by using density functional theory-based calculations,in which the optimal doping configurations were explored for potential applications in adsorbing sulfur *** showed that both B or Si single-atom doping and B-Si codoping could substantially enhance the electron transport properties of GR and GDY,improving their surface ***,B and Si atoms displayed synergistic effects for the codoped configurations,where B-Si codoped GR/GDY exhibited much better performance in the adsorption of sulfurcontaining chemicals than single-atom doped *** addition,results demonstrated that,after B-Si codoping,the adsorption energy and charge transfer amounts of GDY with sulfur compounds were much larger than those of GR,indicating that B-Si codoped GDY might be a favorable material for more effectively interacting with sulfur reagents.

关键词： adsorption density functional theory doping graphdiyne graphene sulfur compounds