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Inhibition mechanisms of CRISPR-Cas9 by AcrⅡA25.1 and AcrⅡA32

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Science China(life sciences) 2024年第9期67卷 1781-1791页

作者： Jianlin Zheng Yuwei Zhu Tengjin Huang Wenbo Gao Jiale He Zhiwei Huang HIT Center for life sciences School of Life Science and TechnologyHarbin Institute of TechnologyHarbin 150080China Westlake Center for Genome Editing Westlake Laboratory of Life Sciences and BiomedicineSchool of Life SciencesWestlake UniversityHangzhou 310024China

In the ongoing arms race between bacteria and bacteriophages,bacteriophages have evolved anti-CRISPR proteins to counteract bacterial CRISPR-Cas ***,AcrⅡA25.1 and AcrⅡA32 have been found to effectively inhibit the activity of Spy Cas9 both in bacterial and human ***,their molecular mechanisms remain ***,we report the cryo-electron microscopy structures of ternary complexes formed by AcrⅡA25.1 and AcrⅡA32 bound to Spy Cas9-sg *** structural analysis and biochemical experiments,we revealed that AcrⅡA25.1 and AcrⅡA32 recognize a novel,previously-unidentified anti-CRISPR binding site on Spy *** found that both AcrⅡA25.1 and AcrⅡA32 directly interact with the WED domain,where they spatially obstruct conformational changes of the WED and PI domains,thereby inhibiting Spy Cas9 from recognizing protospacer adjacent motif(PAM)and unwinding double-stranded *** addition,they may inhibit nuclease activity by blocking the dynamic conformational changes of the Spy Cas9 surveillance *** summary,our data elucidate the inhibition mechanisms of two new anti-CRISPR proteins,provide new strategies for the modulation of Spy Cas9 activity,and expand our understanding of the diversity of anti-CRISPR protein inhibition mechanisms.

关键词： anti-CRISPR cryo-EM Spy Cas9 AcrⅡA25.1 AcrⅡA32 inhibiton

The pathogenesis of Parkinson’s disease and crosstalk with other diseases

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BIOCELL 2024年第8期48卷 1155-1179页

作者： TINGTING LIU DINGYOU GUO JIANSHE WEI institute for Brain sciences Research School of Life SciencesHenan UniversityKaifeng475004China

In China,Parkinson’s disease(PD)is the second most prevalent central nervous system(CNS)degenerative illness affecting middle-aged and older *** disorders including resting tremor,bradykinesia,myotonia,postural instability,and gait instability are the predominant clinical *** two main types of PD are sporadic and familial,with sporadic PD being the more prevalent of the *** environment,genetics,mitochondrial dysfunction,oxidative stress,inflammation,protein aggregation and misfolding,loss of trophic factors,cell death,and gut microbiota may all have a role in the etiology of *** is inversely connected with other cancers and positively correlated with COVID-19,diabetes mellitus(DM),melanoma,and ischemic heart disease(IHD)*** disease progression,managing motor and non-motor symptoms,and avoiding and controlling dysfunction in the middle and later phases of the disease are the key areas of research and development for its ***,the development and progression of PD can be slowed down by using conventional pharmacology,natural items,and innovative *** article reviews the pathogenesis of PD,its correlations with other non-genetic diseases,and the research progress of drugs and technologies for alleviating PD.

关键词： Parkinson’s disease Mitochondrial dysfunction Oxidative stress Inflammation Cancer Therapies

Early response of understory vegetation to the mass dieback of Norway spruce in the European lowland temperate forest

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Forest Ecosystems 2024年第2期11卷 214-225页

作者： Jan Marek Matuszkiewicz Andrzej N.Affek Piotr Zaniewski Ewa Kołaczkowska Faculty of Geography and Regional Studies University of WarsawPoland institute of Geography and Spatial Organization Polish Academy of SciencesPoland institute of Forest sciences Warsaw University of Life SciencesPoland

Spruce-dominated forests are commonly exposed to disturbances associated with mass occurrences of bark *** dieback of trees triggers many physical and chemical processes in the ecosystem resulting in rapid changes in the vegetation of the lower forest *** aimed to determine the response of non-tree understory vegetation to the mass dieback of Norway spruce(Picea abies)in the first years after the disturbance caused by the European spruce bark beetle(Ips typographus)*** study area was the Białowieża Biosphere Reserve covering the Polish part of the emblematic Białowieża Forest,in total 597km^(2).The main data source comprised 3,900 phytosociological relevés(combined spring and summer campaigns)collected from 1,300 systematically distributed forest sites in 2016–2018–the peak years of the bark beetle *** found that the understory responded immediately to mass spruce dieback,with the most pronounced changes observed in the year of the disturbance and the subsequent ***-tolerant forest species declined in the initial years following the mass spruce dieback,while hemicryptophytes,therophytes,light-demanding species associated with non-forest seminatural communities,as well as water-demanding forest species,*** acetosella,the most common understory species in the Białowieża Forest,showed a distinct fluctuation pattern,with strong short-term expansion right after spruce dieback,followed by a gradual decline over the next 3–4 years to a cover level 5 percentage points lower than before the ***,our study revealed that mass spruce dieback selectively affects individual herb species,and their responses can be directional and non-directional(fluctuation).Furthermore,we demonstrated that the mass dieback of spruce temporarily increases plant species diversity(α-diversity).

关键词： Forest disturbance Bark beetle outbreak Picea abies Ips typographus Response of understory vegetation Herbaceous species Biaowieza Forest

Multi-region calcium imaging in freely behaving mice with ultra-compact head-mounted fluorescence microscopes

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National Science Review 2024年第1期11卷 161-173页

作者： Feng Xue Fei Li Ke-ming Zhang Lufeng Ding Yang Wang Xingtao Zhao Fang Xu Danke Zhang Mingzhai Sun Pak-Ming Lau Qingyuan Zhu Pengcheng Zhou Guo-Qiang Bi Department of Precision Machinery and Precision Instruments University of Science and Technology of China Hefei National Laboratory for Physical sciences at the Microscale University of Science and Technology of China Interdisciplinary Center for Brain Information the Brain Cognition and Brain Disease Institute Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Faculty of life and Health sciences Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences School of life sciences University of Science and Technology of China institute of Semiconductors Chinese Academy of Sciences Department of Modern life sciences and Biotecnology Xiongan Institute of Innovation Xiongan New Area Shenzhen-Hong Kong institute of Brain Science-Shenzhen Fundamental Research Institutions Suzhou institute for Advanced Research University of Science and Technology of China institute of Artiflcial Intelligence Hefei Comprehensive National Science Center

To investigate the circuit-level neural mechanisms of behavior, simultaneous imaging of neuronal activity in multiple cortical and subcortical regions is highly desired. Miniature head-mounted microscopes offer the capability of calcium imaging in freely behaving animals. However, implanting multiple microscopes on a mouse brain remains challenging due to space constraints and the cumbersome weight of the ***, we present TINIscope, a Tightly Integrated Neuronal Imaging microscope optimized for electronic and opto-mechanical design. With its compact and lightweight design of 0.43 g, TINIscope enables unprecedented simultaneous imaging of behavior-relevant activity in up to four brain regions in ***-of-concept experiments with TINIscope recorded over 1000 neurons in four hippocampal subregions and revealed concurrent activity patterns spanning across these regions. Moreover, we explored potential multi-modal experimental designs by integrating additional modules for optogenetics, electrical stimulation or local field potential recordings. Overall, TINIscope represents a timely and indispensable tool for studying the brain-wide interregional coordination that underlies unrestrained behaviors.

关键词： miniature microscope multiple sites calcium imaging multimodal integration hippocampus

Shallow sub-lakes are essential for sustaining the successful wintering of waterbirds in Poyang Lake,China

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Avian Research 2024年第2期15卷 219-228页

作者： Mengjie Lu Zhen Zhang Peng Chen Changxin Xu Bin Gao Luzhang Ruan School of life sciences Nanchang UniversityNanchang330031China Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity Center for Watershed EcologyInstitute of Life Science and School of Life SciencesNanchang UniversityNanchang330031China

For migratory waterbirds,the quality of wintering habitat is related to spring migration and successful breeding in the next *** availability of food resources in the habitat is critical and varies within water *** the water-level fluctuations in Poyang Lake have been extremely variable interannually in recent years,the wintering waterbird populations have remained relatively ***,the mechanism of maintaining the stability is worth *** study aimed to compare the distribution of vegetation and herbivorous wa-terbirds in 2015-2016 and 2016-2017,focusing on three shallow sub-lakes and one main lake *** results showed that the emergence of tubers and the growth of Carex *** a continuous food supply and habitat for wintering waterbirds with a gradual decline in the water *** sub-lakes supported almost all of the tuber-eating waterbirds(1.42-1.62×10^(5))and most geese(1.34-1.53×10^(6)).However,the main lake area,covered with Persicaria hydropiper,did not provide adequate and accessible *** resulted in almost no distribution of tuber-eating waterbirds,with only a few geese congregating in early *** results demonstrated that the shallow sub-lakes under human control provided a different environment from the main lake and are key to sustaining the successful wintering of hundreds of thousands of migratory waterbirds in Poyang ***,we recommend refining the anthropogenic management of the shallow sub-lakes to regulate the water level to ensure the carrying capacity of Poyang Lake.

关键词： Anthropogenic management Carrying capacity Seasonal lake Water level Wintering habitat

Rice ONAC016 promotes leaf senescence through abscisic acid signaling pathway involving OsNAP

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The Crop Journal 2024年第3期12卷 709-720页

作者： Eunji Gi Sung-Hwan Cho Suk-Hwan Kim Kiyoon Kang Nam-Chon Paek Department of Agriculture Forestry and BioresourcesPlant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea Division of life sciences Incheon National UniversityIncheon 22012Republic of Korea

Senescence-induced NAC(senNAC)TFs play a crucial role in senescence during the final stage of leaf *** this study,we identified a rice senNAC,ONAC016,which functions as a positive regulator of leaf *** expression of ONAC016 increased rapidly in rice leaves during the progression of dark-induced and natural *** onac016-1 knockout mutant showed a delayed leaf yellowing phenotype,whereas the overexpression of ONAC016 accelerated leaf ***,ONAC016 expression was upregulated by abscisic acid(ABA),and thus detached leaves of the onac016-1 mutant remained green much longer under ABA *** RT-PCR analysis showed that ONAC016 upregulates the genes associated with chlorophyll degradation,senescence,and ABA *** one-hybrid and dual-luciferase assays revealed that ONAC016 binds directly to the promoter regions of OsNAP,a key gene involved in chlorophyll degradation and ABA-induced *** together,these results suggest that ONAC016 plays an important role in promoting leaf senescence through the ABA signaling pathway involving OsNAP.

关键词： Rice ONAC016 OsNAP Leaf senescence Abscisic acid signaling

The RNA m^(6)A demethylase ALKBH5 drives emergency granulopoiesis and neutrophil mobilization by upregulating G-CSFR expression

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Cellular & Molecular Immunology 2024年第1期21卷 6-18页

作者： Yang Liu Renjie Song Zhike Lu Lu Zhao Xinyi Zhan Yini Li Xuetao Cao Department of Immunology Center for ImmunotherapyInstitute of Basic Medical SciencesPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina Suzhou institute of Systems Medicine Chinese Academy of Medical SciencesSuzhouChina Frontier Research Center for Cell Response Institute of ImmunologyCollege of Life SciencesNankai UniversityTianjinChina School of life sciences Westlake UniversityHangzhouChina

Emergency granulopoiesis and neutrophil mobilization that can be triggered by granulocyte colony-stimulating factor(G-CSF)through its receptor G-CSFR are essential for antibacterial innate ***,the epigenetic modifiers crucial for intrinsically regulating G-CSFR expression and the antibacterial response of neutrophils remain largely unclear.N6-methyladenosine(m^(6)A)RNA modification and the related demethylase alkB homolog 5(ALKBH5)are key epigenetic regulators of immunity and inflammation,but their roles in neutrophil production and mobilization are still *** used cecal ligation and puncture(CLP)-induced polymicrobial sepsis to model systemic bacterial infection,and we report that ALKBH5 is required for emergency granulopoiesis and neutrophil ***5 depletion significantly impaired the production of immature neutrophils in the bone marrow of septic *** addition,Alkbh5-deficient septic mice exhibited higher retention of mature neutrophils in the bone marrow and defective neutrophil release into the circulation,which led to fewer neutrophils at the infection site than in their wild-type *** bacterial infection,ALKBH5 imprinted production-and mobilization-promoting transcriptome signatures in both mouse and human ***,ALKBH5 erased m^(6)A methylation on the CSF3R mRNA to increase the mRNA stability and protein expression of G-CSFR,consequently upregulating cell surface G-CSFR expression and downstream STAT3 signaling in *** RIP-qPCR results confirmed the direct binding of ALKBH5 to the CSF3R mRNA,and the binding strength declined upon bacterial infection,accounting for the decrease in G-CSFR expression on bacteria-infected *** these results collectively,we define a new role of ALKBH5 in intrinsically driving neutrophil production and mobilization through m^(6)A demethylation-dependent posttranscriptional regulation,indicating that m^(6)A RNA modification in neutrop

关键词： Emergency granulopoiesis Neutrophil mobilization ALKBH5 m^(6)A RNA modification G-CSF receptor

A zebrafish tufm mutant model for the COXPD4 syndrome of aberrant mitochondrial function

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Journal of Genetics and Genomics 2024年第9期51卷 922-933页

作者： Ting Li Tursunjan Aziz Guangyuan Li Lin Zhang Jihua Yao Shunji Jia School of life sciences Fudan UniversityShanghai 200438China State Key Laboratory of Membrane Biology Tsinghua-Peking Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing 100084China State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

Mitochondrial dysfunction is a critical factor leading to a wide range of clinically heterogeneous and often severe disorders due to its central role in generating cellular *** in the TUFM gene are known to cause combined oxidative phosphorylation deficiency 4(COXPD4),a rare mitochondrial disorder characterized by a comprehensive quantitative deficiency in mitochondrial respiratory chain(MRC)*** development of a reliable animal model for COXPD4 is crucial for elucidating the roles and mechanisms of TUFM in disease pathogenesis and benefiting its medical *** this study,we construct a zebrafish tufm−/−mutant that closely resembles the COXPD4 syndrome,exhibiting compromised mitochondrial protein translation,dysfunctional mitochondria with oxidative phosphorylation defects,and significant metabolic suppression of the tricarboxylic acid *** this COXPD4 zebrafish model,we comprehensively validate the clinical relevance of TUFM mutations and identify probucol as a promising therapeutic approach for managing *** data offer valuable insights for understanding mitochondrial diseases and developing effective treatments.

关键词： Tufm Mitochondria COXPD4 Disease model Zebrafish

Design of antiviral AGO2-dependent short hairpin RNAs

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Virologica Sinica 2024年第4期39卷 645-654页

作者： Yuanyuan Bie Jieling Zhang Jiyao Chen Yumin Zhang Muhan Huang Leike Zhang Xi Zhou Yang Qiu Key Laboratory of Virology and Biosafety Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China State Key Laboratory of Virology Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China University of Chinese Academy of sciences Beijing 100049China School of life sciences Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230027China

The increasing emergence and re-emergence of RNA virus outbreaks underlines the urgent need to develop effective *** interference(RNAi)is a sequence-specific gene silencing mechanism that is triggered by small interfering RNAs(siRNAs)or short hairpin RNAs(shRNAs),which exhibits significant promise for antiviral ***2-dependent shRNA(agshRNA)generates a single-stranded guide RNA and presents significant advantages over traditional siRNA and *** this study,we applied a logistic regression algorithm to a previously published chemically siRNA efficacy dataset and built a machine learning-based model with high predictive *** this model,we designed siRNA sequences targeting diverse RNA viruses,including human enterovirus A71(EV71),Zika virus(ZIKV),dengue virus 2(DENV2),mouse hepatitis virus(MHV)and severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),and transformed them into *** validated the performance of our agshRNA design by evaluating antiviral efficacies of agshRNAs in cells infected with different *** the agshRNA targeting EV71 as an example,we showed that the anti-EV71 effect of agshRNA was more potent compared with the corresponding siRNA and ***,the antiviral effect of agshRNA is dependent on AGO2-processed guide RNA,which can load into the RNA-induced silencing complex(RISC).We also confirmed the antiviral effect of agshRNA in ***,this work develops a novel antiviral strategy that combines machine learning-based algorithm with agshRNA design to custom design antiviral agshRNAs with high efficiency.

关键词： AgshRNA Antiviral strategy Machine learning model