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Matrix metalloproteinase 2 degrades collagen I to regulate ovarian development by association with an insulin-like peptide

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Insect Science 2024年第4期31卷 1090-1106页

作者： Yi Wei Xiao-Lin Zhou Peng Chen Tai-Hang Liu Cheng Lu Min-Hui Pan State Key laboratory of Silkworm Genome Biology Southwest UniversityChongqingChina Key laboratory for Sericulture functional genomics and Biotechnology of Agricultural Ministry Southwest UniversityChongqingChina Wenzhou Institute University of Chinese Academy of SciencesWenzhouZhejiang ProvinceChina

The ovary generally undergoes tissue remodeling during larval to pupal transition,which includes membrane degeneration and ovariole *** the same time,the hormones produced by insects significantly change during ***,the regulatory mechanism for ovarian development and hormones is not fully understood in ***,we found that matrix metalloproteinase 2(MMP2)was highly expressed in the ovarian capsules and ovarioles,and the development was abnormal after knocking out MMP2 in Bombyx *** process of abnormal degradation of collagen I due to MMP2 deletion,which resulted in abnormal development of ovarioles and eggs,was analyzed in *** proteomics of ovaries in the MMP2-knock out and wild type strains showed a critically significant difference in the expression of a protein,insulin-like peptide(ILP).Additional analysis revealed significant alteration of ILP during ovarian development,and abnormal expression of ILP significantly affected ovarian development in vivo and MMP2 expression in vitro and in *** results showed that MMP2 regulation of ovarian tissue remodeling is closely related to ILP *** study provides new insights into the regulatory mechanism of MMP2 and ovarian development in ***.

关键词： Bombyx mori collagen I insulin-like peptide matrix metalloproteinase ovarian development

BSAlign:A Library for Nucleotide Sequence Alignment

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genomics, proteomics & Bioinformatics 2024年第2期22卷 135-142页

作者： Haojing Shao Jue Ruan Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China

Increasing the accuracy of the nucleotide sequence alignment is an essential issue in genomics *** classic dynamic programming(DP)algorithms(e.g.,Smith–Waterman and Needleman–Wunsch)guarantee to produce the optimal result,their time complexity hinders the application of large-scale sequence *** optimization efforts that aim to accelerate the alignment process generally come from three perspectives:redesigning data structures[e.g.,diagonal or striped Single Instruction Multiple Data(SIMD)implementations],increasing the number of parallelisms in SIMD operations(e.g.,difference recurrence relation),or reducing search space(e.g.,banded DP).However,no methods combine all these three aspects to build an ultra-fast *** this study,we developed a Banded Striped Aligner(BSAlign)library that delivers accurate alignment results at an ultra-fast speed by knitting a series of novel methods together to take advantage of all of the aforementioned three perspectives with highlights such as active F-loop in striped vectorization and striped move in banded *** applied our new acceleration design on both regular and edit distance pairwise *** achieved 2-fold speed-up than other SIMD-based implementations for regular pairwise alignment,and 1.5-fold to 4-fold speed-up in edit distance-based implementations for long *** is implemented in C programing language and is available at https://***/ruanjue/bsalign.

关键词： Pairwise alignment Edit distance Striped vectorization Banded dynamic programming F evaluation

A Pt/CeO_(2)Hybrid Nanozyme with Stable Peroxidase Activity for the Detection of Acetylcholine

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Chemical Research in Chinese Universities 2024年第2期40卷 268-271页

作者： CUI Xulian MA Baofu PAN Hui XIA Yu LIU Li ZHAO Baofeng LIANG Zhen ZHANG Lihua ZHANG Yukui State Key laboratory of Medical proteomics Dalian Institute of Chemical PhysicsChinese Academy of ScienceDalian116023P.R.China The Research Center for Medical genomics Key Laboratory of Medical Cell BiologyMinistry of EducationSchool of Life ScienceChina Medical UniversityShenyang110001P.R.China River Fisheries Research Institute Chinese Academy of Fishery SciencesGuangzhou510000P.R.China

Acetylcholine(ACh)is a common neurotransmitterl)that is secreted by cholinergic neurons[2]and is found mainly in the peripheral and central nervous systems.[3]ACh transmits nerve signals from presynaptic to postsynapt... 详细信息

关键词： Acetylcholine/choline Nanozyme Hydrogen peroxide Alzheimer’s disease

Hypoxia-inducible factor-1αin myocardial infarction

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World Journal of Cardiology 2024年第4期16卷 181-185页

作者： IvanaŠkrlec Sergey N Kolomeichuk Faculty of Dental Medicine and Health Josip Juraj Strossmayer University of OsijekOsijek 31000Croatia Institute of Biology Karelia Research Center of Russian Academy of SciencesPetrozavodsk 185910Russia laboratory for genomics Proteomicsand MetabolomicsResearch Institute of Biomedicine and Biomedical TechnologiesTyumen State Medical UniversityTyumen 625023Russia

Hypoxia-inducible factor 1(HIF1)has a crucial function in the regulation of oxygen levels in mammalian cells,especially under hypoxic *** importance in cardiovascular diseases,particularly in cardiac ischemia,is because of its ability to alleviate cardiac *** oxygen-responsive subunit,HIF1α,plays a crucial role in this process,as it has been shown to have cardioprotective effects in myocardial infarction through regulating the expression of genes affecting cellular survival,angiogenesis,and ***,HIF1αexpression induced reperfusion in the ischemic skeletal muscle,and hypoxic skin wounds in diabetic animal models showed reduced HIF1α*** expression of HIF1αhas been shown to reduce apoptosis and oxidative stress in cardiomyocytes during acute myocardial *** variations in HIF1αhave also been found to correlate with altered responses to ischemic cardiovascular *** addition,a link has been established between the circadian rhythm and hypoxic molecular signaling pathways,with HIF1αfunctioning as an oxygen sensor and circadian genes such as period circadian regulator 2 responding to changes in *** editorial analyzes the relationship between HIF1αand the circadian rhythm and highlights its significance in myocardial adaptation to *** the changes in molecular signaling pathways associated with diseases,specifically cardiovascular diseases,provides the opportunity for innovative therapeutic interventions,especially in low-oxygen environments such as myocardial infarction.

关键词： Cardiovascular pathologies Circadian genes Hypoxia-inducible factor 1 Hypoxia Gene-gene interaction

Genetic mapping of plasma proteome on brain structure

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Journal of Genetics and genomics 2024年第7期51卷 774-777页

作者： Shengyi Ma Fengzhe Xu Yuanqing Fu Ju-Sheng Zheng Fudan University Shanghai 200433China School of Life Sciences Westlake UniversityHangzhouZhejiang 310030China Westlake Center for Intelligent proteomics Westlake Laboratory of Life Sciences and BiomedicineHangzhouZhejiang 310030China

The emergence of high-throughput techniques for proteomics measurement has led to an increasing number of proteogenomic studies that aim to reveal protein quantitative trait loci(pQTL)based on large cohorts(Suhre et a... 详细信息

关键词： mapping structure throughput

Cross-sectional network analysis of plasma proteins/metabolites correlated with pathogenesis and therapeutic response in acute promyelocytic leukemia

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Frontiers of Medicine 2024年第2期18卷 327-343页

作者： Niu Qiao Yizhu Lyu Feng Liu Yuliang Zhang Xiaolin Ma Xiaojing Lin Junyu Wang Yinyin Xie Ruihong Zhang Jing Qiao Hongming Zhu Li Chen Hai Fang Tong Yin Zhu Chen Qiang Tian Saijuan Chen Shanghai Institute of Hematology State Key Laboratory of Medical GenomicsNational Research Center for Translational Medicine at ShanghaiRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai200025China Department of Hematology Second Hospital of Dalian Medical UniversityDalian116021China

The treatment of PML/RARA+acute promyelocytic leukemia(APL)with all-trans-retinoic acid and arsenic trioxide(ATRA/ATO)has been recognized as a model for translational medicine *** an altered microenvironment is a general cancer hallmark,how APL blasts shape their plasma composition is poorly ***,we reported a cross-sectional correlation network to interpret multilayered datasets on clinical parameters,proteomes,and metabolomes of paired plasma samples from patients with APL before or after ATRA/ATO induction *** study revealed the two prominent features of the APL plasma,suggesting a possible involvement of APL blasts in modulating plasma *** was characterized by altered secretory protein and metabolite profiles correlating with heightened proliferation and energy consumption in APL blasts,and the other featured APL plasma-enriched proteins or enzymes catalyzing plasma-altered metabolites that were potential trans-regulatory targets of PML/***,results indicated heightened interferon-gamma signaling characterizing a tumor-suppressing function of the immune system at the first hematological complete remission stage,which likely resulted from therapy-induced cell death or senescence and ensuing supraphysiological levels of intracellular ***,our work sheds new light on the pathophysiology and treatment of APL and provides an information-rich reference data cohort for the exploratory and translational study of leukemia microenvironment.

关键词： acute promyelocytic leukemia plasma proteomics plasma metabolomics cross-sectional correlation network pathogenesis treatment

CpG Island Definition and Methylation Mapping of the T2T-YAO Genome

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genomics, proteomics & Bioinformatics 2024年第2期22卷 69-79页

作者： Ming Xiao Rui Wei Jun Yu Chujie Gao Fengyi Yang Le Zhang College of Computer Science Sichuan UniversityChengdu 610065China Key laboratory of Systems Health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China CAS Key laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Precisely defining and mapping all cytosine(C)positions and their clusters,known as CpG islands(CGIs),as well as their methylation status,are pivotal for genome-wide epigenetic studies,especially when population-centric reference genomes are ready for timely ***,we first align the two high-quality reference genomes,T2T-YAO and T2T-CHM13,from different ethnic backgrounds in a base-by-base fashion and compute their genome-wide density-defined and position-defined ***,by mapping some representative genome-wide methylation data from selected organs onto the two genomes,we find that there are about 4.7%–5.8%sequence divergency of variable categories depending on quality *** among the divergent sequences are mostly associated with neurological ***,CGIs associated with the divergent sequences are significantly different with respect to CpG density and observed CpG/expected CpG(O/E)ratio between the two ***,we find that the T2T-YAO genome not only has a greater CpG coverage than that of the T2T-CHM13 genome when whole-genome bisulfite sequencing(WGBS)data from the European and American populations are mapped to each reference,but also shows more hyper-methylated CpG sites as compared to the T2T-CHM13 *** study suggests that future genome-wide epigenetic studies of the Chinese populations rely on both acquisition of high-quality methylation data and subsequent precision CGI mapping based on the Chinese T2T reference.

关键词： T2T-YAO Position-defined CpG island Density-defined CpG island DNA methylation Genome analysis

CRL2^(APPBP2)-mediated TSPYL2 degradation counteracts human mesenchymal stem cell senescence

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Science China(Life Sciences) 2024年第3期67卷 460-474页

作者： Daoyuan Huang Qian Zhao Kuan Yang Jinghui Lei Ying Jing Hongyu Li Chen Zhang Shuai Ma Shuhui Sun Yusheng Cai Guibin Wang Jing Qu Weiqi Zhang Si Wang Guang-Hui Liu Advanced Innovation Centerfor Human Brain Protection National Clinical Research Centerfor Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China State Key laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Aging Translational MedicineCenter International Centerfor Aging and CancerBejing Municipal GeriatricMedical Research CenterXuanwu HospitalCapital Medical UniversityBeijing 100053China State Key laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Beijing Institute for Stem Cell and Regenerative Medicine Beijing100101China CAS Key laboratory of Genomic and Precision Medicine Bejing Institute of Genomics and China National Center for BioinformationChinese Academy of SciencesBeijing 100101China Institute for Stem Cell and Regeneration CASBeijing 100101China The Fifth People's Hospital of Chongqing Chongqing 400062China Sino-Danish Cllege University of Chinese Academy of SciencesBeijing101408China National laboratory of Biomacromolecules CAS Center for Excelence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China State Key laboratory of proteomics Beijing Proteome Research CenterNational Center for Protein Sciences(Beijing)Beijing Institute of LifeomicsBeijing 102206China

Cullin-RING E3 ubiquitin ligases(CRLs),the largest family of multi-subunit E3 ubiquitin ligases in eukaryotic cells,represent core cellular machinery for executing protein degradation and maintaining ***,we asked what roles Cullin proteins play in human mesenchymal stem cell(hMSC)homeostasis and *** this end,we conducted a comparative aging phenotype analysis by individually knocking down Cullin members in three senescence models:replicative senescent hMSCs,Hutchinson-Gilford Progeria Syndrome hMSCs,and Werner syndrome *** all family members,we found that CUL2 deficiency rendered hMSCs the most susceptible to *** investigate CUL2-specific underlying mechanisms,we then applied CRISPR/Cas9-mediated gene editing technology to generate CUL2-deficient human embryonic stem cells(hESCs).When we differentiated these into h MSCs,we found that CUL2 deletion markedly accelerates hMSC ***,we identified that CUL2 targets and promotes ubiquitin proteasome-mediated degradation of TSPYL2(a known negative regulator of proliferation)through the substrate receptor protein APPBP2,which in turn downregulates one of the canonical aging marker-P21^(waf1/cip1),and thereby delays *** work provides important insights into how CRL2^(APPBP2)-mediated TSPYL2 degradation counteracts hMSC senescence,providing a molecular basis for directing intervention strategies against aging and aging-related diseases.

关键词： Cullins stem cell senescence aging proteostasis ubiquitination APPBP2 TSPYL2

GametesOmics:A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice

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genomics, proteomics & Bioinformatics 2024年第1期22卷 121-130页

作者： Jianting An Jing Wang Siming Kong Shi Song Wei Chen Peng Yuan Qilong He Yidong Chen Ye Li Yi Yang Wei Wang Rong Li Liying Yan Zhiqiang Yan Jie Qiao State Key laboratory of Female Fertility Promotion Center for Reproductive MedicineDepartment of Obstetrics and GynecologyPeking University Third HospitalBeijing 100191China National Clinical Research Center for Obstetrics and Gynecology Peking University Third HospitalBeijing 100191China Key laboratory of Assisted Reproduction Ministry of EducationPeking UniversityBeijing 100191China Beijing Key laboratory of Reproductive Endocrinology and Assisted Reproductive Technology Beijing 100191China Peking-Tsinghua Center for Life Sciences Peking UniversityBeijing 100871China Beijing Advanced Innovation Center for genomics Beijing 100191China

Gametogenesis plays an important role in the reproduction and evolution of *** transcriptomic and epigenetic alterations in this process can influence the reproductive capacity,fertilization,and embryonic *** rapidly increasing single-cell studies have provided valuable multi-omics ***,data from different layers and sequencing platforms have not been uniformed and integrated,which greatly limits their use for exploring the molecular mechanisms that underlie oogenesis and ***,we develop GametesOmics,a comprehensive database that integrates the data of gene expression,DNA methylation,and chromatin accessibility during oogenesis and spermatogenesis in humans and *** provides a user-friendly website and various tools,including Search and Advanced Search for querying the expression and epigenetic modification(s)of each gene;Tools with Differentially expressed gene(DEG)analysis for identifying DEGs,Correlation analysis for demonstrating the genetic and epigenetic changes,Visualization for displaying single-cell clusters and screening marker genes as well as master transcription factors(TFs),and MethylView for studying the genomic distribution of epigenetic *** also provides Genome Browser and Ortholog for tracking and comparing gene expression,DNA methylation,and chromatin accessibility between humans and *** offers a comprehensive resource for biologists and clinicians to decipher the cell fate transition in germ cell development,and can be accessed at http://***/.

关键词： Gametogenesis Oogenesis Spermatogenesis Transcriptomics Epigenomics