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JunB condensation attenuates vascular endothelial damage under hyperglycemic condition

Journal of Molecular Cell Biology 2023年第12期15卷 34-49页

作者： Xuxia Ren Zexu Cui Qiaoqiao Zhang Zhiguang Su Wei Xu Jinhui Wu Hao Jiang Laboratory for Aging and Cancer Research Frontiers Science Center Disease-related Molecular NetworkState Key Laboratory of Respiratory Health and Multimorbidity and National Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengdu 610041China Key Laboratory of Gene Engineering of the Ministry of Education State Key Laboratory of BiocontrolSchool of Life SciencesSun Yat-sen UniversityGuangzhou 510275China Molecular Medicine Research Center West China HospitalSichuan UniversityChengdu 610041China Center of Geriatrics and Gerontology National Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengdu 610041China

Endothelial damage is the initial and crucial factor in the occurrence and development of vascular complications in diabetic patients,contributing to morbidity and *** hyperglycemia has been identified as a damaging effector,the detailed mechanisms remain *** this study,identified by ATAC-seq and RNA-seq,JunB reverses the inhibition of proliferation and the promotion of apoptosis in human umbilical vein endothelial cells treated with high glucose,mainly through the cell cycle and p53 signaling ***,JunB undergoes phase separation in the nucleus and in vitro,mediated by its intrinsic disordered region and DNA-binding *** localization and condensation behaviors are required for JunB-mediated proliferation and ***,our study uncovers the roles of JunB and its coacervation in repairing vascular endothelial damage caused by high glucose,elucidating the involvement of phase separation in diabetes and diabetic endothelial dysfunction.

关键词： hyperglycemia JunB phase separation endothelial damage

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Insight into the microbial community of denitrification process using different solid carbon sources: Not only bacteria

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Journal of Environmental Sciences 2024年第10期144卷 87-99页

作者： Congyu Li Yu Ling Yanjie Zhang Haiyan Wang Huan Wang Guokai Yan Weiyang Dong Yang Chang Liang Duan State Key Laboratory of Environmental Criteria and Risk Assessment Chinese Research Academy of Environmental SciencesBeijing 100012China College of Environmental Science and Engineering Tongji UniversityShanghai 200092China College of Water Sciences Beijing Normal UniversityBeijing 100875China Research Center of Environmental Pollution Control Technology Chinese Research Academy of Environmental ScienceBeijing 100012China State Environmental Protection Key Laboratory of Estuarine and Coastal Environment Chinese Research Academy of Environmental SciencesBeijing 100012China

There is a lack of understanding about the bacterial,fungal and archaeal communities’composition of solid-phase denitrification(SPD)*** investigated four SPD systems with different carbon sources by analyzing microbial gene sequences based on operational taxonomic unit(OTU)and amplicon sequence variant(ASV).The results showed that the corncob-polyvinyl alcohol sodium alginate-polycaprolactone(CPSP,0.86±0.04 mg NO_(3)^(−)-N/(g·day))and corncob(0.85±0.06 mg NO_(3)^(−)-N/(g·day))had better denitrification efficiency than polycaprolactone(PCL,0.29±0.11 mg NO_(3)^(−)-N/(g·day))and polyvinyl alcoholsodium alginate(PVA-SA,0.24±0.07 mg NO_(3)^(−)-N/(g·day)).The bacterial,fungal and archaeal microbial composition was significantly different among carbon source types such as Proteobacteria in PCL(OTU:83.72%,ASV:82.49%)and Rozellomycota in PVA-SA(OTU:71.99%,ASV:81.30%).ASV methods can read more microbial units than that of OTU and exhibit higher alpha diversity and classify some species that had not been identified by OTU such as Nanoarchaeota phylum,unclassified_f_Xanthobacteraceae genus,etc.,indicating ASV may be more conducive to understand SPD microbial *** co-occurring network showed some correlation between the bacteria fungi and archaea species,indicating different species may collaborate in SPD *** KEGG function prediction results were obtained in two bioinformatic methods generally and some fungi and archaea functions should not be ignored in SPD *** results may be beneficial for understanding microbial communities in SPD systems.

关键词： Solid-phase denitrification Solid carbon source Microbial community ASV analysis OTU analysis

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genes controlling grain chalkiness in rice

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The Crop Journal 2024年第4期12卷 979-991页

作者： Luo Chen Xiumei Li Minhua Zheng Rui Hu Jingfang Dong Lingyan Zhou Wuge Liu Dilin Liu Wu Yang Rice Research Institute Guangdong Academy of Agricultural SciencesGuangdong Key Laboratory of New Technology in Rice BreedingGuangdong Rice Engineering LaboratoryKey Laboratory of Genetics and Breeding of High Quality Rice in Southern China(Co-construction by Ministry and Province)Ministry of Agriculture and Rural AffairsGuangzhou 510640GuangdongChina College of Agriculture and Biology Zhongkai University of Agriculture and EngineeringGuangzhou 510225GuangdongChina Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization Agro-biological Gene Research CenterGuangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina

With rising living standards,there is an increasing demand for high-quality *** quality is mainly defined by milling quality,appearance quality,cooking and eating quality,and nutrition *** them,chalkiness is a key trait for appearance quality,which adversely affects cooking and eating quality,head rice yield,and commercial ***,chalkiness is undesirable,and reducing chalkiness is a major goal in rice quality ***,chalkiness is a complex trait jointly influenced by genetic and environmental factors,making its genetic study and precision improvement a huge *** the rapid development of molecular techniques,much knowledge has been gained about the genes and molecular networks involved in chalkiness *** present review describes the major environmental factors affecting chalkiness and summarizes the quantitative trait loci(QTL)associated with *** than 150 genes related to chalkiness formation have been *** functions of the genes regulating chalkiness,primarily those involved in starch synthesis,storage protein synthesis,transcription regulation,organelle development,grain shape regulation,and hightemperature response,are ***,we identify the challenges associated with genetic improvement of chalkiness and suggest potential ***,the review offers insight into the molecular dynamics of chalkiness and provides a strong basis for the future breeding of high-quality rice varieties.

关键词： Rice Grain quality Chalkiness QTL identification gene

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Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet

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Journal of Animal Science and Biotechnology 2024年第4期15卷 1494-1511页

作者： Guangliang Gao Rui Liu Silu Hu Mengnan He Jiaman Zhang Dengfeng Gao Jing Li Jiwei Hu Jiwen Wang Qigui Wang Mingzhou Li Long Jin Livestock and Poultry Multi‑Omics Key Laboratory of Ministry of Agriculture and Rural Affairs College of Animal Science and TechnologySichuan Agricultural UniversityChengdu 611130China Chongqing Engineering Research Center of Goose Genetic Improvement Institute of Poultry ScienceChongqing Academy of Animal SciencesRongchang DistrictChongqing 402460China

Background Goose, descendants of migratory ancestors, have undergone extensive selective breeding, resulting in their remarkable ability to accumulate fat in the liver and exhibit a high tolerance for significant energy intake. As a result, goose offers an excellent model for studying obesity, metabolic disorders, and liver diseases in mammals. Although the impact of the three-dimensional arrangement of chromatin within the cell nucleus on gene expression and transcriptional regulation is widely acknowledged, the precise functions of chromatin architecture reorganization during fat deposition in goose liver tissues still need to be fully *** In this study, geese exhibited more pronounced changes in the liver index and triglyceride(TG) content following the consumption of the high-fat diet(HFD) than mice without significant signs of inflammation. Additionally, we performed comprehensive analyses on 10 goose liver tissues(5 HFD, 5 normal), including generating highresolution maps of chromatin architecture, conducting whole-genome gene expression profiling, and identifying H3K27ac peaks in the livers of geese and mice subjected to the HFD. Our results unveiled a multiscale restructuring of chromatin architecture, encompassing Compartment A/B, topologically associated domains, and interactions between promoters and enhancers. The dynamism of the three-dimensional genome architecture, prompted by the HFD, assumed a pivotal role in the transcriptional regulation of crucial genes. Furthermore, we identified genes that regulate chromatin conformation changes, contributing to the metabolic adaptation process of lipid deposition and hepatic fat changes in geese in response to excessive energy intake. Moreover, we conducted a cross-species analysis comparing geese and mice exposed to the HFD, revealing unique characteristics specific to the goose liver compared to a mouse. These chromatin conformation changes help elucidate the observed characteristics of fat

关键词： Compartment A/B Goose fatty liver Promoter-enhancer interactions Regulation of gene expression

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Panicle-3D: A low-cost 3D-modeling method for rice panicles based on deep learning, shape from silhouette, and supervoxel clustering

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The Crop Journal 2022年第5期10卷 1386-1398页

作者： Dan Wu Lejun Yu Junli Ye Ruifang Zhai Lingfeng Duan Lingbo Liu Nai Wu Zedong Geng Jingbo Fu Chenglong Huang Shangbin Chen Qian Liu Wanneng Yang Britton Chance Center for Biomedical Photonics Wuhan National Laboratory for Optoelectronicsand Key Laboratory of Ministry of Education for Biomedical PhotonicsDepartment of Biomedical EngineeringHuazhong University of Science and TechnologyWuhan 430074HubeiChina School of Biomedical Engineering Hainan UniversityHaikou 570228HainanChina National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhan 430070HubeiChina

Self-occlusions are common in rice canopy images and strongly influence the calculation accuracies of panicle traits. Such interference can be largely eliminated if panicles are phenotyped at the 3 D *** on 3 D panicle phenotyping has been limited. Given that existing 3 D modeling techniques do not focus on specified parts of a target object, an efficient method for panicle modeling of large numbers of rice plants is lacking. This paper presents an automatic and nondestructive method for 3 D panicle modeling. The proposed method integrates shoot rice reconstruction with shape from silhouette, 2 D panicle segmentation with a deep convolutional neural network, and 3 D panicle segmentation with ray tracing and supervoxel clustering. A multiview imaging system was built to acquire image sequences of rice canopies with an efficiency of approximately 4 min per rice plant. The execution time of panicle modeling per rice plant using 90 images was approximately 26 min. The outputs of the algorithm for a single rice plant are a shoot rice model, surface shoot rice model, panicle model, and surface panicle model, all represented by a list of spatial coordinates. The efficiency and performance were evaluated and compared with the classical structure-from-motion algorithm. The results demonstrated that the proposed method is well qualified to recover the 3 D shapes of rice panicles from multiview images and is readily adaptable to rice plants of diverse accessions and growth stages. The proposed algorithm is superior to the structure-from-motion method in terms of texture preservation and computational efficiency. The sample images and implementation of the algorithm are available online. This automatic, cost-efficient, and nondestructive method of 3 D panicle modeling may be applied to high-throughput 3 D phenotyping of large rice populations.

关键词： Panicle phenotyping Deep convolutional neural network 3D reconstruction Shape from silhouette Point-cloud segmentation Ray tracing Supervoxel clustering

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Ameliorative effects of Lactobacillus fermentum isolated from individuals following vegan, omnivorous and high-meat diets on ulcerative colitis in mice

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Food Science and Human Wellness 2024年第6期13卷 3181-3192页

作者： Qingsong Zhang Wei Xiao Leilei Yu Fengwei Tian Jianxin Zhao Hao Zhang Wei Chen Qixiao Zhai State Key Laboratory of Food Science and Technology Jiangnan UniversityWuxi 214122China School of Food Science and Technology Jiangnan UniversityWuxi 214122China National Engineering Research Center for Functional Food Jiangnan UniversityWuxi 214122China Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch Wuxi 214122China

Lactobacillus *** be beneficial for the prevention or treatment of ulcerative colitis(UC).In this study,153 participants who followed vegan,omnivorous,or high-meat diet were *** analysis of the Lactobacillus community in feces revealed that Lactobacillus fermentum strains were significantly affected by *** of mixed *** strains from vegans significantly improved inflammation compared to that from omnivores and high-meat consumers,as evidenced by a significant reduction in colonic tissue damage,improvement in inflammatory cytokines,enhanced expression of ZO-1,occludin,and claudin-3,and a significant increase in short chain fatty acids *** effect of a single strain of *** was similar to that of a mixed strains of *** *** analysis suggested that *** strains from the guts of vegans possessed a higher prevalence of genes involved in carbohydrate catabolism than those from the guts of omnivores and high-meat *** particular,the ME2 gene is involved in the biosynthesis of acetate,a compound considered to possess anti-inflammatory *** conclusion,this study indicates strain-specific differences in the ability of *** strains to alleviate UC in mice,influenced by habitual diets。

关键词： Ulcerative colitis Vegan Omnivorous High-meat diet Lactobacillus fermentum

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Anti-PD-L1 antibody ASC22 in combination with a histone deacetylase inhibitor chidamide as a “shock and kill” strategy for ART-free virological control: a phase Ⅱ single-arm study

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Signal Transduction and Targeted Therapy 2024年第10期9卷 4579-4589页

作者： Luling Wu Zhihang Zheng Jingna Xun Li Liu Jiangrong Wang Xinyu Zhang Yueming Shao Yinzhong Shen Renfang Zhang Min Zhang Meiyan Sun Tangkai Qi Zhenyan Wang Shuibao Xu Wei Song Yang Tang Bihe Zhao Zichen Song Jean-Pierre Routy Hongzhou Lu Jun Chen Department of Infectious Diseases and Immunology Shanghai Public Health Clinical CenterFudan UniversityShanghaiChina Institute of Antibiotics Huashan HospitalFudan UniversityShanghaiChina Shanghai Institute of Infectious Disease and Biosecurity Fudan UniversityShanghaiChina State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology Ministry of EducationInstitute of GeneticsSchool of Life SciencesFudan UniversityShanghaiChina Department of Clinical Laboratory Shanghai Public Health Clinical CenterFudan UniversityShanghaiChina Infectious Disease and Immunity in Global Health Program Research Institute of McGill University Health CentreMontrealQCCanada Department of Infectious Diseases and Nursing Research Institution National Clinical Research Center for Infectious DiseasesThe Third People’s Hospital of ShenzhenGuangdongChina

The combination of ASC22, an anti-PD-L1 antibody potentially enhancing HIV-specific immunity and chidamide, a HIV latency reversal agent, may serve as a strategy for antiretroviral therapy-free virological control for HIV. People living with HIV, having achieved virological suppression, were enrolled to receive ASC22 and chidamide treatment in addition to their antiretroviral therapy. Participants were monitored over 24 weeks to measure changes in viral dynamics and the function of HIV-specific CD8^(+) T cells (NCT05129189). 15 participants completed the study. At week 8, CA HIV RNA levels showed a significant increase from baseline, and the values returned to baseline after discontinuing ASC22 and chidamide. The total HIV DNA was only transiently increased at week 4 (P = 0.014). In contrast, integrated HIV DNA did not significantly differ from baseline. Increases in the proportions of effector memory CD4^(+) and CD8^(+) T cells (TEM) were observed from baseline to week 24 (P = 0.034 and P = 0.002, respectively). The combination treatment did not succeed in enhancing the function of HIV Gag/Pol- specific CD8^(+) T cells. Nevertheless, at week 8, a negative correlation was identified between the proportions of HIV Gag-specific TEM cells and alterations in integrated DNA in the T cell function improved group (P = 0.042 and P = 0.034, respectively). Nine adverse events were solicited, all of which were graded 1 and resolved spontaneously. The combined treatment of ASC22 and chidamide was demonstrated to be well-tolerated and effective in activating latent HIV reservoirs. Further investigations are warranted in the context of analytic treatment interruption.

关键词： immunity alterations treatment

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Combining UAV multisensor field phenotyping and genome-wide association studies to reveal the genetic basis of plant height in cotton(Gossypium hirsutum)

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植物表型组学（英文） 2025年第1期7卷 260-271页

作者： Liqiang Fan Jiajie Yang Xuwen Wang Zhao Liu Bowei Xu Li Liu Chenxu Gao Xiantao Ai Fuguang Li Lei Gao Yu Yu Zuoren Yang State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang 455000HenanChina Xinjiang Key Laboratory of Crop Gene Editing and Germplasm Innovation Institute of Western Agricultural of CAASChangji831100Xinjiang China Engineering Research Centre of Cotton Ministry of Education/College of AgricultureXinjiang Agricultural University311 Nongda East RoadUrumqi830052China State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang 455000HenanChina Xinjiang Key Laboratory of Crop Gene Editing and Germplasm Innovation Institute of Western Agricultural of CAASChangji831100Xinjiang China Cotton Research Institute Xinjiang Academy Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding(Xinjiang)Ministry of AgricultureChina Zhengzhou Research Base State Key Laboratory of Cotton Bio-breeding and Integrated UtilizationSchool of Agricultural SciencesZhengzhou UniversityZhengzhou450001HenanChina State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang 455000HenanChina College of Smart Agriculture(Research Institute) Xinjiang UniversityUrumqi830046XinjiangChina State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang 455000HenanChina Xinjiang Key Laboratory of Crop Gene Editing and Germplasm Innovation Institute of Western Agricultural of CAASChangji831100Xinjiang China Zhengzhou Research Base State Key Laboratory of Cotton Bio-breeding and Integrated UtilizationSchool of Agricultural SciencesZhengzhou UniversityZhengzhou450001HenanChina State Key Laboratory of Cotton Bio-breeding and Integrated Utilization Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang

Plant height(PH)is a key agronomic trait influencing plant *** PH values for cotton are important for lodging resistance,high planting density,and mechanized harvesting,making it crucial to elucidate the mechanisms of the genetic regulation of ***,traditional field PH phenotyping largely relies on manual measurements,limiting its large-scale *** this study,a high-throughput phenotyping platform based on UAV-mounted RGB and light detection and ranging(LiDAR)was developed to efficiently and accurately obtain time series PHs of 419 cotton accessions in the *** strategies were used to extract PH values from two sets of sensor data,and the extracted values were used to train using linear regression and machine learning methods to obtain PH *** predictions were consistent with manual measurements of the PH for the LiDAR(R2=0.934)and RGB(R2=0.914)*** predicted PH values were used for GWAS analysis,and 34 PH-related genes,two of which have been demonstrated to regulate PH in cotton,namely,GhPH1 and GhUBP15,were *** further identified significant differences in the expression of a new gene named GhPH_UAV1 in the stems of the *** cultivar ZM24 harvested on the 15th,35th,and 70th days after sowing compared with those from a dwarf mutant(pag1),which presented shortened stem and internode *** overexpression of GhPH_UAV1 significantly promoted cotton stem development,whereas its knockout by CRISPR-Cas9 dramatically inhibited stem growth,suggesting that GhPH_UAV1 plays a positive regulatory role in cotton *** field-scale high-throughput phenotype monitoring platform significantly improves the ability to obtain high-quality phenotypic data from large populations,which helps overcome the imbalance between massive genotypic data and the shortage of field phenotypic data and facilitates the integration of genotype and phenotype research for crop improvement.

关键词： Plant height UAV RGB LiDAR Genome-wide association study

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miR-1205/DNAJB1 reverses docetaxel chemoresistance in human triple negative breast carcinoma cells via regulation of mutp53/TAp63 signaling

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生物化学与生物物理学报（英文版） 2022年第1期54卷 37-46页

作者： Yongxiang Yin Jinqiu Zhang Tao Ma Daozhen Chen Daru Lu State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology School of Life SciencesFudan UniversityShanghai 200438China Department of Pathology The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical UniversityWuxi 214002China Department of Pathology The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical UniversityWuxi 214002China Department of Breast The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical UniversityWuxi 214002China Central Laboratory The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical UniversityWuxi 214002China State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology School of Life SciencesFudan UniversityShanghai 200438China

Chemoresistance is the major cause of therapeutic failure in human triple negative breast carcinoma(TNBC).Docetaxel(DOC),a first-line therapeutic drug in TNBC treatment,is limited for long-term use due to the develop-ment of ***,overcoming chemoresistance of DOC remains an important challenge to improve patient's outcome of *** this study,we aimed to investigate the molecular mechanism behind DOC che-moresistance and the possible therapeutic effects of *** qRT-PCR analysis,we discovered that miR-1205 is gradually downregulated in human triple negative breast carcinoma MDA-MB-231 and docetaxel-resistant MDA-MB-231(MDA-MB-231/DOC)cells compared with Hs 578Bst normal human breast *** viability,cell cycle and apoptosis assays in MDA-MB-231/DOC cells indicated that miR-1205 overexpression enhances doc-etaxel sensitivity by reducing cell viability as well as inducing G2/M cell cycle arrest and cell *** blot analysis,dual-luciferase reporter assay,co-immunoprecipitation assay and chromatin immunoprecipitation assay revealed that miR-1205 overexpression disrupts the stable complex formation of DNAJB1,mutp53 and TAp63 by directly reducing DNAJB1 expression,which abates the sequestrating effect of mutp53 on TAp63,thereby leading to the enhanced DOC sensitivity in MDA-MB-231/DOC *** findings demonstrate the role of the miR-1205/DNAJB1 axis in the docetaxel resistance of TNBC,which may offer a promising therapeutic approach to resolve docetaxel resistance in TNBC.

关键词： docetaxel resistance miR-1205/DNAJB1 mutp53/TAp63 signaling triple negative breast carcinoma

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A recombinase polymerase amplification with lateral flow assay for rapid on-the-spot detection of Aeromonas salmonicida

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Water Biology and Security 2024年第3期3卷 58-64页

作者： Sijie Zhang Yuanxing Zhang Qin Liu Qiyao Wang Yibei Zhang State Key Laboratory of Bioreactor Engineering Laboratory for Aquatic Animal DiseasesEast China University of Science and TechnologyShanghai200237China Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Zhuhai519000China Shanghai Engineering Research Center of Maricultured Animal Vaccines Shanghai200237China

Aeromonas salmonicida is a common pathogen of salmonid fishes that poses a significant threat to the fresh water and marine culture industry,potentially resulting in huge economic *** prevent and control fish diseases caused by ***,rapid and effective diagnostic approaches must be developed,and which are important for routine monitoring and clinical *** combining recombinase polymerase amplification(RPA)technology with a visible lateral flow strip(RPA-LF),we have enhanced both the precision of RPA detection and the convenience of real-time *** this study,we introduce a robust method for detecting *** using *** assay specifically targets the ASA_1441 gene of ***,ensuring high specificity,without cross-reactivity with other prevalent fresh water or marine *** optimal amplification temperature of the RPA assay was 39℃.Its sensitivity extends to as low as 100 fg of purified DNA,representing more than 1000-fold higher sensitivity than conventional PCR ***,to enhance the usability of the RPA-LF assay,we developed a rapid sample preparation method using cellulose dipsticks for nucleic acid *** method achieves a limit of detection(LOD)as low as 1.67 CFU/μL and completes the entire process within 20 *** conclusion,our findings present a rapid and precise tool for monitoring *** infection in aquaculture and marine *** advancement offers valuable insights for effective disease prevention and control strategies.

关键词： Aeromonas salmonicida Recombinase Polymerase Amplification(RPA) Lateral flow On-the-spot detection

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