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Repressor elements provide insights into tissue development and phenotypes in pigs

Zoological Research 2024年第6期45卷 1313-1326页

作者： Yue-Dong Zhang Chao Guo Hang Liu Yun Gao Yongjun Tan Longjian Niu Ligang Wang Lixian Wang david mirwin Chunhui Hou Zhong-Yin Zhou Ya-Ping Zhang Key Laboratory of Genetic Evolution&Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan Yunnan UniversityKunmingYunnan 650091China School of Life Science Yunnan UniversityKunmingYunnan 650091China School of Life Sciences Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui 230026China State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangshaHunan 410125China School of Public Health and Emergency Management Southern University of Science and TechnologyShenzhenGuangdong 518055China Shenzhen Key Laboratory of Cardiovascular Health and Precision Medicine Southern University of Science and TechnologyShenzhenGuangdong 518055China Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100081China Department of Laboratory Medicine and Pathobiology University of TorontoToronto M5S 1A8Canada Yunnan Key Laboratory of Biodiversity Information KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China

Repressor elements significantly influence economically relevant phenotypes in pigs;however,their precise roles and characteristics are inadequately *** the present study,we employed H3K27me3 profiling,assay for transposase-accessible chromatin with highthroughput sequencing(ATAC-seq),and RNA sequencing(RNA-seq)data across six tissues derived from three embryonic layers to identify and map 2034 super repressor elements(SREs) and 22223 typical repressor elements(TREs) in the pig ***,many repressor elements were conserved across mesodermal and ectodermal *** exhibited tight regulation of their target genes,affecting a limited number of genes within a specific genomic region with pronounced effects,while TREs exerted broader but weaker regulation over a wider range of target ***,in neuronal tissues,genes regulated by repressor elements started to be repressed during the differentiation of stem cells into progenitor ***,analysis showed that many repressor elements exhibited cooperative and additive effects on the modulation of KLF4 *** research provides the first comprehensive map of pig repressor elements,serving as an essential reference for future studies on repressor elements.

关键词： Repressor elements Super repressor elements Silencer Regulatory model Tissue development KLF4 Pig

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Integrative analyses of RNA editing,alternative splicing,and expression of young genes in human brain transcriptome by deep RNA sequencing

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Journal of Molecular Cell Biology 2015年第4期7卷 314-325页

作者： Dong-Dong Wu Ling-Qun Ye Yan Li Yan-Bo Sun Yi Shao Chunyan Chen Zhu Zhu Li Zhong Lu Wang david mirwin Yong EZhang Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650204China University of Chinese Academy of Sciences BeijingChina Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijingChina Laboratory for Conservation and Utilization of Bio-resource Yunnan UniversityKunming 650091China Department of Laboratory Medicine and Pathobiology University of TorontoTorontoCanada Banting and Best Diabetes Centre University of TorontoTorontoCanada

Next-generation RNA sequencing has been successfully used for identification of transcript assembly,evaluation of gene expression levels,and detection of post-transcriptional *** these large-scale studies,additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain ***,we provide a total of 6.5 billion RNA-seq reads fromdifferent subregions of the human brain.A significant correlation was observed between the levels of alternative splicing and RNA editing,which might be explained by a competition between the molecularmachineries responsible for the splicing and editing of *** protein-coding genesdemonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to *** found that a significantly greater number of young human protein-coding genes are expressed in the putamen,a tissue that was also observed to have the highest level of RNA-editing *** putamen,which previously received little attention,plays an important role in cognitive ability,and our data suggest a potential contribution of the putamen to human evolution.

关键词： RNA editing human brain transcriptome young gene human brain evolution

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导致狐狸重症腹泻疫情的新型犬冠状病毒的发现与鉴定

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Science Bulletin 2023年第21期68卷 2598-2606,M0006页

作者：刘雨婷邓瑶牛胜朱娜宋敬东张晓爽苏伟婷佴文慧陆柔剑 david mirwin 高福王文玲王奇慧谭文杰张树义 College of Animal Science and Veterinary Medicine Shenyang Agricultural UniversityShenyang 110866China NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China College of Veterinary Medicine Shanxi Agricultural UniversityJinzhong 030801China National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China Tianjin Zoo Tianjin 300381China Kunming Cell Bank State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Department of Laboratory Medicine and Pathobiology University of TorontoToronto ON M5S 1A8Canada CAS Key Laboratory of Pathogen Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China School of Laboratory Medicine and Life Sciences Wenzhou Medical UniversityWenzhou 325035China

2019年末,中国东北地区狐狸群中暴发大规模疫情,发病狐狸表现出急性腹泻症状,并出现大量狐狸死亡.通过对该疫源地发病狐狸肛拭子、血液与发病组织的检测分析,获得了多条全长新型犬冠状病毒(CCoV)基因组序列,研究团队将该病毒命名为VuCC... 详细信息

2019年末,中国东北地区狐狸群中暴发大规模疫情,发病狐狸表现出急性腹泻症状,并出现大量狐狸死亡.通过对该疫源地发病狐狸肛拭子、血液与发病组织的检测分析,获得了多条全长新型犬冠状病毒(CCoV)基因组序列,研究团队将该病毒命名为VuCCoV,并确认VuCCoV是引起该疫情的病原.进一步分析表明,VuCCoV基因组的4个结构基因(S,E,M,N)中的3个(E,M,N)与犬冠状病毒(CCoV)对应基因具有超过90%的核苷酸同一性,但S基因核苷酸序列表现出较大的差异.VuCCoV的RNA依赖的RNA聚合酶与蝙蝠冠状病毒PB025的对应蛋白仅存在2~3个氨基酸差异,系统进化分析提示VuCCoV很可能来源于蝙蝠.表面等离子体共振分析实验表明,VuCCoV刺突蛋白受体结合区(RBD)可与犬和狐狸的氨肽酶N(APN)结合,但不与人APN结合,假病毒感染及病毒分离培养实验进一步证实该VuCCoV不易感染人源细胞.蝙蝠等野生动物宿主的病毒跨物种传播对人类和家畜健康构成了显著威胁,VuCCoV的发现和溯源证实蝙蝠作为疫情出现的潜在驱动因素的重要性.积极监控蝙蝠及其他犬科动物中的病毒感染,发现、鉴定对人兽健康构成潜在威胁的新型冠状病毒并研究其进化变异特征与感染特性,对于防控新发人兽共患传染病、建设国家生物安q全体系具有重要意义.

关键词：犬冠状病毒人兽共患传染病病毒感染表面等离子体共振犬科动物动物宿主氨肽酶N 狐狸

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Making bridges between preclinical and clinical insights into age-related cognitive decline

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Neural Regeneration Research 2025年第8期20卷 2321-2322页

作者： david VC Brito Clévio Nóbrega Algarve Biomedical Center-Research Institute(ABC-RI) Campus GambelasFaroPortugal Algarve Biomedical Center-(ABC) Campus GambelasFaroPortugal Faculty of Medicine and Biomedical Sciences(FMCB) University of AlgarveGambelas CampusFaroPortugal

With people living longer,the societal impact of age-related cognitive decline is becoming more pronounced(Crimmins,2015).Thus,it is increasingly important to comprehend the cognitive shifts linked to aging-whether th... 详细信息

关键词： bridges becoming insight

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Women in visual neural regeneration research

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Neural Regeneration Research 2025年第2期20卷 489-490页

作者： Tonia S.Rex david J.Calkins Vanderbilt Eye Institute Vanderbilt University Medical CenterNashvilleTNUSA

The year 2024 marks the 60^(th)anniversary of Title IX and 25 years since the New York Times revealed bias against female faculty members at the Massachusetts Institute of *** take an opportunity here to examine the state of gender bias in a relatively new yet already prominent field,neural regeneration in the visual system,for which there is a well-defined context useful for this *** National Eye Institute(NEI)provided the first round of research funding for its Audacious Goals Initiative(AGI)on visual neural regeneration in 2013 and the last round in ***,we focus on this *** sources included PubMed,the National Science Foundation(NSF),the NEI,the Blue Ridge Institute for Medical Research and data from the major professional organization for eye and vision research,the Association for Research in Vision and Ophthalmology(ARVO).

关键词： neural visual Times

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Silk-based nerve guidance conduits with macroscopic holes modulate the vascularization of regenerating rat sciatic nerve

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Neural Regeneration Research 2025年第6期20卷 1789-1800页

作者： Carina Hromada Patrick Heimel Markus Kerbl LászlóGál Sylvia Nürnberger Barbara Schaedl James Ferguson Nicole Swiadek Xavier Monforte Johannes C.Heinzel Antal Nógrádi Andreas H.Teuschl-Woller david Hercher Department Life Science Engineering University of Applied Sciences Technikum WienViennaAustria Austrian Cluster for Tissue Regeneration ViennaAustria Ludwig Boltzmann Institute for Traumatology The Research Center in Cooperation with AUVAViennaAustria University Clinic of Dentistry Medical University of ViennaViennaAustria Department of Plastic Reconstructive and Aesthetic SurgeryLandesklinikum Wiener Neustadt2700 Wiener NeustadtAustria Department of Anatomy Histology and EmbryologyAlbert Szent-Györgyi Medical SchoolUniversity of SzegedSzegedHungary Medical University of Vienna Department of Orthopedics and Trauma SurgeryDevision of Trauma SurgeryViennaAustria Department of Hand- PlasticReconstructive and Burn SurgeryBG Unfallklinik TuebingenUniversity of TuebingenTuebingenGermany

Peripheral nerve injuries induce a severe motor and sensory deficit. Since the availability of autologous nerve transplants for nerve repair is very limited, alternative treatment strategies are sought, including the use of tubular nerve guidance conduits(tNGCs). However, the use of tNGCs results in poor functional recovery and central necrosis of the regenerating tissue, which limits their application to short nerve lesion defects(typically shorter than 3 cm). Given the importance of vascularization in nerve regeneration, we hypothesized that enabling the growth of blood vessels from the surrounding tissue into the regenerating nerve within the tNGC would help eliminate necrotic processes and lead to improved regeneration. In this study, we reported the application of macroscopic holes into the tubular walls of silk-based tNGCs and compared the various features of these improved silk^(+) tNGCs with the tubes without holes(silk^(–) tNGCs) and autologous nerve transplants in an 8-mm sciatic nerve defect in rats. Using a combination of micro-computed tomography and histological analyses, we were able to prove that the use of silk^(+) tNGCs induced the growth of blood vessels from the adjacent tissue to the intraluminal neovascular formation. A significantly higher number of blood vessels in the silk^(+) group was found compared with autologous nerve transplants and silk^(–), accompanied by improved axon regeneration at the distal coaptation point compared with the silk^(–) tNGCs at 7 weeks postoperatively. In the 15-mm(critical size) sciatic nerve defect model, we again observed a distinct ingrowth of blood vessels through the tubular walls of silk^(+) tNGCs, but without improved functional recovery at 12 weeks postoperatively. Our data proves that macroporous tNGCs increase the vascular supply of regenerating nerves and facilitate improved axonal regeneration in a short-defect model but not in a critical-size defect model. This study suggests that further optimizatio

关键词： axon regeneration blood vessel functional recovery macroporous nerve lesion peripheral nerve repair sciatic nerve silk-based nerve guidance conduit vascularization

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Complement-dependent neuroinflammation in spinal cord injury:from pathology to therapeutic implications

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Neural Regeneration Research 2025年第5期20卷 1324-1335页

作者： Hassan Saad Bachar El Baba Ali Tfaily Firas Kobeissy Juanmarco Gutierrez Gonzalez Daniel Refai Gerald R.Rodts Christian Mustroph david Gimbel Jonathan Grossberg Daniel L.Barrow Matthew F.Gary Ali M.Alawieh Department of Neurosurgery Emory University School of MedicineAtlantaGAUSA Department of Neurology Yale UniversityNew HavenCTUSA Center for Neurotrauma Multiomics&Biomarkers(CNMB)Morehouse School of MedicineAtlantaGAUSA

Spinal cord injury remains a major cause of disability in young adults,and beyond acute decompression and rehabilitation,there are no pharmacological treatments to limit the progression of injury and optimize recovery in this *** the thorough investigation of the complement system in triggering and propagating cerebral neuroinflammation,a similar role for complement in spinal neuroinflammation is a focus of ongoing *** this work,we survey the current literature investigating the role of complement in spinal cord injury including the sources of complement proteins,triggers of complement activation,and role of effector functions in the *** study relevant data demonstrating the different triggers of complement activation after spinal cord injury including direct binding to cellular debris,and or activation via antibody binding to damage-associated molecular *** effector functions of complement have been implicated in spinal cord injury,and we critically evaluate recent studies on the dual role of complement anaphylatoxins in spinal cord injury while emphasizing the lack of pathophysiological understanding of the role of opsonins in spinal cord *** this pathophysiological review,we systematically review the different translational approaches used in preclinical models of spinal cord injury and discuss the challenges for future translation into human *** review emphasizes the need for future studies to dissect the roles of different complement pathways in the pathology of spinal cord injury,to evaluate the phases of involvement of opsonins and anaphylatoxins,and to study the role of complement in white matter degeneration and regeneration using translational strategies to supplement genetic models.

关键词： complement neuroinflammation neuroplasticity regeneration spinal cord injury targeted therapy

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Software, Software Engineering and Software Engineering Research: Some Unconventional Thoughts

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Journal of Computer Science & Technology 2009年第2期24卷 189-197页

作者： david Notkin Computer Science and Engineering University of Washington Seattle

Software engineering is broadly discussed as falling far short of expectations. Data and examples are used to justify how software itself is often poor, how the engineering of software leaves much to be desired, and how research in software engineering has not made enough progress to help overcome these weaknesses. However, these data and examples are presented and interpreted in ways that are arguably imbalanced. This imbalance, usually taken at face value, may be distracting the field from making significant progress towards improving the effective engineering of software, a goal the entire community shares. Research dichotomies, which tend to pit one approach against another, often subtly hint that there is a best way to engineer software or a best way to perform research on software. This, too, may be distracting the field from important classes of progress.

关键词： software engineering/general software engineering process/life cycle

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The functional properties of synapses made by regenerated axons across spinal cord lesion sites in lamprey

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Neural Regeneration Research 2022年第10期17卷 2272-2277页

作者： david Parker Department of Physiology Developmentand NeuroscienceUniversity of CambridgeCambridgeUK

While the anatomical properties of regenerated axons across spinal cord lesion sites have been studied extensively,little is known of how the functional properties of regenerated synapses compared to those in unlesioned *** study aims to compare the properties of synapses made by regenerated axons with unlesioned axons using the lamprey,a model system for spinal injury research,in which functional locomotor recovery after spinal cord lesions is associated with axonal regeneration across the lesion *** synapses below the lesion site did not differ from synapses from unlesioned axons with respect to the amplitude and duration of single excitatory postsynaptic *** also showed the same activity-dependent depression over spike ***,regenerated synapses did differ from unlesioned synapses as the estimated number of synaptic vesicles was greater and there was evidence for increased postsynaptic quantal *** axons above the lesion site,the amplitude and duration of single synaptic inputs also did not differ significantly from unlesioned ***,in this case,there was evidence of a reduction in release probability and inputs facilitated rather than depressed over spike *** inputs from single regenerated axons below the lesion site thus do not increase in amplitude to compensate for the reduced number of descending axons after functional ***,the postsynaptic input was maintained at the unlesioned level using different synaptic ***,the facilitation from the same initial amplitude above the lesion site made the synaptic input over spike trains functionally *** may help to increase propriospinal activity across the lesion site to compensate for the lesion-induced reduction in supraspinal *** animal experiments were approved by the Animal Ethics Committee of Cambridge University.

关键词： electrophysiology lamprey plasticity regeneration reticulospinal axon spinal cord spinal injury synapse

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Conversion of Solar Energy to Fuels by Inorganic Heterogeneous Systems

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催化学报 2011年第6期32卷 879-890页

作者： Kimfung LI david MARTIN Department of Chemical Engineering University College LondonTorrington PlaceLondonWC1E 7JEUK

Over the last several years,the need to find clean and renewable energy sources has increased rapidly because current fossil fuels will not only eventually be depleted,but their continuous combustion leads to a dramatic increase in the carbon dioxide amount in *** of the Sun's radiation can provide a solution to both *** fuel can be generated by using solar energy to split water,and liquid fuels can be produced via direct CO2 *** would create an essentially free carbon or at least carbon neutral energy *** this tutorial review,the current progress in fuels' generation directly driven by solar energy is *** mechanisms are discussed with suggestions for future research.

关键词：固体超强碱氧化钙硝酸钾氧化铝氧化锆氢氧化钾硝酸钙

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