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SSRN 2024年

作者： Frigaard, Niels-Ulrik Seemann, Stefan E. Marine Biological Section Department of Biology University of Copenhagen Helsingør Denmark Center for non-coding RNA in Technology and Health Department of Veterinary and Animal Sciences University of Copenhagen Frederiksberg Denmark

Methane (CH4) and carbon dioxide (CO2) occur as undesirable waste products in carbon-based fuel productions. Bothgases are major greenhouse gases with CH4 being much more potent than CO2. For this reason, excess CH4 from varioussources is often flared into CO2 rather than releasing the CH4 into the atmosphere, however, some CH4 is still emitteddue to the inefficiency of flare combustion. We have explored how natural microbial communities can be manipulatedinto consuming both CH4 and CO2 from a gas stream and converting the gases into microbial biomass. Natural seawaterwas enriched with inorganic nutrients and injected with a continuous gas stream containing CH4 (4.7% v/v) and CO2(1% v/v) over a period of several days, either in the dark or in the light. Microbial communities established thatcontained methanotrophic bacteria consuming CH4, and cyanobacteria and microalgae consuming CO2. The measureof chemotaxonomic markers revealed that the growth of phototrophs increased greatly only in the light with an earlydominance by cyanobacteria later overtaken by microalgae, and that the growth of methanotrophs increased greatlyonly in the dark. The microbial communities were characterized using near-full-length 16S/18S rrna gene ampliconsequencing with the Nanopore technology. In the incubated cultures, the microbial diversity was drastically lower ascompared to the natural communities. The most abundant microalgae were green algae belonging to Picochlorum,Tetraselmis, Chlamydomonas, and Nannochloris, and the most abundant cyanobacteria were related to Geitlerinemasp. PCC 7105, Symphothece sp. PCC 7002 and Cyanobium sp. PCC 6307 (based on the SILVA reference database).Methylomicrobium and Methylobacter were the most abundant methanotrophs in the dark-incubated cultures, whereasMethylomonas methanica was identified as the single methanotroph with notable abundance under light ***, for optimal CH4 and CO2 consumption it may be necessary to physically separate

关键词： Microalgae

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Discovering and Evaluating Organizational Knowledge from Textual Data: Application to Crisis Management

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SSRN 2023年

作者： Grissa, Dhouha Andonoff, Eric Hanachi, Chihab Center for non-coding RNA in Technology and Health Department of Veterinary and Animal Science University of Copenhagen Frederiksberg C1870 Denmark Université Toulouse - Capitole IRIT 2 rue du Doyen Gabriel Marty Toulouse31042 France

Crisis management effectiveness relies mainly on the quality of the distributed human organization deployed for saving lives, limiting damage and reducing risks. Organizations set up in this context are not always predefined and static;they could evolve and new forms could emerge since actors, such as volunteers or NGO, could join dynamically to collaborate. To improve crisis resolution effectiveness, it is first important to understand, analyze and evaluate such dynamic organizations in order to adjust crisis management plans and ease coordination among actors. Giving a textual experience feedback from past crisis, the objective of this paper is to discover the organizational structure deployed in the considered crisis and then evaluate it according to a set of criteria. For that purpose, we combine in a coherent framework text and association rule mining for pattern discovery and annotation, and multi-agent system models and techniques for formally building and evaluating organizational structures. We present the OSminer algorithm that discovers association rules based on relevant textual patterns and then builds an organizational structure including three main relations between actors: power, control and coordination. A real-life case study, a flood crisis hitting the south west of France, serves as a basis for testing/experimenting our solution. The organizational structure, discovered in this case study, has 24 actors. Its evaluation indicates its efficiency, but shows that it is neither robust nor flexible. Our findings highlight the potential of our approach to discover and evaluate organizational structures from a text recording interactions between stakeholders in a crisis context. © 2023, The Authors. All rights reserved.

关键词： Association rules

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Ribosomal modification protein rimK-like family member A activates betaine-homocysteine S-methyltransferase 1 to ameliorate hepatic steatosis

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Signal Transduction and Targeted Therapy 2024年第9期9卷 4048-4065页

作者： Han Yan Wenjun Liu Rui Xiang Xin Li Song Hou Luzheng Xu Lin Wang Dong Zhao Xingkai Liu Guoqing Wang Yujing Chi Jichun Yang Department of Physiology and Pathophysiology School of Basic Medical SciencesState Key Laboratory of Vascular Homeostasis and RemodelingCenter for Non-coding RNA MedicinePeking University Health Science CenterBeijing 100191China Department of Endocrinology The Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhou 310058China Medical and Health Analysis Center Peking UniversityBeijing 100191China Department of Hepatobiliary Surgery Xi-Jing HospitalFourth Military Medical UniversityXi’an 710032China Department of Endocrinology Beijing Luhe HospitalCapital Medical UniversityBeijing 101100China Department of Hepatobiliary and Pancreatic Surgery General Surgery CentreFirst Hospital of Jilin UniversityChangchun 130061China Key Laboratory of Pathobiology Ministry of Education College of Basic Medical SciencesJilin UniversityChangchun 130012China Department of Central Laboratory and Institute of Clinical Molecular Biology Department of GastroenterologyPeking University People’s HospitalBeijing 100044China Department of Cardiology Peking University Third HospitalBeijing 100191China

nonalcoholic fatty liver disease(NAFLD)is a serious threat to public health,but its underlying mechanism remains poorly *** screening important genes using Gene Importance Calculator(GIC)we developed previously,ribosomal modification protein rimK-like family member A(RIMKLA)was predicted as one essential gene but its functions remained largely *** current study determined the roles of RIMKLA in regulating glucose and lipid *** expression was reduced in livers of human and mouse with *** RIMKLA overexpression ameliorated steatosis and hyperglycemia in obese ***-specific RIMKLA knockout aggravated high-fat diet(HFD)-induced dysregulated glucose/lipid metabolism in ***,RIMKLA is a new protein kinase that phosphorylates betaine-homocysteine S-methyltransferase 1(BHMT1)at threonine 45(Thr45)*** phosphorylation at Thr45 and activation,BHMT1 eliminated homocysteine(Hcy)to inhibit the activity of transcription factor activator protein 1(AP1)and its induction on fatty acid synthase(FASn)and cluster of differentiation 36(CD36)gene transcriptions,concurrently repressing lipid synthesis and uptake in ***45 to alanine(T45A)mutation inactivated BHMT1 to abolish RIMKLA’s repression on Hcy level,AP1 activity,FASn/CD36 expressions,and lipid ***1 overexpression rescued the dysregulated lipid metabolism in RIMKLA-deficient *** summary,RIMKLA is a novel protein kinase that phosphorylates BHMT1 at Thr45 to repress lipid synthesis and *** obese condition,inhibition of RIMKLA impairs BHMT1 activity to promote hepatic lipid deposition.

关键词： metabolism hepatic homocysteine

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Computational discovery of conserved rna structures and functional characterization of a structured lncrna in Leishmania braziliensis

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non-coding rna Research 2025年 14卷 51-64页

作者： Caroline R. Espada Christian Anthon Rubens D.M. Magalhães José Carlos Quilles Junior Natalia M.M. Teles Fabiano S. Pais Lissur A. Orsine Letícia de Almeida Tânia P.A. Defina Adam Dowle Jan Gorodkin Pegine B. Walrad Angela K. Cruz Department of Cell and Molecular Biology Ribeirão Preto Medical School University of São Paulo FMRP-USP Ribeirão Preto São Paulo Brazil Department of Biology York Biomedical Research Institute University of York York United Kingdom Center for Non-coding RNA in Technology and Health Department of Animal and Veterinary Sciences Faculty for Health and Medical Sciences University of Copenhagen Copenhagen Denmark Data Science Lab Metabolomics and Proteomics Lab Bioscience Technology Facility Department of Biology University of York York United Kingdom

Leishmania parasites alternate between hosts, facing environmental changes that demand rapid gene expression adaptation. Lacking canonical rna polymerase II promoters, transcription in these eukaryotes is polycistronic, with gene regulation occurring post-transcriptionally. Although non-coding rnas (ncrnas) have been identified in Leishmania transcriptomes, their functions remain unclear. Recognizing rna structure's importance, we performed a genome-wide alignment of L. braziliensis and related species, identifying conserved rna structures, 38 of which overlap with known ncrnas. One such ncrna, lncrna45 , was functionally characterized. Using a knockout cell line, we demonstrated that lncrna45 is crucial for parasite fitness. Reintroducing the wild type lncrna45 restored fitness, while a version with a single nucleotide substitution in the structured region did not. This mutation also altered rna-protein interactions. These findings suggest that lncrna45 's regulatory role and protein interactions rely on its secondary structure. This study highlights the significance of structured lncrnas in Leishmania biology and their potential as therapeutic targets. Further research into these ncrnas could uncover new parasite regulation mechanisms and inspire novel treatment strategies.

关键词： non-coding rnas Leishmania braziliensis rna structure Gene expression regulation CRISPR- Cas9

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Targeting non-coding rnas to overcome cancer therapy resistance

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Signal Transduction and Targeted Therapy 2022年第5期7卷 1447-1466页

作者： BaoQing Chen Mihnea P.Dragomir Chen Yang Qiaoqiao Li David Horst George A.Calin Department of Radiation Oncology State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat-sen University Cancer CenterGuangzhouGuangdong 510060China Institute of Pathology Charité-Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt-Universität zu Berlin and Berlin Institute of HealthBerlin 10117Germany Berlin Institute of Health Anna-Louisa-Karsch-Straße 210178 BerlinGermany German Cancer Consortium(DKTK) Partner Site BerlinGerman Cancer Research Center(DKFZ)69210 HeidelbergGermany Department of Translational Molecular Pathology The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA Center for RNA Interference and Non-Coding RNAs The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA

It is now well known that non-coding rnas(ncrnas),rather than protein-coding transcripts,are the preponderant rna ***,particularly micrornas(mirnas),long non-coding rnas(lncrnas),and circular rnas(circrnas),are widely appreciated as pervasive regulators of multiple cancer hallmarks such as proliferation,apoptosis,invasion,metastasis,and genomic *** recent discoveries in cancer therapy,resistance to chemotherapy,radiotherapy,targeted therapy.

关键词： chemotherapy metastasis rnas

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Inhibition of KDM6B prevents osteoarthritis by blocking growth plate-like H3K27me3 loss in bivalent genes

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Science China Life Sciences 2025年第5期68卷 1423-1436页

作者： Hao Du Yao Zhang Xi Yu Xuanhe You Diwei Wu Ze Du Yongrui Cai Zhenyu Luo Hanpeng Lu Zhixin Liao Bi-Sen Ding Ya Zhao Yan Wang Ke Xiao Fan Yang Fangji Gan Ning Ning Jiancheng Zeng Peiliang Shi Zongke Zhou Shishu Huang Department of Orthopedic Surgery and Orthopedic Research Institute West China HospitalSichuan University Rehabilitation Medicine Center West China HospitalSichuan University Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE State Key Laboratory of BiotherapyWest China Second University HospitalSichuan University Institute of Translational Medicine Medical CollegeYangzhou University Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research College of Animal Science and Technology Sichuan Agricultural University Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province Sichuan Agricultural University Department of Lower Limb Surgery of Sichuan Province Orthopedic Hospital Central Laboratory of Sichuan Province Orthopedic Hospital Brain Cognition and Brain Disease Institute (BCBDI) Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences (CAS)Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions School of Mechanical Engineering Sichuan University Gem Pharmatech (Chengdu) Co. Ltd.

Osteoarthritis(OA) is the most prevalent joint disorder occurring with articular cartilage degradation. It includes a switch from an articular to a growth plate chondrocyte phenotype. Here, we investigated the histone modification profiles and found significant H3K27me3 loss in OA, which led to disease-associated gene expression. Surprisingly, these genes were occupied by both H3K27me3 and H3K4me3 in normal chondrocytes, showing a poised bivalent state. Furthermore, we observed the derepression of similar bivalent genes in growth plate chondrocytes. Finally, a KDM6B inhibitor GSK-J4 prevented the H3K27me3 loss and cartilage damage in the rat OA model. Our results reveal an inherited bivalent epigenetic signature on developmental genes that makes articular chondrocytes prone to hypertrophy and contributes to a promising epigenetic therapy for OA.

关键词： osteoarthritis histone modifications H3K27me3 bivalency growth plate

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Pluripotent stem cell-derived cardiomyocyte transplantation: marching from bench to bedside

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Science China Life Sciences 2025年

作者： Yi Hong Jiarui Liu Weixuan Wang Hao Li Weijing Kong Xiaoxia Li Wei Zhang Sara Pahlavan Yida Tang Xi Wang Kai Wang Department of Physiology and Pathophysiology School of Basic Medical Sciences State Key Laboratory of Vascular Homeostasis and Remodeling Beijing Advanced Center of Cellular Homeostasis and Aging-Related Diseases Center for Non-coding RNA Medicine Clinical Stem Cell Research Center Peking University Third Hospital Peking University Department of Education Peking University First Hospital Peking University TianXinFu (Beijing) Medical Appliance Co. Ltd. Department of Stem Cells and Developmental Biology Cell Science Research Center Royan Institute for Stem Cell Biology and Technology The Academic Center for Education Culture and Research Department of Cardiology and Institute of Vascular Medicine Key Laboratory of Molecular Cardiovascular Science Ministry of Education Peking University Third Hospital State Key Laboratory of Female Fertility Promotion Department of Obstetrics and Gynecology Peking University Third Hospital Institute of Advanced Clinical Medicine Peking University Hubei Key Laboratory of Embryonic Stem Cell Research Hubei University of Medicine

Cardiovascular diseases such as myocardial infarction, heart failure, and cardiomyopathy, persist as a leading global cause of death. Current treatment options have inherent limitations, particularly in terms of cardiac regeneration due to the limited regenerative capacity of adult human hearts. The transplantation of pluripotent stem cell-derived cardiomyocytes(PSC-CMs) has emerged as a promising and potential solution to address this challenge. This review aims to summarize the latest advancements and prospects of PSC-CM transplantation(PCT), along with the existing constraints, such as immune rejection and engraftment arrhythmias, and corresponding solutions. Encompassing a comprehensive range from fundamental research findings and preclinical experiments to ongoing clinical trials, we hope to offer insights into PCT from bench to bedside.

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Correction: Ribosomal modification protein rimK-like family member A activates betaine-homocysteine S-methyltransferase 1 to ameliorate hepatic steatosis

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Signal Transduction and Targeted Therapy 2025年第1期10卷 471-472页

作者： Han Yan Wenjun Liu Rui Xiang Xin Li Song Hou Luzheng Xu Lin Wang Dong Zhao Xingkai Liu Guoqing Wang Yujing Chi Jichun Yang Department of Physiology and Pathophysiology School of Basic Medical Sciences State Key Laboratory of Vascular Homeostasis and Remodeling Center for Non-coding RNA Medicine Peking University Health Science Center Beijing China Department of Endocrinology The Second Affiliated Hospital School of Medicine Zhejiang University Hangzhou China Department of Cardiology Peking University Third Hospital Beijing China Medical and Health Analysis Center Peking University Beijing China Department of Hepatobiliary Surgery Xi-Jing Hospital Fourth Military Medical University Xi’an China Department of Endocrinology Beijing Luhe Hospital Capital Medical University Beijing China Department of Hepatobiliary and Pancreatic Surgery General Surgery Centre First Hospital of Jilin University Changchun China Key Laboratory of Pathobiology Ministry of Education College of Basic Medical Sciences Jilin University Changchun China Department of Central Laboratory and Institute of Clinical Molecular Biology Department of Gastroenterology Peking University People’s Hospital Beijing China

Correction to:Signal Transduction and Targeted Therapy https://***/10.1038/s41392-024-01914-0,published online 08 August 2024 In the process of collating the raw data,the authors noticed one inadvertent mistake in supplementaryfigure 9f after online publication of the ***β-actin in supplementaryfigure 9d was repeatedly inserted asβ-actin(upper)in supplementaryfigure *** correct data and corresponding original image are provided as *** correction does not affect the keyfindings(the existing published results or the discussion).The original article has been corrected.

关键词： hepatic correction repeatedly

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Single-cell rna sequencing-based immunological feature analysis of a COVID-19 patient with recurrent positive SARS-CoV-2 rna

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Chinese Medical Journal 2022年第8期135卷 1000-1002页

作者： Bin Su Ruya Sun Lili Zhang Jiaying Zhang Xia Feng Zhenhuan Cao Wei Hou Xianghua Guo Qing Ge Qinghua Cui Yuan Zhou Yingmin Ma Ronghua Jin Yingmei Feng Beijing Youan Hospital Capital Medical UniversityBeijing 100069China Department of Biomedical Informatics School of Basic Medical SciencesKey Laboratory of Molecular Cardiovascular Sciences of the Ministry of EducationCenter for Non-coding RNA MedicinePeking University Health Science CenterBeijing 100191China Department of Immunology Key Laboratory of Medical ImmunologyMinistry of HealthSchool of Basic Medical SciencesPeking University Health Science CenterBeijing 100191China Beijing Ditan Hospital Capital Medical UniversityBeijing 100102China

To the Editor:Since the outbreak in December 2019,severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has infected>2.4 billion people worldwide,resulting in>4.9 million *** understand the pathogenesis of SARS-CoV-2 infection,single-cell rna-sequencing(scrna-seq)profiles of peripheral blood mononuclear cells(PBMCs)have been constructed in coronavirus disease-2019(COVID-19)patients at different disease stages.

关键词： acute respiratory pathogenesis

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Using GPU to accelerate the pairwise structural rna alignment with base pair probabilities

Using GPU to accelerate the pairwise structural RNA alignmen...

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作者： Sundfeld, Daniel Teodoro, George Havgaard, Jakob H. Gorodkin, Jan Melo, Alba C. M. A. Information and Communication Technology Brasília Federal Institute Brasília Brazil Department of Computer Science University of Brasília Brasília Brazil Center for Non-Coding RNA in Technology and Health Department of Veterinary and Animal Sciences University of Copenhagen Copenhagen Denmark

Structural alignments of Ribonucleic acid (rna) sequences solved by the Sankoff algorithm are computationally expensive and often require constraints to be used in practice. Modern Graphics Processing Units (GPUs) contain more than 1000 cores, which compute in parallel to speed up applications. Here, we present a GPU-based solution to the rna structural alignment problem that makes use of precalculated base pair probabilities on the individual sequences. We designed and developed an unconstrained version of the Sankoff algorithm, obtaining the optimal result and calculating the entire four-dimension dynamic programming matrix (4D DP). Our approach uses a two-level wavefront strategy to exploit parallelism. The 4D DP matrix is divided in one external matrix (EM) and several internal matrices (IM). We applied wavefront strategies on the EM and IMs in a two-level hierarchical way. At the first level, the wavefront is applied to the EM, calculating the cells that belong to the same diagonal in parallel. In the second level, since each cell in the EM is itself an IM matrix, the cells that belong to the same IM diagonal are calculated in parallel. The results obtained with real rna sequences show that our GPU version is capable of outperforming a multicore CPU version of the unconstrained version of the Sankoff algorithm. Compared with the CPU-based version running on 32 cores, our approach is able to achieve a speedup of 7.81x on the NVidia Tesla P100. In this case, the execution time was reduced from 6 hours and 18 minutes (32 cores) to 48 minutes and 20 seconds (GPU). © 2019 John Wiley & Sons, Ltd.

关键词： Graphics processing unit

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