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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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Quality Assessment of Domesticated Animal Genome Assemblies

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Bioinformatics and Biology Insights 2015年第Suppl 4期9S4卷 49-58页

作者： Seemann, Stefan E. Anthon, Christian Palasca, Oana Gorodkin, Jan Center for non-coding RNA in Technology and Health Department of Veterinary Clinical and Animal Sciences University of Copenhagen København Denmark

The era of high-throughput sequencing has made it relatively simple to sequence genomes and transcriptomes of individuals from many species. In order to analyze the resulting sequencing data, high-quality reference genome assemblies are required. However, this is still a major challenge, and many domesticated animal genomes still need to be sequenced deeper in order to produce high-quality assemblies. In the meanwhile, ironically, the extent to which rna seq and other next-generation data is produced frequently far exceeds that of the genomic sequence. Furthermore, basic comparative analysis is often affected by the lack of genomic sequence. Herein, we quantify the quality of the genome assemblies of 20 domesticated animals and related species by assessing a range of measurable parameters, and we show that there is a positive correlation between the fraction of mappable reads from rnaseq data and genome assembly quality. We rank the genomes by their assembly quality and discuss the implications for genotype analyses. © 2015, © 2015 SAGE Publications.

关键词： assembly quality domesticated animals genome assembly

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SPARSE: Quadratic time simultaneous alignment and folding of rnas without sequence-based heuristics

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17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013

作者： Will, Sebastian Schmiedl, Christina Miladi, Milad Möhl, Mathias Backofen, Rolf Bioinformatics Department of Computer Science University of Freiburg Germany Bioinformatics Department of Computer Science University of Leipzig Germany University of Freiburg Germany University of Freiburg Germany Centre for Non-coding RNA in Technology and Health Bagsvaerd Denmark

ISBN: (纸本)9783642371943

Motivation: There is increasing evidence of pervasive transcription, resulting in hundreds of thousands of ncrnas of unknown function. Standard computational analysis tasks for inferring functional annotations like clustering require fast and accurate rna comparisons based on sequence and structure similarity. The gold standard for the latter is Sankoff's algorithm [3], which simultaneously aligns and folds rnas. Because of its extreme time complexity of O(n6), numerous faster "Sankoff-style" approaches have been suggested. Several such approaches introduce heuristics based on sequence alignment, which compromises the alignment quality for rnas with sequence identities below 60% [1]. Avoiding such heuristics, as e.g. in LocArna [4], has been assumed to prohibit time complexities better than O(n 4), which strongly limits large-scale applications. © 2013 Springer-Verlag.

关键词： Alignment

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Computational strategies to search structured rnas in genomic sequence(and roads towards further analysis)

Computational strategies to search structured RNAs in genomi...

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2011国际基因组学大会

作者： Jan Gorodkin Center for non-coding RNA in Technology and Health IBHVUniversity of CopenhagenDenmark

A key application of early methods for computational rna folding was to aid interpretation of structure probing *** the years computational rna biology has developed in which improved energy models and the availability of multiple genomes have contributed substantially to the development of the *** methods that search for common rna structures in a set of co-regulated rnas have

关键词： rna and roads towards further analysis Computational strategies to search structured rnas in genomic sequence

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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

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 Brasil 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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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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50 shades of rule composition from chemical reactions to higher levels of abstraction

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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2014年 8738卷 115-135页

作者： Andersen, Jakob Lykke Flamm, Christoph Merkle, Daniel Stadler, Peter F. Department of Mathematics and Computer Science University of Southern Denmark Denmark Institute for Theoretical Chemistry University of Vienna Austria Bioinformatics Group Department of Computer Science and Interdisciplinary Center for Bioinformatics Leipzig Germany Max Planck Institute for Mathematics in the Sciences Leipzig Germany Fraunhofer Institute for Cell Therapy and Immunology Leipzig Germany Center for Non-coding RNA in Technology and Health University of Copenhagen Denmark Santa Fe Institute United States

ISBN: (纸本)9783319103976

Graph rewriting has been applied quite successfully to model chemical and biological systems at different levels of abstraction. A particularly powerful feature of rule-based models that are rigorously grounded in category theory, is, that they admit a well-defined notion of rule composition, hence, provide their users with an intrinsic mechanism for compressing trajectories and coarse grained representations of dynamical aspects. The same formal framework, however, also allows the detailed analysis of transitions in which the final and initial states are known, but the detailed stepwise mechanism remains hidden. To demonstrate the general principle we consider here how rule composition is used to determine accurate atom maps for complex enzyme reactions. This problem not only exemplifies the paradigm but is also of considerable practical importance for many down-stream analyses of metabolic networks and it is a necessary prerequisite for predicting atom traces for the analysis of isotope labelling experiments. © Springer International Publishing Switzerland 2014.

关键词： Biological systems

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Comparative ncrna gene and structure prediction using foldalign and foldalignM

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Current Protocols in Bioinformatics 2012年第SUPPL.39期39卷

作者： Havgaard, Jakob Kaur, Simranjeet Gorodkin, Jan Center for Non-Coding RNA in Technology and Health Department of Veterinary Clinical and Animal Sciences University of Copenhagen Copenhagen Denmark

This unit describes how to use Foldalign and FoldalignM to make structural alignments of non-protein-coding-rna (ncrna). These tools can be used to find new ncrnas, to find the structure of novel ncrnas, and to improv... 详细信息

关键词： ncrna ncrna gene finding non-coding rna rna multiple sequence alignment rna structural alignment rna structure prediction

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Identification of valid reference genes for microrna expression studies in a hepatitis B virus replicating liver cell line

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BMC Research Notes 2016年第1期9卷 1-7页

作者： Jacobsen, Kari Stougaard Nielsen, Kirstine Overgaard Winther, Thilde Nordmann Glebe, Dieter Pociot, Flemming Hogh, Birthe Department of Paediatrics Hvidovre Hospital University of Copenhagen Copenhagen Denmark Department of Paediatrics Center for Non-Coding RNA in Technology and Health Herlev Hospital University of Copenhagen Copenhagen Denmark Institute of Medical Virology National Reference Center for Hepatitis B and D Viruses German Center for Infection Research Biomedical Research Center Seltersberg Justus-Liebig University Giessen Giessen Germany

Background: Micrornas are regulatory molecules and suggested as non-invasive biomarkers for molecular diagnostics and prognostics. Altered expression levels of specific micrornas are associated with hepatitis B virus infection and hepatocellular carcinoma. We previously identified differentially expressed micrornas with liver-specific target genes in plasma from children with chronic hepatitis B. To further understand the biological role of these micrornas in the pathogenesis of chronic hepatitis B, we have used the human liver cell line HepG2, with and without HBV replication, after transfection of hepatitis B virus expression vectors. RT-qPCR is the preferred method for microrna studies, and a careful normalisation strategy, verifying the optimal set of reference genes, is decisive for correctly evaluating microrna expression levels. The aim of this study was to provide valid reference genes for the human HCC-derived cell line HepG2. Results: A panel of 739 micrornas was screened to identify the most stably expressed micrornas, followed by a PubMed search identifying micrornas previously used as reference genes. Sixteen candidate reference genes were validated by RT-qPCR. Reference gene stabilities were calculated first by standard deviations of ΔCt values and then by geNorm and NormFinder analyses, taking into account the amplification efficiency of each microrna primer set. The optimal set of reference genes was verified by a target analysis using RT-qPCR on miR-215-5p. Conclusion: We identified miR-24-3p, miR-151a-5p, and miR-425-5p as the most valid combination of reference genes for microrna RT-qPCR studies in our hepatitis B virus replicating HepG2 cell model. © 2016 Jacobsen et al.

关键词： Hepatitis B virus microrna Normalisation Reference genes RT-qPCR

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Methane and Co2 Consumption from a Synthetic Waste Gas by Microbial Communities in Enriched Seawater

SSRN

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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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