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ARNA: Interactive Comparison and Alignment of RNA Secondary Structure

G. Gainant, D. Auber
IEEE Symposium on Information Visualization  
Figure 1 : Comparing the secondary structure of two RNA sequences with ARNA. ABSTRACT ARNA is an interactive visualization system that supports comparison and alignment of RNA secondary structure.  ...  We present a new approach to RNA alignment that exploits the complex structure of the Smith-Waterman local distance matrix, allowing people to explore the space of possible partial alignments to discover  ...  We focus here on the problem of aligning RNA. ALIGNING RNA The problem of multiple sequence alignment has been well studied [4] .  ... 
doi:10.1109/infvis.2004.7 dblp:conf/infovis/GainantA04 fatcat:43nospsggjcvphbtqfnzo62yui

Structure and interactions of the archaeal motility repression module ArnA-ArnB that modulates archaellum gene expression in Sulfolobus acidocaldarius

Lena Hoffmann, Katrin Anders, Lisa F. Bischof, Xing Ye, Julia Reimann, Sunia Khadouma, Trong K. Pham, Chris van der Does, Phillip C. Wright, Lars-Oliver Essen, Sonja-Verena Albers
2019 Journal of Biological Chemistry  
In summary, our findings unravel the structural features in ArnA and ArnB important for their interaction and functional archaellum expression and reveal how nutrient conditions affect this interaction  ...  Here, we report the structural base for such an interacting pair of FHA and vWA domain-containing proteins, ArnA and ArnB, in the thermoacidophilic archaeon Sulfolobus acidocaldarius, where they act synergistically  ...  Acknowledgements: We thank the beamline staff of the ESRF, Grenoble, and BESSY-II, Berlin for support, Holger Steuber for his help in structure solution, Petra Gnau and Ralf Pöschke for technical support  ... 
doi:10.1074/jbc.ra119.007709 pmid:30902813 pmcid:PMC6509490 fatcat:ghpigxjp2bagfmgdlwgk2n7xsy

Real-time monitoring of aRNA production during T7 amplification to prevent the loss of sample representation during microarray hybridization sample preparation

Isabelle Gilbert, Sara Scantland, Isabelle Dufort, Olga Gordynska, Aurélie Labbe, Marc-André Sirard, Claude Robert
2009 Nucleic Acids Research  
This second phase leads to modifications in transcript abundance that biases comparison between samples of different types.  ...  candidates undetected and distorting the true proportional differences of all candidates analyzed.  ...  ACKNOWLEDGEMENTS We thank Isabelle Laflamme for her technical assistance during the embryo production in addition to Dr Marc-Andre´Laniel and Dr Julie Nieminen for critical review of the manuscript.  ... 
doi:10.1093/nar/gkp193 pmid:19336411 pmcid:PMC2677895 fatcat:iwu6mqiq5rbj7bn5hrgb7bg4iy

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival [article]

Oliver Smith, Glenn Dunshea, Mikkel-Holger S Sinding, Sergey Fedorov, Mietje Germonpre, Hervé Bocherens, M.T.P. Gilbert
2019 biorxiv/medrxiv   pre-print
Other hallmarks of RNA-seq data such as exon-exon junction presence and high endogenous ribosomal RNA content confirms our data's authenticity.  ...  Here we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid.  ...  Shyam Gopalakrishnan for his valuable insights on our data analysis, and finally, we thank Kristian Gregersen at the Natural History Museum of Denmark for access to wolf hides. Author Contributions  ... 
doi:10.1101/546820 fatcat:eoenfg5xwbgy5ppzxjauzcpqaa

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival

Oliver Smith, Glenn Dunshea, Mikkel-Holger S. Sinding, Sergey Fedorov, Mietje Germonpre, Hervé Bocherens, M. T. P. Gilbert, Chris Tyler-Smith
2019 PLoS Biology  
Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data's authenticity.  ...  Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid.  ...  Shyam Gopalakrishnan for his valuable insights on our data analysis, and finally, we thank Kristian Gregersen at the Natural History Museum of Denmark for access to wolf hides. Author Contributions  ... 
doi:10.1371/journal.pbio.3000166 pmid:31361744 pmcid:PMC6667121 fatcat:v5djwrbsonc3xnjgqcy2tyrvui

Efficient drawing of RNA secondary structure

David Auber, Maylis Delest, Jean-Philippe Domenger, Serge Dulucq
2006 Journal of Graph Algorithms and Applications  
In order to allow a visual comparison of two RNAs, we use an heuristic that places the biggest similar part of the two structures in the same position and orientation.  ...  In this paper, we propose a new layout algorithm that draws the secondary structure of a Ribonucleic Acid (RNA) automatically according to some of the biologists' aesthetic criteria.  ...  Efficient comparison must allow the user to visually compare two RNA secondary structures.  ... 
doi:10.7155/jgaa.00131 fatcat:d4mzzkfcdrachpacpydxxgjkp4

Comparative transcriptome analysis of stylar canal cells identifies novel candidate genes implicated in the self-incompatibility response of Citrus clementina

Marco Caruso, Paz Merelo, Gaetano Distefano, Stefano La Malfa, Angela Lo Piero, Francisco R Tadeo, Manuel Talon, Alessandra Gentile
2012 BMC Plant Biology  
Here we report the identification of candidate genes involved in pollen-pistil interaction and self-incompatibility in clementine (Citrus clementina Hort. ex Tan.).  ...  cultivar and 'Monreal', a selfcompatible mutation of 'Comune').  ...  This work was supported by: the Italian Ministry of the University -Project PRIN "The productive process in fruit tree species: molecular, physiological and agronomical aspects of floral incompatibility  ... 
doi:10.1186/1471-2229-12-20 pmid:22333138 pmcid:PMC3305554 fatcat:27k4yuyzgnh4rn2b4skgrxahxe

Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

Kimberly A. Stanek, Jennifer Patterson-West, Peter S. Randolph, Cameron Mura
2017 Acta Crystallographica Section D: Structural Biology  
ThisAaeHfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further  ...  Structures ofAaeHfq were determined in space groupsP1 andP6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered.  ...  Huber (Regensburg) for providing a sample of A. aeolicus genomic material, J. Bushweller (UVa) for access to a fluorescence plate reader, J.  ... 
doi:10.1107/s2059798317000031 pmid:28375142 pmcid:PMC5379935 fatcat:h34l4rogkfajpmr5ur4edbmrle

Gene Expression Profiling of Liver Cancer Stem Cells by RNA-Sequencing

David W. Y. Ho, Zhen Fan Yang, Kang Yi, Chi Tat Lam, Michael N. P. Ng, Wan Ching Yu, Joyce Lau, Timothy Wan, Xiaoqi Wang, Zhixiang Yan, Hang Liu, Yong Zhang (+2 others)
2012 PLoS ONE  
Acknowledgments We thank Xueda Hu, Li Chen, and Xuemei Tan for conducting the RNA-Sequencing experiments, and Dr. Chi Keung Lau for designing the primers.  ...  (A) Alignment of RNA-Seq sequence reads to GPC3 gene.  ...  After amplification, an average of 114 mg of amplified RNA (aRNA) was obtained.  ... 
doi:10.1371/journal.pone.0037159 pmid:22606345 pmcid:PMC3351419 fatcat:vpm2rukqnfbrpnzm6ohgk7x3xi

An overview of gene expression dynamics during early ovarian folliculogenesis: specificity of follicular compartments and bi-directional dialog

Agnes Bonnet, Cedric Cabau, Olivier Bouchez, Julien Sarry, Nathalie Marsaud, Sylvain Foissac, Florent Woloszyn, Philippe Mulsant, Beatrice Mandon-Pepin
2013 BMC Genomics  
In addition, signaling pathways (VEGF, NOTCH, IGF1, etc.) and GC transzonal projections suggest the existence of complex cell-cell interactions.  ...  Results: We used a laser capture microdissection method combined with RNA-seq technology to explore the transcriptome in oocytes and granulosa cells (GCs) during development of the sheep ovarian follicle  ...  RNA sequencing was processed at the genomic platform Toulouse, Genopole (http://genomique.genotoul.fr/). We thank Katia Feve for her help with Fluidigm experiment.  ... 
doi:10.1186/1471-2164-14-904 pmid:24350644 pmcid:PMC3890531 fatcat:a6q6jkdpsvcixksak6eunyh3oe

Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression

Loren A Honaas, Eric K Wafula, Zhenzhen Yang, Joshua P Der, Norman J Wickett, Naomi S Altman, Christopher G Taylor, John I Yoder, Michael P Timko, James H Westwood, Claude W dePamphilis
2013 BMC Plant Biology  
Results The interaction of Triphysaria with the distantly related hosts Zea mays and Medicago truncatula reveals dramatic host-specific gene expression patterns.  ...  Results: The interaction of Triphysaria with the distantly related hosts Zea mays and Medicago truncatula reveals dramatic host-specific gene expression patterns.  ...  and IOS-1104334 to Taylor CG, McIntyre L and Koch, K, and the Intercollege Graduate Program in Plant Biology and Department of Biology of Penn State University.  ... 
doi:10.1186/1471-2229-13-9 pmid:23302495 pmcid:PMC3636017 fatcat:rtm27roorrf37nvyefg52n2yq4

In vitro selection of RNA lectins: using combinatorial chemistry to interpret ribozyme evolution

Susan M. Lato, Amy R. Boles, Andrew D. Ellington
1995 Chemistry and Biology  
No predominant secondary structural feature appears in the selected RNAs.  ...  Ribosomal RNA and group I introns have no obvious similarity at the level of secondary structure, and there is no reason to believe that their tertiary folds are similar.  ...  High-salt-eluted and affinity-eluted RNAs from round 3 were separately selected in round 4.  ... 
doi:10.1016/1074-5521(95)90048-9 pmid:9383431 fatcat:pjd4stmoubb55mgtdqr4zrnxum

Protein phosphorylation and its role in archaeal signal transduction

Dominik Esser, Lena Hoffmann, Trong Khoa Pham, Christopher Bräsen, Wen Qiu, Phillip C. Wright, Sonja-Verena Albers, Bettina Siebers, Alain Filloux
2016 FEMS Microbiology Reviews  
It combines results from identified phosphoproteins, biochemical characterization of protein kinases and protein phosphatases as well as target enzymes and first insights into archaeal signal transduction  ...  Reversible protein phosphorylation is the main mechanism of signal transduction that enables cells to rapidly respond to environmental changes by controlling the functional properties of proteins in response  ...  Secondary structure elements of the solved Sso-PTP structure are shown above the sequence with β-sheets depicted as orange arrows and α helices as green boxes (Chu and Wang 2007) .  ... 
doi:10.1093/femsre/fuw020 pmid:27476079 pmcid:PMC5007285 fatcat:2ey67sswajaz5ieugmvqj3s33m

Chronic Endoplasmic Reticulum Stress Activates Unfolded Protein Response in Arterial Endothelium in Regions of Susceptibility to Atherosclerosis

Mete Civelek, Elisabetta Manduchi, Rebecca J. Riley, Christian J. Stoeckert, Peter F. Davies
2009 Circulation Research  
Rationale: Endothelial function and dysfunction are central to the focal origin and regional development of atherosclerosis; however, an in vivo endothelial phenotypic footprint of susceptibility to atherosclerosis  ...  ER transmembrane signal transducers IRE1␣ and ATF6␣ and their downstream effectors, but not PERK, were activated concomitant with a higher transcript expression of protein folding enzymes and chaperones  ...  Diamond and Craig A. Simmons for critical reading of the manuscript, and Drs Marie Guerraty and Yun Fang for helpful discussions.  ... 
doi:10.1161/circresaha.109.203711 pmid:19661457 pmcid:PMC2746924 fatcat:mv2fmo7ybffgbhcvuwzjnank3u

Differentially expressed genes in embryonic cardiac tissues of mice lacking Folr1 gene activity

Huiping Zhu, Robert M Cabrera, Bogdan J Wlodarczyk, Daniel Bozinov, Deli Wang, Robert J Schwartz, Richard H Finnell
2007 BMC Developmental Biology  
Gene ontology analysis highlighted the following ontology groups: cell migration, cell motility and localization of cells, structural constituent of cytoskeleton, cell-cell adhesion, oxidoreductase, protein  ...  These changes affected normal cytoskeleton structures, cell migration and motility as well as cellular redox status, which may contribute to cardiovascular abnormalities in mouse embryos lacking Folr1  ...  Michelle Merriweather and Ms. Melissa Scott, who were responsible for the care and well being of the mouse colony.  ... 
doi:10.1186/1471-213x-7-128 pmid:18028541 pmcid:PMC2206038 fatcat:h2abkpv5f5acxkfbssl5gly2dq
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