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Correction to: Detailed prediction of protein sub-nuclear localization

Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén, Burkhard Rost
2019 BMC Bioinformatics  
Following publication of the original article [1], the author reported that an incorrect figure has been published as Figure 2. The correct Figure 2 is shown below.  ...  13 nuclear sub-structures, 19% of all proteins were predicted at RI > 60 (point marked by dotted lines).  ...  It related the prediction strength to the performance. The data for this figure were binned in intervals of 20.  ... 
doi:10.1186/s12859-019-3305-4 pmid:31861997 pmcid:PMC6925513 fatcat:ilov2jm73rgyncgc3axzsg4k3e

Detailed prediction of protein sub-nuclear localization

Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén, Burkhard Rost
2019 BMC Bioinformatics  
Sub-nuclear structures or locations are associated with various nuclear processes. Proteins localized in these substructures are important to understand the interior nuclear mechanisms.  ...  It distinguishes sub-nuclear localization in 13 distinct substructures and distinguishes between nuclear proteins confined to the nucleus and those that are also native to other compartments (traveler  ...  ML refined the existing implementation, performed GO enrichment analysis and analysis of protein-protein interactions for nuclear proteins and did the major part of writing the manuscript.  ... 
doi:10.1186/s12859-019-2790-9 pmid:31014229 pmcid:PMC6480651 fatcat:l6nkndl4tjhovpzj4cywqq3pvy

Retraction Note to: correction: Low nitrate: phosphate ratios in the global ocean

T. Tyrrell, C. S. Law
1998 Nature  
This work was supported in part by Grants-in-Aid from the Ministry of Education, Science, Sports and Culture in Japan. Correspondence and requests for materials should be addressed to S.N.  ...  This work was supported in part by the National Science Foundation, the Office of Naval Research, the Packard Foundation, and the A.P. Sloan Foundation.  ...  When CAD protein is synthesized, ICAD may bind to the nascent chain of CAD to allow its correct folding.  ... 
doi:10.1038/30780 fatcat:j34jemzflbhrjh2pdwv3flr37a

The protein domains of theDictyosteliummicroprocessor that are required for correct subcellular localization and for microRNA maturation

Janis Kruse, Doreen Meier, Fides Zenk, Maren Rehders, Wolfgang Nellen, Christian Hammann
2016 RNA Biology  
Based on the unique setup of the Dictyostelium microprocessor with a subcellular localization similar to plants, but a protein domain composition similar to animals, we propose a model for the evolutionary  ...  An investigation of DrnB variants revealed that its newly identified nuclear localization signal is necessary, but not sufficient for the perinucleolar localization.  ...  Funding This work was in part supported by grants of the Deutsche Forschungsgemeinschaft (HA3459/5) to CH and (Ne285/14) to WN. DM acknowledges support by a Graduiertenstipendium desLandes Hessen.  ... 
doi:10.1080/15476286.2016.1212153 pmid:27416267 pmcid:PMC5056781 fatcat:6wk7eikdqvbctkuyzyw2k2n7ju

CORRECTION

2004 British Journal of Ophthalmology  
Acknowledgements We are grateful to Robert Harvey and Salman Mirza for their help in this study. C M G Cheung, O M Durrani, P I Murray  ...  Ki-67 is a nuclear antigen expressed in all stages of the cell cycle except the resting stage.  ...  Enhanced expression of MIB-1 and presence of mutant p53 protein in the absence of bcl-2 may contribute to the aggressive biology of OSSN.  ... 
doi:10.1136/bjo.2003.021055corr1 fatcat:aax7r4ytw5bgxhgif2yaerl5s4

RNA-targeted splice-correction therapy for neuromuscular disease

M. J. A. Wood, M. J. Gait, H. Yin
2010 Brain  
Splice-modulation therapy, whereby molecular manipulation of premessenger RNA splicing is engineered to yield genetic correction, is a promising novel therapy for genetic diseases of muscle and nerve-the  ...  Duchenne muscular dystrophy arises due to mutations that disrupt the open-reading-frame in the DMD gene leading to the absence of the essential muscle protein dystrophin.  ...  Acknowledgements The authors wish to thank Yiqi Seow for expert help in the design of the figures.  ... 
doi:10.1093/brain/awq002 pmid:20150322 fatcat:hixqhmsctvcr5nb5yc5tzudbza

Investigating and Correcting Plasma DNA Sequencing Coverage Bias to Enhance Aneuploidy Discovery

Dineika Chandrananda, Natalie P. Thorne, Devika Ganesamoorthy, Damien L. Bruno, Yuval Benjamini, Terence P. Speed, Howard R. Slater, Melanie Bahlo, Fengfeng Zhou
2014 PLoS ONE  
The improved bias corrections that we demonstrate in this work can be readily adopted into existing fetal trisomy detection protocols and should also lead to improvements in sub-chromosomal copy number  ...  We propose a model to correct this fragmentation bias and observe that incorporating this bias does not lead to any further improvements in the detection of fetal trisomy.  ...  Acknowledgments The authors are grateful to the pregnant women who participated in this study. We would like to thank Keith Satterley for his help with technical issues in data storage, Dr.  ... 
doi:10.1371/journal.pone.0086993 pmid:24489824 pmcid:PMC3906086 fatcat:hivmipcs35dv5k65i3c7nkvfga

SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent

N. E. Davey
2006 Nucleic Acids Research  
Prediction of motifs among sets of biologically related proteins, including those both with and without detectable similarity, were made using the TEIRESIAS algorithm.  ...  The number of motif occurrences arising through common evolutionary descent were normalized based on treatment of BLAST local alignments.  ...  Funding to pay the Open Access publication charges for this article was provided by Science Foundation Ireland. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkl486 pmid:16855291 pmcid:PMC1524906 fatcat:iu3vq56xsvg5dpafyeo3q4ldqi

SOT1, a pentatricopeptide repeat protein with a small MutS-related domain, is required for correct processing of plastid 23S-4.5S rRNA precursors in Arabidopsis thaliana

Wenjuan Wu, Sheng Liu, Hannes Ruwe, Delin Zhang, Joanna Melonek, Yajuan Zhu, Xupeng Hu, Sandra Gusewski, Ping Yin, Ian D. Small, Katharine A. Howell, Jirong Huang
2016 The Plant Journal  
Visualization of the gel to check loading also shows a reduced amount of RbcL protein in the sot1 mutant plants.  ...  Here, we show that SUPPRESSOR OF THYLAKOID FORMATION1 (SOT1), a plastid-localized pentatricopeptide repeat (PPR) protein with a small MutS-related domain, is required for maturation of the 23S-4.5S rRNA  ...  ACKNOWLEDGEMENTS We thank Steven Rodermel (Department of Botany, Iowa State University) for providing the var2 seeds, Alice Barkan (Department of Biology, University of Oregon) for providing the AtpE antibody  ... 
doi:10.1111/tpj.13126 pmid:26800847 fatcat:rb27dwewyrdjdaaynfmpx6utfa

Automatic 13C chemical shift reference correction for unassigned protein NMR spectra

Xi Chen, Andrey Smelter, Hunter N. B. Moseley
2018 Journal of Biomolecular NMR  
Poor chemical shift referencing, especially for 13 C in protein Nuclear Magnetic Resonance (NMR) experiments, fundamentally limits and even prevents effective study of biomacromolecules via NMR, including  ...  To solve this problem, we constructed a Bayesian probabilistic framework that circumvents the limitations of previous reference correction methods that required protein resonance assignment and/or three-dimensional  ...  Moseley) and National Institutes of Health grant NIH UL1TR001998-01 (Philip Kern).  ... 
doi:10.1007/s10858-018-0202-5 pmid:30097912 fatcat:nyvwwwsi5vbklo7pez5gwzpbt4

Fine spatiotemporal activity in contracting myometrium revealed by motion-corrected calcium imaging

Fiona C. Loftus, Anatoly Shmygol, Magnus J. E. Richardson
2014 Journal of Physiology  
Applied to our data, we illustrate that the method allows for analyses of calcium dynamics in contracting myometrium in unprecedented spatiotemporal detail.  ...  Additionally, we use the kinematics of tissue motion to compare calcium signals at the subcellular level and local contractile motion.  ...  Details of the motion-correction algorithm Identification of landmarks for tracking.  ... 
doi:10.1113/jphysiol.2014.275412 pmid:25085893 pmcid:PMC4280886 fatcat:dnzclthbqvea3ee5pftdmncgay

Insulin-like growth factor-1 activates AMPK to augment mitochondrial function and correct neuronal metabolism in sensory neurons in type 1 diabetes

Mohamad-Reza Aghanoori, Darrell R. Smith, Shiva Shariati-Ievari, Andrew Ajisebutu, Annee Nguyen, Fiona Desmond, Carlos H.A. Jesus, Xiajun Zhou, Nigel A. Calcutt, Michel Aliani, Paul Fernyhough
2019 Molecular Metabolism  
We hypothesized that sub-optimal insulin-like growth factor 1 (IGF-1) signaling in diabetes drives loss of AMPK activity and mitochondrial function, both contributing to development of DSPN.  ...  There is impaired neurotrophic growth factor signaling, AMP-activated protein kinase (AMPK) activity and mitochondrial function in dorsal root ganglia (DRG) of animal models of type 1 and type 2 diabetes  ...  ACKNOWLEDGMENTS We would like to thank Dr. Mohammad Golam Sabbir, St Boniface Research Centre, for his contribution to 2D gel set up and Alex Marquez and Katie Frizzi for excellent technical support.  ... 
doi:10.1016/j.molmet.2018.11.008 pmid:30545741 pmcid:PMC6358538 fatcat:nwf6uihghveulgbmuuvppsswty

Erratum: correction: A caspase-activated DNase that degrades DNA during apoptosis and its inhibitor ICAD

Masato Enari, Hideki Sakahira, Hideki Yokoyama, Katsuya Okawa, Akihiro Iwamatsu, Shigekazu Nagata
1998 Nature  
This work was supported in part by Grants-in-Aid from the Ministry of Education, Science, Sports and Culture in Japan. Correspondence and requests for materials should be addressed to S.N.  ...  This work was supported in part by the National Science Foundation, the Office of Naval Research, the Packard Foundation, and the A.P. Sloan Foundation.  ...  When CAD protein is synthesized, ICAD may bind to the nascent chain of CAD to allow its correct folding.  ... 
doi:10.1038/30782 fatcat:yegmvzcvpnb4rncxngpwn66sne

Molecular Mechanisms and Determinants of Innovative Correction Approaches in Coagulation Factor Deficiencies

Dario Balestra, Alessio Branchini
2019 International Journal of Molecular Sciences  
; (iii) the rescue of protein synthesis/function through the induction of ribosome readthrough targeting nonsense variants or the correction of folding defects caused by amino acid substitutions.  ...  ; (ii) the rescue of altered pre-mRNA processing through the engineering of key spliceosome components able to promote correct exon recognition and, in turn, the synthesis and secretion of functional factors  ...  correct protein.  ... 
doi:10.3390/ijms20123036 pmid:31234407 pmcid:PMC6627357 fatcat:t5imw64jmrh4hmzuvhobkc5tdq

RNA-GPS Predicts SARS-CoV-2 RNA Localization to Host Mitochondria and Nucleolus [article]

Kevin E Wu, James Zou, Howard Y Chang
2020 biorxiv/medrxiv  
We compare hundreds of SARS-CoV-2 genomes to the human transcriptome and other coronaviruses and perform systematic sub-sequence analyses to identify the responsible signals.  ...  We discuss the mitochondrial localization signal in relation to the formation of double-membrane vesicles, a critical stage in the coronavirus life cycle.  ...  Fazal provided particularly helpful feedback regarding biological interpretation of localization results. H.Y.C. is supported by RM1-HG007735 and R01-HG004361.  ... 
doi:10.1101/2020.04.28.065201 pmid:32511373 pmcid:PMC7263502 fatcat:iq4k2u72qfh6jh5nhtdpsr2ckq
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