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Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence
2008
BMC Bioinformatics
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We have developed a method to cluster cognate proteins from multiple organisms beginning with only one sequence, through connectivity saturation with that Seed sequence. ...
It is extremely important to comparative biology that related proteins be identified as members of the same cognate group, since a characterized putative homolog could be used to find clues about the function ...
Acknowledgements We would like to sincerely thank Darren A. ...
doi:10.1186/1471-2105-9-141
pmid:18321373
pmcid:PMC2277401
fatcat:lutdw2pgcvevpf7nbd7plmpfry
Archaeosortases and Exosortases Are Widely Distributed Systems Linking Membrane Transit with Posttranslational Modification
2011
Journal of Bacteriology
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Multiple new prokaryotic C-terminal protein-sorting signals were found that reprise the tripartite architecture shared by LPXTG and PEP-CTERM: motif, TM helix, basic cluster. ...
A picture emerges of an ancient and now well-differentiated superfamily of deeply membrane-embedded protein-processing enzymes. ...
Alignment of multiple C-terminal putative protein-sorting signals from a single species often shows apparent sequence homology that runs through the TM domain and is not limited to the signature motif ...
doi:10.1128/jb.06026-11
pmid:22037399
pmcid:PMC3256604
fatcat:pefplcacfjfkre4mk4dspvw5ju
mRNA/protein sequence complementarity and its determinants: The impact of affinity scales
2017
PLoS Computational Biology
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It has recently been demonstrated that the nucleobase-density profiles of mRNA coding sequences are related in a complementary manner to the nucleobase-affinity profiles of their cognate protein sequences ...
obtained from experimental structures of RNA-protein complexes. ...
The sequences of mRNAs and their cognate proteins are, of course, linked by the universal genetic code. ...
doi:10.1371/journal.pcbi.1005648
pmid:28750009
pmcid:PMC5549747
fatcat:vvdrz5dds5aivpsqdv5zvq4kw4
Developing microRNA screening as a functional genomics tool for disease research
2013
Frontiers in Physiology
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ACKNOWLEDGMENTS Mark Mercola acknowledges research support from the NIH (R33HL088266 and R01HL113601), Mathers Charitable Trust, California Institute for Regenerative Medicine (RC1-000132) and the Fondation ...
Shankar Subramaniam acknowledges research support from the NIH (R33HL087375, U54GM69338, P01DK074868, R01HL106579, and R01HL108735). miRNA screening is supported by NIH P30AR061303 and P30CA030199. ...
One approach FIGURE 2 | Computational and experimental strategies to identify miRNA targets. miRNAs target multiple proteins, and in certain instances a single family of miRNAs target multiple proteins ...
doi:10.3389/fphys.2013.00223
pmid:23986717
pmcid:PMC3753477
fatcat:vkfd2mejk5ejvem5heyoagx3ae
Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans
2010
Nature Structural & Molecular Biology
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A single miRNA can potentially repress hundreds of genes by binding with partial sequence complementarity to mRNAs 3,4 . ...
The identification and analysis of sequences directly associated with Argonaute protein in vivo in C. elegans has enabled the discovery of distinct features related to this core component of the miRNA-induced ...
To characterize the sequence properties of ALG-1 binding sites, we subjected CDCs and a control set of random derived clusters (RDCs) to a battery of computational analyses. ...
doi:10.1038/nsmb.1745
pmid:20062054
pmcid:PMC2834287
fatcat:hohuu3ski5dtbea4ink5i54eha
Reshaping of the Arabidopsis thaliana proteome landscape and co-regulation of proteins in development and immunity
[article]
2020
bioRxiv
pre-print
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Among others, the data suggest a potential function of RD26 and other NAC transcription factors in seed development related to desiccation tolerance as well as a possible function of Cysteine-rich Receptor-like ...
The extensive coverage of the Arabidopsis proteome in various biological scenarios presents a rich resource to plant biologists that we make available to the community. ...
The proteins in cluster 7 are very specific to the seed proteome. ...
doi:10.1101/2020.03.09.978627
fatcat:n6beqrdamrb4hb4wqh6f3bfnvi
Transcriptional profiling reveals distinct classes of parathyroid tumors in PHPT
2018
Endocrine-Related Cancer
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RNAseq and proteomic analysis identified a candidate set of differentially expressed genes highly correlated with calcium-sensing capacity. ...
Subsequent quantitative assessment of the expression levels of these genes in an independent cohort of parathyroid tumors confirmed that calcium-sensitive tumors cluster in a discrete transcriptional profile ...
Tumors derived from PHPT patients with osteoporosis fell almost exclusively within Clusters 2 and 3, with only a single instance found in Cluster 1. ...
doi:10.1530/erc-17-0470
pmid:29475894
fatcat:ruorcgapmzajzejc5qc25q52ne
Origins and Diversification of a Complex Signal Transduction System in Prokaryotes
2010
Science Signaling
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While tracing its evolutionary history, we also developed a classification scheme that revealed more than a dozen distinct classes of chemotaxis systems, enabling future predictive modeling of chemotactic ...
Article Tools http://stke.sciencemag.org/cgi/content/full/sigtrans;3/128/ra50 Visit the online version of this article to access the personalization and article tools: Materials Supplemental http://stke.sciencemag.org ...
domains of cognate response regulators primarily targeting multiple DNA promoters) to the system that links multiple inputs (sensory domains of MCPs) to a single output (CheY to the flagellar motor). ...
doi:10.1126/scisignal.2000724
pmid:20587806
pmcid:PMC3401578
fatcat:yqpg5mnj25aotbe6hxzwwkcuta
Evolution of Function of a Fused Metazoan tRNA Synthetase
2010
Molecular biology and evolution
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The ERS and PRS catalytic domains in multiple bilaterian taxa are linked by variable number of helix-turn-helix domains referred to as WHEP-TRS domains. ...
The glutamyl-prolyl tRNA synthetase (EPRS) of bilaterian animals is unique among AARSs, containing two functional enzymes catalyzing ligation of glutamate and proline to their cognate transfer RNAs (tRNAs ...
Acknowledgment This work was supported by the National Institute of Health grants P01 HL029582, P01 HL076491, and R01 GM086430 (to P.L.F.). ...
doi:10.1093/molbev/msq246
pmid:20829344
pmcid:PMC3002251
fatcat:fj6hwv4omnhthbukompqcypqaa
Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level
2016
Proteomics
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The ten control animals clustered tightly together, distinct from the ten heat-shocked individ-uals. ...
Results
Optimization of protein extraction and data acquisition from single nematodes We optimized a lysis workflow that allows proteome extraction from single nematodes, reducing losses using a single ...
doi:10.1002/pmic.201500264
pmid:26552604
pmcid:PMC4819713
fatcat:4q7lcjdulfgu5esk2xhmbhggri
From Fuzziness to Precision Medicine: On the Rapidly Evolving Proteomics with Implications in Mitochondrial Connectivity to Rare Human Disease
2021
iScience
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In this perspective article, we identified 21 mt proteins from public repositories that associate with RCC deficiency, MELAS, or ARSACS, engaging in a relatively small number of protein-protein interactions ...
(PPIs), underscoring the need for advanced proteomic and interactomic platforms to uncover the complete scope of mt connectivity to RDs. ...
Rapid developments in sorting techniques and single-cell RNA sequencing have made it possible to capture cell types of interest on a single cell level. ...
doi:10.1016/j.isci.2020.102030
pmid:33521598
pmcid:PMC7820543
fatcat:awxqyvbttrdyvnihnqxvn2qlme
Intraspecies Competition in Serratia marcescens Is Mediated by Type VI-Secreted Rhs Effectors and a Conserved Effector-Associated Accessory Protein
2015
Journal of Bacteriology
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Multiple antibacterial effectors can be delivered by these systems, with diverse activities against target cells and distinct modes of secretion. ...
One of these was shown to act as a DNase toxin, while the other contains a novel, cytoplasmic-acting toxin domain. ...
ACKNOWLEDGMENTS We thank Maximilian Fritsch for construction of strain MJF15, N. Gotoh for strain SM39, and Bill Hunter and all the members of the S.J.C. group for advice and discussion. ...
doi:10.1128/jb.00199-15
pmid:25939831
pmcid:PMC4524185
fatcat:k3qsa3d66jhnnnu35b2gj3m3ma
Combined Proteomics/Genomics Approach Reveals Proteomic Changes of Mature Virions as a Novel Poxvirus Adaptation Mechanism
2017
Viruses
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While the overall viral genome sequence was stable during passaging, proteomics revealed multiple changes in the virion composition. ...
To elucidate adaptation mechanisms of poxviruses, we isolated cowpox virus particles from a rat and passaged them five times in a human and a rat cell line. ...
The authors are grateful to Andreas Kurth for providing crust material from infected rats.
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/v9110337
pmid:29125539
pmcid:PMC5707544
fatcat:icaaryymh5dfblxcwmxrtersdq
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
2005
BMC Biology
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Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. ...
However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications. ...
Finally, we are indebted to NSF for their long and continuous support of this project (Cooperative Agreement. DBI 9813586). ...
doi:10.1186/1741-7007-3-7
pmid:15784138
pmcid:PMC1082884
fatcat:jw5tyx6eubea7fb5yczxnc4ynq
Global Analysis of Protein Palmitoylation in African Trypanosomes
2010
Eukaryotic Cell
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A total of 124 palmitoylated proteins were identified, with an estimated false discovery rate of 1.0%. ...
This palmitoyl proteome includes all of the known palmitoyl proteins in procyclic-stage T. brucei as well as several proteins whose homologues are palmitoylated in other organisms. ...
5G12RR008124-16A1) for use of the LC-MS instrument. ...
doi:10.1128/ec.00248-10
pmid:21193548
pmcid:PMC3067466
fatcat:cib2fd3wcfa4zblb27rtabmnrq
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