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The Protein Naming Utility: a rules database for protein nomenclature

Johannes Goll, Robert Montgomery, Lauren M. Brinkac, Seth Schobel, Derek M. Harkins, Yinong Sebastian, Susmita Shrivastava, Scott Durkin, Granger Sutton
2009 Nucleic Acids Research  
The need for consistent and unambiguous names has led to the development of a number of conventions for naming genes and proteins [UniProt protein nomenclature (2), HUGO human gene name nomenclature (  ...  DISCUSSION In this article, we have presented the PNU, a new webbased database for storing and applying protein naming rules.  ...  FUNDING Funding for open access charge: National Institute of Allergy and Infectious Disease (contract HHSN266200400038C). Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkp958 pmid:20007151 pmcid:PMC2808875 fatcat:4yuswvqko5hjbpbuhhrxp56x64

Quantitative Assessment of Dictionary-based Protein Named Entity Tagging

H. Liu, Z.-Z. Hu, M. Torii, C. Wu, C. Friedman
2006 JAMIA Journal of the American Medical Informatics Association  
Conclusion: The study indicated that names for genes/proteins are highly ambiguous and there are usually multiple names for the same gene or protein.  ...  The aim of this study was to provide quantitative assessment of the complexity of BNET on protein entities through BioThesaurus, a thesaurus of gene/protein names for UniProt knowledgebase (UniProtKB)  ...  This feature is helpful in literature-based protein database annotation and indeed is already used for semi-automatic mapping of gene/protein names to UniProtKB entries from a rule-based text mining system  ... 
doi:10.1197/jamia.m2085 pmid:16799122 pmcid:PMC1561801 fatcat:slluxn6gknhx5hpvexewpnr47a

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment

A. K. Arakaki, Y. Zhang, J. Skolnick
2004 Bioinformatics  
For 35% of decoy structures, our method identifies the active site in models having 3-4 Å coordinate root mean square deviation from the native structure, a quality that is reachable using state of the  ...  Results: A method that automatically generates a library of 3D functional descriptors for the structure-based prediction of enzyme active sites (automated functional templates, 593 in total for 162 different  ...  A.K.A. also acknowledges partial support from the Pew Latin American Fellows Program in Biomedical Sciences.  ... 
doi:10.1093/bioinformatics/bth044 pmid:14764543 fatcat:lodymfq5bngmtdsvsfahuh5lqu

Two Type VI Secretion DNase Effectors are Utilized for Interbacterial Competition in the Fish Pathogen Pseudomonas plecoglossicida

Yanyan Li, Xiaojun Yan, Zhen Tao
2022 Frontiers in Microbiology  
Pseudomonas plecoglossicida is a facultative fish pathogen that possesses three distinct type VI secretion systems (named T6SS-1, T6SS-2, and T6SS-3).  ...  We first identified four putative antibacterial effectors (denoted as Txe1, Txe2, Txe3, and Txe4) and their cognate immunity proteins encoded in P. plecoglossicida strain XSDHY-P by analyzing the regions  ...  of the same T6SS system (namely, T6SS-2) for toxin delivery .  ... 
doi:10.3389/fmicb.2022.869278 pmid:35464968 pmcid:PMC9020831 fatcat:4t5bbxievfflvlr7scbax64cdu

Novel QTL Conferring Phosphorus Acquisition and Utilization Efficiencies in Barley

Shangqing Gao, Jiaqi Xia, Shu Yuan, Youjie Shen, Xinting Zhong, Senfeng Zhang, Yuhang Li, Deyi Hu, Jian Zeng, Ting Lan, Yaxi Liu, Guangdeng Chen
2020 Frontiers in Genetics  
Based on the analysis of a recombinant inbred lines (RILs) population derived from a cross between a malting barley variety and a wild barley accession, 17 QTL controlling PAE, PUE and yield traits were  ...  Phosphorus (P) deficiency in agricultural soil is a major constraint for crop production and increasing P acquisition efficiency (PAE) of plants is considered as one of the most cost-effective solutions  ...  All the authors read and approved the final manuscript.  ... 
doi:10.3389/fgene.2020.580452 pmid:33101396 pmcid:PMC7500284 fatcat:smxcnra7jfei3gv3gtvobnhrpu

BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins

Suresh Panneerselvam, Ruchir Mishra, Colin Berry, Neil Crickmore, Bryony C Bonning
2022 Database: The Journal of Biological Databases and Curation  
The associated website also provides a portal for users to submit protein sequences for naming.  ...  In association with a revised nomenclature for these proteins, BPPRC contains a database that allows users to browse and download sequences.  ...  on database functionality during development.  ... 
doi:10.1093/database/baac022 pmid:35396594 pmcid:PMC9216523 fatcat:5t2wma2lrjczfoedwtxmjepp7i

Burkholderia cenocepacia utilizes a type VI secretion system for bacterial competition

Helena L. Spiewak, Sravanthi Shastri, Lili Zhang, Stephan Schwager, Leo Eberl, Annette C. Vergunst, Mark S. Thomas
2019 MicrobiologyOpen  
of species that utilize the T6SS for this purpose.  ...  It possesses a type VI secretion system (T6SS), a secretory apparatus that can perforate the cellular membrane of other bacterial species and/or eukaryotic targets, to deliver an arsenal of effector proteins  ...  PAAR domain-containing protein in A. baylyi and named accordingly (Weber et al., 2016) .  ... 
doi:10.1002/mbo3.774 pmid:30628184 pmcid:PMC6612558 fatcat:clkptu23hzfr3jwcub6wc6kriq

Protein biomarker discovery and validation: the long and uncertain path to clinical utility

Nader Rifai, Michael A Gillette, Steven A Carr
2006 Nature Biotechnology  
This is due in part to the lack of a coherent pipeline connecting marker discovery with well-established methods for validation.  ...  Proteomics methods based on mass spectrometry hold special promise for the discovery of novel biomarkers that might form the foundation for new clinical blood tests, but to date their contribution to the  ...  Therefore, in the absence of a predicate device and depending on the intended use and clinical utility, either a PMA or a de novo process will be required for a new protein of interest before it achieves  ... 
doi:10.1038/nbt1235 pmid:16900146 fatcat:2da6k2dqtfewxby2parhgwxz2q

Flavobacterium johnsoniae GldH Is a Lipoprotein That Is Required for Gliding Motility and Chitin Utilization

M. J. McBride, T. F. Braun, J. L. Brust
2003 Journal of Bacteriology  
GldH does not exhibit significant amino acid similarity to proteins of known function in the databases.  ...  . gldH encodes a predicted 141-amino-acid protein that localized to the membrane fraction.  ...  ACKNOWLEDGMENTS This research was supported by grants from the National Science Foundation (MCB-9727825 and MCB-0130967) and by a Shaw Scientist Award to M.J.M. from The Milwaukee Foundation.  ... 
doi:10.1128/jb.185.22.6648-6657.2003 pmid:14594839 pmcid:PMC262120 fatcat:6vqwtvdol5ashipoj5istvzddu

Utilization of alternate chirality enantiomers in microbial communities

Elena V. Pikuta, Richard B. Hoover, Richard B. Hoover, Gilbert V. Levin, Alexei Y. Rozanov, Paul C. W. Davies
2010 Instruments, Methods, and Missions for Astrobiology XIII  
Our previous study of chirality led to interesting findings for some anaerobic extremophiles: the ability to metabolize substrates with alternate chirality enantiomers of amino acids and sugars.  ...  The functional division within a microbial community on proteo-and sugarlytic links was also reflected in a microbial diet with Lsugars and D-amino acids.  ...  Acknowledgments We thank the administration of the National Space Sciences and Technologies Center and Von Broun Center for Science & Innovation, Inc. and Delaware State University for providing funding  ... 
doi:10.1117/12.862232 fatcat:x5vxgnuhfjdqbcspuvyxp2rl34

Adding clinical utility to the laboratory reports: automation of interpretative comments

Wytze Oosterhuis
2018 Clinical Chemistry and Laboratory Medicine  
Patients have in general little understanding of these results, and consultation of patients could add a new dimension to the service of the laboratory.  ...  These developments have been recognized by the European Federation of Clinical Chemistry and Laboratory Medicine, which has established the working group on Patient Focused Laboratory Medicine for work  ...  The use of international standards, e.g. for nomenclature and coding of laboratory results, will be necessary for proper transferability.  ... 
doi:10.1515/cclm-2018-0623 pmid:30367781 fatcat:2w4kywzucvfkvnr4m4kxgaffjm

Towards Better Test Utilization - Strategies to Improve Physician Ordering and Their Impact on Patient Outcomes

Danielle B Freedman
2015 EJIFCC  
In order to improve patient outcomes, laboratory tests must be appropriately ordered, properly conducted, reported in a timely manner, correctly interpreted and affect a decision for future diagnosis and  ...  Laboratory medicine is the single highest volume medical activity in healthcare and demand for laboratory testing is increasing disproportionately to medical activity.  ...  HARMONIZATION OF NOMENCLATURE CLIHC have also examined the issue of the wide inconsistencies in test nomenclature as a significant barrier to physicians ordering the correct test.  ... 
pmid:27683478 pmcid:PMC4975220 fatcat:kqiakt7qwvfrhkyzemt7d6kjqm

Microbial Cellulose Utilization: Fundamentals and Biotechnology

L. R. Lynd, P. J. Weimer, W. H. van Zyl, I. S. Pretorius
2002 Microbiology and Molecular Biology Reviews  
Generally, only a few species within each of the above-named genera are actively cellulolytic.  ...  Examination of the rapidly expanding genomics database may reveal similar surprises in the future.  ... 
doi:10.1128/mmbr.66.3.506-577.2002 pmid:12209002 pmcid:PMC120791 fatcat:cxf3za5pnrhhzf2p4wslosrhna

Cytochrome P450 Monooxygenase-Mediated Metabolic Utilization of Benzo[a]Pyrene by Aspergillus Species

Erin M. Ostrem Loss, Mi-Kyung Lee, Ming-Yueh Wu, Julia Martien, Wanping Chen, Daniel Amador-Noguez, Colin Jefcoate, Christina Remucal, Seunho Jung, Sun-Chang Kim, Jae-Hyuk Yu, Reinhard Fischer
2019 mBio  
Importantly, we identify and characterize the conserved bapA gene encoding a cytochrome P450 monooxygenase that is necessary for the metabolic utilization of BaP in Aspergillus.  ...  Importantly, this study reveals key components of the metabolic utilization of BaP, notably a cytochrome P450 monooxygenase and the fungal NF-κB-type transcriptional regulators.  ...  These proteins can be classified into the same subfamily, CYP617D, based on the rules of the International P450 Nomenclature Committee. For the expanded information, see Fig. S5 and Table S3.  ... 
doi:10.1128/mbio.00558-19 fatcat:ebhz3s5cvbdshcrits6p6khzv4

The Opportunistic Pathogen Serratia marcescens Utilizes Type VI Secretion To Target Bacterial Competitors

S. L. Murdoch, K. Trunk, G. English, M. J. Fritsch, E. Pourkarimi, S. J. Coulthurst
2011 Journal of Bacteriology  
The type VI secretion system (T6SS) is the most recently described and least understood of the protein secretion systems of Gram-negative bacteria.  ...  Serratia marcescens is an opportunistic enteric pathogen, a class of bacteria responsible for a significant proportion of hospital-acquired infections.  ...  We also gratefully acknowledge the contribution of the Pathogen Sequencing Unit at the Wellcome Trust Sanger Institute, Hinxton, United Kingdom, for performing the Serratia marcescens Db11 genome sequencing  ... 
doi:10.1128/jb.05671-11 pmid:21890705 pmcid:PMC3194891 fatcat:rr43bhsbvbafdann4r43bzvfgu
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