51
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Gurbanov R, Bilgin M, Severcan F. Restoring effect of selenium on the molecular content, structure and fluidity of diabetic rat kidney brush border cell membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:845-54. [DOI: 10.1016/j.bbamem.2016.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 01/28/2016] [Accepted: 02/01/2016] [Indexed: 02/02/2023]
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52
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Ding H, Liang ZY, Guo FB, Huang J, Chen W, Lin H. Predicting bacteriophage proteins located in host cell with feature selection technique. Comput Biol Med 2016; 71:156-61. [PMID: 26945463 DOI: 10.1016/j.compbiomed.2016.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/18/2016] [Accepted: 02/18/2016] [Indexed: 10/22/2022]
Abstract
A bacteriophage is a virus that can infect a bacterium. The fate of an infected bacterium is determined by the bacteriophage proteins located in the host cell. Thus, reliably identifying bacteriophage proteins located in the host cell is extremely important to understand their functions and discover potential anti-bacterial drugs. Thus, in this paper, a computational method was developed to recognize bacteriophage proteins located in host cells based only on their amino acid sequences. The analysis of variance (ANOVA) combined with incremental feature selection (IFS) was proposed to optimize the feature set. Using a jackknife cross-validation, our method can discriminate between bacteriophage proteins located in a host cell and the bacteriophage proteins not located in a host cell with a maximum overall accuracy of 84.2%, and can further classify bacteriophage proteins located in host cell cytoplasm and in host cell membranes with a maximum overall accuracy of 92.4%. To enhance the value of the practical applications of the method, we built a web server called PHPred (〈http://lin.uestc.edu.cn/server/PHPred〉). We believe that the PHPred will become a powerful tool to study bacteriophage proteins located in host cells and to guide related drug discovery.
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Affiliation(s)
- Hui Ding
- Key Laboratory for NeuroInformation of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology and Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Zhi-Yong Liang
- Key Laboratory for NeuroInformation of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology and Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Feng-Biao Guo
- Key Laboratory for NeuroInformation of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology and Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jian Huang
- Key Laboratory for NeuroInformation of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology and Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wei Chen
- Key Laboratory for NeuroInformation of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology and Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China; Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063000, China.
| | - Hao Lin
- Key Laboratory for NeuroInformation of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology and Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China.
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53
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Friis-Nielsen J, Kjartansdóttir KR, Mollerup S, Asplund M, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Nielsen IB, Alquezar-Planas DE, Olsen PVS, Vinner L, Fridholm H, Nielsen LP, Willerslev E, Sicheritz-Pontén T, Lund O, Hansen AJ, Izarzugaza JMG, Brunak S. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers. Viruses 2016; 8:E53. [PMID: 26907326 PMCID: PMC4776208 DOI: 10.3390/v8020053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 12/17/2022] Open
Abstract
Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified.
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Affiliation(s)
- Jens Friis-Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Kristín Rós Kjartansdóttir
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Maria Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Stine Raith Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Ida Broman Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Pernille V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen S, Denmark.
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Jose M G Izarzugaza
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
- NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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54
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Illuminating structural proteins in viral "dark matter" with metaproteomics. Proc Natl Acad Sci U S A 2016; 113:2436-41. [PMID: 26884177 DOI: 10.1073/pnas.1525139113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses are ecologically important, yet environmental virology is limited by dominance of unannotated genomic sequences representing taxonomic and functional "viral dark matter." Although recent analytical advances are rapidly improving taxonomic annotations, identifying functional dark matter remains problematic. Here, we apply paired metaproteomics and dsDNA-targeted metagenomics to identify 1,875 virion-associated proteins from the ocean. Over one-half of these proteins were newly functionally annotated and represent abundant and widespread viral metagenome-derived protein clusters (PCs). One primarily unannotated PC dominated the dataset, but structural modeling and genomic context identified this PC as a previously unidentified capsid protein from multiple uncultivated tailed virus families. Furthermore, four of the five most abundant PCs in the metaproteome represent capsid proteins containing the HK97-like protein fold previously found in many viruses that infect all three domains of life. The dominance of these proteins within our dataset, as well as their global distribution throughout the world's oceans and seas, supports prior hypotheses that this HK97-like protein fold is the most abundant biological structure on Earth. Together, these culture-independent analyses improve virion-associated protein annotations, facilitate the investigation of proteins within natural viral communities, and offer a high-throughput means of illuminating functional viral dark matter.
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55
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Kryshtafovych A, Moult J, Baslé A, Burgin A, Craig TK, Edwards RA, Fass D, Hartmann MD, Korycinski M, Lewis RJ, Lorimer D, Lupas AN, Newman J, Peat TS, Piepenbrink KH, Prahlad J, van Raaij MJ, Rohwer F, Segall AM, Seguritan V, Sundberg EJ, Singh AK, Wilson MA, Schwede T. Some of the most interesting CASP11 targets through the eyes of their authors. Proteins 2015; 84 Suppl 1:34-50. [PMID: 26473983 PMCID: PMC4834066 DOI: 10.1002/prot.24942] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/17/2015] [Accepted: 10/11/2015] [Indexed: 11/17/2022]
Abstract
The Critical Assessment of protein Structure Prediction (CASP) experiment would not have been possible without the prediction targets provided by the experimental structural biology community. In this article, selected crystallographers providing targets for the CASP11 experiment discuss the functional and biological significance of the target proteins, highlight their most interesting structural features, and assess whether these features were correctly reproduced in the predictions submitted to CASP11. Proteins 2016; 84(Suppl 1):34–50. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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Affiliation(s)
| | - John Moult
- Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Alex Burgin
- Broad Institute, Cambridge, Massachusetts, 02142
| | | | - Robert A Edwards
- Department of Biology, San Diego State University, San Diego, California, 92182.,Department of Computer Science, San Diego State University, San Diego, California, 92182
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Mateusz Korycinski
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | | | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Janet Newman
- Biomedical Manufacturing Program, CSIRO, Parkville, VIC, Australia
| | - Thomas S Peat
- Biomedical Manufacturing Program, CSIRO, Parkville, VIC, Australia
| | - Kurt H Piepenbrink
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - Janani Prahlad
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588
| | - Mark J van Raaij
- Centro Nactional De Biotecnologia (CNB-CSIC), Madrid, E-28049, Spain
| | - Forest Rohwer
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, California, 92182
| | - Anca M Segall
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, California, 92182
| | | | - Eric J Sundberg
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, 21201.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, 21201.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - Abhimanyu K Singh
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, 4056, Switzerland. .,SIB Swiss Institute of Bioinformatics, Basel, 4056, Switzerland.
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56
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Ogilvie LA, Jones BV. The human gut virome: a multifaceted majority. Front Microbiol 2015; 6:918. [PMID: 26441861 PMCID: PMC4566309 DOI: 10.3389/fmicb.2015.00918] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 08/21/2015] [Indexed: 12/21/2022] Open
Abstract
Here, we outline our current understanding of the human gut virome, in particular the phage component of this ecosystem, highlighting progress, and challenges in viral discovery in this arena. We reveal how developments in high-throughput sequencing technologies and associated data analysis methodologies are helping to illuminate this abundant 'biological dark matter.' Current evidence suggests that the human gut virome is a highly individual but temporally stable collective, dominated by phages exhibiting a temperate lifestyle. This viral community also appears to encode a surprisingly rich functional repertoire that confers a range of attributes to their bacterial hosts, ranging from bacterial virulence and pathogenesis to maintaining host-microbiome stability and community resilience. Despite the significant advances in our understanding of the gut virome in recent years, it is clear that we remain in a period of discovery and revelation, as new methods and technologies begin to provide deeper understanding of the inherent ecological characteristics of this viral ecosystem. As our understanding increases, the nature of the multi-partite interactions occurring between host and microbiome will become clearer, helping us to more rationally define the concepts and principles that will underpin approaches to using human gut virome components for medical or biotechnological applications.
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Affiliation(s)
- Lesley A. Ogilvie
- School of Pharmacy and Biomolecular Sciences, University of BrightonBrighton, UK
- Alacris Theranostics GmbHBerlin, Germany
| | - Brian V. Jones
- School of Pharmacy and Biomolecular Sciences, University of BrightonBrighton, UK
- Queen Victoria Hospital NHS Foundation TrustEast Grinstead, UK
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57
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Zhang L, Zhang C, Gao R, Yang R. An Ensemble Method to Distinguish Bacteriophage Virion from Non-Virion Proteins Based on Protein Sequence Characteristics. Int J Mol Sci 2015; 16:21734-58. [PMID: 26370987 PMCID: PMC4613277 DOI: 10.3390/ijms160921734] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/16/2015] [Accepted: 08/25/2015] [Indexed: 11/16/2022] Open
Abstract
Bacteriophage virion proteins and non-virion proteins have distinct functions in biological processes, such as specificity determination for host bacteria, bacteriophage replication and transcription. Accurate identification of bacteriophage virion proteins from bacteriophage protein sequences is significant to understand the complex virulence mechanism in host bacteria and the influence of bacteriophages on the development of antibacterial drugs. In this study, an ensemble method for bacteriophage virion protein prediction from bacteriophage protein sequences is put forward with hybrid feature spaces incorporating CTD (composition, transition and distribution), bi-profile Bayes, PseAAC (pseudo-amino acid composition) and PSSM (position-specific scoring matrix). When performing on the training dataset 10-fold cross-validation, the presented method achieves a satisfactory prediction result with a sensitivity of 0.870, a specificity of 0.830, an accuracy of 0.850 and Matthew's correlation coefficient (MCC) of 0.701, respectively. To evaluate the prediction performance objectively, an independent testing dataset is used to evaluate the proposed method. Encouragingly, our proposed method performs better than previous studies with a sensitivity of 0.853, a specificity of 0.815, an accuracy of 0.831 and MCC of 0.662 on the independent testing dataset. These results suggest that the proposed method can be a potential candidate for bacteriophage virion protein prediction, which may provide a useful tool to find novel antibacterial drugs and to understand the relationship between bacteriophage and host bacteria. For the convenience of the vast majority of experimental Int. J. Mol. Sci. 2015, 16,21735 scientists, a user-friendly and publicly-accessible web-server for the proposed ensemble method is established.
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Affiliation(s)
- Lina Zhang
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
| | - Chengjin Zhang
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
- School of Mechanical, Electrical and Information Engineering, Shandong University, Weihai 264209, China.
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
| | - Runtao Yang
- School of Control Science and Engineering, Shandong University, Jinan 250061, China.
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58
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Sanchez SE, Cuevas DA, Rostron JE, Liang TY, Pivaroff CG, Haynes MR, Nulton J, Felts B, Bailey BA, Salamon P, Edwards RA, Burgin AB, Segall AM, Rohwer F. Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins. J Vis Exp 2015:e52854. [PMID: 26132888 PMCID: PMC4544906 DOI: 10.3791/52854] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysis by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.
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Affiliation(s)
| | - Daniel A Cuevas
- Computational Science Research Center, San Diego State University
| | | | - Tiffany Y Liang
- Bioinformatics and Medical Informatics Research Center, San Diego State University
| | | | | | - Jim Nulton
- Department of Mathematics and Statistics, San Diego State University
| | - Ben Felts
- Department of Mathematics and Statistics, San Diego State University
| | - Barbara A Bailey
- Department of Mathematics and Statistics, San Diego State University
| | - Peter Salamon
- Department of Mathematics and Statistics, San Diego State University
| | - Robert A Edwards
- Department of Biology, San Diego State University; Department of Computer Science, San Diego State University; Mathematics and Computer Science Division, Argonne National Laboratory
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59
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Ding H, Feng PM, Chen W, Lin H. Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis. MOLECULAR BIOSYSTEMS 2015; 10:2229-35. [PMID: 24931825 DOI: 10.1039/c4mb00316k] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bacteriophage virion proteins play extremely important roles in the fate of host bacterial cells. Accurate identification of bacteriophage virion proteins is very important for understanding their functions and clarifying the lysis mechanism of bacterial cells. In this study, a new sequence-based method was developed to identify phage virion proteins. In the new method, the protein sequences were initially formulated by the g-gap dipeptide compositions. Subsequently, the analysis of variance (ANOVA) with incremental feature selection (IFS) was used to search for the optimal feature set. It was observed that, in jackknife cross-validation, the optimal feature set including 160 optimized features can produce the maximum accuracy of 85.02%. By performing feature analysis, we found that the correlation between two amino acids with one gap was more important than other correlations for phage virion protein prediction and that some of the 1-gap dipeptides were important and mainly contributed to the virion protein prediction. This analysis will provide novel insights into the function of phage virion proteins. On the basis of the proposed method, an online web-server, PVPred, was established and can be freely accessed from the website (http://lin.uestc.edu.cn/server/PVPred). We believe that the PVPred will become a powerful tool to study phage virion proteins and to guide the related experimental validations.
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Affiliation(s)
- Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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60
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Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat Rev Microbiol 2015; 13:147-59. [PMID: 25639680 DOI: 10.1038/nrmicro3404] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Marine viruses have important roles in microbial mortality, gene transfer, metabolic reprogramming and biogeochemical cycling. In this Review, we discuss recent technological advances in marine virology including the use of near-quantitative, reproducible metagenomics for large-scale investigation of viral communities and the emergence of gene-based viral ecology. We also describe the reprogramming of microbially driven processes by viral metabolic genes, the identification of novel viruses using cultivation-dependent and cultivation-independent tools, and the potential for modelling studies to provide a framework for studying virus-host interactions. These transformative advances have set a rapid pace in exploring and predicting how marine viruses manipulate and respond to their environment.
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61
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Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GGZ, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK, Felts B, Dinsdale EA, Mokili JL, Edwards RA. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun 2014; 5:4498. [PMID: 25058116 PMCID: PMC4111155 DOI: 10.1038/ncomms5498] [Citation(s) in RCA: 502] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/25/2014] [Indexed: 01/20/2023] Open
Abstract
Metagenomics, or sequencing of the genetic material from a complete microbial community, is a
promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many
unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present
in the majority of published human faecal metagenomes, which we refer to as crAssphage. Its
~97 kbp genome is six times more abundant in publicly available metagenomes than all other
known phages together; it comprises up to 90% and 22% of all reads in virus-like particle
(VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all
human faecal metagenomic sequencing reads in the public databases. The majority of
crAssphage-encoded proteins match no known sequences in the database, which is why it was not
detected before. Using a new co-occurrence profiling approach, we predict a Bacteroides host
for this phage, consistent with Bacteroides-related protein homologues and a unique
carbohydrate-binding domain encoded in the phage genome. Metagenomic studies of microbial communities often report DNA sequences from
unidentified viruses. Here, Dutilh et al. analyse metagenomic data to reveal the complete
genome of an abundant, ubiquitous virus from human faeces, and predict that the virus infects
bacteria of the Bacteroides group.
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Affiliation(s)
- Bas E Dutilh
- 1] Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands [2] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [3] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [4] Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo. 373, Prédio Anexo ao Bloco A do Centro de Ciências da Saúde, Ilha do Fundão, CEP 21941-902 Rio de Janeiro, Brazil
| | - Noriko Cassman
- 1] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2]
| | - Katelyn McNair
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Savannah E Sanchez
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Genivaldo G Z Silva
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Lance Boling
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Jeremy J Barr
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Daan R Speth
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Victor Seguritan
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Ramy K Aziz
- 1] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt
| | - Ben Felts
- Department of Mathematics, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Elizabeth A Dinsdale
- 1] Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - John L Mokili
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA
| | - Robert A Edwards
- 1] Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [2] Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo. 373, Prédio Anexo ao Bloco A do Centro de Ciências da Saúde, Ilha do Fundão, CEP 21941-902 Rio de Janeiro, Brazil [3] Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, California 92182, USA [4] Division of Mathematics and Computer Science, Argonne National Laboratory, 9700 S Cass Ave B109, Argonne, Illinois 60439, USA
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Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins 2014; 82 Suppl 2:26-42. [PMID: 24318984 PMCID: PMC4072496 DOI: 10.1002/prot.24489] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 11/01/2013] [Accepted: 11/09/2013] [Indexed: 11/12/2022]
Abstract
For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, more than 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this article, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict transmembrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin (IL)-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fiber protein gene product 17 from bacteriophage T7; the bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally, an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins.
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Affiliation(s)
- Andriy Kryshtafovych
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616,
| | - John Moult
- Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA;
| | - Patrick Bales
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA;
| | - J. Fernando Bazan
- (1) Departments of Protein Engineering and (2) Structural Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, (3) Present address: 44th & Aspen Life Sciences, 924 4th St. N., Stillwater, MN 55082,
| | - Marco Biasini
- (1) Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; (2) SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50, 4056 Basel, Switzerland;
| | - Alex Burgin
- Broad Institute, 5 Cambridge Center, Cambridge, MA 02142, USA;
| | - Chen Chen
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA;
| | - Frank V. Cochran
- Department of Biochemistry, Stanford University, Stanford, California, 94305, USA;
| | | | - Rhiju Das
- (1) Department of Biochemistry, Stanford University, Stanford, California, 94305, USA; (2) Department of Physics, Stanford University, Stanford, California, 94305, USA,
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100 Israel, Tel: +972-8-934-3214; Fax: +972-8-934-4136;
| | - Carmela Garcia-Doval
- Centro Nactional de Biotecnologia (CNB-CSIC), calle Darwin 3, E-28049 Madrid, Spain.
| | - Osnat Herzberg
- (1) Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA; (2) Department of Chemistry and Biochemistry, University of Maryland, College Park;
| | - Donald Lorimer
- Emerald Bio, 7869 NE Day Rd W, Bainbridge Isle, WA 98110, USA;
| | - Hartmut Luecke
- Center for Biomembrane Systems and Depts. of Biochemistry, Biophysics & Computer Science, 3205 McGaugh Hall, University of California, Irvine, CA 92697-3900, USA;
| | - Xiaolei Ma
- (1) Departments of Protein Engineering and (2) Structural Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080 (3) Present address: Novartis Institutes for Biomedical Research, 4560 Horton St., Emeryville, CA 94608, USA;
| | - Daniel C. Nelson
- (1) Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA; (2) Department of Veterinary Medicine, University of Maryland, College Park,
| | - Mark J. van Raaij
- Centro Nactional de Biotecnologia (CNB-CSIC), calle Darwin 3, E-28049 Madrid, Spain.
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA 92182, USA;
| | - Anca Segall
- Department of Biology, San Diego State University, San Diego, CA 92182, USA;
| | - Victor Seguritan
- Department of Biology, San Diego State University, San Diego, CA 9218
| | - Kornelius Zeth
- Unidad de Biofisica (CSIC-UPV/EHU), Barrio Sarriena s/n 48940, Leioa, Vizcaya, SPAIN, and IKERBASQUE, Basque Foundation for Science, Bilbao, Spain;
| | - Torsten Schwede
- (1) Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; (2) SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50, 4056 Basel, Switzerland;
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63
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Ding H, Feng PM, Chen W, Lin H. Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis. MOLECULAR BIOSYSTEMS 2014. [DOI: 10.1039/c4mb00316k pmid: 24931825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bacteriophage virion proteins play extremely important roles in the fate of host bacterial cells.
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Affiliation(s)
- Hui Ding
- Key Laboratory for Neuro-Information of Ministry of Education
- Center of Bioinformatics
- School of Life Science and Technology
- University of Electronic Science and Technology of China
- Chengdu 610054, China
| | - Peng-Mian Feng
- School of Public Health
- Hebei United University
- Tangshan 063000, China
| | - Wei Chen
- Department of Physics
- School of Sciences
- and Center for Genomics and Computational Biology
- Hebei United University
- Tangshan 063000, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education
- Center of Bioinformatics
- School of Life Science and Technology
- University of Electronic Science and Technology of China
- Chengdu 610054, China
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64
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Phylogenomic network and comparative genomics reveal a diverged member of the ΦKZ-related group, marine vibrio phage ΦJM-2012. J Virol 2013; 87:12866-78. [PMID: 24067958 DOI: 10.1128/jvi.02656-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages are the largest reservoir of genetic diversity. Here we describe the novel phage ΦJM-2012. This natural isolate from marine Vibrio cyclitrophicus possesses very few gene contents relevant to other well-studied marine Vibrio phages. To better understand its evolutionary history, we built a mathematical model of pairwise relationships among 1,221 phage genomes, in which the genomes (nodes) are linked by edges representing the normalized number of shared orthologous protein families. This weighted network revealed that ΦJM-2012 was connected to only five members of the Pseudomonas ΦKZ-like phage family in an isolated network, strongly indicating that it belongs to this phage group. However, comparative genomic analyses highlighted an almost complete loss of colinearity with the ΦKZ-related genomes and little conservation of gene order, probably reflecting the action of distinct evolutionary forces on the genome of ΦJM-2012. In this phage, typical conserved core genes, including six RNA polymerase genes, were frequently displaced and the hyperplastic regions were rich in both unique genes and predicted unidirectional promoters with highly correlated orientations. Further, analysis of the ΦJM-2012 genome showed that segments of the conserved N-terminal parts of ΦKZ tail fiber paralogs exhibited evidence of combinatorial assortment, having switched transcriptional orientation, and there was recruitment and/or structural changes among phage endolysins and tail spike protein. Thus, this naturally occurring phage appears to have branched from a common ancestor of the ΦKZ-related groups, showing a distinct genomic architecture and unique genes that most likely reflect adaptation to its chosen host and environment.
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65
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Schmid T, Bogdan M, Günzel D. Discerning apical and basolateral properties of HT-29/B6 and IPEC-J2 cell layers by impedance spectroscopy, mathematical modeling and machine learning. PLoS One 2013; 8:e62913. [PMID: 23840862 PMCID: PMC3698131 DOI: 10.1371/journal.pone.0062913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Accepted: 03/26/2013] [Indexed: 11/19/2022] Open
Abstract
Quantifying changes in partial resistances of epithelial barriers in vitro is a challenging and time-consuming task in physiology and pathophysiology. Here, we demonstrate that electrical properties of epithelial barriers can be estimated reliably by combining impedance spectroscopy measurements, mathematical modeling and machine learning algorithms. Conventional impedance spectroscopy is often used to estimate epithelial capacitance as well as epithelial and subepithelial resistance. Based on this, the more refined two-path impedance spectroscopy makes it possible to further distinguish transcellular and paracellular resistances. In a next step, transcellular properties may be further divided into their apical and basolateral components. The accuracy of these derived values, however, strongly depends on the accuracy of the initial estimates. To obtain adequate accuracy in estimating subepithelial and epithelial resistance, artificial neural networks were trained to estimate these parameters from model impedance spectra. Spectra that reflect behavior of either HT-29/B6 or IPEC-J2 cells as well as the data scatter intrinsic to the used experimental setup were created computationally. To prove the proposed approach, reliability of the estimations was assessed with both modeled and measured impedance spectra. Transcellular and paracellular resistances obtained by such neural network-enhanced two-path impedance spectroscopy are shown to be sufficiently reliable to derive the underlying apical and basolateral resistances and capacitances. As an exemplary perturbation of pathophysiological importance, the effect of forskolin on the apical resistance of HT-29/B6 cells was quantified.
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Affiliation(s)
- Thomas Schmid
- Department of Mathematics and Computer Science, Universität Leipzig, Leipzig, Germany
| | - Martin Bogdan
- Department of Mathematics and Computer Science, Universität Leipzig, Leipzig, Germany
| | - Dorothee Günzel
- Institute of Clinical Physiology, Charité Universitätsmedizin Berlin, Berlin, Germany
- * E-mail:
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66
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Klumpp J, Fouts DE, Sozhamannan S. Bacteriophage functional genomics and its role in bacterial pathogen detection. Brief Funct Genomics 2013; 12:354-65. [DOI: 10.1093/bfgp/elt009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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67
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Liu X, Pei X, Li N, Zhang Y, Zhang X, Chen J, Lv L, Ma H, Wu X, Zhao W, Lou T. Improved glomerular filtration rate estimation by an artificial neural network. PLoS One 2013; 8:e58242. [PMID: 23516450 PMCID: PMC3596400 DOI: 10.1371/journal.pone.0058242] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 02/01/2013] [Indexed: 12/02/2022] Open
Abstract
Background Accurate evaluation of glomerular filtration rates (GFRs) is of critical importance in clinical practice. A previous study showed that models based on artificial neural networks (ANNs) could achieve a better performance than traditional equations. However, large-sample cross-sectional surveys have not resolved questions about ANN performance. Methods A total of 1,180 patients that had chronic kidney disease (CKD) were enrolled in the development data set, the internal validation data set and the external validation data set. Additional 222 patients that were admitted to two independent institutions were externally validated. Several ANNs were constructed and finally a Back Propagation network optimized by a genetic algorithm (GABP network) was chosen as a superior model, which included six input variables; i.e., serum creatinine, serum urea nitrogen, age, height, weight and gender, and estimated GFR as the one output variable. Performance was then compared with the Cockcroft-Gault equation, the MDRD equations and the CKD-EPI equation. Results In the external validation data set, Bland-Altman analysis demonstrated that the precision of the six-variable GABP network was the highest among all of the estimation models; i.e., 46.7 ml/min/1.73 m2 vs. a range from 71.3 to 101.7 ml/min/1.73 m2, allowing improvement in accuracy (15% accuracy, 49.0%; 30% accuracy, 75.1%; 50% accuracy, 90.5% [P<0.001 for all]) and CKD stage classification (misclassification rate of CKD stage, 32.4% vs. a range from 47.3% to 53.3% [P<0.001 for all]). Furthermore, in the additional external validation data set, precision and accuracy were improved by the six-variable GABP network. Conclusions A new ANN model (the six-variable GABP network) for CKD patients was developed that could provide a simple, more accurate and reliable means for the estimation of GFR and stage of CKD than traditional equations. Further validations are needed to assess the ability of the ANN model in diverse populations.
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Affiliation(s)
- Xun Liu
- Division of Nephrology, Department of Internal Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Department of Biomedical Engineering, South China University of Technology, Guangzhou, China
| | - Xiaohua Pei
- Division of Nephrology, Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ningshan Li
- Department of Biomedical Engineering, South China University of Technology, Guangzhou, China
- Department of Radiation Oncology, Chengdu International Cancer Treatment Hospital, Chengdu, China
| | - Yunong Zhang
- School of Information Science & Technology, Sun Yat-sen University, Guangzhou, China
| | - Xiang Zhang
- Department of Internal Medicine, JieYang People's Hospital, Jieyang, China
| | - Jinxia Chen
- Division of Nephrology, Department of Internal Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Linsheng Lv
- Operating Room, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Huijuan Ma
- Division of Nephrology, Department of Internal Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoming Wu
- Department of Biomedical Engineering, South China University of Technology, Guangzhou, China
- * E-mail: (TL); (WZ); (XW)
| | - Weihong Zhao
- Division of Nephrology, Department of Geriatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- * E-mail: (TL); (WZ); (XW)
| | - Tanqi Lou
- Division of Nephrology, Department of Internal Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- * E-mail: (TL); (WZ); (XW)
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