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Semi-supervised learning for MALDI–TOF mass spectrometry data classification: an application in the salmon industry. Neural Comput Appl 2023. [DOI: 10.1007/s00521-023-08333-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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Radmehr B, Zaferanloo B, Tran T, Beale DJ, Palombo EA. Prevalence and Characteristics of Bacillus cereus Group Isolated from Raw and Pasteurised Milk. Curr Microbiol 2020; 77:3065-3075. [PMID: 32696237 DOI: 10.1007/s00284-020-02129-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/11/2020] [Indexed: 12/12/2022]
Abstract
The elimination of spore-forming bacteria is not guaranteed by current pasteurisation processes and is a challenging problem for the dairy industry. Given that Bacillus cereus sensu lato (B. cereus group) is an important foodborne pathogen and spoiler in the dairy industry, this study aimed at evaluating the prevalence and characteristics of B. cereus group in raw and pasteurised milk samples collected in Victoria, Australia. Isolated B. cereus group were tested for antimicrobial susceptibility, biofilm formation and virulence properties. Genetic diversity was assessed using ERIC-PCR. Proteomic profiling using MALDI-TOF MS and chemical profiling using Fourier-transform infrared (FTIR) spectroscopy were also applied for clustering of the isolates. Results showed 42.3% of milk samples contained B. cereus group, with a higher contamination level for pasteurised milk. Virulence studies identified genes nheA, nheB, hblA and nheC in most isolates and cyk gene in 46% of all isolates. Antimicrobial susceptibility testing showed a high prevalence of resistance towards ampicillin, ceftriaxone and penicillin. The biofilm-forming capacity of our isolates showed that most (53.7%) had the ability to form a biofilm. Genetic profiling using ERIC-PCR placed most B. cereus group isolates from pasteurised milk in the same cluster, indicating that they probably originated from a similar source. Raw milk isolates showed greater diversity indicating various sources. FTIR spectroscopy showed high agreement with genetic profiling. In contrast, low agreement between proteomic (MALDI-TOF MS) and genetic typing was observed. The present study showed that the FTIR spectroscopy could be adopted as a rapid tool for the typing of B. cereus group. Overall, the virulence and antimicrobial resistance characteristics, together with the ability of isolates to produce biofilm, indicate the importance of B. cereus group in the Australian dairy industry.
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Affiliation(s)
- Behrad Radmehr
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
| | - Bita Zaferanloo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
| | - Thien Tran
- Bruker Pty Ltd, Preston, VIC, 3072, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD, 4102, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia.
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López-Fernández H, Santos HM, Capelo JL, Fdez-Riverola F, Glez-Peña D, Reboiro-Jato M. Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery. BMC Bioinformatics 2015; 16:318. [PMID: 26437641 PMCID: PMC4595311 DOI: 10.1186/s12859-015-0752-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/28/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mass spectrometry is one of the most important techniques in the field of proteomics. MALDI-TOF mass spectrometry has become popular during the last decade due to its high speed and sensitivity for detecting proteins and peptides. MALDI-TOF-MS can be also used in combination with Machine Learning techniques and statistical methods for knowledge discovery. Although there are many software libraries and tools that can be combined for these kind of analysis, there is still a need for all-in-one solutions with graphical user-friendly interfaces and avoiding the need of programming skills. RESULTS Mass-Up, an open software multiplatform application for MALDI-TOF-MS knowledge discovery is herein presented. Mass-Up software allows data preprocessing, as well as subsequent analysis including (i) biomarker discovery, (ii) clustering, (iii) biclustering, (iv) three-dimensional PCA visualization and (v) classification of large sets of spectra data. CONCLUSIONS Mass-Up brings knowledge discovery within reach of MALDI-TOF-MS researchers. Mass-Up is distributed under license GPLv3 and it is open and free to all users at http://sing.ei.uvigo.es/mass-up.
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Affiliation(s)
- H López-Fernández
- Informatics Department, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain. .,Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Pontevedra, Spain.
| | - H M Santos
- BIOSCOPE Research Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de Lisboa, Caparica, Setubal, Portugal.
| | - J L Capelo
- BIOSCOPE Research Group, UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, Universidade NOVA de Lisboa, Caparica, Setubal, Portugal.
| | - F Fdez-Riverola
- Informatics Department, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain. .,Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Pontevedra, Spain.
| | - D Glez-Peña
- Informatics Department, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain. .,Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Pontevedra, Spain.
| | - M Reboiro-Jato
- Informatics Department, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain. .,Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Pontevedra, Spain.
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Characterization of the Edwardsiella tarda proteome in response to different environmental stresses. J Proteomics 2013; 80:320-33. [DOI: 10.1016/j.jprot.2013.01.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 12/17/2012] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
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Tanz SK, Castleden I, Small ID, Millar AH. Fluorescent protein tagging as a tool to define the subcellular distribution of proteins in plants. FRONTIERS IN PLANT SCIENCE 2013; 4:214. [PMID: 23805149 PMCID: PMC3690342 DOI: 10.3389/fpls.2013.00214] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/05/2013] [Indexed: 05/18/2023]
Abstract
Fluorescent protein (FP) tagging approaches are widely used to determine the subcellular location of plant proteins. Here we give a brief overview of FP approaches, highlight potential technical problems, and discuss what to consider when designing FP/protein fusion constructs and performing transformation assays. We analyze published FP tagging data sets along with data from proteomics studies collated in SUBA3, a subcellular location database for Arabidopsis proteins, and assess the reliability of these data sets by comparing them. We also outline the limitations of the FP tagging approach for defining protein location and investigate multiple localization claims by FP tagging. We conclude that the collation of localization datasets in databases like SUBA3 is helpful for revealing discrepancies in location attributions by different techniques and/or by different research groups.
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Affiliation(s)
- Sandra K. Tanz
- ARC Centre of Excellence in Plant Energy Biology, The University of Western AustraliaPerth, WA, Australia
- *Correspondence: Sandra K. Tanz, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia e-mail:
| | - Ian Castleden
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
| | - Ian D. Small
- ARC Centre of Excellence in Plant Energy Biology, The University of Western AustraliaPerth, WA, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
| | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western AustraliaPerth, WA, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western AustraliaPerth, WA, Australia
- Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western AustraliaPerth, WA, Australia
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