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Lukáčová A, Beck T, Trnková K, Trniková M, Krajčovič J, Vesteg M. Discrimination of Euglena gracilis strains Z and bacillaris by MALDI-TOF MS. J Appl Microbiol 2022; 133:930-942. [PMID: 35483969 DOI: 10.1111/jam.15600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/31/2022] [Accepted: 04/26/2022] [Indexed: 12/01/2022]
Abstract
AIMS Euglena gracilis is used as model organism for various microbiological, molecular biological and biotechnological studies. Its most studied wild type strains are Z and bacillaris, but their discrimination by standard molecular methods is difficult. Therefore, we decided to test the suitability of MALDI-TOF MS (matrix assisted laser desorption/ionization - time of flight mass spectrometry) for identification of E. gracilis and for discrimination of these two strains possessing functional chloroplasts. MALDI-TOF MS profiling was also tested for two white (non-photosynthetic) stable E. gracilis mutant strains Wgm ZOflL and W10 BSmL. METHODS AND RESULTS We have successfully obtained main spectrum profiles (MSPs) of E. gracilis strains Z, SAG 1224-5/25 and bacillaris, SAG 1224-5/15 using protein extraction procedure. Subsequent MALDI-TOF MS profiling of a number of tested samples and the comparison of the obtained protein profiles with our in-house database including MSPs of both strains has revealed that these two strains can be easily distinguished by MALDI-TOF MS based on score values over two in most cases. This method has also confirmed the ancestry of white mutant strains Wgm ZOflL and W10 BSmL, originally derived from strains Z and bacillaris, respectively. CONCLUSIONS MALDI-TOF MS is suitable, accurate and rapid method for discrimination of E. gracilis strains. SIGNIFICANCE AND IMPACT OF STUDY These results can have broad practical implications for laboratories cultivating various strains of euglenids, and they can be applied for their discrimination by MALDI-TOF MS.
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Affiliation(s)
- Alexandra Lukáčová
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, Banská Bystrica, Slovakia
| | - Terézia Beck
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, Banská Bystrica, Slovakia
| | - Katarína Trnková
- Department of the Environment, Faculty of Natural Sciences, Matej Bel University, Banská Bystrica, Slovakia
| | - Miriam Trniková
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, Banská Bystrica, Slovakia
| | - Juraj Krajčovič
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Trnava, Slovakia
| | - Matej Vesteg
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, Banská Bystrica, Slovakia
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2
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Fidelis CE, Franke M, de Abreu LCR, Jagielski T, Ribeiro MG, Dos Santos MV, Gonçalves JL. MALDI-TOF MS identification of Prototheca algae associated with bovine mastitis. J Vet Diagn Invest 2021; 33:1168-1171. [PMID: 34353173 DOI: 10.1177/10406387211036459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We evaluated the use of MALDI-TOF MS for the identification of 3 major, dairy-associated Prototheca species, namely, Prototheca bovis (formerly P. zopfii genotype 2), P. blaschkeae, and P. ciferrii (formerly P. zopfii genotype 1). The MALDI-TOF MS spectra established for those species were introduced into the reference spectra library of the Bruker Biotyper MALDI-TOF MS analysis software. Next, 31 Prototheca isolates from Holstein cows with mastitis, from herds located in the midwestern area of São Paulo State, Brazil, were subjected to MALDI-TOF MS profiling. MALDI-TOF MS allowed identification of 22 of 27 P. bovis and 3 of 4 P. blaschkeae isolates with scores >2.0, with 5 of 27 P. bovis and 1 of 4 P. blaschkeae isolates identified only to the genus level. With our extended algae database, MALDI-TOF MS can contribute to quick and effective speciation of Prototheca from mastitis cases.
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Affiliation(s)
- Carlos E Fidelis
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo-USP, Pirassununga, São Paulo, Brazil
| | - Manoela Franke
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo-USP, Pirassununga, São Paulo, Brazil
| | - Letícia C R de Abreu
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo-USP, Pirassununga, São Paulo, Brazil
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Márcio G Ribeiro
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Sciences, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Marcos V Dos Santos
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo-USP, Pirassununga, São Paulo, Brazil
| | - Juliano L Gonçalves
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo-USP, Pirassununga, São Paulo, Brazil.,Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
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3
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Masuda M, Jagielski T, Danesi P, Falcaro C, Bertola M, Krockenberger M, Malik R, Kano R. Protothecosis in Dogs and Cats-New Research Directions. Mycopathologia 2020; 186:143-152. [PMID: 33206310 DOI: 10.1007/s11046-020-00508-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 11/02/2020] [Indexed: 11/25/2022]
Abstract
Protothecosis refers to disease of humans and animals caused by infection with fungus-like, colourless microalgae of the genus Prototheca. Although protothecosis remains an uncommon infection, increasing numbers of human and animal cases are being diagnosed worldwide. This review summarises major new findings in basic science (sequencing analyses of sterol 14α-demethylase (CYP51/ERG11) genes and organelle genomes of Prototheca wickerhamii) to elucidate taxonomic features of this pathogen. Furthermore, this review updates and summarises the clinical features, diagnosis and treatment of protothecosis in dogs and cats. This content of this review is based on information presented at the medical phycology symposium held in the 20th Congress of the International Society for Human and Animal Mycology ( https://www.isham.org/ ).
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Affiliation(s)
- Michiaki Masuda
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi, Japan
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Patrizia Danesi
- Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, PD, Italy
| | - Christian Falcaro
- Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, PD, Italy
| | - Michela Bertola
- Istituto Zooprofilattico Sperimentale Delle Venezie, Legnaro, PD, Italy
| | - Mark Krockenberger
- Veterinary Pathology Diagnostic Services (VPDS), Sydney School of Veterinary Science, The University of Sydney, B14, Sydney, NSW, Australia
| | - Richard Malik
- Centre for Veterinary Education, The University of Sydney, B22, Sydney, NSW, 2006, Australia
| | - Rui Kano
- Department of Veterinary Dermatology, Nihon University School of Veterinary Medicine, 1866, Kameino, Fujisawa, Kanagawa, 252-0880, Japan.
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4
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Teng SY, Yew GY, Sukačová K, Show PL, Máša V, Chang JS. Microalgae with artificial intelligence: A digitalized perspective on genetics, systems and products. Biotechnol Adv 2020; 44:107631. [PMID: 32931875 DOI: 10.1016/j.biotechadv.2020.107631] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022]
Abstract
With recent advances in novel gene-editing tools such as RNAi, ZFNs, TALENs, and CRISPR-Cas9, the possibility of altering microalgae toward designed properties for various application is becoming a reality. Alteration of microalgae genomes can modify metabolic pathways to give elevated yields in lipids, biomass, and other components. The potential of such genetically optimized microalgae can give a "domino effect" in further providing optimization leverages down the supply chain, in aspects such as cultivation, processing, system design, process integration, and revolutionary products. However, the current level of understanding the functional information of various microalgae gene sequences is still primitive and insufficient as microalgae genome sequences are long and complex. From this perspective, this work proposes to link up this knowledge gap between microalgae genetic information and optimized bioproducts using Artificial Intelligence (AI). With the recent acceleration of AI research, large and complex data from microalgae research can be properly analyzed by combining the cutting-edge of both fields. In this work, the most suitable class of AI algorithms (such as active learning, semi-supervised learning, and meta-learning) are discussed for different cases of microalgae applications. This work concisely reviews the current state of the research milestones and highlight some of the state-of-art that has been carried out, providing insightful future pathways. The utilization of AI algorithms in microalgae cultivation, system optimization, and other aspects of the supply chain is also discussed. This work opens the pathway to a digitalized future for microalgae research and applications.
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Affiliation(s)
- Sin Yong Teng
- Brno University of Technology, Institute of Process Engineering, Technická 2896/2, 616 69, Brno, Czech Republic.
| | - Guo Yong Yew
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.
| | - Kateřina Sukačová
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, Brno 603 00, Czech Republic.
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.
| | - Vítězslav Máša
- Brno University of Technology, Institute of Process Engineering, Technická 2896/2, 616 69, Brno, Czech Republic.
| | - Jo-Shu Chang
- Department of Chemical and Materials Engineering, College of Engineering, Tunghai University, Taichung 407, Taiwan; Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan.
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5
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Nikoghosyan M, Schmidt M, Margaryan K, Loeffler-Wirth H, Arakelyan A, Binder H. SOMmelier-Intuitive Visualization of the Topology of Grapevine Genome Landscapes Using Artificial Neural Networks. Genes (Basel) 2020; 11:genes11070817. [PMID: 32709105 PMCID: PMC7397337 DOI: 10.3390/genes11070817] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/26/2020] [Accepted: 07/15/2020] [Indexed: 01/02/2023] Open
Abstract
Background: Whole-genome studies of vine cultivars have brought novel knowledge about the diversity, geographical relatedness, historical origin and dissemination, phenotype associations and genetic markers. Method: We applied SOM (self-organizing maps) portrayal, a neural network-based machine learning method, to re-analyze the genome-wide Single Nucleotide Polymorphism (SNP) data of nearly eight hundred grapevine cultivars. The method generates genome-specific data landscapes. Their topology reflects the geographical distribution of cultivars, indicates paths of cultivar dissemination in history and genome-phenotype associations about grape utilization. Results: The landscape of vine genomes resembles the geographic map of the Mediterranean world, reflecting two major dissemination paths from South Caucasus along a northern route via Balkan towards Western Europe and along a southern route via Palestine and Maghreb towards Iberian Peninsula. The Mediterranean and Black Sea, as well as the Pyrenees, constitute barriers for genetic exchange. On the coarsest level of stratification, cultivars divide into three major groups: Western Europe and Italian grapes, Iberian grapes and vine cultivars from Near East and Maghreb regions. Genetic landmarks were associated with agronomic traits, referring to their utilization as table and wine grapes. Pseudotime analysis describes the dissemination of grapevines in an East to West direction in different waves of cultivation. Conclusion: In analogy to the tasks of the wine waiter in gastronomy, the sommelier, our ‘SOMmelier’-approach supports understanding the diversity of grapevine genomes in the context of their geographic and historical background, using SOM portrayal. It offers an option to supplement vine cultivar passports by genome fingerprint portraits.
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Affiliation(s)
- Maria Nikoghosyan
- Research Group of Bioinformatics, Institute of Molecular Biology of National Academy of Sciences RA, Yerevan 0014, Armenia; (M.N.); (A.A.)
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia
| | - Maria Schmidt
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany; (M.S.); (H.L.-W.)
| | - Kristina Margaryan
- Research Group of Plant Genetics and Immunology, Institute of Molecular Biology of National Academy of Sciences RA, Yerevan 0014, Armenia;
- Department of Genetics and Cytology, Yerevan State University, Yerevan 0025, Armenia
| | - Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany; (M.S.); (H.L.-W.)
| | - Arsen Arakelyan
- Research Group of Bioinformatics, Institute of Molecular Biology of National Academy of Sciences RA, Yerevan 0014, Armenia; (M.N.); (A.A.)
- Institute of Biomedicine and Pharmacy, Russian-Armenian University, Yerevan 0051, Armenia
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany; (M.S.); (H.L.-W.)
- Correspondence:
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Bilz NC, Willscher E, Binder H, Böhnke J, Stanifer ML, Hübner D, Boulant S, Liebert UG, Claus C. Teratogenic Rubella Virus Alters the Endodermal Differentiation Capacity of Human Induced Pluripotent Stem Cells. Cells 2019; 8:cells8080870. [PMID: 31405163 PMCID: PMC6721684 DOI: 10.3390/cells8080870] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 12/31/2022] Open
Abstract
The study of congenital virus infections in humans requires suitable ex vivo platforms for the species-specific events during embryonal development. A prominent example for these infections is rubella virus (RV) which most commonly leads to defects in ear, heart, and eye development. We applied teratogenic RV to human induced pluripotent stem cells (iPSCs) followed by differentiation into cells of the three embryonic lineages (ecto-, meso-, and endoderm) as a cell culture model for blastocyst- and gastrulation-like stages. In the presence of RV, lineage-specific differentiation markers were expressed, indicating that lineage identity was maintained. However, portrait analysis of the transcriptomic expression signatures of all samples revealed that mock- and RV-infected endodermal cells were less related to each other than their ecto- and mesodermal counterparts. Markers for definitive endoderm were increased during RV infection. Profound alterations of the epigenetic landscape including the expression level of components of the chromatin remodeling complexes and an induction of type III interferons were found, especially after endodermal differentiation of RV-infected iPSCs. Moreover, the eye field transcription factors RAX and SIX3 and components of the gene set vasculogenesis were identified as dysregulated transcripts. Although iPSC morphology was maintained, the formation of embryoid bodies as three-dimensional cell aggregates and as such cellular adhesion capacity was impaired during RV infection. The correlation of the molecular alterations induced by RV during differentiation of iPSCs with the clinical signs of congenital rubella syndrome suggests mechanisms of viral impairment of human development.
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Affiliation(s)
- Nicole C Bilz
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany
| | - Edith Willscher
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Janik Böhnke
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany
| | - Megan L Stanifer
- Schaller Research Group at CellNetworks, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Denise Hübner
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany
| | - Steeve Boulant
- Schaller Research Group at CellNetworks, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Research Group "Cellular Polarity and Viral Infection" (F140), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Uwe G Liebert
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany
| | - Claudia Claus
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany.
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7
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Crossay T, Antheaume C, Redecker D, Bon L, Chedri N, Richert C, Guentas L, Cavaloc Y, Amir H. New method for the identification of arbuscular mycorrhizal fungi by proteomic-based biotyping of spores using MALDI-TOF-MS. Sci Rep 2017; 7:14306. [PMID: 29084976 PMCID: PMC5662746 DOI: 10.1038/s41598-017-14487-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/11/2017] [Indexed: 12/20/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF, Glomeromycota) are mutualistic symbionts associated with majority of land plants. These fungi play an important role in plant growth, but their taxonomic identification remains a challenge for academic research, culture collections and inoculum producers who need to certify their products. Identification of these fungi was traditionally performed based on their spore morphology. DNA sequence data have successfully been used to study the evolutionary relationships of AMF, develop molecular identification tools and assess their diversity in the environment. However, these methods require considerable expertise and are not well-adapted for "routine" quality control of culture collections and inoculum production. Here, we show that Matrix-Assisted Laser Desorption Ionisation Time of Flight Mass Spectrometry proteomic-based biotyping is a highly efficient approach for AMF identification. Nineteen isolates belonging to fourteen species, seven genera and five families were clearly differentiated by MALDI biotyping at the species level, and intraspecific differentiation was achieved for the majority. AMF identification by MALDI biotyping could be highly useful, not only for research but also in agricultural and environmental applications. Fast, accurate and inexpensive molecular mass determination and the possibility of automation make MALDI-TOF-MS a real alternative to conventional morphological and molecular methods for AMF identification.
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Affiliation(s)
- Thomas Crossay
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France
| | - Cyril Antheaume
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France. .,Plate-forme d'Analyse Chimique Strasbourg-Illkirch. Université de Strasbourg, F-67400, Illkirch, France.
| | - Dirk Redecker
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Lucie Bon
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France
| | - Nicolas Chedri
- Institut Pasteur, Bacteriology Research Unit, 98800, Nouméa, Nouvelle-Calédonie, France
| | | | - Linda Guentas
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France
| | - Yvon Cavaloc
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France
| | - Hamid Amir
- Institut des Sciences Exactes et Appliquées (EA 7484), Université de Nouvelle-Calédonie, BP R4, 98851, Nouméa, Nouvelle-Calédonie, France.
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Hirose N, Hua Z, Kato Y, Zhang Q, Li R, Nishimura K, Masuda M. Molecular Characterization of Prototheca strains isolated in China revealed the first cases of protothecosis associated with Prototheca zopfii genotype 1. Med Mycol 2017; 56:279-287. [DOI: 10.1093/mmy/myx039] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Noriyuki Hirose
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi 321-0293, Japan
- BD Japan, Co., Ltd., Tokyo 107-0052, Japan
| | - Zhensheng Hua
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi 321-0293, Japan
| | - Yuichi Kato
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi 321-0293, Japan
| | - Qiangqiang Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Ruoyu Li
- Department of Dermatology, Peking University First Hospital, Beijing, China
| | - Kazuko Nishimura
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi 321-0293, Japan
- First Laboratories, Co. Ltd., Kanagawa 211-0013, Japan
| | - Michiaki Masuda
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi 321-0293, Japan
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9
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Zhao H, Jia J, Chen Y, Tang J, Jiang Y, Wang J, Li Z, Zhao L. Strain-level characterization of cold-stressed Listeria monocytogenes
using maldi-tof mass fingerprinting. J Food Saf 2017. [DOI: 10.1111/jfs.12339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Han Zhao
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
| | - Juntao Jia
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
| | - Ying Chen
- Research Institute for Food Safety; Chinese Academy of Inspection and Quarantine; Beijing China
| | - Jing Tang
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
| | - Yinghui Jiang
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
| | - Jing Wang
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
| | - Zhengyi Li
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
| | - Liqing Zhao
- Technological Center; Shandong Entry-Exit Inspection and Quarantine Bureau; Qingdao China
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10
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Arakelyan A, Nersisyan L, Petrek M, Löffler-Wirth H, Binder H. Cartography of Pathway Signal Perturbations Identifies Distinct Molecular Pathomechanisms in Malignant and Chronic Lung Diseases. Front Genet 2016; 7:79. [PMID: 27200087 PMCID: PMC4859092 DOI: 10.3389/fgene.2016.00079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/20/2016] [Indexed: 12/16/2022] Open
Abstract
Lung diseases are described by a wide variety of developmental mechanisms and clinical manifestations. Accurate classification and diagnosis of lung diseases are the bases for development of effective treatments. While extensive studies are conducted toward characterization of various lung diseases at molecular level, no systematic approach has been developed so far. Here we have applied a methodology for pathway-centered mining of high throughput gene expression data to describe a wide range of lung diseases in the light of shared and specific pathway activity profiles. We have applied an algorithm combining a Pathway Signal Flow (PSF) algorithm for estimation of pathway activity deregulation states in lung diseases and malignancies, and a Self Organizing Maps algorithm for classification and clustering of the pathway activity profiles. The analysis results allowed clearly distinguish between cancer and non-cancer lung diseases. Lung cancers were characterized by pathways implicated in cell proliferation, metabolism, while non-malignant lung diseases were characterized by deregulations in pathways involved in immune/inflammatory response and fibrotic tissue remodeling. In contrast to lung malignancies, chronic lung diseases had relatively heterogeneous pathway deregulation profiles. We identified three groups of interstitial lung diseases and showed that the development of characteristic pathological processes, such as fibrosis, can be initiated by deregulations in different signaling pathways. In conclusion, this paper describes the pathobiology of lung diseases from systems viewpoint using pathway centered high-dimensional data mining approach. Our results contribute largely to current understanding of pathological events in lung cancers and non-malignant lung diseases. Moreover, this paper provides new insight into molecular mechanisms of a number of interstitial lung diseases that have been studied to a lesser extent.
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Affiliation(s)
- Arsen Arakelyan
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of SciencesYerevan, Armenia; College of Science and Engineering, American University of ArmeniaYerevan, Armenia
| | - Lilit Nersisyan
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of SciencesYerevan, Armenia; College of Science and Engineering, American University of ArmeniaYerevan, Armenia
| | - Martin Petrek
- Laboratory of Immunogenomics, Department of Pathological Physiology, Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University Olomouc Olomouc, Czech Republic
| | - Henry Löffler-Wirth
- Interdisciplinary Centre for Bioinformatics, University of Leipzig Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, University of Leipzig Leipzig, Germany
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11
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Masuda M, Hirose N, Ishikawa T, Ikawa Y, Nishimura K. Prototheca miyajii sp. nov., isolated from a patient with systemic protothecosis. Int J Syst Evol Microbiol 2016; 66:1510-1520. [DOI: 10.1099/ijsem.0.000911] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Michiaki Masuda
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi 321-0293, Japan
| | - Noriyuki Hirose
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi 321-0293, Japan
- BD Japan, Co., Ltd, Tokyo 107-0052, Japan
| | - Tomohiro Ishikawa
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi 321-0293, Japan
| | - Yoshiya Ikawa
- Laboratory of Biofunctional Chemistry, Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Kazuko Nishimura
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi 321-0293, Japan
- First Laboratories, Co. Ltd, Kanagawa 211-0013, Japan
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12
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Barbano D, Diaz R, Zhang L, Sandrin T, Gerken H, Dempster T. Rapid Characterization of Microalgae and Microalgae Mixtures Using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS). PLoS One 2015; 10:e0135337. [PMID: 26271045 PMCID: PMC4536233 DOI: 10.1371/journal.pone.0135337] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/21/2015] [Indexed: 11/28/2022] Open
Abstract
Current molecular methods to characterize microalgae are time-intensive and expensive. Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) may represent a rapid and economical alternative approach. The objectives of this study were to determine whether MALDI-TOF MS can be used to: 1) differentiate microalgae at the species and strain levels and 2) characterize simple microalgal mixtures. A common protein extraction sample preparation method was used to facilitate rapid mass spectrometry-based analysis of 31 microalgae. Each yielded spectra containing between 6 and 56 peaks in the m/z 2,000 to 20,000 range. The taxonomic resolution of this approach appeared higher than that of 18S rDNA sequence analysis. For example, two strains of Scenedesmus acutus differed only by two 18S rDNA nucleotides, but yielded distinct MALDI-TOF mass spectra. Mixtures of two and three microalgae yielded relatively complex spectra that contained peaks associated with members of each mixture. Interestingly, though, mixture-specific peaks were observed at m/z 11,048 and 11,230. Our results suggest that MALDI-TOF MS affords rapid characterization of individual microalgae and simple microalgal mixtures.
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Affiliation(s)
- Duane Barbano
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, Arizona, United States of America
| | - Regina Diaz
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, Arizona, United States of America
| | - Lin Zhang
- School of Mathematical and Natural Sciences, Arizona State University, MC 2352, P.O. Box 37100, Phoenix, Arizona, United States of America
| | - Todd Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, MC 2352, P.O. Box 37100, Phoenix, Arizona, United States of America
- * E-mail:
| | - Henri Gerken
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Building ISTB-3, Room 103, Mesa, Arizona, United States of America
| | - Thomas Dempster
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Building ISTB-3, Room 103, Mesa, Arizona, United States of America
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Strain-level visualized analysis of cold-stressed Vibrio parahaemolyticus based on MALDI-TOF mass fingerprinting. Microb Pathog 2015; 88:16-21. [PMID: 26255031 DOI: 10.1016/j.micpath.2015.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 07/29/2015] [Accepted: 08/03/2015] [Indexed: 11/23/2022]
Abstract
In this study, strain-level visualized analysis of cold-stressed Vibrio parahaemolyticus based on matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass fingerprinting was investigated. All the peptide mass fingerprinting profiles obtained were analyzed by self-organized map (SOM) and cluster analysis. Our results showed that the peptide mass fingerprinting profiles of V. parahaemolyticus substantially changed under cold stress at strain level. The cold-stressed V. parahaemolyticus strains were distributed to 14 neurons by SOM classification, almost totally different from the controls. This is the first time that so many strains had been chosen to study bacterial cold stress responses, which can help promote an overall understanding to stress responses of cold-stressed strains.
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Löffler-Wirth H, Kalcher M, Binder H. oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor. Bioinformatics 2015; 31:3225-7. [PMID: 26063839 DOI: 10.1093/bioinformatics/btv342] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 05/29/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Comprehensive analysis of genome-wide molecular data challenges bioinformatics methodology in terms of intuitive visualization with single-sample resolution, biomarker selection, functional information mining and highly granular stratification of sample classes. oposSOM combines those functionalities making use of a comprehensive analysis and visualization strategy based on self-organizing maps (SOM) machine learning which we call 'high-dimensional data portraying'. The method was successfully applied in a series of studies using mostly transcriptome data but also data of other OMICs realms. AVAILABILITY AND IMPLEMENTATION oposSOM is now publicly available as Bioconductor R package. CONTACT wirth@izbi.uni-leipzig.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Henry Löffler-Wirth
- Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig 04107, Germany
| | - Martin Kalcher
- Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig 04107, Germany
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, Leipzig University, Leipzig 04107, Germany
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15
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Emami K, Hack E, Nelson A, Brain CM, Lyne FM, Mesbahi E, Day JG, Caldwell GS. Proteomic-based biotyping reveals hidden diversity within a microalgae culture collection: An example using Dunaliella. Sci Rep 2015; 5:10036. [PMID: 25963242 PMCID: PMC4650328 DOI: 10.1038/srep10036] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/24/2015] [Indexed: 11/16/2022] Open
Abstract
Accurate and defendable taxonomic identification of microalgae strains is vital for culture collections, industry and academia; particularly when addressing issues of intellectual property. We demonstrate the remarkable effectiveness of Matrix Assisted Laser Desorption Ionisation Time of Flight Mass Spectrometry (MALDI-TOF-MS) biotyping to deliver rapid and accurate strain separation, even in situations where standard molecular tools prove ineffective. Highly distinctive MALDI spectra were obtained for thirty two biotechnologically interesting Dunaliella strains plus strains of Arthrospira, Chlorella, Isochrysis, Tetraselmis and a range of culturable co-occurring bacteria. Spectra were directly compared with genomic DNA sequences (internal transcribed spacer, ITS). Within individual Dunaliella isolates MALDI discriminated between strains with identical ITS sequences, thereby emphasising and enhancing knowledge of the diversity within microalgae culture collections. Further, MALDI spectra did not vary with culture age or growth stage during the course of the experiment; therefore MALDI presents stable and accurate strain-specific signature spectra. Bacterial contamination did not affect MALDI’s discriminating power. Biotyping by MALDI-TOF-MS will prove effective in situations wherein precise strain identification is vital, for example in cases involving intellectual property disputes and in monitoring and safeguarding biosecurity. MALDI should be accepted as a biotyping tool to complement and enhance standard molecular taxonomy for microalgae.
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Affiliation(s)
- Kaveh Emami
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Ethan Hack
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST
| | - Chelsea M Brain
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Fern M Lyne
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Ehsan Mesbahi
- Faculty of Science, Agriculture and Engineering (SAgE), Devonshire Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - John G Day
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, UK
| | - Gary S Caldwell
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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16
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Monitoring fungal growth on brown rice grains using rapid and non-destructive hyperspectral imaging. Int J Food Microbiol 2015; 199:93-100. [DOI: 10.1016/j.ijfoodmicro.2015.01.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 12/02/2014] [Accepted: 01/01/2015] [Indexed: 01/08/2023]
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17
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Siripatrawan U, Harte BR. Data visualization of Salmonella Typhimurium contamination in packaged fresh alfalfa sprouts using a Kohonen network. Talanta 2014; 136:128-35. [PMID: 25702994 DOI: 10.1016/j.talanta.2014.11.070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/01/2014] [Accepted: 11/03/2014] [Indexed: 10/24/2022]
Abstract
Class visualization of multi-dimensional data from analysis of volatile metabolic compounds monitored using an electronic nose based on metal oxide sensor array was attained using a Kohonen network. An array of 12 metal oxide based chemical sensors was used to monitor changes in the volatile compositions from the headspace of packaged fresh sprouts with and without Salmonella Typhimurium contamination. Kohonen׳s self-organizing map (SOM) was then created for learning different patterns of volatile metabolites. The Kohonen network comprising 225 nodes arranged into a two-dimensional hexagonal map was used to locate the samples on the map to facilitate sample classification. Graphical maps including the unified matrix, component planes, and hit histograms were described to characterize the relation between samples. The clustering of samples with different levels of S. Typhimurium contamination could be visually distinguishable on the SOM. The Kohonen network proved to be advantageous in visualization of multi-dimensional nonlinear data and provided a clearer separation of different sample groups than a conventional linear principal component analysis (PCA) approach. The sensor array integrated with the Kohonen network could be used as a rapid and nondestructive method to distinguish samples with different levels of S. Typhimurium contamination. Although the analyses were performed on samples with natural background microbiota of about 7 Log(CFU/g), this microbiota did not affect the S. Typhimurium detection. The proposed method has potential to rapidly detect a target foodborne pathogen in real-life food samples instantaneously without subsequently culturing stages.
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Affiliation(s)
- Ubonrat Siripatrawan
- Department of Food Technology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
| | - Bruce R Harte
- School of Packaging, Michigan State University, East Lansing, MI, USA
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18
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Binder H, Wirth H, Arakelyan A, Lembcke K, Tiys ES, Ivanisenko VA, Kolchanov NA, Kononikhin A, Popov I, Nikolaev EN, Pastushkova LK, Larina IM. Time-course human urine proteomics in space-flight simulation experiments. BMC Genomics 2014; 15 Suppl 12:S2. [PMID: 25563515 PMCID: PMC4303941 DOI: 10.1186/1471-2164-15-s12-s2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Long-term space travel simulation experiments enabled to discover different aspects of human metabolism such as the complexity of NaCl salt balance. Detailed proteomics data were collected during the Mars105 isolation experiment enabling a deeper insight into the molecular processes involved. RESULTS We studied the abundance of about two thousand proteins extracted from urine samples of six volunteers collected weekly during a 105-day isolation experiment under controlled dietary conditions including progressive reduction of salt consumption. Machine learning using Self Organizing maps (SOM) in combination with different analysis tools was applied to describe the time trajectories of protein abundance in urine. The method enables a personalized and intuitive view on the physiological state of the volunteers. The abundance of more than one half of the proteins measured clearly changes in the course of the experiment. The trajectory splits roughly into three time ranges, an early (week 1-6), an intermediate (week 7-11) and a late one (week 12-15). Regulatory modes associated with distinct biological processes were identified using previous knowledge by applying enrichment and pathway flow analysis. Early protein activation modes can be related to immune response and inflammatory processes, activation at intermediate times to developmental and proliferative processes and late activations to stress and responses to chemicals. CONCLUSIONS The protein abundance profiles support previous results about alternative mechanisms of salt storage in an osmotically inactive form. We hypothesize that reduced NaCl consumption of about 6 g/day presumably will reduce or even prevent the activation of inflammatory processes observed in the early time range of isolation. SOM machine learning in combination with analysis methods of class discovery and functional annotation enable the straightforward analysis of complex proteomics data sets generated by means of mass spectrometry.
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Affiliation(s)
- Hans Binder
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Henry Wirth
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | | | - Kathrin Lembcke
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Evgeny S Tiys
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | | | | | - Alexey Kononikhin
- Talrose Institute for Energy Problems of Chemical Physics, RAS, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
| | - Igor Popov
- Emanuel Institute for Biochemical Physics, RAS, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
| | - Evgeny N Nikolaev
- Talrose Institute for Energy Problems of Chemical Physics, RAS, Moscow, Russia
- Emanuel Institute for Biochemical Physics, RAS, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Lyudmila Kh Pastushkova
- Institute of Biomedical Problems - Russian Federation State Scientific Research Center RAS, Moscow, Russia
| | - Irina M Larina
- Institute of Biomedical Problems - Russian Federation State Scientific Research Center RAS, Moscow, Russia
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19
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How stemlike are sphere cultures from long-term cancer cell lines? Lessons from mouse glioma models. J Neuropathol Exp Neurol 2014; 73:1062-77. [PMID: 25289892 DOI: 10.1097/nen.0000000000000130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cancer stem cells may mediate therapy resistance and recurrence in various types of cancer, including glioblastoma. Cancer stemlike cells can be isolated from long-term cancer cell lines, including glioma lines. Using sphere formation as a model for cancer cell stemness in vitro, we derived sphere cultures from SMA-497, SMA-540, SMA-560, and GL-261 glioma cells. Gene expression and proteomics profiling demonstrated that sphere cultures uniformly showed an elevated expression of stemness-associated genes, notably including CD44. Differences in neural lineage marker expression between nonsphere and sphere cultures were heterogeneous except for a uniform reduction of β-III-tubulin in sphere cultures. All sphere cultures showed slower growth. Self-renewal capacity was influenced by medium conditions but not nonsphere versus sphere culture phenotype. Sphere cultures were more resistant to irradiation, whereas both nonsphere and sphere cultures were highly resistant to temozolomide. Nonsphere cells formed more aggressive tumors in syngeneic mice than sphere cells in all models except SMA-560. There were no major differences in vascularization or infiltration by T cells or microglia/macrophages between nonsphere and sphere cell-derived tumors implanted in syngeneic hosts. Together, these data indicate that mouse glioma cell lines may be induced in vitro to form spheres that acquire features of stemness, but they do not exhibit a uniform biologic phenotype, thereby challenging the view that they represent a superior model system.
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20
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Hopp L, Wirth H, Fasold M, Binder H. Portraying the expression landscapes of cancer subtypes. ACTA ACUST UNITED AC 2014. [DOI: 10.4161/sysb.25897] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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21
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Algal biomass analysis by laser-based analytical techniques--a review. SENSORS 2014; 14:17725-52. [PMID: 25251409 PMCID: PMC4208246 DOI: 10.3390/s140917725] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 09/05/2014] [Accepted: 09/11/2014] [Indexed: 12/12/2022]
Abstract
Algal biomass that is represented mainly by commercially grown algal strains has recently found many potential applications in various fields of interest. Its utilization has been found advantageous in the fields of bioremediation, biofuel production and the food industry. This paper reviews recent developments in the analysis of algal biomass with the main focus on the Laser-Induced Breakdown Spectroscopy, Raman spectroscopy, and partly Laser-Ablation Inductively Coupled Plasma techniques. The advantages of the selected laser-based analytical techniques are revealed and their fields of use are discussed in detail.
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22
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Hopp L, Lembcke K, Binder H, Wirth H. Portraying the Expression Landscapes of B-CellLymphoma-Intuitive Detection of Outlier Samples and of Molecular Subtypes. BIOLOGY 2013; 2:1411-37. [PMID: 24833231 PMCID: PMC4009791 DOI: 10.3390/biology2041411] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/01/2013] [Accepted: 11/05/2013] [Indexed: 01/03/2023]
Abstract
We present an analytic framework based on Self-Organizing Map (SOM) machine learning to study large scale patient data sets. The potency of the approach is demonstrated in a case study using gene expression data of more than 200 mature aggressive B-cell lymphoma patients. The method portrays each sample with individual resolution, characterizes the subtypes, disentangles the expression patterns into distinct modules, extracts their functional context using enrichment techniques and enables investigation of the similarity relations between the samples. The method also allows to detect and to correct outliers caused by contaminations. Based on our analysis, we propose a refined classification of B-cell Lymphoma into four molecular subtypes which are characterized by differential functional and clinical characteristics.
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Affiliation(s)
- Lydia Hopp
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, Leipzig 04107, Germany.
| | - Kathrin Lembcke
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, Leipzig 04107, Germany.
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, Leipzig 04107, Germany.
| | - Henry Wirth
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, Leipzig 04107, Germany.
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23
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Hirose N, Nishimura K, Inoue-Sakamoto M, Masuda M. Ribosomal internal transcribed spacer of Prototheca wickerhamii has characteristic structure useful for identification and genotyping. PLoS One 2013; 8:e81223. [PMID: 24312279 PMCID: PMC3842318 DOI: 10.1371/journal.pone.0081223] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/09/2013] [Indexed: 11/19/2022] Open
Abstract
Prototheca species are achlorophyllous algae ubiquitous in nature and known to cause localized and systemic infection both in humans and animals. Although identification of the Prototheca species in clinical specimens is a challenge, there are an increasing number of cases in which molecular techniques have successfully been used for diagnosis of protothecosis. In this study, we characterized nuclear ribosomal DNA (rDNA) of a strain of Prototheca (FL11-0001) isolated from a dermatitis patient in Japan for its species identification. When nuclear rDNA of FL11-0001 and that of various other Prototheca strains were compared by polymerase chain reaction (PCR), the results indicated that the sizes of ribosomal internal transcribed spacer (ITS) were different in a species-dependent manner, suggesting that the variation might be useful for differentiation of Prototheca spp. Especially, ITS of P. wickerhamii, the most common cause of human protothecosis, was distinctively larger than that of other Prototheca spp. FL11-0001, whose ITS was comparably large, could easily be identified as P. wickerhamii. The usefulness of the PCR analysis of ITS was also demonstrated by the discovery that one of the clinical isolates that had previously been designated as P. wickerhamii was likely a novel species. Furthermore, our data demonstrated that nucleotide sequences of P. wickerhamii ITS are heterogenous between different rDNA copies in each strain and also polymorphic between strains. Phylogenetic analysis suggested that the ITS sequences could be classified to four clades, based on which P. wickerhamii strains might be grouped into at least two genotypes. Comprehensive characterization of Prototheca rDNA may provide valuable insights into diagnosis and epidemiology of protothecosis, as well as evolution and taxonomy of Prototheca and related organisms.
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Affiliation(s)
- Noriyuki Hirose
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi, Japan
- Fukushima Plant, BD Japan, Co., Ltd., Fukushima, Japan
| | - Kazuko Nishimura
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi, Japan
- First Laboratories, Co. Ltd., Kanagawa, Japan
| | - Maki Inoue-Sakamoto
- Dermatology Division, Amakusa Chuo General Hospital, Kumamoto, Japan
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Michiaki Masuda
- Department of Microbiology, Dokkyo Medical University School of Medicine, Tochigi, Japan
- * E-mail:
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Murugaiyan J, Weise C, von Bergen M, Roesler U. Two-dimensional proteome reference map of Prototheca zopfii
revealed reduced metabolism and enhanced signal transduction as adaptation to an infectious life style. Proteomics 2013; 13:2664-9. [DOI: 10.1002/pmic.201300037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/03/2013] [Accepted: 06/26/2013] [Indexed: 02/04/2023]
Affiliation(s)
- Jayaseelan Murugaiyan
- Institute of Animal Health and Environmental Hygiene; Freie Universitaet-Berlin; Berlin Germany
| | - Christoph Weise
- Institute for Chemistry and Biochemistry; Freie Universitaet-Berlin; Berlin Germany
| | - Martin von Bergen
- Department of Proteomics; Helmholtz Centre for Environmental Research-UFZ; Leipzig Germany
- Department of Metabolomics; Helmholtz Centre for Environmental Research-UFZ; Leipzig Germany
- Department of Biotechnology; Chemistry and Environmental Engineering; Aalborg University; Aalborg Denmark
| | - Uwe Roesler
- Institute of Animal Health and Environmental Hygiene; Freie Universitaet-Berlin; Berlin Germany
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Zampieri D, Santos VG, Braga PAC, Ferreira CR, Ballottin D, Tasic L, Basso AC, Sanches BV, Pontes JHF, da Silva BP, Garboggini FF, Eberlin MN, Tata A. Microorganisms in cryopreserved semen and culture media used in the in vitro production (IVP) of bovine embryos identified by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). Theriogenology 2013; 80:337-45. [PMID: 23756041 DOI: 10.1016/j.theriogenology.2013.04.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/15/2013] [Accepted: 04/22/2013] [Indexed: 01/04/2023]
Abstract
Commercial cattle breeders produce their own herd offspring for the dairy and beef market using artificial insemination. The procedure involves sanitary risks associated with the collection and commercialization of the germplasm, and the in vitro production and transfer of the bovine embryos must be monitored by strict health surveillance. To avoid the spreading of infectious diseases, one must rely on using controlled and monitored germplasm, media, and reagents that are guaranteed free of pathogens. In this article, we investigated the use of a new mass spectrometric approach for fast and accurate identification of bacteria and fungi in bovine semen and in culture media employed in the embryo in vitro production process. The microorganisms isolated from samples obtained in a commercial bovine embryo IVP setting were identified in a few minutes by their conserved peptide/protein profile, obtained applying matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS), matched against a commercial database. The successful microorganisms MS identification has been confirmed by DNA amplification and sequencing. Therefore, the MS technique seems to offer a powerful tool for rapid and accurate microorganism identification in semen and culture media samples.
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Affiliation(s)
- Dávila Zampieri
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, Sao Paulo, Brazil
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26
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Braga PAC, Tata A, Gonçalves dos Santos V, Barreiro JR, Schwab NV, Veiga dos Santos M, Eberlin MN, Ferreira CR. Bacterial identification: from the agar plate to the mass spectrometer. RSC Adv 2013. [DOI: 10.1039/c2ra22063f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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