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Dawes IW. Ian Dawes-the third Pope-lucky to be a researcher. FEMS Yeast Res 2016; 16:fow040. [PMID: 27189365 DOI: 10.1093/femsyr/fow040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2016] [Indexed: 11/14/2022] Open
Abstract
Retrospective articles are an excuse for a rosy tinted view of one's life. This fully expurgated version is no exception. No "what the butler saw" or the vilification of enemies that one finds in political autobiographies - merely the account of one born to a generation of those whose forebears never had the chance to go to university and enjoy the subsequent fruits of that education - and of one who by chance stumbled into the world of yeast genetics and molecular biology, who had a lot of fun on the way and who never sought to leave it.
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Affiliation(s)
- Ian W Dawes
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Australia, Sydney, NSW 2052, Australia
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2
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Abstract
In recent years, there has been a noticeable rise in fungal infections related to non-albicans Candida species, including Candida glabrata which has both intrinsic resistance to and commonly acquired resistance to azole antifungals. Phylogenetically, C. glabrata is more closely related to the mostly non-pathogenic model organism Saccharomyces cerevisiae than to other Candida species. Despite C. glabrata's designation as a pathogen by Wickham in 1957, relatively little is known about its mechanism of virulence. Over the past few years, technology to analyse the molecular basis of infection has developed rapidly, and here we briefly review the major advances in tools and technologies available to explore and investigate the virulence of C. glabrata that have occurred over the past decade.
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Affiliation(s)
- Hsueh-lui Ho
- Biosciences, University of Exeter, Stocker Road, Exeter, Devon EX4 4QD, UK
| | - Ken Haynes
- Biosciences, University of Exeter, Stocker Road, Exeter, Devon EX4 4QD, UK
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Memorial Issue Dedicated to François Jacob. Res Microbiol 2014; 165:311-98. [PMID: 25756095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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Abstract
Although this volume is dedicated to honoring François Jacob, I would like my contribution to broaden the context by recalling the background within which the scientists of those times operated. The specific scientific accomplishments of Jacob will certainly be covered by the other contributors who collaborated with him. My handful of recollections presented here largely as vignettes is intended to give the reader a feeling for the elements, many social, that shaped the generation of scientists that included such central figures, Jacob, Lwoff, Monod. It is the tale of a generation trying to express its creativity in a world caught up in war, irrational values and unforgivable inhumanity. Even this limited account is a great story bringing us important lessons for thought.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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5
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Affiliation(s)
- Thomas D Bruns
- Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 97720-3102, USA
| | | | - Karen W Hughes
- Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996-1610, USA
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6
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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7
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Worden AZ, Cuvelier ML, Bartlett DH. In-depth analyses of marine microbial community genomics. Trends Microbiol 2006; 14:331-6. [PMID: 16820296 DOI: 10.1016/j.tim.2006.06.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 05/18/2006] [Accepted: 06/19/2006] [Indexed: 11/21/2022]
Abstract
Marine microbes have evolved to live along extreme environmental gradients, whether at the microscale, in proximity to particles or over the entire water column. Using community genomics, DeLong et al. highlight deduced biological differences that result from open-ocean depth gradients. The power of the large-insert libraries used is that both phylogeny and function can be inferred from the genetic material obtained--even for uncultured microbes. Together with complete genomes of marine isolates and advances in physiology and ecology, this study paves the way for ecosystems biology approaches to dynamics and controls of marine microbial populations.
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Affiliation(s)
- Alexandra Z Worden
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, FL 33149, USA.
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8
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Abstract
Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic genomes, a result consistent with those from multilocus sequence typing and representational difference analyses. The integration of various levels of ecological analyses coupled to the application and further development of high throughput technologies are accelerating the pace of discovery in microbial ecology.
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Affiliation(s)
- Jianping Xu
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.
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9
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Abstract
Lactococci are one of the most exploited microorganisms used in the manufacture of food. These intensively used cultures are generally characterized by having a rich plasmid complement. It could be argued that it is the plasmid complement of commercially utilized cultures that gives them their technical superiority and individuality. Consequently, it is timely to reflect on the desirable characteristics encoded on lactococcal plasmids. It is argued that plasmids play a key role in the evolution of modern starter strains and are a lot more than just selfish replicosomes but more essential necessities of intensively used commercial starters. Moreover, the study of plasmid biology provides a genetic blueprint that has proved essential for the generation of molecular tools for the genetic improvement of Lactococcus lactis.
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Affiliation(s)
- Susan Mills
- Teagasc, Dairy Products Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
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Abstract
Although genomics has classically focused on pure, easy-to-obtain samples, such as microbes that grow readily in culture or large animals and plants, these organisms represent only a fraction of the living or once-living organisms of interest. Many species are difficult to study in isolation because they fail to grow in laboratory culture, depend on other organisms for critical processes, or have become extinct. Methods that are based on DNA sequencing circumvent these obstacles, as DNA can be isolated directly from living or dead cells in various contexts. Such methods have led to the emergence of a new field, which is referred to as metagenomics.
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Affiliation(s)
- Susannah Green Tringe
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
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Abstract
As the global threat of drug-resistant pathogens continues to rise, new strategies and resources are required to accelerate and advance the drug discovery process. We believe that rapid progress in metagenomics has opened up a new era in the study of marine microbial diversity that enables direct access to the genomes of numerous uncultivable microorganisms. This review outlines recent developments and future trends in metagenomics-based drug discovery in marine microbial communities and their associated chemical prosperity.
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Affiliation(s)
- Xiang Li
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, China 510301.
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Cowan D, Meyer Q, Stafford W, Muyanga S, Cameron R, Wittwer P. Metagenomic gene discovery: past, present and future. Trends Biotechnol 2005; 23:321-9. [PMID: 15922085 DOI: 10.1016/j.tibtech.2005.04.001] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Revised: 02/22/2005] [Accepted: 04/04/2005] [Indexed: 11/29/2022]
Abstract
It is now widely accepted that the application of standard microbiological methods for the recovery of microorganisms from the environment has had limited success in providing access to the true extent of microbial biodiversity. It follows that much of the extant microbial genetic diversity (collectively termed the metagenome) remains unexploited, an issue of considerable relevance to a wider understanding of microbial communities and of considerable importance to the biotechnology industry. The recent development of technologies designed to access this wealth of genetic information through environmental nucleic acid extraction has provided a means of avoiding the limitations of culture-dependent genetic exploitation.
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Affiliation(s)
- Don Cowan
- Advanced Research Centre for Applied Microbiology, Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa.
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Abstract
Recent advances in shotgun sequencing and computational methods for genome assembly have advanced the field of metagenomics, the culture-independent cloning and analysis of microbial DNA extracted directly from an environmental sample, to provide glimpses into the life of uncultured microorganisms. More than 99% of prokaryotes in the environment cannot be cultured in the laboratory, a phenomenon that limits our understanding of microbial physiology, genetics, and community ecology. One way around this problem is metagenomics, the culture-independent cloning and analysis of microbial DNA extracted directly from an environmental sample. Recent advances in shotgun sequencing and computational methods for genome assembly have advanced the field of metagenomics to provide glimpses into the life of uncultured microorganisms.
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Affiliation(s)
- Patrick D Schloss
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, USA
| | - Jo Handelsman
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, USA
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Poxton IR. Molecular techniques in the diagnosis and management of infectious diseases: do they have a role in bacteriology? Med Princ Pract 2005; 14 Suppl 1:20-6. [PMID: 16103710 DOI: 10.1159/000086181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2004] [Accepted: 11/09/2004] [Indexed: 11/19/2022] Open
Abstract
The diagnosis and management of bacterial diseases has been done by traditional methods for a century or more. With the advent of molecular methods, however, these traditional approaches are being challenged. This review examines the pros and cons of traditional versus modern methods and tries to answer the question: when are molecular methods useful or essential? The following topics are addressed with appropriate examples: diagnosis; identification, typing and fingerprinting; pathogenesis; patient management; susceptibility to disease, and resistance to antimicrobial agents. It was concluded that there is still a place for both traditional and modern molecular methods, and training of staff must include both methodologies. Innovation is encouraged--but new technologies must be thoroughly tested before introduction into the routine lab. Liaison between laboratory scientist and physician is important, but above all experience is paramount.
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Affiliation(s)
- Ian R Poxton
- Division of Medical Microbiology, Centre for Infectious Diseases, University of Edinburgh College of Medicine and Veterinary Medicine, Edinburgh, UK.
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Mustafa AS. Mycobacterial gene cloning and expression, comparative genomics, bioinformatics and proteomics in relation to the development of new vaccines and diagnostic reagents. Med Princ Pract 2005; 14 Suppl 1:27-34. [PMID: 16103711 DOI: 10.1159/000086182] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2004] [Accepted: 07/17/2004] [Indexed: 11/19/2022] Open
Abstract
Recent advances in molecular and genomic techniques have facilitated research on several aspects of mycobacteriology, such as diagnosis and the identification of new vaccines and therapeutic targets for various diseases, including tuberculosis. The aim of this review was to analyze the implications of advances in molecular and genomic techniques on the development of new vaccines for tuberculosis as well as immunological reagents to diagnose the disease. Gene cloning and expression, DNA and protein sequencing, polymerase chain reaction, comparative genomics, bioinformatics, proteomics and DNA and peptide synthesis coupled with the application of cellular immunology techniques have led to the identification of several antigens of Mycobacterium tuberculosis, which have potential for diagnosis and vaccine applications. For example, cross-reactive mycobacterial antigens like heat shock proteins, MTB32 and MTB39, have been identified as new vaccine candidates, and antigens encoded by M. tuberculosis-specific genomic regions as new reagents for diagnosis.
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Affiliation(s)
- A S Mustafa
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait.
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Fraser CM. Exploring the boundaries of life. Trends Microbiol 2004; 12:404-5. [PMID: 15337160 DOI: 10.1016/j.tim.2004.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Claire M Fraser
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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Clewley JP. Shotgun sequencing the microbial diversity of the Earth. Commun Dis Public Health 2004; 7:229-30. [PMID: 15481219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- J P Clewley
- Virus Reference Division, Health Protection Agency Central Public Health Labortory
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20
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Abstract
Bacterial benefactors—and other prokaryotic pursuits
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Affiliation(s)
- Ariane Toussaint
- Belgian Fonds National de la Recherche Scientifique, Université Libre de Bruxelles, Brussels, Belgium.
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Abstract
Animal model systems are an intricate part of the discovery and development of new medicines. The sequencing of not only the human genome but also those of the various pathogenic bacteria, the nematode Caenorhabditis elegans, the fruitfly Drosophila, and the mouse has enabled the discovery of new drug targets to push forward at an unprecedented pace. The knowledge and tools in these "model" systems are allowing researchers to carry out experiments more efficiently and are uncovering previously hidden biological connections. While the history of bacteria, yeast, and mice in drug discovery are long, their roles are ever evolving. In contrast, the history of Drosophila and C. elegans at pharmaceutical companies is short. We will briefly review the historic role of each model organism in drug discovery and then update the readers as to the abilities and liabilities of each model within the context of drug development.
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Affiliation(s)
- Pamela M Carroll
- Department of Applied Genomics, Bristol-Myers Squibb, Pennington NJ 08534, USA
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Prickett K. Microbial genotyping is an underserved market. Pharmacogenomics 2003; 4:374. [PMID: 12831315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Affiliation(s)
- Katie Prickett
- Phermacogenomics, Ashley Publications Ltd, Unitec House, London, UK.
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Abstract
Richard Lenski is the John Hannah Distinguished Professor of Microbial Ecology at Michigan State University. He studies the ecology, genetics and evolution of bacteria in an experimental setting that enables him to observe the dynamical processes and outcomes across many generations. One of his experiments with Escherichia coli has passed 30,000 generations and is still on-going. A few years ago, he also began studying artificial life in the form of 'digital organisms' - computer programs that replicate, mutate, compete, and therefore evolve and adapt.
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Affiliation(s)
- Richard Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing 48824, USA.
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Boyce N. An ocean of genes. Speed-reading all the DNA in the sea--and the gut--could reveal worlds of unknown organisms. US News World Rep 2003; 134:62. [PMID: 12747119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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Abstract
In the last decade, DNA fingerprint techniques have become available to study the interperson transmission of tuberculosis and other mycobacterial infections. These methods have facilitated epidemiological studies at a population level. In addition, the species identification of rarely encountered mycobacteria has improved significantly. This article describes the state of the art of the main molecular typing methods for Mycobacterium tuberculosis complex and non-M. tuberculosis complex (atypical) mycobacteria. Important new insights that have been gained through molecular techniques into epidemiological aspects and diagnosis of mycobacterial diseases are highlighted.
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MESH Headings
- Animals
- Contact Tracing
- DNA Fingerprinting
- DNA, Bacterial/genetics
- Genetics, Microbial/trends
- Genotype
- Humans
- Molecular Epidemiology/methods
- Mycobacterium/classification
- Mycobacterium/genetics
- Mycobacterium/isolation & purification
- Mycobacterium Infections, Nontuberculous/epidemiology
- Mycobacterium Infections, Nontuberculous/genetics
- Mycobacterium Infections, Nontuberculous/transmission
- Mycobacterium tuberculosis/genetics
- Nontuberculous Mycobacteria/genetics
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- Reproducibility of Results
- Sequence Analysis, DNA
- Sequence Analysis, RNA
- Transformation, Bacterial
- Tuberculosis/epidemiology
- Tuberculosis/genetics
- Tuberculosis/transmission
- Tuberculosis, Multidrug-Resistant/epidemiology
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Affiliation(s)
- D Van Soolingen
- Mycobacteria Reference Department, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
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Affiliation(s)
- J C Post
- Center for Genomic Sciences, Allegheny Singer Research Institute, and the Department of Surgery, Allegheny General Hospital, MCP-Hahnemann University School of Medicine, Pittsburgh, PA 15212, USA
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Abstract
Complete genomic sequences of microbial pathogens and hosts offer sophisticated new strategies for studying host-pathogen interactions. DNA microarrays exploit primary sequence data to measure transcript levels and detect sequence polymorphisms, for every gene, simultaneously. The design and construction of a DNA microarray for any given microbial genome are straightforward. By monitoring microbial gene expression, one can predict the functions of uncharacterized genes, probe the physiologic adaptations made under various environmental conditions, identify virulence-associated genes, and test the effects of drugs. Similarly, by using host gene microarrays, one can explore host response at the level of gene expression and provide a molecular description of the events that follow infection. Host profiling might also identify gene expression signatures unique for each pathogen, thus providing a novel tool for diagnosis, prognosis, and clinical management of infectious disease.
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Davies J. The renaissance of microbiology. Int Microbiol 1998; 1:255-8. [PMID: 10943371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Microbiology is finally occupying its true position as the pre-eminent field in life sciences. This is due to advances in molecular techniques that confirm the evolutionary significance of the biology of microbes. It is anticipated that the use of comparative genomics will provide information that will advance the understanding of mechanisms of pathogenesis and the importance of secondary metabolism in social microbiology. More emphasis on studies of microbial diversity will increase its value in both fundamental microbiology and its industrial applications.
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Affiliation(s)
- J Davies
- TerraGen Diversity, Inc., Vancouver, B.C., Canada.
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Regueiro BJ. [Genetic therapy; the role of the microbiologist and his future]. Enferm Infecc Microbiol Clin 1997; 15:57-9. [PMID: 9101747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Stephenson J. Disease detectives are turning to molecular techniques to uncover emerging microbes. JAMA 1996; 275:176. [PMID: 8604157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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