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Bioinformatics and Microarray-Based Technologies to Viral Genome Sequence Analysis. MICROBIAL GENOMICS IN SUSTAINABLE AGROECOSYSTEMS 2019. [PMCID: PMC7121691 DOI: 10.1007/978-981-13-8739-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Identification of microbial pathogen is an important event which lead to diagnosis, treatment, and control of infections produce by them. The high-throughput technology like microarray and new-generation sequencing machine are able to generate huge amount of nucleotide sequences of viral and bacterial genome of both known and unknown pathogens. Few years ago it was the DNA microarrays which had great potential to screen all the known pathogens and yet to be identified pathogen simultaneously. But after the development of a new generation sequencing, technologies and advance computational approach researchers are looking forward for a complete understanding of microbes and host interactions. The powerful sequencing platform is rapidly transforming the landscape of microbial identification and characterization. As bioinformatics analysis tools and databases are easily available to researchers, the enormous amount of data generated can be meaningfully handled for better understanding of the microbial world. Here in this chapter, we present commentary on how the computational method incorporated with sequencing technique made easy for microbial detection and characterization.
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Marcato F, van den Brand H, Kemp B, van Reenen K. Evaluating Potential Biomarkers of Health and Performance in Veal Calves. Front Vet Sci 2018; 5:133. [PMID: 29977895 PMCID: PMC6021515 DOI: 10.3389/fvets.2018.00133] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 05/30/2018] [Indexed: 11/13/2022] Open
Abstract
Veal calves undergo many challenges in the early stages of their life. Such challenges, including mixing procedures and transportation of calves to the veal farm, may have a negative influence on growth rate, feed intake, metabolism, immunity and disease susceptibility of calves. As a consequence, many hematological, physiological, metabolic and immunological parameters of stressed calves might be altered on arrival at the veal farm. Some of these response variables might be useful as biomarkers of performance of calves at the veal farm as they might provide information about an ongoing disease process, or may predict future diseases. Biomarkers might be helpful to group and manage calves in different risk categories after arrival. By adopting treatment decisions and protocols on a risk-group or individual basis, it would be possible to improve animal health and reduce both disease incidence and antibiotic use. Moreover, the use of biomarkers might be an economically feasible approach as some of them do not need invasive techniques and others can be measured in blood already taken during routine checks. Previous literature mainly assessed the physiological responses of calves to transportation. However, information on the link between on-farm arrival data and future health and performance of veal calves is limited. This review, therefore, examined a wide range of papers and aimed to identify potential biomarkers of future health and performance.
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Affiliation(s)
- Francesca Marcato
- Adaptation Physiology Group, Wageningen University & Research, Wageningen, Netherlands
- Animal Production Systems Group, Livestock Research, Wageningen University & Research, Wageningen, Netherlands
| | - Henry van den Brand
- Adaptation Physiology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Bas Kemp
- Adaptation Physiology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Kees van Reenen
- Animal Production Systems Group, Livestock Research, Wageningen University & Research, Wageningen, Netherlands
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Moore RE, Kirwan J, Doherty MK, Whitfield PD. Biomarker Discovery in Animal Health and Disease: The Application of Post-Genomic Technologies. Biomark Insights 2017. [DOI: 10.1177/117727190700200040] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The causes of many important diseases in animals are complex and multifactorial, which present unique challenges. Biomarkers indicate the presence or extent of a biological process, which is directly linked to the clinical manifestations and outcome of a particular disease. Identifying biomarkers or biomarker profiles will be an important step towards disease characterization and management of disease in animals. The emergence of post-genomic technologies has led to the development of strategies aimed at identifying specific and sensitive biomarkers from the thousands of molecules present in a tissue or biological fluid. This review will summarize the current developments in biomarker discovery and will focus on the role of transcriptomics, proteomics and metabolomics in biomarker discovery for animal health and disease.
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Affiliation(s)
- Rowan E. Moore
- Proteomics and Functional Genomics Research Group, Faculty of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
| | - Jennifer Kirwan
- Proteomics and Functional Genomics Research Group, Faculty of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
| | - Mary K. Doherty
- Proteomics and Functional Genomics Research Group, Faculty of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
| | - Phillip D. Whitfield
- Proteomics and Functional Genomics Research Group, Faculty of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
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Hostetter G, Collins E, Varlan P, Edewaard E, Harbach PR, Hudson EA, Feenstra KJ, Turner LM, Berghuis BD, Resau JH, Jewell SD. Veterinary and human biobanking practices: enhancing molecular sample integrity. Vet Pathol 2013; 51:270-80. [PMID: 24227009 DOI: 10.1177/0300985813510532] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Animal models have historically informed veterinary and human pathophysiology. Next-generation genomic sequencing and molecular analyses using analytes derived from tissue require integrative approaches to determine macroanalyte integrity as well as morphology for imaging algorithms that can extend translational applications. The field of biospecimen science and biobanking will play critical roles in tissue sample collection and processing to ensure the integrity of macromolecules, aid experimental design, and provide more accurate and reproducible downstream genomic data. Herein, we employ animal experiments to combine protein expression analysis by microscopy with RNA integrity number and quantitative measures of morphologic changes of autolysis. These analyses can be used to predict the effect of preanalytic variables and provide the basis for standardized methods in tissue sample collection and processing. We also discuss the application of digital imaging with quantitative RNA and tissue-based protein measurements to show that genomic methods augment traditional in vivo imaging to support biospecimen science. To make these observations, we have established a time course experiment of murine kidney tissues that predicts conventional measures of RNA integrity by RIN analysis and provides reliable and accurate measures of biospecimen integrity and fitness, in particular for time points less than 3 hours post-tissue resection.
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Affiliation(s)
- G Hostetter
- Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA.
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Kort EJ, Norton P, Haak P, Berghuis B, Ramirez S, Resau J. Review Paper: Gene Expression Profiling in Veterinary and Human Medicine: Overview of Applications and Proposed Quality Control Practices. Vet Pathol 2009; 46:598-603. [DOI: 10.1354/vp.08-vp-0276-r-rev] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
High throughput molecular analysis of veterinary tissue samples is being applied to a wide range of research questions aimed at improving survival, development of diagnostic assays, and improving the economics of commercial production of animal products. Many of these efforts also, implicitly or explicitly, have ramifications for the clinical care of humans and, potentially, animals. Here we provide an overview of applications of gene expression profiling in veterinary research and practice. We then focus on the current state of quality control and quality assurance efforts in gene expression profiling studies, underscoring lessons learned from such analysis of human samples. Finally, we propose practices aimed at ensuring the reliability and reproducibility of such assays. The implementation of quality assurance practices by a trained pathologist is an essential link in the chain of events leading ultimately to reliable and reproducible research findings and appropriate clinical care.
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Affiliation(s)
- E. J. Kort
- Laboratorie of Molecular Epidemiology, Van Andel Research Institute, Grand Rapids, MI
| | - P. Norton
- Laboratorie of Molecular Epidemiology, Van Andel Research Institute, Grand Rapids, MI
| | - P. Haak
- Laboratorie of Molecular Epidemiology, Van Andel Research Institute, Grand Rapids, MI
| | - B. Berghuis
- Laboratorie of Analytical, Cellular, and Molecular Microscopy, Van Andel Research Institute, Grand Rapids, MI
| | - S. Ramirez
- Laboratorie of Analytical, Cellular, and Molecular Microscopy, Van Andel Research Institute, Grand Rapids, MI
| | - J. Resau
- Laboratorie of Molecular Epidemiology, Van Andel Research Institute, Grand Rapids, MI
- Laboratorie of Analytical, Cellular, and Molecular Microscopy, Van Andel Research Institute, Grand Rapids, MI
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Plummer PJ. Molecular diagnostics for the food animal practitioner. Vet Clin North Am Food Anim Pract 2007; 23:481-501, vi. [PMID: 17920458 DOI: 10.1016/j.cvfa.2007.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Molecular diagnostics are becoming widely used as routine diagnostic tests performed by food animal practitioners. This article discusses the variations of several commonly performed molecular assays with regard to their molecular basis and the appropriate interpretation of the results. Applications of these methods are discussed in the context of infectious disease testing and genetic testing of food animal species.
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Affiliation(s)
- Paul J Plummer
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, 1710 Veterinary Medicine Complex, Ames, IA 50011-1250, USA.
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Ghindilis AL, Smith MW, Schwarzkopf KR, Roth KM, Peyvan K, Munro SB, Lodes MJ, Stöver AG, Bernards K, Dill K, McShea A. CombiMatrix oligonucleotide arrays: Genotyping and gene expression assays employing electrochemical detection. Biosens Bioelectron 2007; 22:1853-60. [PMID: 16891109 DOI: 10.1016/j.bios.2006.06.024] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Revised: 06/14/2006] [Accepted: 06/20/2006] [Indexed: 11/15/2022]
Abstract
Electrochemical detection has been developed and assay performances studied for the CombiMatrix oligonucleotide microarray platform that contains 12,544 individually addressable microelectrodes (features) in a semiconductor matrix. The approach is based on the detection of redox active chemistries (such as horseradish peroxidase (HRP) and the associated substrate TMB) proximal to specific microarray electrodes. First, microarray probes are hybridized to biotin-labeled targets, second, the HRP-streptavidin conjugate binds to biotin, and enzymatic oxidation of the electron donor substrate then occurs. The detection current is generated due to electro-reduction of the HRP reaction product, and it is measured with the CombiMatrix ElectraSense Reader. Performance of the ElectraSense platform has been characterized using gene expression and genotyping assays to analyze: (i) signal to concentration dependence, (ii) assay resolution, (iii) coefficients of variation, (CV) and (iv) array-to-array reproducibility and data correlation. The ElectraSense platform was also compared to the standard fluorescent detection, and good consistency was observed between these two different detection techniques. A lower detection limit of 0.75 pM was obtained for ElectraSense as compared to the detection limit of 1.5 pM obtained for fluorescent detection. Thus, the ElectraSense platform has been used to develop nucleic acid assays for highly accurate genotyping of a variety of pathogens including bio-threat agents (such as Bacillus anthracis, Yersinia pestis, and other microorganisms including Escherichia coli, Bacillus subtilis, etc.) and common pathogens of the respiratory tract (e.g. influenza A virus).
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Affiliation(s)
- Andrey L Ghindilis
- CombiMatrix Corporation, 6500 Harbour Heights Pkwy, 301, Mukilteo, WA 98275, USA.
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