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Wanapat M, Dagaew G, Sommai S, Matra M, Suriyapha C, Prachumchai R, Muslykhah U, Phupaboon S. The application of omics technologies for understanding tropical plants-based bioactive compounds in ruminants: a review. J Anim Sci Biotechnol 2024; 15:58. [PMID: 38689368 PMCID: PMC11062008 DOI: 10.1186/s40104-024-01017-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 02/29/2024] [Indexed: 05/02/2024] Open
Abstract
Finding out how diet impacts health and metabolism while concentrating on the functional qualities and bioactive components of food is the crucial scientific objective of nutritional research. The complex relationship between metabolism and nutrition could be investigated with cutting-edge "omics" and bioinformatics techniques. This review paper provides an overview of the use of omics technologies in nutritional research, with a particular emphasis on the new applications of transcriptomics, proteomics, metabolomics, and genomes in functional and biological activity research on ruminant livestock and products in the tropical regions. A wealth of knowledge has been uncovered regarding the regulation and use of numerous physiological and pathological processes by gene, mRNA, protein, and metabolite expressions under various physiological situations and guidelines. In particular, the components of meat and milk were assessed using omics research utilizing the various methods of transcriptomics, proteomics, metabolomics, and genomes. The goal of this review is to use omics technologies-which have been steadily gaining popularity as technological tools-to develop new nutritional, genetic, and leadership strategies to improve animal products and their quality control. We also present an overview of the new applications of omics technologies in cattle production and employ nutriomics and foodomics technologies to investigate the microbes in the rumen ecology. Thus, the application of state-of-the-art omics technology may aid in our understanding of how species and/or breeds adapt, and the sustainability of tropical animal production, in the long run, is becoming increasingly important as a means of mitigating the consequences of climate change.
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Affiliation(s)
- Metha Wanapat
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Gamonmas Dagaew
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sukruthai Sommai
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Maharach Matra
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chaichana Suriyapha
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Rittikeard Prachumchai
- Department of Animal Science, Faculty of Agricultural Technology, University of Technology Thanyaburi, Rajamangala Pathum Thani, 12130, Thailand
| | - Uswatun Muslykhah
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Srisan Phupaboon
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand.
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Narasaka S, Endo Y, Fu Z, Moriyama M, Arai S, Abe K, Kato H. Safety Evaluation of Hypoallergenic Wheat Flour by Using a DNA Microarray. Biosci Biotechnol Biochem 2014; 70:1464-70. [PMID: 16751703 DOI: 10.1271/bbb.60002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The effect of the consumption of hypoallergenic wheat flour (HWF) on the expression of a wide spectrum of genes was analyzed by using a DNA microarray. Gene expression profiles in the liver and intestines of rats fed on a diet composed mainly of HWF were compared with those of rats fed on a normal flour-based diet. Among the eight thousand transcripts represented on the GeneChip microarray, no more than 30 genes exhibited up- or down-regulation of two-fold or more after one week or two months of HWF consumption. No adverse effects were apparent. Up-regulation of some of the genes known to respond to the interferon-gamma signal was apparent in the one-week experiment, which may be related to possible oral immunotolerance resulting from HWF feeding. This DNA microarray technology presents an efficient method for evaluating the safety of foods.
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Affiliation(s)
- Sachiko Narasaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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Coffee intake down-regulates the hepatic gene expression of peroxisome proliferator-activated receptor gamma in C57BL/6J mice fed a high-fat diet. J Funct Foods 2014. [DOI: 10.1016/j.jff.2013.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Takahashi S, Masuda J, Shimagami H, Ohta Y, Kanda T, Saito K, Kato H. Mild caloric restriction up-regulates the expression of prohibitin: A proteome study. Biochem Biophys Res Commun 2011; 405:462-7. [DOI: 10.1016/j.bbrc.2011.01.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 01/15/2011] [Indexed: 02/07/2023]
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Effect of mild restriction of food intake on gene expression profile in the liver of young rats: reference data for in vivo nutrigenomics study. Br J Nutr 2010; 104:941-50. [PMID: 20447325 DOI: 10.1017/s0007114510001625] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Recent transcriptomics studies on the effect of long-term or severe energy restriction (ER) have revealed that many genes are dynamically modulated by this condition in rodents. The present study was conducted to define the global gene expression profile in response to mild ER treatment. Growing rats were fed with reduced amount of diet (5-30 % ER) for 1 week or 1 month. Using DNA microarray analysis of the liver, seventy-two genes that were consistently changed through the different ER levels were identified. Many were related to lipid metabolism including genes encoding key enzymes such as carnitine palmitoyltransferase 1 and fatty acid synthase. Interestingly, a number of genes were altered even by 5 % ER for 1 week where no differences in weight gain were observed. The information obtained in the present study can be used as a valuable reference data source in the transcriptomics studies of food and nutrition in which subtle differences in food intake sometimes hinder appropriate interpretation of the data.
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A tool for sheep product quality: custom microarrays from public databases. Nutrients 2009; 1:235-50. [PMID: 22253981 PMCID: PMC3257605 DOI: 10.3390/nu1020235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 12/01/2009] [Indexed: 01/12/2023] Open
Abstract
Milk and dairy products are an essential food and an economic resource in many countries. Milk component synthesis and secretion by the mammary gland involve expression of a large number of genes whose nutritional regulation remains poorly defined. The purpose of this study was to gain an understanding of the genomic influence on milk quality and synthesis by comparing two sheep breeds with different milking attitude (Sarda and Gentile di Puglia) using sheep-specific microarray technology. From sheep ESTs deposited at NCBI, we have generated the first annotated microarray developed for sheep with a coverage of most of the genome.
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Rouillard JM, Gulari E. OligoArrayDb: pangenomic oligonucleotide microarray probe sets database. Nucleic Acids Res 2008; 37:D938-41. [PMID: 18948290 PMCID: PMC2686523 DOI: 10.1093/nar/gkn761] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OligoArrayDb is a comprehensive database containing pangenomic oligonucleotide microarray probe sets designed for most of the sequenced genomes that are not covered by commercial catalog arrays. The availability of probe sequences, associated with custom microarray fabrication services offered by many companies and cores presents the unequalled possibility to perform microarray experiments on most of the sequenced organisms. OligoArrayDb contains more than 2.8 probes per gene in average for more than 600 organisms, mostly archaea and bacteria strains available from public database. On average, 98% of the annotated genes have at least one probe which is predicted to be specific to its intended target in >94% of the cases. OligoArrayDb is weekly updated as new sequenced genomes become available. Probe sequences, in addition to a comprehensive set of annotations can be downloaded from this database. OligoArrayDb is publicly accessible online at http://berry.engin.umich.edu/oligoarraydb.
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Affiliation(s)
- Jean-Marie Rouillard
- Chemical Engineering Department, University of Michigan, 2300 Hayward Street, Ann Arbor, MI 48109, USA.
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Roy S, Sen CK. cDNA microarray screening in food safety. Toxicology 2006; 221:128-33. [PMID: 16466843 PMCID: PMC2667801 DOI: 10.1016/j.tox.2005.12.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2005] [Revised: 12/06/2005] [Accepted: 12/10/2005] [Indexed: 11/17/2022]
Abstract
The cDNA microarray technology and related bioinformatics tools presents a wide range of novel application opportunities. The technology may be productively applied to address food safety. In this mini-review article, we present an update highlighting the late breaking discoveries that demonstrate the vitality of cDNA microarray technology as a tool to analyze food safety with reference to microbial pathogens and genetically modified foods. In order to bring the microarray technology to mainstream food safety, it is important to develop robust user-friendly tools that may be applied in a field setting. In addition, there needs to be a standardized process for regulatory agencies to interpret and act upon microarray-based data. The cDNA microarray approach is an emergent technology in diagnostics. Its values lie in being able to provide complimentary molecular insight when employed in addition to traditional tests for food safety, as part of a more comprehensive battery of tests.
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Affiliation(s)
- Sashwati Roy
- Laboratory of Molecular Medicine and DNA Microarray & Genetics Facility, Dorothy M. Davis Heart and Lung Research Institute, Department of Surgery, The Ohio State University Medical Center, Columbus, OH 43210, USA
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