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González-Sálamo J, Varela-Martínez DA, González-Curbelo MÁ, Hernández-Borges J. The Role of Chromatographic and Electromigration Techniques in Foodomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1336:31-49. [PMID: 34628626 DOI: 10.1007/978-3-030-77252-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Foodomics is the discipline aimed at studying the prevention of diseases by food, identifying chemical, biological and biochemical food contaminants, determining changes in genetically modified foods, identifying biomarkers able to confirm the authenticity and quality of foods or studying the safety, quality and traceability of foods, among other issues. It is mainly based on the use of genomic, transcriptomic, proteomic and metabolomic tools, among others, in order to understand the effect of food on animals and humans at the level of genes, messenger ribonucleic acid, proteins and metabolites. Since the first definition of Foodomics, a reasonable number of works have shown the extremely high possibilities of this discipline, which is highly based on the use of advanced analytical hyphenated techniques - especially for proteomics and metabolomics. This book chapter aims at providing a general description of the role of chromatographic and electromigration techniques that are currently being applied to achieve the main objectives of Foodomics, particularly in the proteomic and metabolomic fields, since most published works have been focused on these approaches, and to highlight relevant applications.
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Affiliation(s)
- Javier González-Sálamo
- Departamento de Química, Unidad Departamental de Química Analítica, Facultad de Ciencias, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - Diana Angélica Varela-Martínez
- Departamento de Química, Unidad Departamental de Química Analítica, Facultad de Ciencias, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain.,Departamento de Ciencias Básicas, Facultad de Ingeniería, Universidad EAN, Bogotá D.C., Colombia
| | | | - Javier Hernández-Borges
- Departamento de Química, Unidad Departamental de Química Analítica, Facultad de Ciencias, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain. .,Instituto Universitario de Enfermedades Tropicales y Salud Pública, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain.
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Nash T, Huff M, Glen WB, Hardiman G. Pipeline for Integrated Microarray Expression Normalization Tool Kit (PIMENTo) for Tumor Microarray Profiling Experiments. Methods Mol Biol 2019; 1908:153-168. [PMID: 30649727 DOI: 10.1007/978-1-4939-9004-7_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
We have developed a Pipeline for Integrated Microarray Expression & Normalization Tool kit (PIMENTo) with the aim of streamlining the processes necessary for gene expression analysis in tumor tissue using DNA microarrays. Built with the R programming language and leveraging several open-source packages available through CRAN and Bioconductor, PIMENTo enables researchers to perform complex tasks with a minimal number of operations. Here, we describe the pipeline, review necessary data inputs, examine data outputs and quality control assessments and explore the commands to perform such analysis.
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Affiliation(s)
- Thomas Nash
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA.,Department of Computer Science, College of Charleston, Charleston, SC, USA
| | - Matthew Huff
- MS in Biomedical Sciences Program, Medical University of South Carolina (MUSC), Charleston, SC, USA
| | - W Bailey Glen
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA.,Department of Pathology and Laboratory Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA
| | - Gary Hardiman
- MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA. .,Department of Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA. .,Department of Public Health Sciences, Medical University of South Carolina (MUSC), Charleston, SC, USA. .,School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Stranmillis Road, Belfast, BT9 5AG, UK.
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Pant Pai N, Daher J. Multiplexed testing for HIV and related bacterial and viral co-infections at the point-of-care: quo vadis? Expert Rev Mol Diagn 2015; 15:463-9. [PMID: 25795042 DOI: 10.1586/14737159.2015.1021335] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recently, there has been a paradigm shift toward an understanding of the need to screen select sub-populations for several sexually transmitted and blood-borne infections simultaneously, at one time with various rapid point-of-care (POC) technologies, rather than one infection at a time. This is an encouraging and promising change, however many contextual factors need to be considered before implementing such technologies. In this editorial, we highlight some challenges, issues and concerns regarding implementation, integration, and uptake of these technologies across global settings. However, careful planning and well thought out implementation plan that include investments in training health care professionals, improving test and treat algorithms, rapid protocols on communicating actionable results to providers, and timely action, will bring about the desired impact in patient's lives. This is especially true in settings where they stand to achieve the maximum desired public health and social impact.
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Affiliation(s)
- Nitika Pant Pai
- Department of Medicine, McGill University, Montreal, Quebec, Canada
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Forster L, McCooke J, Bellgard M, Joske D, Finlayson J, Ghassemifar R. Differential gene expression analysis in early and late erythroid progenitor cells in β-thalassaemia. Br J Haematol 2015; 170:257-67. [DOI: 10.1111/bjh.13432] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/19/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Luke Forster
- School of Pathology and Laboratory Medicine; University of Western Australia; Nedlands WA Australia
| | - John McCooke
- Centre for Comparative Genomics; Murdoch University; Murdoch WA Australia
| | - Matthew Bellgard
- Centre for Comparative Genomics; Murdoch University; Murdoch WA Australia
| | - David Joske
- Department of Haematology; PathWest Laboratory Medicine; Queen Elizabeth II Medical Centre; Nedlands WA Australia
| | - Jill Finlayson
- School of Pathology and Laboratory Medicine; University of Western Australia; Nedlands WA Australia
- Department of Haematology; PathWest Laboratory Medicine; Queen Elizabeth II Medical Centre; Nedlands WA Australia
| | - Reza Ghassemifar
- School of Pathology and Laboratory Medicine; University of Western Australia; Nedlands WA Australia
- Department of Haematology; PathWest Laboratory Medicine; Queen Elizabeth II Medical Centre; Nedlands WA Australia
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Baker ME, Hardiman G. Transcriptional analysis of endocrine disruption using zebrafish and massively parallel sequencing. J Mol Endocrinol 2014; 52:R241-56. [PMID: 24850832 PMCID: PMC4145605 DOI: 10.1530/jme-13-0219] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Endocrine-disrupting chemicals (EDCs), including plasticizers, pesticides, detergents, and pharmaceuticals, affect a variety of hormone-regulated physiological pathways in humans and wildlife. Many EDCs are lipophilic molecules and bind to hydrophobic pockets in steroid receptors, such as the estrogen receptor and androgen receptor, which are important in vertebrate reproduction and development. Indeed, health effects attributed to EDCs include reproductive dysfunction (e.g. reduced fertility, reproductive tract abnormalities, and skewed male:female sex ratios in fish), early puberty, various cancers, and obesity. A major concern is the effects of exposure to low concentrations of endocrine disruptors in utero and post partum, which may increase the incidence of cancer and diabetes in adults. EDCs affect transcription of hundreds and even thousands of genes, which has created the need for new tools to monitor the global effects of EDCs. The emergence of massive parallel sequencing for investigating gene transcription provides a sensitive tool for monitoring the effects of EDCs on humans and other vertebrates, as well as elucidating the mechanism of action of EDCs. Zebrafish conserve many developmental pathways found in humans, which makes zebrafish a valuable model system for studying EDCs, especially on early organ development because their embryos are translucent. In this article, we review recent advances in massive parallel sequencing approaches with a focus on zebrafish. We make the case that zebrafish exposed to EDCs at different stages of development can provide important insights on EDC effects on human health.
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Affiliation(s)
- Michael E Baker
- Department of MedicineUniversity of California San Diego, 9500 Gilman Drive 0605, La Jolla, California 92093-0605, USACSRC and BIMRCSan Diego State University, 5500 Campanile Drive, San Diego, California 92182-7720, USADepartment of MedicineMedical University of South Carolina, 135 Cannon Street, Suite 303 MSC 835, Charleston, South Carolina 29425, USA
| | - Gary Hardiman
- Department of MedicineUniversity of California San Diego, 9500 Gilman Drive 0605, La Jolla, California 92093-0605, USACSRC and BIMRCSan Diego State University, 5500 Campanile Drive, San Diego, California 92182-7720, USADepartment of MedicineMedical University of South Carolina, 135 Cannon Street, Suite 303 MSC 835, Charleston, South Carolina 29425, USADepartment of MedicineUniversity of California San Diego, 9500 Gilman Drive 0605, La Jolla, California 92093-0605, USACSRC and BIMRCSan Diego State University, 5500 Campanile Drive, San Diego, California 92182-7720, USADepartment of MedicineMedical University of South Carolina, 135 Cannon Street, Suite 303 MSC 835, Charleston, South Carolina 29425, USA
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Molecular fixative enables expression microarray analysis of microdissected clinical cervical specimens. Exp Mol Pathol 2014; 96:168-77. [PMID: 24412268 DOI: 10.1016/j.yexmp.2013.12.007] [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: 11/21/2013] [Accepted: 12/06/2013] [Indexed: 11/21/2022]
Abstract
Formalin-fixed tissue has been a mainstay of clinical pathology laboratories, but formalin alters many biomolecules, including nucleic acids and proteins. Meanwhile, frozen tissues contain better-preserved biomolecules, but tissue morphology is affected, limiting their diagnostic utility. Molecular fixatives promise to bridge this gap by simultaneously preserving morphology and biomolecules, enabling clinical diagnosis and molecular analyses on the same specimen. While previous reports have broadly evaluated the use of molecular fixative in various human tissues, we present here the first detailed assessment of the applicability of molecular fixative to both routine histopathological diagnosis and molecular analysis of cervical tissues. Ten specimens excised via the loop electrosurgical excision procedure, which removes conical tissue samples from the cervix, were cut into alternating pieces preserved in either formalin or molecular fixative. Cervical specimens preserved in molecular fixative were easily interpretable, despite featuring more eosinophilic cytoplasm and more recognizable chromatin texture than formalin-fixed specimens. Immunohistochemical staining patterns of p16 and Ki-67 were similar between fixatives, although Ki-67 staining was stronger in the molecular fixative specimens. The RNA of molecular fixative specimens from seven cases representing various dysplasia grades was assessed for utility in expression microarray analysis. Cluster analysis and scatter plots of duplicate samples suggest that data of sufficient quality can be obtained from as little as 50ng of RNA from molecular fixative samples. Taken together, our results show that molecular fixative may be a more versatile substitute for formalin, simultaneously preserving tissue morphology for clinical diagnosis and biomolecules for immunohistochemistry and gene expression analysis.
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Streit A, Tambalo M, Chen J, Grocott T, Anwar M, Sosinsky A, Stern CD. Experimental approaches for gene regulatory network construction: the chick as a model system. Genesis 2012; 51:296-310. [PMID: 23174848 DOI: 10.1002/dvg.22359] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/09/2012] [Accepted: 11/11/2012] [Indexed: 01/23/2023]
Abstract
Setting up the body plan during embryonic development requires the coordinated action of many signals and transcriptional regulators in a precise temporal sequence and spatial pattern. The last decades have seen an explosion of information describing the molecular control of many developmental processes. The next challenge is to integrate this information into logic "wiring diagrams" that visualize gene actions and outputs, have predictive power and point to key control nodes. Here, we provide an experimental workflow on how to construct gene regulatory networks using the chick as model system.
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Affiliation(s)
- Andrea Streit
- Department of Craniofacial Development and Stem Cell Biology, King's College London, London, United Kingdom.
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Li W. Volcano plots in analyzing differential expressions with mRNA microarrays. J Bioinform Comput Biol 2012; 10:1231003. [PMID: 23075208 DOI: 10.1142/s0219720012310038] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log(10)(p-value) from the t-test). We review the basic and interactive use of the volcano plot and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide a unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility of applying volcano plots to other fields beyond microarray.
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Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, 350 Community Drive, NY 11030, USA.
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