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Chukwudi CU. Consolidating and Upscaling Molecular Research Capacity in Nigeria: On Who's Account? Front Res Metr Anal 2022; 6:788673. [PMID: 35071971 PMCID: PMC8766846 DOI: 10.3389/frma.2021.788673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/02/2021] [Indexed: 11/25/2022] Open
Abstract
Molecular research and researchers engage in studies that seek to understand the structures, functions, and interactions of biomolecules as the basis for cellular and systemic effects in living organisms. This research approach was made possible by considerable technological advancements that equip researchers with tools to view biomolecules. Although molecular research holds great promises for improving lives and living, the technological requirements and equipment to undertake molecular research are quite expensive, often requiring a heavy start-up capital or investment. In developing countries such as Nigeria, where the majority of the population lives below the poverty line and research funding is abysmally low, such heavy investments into research that do not provide immediate solutions to societal problems are difficult. This is mostly due to limited resources available to tackle many urgent and pressing needs, and limited perspective and understanding of policymakers, leading to infrastructural and skilled personnel deficit to support molecular research. Despite all these, the field of molecular research continues to grow exponentially globally, hence, funding and investments into this critical life science research area have become imperative. With the rich biodiversity of humans, animals, and plants in Nigeria, and the huge burden of infectious diseases in the country or region, global advances in genomics and proteomics studies will be incomplete without adequate contribution from Nigeria and sub-Saharan Africa region. This paper examines the progression and challenges of undertaking molecular research in Nigeria, and how Nigerian molecular research scientists are tackling these issues, with recommendations for improved molecular research capacity and output in the country or region.
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Li HK, Zhang WD, Gu Y, Wu GS. Strategy of systems biology for visualizing the “Black box” of traditional Chinese medicine. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2020. [DOI: 10.4103/wjtcm.wjtcm_31_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Informatics for Nutritional Genetics and Genomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1005:143-166. [PMID: 28916932 DOI: 10.1007/978-981-10-5717-5_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
While traditional nutrition science is focusing on nourishing population, modern nutrition is aiming at benefiting individual people. The goal of modern nutritional research is to promote health, prevent diseases, and improve performance. With the development of modern technologies like bioinformatics, metabolomics, and molecular genetics, this goal is becoming more attainable. In this chapter, we will discuss the new concepts and technologies especially in informatics and molecular genetics and genomics, and how they have been implemented to change the nutrition science and lead to the emergence of new branches like nutrigenomics, nutrigenetics, and nutritional metabolomics.
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Loor JJ, Vailati-Riboni M, McCann JC, Zhou Z, Bionaz M. TRIENNIAL LACTATION SYMPOSIUM: Nutrigenomics in livestock: Systems biology meets nutrition. J Anim Sci 2016; 93:5554-74. [PMID: 26641165 DOI: 10.2527/jas.2015-9225] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The advent of high-throughput technologies to study an animal's genome, proteome, and metabolome (i.e., "omics" tools) constituted a setback to the use of reductionism in livestock research. More recent development of "next-generation sequencing" tools was instrumental in allowing in-depth studies of the microbiome in the rumen and other sections of the gastrointestinal tract. Omics, along with bioinformatics, constitutes the foundation of modern systems biology, a field of study widely used in model organisms (e.g., rodents, yeast, humans) to enhance understanding of the complex biological interactions occurring within cells and tissues at the gene, protein, and metabolite level. Application of systems biology concepts is ideal for the study of interactions between nutrition and physiological state with tissue and cell metabolism and function during key life stages of livestock species, including the transition from pregnancy to lactation, in utero development, or postnatal growth. Modern bioinformatic tools capable of discerning functional outcomes and biologically meaningful networks complement the ever-increasing ability to generate large molecular, microbial, and metabolite data sets. Simultaneous visualization of the complex intertissue adaptations to physiological state and nutrition can now be discerned. Studies to understand the linkages between the microbiome and the absorptive epithelium using the integrative approach are emerging. We present examples of new knowledge generated through the application of functional analyses of transcriptomic, proteomic, and metabolomic data sets encompassing nutritional management of dairy cows, pigs, and poultry. Published work to date underscores that the integrative approach across and within tissues may prove useful for fine-tuning nutritional management of livestock. An important goal during this process is to uncover key molecular players involved in the organismal adaptations to nutrition.
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Sahebi M, Hanafi MM, Azizi P, Hakim A, Ashkani S, Abiri R. Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives. Mol Biotechnol 2016; 57:880-903. [PMID: 26271955 DOI: 10.1007/s12033-015-9884-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.
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Affiliation(s)
- Mahbod Sahebi
- Laboratory of Plantation Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia,
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Talwar P, Silla Y, Grover S, Gupta M, Grewal GK, Kukreti R. Systems Pharmacology and Pharmacogenomics for Drug Discovery and Development. SYSTEMS AND SYNTHETIC BIOLOGY 2015. [DOI: 10.1007/978-94-017-9514-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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The future of molecular imaging in paradigm shift from reactive to proactive (P4) medicine: predictive, preventive, personalized and participatory. Nucl Med Commun 2014; 35:1193-6. [PMID: 25211627 DOI: 10.1097/mnm.0000000000000205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Hadd AG, Brown JT, Andruss BF, Ye F, WalkerPeach CR. Adoption of array technologies into the clinical laboratory. Expert Rev Mol Diagn 2014; 5:409-20. [PMID: 15934817 DOI: 10.1586/14737159.5.3.409] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Array-based methods are making substantial contributions to the discovery of disease biomarkers and are fueling the growth of multianalyte testing for disease diagnosis and treatment. The distillation of high-density array results into sets of signature markers promises to improve disease staging, risk stratification and treatment decisions. To accommodate the growing requirement for multiplex testing, clinical laboratories are converting several single-analyte tests into array-based formats. However, adoption of array technologies provides several challenges to the laboratory, which must evaluate these new formats, train laboratory personnel, market the new services and obtain reimbursement for new analytes. Liquid-bead arrays are an attractive format for routine clinical diagnostics due to a combination of appropriate analyte density, simultaneous array decoding and detection, and flexibility for rapid customization. In this review, the suitability of several array platforms to diagnostic testing and applications of liquid-bead arrays for cystic fibrosis testing, multidisease carrier status assays and leukemia subtyping are discussed. As our understanding of the clinical utility of new or established biomarkers and recommendations for testing change, flexibility and adaptability of array platforms will be imperative. Future development of novel assay formats and improved quantitation will expand the number of diseases tested and lead to further integration into the diagnostic laboratory.
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Affiliation(s)
- Andrew G Hadd
- Ambion Diagnostics, 2130 Woodward Street, Austin, TX 78744, USA.
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Abstract
Studying complex biological systems in a holistic rather than a "one gene or one protein" at a time approach requires the concerted effort of scientists from a wide variety of disciplines. The Institute for Systems Biology (ISB) has seamlessly integrated these disparate fields to create a cross-disciplinary platform and culture in which "biology drives technology drives computation." To achieve this platform/culture, it has been necessary for cross-disciplinary ISB scientists to learn one another's languages and work together effectively in teams. The focus of this "systems" approach on disease has led to a discipline denoted systems medicine. The advent of technological breakthroughs in the fields of genomics, proteomics, and, indeed, the other "omics" is catalyzing striking advances in systems medicine that have and are transforming diagnostic and therapeutic strategies. Systems medicine has united genomics and genetics through family genomics to more readily identify disease genes. It has made blood a window into health and disease. It is leading to the stratification of diseases (division into discrete subtypes) for proper impedance match against drugs and the stratification of patients into subgroups that respond to environmental challenges in a similar manner (e.g. response to drugs, response to toxins, etc.). The convergence of patient-activated social networks, big data and their analytics, and systems medicine has led to a P4 medicine that is predictive, preventive, personalized, and participatory. Medicine will focus on each individual. It will become proactive in nature. It will increasingly focus on wellness rather than disease. For example, in 10 years each patient will be surrounded by a virtual cloud of billions of data points, and we will have the tools to reduce this enormous data dimensionality into simple hypotheses about how to optimize wellness and avoid disease for each individual. P4 medicine will be able to detect and treat perturbations in healthy individuals long before disease symptoms appear, thus optimizing the wellness of individuals and avoiding disease. P4 medicine will 1) improve health care, 2) reduce the cost of health care, and 3) stimulate innovation and new company creation. Health care is not the only subject that can benefit from such integrative, cross-disciplinary, and systems-driven platforms and cultures. Many other challenges plaguing our planet, such as energy, environment, nutrition, and agriculture can be transformed by using such an integrated and systems-driven approach.
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Affiliation(s)
- Leroy Hood
- To whom correspondence should be addressed. E-mail:
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Osiri JK, Shadpour H, Witek MA, Soper SA. Integrated multifunctional microfluidics for automated proteome analyses. Top Curr Chem (Cham) 2011; 304:261-94. [PMID: 21678138 DOI: 10.1007/128_2011_152] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Proteomics is a challenging field for realizing totally integrated microfluidic systems for complete proteome processing due to several considerations, including the sheer number of different protein types that exist within most proteomes, the large dynamic range associated with these various protein types, and the diverse chemical nature of the proteins comprising a typical proteome. For example, the human proteome is estimated to have >10(6) different components with a dynamic range of >10(10). The typical processing pipeline for proteomics involves the following steps: (1) selection and/or extraction of the particular proteins to be analyzed; (2) multidimensional separation; (3) proteolytic digestion of the protein sample; and (4) mass spectral identification of either intact proteins (top-down proteomics) or peptide fragments generated from proteolytic digestions (bottom-up proteomics). Although a number of intriguing microfluidic devices have been designed, fabricated and evaluated for carrying out the individual processing steps listed above, work toward building fully integrated microfluidic systems for protein analysis has yet to be realized. In this chapter, information will be provided on the nature of proteomic analysis in terms of the challenges associated with the sample type and the microfluidic devices that have been tested to carry out individual processing steps. These include devices such as those for multidimensional electrophoretic separations, solid-phase enzymatic digestions, and solid-phase extractions, all of which have used microfluidics as the functional platform for their implementation. This will be followed by an in-depth review of microfluidic systems, which are defined as units possessing two or more devices assembled into autonomous systems for proteome processing. In addition, information will be provided on the challenges involved in integrating processing steps into a functional system and the approaches adopted for device integration. In this chapter, we will focus exclusively on the front-end processing microfluidic devices and systems for proteome processing, and not on the interface technology of these platforms to mass spectrometry due to the extensive reviews that already exist on these types of interfaces.
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Affiliation(s)
- John K Osiri
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70817, USA
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Osiri JK, Shadpour H, Park S, Snowden BC, Chen ZY, Soper SA. Generating high peak capacity 2-D maps of complex proteomes using PMMA microchip electrophoresis. Electrophoresis 2008; 29:4984-92. [DOI: 10.1002/elps.200800496] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Identification of dominant signaling pathways from proteomics expression data. J Proteomics 2008; 71:89-96. [PMID: 18541477 DOI: 10.1016/j.jprot.2008.01.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 01/03/2008] [Accepted: 01/04/2008] [Indexed: 11/20/2022]
Abstract
The availability of the results of high-throughput analyses coming from 'omic' technologies has been one of the major driving forces of pathway biology. Analytical pathway biology strives to design a 'pathway search engine', where the input is the 'omic' data and the output is the list of activated or dominant pathways in a given sample. Here we describe the first attempt to design and validate such a pathway search engine using as input expression proteomics data. The engine represents a specific workflow in computational tools developed originally for mRNA analysis (BMC Bioinformatics 2006, 7 (Suppl 2), S13). Using our own datasets as well as data from recent proteomics literature we demonstrate that different dominant pathways (EGF, TGF(beta), stress, and Fas pathways) can be correctly identified even from limited datasets. Pathway search engines can find application in a variety of proteomics-related fields, from fundamental molecular biology to search for novel types of disease biomarkers.
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Hood L. A personal journey of discovery: developing technology and changing biology. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:1-43. [PMID: 20636073 DOI: 10.1146/annurev.anchem.1.031207.113113] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
This autobiographical article describes my experiences in developing chemically based, biological technologies for deciphering biological information: DNA, RNA, proteins, interactions, and networks. The instruments developed include protein and DNA sequencers and synthesizers, as well as ink-jet technology for synthesizing DNA chips. Diverse new strategies for doing biology also arose from novel applications of these instruments. The functioning of these instruments can be integrated to generate powerful new approaches to cloning and characterizing genes from a small amount of protein sequence or to using gene sequences to synthesize peptide fragments so as to characterize various properties of the proteins. I also discuss the five paradigm changes in which I have participated: the development and integration of biological instrumentation; the human genome project; cross-disciplinary biology; systems biology; and predictive, personalized, preventive, and participatory (P4) medicine. Finally, I discuss the origins, the philosophy, some accomplishments, and the future trajectories of the Institute for Systems Biology.
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Affiliation(s)
- Lee Hood
- Institute for Systems Biology, Seattle, Washington 98103, USA.
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An Y, Cooper JW, Balgley BM, Lee CS. Selective enrichment and ultrasensitive identification of trace peptides in proteome analysis using transient capillary isotachophoresis/zone electrophoresis coupled with nano-ESI-MS. Electrophoresis 2006; 27:3599-608. [PMID: 16927423 DOI: 10.1002/elps.200600093] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Besides the complexity in protein samples of biological origin, probably the greatest challenge presently facing comprehensive proteome analysis is related to the large variation of protein relative abundances (>6 orders of magnitude), having potential biological significance in mammalian systems. As demonstrated in this work, transient capillary ITP/zone electrophoresis (CITP/CZE) provides selective analyte enrichment through electrokinetic stacking and extremely high resolving power toward protein and peptide mixtures. The result of the CITP process is that major components may be diluted, but trace compounds are concentrated. The on-column transition of CITP to CZE minimizes additional band broadening while providing superior analyte resolution. Online coupling of transient CITP/CZE with nano-ESI-MS allows ultrasensitive detection of trace peptides at levels of subnanomolar concentration or subfemtomole mass in complex peptide mixtures. More importantly, selective enrichment of trace peptides enables the identification and sequence analysis of low-abundance peptides co-migrated with highly abundant species at a concentration ratio of 1:500,000. The combined CITP/CZE-nano-ESI-MS system is demonstrated to be at least one to two orders of magnitude more sensitive than that attained in conventional electrophoretic and chromatographic-based proteome technologies over a wide dynamic concentration range, potentially allowing comprehensive analysis of protein profiles within a small cell population and limited tissue samples using conventional mass spectrometers. Furthermore, the speed of CITP/CZE separation and the lack of column equilibration in CITP/CZE not only improve the throughput of proteome analysis, but also facilitate its seamless integration with other separation technologies in a multidimensional protein identification platform.
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Affiliation(s)
- Yanming An
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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Huang YF, Huang CC, Hu CC, Chang HT. Capillary electrophoresis-based separation techniques for the analysis of proteins. Electrophoresis 2006; 27:3503-22. [PMID: 16927348 DOI: 10.1002/elps.200600100] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
CE offers the advantages of high speed, great efficiency, as well as the requirement of minimum amounts of sample and buffer for the analysis of proteins. In this review, we summarize the CE-based techniques coupled with absorption, LIF, and MS detection systems for the analysis of proteins mostly within the past 5 years. The basic principle of each technique and its advantages and disadvantages for protein analysis are discussed in brief. Advanced CE techniques, including on-column concentration techniques and high-efficiency multidimensional separation techniques, for high-throughput protein profiling of complex biological samples and/or of single cells are emphasized. Although the developed techniques provide improved peak capacity, they have not become practical tools for proteomics, mainly because of poor reproducibility, low-sample lading capacity, and low throughput due to ineffective interfaces between two separation dimensions and that between separation and MS systems. In order to identify the complexities and dynamics of the proteomes expressed by cells, tissues, or organisms, techniques providing improved analytical sensitivity, throughput, and dynamic ranges are still demanded.
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Affiliation(s)
- Yu-Fen Huang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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Schasfoort RBM. Proteomics-on-a-chip: the challenge to couple lab-on-a-chip unit operations. Expert Rev Proteomics 2006; 1:123-32. [PMID: 15966805 DOI: 10.1586/14789450.1.1.123] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This review describes a vision of a proteomics-on-a-chip device to separate, detect and identify the proteome. It guides the reader towards a development strategy, avoiding some of the pitfalls. It also describes the current state-of-the-art developments in proteomic analysis including available technologies, current market issues, the elements of an envisaged proteomics-on-a-chip device, the required microfabrication processes and the integration of the elements into one device. Address-flow microfluidics is a tool for connecting separation and detection platforms. The final section contains an expert opinion on the recommended development strategies, benefits of proteomics-on-a-chip in the life sciences and the anticipated market.
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Affiliation(s)
- Richard B M Schasfoort
- Biochip Group, Faculty of Science and Technology, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands.
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Abstract
The emergent properties of biological systems, organized around complex networks of irregularly connected elements, limit the applications of the direct scientific method to their study. The current lack of knowledge opens new perspectives to the inverse scientific paradigm where observations are accumulated and analysed by advanced data-mining techniques to enable a better understanding and the formulation of testable hypotheses about the structure and functioning of these systems. The current technology allows for the wide application of omics analytical methods in the determination of time-resolved molecular profiles of biological samples. Here it is proposed that the theory of dynamical systems could be the natural framework for the proper analysis and interpretation of such experiments. A new method is described, based on the techniques of non-linear time series analysis, which is providing a global view on the dynamics of biological systems probed with time-resolved omics experiments.
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Affiliation(s)
- Martin G Grigorov
- Nestlé Research Center, BioAnalytical Science CH-1000 Lausanne 26, Switzerland.
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Vemuri GN, Aristidou AA. Metabolic engineering in the -omics era: elucidating and modulating regulatory networks. Microbiol Mol Biol Rev 2006; 69:197-216. [PMID: 15944454 PMCID: PMC1197421 DOI: 10.1128/mmbr.69.2.197-216.2005] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The importance of regulatory control in metabolic processes is widely acknowledged, and several enquiries (both local and global) are being made in understanding regulation at various levels of the metabolic hierarchy. The wealth of biological information has enabled identifying the individual components (genes, proteins, and metabolites) of a biological system, and we are now in a position to understand the interactions between these components. Since phenotype is the net result of these interactions, it is immensely important to elucidate them not only for an integrated understanding of physiology, but also for practical applications of using biological systems as cell factories. We present some of the recent "-omics" approaches that have expanded our understanding of regulation at the gene, protein, and metabolite level, followed by analysis of the impact of this progress on the advancement of metabolic engineering. Although this review is by no means exhaustive, we attempt to convey our ideology that combining global information from various levels of metabolic hierarchy is absolutely essential in understanding and subsequently predicting the relationship between changes in gene expression and the resulting phenotype. The ultimate aim of this review is to provide metabolic engineers with an overview of recent advances in complementary aspects of regulation at the gene, protein, and metabolite level and those involved in fundamental research with potential hurdles in the path to implementing their discoveries in practical applications.
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Affiliation(s)
- Goutham N Vemuri
- Center for Molecular BioEngineering, Drifmier Engineering Center, University of Georgia, Athens, 30605, USA
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Lipan O, Wong WH. Is the future biology Shakespearean or Newtonian? MOLECULAR BIOSYSTEMS 2006; 2:411-6. [PMID: 17153137 DOI: 10.1039/b607243g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
"Cells do not care about mathematics" thus concluded a biologist friend after a discussion on the future of biology. And indeed, why should they care? But if we exchange the word "cell" with "rock", "Moon" or "electrons", do we have to change the sentence also? Starting from this line of thought, we review some recent developments in understanding the stochastic behavior of biological systems. We emphasize the importance of a molecular Signal Generator in the study of genetic networks.
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Affiliation(s)
- Ovidiu Lipan
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, 1120 15th St. CA-4139, Augusta, GA, 30912, USA.
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Van Regenmortel MHV. 15th meeting on Methods in Protein Structure Analysis. 29th August-2nd September, 2004, University of Washington, WA, USA. Expert Rev Proteomics 2005; 1:397-9. [PMID: 15966836 DOI: 10.1586/14789450.1.4.397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Davidov E, Clish CB, Oresic M, Meys M, Stochaj W, Snell P, Lavine G, Londo TR, Adourian A, Zhang X, Johnston M, Morel N, Marple EW, Plasterer TN, Neumann E, Verheij E, Vogels JTWE, Havekes LM, van der Greef J, Naylor S. Methods for the differential integrative omic analysis of plasma from a transgenic disease animal model. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2005; 8:267-88. [PMID: 15703476 DOI: 10.1089/omi.2004.8.267] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Multitiered quantitative analysis of biological systems is rapidly becoming the desired approach to study hierarchical functional interactions between proteins and metabolites. We describe here a novel systematic approach to analyze organisms with complex metabolic regulatory networks. By using precise analytical methods to measure biochemical constituents and their relative abundance in whole plasma of transgenic ApoE*3-Leiden mice and an isogenic wild-type control group, simultaneous snapshots of metabolic and protein states were obtained. Novel data processing and multivariate analysis tools such as Impurity Resolution Software (IMPRESS) and Windows-based linear fit program (WINLIN) were used to compare protein and metabolic profiles in parallel. Canonical correlations of the resulting data show quantitative relationships between heterogeneous components in the TG animals. These results, obtained solely from whole plasma analysis allowed us, in a rapid manner, to corroborate previous findings as well as find new events pertaining to dominant and peripheral events in lipoprotein metabolism of a genetically modified mammalian organism in relation to ApoE3, a key mediator of lipoprotein metabolism.
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Abstract
The sequencing of several organisms' genomes, including the human's one, has opened the way for the so-called postgenomic era, which is now routinely coined as "proteomics". The most basic task in proteomics remains the detection and identification of proteins from a biological sample, and the most traditional way to achieve this goal consists of protein separations performed by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Still, the 2-D PAGE-mass spectrometry (MS) approach remains lacking in proteome coverage (for proteins having extreme isoelectric points or molecular masses as well as for membrane proteins), dynamic range, sensitivity, and throughput. Consequently, considerable efforts have been devoted to the development of non-gel-based proteome separation technologies in an effort to alleviate the shortcomings in 2-D PAGE while reserving the ability to resolve complex protein and peptide mixtures prior to MS analysis. This review focuses on the most recent advances in capillary-based separation techniques, including capillary liquid chromatography, capillary electrophoresis, and capillary electrokinetic chromatography, and combinations of multiples of these mechanisms, along with the coupling of these techniques to MS. Developments in capillary separations capable of providing extremely high resolving power and selective analyte enrichment are particularly highlighted for their roles within the broader context of a state-of-the-art integrated proteome effort. Miniaturized and integrated multidimensional peptide/protein separations using microfluidics are further summarized for their potential applications in high-throughput protein profiling toward biomarker discovery and clinical diagnosis.
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Qutub AA, Hunt CA. Glucose transport to the brain: a systems model. ACTA ACUST UNITED AC 2005; 49:595-617. [PMID: 16269321 DOI: 10.1016/j.brainresrev.2005.03.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2004] [Revised: 03/02/2005] [Accepted: 03/09/2005] [Indexed: 02/07/2023]
Abstract
Glucose transport to the brain involves sophisticated interactions of solutes, transporters, enzymes, and cell signaling processes, within an intricate spatial architecture. The dynamics of the transport are influenced by the adaptive nature of the blood-brain barrier (BBB), the semi-impermeable membranes of brain capillaries. As both the gate and the gatekeeper between blood-borne nutrients and brain tissue, the BBB helps govern brain homeostasis. Glucose in the blood must cross the BBB's luminal and abluminal membranes to reach neural tissue. A robust representation of the glucose transport mechanism can highlight a target for brain therapeutic intervention, help characterize mechanisms behind several disease phenotypes, or suggest a new delivery route for drugs. The challenge for researchers is understanding the relationships between influential physiological variables in vivo, and using that knowledge to predict how alterations or interventions affect glucose transport. This paper reviews factors influencing glucose transport and approaches to representing blood-to-brain glucose transport including in vitro, in vivo, and kinetic models. Applications for different models are highlighted, while their limitations in answering arising questions about the human in vivo BBB lead to a discussion of an alternate approach. A developing complex systems simulation is introduced, initiating a single platform to represent the dynamics of glucose transport across the adapting human blood-brain barrier.
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Affiliation(s)
- Amina A Qutub
- Joint Graduate Group in Bioengineering, University of California, Berkeley and San Francisco, USA.
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Feder ME. Aims of undergraduate physiology education: a view from the University of Chicago. ADVANCES IN PHYSIOLOGY EDUCATION 2005; 29:3-10. [PMID: 15718377 DOI: 10.1152/advan.00028.2004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Physiology may play an important, if not essential role, in a liberal arts education because it provides a context for integrating information and concepts from diverse biological and extra-biological disciplines. Instructors of physiology may aid in fulfilling this role by clarifying the core concepts that physiological details exemplify. As an example, presented here are the core principles that are the basis for an undergraduate physiology course taught at the University of Chicago. The first of these is: Evolution has resulted in organisms comprising mechanisms for maintenance, growth, and reproduction, despite perturbations of the internal and external environment. Such principles necessitate a coupling of physiology to diverse disciplines (i.e., "sciomics") and provide a basis for integrating discoveries in other disciplines.
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Affiliation(s)
- Martin E Feder
- Department of Organismal Biology & Anatomy, The University of Chicago, Chicago, Illinois, USA.
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Morel NM, Holland JM, van der Greef J, Marple EW, Clish C, Loscalzo J, Naylor S. Primer on medical genomics. Part XIV: Introduction to systems biology--a new approach to understanding disease and treatment. Mayo Clin Proc 2004; 79:651-8. [PMID: 15132407 DOI: 10.4065/79.5.651] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The advent of the "-omics revolution" has forced us to reevaluate our ability to acquire, measure, and handle large data sets. Omic platforms such as expression arrays and mass spectrometry, with their exquisite selectivity, sensitivity, and specificity, are unrivaled technologies for detection, quantitation, and identification of DNA, messenger RNA, proteins, and metabolites derived from complex body tissue and fluids. More recently, attempts have been made to capture the utility of these platform technologies and combine them under the umbrella of systems biology, also referred to as pathway, network, or integrative biology. Applied systems biology is the integrated analysis of genetic, genomic, protein, metabolite, cellular, and pathway events that are in flux and interdependent. It necessitates the use of a variety of analytic platforms as well as biostatistics, bioinformatics, data integration, computational biology, modeling, and knowledge assembly protocols. Such sophisticated analyses may provide new insight into the understanding of disease processes and mechanisms of action of pharmaceutical agents. Ultimately, this requires a perspective on how complex systems behave and are modulated. In this regard, systems biology, more appropriately considered as a process containing a series of modules, aims to provide tools and capabilities to carry out such tasks. We describe the essentials required to carry out systems biology experiments, the method in which integrated data in the form of a systems biology correlation network affords new insight into understanding disease, and the vista of developing more efficient biomarkers and therapeutic agents.
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Chen J, Balgley BM, DeVoe DL, Lee CS. Capillary isoelectric focusing-based multidimensional concentration/separation platform for proteome analysis. Anal Chem 2003; 75:3145-52. [PMID: 12964763 DOI: 10.1021/ac034014+] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An integrated proteome concentration/separation approach involving on-line combination of capillary isoelectric focusing (CIEF) with capillary reversed-phase liquid chromatography (CRPLC) is developed for providing significant analyte concentration and extremely high resolving power toward protein and peptide mixtures. Upon completion of analyte focusing, the self-sharpening effect greatly restricts analyte diffusion and contributes to analyte stacking in narrowly focused bands with a concentration factor of approximately 240. In addition to analyte focusing, CIEF as the first separation dimension resolves proteins/peptides on the basis of their differences in pI and offers greater resolving power than that achieved in strong cation exchange chromatography. The grouping of two highly resolving and completely orthogonal separation techniques of CIEF and CRPLC, together with analyte focusing and concentration, significantly enhances the dynamic range and sensitivity of conventional mass spectrometry toward the identification of low-abundance proteins. The CIEF-based multidimensional separation/concentration platform enables the identification of a greater number of yeast soluble proteins than methods presented in the literature, yet requires a protein loading of only 9.6 microg. This protein loading is 2-3 orders of magnitude lower than those employed by the reported non-gel-based proteome techniques. The distribution of a codon adaptation index value for identified yeast proteins approximates to that predicted for the entire yeast proteome and supports the capability of CIEF-based proteome separation technology for achieving comprehensive proteome analysis. By reducing the inner diameter of chromatography columns from 180 microm to 100 microm, the required protein loading is further decreased from 9.6 microg to 960 ng, illustrating the potential usage of this proteome technology for the analysis of protein profiles within small cell populations or limited tissue samples.
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Affiliation(s)
- Jinzhi Chen
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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Abstract
The Human Genome Project has changed the worlds of biology and medicine-helping to catalyze two major paradigm changes: systems biology and predictive, preventive and personalized medicine. These two themes will dominate 21st century biology and medicine. I will discuss these changes and indicate how they may interface with with the process of aging.
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Affiliation(s)
- Leroy Hood
- Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA.
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