1
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Shankar A, Sharma KK. Fungal secondary metabolites in food and pharmaceuticals in the era of multi-omics. Appl Microbiol Biotechnol 2022; 106:3465-3488. [PMID: 35546367 PMCID: PMC9095418 DOI: 10.1007/s00253-022-11945-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/12/2022] [Accepted: 04/24/2022] [Indexed: 01/16/2023]
Abstract
Fungi produce several bioactive metabolites, pigments, dyes, antioxidants, polysaccharides, and industrial enzymes. Fungal products are also the primary sources of functional food and nutrition, and their pharmacological products are used for healthy aging. Their molecular properties are validated through the use of recent high-throughput genomic, transcriptomic, and metabolomic tools and techniques. Together, these updated multi-omic tools have been used to study fungal metabolites structure and their mode of action on biological and cellular processes. Diverse groups of fungi produce different proteins and secondary metabolites, which possess tremendous biotechnological and pharmaceutical applications. Furthermore, its use and acceptability can be accelerated by adopting multi-omics, bioinformatics, and machine learning tools that generate a huge amount of molecular data. The integration of artificial intelligence and machine learning tools in the era of omics and big data has opened up a new outlook in both basic and applied researches in the area of nutraceuticals and functional food and nutrition. KEY POINTS: • Multi-omic tool helps in the identification of novel fungal metabolites • Intra-omic data from genomics to bioinformatics • Novel metabolites and application in human health.
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Affiliation(s)
- Akshay Shankar
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India.
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2
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Sharma A, Colonna G. System-Wide Pollution of Biomedical Data: Consequence of the Search for Hub Genes of Hepatocellular Carcinoma Without Spatiotemporal Consideration. Mol Diagn Ther 2021; 25:9-27. [PMID: 33475988 PMCID: PMC7847983 DOI: 10.1007/s40291-020-00505-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 12/17/2022]
Abstract
Biomedical institutions rely on data evaluation and are turning into data factories. Big-data storage centers, supercomputing systems, and increased algorithmic efficiency allow us to analyze the ever-increasing amount of data generated every day in biomedical research centers. In network science, the principal intrinsic problem is how to integrate the data and information from different experiments on genes or proteins. Data curation is an essential process in annotating new functional data to known genes or proteins, undertaken by a biobank curator, which is then reflected in the calculated networks. We provide an example of how protein-protein networks today have space-time limits. The next step is the integration of data and information from different biobanks. Omics data and networks are essential parts of this step but also have flawed protocols and errors. Consider data from patients with cancer: from biopsy procedures to experimental tests, to archiving methods and computational algorithms, these are continuously handled so require critical and continuous "updates" to obtain reproducible, reliable, and correct results. We show, as a second example, how all this distorts studies in cellular hepatocellular carcinoma. It is not unlikely that these flawed data have been polluting biobanks for some time before stringent conditions for the veracity of data were implemented in Big data. Therefore, all this could contribute to errors in future medical decisions.
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Affiliation(s)
- Ankush Sharma
- Department of Biosciences, University of Oslo, Oslo, Norway.
- Department of Informatics, University of Oslo, Oslo, Norway.
- Institute of Cancer Research, Institute of Clinical medicine, University of Oslo, Oslo, Norway.
| | - Giovanni Colonna
- Medical Informatics, AOU-Vanvitelli, Università della Campania, Naples, Italy
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3
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Rivas-Astroza M, Conejeros R. Metabolic flux configuration determination using information entropy. PLoS One 2020; 15:e0243067. [PMID: 33275628 PMCID: PMC7717585 DOI: 10.1371/journal.pone.0243067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 11/14/2020] [Indexed: 11/20/2022] Open
Abstract
Constraint-based models use steady-state mass balances to define a solution space of flux configurations, which can be narrowed down by measuring as many fluxes as possible. Due to loops and redundant pathways, this process typically yields multiple alternative solutions. To address this ambiguity, flux sampling can estimate the probability distribution of each flux, or a flux configuration can be singled out by further minimizing the sum of fluxes according to the assumption that cellular metabolism favors states where enzyme-related costs are economized. However, flux sampling is susceptible to artifacts introduced by thermodynamically infeasible cycles and is it not clear if the economy of fluxes assumption (EFA) is universally valid. Here, we formulated a constraint-based approach, MaxEnt, based on the principle of maximum entropy, which in this context states that if more than one flux configuration is consistent with a set of experimentally measured fluxes, then the one with the minimum amount of unwarranted assumptions corresponds to the best estimation of the non-observed fluxes. We compared MaxEnt predictions to Escherichia coli and Saccharomyces cerevisiae publicly available flux data. We found that the mean square error (MSE) between experimental and predicted fluxes by MaxEnt and EFA-based methods are three orders of magnitude lower than the median of 1,350,000 MSE values obtained using flux sampling. However, only MaxEnt and flux sampling correctly predicted flux through E. coli’s glyoxylate cycle, whereas EFA-based methods, in general, predict no flux cycles. We also tested MaxEnt predictions at increasing levels of overflow metabolism. We found that MaxEnt accuracy is not affected by overflow metabolism levels, whereas the EFA-based methods show a decreasing performance. These results suggest that MaxEnt is less sensitive than flux sampling to artifacts introduced by thermodynamically infeasible cycles and that its predictions are less susceptible to overfitting than EFA-based methods.
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Affiliation(s)
- Marcelo Rivas-Astroza
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- * E-mail:
| | - Raúl Conejeros
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
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4
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García-Romero I, Nogales J, Díaz E, Santero E, Floriano B. Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling. Sci Rep 2020; 10:8651. [PMID: 32457330 PMCID: PMC7250832 DOI: 10.1038/s41598-020-65258-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/30/2020] [Indexed: 11/23/2022] Open
Abstract
Sphingopyxis granuli strain TFA is an α-proteobacterium that belongs to the sphingomonads, a group of bacteria well-known for its degradative capabilities and oligotrophic metabolism. Strain TFA is the only bacterium in which the mineralisation of the aromatic pollutant tetralin has been completely characterized at biochemical, genetic, and regulatory levels and the first Sphingopyxis characterised as facultative anaerobe. Here we report additional metabolic features of this α-proteobacterium using metabolic modelling and the functional integration of genomic and transcriptomic data. The genome-scale metabolic model (GEM) of strain TFA, which has been manually curated, includes information on 743 genes, 1114 metabolites and 1397 reactions. This represents the largest metabolic model for a member of the Sphingomonadales order thus far. The predictive potential of this model was validated against experimentally calculated growth rates on different carbon sources and under different growth conditions, including both aerobic and anaerobic metabolisms. Moreover, new carbon and nitrogen sources were predicted and experimentally validated. The constructed metabolic model was used as a platform for the incorporation of transcriptomic data, generating a more robust and accurate model. In silico flux analysis under different metabolic scenarios highlighted the key role of the glyoxylate cycle in the central metabolism of strain TFA.
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Affiliation(s)
- Inmaculada García-Romero
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, ES-41013, Seville, Spain
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, United Kingdom
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Eduardo Díaz
- Department of Microbial and Plant Biotechnology. Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), 28040, Madrid, Spain
| | - Eduardo Santero
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, ES-41013, Seville, Spain
| | - Belén Floriano
- Department of Molecular Biology and Biochemical Engineering. Universidad Pablo de Olavide, ES-41013, Seville, Spain.
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5
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Modeling the Interplay between Photosynthesis, CO 2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium. Sci Rep 2019; 9:12638. [PMID: 31477760 PMCID: PMC6718658 DOI: 10.1038/s41598-019-49079-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/19/2019] [Indexed: 11/17/2022] Open
Abstract
Rhodopseudomonas palustris CGA009 is a purple non-sulfur bacterium that can fix carbon dioxide (CO2) and nitrogen or break down organic compounds for its carbon and nitrogen requirements. Light, inorganic, and organic compounds can all be used for its source of energy. Excess electrons produced during its metabolic processes can be exploited to produce hydrogen gas or biodegradable polyesters. A genome-scale metabolic model of the bacterium was reconstructed to study the interactions between photosynthesis, CO2 fixation, and the redox state of the quinone pool. A comparison of model-predicted flux values with available Metabolic Flux Analysis (MFA) fluxes yielded predicted errors of 5–19% across four different growth substrates. The model predicted the presence of an unidentified sink responsible for the oxidation of excess quinols generated by the TCA cycle. Furthermore, light-dependent energy production was found to be highly dependent on the quinol oxidation rate. Finally, the extent of CO2 fixation was predicted to be dependent on the amount of ATP generated through the electron transport chain, with excess ATP going toward the energy-demanding Calvin-Benson-Bassham (CBB) pathway. Based on this analysis, it is hypothesized that the quinone redox state acts as a feed-forward controller of the CBB pathway, signaling the amount of ATP available.
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6
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Human Systems Biology and Metabolic Modelling: A Review-From Disease Metabolism to Precision Medicine. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8304260. [PMID: 31281846 PMCID: PMC6590590 DOI: 10.1155/2019/8304260] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/07/2019] [Accepted: 05/20/2019] [Indexed: 01/06/2023]
Abstract
In cell and molecular biology, metabolism is the only system that can be fully simulated at genome scale. Metabolic systems biology offers powerful abstraction tools to simulate all known metabolic reactions in a cell, therefore providing a snapshot that is close to its observable phenotype. In this review, we cover the 15 years of human metabolic modelling. We show that, although the past five years have not experienced large improvements in the size of the gene and metabolite sets in human metabolic models, their accuracy is rapidly increasing. We also describe how condition-, tissue-, and patient-specific metabolic models shed light on cell-specific changes occurring in the metabolic network, therefore predicting biomarkers of disease metabolism. We finally discuss current challenges and future promising directions for this research field, including machine/deep learning and precision medicine. In the omics era, profiling patients and biological processes from a multiomic point of view is becoming more common and less expensive. Starting from multiomic data collected from patients and N-of-1 trials where individual patients constitute different case studies, methods for model-building and data integration are being used to generate patient-specific models. Coupled with state-of-the-art machine learning methods, this will allow characterizing each patient's disease phenotype and delivering precision medicine solutions, therefore leading to preventative medicine, reduced treatment, and in silico clinical trials.
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7
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McCombe PA, Henderson RD, Lee A, Lee JD, Woodruff TM, Restuadi R, McRae A, Wray NR, Ngo S, Steyn FJ. Gut microbiota in ALS: possible role in pathogenesis? Expert Rev Neurother 2019; 19:785-805. [PMID: 31122082 DOI: 10.1080/14737175.2019.1623026] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: The gut microbiota has important roles in maintaining human health. The microbiota and its metabolic byproducts could play a role in the pathogenesis of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Areas covered: The authors evaluate the methods of assessing the gut microbiota, and also review how the gut microbiota affects the various physiological functions of the gut. The authors then consider how gut dysbiosis could theoretically affect the pathogenesis of ALS. They present the current evidence regarding the composition of the gut microbiota in ALS and in rodent models of ALS. Finally, the authors review therapies that could improve gut dysbiosis in the context of ALS. Expert opinion: Currently reported studies suggest some instances of gut dysbiosis in ALS patients and mouse models; however, these studies are limited, and more information with well-controlled larger datasets is required to make a definitive judgment about the role of the gut microbiota in ALS pathogenesis. Overall this is an emerging field that is worthy of further investigation. The authors advocate for larger studies using modern metagenomic techniques to address the current knowledge gaps.
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Affiliation(s)
- Pamela A McCombe
- Centre for Clinical Research, The University of Queensland , Brisbane , Australia.,Wesley Medical Research, Level 8 East Wing, The Wesley Hospital , Brisbane , Australia.,Department of Neurology, Royal Brisbane & Women's Hospital , Brisbane , Australia.,School of Medicine, The University of Queensland , Brisbane , Australia
| | - Robert D Henderson
- Wesley Medical Research, Level 8 East Wing, The Wesley Hospital , Brisbane , Australia.,Department of Neurology, Royal Brisbane & Women's Hospital , Brisbane , Australia.,School of Medicine, The University of Queensland , Brisbane , Australia.,Queensland Brain Institute, The University of Queensland , Brisbane , Australia
| | - Aven Lee
- Centre for Clinical Research, The University of Queensland , Brisbane , Australia
| | - John D Lee
- School of Biomedical Sciences, The University of Queensland , Brisbane , Australia
| | - Trent M Woodruff
- School of Biomedical Sciences, The University of Queensland , Brisbane , Australia
| | - Restuadi Restuadi
- Institute for Molecular Bioscience, The University of Queensland , Brisbane , Australia
| | - Allan McRae
- Institute for Molecular Bioscience, The University of Queensland , Brisbane , Australia
| | - Naomi R Wray
- Queensland Brain Institute, The University of Queensland , Brisbane , Australia.,Institute for Molecular Bioscience, The University of Queensland , Brisbane , Australia
| | - Shyuan Ngo
- Centre for Clinical Research, The University of Queensland , Brisbane , Australia.,Wesley Medical Research, Level 8 East Wing, The Wesley Hospital , Brisbane , Australia.,Department of Neurology, Royal Brisbane & Women's Hospital , Brisbane , Australia.,Queensland Brain Institute, The University of Queensland , Brisbane , Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane , Australia
| | - Frederik J Steyn
- Centre for Clinical Research, The University of Queensland , Brisbane , Australia.,Wesley Medical Research, Level 8 East Wing, The Wesley Hospital , Brisbane , Australia.,Department of Neurology, Royal Brisbane & Women's Hospital , Brisbane , Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane , Australia
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8
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Shen T, Zhang Z, Chen Z, Gu D, Liang S, Xu Y, Li R, Wei Y, Liu Z, Yi Y, Xie X. A genome-scale metabolic network alignment method within a hypergraph-based framework using a rotational tensor-vector product. Sci Rep 2018; 8:16376. [PMID: 30401914 PMCID: PMC6219566 DOI: 10.1038/s41598-018-34692-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/23/2018] [Indexed: 12/14/2022] Open
Abstract
Biological network alignment aims to discover important similarities and differences and thus find a mapping between topological and/or functional components of different biological molecular networks. Then, the mapped components can be considered to correspond to both their places in the network topology and their biological attributes. Development and evolution of biological network alignment methods has been accelerated by the rapidly increasing availability of such biological networks, yielding a repertoire of tens of methods based upon graph theory. However, most biological processes, especially the metabolic reactions, are more sophisticated than simple pairwise interactions and contain three or more participating components. Such multi-lateral relations are not captured by graphs, and computational methods to overcome this limitation are currently lacking. This paper introduces hypergraphs and association hypergraphs to describe metabolic networks and their potential alignments, respectively. Within this framework, metabolic networks are aligned by identifying the maximal Z-eigenvalue of a symmetric tensor. A shifted higher-order power method was utilized to identify a solution. A rotational strategy has been introduced to accelerate the tensor-vector product by 250-fold on average and reduce the storage cost by up to 1,000-fold. The algorithm was implemented on a spark-based distributed computation cluster to significantly increase the convergence rate further by 50- to 80-fold. The parameters have been explored to understand their impact on alignment accuracy and speed. In particular, the influence of initial value selection on the stationary point has been simulated to ensure an accurate approximation of the global optimum. This framework was demonstrated by alignments among the genome-wide metabolic networks of Escherichia coli MG-1655 and Halophilic archaeon DL31. To our knowledge, this is the first genome-wide metabolic network alignment at both the metabolite level and the enzyme level. These results demonstrate that it can supply quite a few valuable insights into metabolic networks. First, this method can access the driving force of organic reactions through the chemical evolution of metabolic network. Second, this method can incorporate the chemical information of enzymes and structural changes of compounds to offer new way defining reaction class and module, such as those in KEGG. Third, as a vertex-focused treatment, this method can supply novel structural and functional annotation for ill-defined molecules. The related source code is available on request.
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Affiliation(s)
- Tie Shen
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou, China.
| | - Zhengdong Zhang
- College of Mathematics and Information Science, Guiyang University, Guiyang, Guizhou, China
| | - Zhen Chen
- College of Mathematical Science, Guizhou Normal University, Guiyang, Guizhou, China
| | - Dagang Gu
- College of Mathematics and Information Science, Guiyang University, Guiyang, Guizhou, China
| | - Shen Liang
- College of Mathematics and Information Science, Guiyang University, Guiyang, Guizhou, China
| | - Yang Xu
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou, China
| | - Ruiyuan Li
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou, China
| | - Yimin Wei
- School of Mathematics Sciences and Key Laboratory of Mathematics for Nonlinear Sciences, Fudan University, Shanghai, China
| | - Zhijie Liu
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou, China
| | - Yin Yi
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst of Southwest Areas China, Guizhou Normal University, Guiyang, Guizhou, China.
| | - Xiaoyao Xie
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou, China.
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9
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Sinha N, Suarez-Diez M, Hooiveld GJEJ, Keijer J, Martin Dos Santos V, van Schothorst EM. A Constraint-Based Model Analysis of Enterocyte Mitochondrial Adaptation to Dietary Interventions of Lipid Type and Lipid Load. Front Physiol 2018; 9:749. [PMID: 29962969 PMCID: PMC6013923 DOI: 10.3389/fphys.2018.00749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/28/2018] [Indexed: 12/12/2022] Open
Abstract
Computational modeling of mitochondrial adaptability and flexibility in the small intestine upon different nutritional exposures will provide insights that will help to define healthy diet interventions. Therefore, a murine enterocyte-specific mitochondrial constraint-based metabolic model (named MT_mmuENT127) was constructed and used to simulate mitochondrial behavior under different dietary conditions, representing various levels and composition of nutrients absorbed by the enterocytes in mice, primarily focusing on metabolic pathways. Our simulations predicted that increasing the fraction of marine fatty acids in the diet, or increasing the dietary lipid/carbohydrate ratio resulted in (i) an increase in mitochondrial fatty acid beta oxidation, and (ii) changes in only a limited subset of mitochondrial reactions, which appeared to be independent of gene expression regulation. Moreover, transcript levels of mitochondrial proteins suggested unaltered fusion–fission dynamics by an increased lipid/carbohydrates ratio or by increased fractions of marine fatty acids. In conclusion, our enterocytic mitochondrial constraint-based model was shown to be a suitable platform to investigate effects of dietary interventions on mitochondrial adaptation and provided novel and deeper insights in mitochondrial metabolism and regulation.
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Affiliation(s)
- Neeraj Sinha
- Nutrition, Metabolism and Genomics, Division of Human Nutrition, Wageningen University & Research, Wageningen, Netherlands.,Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands.,Human and Animal Physiology, Wageningen University & Research, Wageningen, Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Guido J E J Hooiveld
- Nutrition, Metabolism and Genomics, Division of Human Nutrition, Wageningen University & Research, Wageningen, Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University & Research, Wageningen, Netherlands
| | - Vitor Martin Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands.,LifeGlimmer GmbH, Berlin, Germany
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10
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Ghazaei C. Pathogenic Leptospira: Advances in understanding the molecular pathogenesis and virulence. Open Vet J 2018; 8:13-24. [PMID: 29445617 PMCID: PMC5806663 DOI: 10.4314/ovj.v8i1.4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 01/08/2018] [Indexed: 12/16/2022] Open
Abstract
Leptospirosis is a common zoonotic disease has emerged as a major public health problem, with developing countries bearing disproportionate burdens. Although the diverse range of clinical manifestations of the leptospirosis in humans is widely documented, the mechanisms through which the pathogen causes disease remain undetermined. In addition, leptospirosis is a much-neglected life-threatening disease although it is one of the most important zoonoses occurring in a diverse range of epidemiological distribution. Recent advances in molecular profiling of pathogenic species of the genus Leptospira have improved our understanding of the evolutionary factors that determine virulence and mechanisms that the bacteria employ to survive. However, a major impediment to the formulation of intervention strategies has been the limited understanding of the disease determinants. Consequently, the association of the biological mechanisms to the pathogenesis of Leptospira, as well as the functions of numerous essential virulence factors still remain implicit. This review examines recent advances in genetic screening technologies, the underlying microbiological processes, the virulence factors and associated molecular mechanisms driving pathogenesis of Leptospira species.
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Affiliation(s)
- Ciamak Ghazaei
- Department of Microbiology, University of Mohaghegh Ardabili, P.O. Box 179, Ardabil, Iran
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11
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Abstract
Bioprocesses are of critical importance in several industries such as the food and pharmaceutical industries. Despite their importance and widespread application, bioprocess models remain rather simplistic and based on unstructured models. These simple models have limitations, making it very difficult to model complex bioprocesses. With dynamic flux balance analysis (DFBA) more comprehensive bioprocess models can be obtained. DFBA simulations are difficult to carry out because they result in dynamic systems with linear programs embedded. Therefore, the use of DFBA as a modeling tool has been limited. With DFBAlab, a MATLAB code that performs efficient and reliable DFBA simulations, the use of DFBA as a modeling tool has become more accessible. Here, we illustrate with an example how to implement bioprocess models in DFBAlab.
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Affiliation(s)
| | - Paul I Barton
- Process Systems Engineering Laboratory, Cambridge, MA, USA.
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12
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13
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Ye C, Xu N, Dong C, Ye Y, Zou X, Chen X, Guo F, Liu L. IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models. Sci Rep 2017; 7:727. [PMID: 28389638 PMCID: PMC5429687 DOI: 10.1038/s41598-017-00820-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/16/2017] [Indexed: 11/12/2022] Open
Abstract
Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into microbial physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.
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Affiliation(s)
- Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Nan Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Chuan Dong
- Key Laboratory for Neuroinformation of Ministry of Education, University of Electronic Science and Technology of China, No. 4, 2nd Section, North Jianshe Road, Chengdu, Sichuan, 610054, China
| | - Yuannong Ye
- School of Biology and Engineering, Guizhou Medical University, Dongqing Road, Huaxi District, Guiyang, Guizhou, 550025, China
- School of Big Health, Guizhou Medical University, Dongqing Road, Huaxi District, Guiyang, Guizhou, 550025, China
| | - Xuan Zou
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Fengbiao Guo
- Key Laboratory for Neuroinformation of Ministry of Education, University of Electronic Science and Technology of China, No. 4, 2nd Section, North Jianshe Road, Chengdu, Sichuan, 610054, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
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14
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Santero E, Floriano B, Govantes F. Harnessing the power of microbial metabolism. Curr Opin Microbiol 2016; 31:63-69. [DOI: 10.1016/j.mib.2016.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 01/12/2023]
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Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento ALT, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA, Yang XF, Zhang JJ, Vinetz JM. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. PLoS Negl Trop Dis 2016; 10:e0004403. [PMID: 26890609 PMCID: PMC4758666 DOI: 10.1371/journal.pntd.0004403] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/03/2016] [Indexed: 12/20/2022] Open
Abstract
Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade's refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic) vs. non-infectious Leptospira, this work provides new insights into the evolution of a genus of bacterial pathogens. This work will be a comprehensive roadmap for understanding leptospirosis pathogenesis. More generally, it provides new insights into mechanisms by which bacterial pathogens adapt to mammalian hosts.
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Affiliation(s)
- Derrick E. Fouts
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Michael A. Matthias
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Haritha Adhikarla
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Ben Adler
- Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Australia
| | - Luciane Amorim-Santos
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia, Brazil
| | - Douglas E. Berg
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Dieter Bulach
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia
| | - Alejandro Buschiazzo
- Institut Pasteur de Montevideo, Laboratory of Molecular and Structural Microbiology, Montevideo, Uruguay
- Institut Pasteur, Department of Structural Biology and Chemistry, Paris, France
| | - Yung-Fu Chang
- Department of Population Medicine & Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Renee L. Galloway
- Centers for Disease Control and Prevention (DHHS, CDC, OID, NCEZID, DHCPP, BSPB), Atlanta, Georgia, United States of America
| | - David A. Haake
- VA Greater Los Angeles Healthcare System, Los Angeles, California, United States of America
- David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Daniel H. Haft
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Rudy Hartskeerl
- WHO/FAO/OIE and National Collaborating Centre for Reference and Research on Leptospirosis, KIT Biomedical Research, Royal Tropical Institute (KIT), Amsterdam, The Netherlands
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia, Brazil
| | - Paul N. Levett
- Government of Saskatchewan, Disease Control Laboratory Regina, Canada
| | - James Matsunaga
- VA Greater Los Angeles Healthcare System, Los Angeles, California, United States of America
- David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Ariel E. Mechaly
- Institut Pasteur de Montevideo, Laboratory of Molecular and Structural Microbiology, Montevideo, Uruguay
| | - Jonathan M. Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Ana L. T. Nascimento
- Centro de Biotecnologia, Instituto Butantan, São Paulo, SP, Brazil
- Programa Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, USP, São Paulo, SP, Brazil
| | - Karen E. Nelson
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Mathieu Picardeau
- Institut Pasteur, Biology of Spirochetes Unit, National Reference Centre and WHO Collaborating Center for Leptospirosis, Paris, France
| | - Jessica N. Ricaldi
- Instituto de Medicina Tropical Alexander von Humboldt; Facultad de Medicina Alberto Hurtado, Universidd Peruana Cayetano Heredia, Lima, Peru
| | | | - Elsio A. Wunder
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia, Brazil
| | - X. Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Jun-Jie Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Joseph M. Vinetz
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
- Instituto de Medicina Tropical Alexander von Humboldt; Facultad de Medicina Alberto Hurtado, Universidd Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina “Alexander von Humboldt,” Universidad Peruana Cayetano Heredia, Lima, Peru
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