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Silva-Andrade C, Rodriguez-Fernández M, Garrido D, Martin AJM. Using metabolic networks to predict cross-feeding and competition interactions between microorganisms. Microbiol Spectr 2024; 12:e0228723. [PMID: 38506512 PMCID: PMC11064492 DOI: 10.1128/spectrum.02287-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 02/06/2024] [Indexed: 03/21/2024] Open
Abstract
Understanding the interactions between microorganisms and their impact on bacterial behavior at the community level is a key research topic in microbiology. Different methods, relying on experimental or mathematical approaches based on the diverse properties of bacteria, are currently employed to study these interactions. Recently, the use of metabolic networks to understand the interactions between bacterial pairs has increased, highlighting the relevance of this approach in characterizing bacteria. In this study, we leverage the representation of bacteria through their metabolic networks to build a predictive model aimed at reducing the number of experimental assays required for designing bacterial consortia with specific behaviors. Our novel method for predicting cross-feeding or competition interactions between pairs of microorganisms utilizes metabolic network features. Machine learning classifiers are employed to determine the type of interaction from automatically reconstructed metabolic networks. Several algorithms were assessed and selected based on comprehensive testing and careful separation of manually compiled data sets obtained from literature sources. We used different classification algorithms, including K Nearest Neighbors, XGBoost, Support Vector Machine, and Random Forest, tested different parameter values, and implemented several data curation approaches to reduce the biological bias associated with our data set, ultimately achieving an accuracy of over 0.9. Our method holds substantial potential to advance the understanding of community behavior and contribute to the development of more effective approaches for consortia design.IMPORTANCEUnderstanding bacterial interactions at the community level is critical for microbiology, and leveraging metabolic networks presents an efficient and effective approach. The introduction of this novel method for predicting interactions through machine learning classifiers has the potential to advance the field by reducing the number of experimental assays required and contributing to the development of more effective bacterial consortia.
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Affiliation(s)
- Claudia Silva-Andrade
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - María Rodriguez-Fernández
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alberto J. M. Martin
- Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Escuela de Ingeniería, Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
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Pereira PDC, Henrique EP, da Costa ER, Falcão ADJ, de Melo MAD, Schneider MPC, Burbano RMR, Diniz DG, Magalhães NGDM, Sherry DF, Diniz CWP, Guerreiro-Diniz C. Molecular Changes in the Brain of the Wintering Calidris pusilla in the Mangroves of the Amazon River Estuary. Int J Mol Sci 2023; 24:12712. [PMID: 37628893 PMCID: PMC10454129 DOI: 10.3390/ijms241612712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Migrant birds prepare differently to fly north for breeding in the spring and for the flight to lower latitudes during autumn, avoiding the cold and food shortages of the Northern Hemisphere's harsh winter. The molecular events associated with these fundamental stages in the life history of migrants include the differential gene expression in different tissues. Semipalmated sandpipers (Calidris pusilla) are Arctic-breeding shorebirds that migrate to the coast of South America during the non-breeding season. In a previous study, we demonstrated that between the beginning and the end of the wintering period, substantial glial changes and neurogenesis occur in the brain of C. pusilla. These changes follow the epic journey of the autumn migration when a 5-day non-stop transatlantic flight towards the coast of South America and the subsequent preparation for the long-distance flight of the spring migration takes place. Here, we tested the hypothesis that the differential gene expressions observed in the brains of individuals captured in the autumn and spring windows are consistent with the previously described cellular changes. We searched for differential gene expressions in the brain of the semipalmated sandpiper, of recently arrived birds (RA) from the autumnal migration, and that of individuals in the premigratory period (PM) in the spring. All individuals were collected in the tropical coastal of northern Brazil in the mangrove region of the Amazon River estuary. We generated a de novo neurotranscriptome for C. pusilla individuals and compared the gene expressions across libraries. To that end, we mapped an RNA-Seq that reads to the C. pusilla neurotranscriptome in four brain samples of each group and found that the differential gene expressions in newly arrived and premigratory birds were related with neurogenesis, metabolic pathways (ketone body biosynthetic and the catabolic and lipid biosynthetic processes), and glial changes (astrocyte-dopaminergic neuron signaling, astrocyte differentiation, astrocyte cell migration, and astrocyte activation involved in immune response), as well as genes related to the immune response to virus infections (Type I Interferons), inflammatory cytokines (IL-6, IL-1β, TNF, and NF-κB), NLRP3 inflammasome, anti-inflammatory cytokines (IL-10), and cell death pathways (pyroptosis- and caspase-related changes).
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Affiliation(s)
- Patrick Douglas Corrêa Pereira
- Laboratório de Biologia Molecular e Neuroecologia, Campus Bragança, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança 68600-000, PA, Brazil; (P.D.C.P.)
| | - Ediely Pereira Henrique
- Laboratório de Biologia Molecular e Neuroecologia, Campus Bragança, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança 68600-000, PA, Brazil; (P.D.C.P.)
| | - Emanuel Ramos da Costa
- Laboratório de Biologia Molecular e Neuroecologia, Campus Bragança, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança 68600-000, PA, Brazil; (P.D.C.P.)
| | - Anderson de Jesus Falcão
- Laboratório de Biologia Molecular e Neuroecologia, Campus Bragança, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança 68600-000, PA, Brazil; (P.D.C.P.)
| | - Mauro André Damasceno de Melo
- Laboratório de Biologia Molecular e Neuroecologia, Campus Bragança, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança 68600-000, PA, Brazil; (P.D.C.P.)
| | | | | | - Daniel Guerreiro Diniz
- Laboratório de Investigações em Neurodegeneração e Infecção, Hospital Universitário João de Barros Barreto, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
- Laboratório de Microscopia Eletrônica, Seção de Hepatologia, Instituto Evandro Chagas, Belém 66093-020, PA, Brazil
| | - Nara Gyzely de Morais Magalhães
- Laboratório de Biologia Molecular e Neuroecologia, Campus Bragança, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança 68600-000, PA, Brazil; (P.D.C.P.)
| | - David Francis Sherry
- Department of Psychology, Advanced Facility for Avian Research, University of Western Ontario, London, ON N6G 1G9, Canada
| | - Cristovam Wanderley Picanço Diniz
- Laboratório de Investigações em Neurodegeneração e Infecção, Hospital Universitário João de Barros Barreto, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | - Cristovam Guerreiro-Diniz
- Laboratório de Biologia Molecular e Neuroecologia, Campus Bragança, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Bragança 68600-000, PA, Brazil; (P.D.C.P.)
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Yenkin AL, Bramley JC, Kremitzki CL, Waligorski JE, Liebeskind MJ, Xu XE, Chandrasekaran VD, Vakaki MA, Bachman GW, Mitra RD, Milbrandt JD, Buchser WJ. Pooled image-base screening of mitochondria with microraft isolation distinguishes pathogenic mitofusin 2 mutations. Commun Biol 2022; 5:1128. [PMID: 36284160 PMCID: PMC9596453 DOI: 10.1038/s42003-022-04089-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/11/2022] [Indexed: 11/08/2022] Open
Abstract
Most human genetic variation is classified as variants of uncertain significance. While advances in genome editing have allowed innovation in pooled screening platforms, many screens deal with relatively simple readouts (viability, fluorescence) and cannot identify the complex cellular phenotypes that underlie most human diseases. In this paper, we present a generalizable functional genomics platform that combines high-content imaging, machine learning, and microraft isolation in a method termed "Raft-Seq". We highlight the efficacy of our platform by showing its ability to distinguish pathogenic point mutations of the mitochondrial regulator Mitofusin 2, even when the cellular phenotype is subtle. We also show that our platform achieves its efficacy using multiple cellular features, which can be configured on-the-fly. Raft-Seq enables a way to perform pooled screening on sets of mutations in biologically relevant cells, with the ability to physically capture any cell with a perturbed phenotype and expand it clonally, directly from the primary screen.
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Affiliation(s)
- Alex L Yenkin
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Functional Imaging for Variant Elucidation at the McDonnell Genome Institute, St Louis, MO, USA
| | - John C Bramley
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Functional Imaging for Variant Elucidation at the McDonnell Genome Institute, St Louis, MO, USA
| | - Colin L Kremitzki
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Functional Imaging for Variant Elucidation at the McDonnell Genome Institute, St Louis, MO, USA
| | - Jason E Waligorski
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Functional Imaging for Variant Elucidation at the McDonnell Genome Institute, St Louis, MO, USA
| | - Mariel J Liebeskind
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Functional Imaging for Variant Elucidation at the McDonnell Genome Institute, St Louis, MO, USA
| | - Xinyuan E Xu
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Functional Imaging for Variant Elucidation at the McDonnell Genome Institute, St Louis, MO, USA
| | - Vinay D Chandrasekaran
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Functional Imaging for Variant Elucidation at the McDonnell Genome Institute, St Louis, MO, USA
| | - Maria A Vakaki
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Functional Imaging for Variant Elucidation at the McDonnell Genome Institute, St Louis, MO, USA
| | - Graham W Bachman
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Functional Imaging for Variant Elucidation at the McDonnell Genome Institute, St Louis, MO, USA
| | - Robi D Mitra
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Functional Imaging for Variant Elucidation at the McDonnell Genome Institute, St Louis, MO, USA
| | - Jeffrey D Milbrandt
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Functional Imaging for Variant Elucidation at the McDonnell Genome Institute, St Louis, MO, USA
| | - William J Buchser
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.
- Functional Imaging for Variant Elucidation at the McDonnell Genome Institute, St Louis, MO, USA.
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Identifying Obstructive Sleep Apnea Syndrome-Associated Genes and Pathways through Weighted Gene Coexpression Network Analysis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:3993509. [PMID: 35132330 PMCID: PMC8817882 DOI: 10.1155/2022/3993509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022]
Abstract
Background Obstructive sleep apnea syndrome (OSAS) is the most common type of sleep apnea disorder. The disease seriously affects the patient's respiratory system. At present, the prognosis of the disease is poor and there is a lack of effective treatments. Therefore, it is urgent to explore its pathogenesis and treatment methods. Method We downloaded a set of expression profile data from GSE75097 related to OSAS based on the Gene Expression Omnibus (GEO) database and selected the representative differentially expressed genes (DEGs) from the sample of the GSE75097 dataset. WGCNA was used to find genes related to OSAS and obtain coexpression modules. The Gene Ontology (GO) function and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were used to analyze genes from key modules. Finally, Cytoscape software was used to construct a protein-protein interaction (PPI) network and analyze the hub genes. Result We obtained a total of 7565 DEGs. Through WGCNA, we got four coexpression modules and the modules most related to OSAS were green-yellow, magenta, purple, and turquoise, and we screened out eight hub genes (DDX46, RNF115, COPA, FBXO4, PA2G4, NHP2L1, CDC20, and PCNA). GO and KEGG analyses indicated that the key modules were mainly enriched in tRNA modification, nucleobase metabolic process, DNA ligation, regulation of cellular component movement, basal transcription factors, Huntington disease, and vitamin digestion and absorption. Conclusion These pathways and hub genes can facilitate understanding the molecular mechanism of OSAS and provide a meaningful reference for finding biological targets of OSAS treatment.
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Karlson CKS, Mohd-Noor SN, Nolte N, Tan BC. CRISPR/dCas9-Based Systems: Mechanisms and Applications in Plant Sciences. PLANTS 2021; 10:plants10102055. [PMID: 34685863 PMCID: PMC8540305 DOI: 10.3390/plants10102055] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022]
Abstract
RNA-guided genomic transcriptional regulation tools, namely clustered regularly interspaced short palindromic repeats interference (CRISPRi) and CRISPR-mediated gene activation (CRISPRa), are a powerful technology for gene functional studies. Deriving from the CRISPR/Cas9 system, both systems consist of a catalytically dead Cas9 (dCas9), a transcriptional effector and a single guide RNA (sgRNA). This type of dCas9 is incapable to cleave DNA but retains its ability to specifically bind to DNA. The binding of the dCas9/sgRNA complex to a target gene results in transcriptional interference. The CRISPR/dCas9 system has been explored as a tool for transcriptional modulation and genome imaging. Despite its potential applications and benefits, the challenges and limitations faced by the CRISPR/dCas9 system include the off-target effects, protospacer adjacent motif (PAM) sequence requirements, efficient delivery methods and the CRISPR/dCas9-interfered crops being labeled as genetically modified organisms in several countries. This review highlights the progression of CRISPR/dCas9 technology as well as its applications and potential challenges in crop improvement.
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Affiliation(s)
- Chou Khai Soong Karlson
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Siti Nurfadhlina Mohd-Noor
- Institute of Microengineering and Nanoelectronics (IMEN), Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia;
| | - Nadja Nolte
- Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands;
| | - Boon Chin Tan
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia;
- Correspondence: ; Tel.: +60-3-7967-7982
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Abstract
Purpose of Review To summarize the recent advances in transcriptomics and proteomics studies of keratoconus using advanced genome-wide gene and protein expression profiling techniques. Recent Findings Second-generation sequencing including RNA sequencing has been widely used to characterize the genome-wide gene expression in corneal tissues or cells affected by keratoconus. Due to different sample types, sequencing platforms, and analysis pipeline, different lists of genes have been identified to be differentially expressed in KC-affected samples. Gene ontology and pathway/network analyses have indicated the involvement of genes related with extracellular matrix, WNT-signaling, TGFβ pathway, and NRF2-regulated network. High throughput proteomics studies using mass spectrometry have uncovered many KC-related protein molecules in pathways related with cytoskeleton, cell matrix, TGFβ signaling, and extracellular matrix remodeling, consistent with gene expression profiling. Summary Both transcriptomics and proteomics studies using genome-wide gene/protein expression profiling techniques have identified significant genes/proteins that may contribute to the pathogenesis of keratoconus. These molecules may be involved in functional categories related with extracellular matrix and TGFβ signaling. It is necessary to perform comprehensive gene/protein expression studies using larger sample size, same type of samples, up-to-date platform and bioinformatics tools.
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The History of Colistin Resistance Mechanisms in Bacteria: Progress and Challenges. Microorganisms 2021; 9:microorganisms9020442. [PMID: 33672663 PMCID: PMC7924381 DOI: 10.3390/microorganisms9020442] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022] Open
Abstract
Since 2015, the discovery of colistin resistance genes has been limited to the characterization of new mobile colistin resistance (mcr) gene variants. However, given the complexity of the mechanisms involved, there are many colistin-resistant bacterial strains whose mechanism remains unknown and whose exploitation requires complementary technologies. In this review, through the history of colistin, we underline the methods used over the last decades, both old and recent, to facilitate the discovery of the main colistin resistance mechanisms and how new technological approaches may help to improve the rapid and efficient exploration of new target genes. To accomplish this, a systematic search was carried out via PubMed and Google Scholar on published data concerning polymyxin resistance from 1950 to 2020 using terms most related to colistin. This review first explores the history of the discovery of the mechanisms of action and resistance to colistin, based on the technologies deployed. Then we focus on the most advanced technologies used, such as MALDI-TOF-MS, high throughput sequencing or the genetic toolbox. Finally, we outline promising new approaches, such as omics tools and CRISPR-Cas9, as well as the challenges they face. Much has been achieved since the discovery of polymyxins, through several innovative technologies. Nevertheless, colistin resistance mechanisms remains very complex.
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Housman G, Gilad Y. Prime time for primate functional genomics. Curr Opin Genet Dev 2020; 62:1-7. [PMID: 32544775 DOI: 10.1016/j.gde.2020.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022]
Abstract
Functional genomics research is continually improving our understanding of genotype-phenotype relationships in humans, and comparative genomics perspectives can provide additional insight into the evolutionary histories of such relationships. To specifically identify conservation or species-specific divergence in humans, we must look to our closest extant evolutionary relatives. Primate functional genomics research has been steadily advancing and expanding, in spite of several limitations and challenges that this field faces. New technologies and cheaper sequencing provide a unique opportunity to enhance and expand primate comparative studies, and we outline possible paths going forward. The potential human-specific insights that can be gained from primate functional genomics research are substantial, and we propose that now is a prime time to expand such endeavors.
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Affiliation(s)
- Genevieve Housman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, 5841 S. Maryland Ave., N417, MC6091, Chicago, IL 60637 USA.
| | - Yoav Gilad
- Section of Genetic Medicine, Department of Medicine, University of Chicago, 5841 S. Maryland Ave., N417, MC6091, Chicago, IL 60637 USA; Department of Human Genetics, University of Chicago, Cummings Life Science Center, 928 E. 58th St., Chicago, IL 60637 USA
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