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Li F, Wang C, Xu J, Wang X, Cao M, Wang S, Zhang T, Xu Y, Wang J, Pan S, Hu W. Evaluation of the antibacterial activity of Elsholtzia ciliate essential oil against halitosis-related Fusobacterium nucleatum and Porphyromonas gingivalis. Front Microbiol 2023; 14:1219004. [PMID: 37608950 PMCID: PMC10440386 DOI: 10.3389/fmicb.2023.1219004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/24/2023] [Indexed: 08/24/2023] Open
Abstract
The broad-spectrum antimicrobial activity of Elsholtzia ciliate essential oil (ECO) has been previously reported, but its effectiveness against halitosis-causing bacteria such as Fusobacterium nucleatum and Porphyromonas gingivalis is not well understood. In this study, we investigated the bacteriostatic activity of ECO against planktonic cells and biofilms of F. nucleatum and P. gingivalis, as well as its ability to inhibit bacterial metabolism and production of volatile sulfur compounds (VSCs) at sub-lethal concentrations. Our findings revealed that ECO exhibited comparable activities to chlorhexidine against these oral bacteria. Treatment with ECO significantly reduced the production of VSCs, including hydrogen sulfide, dimethyl disulfide, and methanethiol, which are major contributors to bad breath. As the major chemical components of ECO, carvacrol, p-cymene, and phellandrene, were demonstrated in vitro inhibitory effects on F. nucleatum and P. gingivalis, and their combined use showed synergistic and additive effects, suggesting that the overall activity of ECO is derived from the cumulative or synergistic effect of multiple active components. ECO was found to have a destructive effect on the bacterial cell membrane by examining the cell morphology and permeability. Furthermore, the application of ECO induced significant changes in the bacterial composition of saliva-derived biofilm, resulting in the elimination of bacterial species that contribute to halitosis, including Fusobacterium, Porphyromonas, and Prevotella. These results provide experimental evidence for the potential clinical applications of ECOs in the prevention and treatment of halitosis.
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Affiliation(s)
- Fengjiao Li
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chuandong Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Jing Xu
- Shenzhen RELX Technology Co., Ltd., Shenzhen, China
| | - Xiaoyu Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Meng Cao
- Shandong Aobo Biotechnology Co., Ltd., Liaocheng, China
| | - Shuhua Wang
- Shandong Aobo Biotechnology Co., Ltd., Liaocheng, China
| | | | - Yanyong Xu
- Beijing Xinyue Technology Co., Ltd., Beijing, China
| | - Jing Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shaobin Pan
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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Lokmic-Tomkins Z, Bhandari D, Bain C, Borda A, Kariotis TC, Reser D. Lessons Learned from Natural Disasters around Digital Health Technologies and Delivering Quality Healthcare. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:4542. [PMID: 36901559 PMCID: PMC10001761 DOI: 10.3390/ijerph20054542] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
As climate change drives increased intensity, duration and severity of weather-related events that can lead to natural disasters and mass casualties, innovative approaches are needed to develop climate-resilient healthcare systems that can deliver safe, quality healthcare under non-optimal conditions, especially in remote or underserved areas. Digital health technologies are touted as a potential contributor to healthcare climate change adaptation and mitigation, through improved access to healthcare, reduced inefficiencies, reduced costs, and increased portability of patient information. Under normal operating conditions, these systems are employed to deliver personalised healthcare and better patient and consumer involvement in their health and well-being. During the COVID-19 pandemic, digital health technologies were rapidly implemented on a mass scale in many settings to deliver healthcare in compliance with public health interventions, including lockdowns. However, the resilience and effectiveness of digital health technologies in the face of the increasing frequency and severity of natural disasters remain to be determined. In this review, using the mixed-methods review methodology, we seek to map what is known about digital health resilience in the context of natural disasters using case studies to demonstrate what works and what does not and to propose future directions to build climate-resilient digital health interventions.
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Affiliation(s)
- Zerina Lokmic-Tomkins
- School of Nursing and Midwifery, Monash University, 35 Rainforest Walk, Clayton, Melbourne, VIC 3800, Australia
| | - Dinesh Bhandari
- School of Nursing and Midwifery, Monash University, 35 Rainforest Walk, Clayton, Melbourne, VIC 3800, Australia
| | - Chris Bain
- Digital Health Theme, Department of Human-Centered Computing, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
| | - Ann Borda
- Melbourne Medical School, The University of Melbourne, Parkville, VIC 3010, Australia
- Department of Information Studies, University College London, London WC1E 6BT, UK
| | - Timothy Charles Kariotis
- School of Computing and Information System, The University of Melbourne, Melbourne, VIC 3010, Australia
- Melbourne School of Government, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - David Reser
- Graduate Entry Medicine Program, Monash Rural Health-Churchill, Churchill, VIC 3842, Australia
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3
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Waclawiková B, Cesar Telles de Souza P, Schwalbe M, Neochoritis CG, Hoornenborg W, Nelemans SA, Marrink SJ, El Aidy S. Potential binding modes of the gut bacterial metabolite, 5-hydroxyindole, to the intestinal L-type calcium channels and its impact on the microbiota in rats. Gut Microbes 2023; 15:2154544. [PMID: 36511640 PMCID: PMC9754111 DOI: 10.1080/19490976.2022.2154544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Intestinal microbiota and microbiota-derived metabolites play a key role in regulating the host physiology. Recently, we have identified a gut-bacterial metabolite, namely 5-hydroxyindole, as a potent stimulant of intestinal motility via its modulation of L-type voltage-gated calcium channels located on the intestinal smooth muscle cells. Dysregulation of L-type voltage-gated calcium channels is associated with various gastrointestinal motility disorders, including constipation, making L-type voltage-gated calcium channels an important target for drug development. Nonetheless, the majority of currently available drugs are associated with alteration of the gut microbiota. Using 16S rRNA sequencing this study shows that, when administered orally, 5-hydroxyindole has only marginal effects on the rat cecal microbiota. Molecular dynamics simulations propose potential-binding pockets of 5-hydroxyindole in the α1 subunit of the L-type voltage-gated calcium channels and when its stimulatory effect on the rat colonic contractility was compared to 16 different analogues, ex-vivo, 5-hydroxyindole stood as the most potent enhancer of the intestinal contractility. Overall, the present findings imply a potential role of microbiota-derived metabolites as candidate therapeutics for targeted treatment of slow intestinal motility-related disorders including constipation.
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Affiliation(s)
- Barbora Waclawiková
- Host-Microbe Metabolic Interactions, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Paulo Cesar Telles de Souza
- Molecular Microbiology and Structural Biochemistry (MMSB - UMR 5086), CNRS & University of Lyon, Lyon, France
| | - Markus Schwalbe
- Host-Microbe Metabolic Interactions, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | | | - Warner Hoornenborg
- Department of Behavioral Neurosciences, Cluster Neurobiology, Groningen Institute of for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Sieger A. Nelemans
- Department of Molecular Neurobiology, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Siewert J. Marrink
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Sahar El Aidy
- Host-Microbe Metabolic Interactions, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands,CONTACT Sahar El Aidy Host-Microbe Metabolic Interactions, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
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4
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de Chaves MG, Merloti LF, de Souza LF, Américo-Pinheiro JHP, Kozusny-Andreani DI, de Souza Moreira FM, Tsai SM, Navarrete AA. Ecological co-occurrence and soil physicochemical factors drive the archaeal community in Amazonian soils. Arch Microbiol 2023; 205:31. [DOI: 10.1007/s00203-022-03372-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/18/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
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Greenspan SE, Peloso P, Fuentes-González JA, Bletz M, Lyra ML, Machado IF, Martins RA, Medina D, Moura-Campos D, Neely WJ, Preuss J, Sturaro MJ, Vaz RI, Navas CA, Toledo LF, Tozetti AM, Vences M, Woodhams DC, Haddad CFB, Pienaar J, Becker CG. Low microbiome diversity in threatened amphibians from two biodiversity hotspots. Anim Microbiome 2022; 4:69. [PMID: 36582011 PMCID: PMC9801548 DOI: 10.1186/s42523-022-00220-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
Microbial diversity positively influences community resilience of the host microbiome. However, extinction risk factors such as habitat specialization, narrow environmental tolerances, and exposure to anthropogenic disturbance may homogenize host-associated microbial communities critical for stress responses including disease defense. In a dataset containing 43 threatened and 90 non-threatened amphibian species across two biodiversity hotspots (Brazil's Atlantic Forest and Madagascar), we found that threatened host species carried lower skin bacterial diversity, after accounting for key environmental and host factors. The consistency of our findings across continents suggests the broad scale at which low bacteriome diversity may compromise pathogen defenses in species already burdened with the threat of extinction.
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Affiliation(s)
- Sasha E. Greenspan
- grid.411015.00000 0001 0727 7545Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Pedro Peloso
- grid.452671.30000 0001 2175 1274Programa de Pós Gradução em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, Pará 66077-530 Brazil ,Instituto Boitatá de Etnobiologia e Conservação da Fauna, Goiânia, Goiás 74085-480 Brazil
| | - Jesualdo A. Fuentes-González
- grid.65456.340000 0001 2110 1845The Department of Biology and the Institute of Environment, Florida International University, Miami, FL 33199 USA
| | - Molly Bletz
- grid.266685.90000 0004 0386 3207Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Mariana L. Lyra
- grid.410543.70000 0001 2188 478XDepartment of Biodiversity and Aquaculture Center (CAUNESP), Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900 Brazil
| | - Ibere F. Machado
- Instituto Boitatá de Etnobiologia e Conservação da Fauna, Goiânia, Goiás 74085-480 Brazil
| | - Renato A. Martins
- grid.411247.50000 0001 2163 588XPrograma de Pós-Graduação em Conservação da Fauna, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905 Brazil
| | - Daniel Medina
- Sistema Nacional de Investigación, SENACYT; City of Knowledge, Clayton, Panama, Republic of Panama ,grid.29857.310000 0001 2097 4281Department of Biology, The Pennsylvania State University, University Park, PA 16803 USA
| | - Diego Moura-Campos
- grid.411087.b0000 0001 0723 2494Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862 Brazil ,grid.1001.00000 0001 2180 7477Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, 2601 Australia
| | - Wesley J. Neely
- grid.411015.00000 0001 0727 7545Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Jackson Preuss
- grid.412292.e0000 0004 0417 7532Departamento de Ciências da Vida, Universidade do Oeste de Santa Catarina, São Miguel Do Oeste, Santa Catarina 89900-000 Brazil
| | - Marcelo J. Sturaro
- grid.411249.b0000 0001 0514 7202Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, São Paulo 09972-270 Brazil
| | - Renata I. Vaz
- grid.11899.380000 0004 1937 0722Departamento de Fisiologia Geral, Instituto de Biociencias, Universidade de São Paulo, São Paulo, São Paulo 05508-090 Brazil
| | - Carlos A. Navas
- grid.11899.380000 0004 1937 0722Departamento de Fisiologia Geral, Instituto de Biociencias, Universidade de São Paulo, São Paulo, São Paulo 05508-090 Brazil
| | - Luís Felipe Toledo
- grid.411087.b0000 0001 0723 2494Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862 Brazil
| | - Alexandro M. Tozetti
- grid.412302.60000 0001 1882 7290Programa de Pos-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, Rio Grande Do Sul 93022-750 Brazil
| | - Miguel Vences
- grid.6738.a0000 0001 1090 0254Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, Brunswick, Germany
| | - Douglas C. Woodhams
- grid.266685.90000 0004 0386 3207Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Célio F. B. Haddad
- grid.410543.70000 0001 2188 478XDepartment of Biodiversity and Aquaculture Center (CAUNESP), Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900 Brazil
| | - Jason Pienaar
- grid.65456.340000 0001 2110 1845The Department of Biology and the Institute of Environment, Florida International University, Miami, FL 33199 USA
| | - C. Guilherme Becker
- grid.29857.310000 0001 2097 4281Department of Biology, The Pennsylvania State University, University Park, PA 16803 USA
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Yu J, Zhao J, Xie H, Cai M, Yao L, Li J, Han L, Chen W, Yu N, Peng D. Dendrobium huoshanense polysaccharides ameliorate ulcerative colitis by improving intestinal mucosal barrier and regulating gut microbiota. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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Mähler B, Janssen K, Tahoun M, Tomaschek F, Schellhorn R, Müller CE, Bierbaum G, Rust J. Adipocere formation in biofilms as a first step in soft tissue preservation. Sci Rep 2022; 12:10122. [PMID: 35710834 PMCID: PMC9203803 DOI: 10.1038/s41598-022-14119-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/01/2022] [Indexed: 12/03/2022] Open
Abstract
The preservation of soft tissue in the fossil record is mostly due to the replacement of organic structures by minerals (e.g. calcite, aragonite or apatite) called pseudomorphs. In rare cases soft tissues were preserved by pyrite. We assume that adipocere, as the shaping component, might be a preliminary stage in the pyritisation of soft tissues under anaerobic conditions. Using high-performance liquid chromatography coupled to ultraviolet and mass spectrometric detection (HPLC–UV/MS) and confocal Raman spectroscopy (CRS) we were able to demonstrate the transformation of the hepatopancreas (digestive gland) of the crayfish Cambarellus diminutus [Hobbs 1945] into adipocere within only 9 days, just inside a biofilm. Microorganisms (bacteria and fungi) which were responsible for the biofilm (Sphaerotilus [Kutzig 1833] and Pluteus [Fries 1857]) and maybe the adipocere formation (Clostridium [Prazmowski 1880]) were detected by 16S rRNA gene amplicon sequencing. Furthermore, micro-computed tomography (µ-CT) analyses revealed a precipitation of calcite and further showed that in animals with biofilm formation calcite precipitates in finer grained crystals than in individuals without biofilm formation, and that the precipitates were denser and replicated the structures of the cuticles better than the coarse precipitates.
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Affiliation(s)
- Bastian Mähler
- Section Palaeontology, Institute of Geosciences, Rheinische Friedrich-Wilhelms Universität Bonn, 53115, Bonn, Germany.
| | - Kathrin Janssen
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, Rheinische Friedrich-Wilhelms Universität, 53127, Bonn, Germany
| | - Mariam Tahoun
- Pharmazeutisches Institut, Pharmazeutische und Medizinische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53121, Bonn, Germany
| | - Frank Tomaschek
- Section Geochemistry/Petrology, Institute of Geosciences, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115, Bonn, Germany
| | - Rico Schellhorn
- Section Palaeontology, Institute of Geosciences, Rheinische Friedrich-Wilhelms Universität Bonn, 53115, Bonn, Germany
| | - Christa E Müller
- Pharmazeutisches Institut, Pharmazeutische und Medizinische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53121, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, Rheinische Friedrich-Wilhelms Universität, 53127, Bonn, Germany
| | - Jes Rust
- Section Palaeontology, Institute of Geosciences, Rheinische Friedrich-Wilhelms Universität Bonn, 53115, Bonn, Germany
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8
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Vachon MA, Engel K, Beaver RC, Slater GF, Binns WJ, Neufeld JD. Fifteen shades of clay: distinct microbial community profiles obtained from bentonite samples by cultivation and direct nucleic acid extraction. Sci Rep 2021; 11:22349. [PMID: 34785699 PMCID: PMC8595889 DOI: 10.1038/s41598-021-01072-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/11/2021] [Indexed: 11/19/2022] Open
Abstract
Characterizing the microbiology of swelling bentonite clays can help predict the long-term behaviour of deep geological repositories (DGRs), which are proposed as a solution for the management of used nuclear fuel worldwide. Such swelling clays represent an important component of several proposed engineered barrier system designs and, although cultivation-based assessments of bentonite clay are routinely conducted, direct nucleic acid detection from these materials has been difficult due to technical challenges. In this study, we generated direct comparisons of microbial abundance and diversity captured by cultivation and direct nucleic acid analyses using 15 reference bentonite clay samples. Regardless of clay starting material, the corresponding profiles from cultivation-based approaches were consistently associated with phylogenetically similar sulfate-reducing bacteria, denitrifiers, aerobic heterotrophs, and fermenters, demonstrating that any DGR-associated growth may be consistent, regardless of the specific bentonite clay starting material selected for its construction. Furthermore, dominant nucleic acid sequences in the as-received clay microbial profiles did not correspond with the bacteria that were enriched or isolated in culture. Few core taxa were shared among cultivation and direct nucleic acid analysis profiles, yet those in common were primarily affiliated with Streptomyces, Micrococcaceae, Bacillus, and Desulfosporosinus genera. These putative desiccation-resistant bacteria associated with diverse bentonite clay samples can serve as targets for experiments that evaluate microbial viability and growth within DGR-relevant conditions. Our data will be important for global nuclear waste management organizations, demonstrating that identifying appropriate design conditions with suitable clay swelling properties will prevent growth of the same subset of clay-associated bacteria, regardless of clay origin or processing conditions.
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Affiliation(s)
- Melody A Vachon
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Katja Engel
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Rachel C Beaver
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Greg F Slater
- School of Geography and Earth Sciences, McMaster University, Hamilton, ON, Canada
| | | | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
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9
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Ford CT, Alemayehu GS, Blackburn K, Lopez K, Dieng CC, Golassa L, Lo E, Janies D. Modeling Plasmodium falciparum Diagnostic Test Sensitivity Using Machine Learning With Histidine-Rich Protein 2 Variants. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.707313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Malaria, predominantly caused by Plasmodium falciparum, poses one of largest and most durable health threats in the world. Previously, simplistic regression-based models have been created to characterize malaria rapid diagnostic test performance, though these models often only include a couple genetic factors. Specifically, the Baker et al., 2005 model uses two types of particular repeats in histidine-rich protein 2 (PfHRP2) to describe a P. falciparum infection, though the efficacy of this model has waned over recent years due to genetic mutations in the parasite. In this work, we use a dataset of 100 P. falciparum PfHRP2 genetic sequences collected in Ethiopia and derived a larger set of motif repeat matches for use in generating a series of diagnostic machine learning models. Here we show that the usage of additional and different motif repeats in more sophisticated machine learning methods proves effective in characterizing PfHRP2 diversity. Furthermore, we use machine learning model explainability methods to highlight which of the repeat types are most important with regards to rapid diagnostic test sensitivity, thereby showcasing a novel methodology for identifying potential targets for future versions of rapid diagnostic tests.
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Chung Y, Ryu Y, An BC, Yoon YS, Choi O, Kim TY, Yoon J, Ahn JY, Park HJ, Kwon SK, Kim JF, Chung MJ. A synthetic probiotic engineered for colorectal cancer therapy modulates gut microbiota. MICROBIOME 2021; 9:122. [PMID: 34039418 PMCID: PMC8157686 DOI: 10.1186/s40168-021-01071-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/06/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Successful chemoprevention or chemotherapy is achieved through targeted delivery of prophylactic agents during initial phases of carcinogenesis or therapeutic agents to malignant tumors. Bacteria can be used as anticancer agents, but efforts to utilize attenuated pathogenic bacteria suffer from the risk of toxicity or infection. Lactic acid bacteria are safe to eat and often confer health benefits, making them ideal candidates for live vehicles engineered to deliver anticancer drugs. RESULTS In this study, we developed an effective bacterial drug delivery system for colorectal cancer (CRC) therapy using the lactic acid bacterium Pediococcus pentosaceus. It is equipped with dual gene cassettes driven by a strong inducible promoter that encode the therapeutic protein P8 fused to a secretion signal peptide and a complementation system. In an inducible CRC cell-derived xenograft mouse model, our synthetic probiotic significantly reduced tumor volume and inhibited tumor growth relative to the control. Mice with colitis-associated CRC induced by azoxymethane and dextran sodium sulfate exhibited polyp regression and recovered taxonomic diversity when the engineered bacterium was orally administered. Further, the synthetic probiotic modulated gut microbiota and alleviated the chemically induced dysbiosis. Correlation analysis demonstrated that specific bacterial taxa potentially associated with eubiosis or dysbiosis, such as Akkermansia or Turicibacter, have positive or negative relationships with other microbial members. CONCLUSIONS Taken together, our work illustrates that an effective and stable synthetic probiotic composed of P. pentosaceus and the P8 therapeutic protein can reduce CRC and contribute to rebiosis, and the validity and feasibility of cell-based designer biopharmaceuticals for both treating CRC and ameliorating impaired microbiota. Video abstract.
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Affiliation(s)
- Yusook Chung
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Yongku Ryu
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Byung Chull An
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Yeo-Sang Yoon
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Oksik Choi
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Tai Yeub Kim
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Jaekyung Yoon
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jun Young Ahn
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Ho Jin Park
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Soon-Kyeong Kwon
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Division of Applied Life Science (BK21), Gyeongsang National University, 501 Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Myung Jun Chung
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea.
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Peña-Chilet M, Roldán G, Perez-Florido J, Ortuño FM, Carmona R, Aquino V, Lopez-Lopez D, Loucera C, Fernandez-Rueda JL, Gallego A, García-Garcia F, González-Neira A, Pita G, Núñez-Torres R, Santoyo-López J, Ayuso C, Minguez P, Avila-Fernandez A, Corton M, Moreno-Pelayo MÁ, Morin M, Gallego-Martinez A, Lopez-Escamez JA, Borrego S, Antiñolo G, Amigo J, Salgado-Garrido J, Pasalodos-Sanchez S, Morte B, Carracedo Á, Alonso Á, Dopazo J. CSVS, a crowdsourcing database of the Spanish population genetic variability. Nucleic Acids Res 2021; 49:D1130-D1137. [PMID: 32990755 PMCID: PMC7778906 DOI: 10.1093/nar/gkaa794] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 01/01/2023] Open
Abstract
The knowledge of the genetic variability of the local population is of utmost importance in personalized medicine and has been revealed as a critical factor for the discovery of new disease variants. Here, we present the Collaborative Spanish Variability Server (CSVS), which currently contains more than 2000 genomes and exomes of unrelated Spanish individuals. This database has been generated in a collaborative crowdsourcing effort collecting sequencing data produced by local genomic projects and for other purposes. Sequences have been grouped by ICD10 upper categories. A web interface allows querying the database removing one or more ICD10 categories. In this way, aggregated counts of allele frequencies of the pseudo-control Spanish population can be obtained for diseases belonging to the category removed. Interestingly, in addition to pseudo-control studies, some population studies can be made, as, for example, prevalence of pharmacogenomic variants, etc. In addition, this genomic data has been used to define the first Spanish Genome Reference Panel (SGRP1.0) for imputation. This is the first local repository of variability entirely produced by a crowdsourcing effort and constitutes an example for future initiatives to characterize local variability worldwide. CSVS is also part of the GA4GH Beacon network. CSVS can be accessed at: http://csvs.babelomics.org/.
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Affiliation(s)
- María Peña-Chilet
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Bioinformatics in Rare Diseases (BiER), Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Sevilla 41013, Spain
- Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS) Hospital Virgen del Rocío, Sevilla 41013, Spain
| | - Gema Roldán
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
| | - Javier Perez-Florido
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS) Hospital Virgen del Rocío, Sevilla 41013, Spain
- Functional Genomics Node, FPS/ELIXIR-ES, Hospital Virgen del Rocío, Sevilla 41013, Spain
| | - Francisco M Ortuño
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS) Hospital Virgen del Rocío, Sevilla 41013, Spain
- Functional Genomics Node, FPS/ELIXIR-ES, Hospital Virgen del Rocío, Sevilla 41013, Spain
| | - Rosario Carmona
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
| | - Virginia Aquino
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
| | - Daniel Lopez-Lopez
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS) Hospital Virgen del Rocío, Sevilla 41013, Spain
| | - Carlos Loucera
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS) Hospital Virgen del Rocío, Sevilla 41013, Spain
| | - Jose L Fernandez-Rueda
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
| | | | - Francisco García-Garcia
- Unidad de Bioinformática y Bioestadística, Centro de Investigación Príncipe Felipe (CIPF), Valencia 46012, Spain
| | - Anna González-Neira
- Human Genotyping Unit–Centro Nacional de Genotipado (CEGEN), Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Guillermo Pita
- Human Genotyping Unit–Centro Nacional de Genotipado (CEGEN), Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Rocío Núñez-Torres
- Human Genotyping Unit–Centro Nacional de Genotipado (CEGEN), Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | | | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid 28040, Spain
| | - Pablo Minguez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid 28040, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid 28040, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid 28040, Spain
| | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid 28040, Spain
| | - Miguel Ángel Moreno-Pelayo
- Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), Madrid 28034, Spain
| | - Matías Morin
- Servicio de Genética, Ramón y Cajal Institute of Health Research (IRYCIS) and Biomedical Network Research Centre on Rare Diseases (CIBERER), Madrid 28034, Spain
| | - Alvaro Gallego-Martinez
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENYO), Pfizer University of Granada, Granada 18016, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria, IBS. GRANADA, Hospital Universitario Virgen de las Nieves, Universidad de Granada, Granada 18016, Spain
| | - Jose A Lopez-Escamez
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENYO), Pfizer University of Granada, Granada 18016, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria, IBS. GRANADA, Hospital Universitario Virgen de las Nieves, Universidad de Granada, Granada 18016, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville 41013, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville 41013, Spain
| | - Jorge Amigo
- Fundación Pública Galega de Medicina Xenómica, SERGAS, IDIS, Santiago de Compostela 15706, Spain
| | - Josefa Salgado-Garrido
- Navarrabiomed-IdiSNA, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), Pamplona, Navarra 31008, Spain
| | - Sara Pasalodos-Sanchez
- Navarrabiomed-IdiSNA, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), Pamplona, Navarra 31008, Spain
| | - Beatriz Morte
- Undiagnosed Rare Diseases Programme (ENoD). Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid 28029, Spain
| | - Ángel Carracedo
- Fundación Pública Galega de Medicina Xenómica, SERGAS, IDIS, Santiago de Compostela 15706, Spain
- Grupo de Medicina Xenómica, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela, España
| | - Ángel Alonso
- Navarrabiomed-IdiSNA, Complejo Hospitalario de Navarra, Universidad Pública de Navarra (UPNA), IdiSNA (Navarra Institute for Health Research), Pamplona, Navarra 31008, Spain
| | - Joaquín Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla 41013, Spain
- Bioinformatics in Rare Diseases (BiER), Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Sevilla 41013, Spain
- Computational Systems Medicine group, Institute of Biomedicine of Seville (IBIS) Hospital Virgen del Rocío, Sevilla 41013, Spain
- Functional Genomics Node, FPS/ELIXIR-ES, Hospital Virgen del Rocío, Sevilla 41013, Spain
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'If I had a hedge fund, I would cure diabetes': endogenous mechanisms for creating public goods. SN BUSINESS & ECONOMICS 2021; 1:120. [PMID: 34778817 PMCID: PMC8419655 DOI: 10.1007/s43546-021-00115-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/26/2021] [Indexed: 02/08/2023]
Abstract
We consider the problem of organizing capital to produce public goods with broad societal value. We review why market corrections via government subsidies or philanthropic initiatives are inadequate, in addition to considering the paradox of patents. Our proposed mechanism (an Ever-growing Prize and a Patent Repository) directs capital towards two innovation problems routinely overlooked: (1) problems for which the reward is insufficient even with established mechanisms (e.g. patents or academic prestige), and (2) problems for which the reward is large, but the effort risk is incalculable. The proposed hedge fund mechanism facilitates crowdsourcing, addressing the challenge of determining problems with broad societal interest; the ever-growing prize allows for an emergent rather than predetermined reward; the patent repository turns private intellectual property into a public good for target problems while circumventing the inventors' threat of patent expiration. We guide this discussion by considering two problems: treating Cystic Fibrosis and curing Diabetes.
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Thompson DC, Bentzien J. Crowdsourcing and open innovation in drug discovery: recent contributions and future directions. Drug Discov Today 2020; 25:2284-2293. [PMID: 33011343 PMCID: PMC7529695 DOI: 10.1016/j.drudis.2020.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/27/2020] [Accepted: 09/17/2020] [Indexed: 01/03/2023]
Abstract
The past decade has seen significant growth in the use of 'crowdsourcing' and open innovation approaches to engage 'citizen scientists' to perform novel scientific research. Here, we quantify and summarize the current state of adoption of open innovation by major pharmaceutical companies. We also highlight recent crowdsourcing and open innovation research contributions to the field of drug discovery, and interesting future directions.
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Affiliation(s)
| | - Jörg Bentzien
- Alkermes, Inc. 852 Winter Street, Waltham, MA 02451-1420, USA
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Qu Z, Zhao H, Zhang H, Wang Q, Yao Y, Cheng J, Lin Y, Xie J, Fu Y, Jiang D. Bio-priming with a hypovirulent phytopathogenic fungus enhances the connection and strength of microbial interaction network in rapeseed. NPJ Biofilms Microbiomes 2020; 6:45. [PMID: 33127920 PMCID: PMC7603479 DOI: 10.1038/s41522-020-00157-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/23/2020] [Indexed: 12/11/2022] Open
Abstract
Plant disease is one of the most important causes of crop losses worldwide. The effective control of plant disease is related to food security. Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum leads to serious yield losses in rapeseed (Brassica napus) production. Hypovirulent strain DT-8 of S. sclerotiorum, infected with Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1), has the potential to control SSR. In this study, we found rapeseed bio-priming with strain DT-8 could significantly decrease the disease severity of SSR and increase yield in the field. After bio-priming, strain DT-8 could be detected on the aerial part of the rapeseed plant. By 16S rRNA gene and internal transcribed spacer (ITS) sequencing technique, the microbiome on different parts of the SSR lesion on bioprimed and non-bioprimed rapeseed stem was determined. The results indicated that SSR and bio-priming treatment could influence the structure and composition of fungal and bacterial communities. Bio-priming treatment could reduce the total abundance of possible plant pathogens and enhance the connectivity and robustness of the interaction network at the genus level. This might be one of the mechanisms that rapeseed bioprimed with strain DT-8 had excellent tolerance on SSR. It might be another possible mechanism of biocontrol and will provide a theoretical guide for agricultural practical production.
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Affiliation(s)
- Zheng Qu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Huizhang Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Hongxiang Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Qianqian Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Yao Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.
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Ford CT, Janies D. Ensemble machine learning modeling for the prediction of artemisinin resistance in malaria. F1000Res 2020; 9:62. [PMID: 35903243 PMCID: PMC9274019 DOI: 10.12688/f1000research.21539.5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 11/20/2022] Open
Abstract
Resistance in malaria is a growing concern affecting many areas of Sub-Saharan Africa and Southeast Asia. Since the emergence of artemisinin resistance in the late 2000s in Cambodia, research into the underlying mechanisms has been underway. The 2019 Malaria Challenge posited the task of developing computational models that address important problems in advancing the fight against malaria. The first goal was to accurately predict artemisinin drug resistance levels of Plasmodium falciparum isolates, as quantified by the IC50. The second goal was to predict the parasite clearance rate of malaria parasite isolates based on in vitro transcriptional profiles. In this work, we develop machine learning models using novel methods for transforming isolate data and handling the tens of thousands of variables that result from these data transformation exercises. This is demonstrated by using massively parallel processing of the data vectorization for use in scalable machine learning. In addition, we show the utility of ensemble machine learning modeling for highly effective predictions of both goals of this challenge. This is demonstrated by the use of multiple machine learning algorithms combined with various scaling and normalization preprocessing steps. Then, using a voting ensemble, multiple models are combined to generate a final model prediction.
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Affiliation(s)
- Colby T. Ford
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, 28223, USA
- School of Data Science, University of North Carolina at Charlotte, Charlotte, North Carolina, 28223, USA
| | - Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, 28223, USA
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Abstract
PURPOSE OF REVIEW We critically evaluate the future potential of machine learning (ML), deep learning (DL), and artificial intelligence (AI) in precision medicine. The goal of this work is to show progress in ML in digital health, to exemplify future needs and trends, and to identify any essential prerequisites of AI and ML for precision health. RECENT FINDINGS High-throughput technologies are delivering growing volumes of biomedical data, such as large-scale genome-wide sequencing assays; libraries of medical images; or drug perturbation screens of healthy, developing, and diseased tissue. Multi-omics data in biomedicine is deep and complex, offering an opportunity for data-driven insights and automated disease classification. Learning from these data will open our understanding and definition of healthy baselines and disease signatures. State-of-the-art applications of deep neural networks include digital image recognition, single-cell clustering, and virtual drug screens, demonstrating breadths and power of ML in biomedicine. SUMMARY Significantly, AI and systems biology have embraced big data challenges and may enable novel biotechnology-derived therapies to facilitate the implementation of precision medicine approaches.
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Affiliation(s)
- Fabian V. Filipp
- Cancer Systems Biology, Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 München, Germany
- School of Life Sciences Weihenstephan, Technical University München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
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