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Matthew S, Carter F, Cooper J, Dippel M, Green E, Hodges S, Kidwell M, Nickerson D, Rumsey B, Reeve J, Petzold LR, Sanft KR, Drawert B. GillesPy2: A Biochemical Modeling Framework for Simulation Driven Biological Discovery. LETTERS IN BIOMATHEMATICS 2023; 10:87-103. [PMID: 37655179 PMCID: PMC10470263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Stochastic modeling has become an essential tool for studying biochemical reaction networks. There is a growing need for user-friendly and feature-complete software for model design and simulation. To address this need, we present GillesPy2, an open-source framework for building and simulating mathematical and biochemical models. GillesPy2, a major upgrade from the original GillesPy package, is now a stand-alone Python 3 package. GillesPy2 offers an intuitive interface for robust and reproducible model creation, facilitating rapid and iterative development. In addition to expediting the model creation process, GillesPy2 offers efficient algorithms to simulate stochastic, deterministic, and hybrid stochastic-deterministic models.
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Affiliation(s)
- Sean Matthew
- National Environmental Modeling and Analysis Center (NEMAC), University of North Carolina, Asheville, NC 28804
| | - Fin Carter
- Department of Computer Science, University of North Carolina, Asheville, NC 28804
| | - Joshua Cooper
- Department of Computer Science, University of North Carolina, Asheville, NC 28804
| | - Matthew Dippel
- Department of Computer Science, University of North Carolina, Asheville, NC 28804
| | - Ethan Green
- Department of Computer Science, University of North Carolina, Asheville, NC 28804
| | - Samuel Hodges
- Department of Computer Science, North Carolina State University, NC 27695
| | - Mason Kidwell
- Department of Computer Science, University of North Carolina, Asheville, NC 28804
| | - Dalton Nickerson
- Department of Computer Science, University of North Carolina, Asheville, NC 28804
| | - Bryan Rumsey
- National Environmental Modeling and Analysis Center (NEMAC), University of North Carolina, Asheville, NC 28804
| | - Jesse Reeve
- Department of Computer Science, University of North Carolina, Asheville, NC 28804
| | - Linda R. Petzold
- Department of Computer Science and Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Kevin R. Sanft
- Department of Computer Science, University of North Carolina, Asheville, NC 28804
| | - Brian Drawert
- National Environmental Modeling and Analysis Center (NEMAC), University of North Carolina, Asheville, NC 28804
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Efficacy of Plant-Derived Fungicides at Inhibiting Batrachochytrium salamandrivorans Growth. J Fungi (Basel) 2022; 8:jof8101025. [PMID: 36294589 PMCID: PMC9605044 DOI: 10.3390/jof8101025] [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: 08/20/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 11/21/2022] Open
Abstract
The emerging fungal amphibian pathogen, Batrachochytrium salamandrivorans (Bsal), is currently spreading across Europe and given its estimated invasion potential, has the capacity to decimate salamander populations worldwide. Fungicides are a promising in situ management strategy for Bsal due to their ability to treat the environment and infected individuals. However, antifungal drugs or pesticides could adversely affect the environment and non-target hosts, thus identifying safe, effective candidate fungicides for in situ treatment is needed. Here, we estimated the inhibitory fungicidal efficacy of five plant-derived fungicides (thymol, curcumin, allicin, 6-gingerol, and Pond Pimafix®) and one chemical fungicide (Virkon® Aquatic) against Bsal zoospores in vitro. We used a broth microdilution method in 48-well plates to test the efficacy of six concentrations per fungicide on Bsal zoospore viability. Following plate incubation, we performed cell viability assays and agar plate growth trials to estimate the minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) of each fungicide. All six fungicides exhibited inhibitory and fungicidal effects against Bsal growth, with estimated MIC concentrations ranging from 60 to 0.156 μg/mL for the different compounds. Allicin showed the greatest efficacy (i.e., lowest MIC and MFC) against Bsal zoospores followed by curcumin, Pond Pimafix®, thymol, 6-gingerol, and Virkon® Aquatic, respectively. Our results provide evidence that plant-derived fungicides are effective at inhibiting and killing Bsal zoospores in vitro and may be useful for in situ treatment. Additional studies are needed to estimate the efficacy of these fungicides at inactivating Bsal in the environment and treating Bsal-infected amphibians.
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Knapp RA, Joseph MB, Smith TC, Hegeman EE, Vredenburg VT, Erdman Jr JE, Boiano DM, Jani AJ, Briggs CJ. Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog. PeerJ 2022; 10:e12712. [PMID: 35036095 PMCID: PMC8742549 DOI: 10.7717/peerj.12712] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023] Open
Abstract
The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies. We conducted in-situ antifungal treatment experiments in wild populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of treatments was to reduce Bd infection intensity ("load") and in doing so alter frog-Bd dynamics and increase the probability of frog population persistence despite ongoing Bd infection. Experiments included treatment of early life stages (tadpoles and subadults) with the antifungal drug itraconazole, treatment of adults with itraconazole, and augmentation of the skin microbiome of subadults with Janthinobacterium lividum, a commensal bacterium with antifungal properties. All itraconazole treatments caused immediate reductions in Bd load, and produced longer-term effects that differed between life stages. In experiments focused on early life stages, Bd load was reduced in the 2 months immediately following treatment and was associated with increased survival of subadults. However, Bd load and frog survival returned to pre-treatment levels in less than 1 year, and treatment had no effect on population persistence. In adults, treatment reduced Bd load and increased frog survival over the entire 3-year post-treatment period, consistent with frogs having developed an effective adaptive immune response against Bd. Despite this protracted period of reduced impacts of Bd on adults, recruitment into the adult population was limited and the population eventually declined to near-extirpation. In the microbiome augmentation experiment, exposure of subadults to a solution of J. lividum increased concentrations of this potentially protective bacterium on frogs. However, concentrations declined to baseline levels within 1 month and did not have a protective effect against Bd infection. Collectively, these results indicate that our mitigation efforts were ineffective in causing long-term changes in frog-Bd dynamics and increasing population persistence, due largely to the inability of early life stages to mount an effective immune response against Bd. This results in repeated recruitment failure and a low probability of population persistence in the face of ongoing Bd infection.
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Affiliation(s)
- Roland A. Knapp
- Sierra Nevada Aquatic Research Laboratory, University of California, Mammoth Lakes, California, United States
- Earth Research Institute, University of California, Santa Barbara, California, United States
| | | | - Thomas C. Smith
- Sierra Nevada Aquatic Research Laboratory, University of California, Mammoth Lakes, California, United States
- Earth Research Institute, University of California, Santa Barbara, California, United States
| | - Ericka E. Hegeman
- Sierra Nevada Aquatic Research Laboratory, University of California, Mammoth Lakes, California, United States
- Earth Research Institute, University of California, Santa Barbara, California, United States
| | - Vance T. Vredenburg
- Department of Biology, San Francisco State University, San Francisco, California, United States
| | - James E. Erdman Jr
- California Department of Fish and Wildlife, Bishop, California, United States
| | - Daniel M. Boiano
- Sequoia and Kings Canyon National Parks, National Park Service, Three Rivers, California, United States
| | - Andrea J. Jani
- Pacific Biosciences Research Center, University of Hawai’i at Mànoa, Honolulu, Hawai’i, United States
| | - Cheryl J. Briggs
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California, United States
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Warne DJ, Baker RE, Simpson MJ. Rapid Bayesian Inference for Expensive Stochastic Models. J Comput Graph Stat 2021. [DOI: 10.1080/10618600.2021.2000419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- David J. Warne
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Ruth E. Baker
- Mathematical Institute, University of Oxford, Oxford, UK
| | - Matthew J. Simpson
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
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Rollins-Smith LA. Global Amphibian Declines, Disease, and the Ongoing Battle between Batrachochytrium Fungi and the Immune System. HERPETOLOGICA 2020. [DOI: 10.1655/0018-0831-76.2.178] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Louise A. Rollins-Smith
- Departments of Pathology, Microbiology and Immunology and Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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Fletcher QE, Webber QMR, Willis CKR. Modelling the potential efficacy of treatments for white‐nose syndrome in bats. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13619] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Quinn E. Fletcher
- Department of Biology and Centre for Forest Interdisciplinary Research (C‐FIR) University of Winnipeg Winnipeg MB Canada
| | - Quinn M. R. Webber
- Department of Biology and Centre for Forest Interdisciplinary Research (C‐FIR) University of Winnipeg Winnipeg MB Canada
- Cognitive and Behavioural Ecology Interdisciplinary Program Memorial University of Newfoundland St. John's NL Canada
| | - Craig K. R. Willis
- Department of Biology and Centre for Forest Interdisciplinary Research (C‐FIR) University of Winnipeg Winnipeg MB Canada
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Wells K, Hamede RK, Jones ME, Hohenlohe PA, Storfer A, McCallum HI. Individual and temporal variation in pathogen load predicts long-term impacts of an emerging infectious disease. Ecology 2019; 100:e02613. [PMID: 30636287 PMCID: PMC6415924 DOI: 10.1002/ecy.2613] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/20/2018] [Accepted: 12/20/2018] [Indexed: 01/06/2023]
Abstract
Emerging infectious diseases increasingly threaten wildlife populations. Most studies focus on managing short-term epidemic properties, such as controlling early outbreaks. Predicting long-term endemic characteristics with limited retrospective data is more challenging. We used individual-based modeling informed by individual variation in pathogen load and transmissibility to predict long-term impacts of a lethal, transmissible cancer on Tasmanian devil (Sarcophilus harrisii) populations. For this, we employed approximate Bayesian computation to identify model scenarios that best matched known epidemiological and demographic system properties derived from 10 yr of data after disease emergence, enabling us to forecast future system dynamics. We show that the dramatic devil population declines observed thus far are likely attributable to transient dynamics (initial dynamics after disease emergence). Only 21% of matching scenarios led to devil extinction within 100 yr following devil facial tumor disease (DFTD) introduction, whereas DFTD faded out in 57% of simulations. In the remaining 22% of simulations, disease and host coexisted for at least 100 yr, usually with long-period oscillations. Our findings show that pathogen extirpation or host-pathogen coexistence are much more likely than the DFTD-induced devil extinction, with crucial management ramifications. Accounting for individual-level disease progression and the long-term outcome of devil-DFTD interactions at the population-level, our findings suggest that immediate management interventions are unlikely to be necessary to ensure the persistence of Tasmanian devil populations. This is because strong population declines of devils after disease emergence do not necessarily translate into long-term population declines at equilibria. Our modeling approach is widely applicable to other host-pathogen systems to predict disease impact beyond transient dynamics.
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Affiliation(s)
- Konstans Wells
- Department of Biosciences, Swansea University, Singleton Campus, Wallace Building, Swansea, SA2 8PP, United Kingdom
- Environmental Futures Research Institute, Griffith University, Brisbane, Queensland, 4111, Australia
| | - Rodrigo K Hamede
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Menna E Jones
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, 83844, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164-4236, USA
| | - Hamish I McCallum
- Environmental Futures Research Institute, Griffith University, Brisbane, Queensland, 4111, Australia
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Ogden NH, Wilson JRU, Richardson DM, Hui C, Davies SJ, Kumschick S, Le Roux JJ, Measey J, Saul WC, Pulliam JRC. Emerging infectious diseases and biological invasions: a call for a One Health collaboration in science and management. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181577. [PMID: 31032015 PMCID: PMC6458372 DOI: 10.1098/rsos.181577] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/18/2019] [Indexed: 05/11/2023]
Abstract
The study and management of emerging infectious diseases (EIDs) and of biological invasions both address the ecology of human-associated biological phenomena in a rapidly changing world. However, the two fields work mostly in parallel rather than in concert. This review explores how the general phenomenon of an organism rapidly increasing in range or abundance is caused, highlights the similarities and differences between research on EIDs and invasions, and discusses shared management insights and approaches. EIDs can arise by: (i) crossing geographical barriers due to human-mediated dispersal, (ii) crossing compatibility barriers due to evolution, and (iii) lifting of environmental barriers due to environmental change. All these processes can be implicated in biological invasions, but only the first defines them. Research on EIDs is embedded within the One Health concept-the notion that human, animal and ecosystem health are interrelated and that holistic approaches encompassing all three components are needed to respond to threats to human well-being. We argue that for sustainable development, biological invasions should be explicitly considered within One Health. Management goals for the fields are the same, and direct collaborations between invasion scientists, disease ecologists and epidemiologists on modelling, risk assessment, monitoring and management would be mutually beneficial.
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Affiliation(s)
- Nick H. Ogden
- National Microbiology Laboratory, Public Health Agency of Canada, Canada
- South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, South Africa
| | - John R. U. Wilson
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, Cape Town, South Africa
| | - David M. Richardson
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
| | - Cang Hui
- Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, Matieland 7602, South Africa
- Mathematical and Physical Biosciences, African Institute for Mathematical Sciences (AIMS), Muizenberg 7945, South Africa
| | - Sarah J. Davies
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
| | - Sabrina Kumschick
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, Cape Town, South Africa
| | - Johannes J. Le Roux
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
- Department of Biological Sciences, Macquarie University, Sydney 2109, Australia
| | - John Measey
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
| | - Wolf-Christian Saul
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
- Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, Matieland 7602, South Africa
| | - Juliet R. C. Pulliam
- South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, South Africa
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Christie MR, Searle CL. Evolutionary rescue in a host-pathogen system results in coexistence not clearance. Evol Appl 2018; 11:681-693. [PMID: 29875810 PMCID: PMC5979755 DOI: 10.1111/eva.12568] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/17/2017] [Indexed: 01/14/2023] Open
Abstract
The evolutionary rescue of host populations may prevent extinction from novel pathogens. However, the conditions that facilitate rapid evolution of hosts, in particular the population variation in host susceptibility, and the effects of host evolution in response to pathogens on population outcomes remain largely unknown. We constructed an individual-based model to determine the relationships between genetic variation in host susceptibility and population persistence in an amphibian-fungal pathogen (Batrachochytrium dendrobatidis) system. We found that host populations can rapidly evolve reduced susceptibility to a novel pathogen and that this rapid evolution led to a 71-fold increase in the likelihood of host-pathogen coexistence. However, the increased rates of coexistence came at a cost to host populations; fewer populations cleared infection, population sizes were depressed, and neutral genetic diversity was lost. Larger adult host population sizes and greater adaptive genetic variation prior to the onset of pathogen introduction led to substantially reduced rates of extinction, suggesting that populations with these characteristics should be prioritized for conservation when species are threatened by novel infectious diseases.
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Affiliation(s)
- Mark Redpath Christie
- Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteINUSA
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More S, Angel Miranda M, Bicout D, Bøtner A, Butterworth A, Calistri P, Depner K, Edwards S, Garin-Bastuji B, Good M, Michel V, Raj M, Saxmose Nielsen S, Sihvonen L, Spoolder H, Stegeman JA, Thulke HH, Velarde A, Willeberg P, Winckler C, Baláž V, Martel A, Murray K, Fabris C, Munoz-Gajardo I, Gogin A, Verdonck F, Gortázar Schmidt C. Risk of survival, establishment and spread of Batrachochytrium salamandrivorans (Bsal) in the EU. EFSA J 2018; 16:e05259. [PMID: 32625888 PMCID: PMC7009437 DOI: 10.2903/j.efsa.2018.5259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Batrachochytrium salamandrivorans (Bsal) is an emerging fungal pathogen of salamanders. Despite limited surveillance, Bsal was detected in kept salamanders populations in Belgium, Germany, Spain, the Netherlands and the United Kingdom, and in wild populations in some regions of Belgium, Germany and the Netherlands. According to niche modelling, at least part of the distribution range of every salamander species in Europe overlaps with the climate conditions predicted to be suitable for Bsal. Passive surveillance is considered the most suitable approach for detection of Bsal emergence in wild populations. Demonstration of Bsal absence is considered feasible only in closed populations of kept susceptible species. In the wild, Bsal can spread by both active (e.g. salamanders, anurans) and passive (e.g. birds, water) carriers; it is most likely maintained/spread in infected areas by contacts of salamanders or by interactions with anurans, whereas human activities most likely cause Bsal entry into new areas and populations. In kept amphibians, Bsal contamination via live silent carriers (wild birds and anurans) is considered extremely unlikely. The risk‐mitigation measures that were considered the most feasible and effective: (i) for ensuring safer international or intra‐EU trade of live salamanders, are: ban or restrictions on salamander imports, hygiene procedures and good practice manuals; (ii) for protecting kept salamanders from Bsal, are: identification and treatment of positive collections; (iii) for on‐site protection of wild salamanders, are: preventing translocation of wild amphibians and release/return to the wild of kept/temporarily housed wild salamanders, and setting up contact points/emergency teams for passive surveillance. Combining several risk‐mitigation measures improve the overall effectiveness. It is recommended to: introduce a harmonised protocol for Bsal detection throughout the EU; improve data acquisition on salamander abundance and distribution; enhance passive surveillance activities; increase public and professionals’ awareness; condition any movement of captive salamanders on Bsal known health status.
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