Progress 09/01/23 to 08/31/24
Outputs
Target Audience:The target audience reached by our efforts during this reporting period includes the greater scientific community as well as graduate and undergraduate students. Part of the project seeks to broadening participation in STEM. We continue to recruit students underrepresented in STEM research to our labs and create opportunities for undergraduate researchers to contribute to active research projects. One of them that we would like to highlight this year is a first-generation student of Puerto Rican descent, Ben Erdozain, who works in the PD Elderd's lab. Ben was recently awarded a highly competitive Beckman scholarship to continue working on a project related to host-pathogen evolution. The results from the project will presented at the LSU Discovery Day in the Spring of 2025.In the Dassanayake Lab, afirst-year Hispanic graduate student in the Dassanayake Lab is leading RNA extractions and currently analyzing RNA-Seq data from over 200 fall armyworm samples across multiple generations as part of this project. Additionally, a post-baccalaureate student, recruited and supported by the NSF-RAMP program, who is both a first-generation college student and of Hispanic heritage, was trained in DNA and RNA extractions and other essential molecular biology techniques during the experiments for this project. The postdoctoral scientist working on this project during most of 2023-2024 leveraged his experience in genomic and transcriptomic data analysis to successfully secure a position at an agricultural company. This project facilitated the development of computational tools and pipelines for processing large datasets in molecular evolutionary analysis, which we plan to release as a community resource upon the project's completion.Additionally, a post-doctoral researcher, graduate students, post-graduate students, and undergraduate students have been trained in a variety of experimental and computational techniques needed to complete the research. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Over the course of the last reporting period, one post-doctoral researcher, two post-graduate students, five graduate students, and sixundergraduate students have been mentored on multiple aspects of this project. This project allowed undergraduate student training for methods widely used in molecular biology (e.g. DNA/RNA extractions, DNA/RNA quantification using Qubit fluorometers, and gel electrophoresis) and data processing and analyses using RNAseq data.A postdoctoral scientist (Pramod Pantha) used this grant to gain research and student mentoring experience aligned with his long-term goals in agricultural applications and successfully secured a position at a leading agricultural company. The post-baccalaureate student (Jorge Pardo) used the skills acquired from this project to conduct independent RNA-Seq research, presented his findings at LSU's Discover Day Undergraduate Research Symposium, and was successfully admitted to the evolutionary biology graduate program at Tulane University. Agraduate student (Jason Garcia) involved in this project plans to present his research at the 2025 Evolution meeting and is preparing for a publication. An undergraduate student, trained in RNA extractions and contributing to the analysis, will be included as a co-author in this publication. As previously mentioned, training in the PD Elderd's lab, besides that directly associated with the research, included reading and discussion of the primary literature related to the projected. Additionally, computational aspects of the research have been used in developing new courses (PD Elderd) and coding initiatives at LSU (PD Elderd and Co-PD Dassanayake). How have the results been disseminated to communities of interest?During this reporting period, onejournal articles and onebook chapter have been published. Additionally, one presentationat an international conferencewasgiven and at two invited departmental seminar. Individuals involved in this research also have a number of other manuscripts near submission. What do you plan to do during the next reporting period to accomplish the goals?Over the course of the next reporting period as in the previous reporting period, we will continue to develop Bayesian hierarchical approaches while also moving forward with evolving/co-evolving host and pathogen. We will also analyze the collected data associated with individual risk of pathogen exposure via the dose-response experiments and population level risk via the experimental epizootics to examine how coevolutionary processes under varying temperature regimes affect disease susceptibility and transmission. We are advancing our computational analysis to identify key metabolic networks that respond to the infection process, as well as molecular targets that exhibit greater plasticity in their expression and evolutionary rates across distinct lineages.The primary computational analysis is planned for a joint publication with the Elderd Lab and the computational tools will be released on GitHub as community tools with another accompanying publication. All RNA sequencing data will be made available via NCBI databases and made accessible through our lab websites.
Impacts
What was accomplished under these goals?
Objectives: 1. We have been focusing our efforts over the past year on two fall armyworms line that were collected near Purdue University in Lafayette, Indiana and another line reared at Mississippi State University. We reared the Purdue line to 10 to 20 generations depending on the temperature that they were experimentally reared under. For the Mississippi line, we are currently on the 4th to 12th generation depending on the rearing temperature. For both lines, we have been rearing them under three different temperature regimes that correspond to below the thermal optimum, near the thermal optimum, and above the thermal optimum. For each temperature, the populations have been further divided into lines that we are exposing to virus (co-evolved lines) and to lines that we are keeping free of virus exposure (control lines). For the lines established at an average day time temperature of 34 C, above the thermal optimum, the lines for both populations collapsed. This collapse occurred in both the co-evolved and control lines. Thus, the collapse was likely due to heat stress associated with the relatively high temperature at which the lines were being reared. It should be noted that this relatively high temperature is well within the bounds of forecasted average day time temperatures in the Southeast under climate change. We have also established a line of fall armyworm from the Southern United States, Mississippi. We are rearing this line under the same conditions as the line collected in Indiana. Similar to the Indiana line, the line reared at 34C collapsed. In the upcoming year, we will continue to rear the Mississippi colony, which will allow us to compare across population lines. 2. During the past year, we have been using our established lines to evolve the pathogen alone and co-evolve the host and the pathogen at each of the selected temperatures. For the co-evolved host population, we have been exposing the population to doses that would result in the mortality of 50% of the population. These doses are based on dose-response experiments conducted on the previous generation. For the evolved virus line, we have been feeding lethal doses of the virus to the control population, which hasn't been previously exposed to virus, and collecting the subsequently produced virus. 3. Over the course of the last year, we have collected numerous samples of the host and the virus and will be using those samples to complete genome and transcriptome analyses. The samples for the Purdue line have been recently processed. We are currently collecting high quality genomic DNA and total RNA for high throughput sequencing libraries designed to generate data for Objectives 3-5. While standard DNA extraction protocols could be used with minimum modifications, we needed to optimize our extraction protocols to yield high quality RNA from host samples. This was especially challenging for virus infected larval samples that had low input due to their limited growth. We have been able to optimize our protocols and create sufficiently high quality RNA for the targeted sequencing plan. We have been testing computational analyses methods beyond standard RNAseq pipelines to effectively identify and quantify viral transcript signals in host tissue where the host transcriptome is overrepresented. We have also tested modifications to identifying sequence variant detection in the genomes from individual to population level over successive generations. In virus-infected populations, we observed the strongest transcriptional response 48 hours post-infection, compared to 24 and 72 hours. Our current analysis also indicates that virus-selected lines exhibit a greater transcriptional response than control lines, while coevolved lines show a reduced response. Elevated temperatures further decreased transcriptional divergence among the treatments. We are advancing our computational analysis to identify key metabolic networks that respond to the infection process, as well as molecular targets that exhibit greater plasticity in their expression and evolutionary rates across distinct lineages. 4. Besides evolving and co-evolving the populations, we have also been conducting additional experiments examining thermal performance for the lines, hemocyte production for each of the lines, and the dose-response of the lines to virus exposure. We are analyzing the associated data for these experiments and presented preliminary results at CRWAD 2024. 5. We are also conducting a series of experiments looking at population-level transmission at the varying temperature lines under which each of the populations have been reared at. We are in the process of analyzing the data associated with these experiments. The experiments are on-going and we will be collecting additional data in subsequent generations. 6. As in the previous year, we have continued to develop Bayesian models and methods related to this objective. Some of this work includes examining computational and theoretical aspects of multiscale ecological state space models. In general, all of this work has led to the publication of one journal articleand one book chapter over the reporting period. The research was also presented at an internationalconferenceand at twoinvited departmental seminars. Additionally, a graduate student in PD Elderd's lab completed his Master's Thesis on neural networks and machine learning related to the virus and hemocyte data being collected. The graduate student is close to submitting a manuscript based on his research. Another member of the PD Elderd's lab defended his PhD and analyzed the effects of coevolution and temperature on pathogen virulence as part of his dissertation. A manuscript related to this research is currently being prepared. Additional publications are close to completion and will be submitted soon. 7. During the past year, a number of individuals have been trained on the grant. This includes one post-doctoral researcher, fivegraduate students, two post-graduate students, and sixundergraduate students. Pramod Pantha in Co-PD Dassanayake's lab was trained in evolutionary genomics analysis methods. A graduate student in Co-PD Dukic's lab successfully defended her thesis and is currently employed in industry. Additionally, an undergraduate student in PD Elderd's lab finished her thesis related to the research that she helped with over the previous reporting period and presented the results, which were well received, at LSU Discovery Day. Two other undergraduate students in the Elderd lab started advanced research projects related to host-pathogen coevolution. Part of the training for the undergraduate, post graduate, and graduate students in PD Elderd's lab included weekly meetings where the students read and discussed primary literature related to the project.
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2024
Citation:
Conference of Research Workers in Animal Diseases. Disease transmission dynamics and host-pathogen coevolution under varying temperatures. (B.D. Elderd (presenter), S. Grimmell, K. Costanza, N. Haulk).
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2024
Citation:
Mathematical Biology Seminar, Georgia Institute of Technology. (V. Dukic).
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Bortz, D., D. Messenger, and V. Dukic. Direct estimation of parameters in ODE models using WENDy: Weak-form estimation of nonlinear dynamics. Bulletin of Mathematic Biology 85 (110).
- Type:
Book Chapters
Status:
Published
Year Published:
2024
Citation:
Arehart, C., J. Arehart, M. David, B. D'Amico, E. Sozzi, V. Dukic, and F. Pomponi. MONOPOLI: A customizable model for forecasting COVID-19 around the world using alternative nonpharmaceutical intervention policy scenarios, human movement data, and regional demographics. Handbook of visual, experimental and computational mathematics: Bridges through data. Springer International Publishing.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
How variability affects disease transmission: Insights from an agricultural pest
|
Progress 09/01/22 to 08/31/23
Outputs
Target Audience: The target audience reached by our efforts during this reporting period includes the greater scientific community as well as graduate and undergraduate students. Part of the project seeks to broadening participation in STEM. We continue to recruit students underrepresented in STEM research to our labs and createopportunities for undergraduate researchers to contribute to active research projects. One of them is a high-school student that completed a summer research internship in Co-PD Dassanayake's lab. An undergraduate Hispanic student, Jason Garcia joined the Dassanayake lab to get basic research training in molecular biology methods in 2022. He is currently enrolled as a temporary research assistant following his graduation in May 2023 and now actively engaged in contributing to research for this project. He plans to apply for graduate school with his recent experience in research. He presented his preliminary research at Discover Day, 2023 for undergraduate research at LSU. Additionally, a post-doctoral researcher, graduate students, post-graduate students, and undergraduate students have been trained in a variety of experimental and computational techniques needed to complete the research. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Over the course of the last reporting period, one post-doctoral researcher, twopost-graduate students, three graduate students, and eight undergraduate students have been mentored on multiple aspects of this project. This project allowed undergraduate student training for methods widely used in molecular biology (e.g. DNA/RNA extractions, DNA/RNA quantification using Qubit fluorometers, and gel electrophoresis) and data processing and analyses using RNAseq data. The project also facilitated career development and provided networking opportunities for a postdoctoral researcher (Pramod Pantha) at an applied science conference organized with industry partnerships and NIH scientists on the use of baculoviruses as biotechnology tools.As previously mentioned, training in the PDElderd's lab, besides that directly associated with the research, included reading and discussion of the primary literature related to the projected. Additionally, computational aspects of the research have been used in developing new courses (PD Elderd) and coding initiatives at LSU (PD Elderd and Co-PD Dassanayake). How have the results been disseminated to communities of interest? During this reporting period, three journal articles and one book chapter have been published. Additionally, two presentations atinternational conferences weregiven. Individuals involved in this research also have a number of other manuscripts near submission. What do you plan to do during the next reporting period to accomplish the goals? Over the course of the next reporting period as in the previous reporting period, we will continue to develop Bayesian hierarchical approaches while also moving forward with evolving/co-evolving host and pathogen. We will also analyze the collected data associated with individual risk of pathogen exposure via the dose-response experiments and population level risk via the experimental epizootics to examine how coevolutionary processes under varying temperature regimes affect disease susceptibility and transmission. Additionally, we will begin sequencing the host and pathogen in both control and coevolutionary lines and start to analyze that associated data as well.
Impacts
What was accomplished under these goals?
Objectives: 1. We have been focusing our efforts over the past year on the fall armyworm line that we collected near Purdue University in Lafayette, Indiana. We are currently on the 17th to 19th generation of the line depending on the temperatures at which we are rearing the insects. We have been rearing them under three different temperature regimes and have divided the populations at each temperature into lines that we are exposing to virus (co-evolved lines) and to lines that we are keeping free of virus exposure (control lines). The line established at an average day time temperature of 34 C collapsed around the 10th generation. This collapse occurred in both the co-evolved and control lines. Thus, the collapse was likely due to heat stress associated with the relatively high temperature at which the lines were being reared. It should be noted that this relatively high temperature is well within the bounds of forecasted average day time temperatures in the Southeast under climate change. We have also established a line of fall armyworm from the Southern United States, Mississippi. We are rearing this line under the same conditions as the line collected in Indiana. Similar to the Indiana line, the line reared at 34C collapsed. For the other temperatures, we are currently on the 3rd to 5th generation dependending upon the temperatures that the insects are being reared at. In the upcoming year, we will continue to rear these colonies. 2. During the past year, we have been using our established lines to evolve the pathogen alone and co-evolve the host and the pathogen at each of the selected temperatures. For the co-evolved host population, we have been exposing the population to doses that would result in the mortality of 50% of the population. These doses are based on dose-response experiments conducted on the previous generation. For the evolved virus line, we have been feeding lethal doses of the virus to the control population, which hasn't been previously exposed to virus, and collecting the subsequently produced virus. 3. Over the course of the last year, we have collected numerous samples of the host and the virus and will be using those samples to complete genome and transcriptome analyses. We are waiting to process the samples in order to process them in bulk.We are currently collecting high quality genomic DNA and total RNA for high throughput sequencing libraries designed to generate data for Objectives 3-5. While standard DNA extraction protocols could be used with minimum modifications, we needed to optimize our extraction protocols to yield high quality RNA from host samples. This was especially challenging for virus infected larval samples that had low input due to their limited growth. We have been able to optimize our protocols and create sufficiently high quality RNA for the targeted sequencing plan. We have been testing computational analyses methods beyond standard RNAseq pipelines to effectively identify and quantify viral transcript signals in host tissue where the host transcriptome is overrepresented. We have also tested modifications to identifying sequence variant detection in the genomes from individual to population level over successive generations. 4. Besides evolving and co-evolving the populations, we have also been conducting additional experiments examining thermal performance for the lines, hemocyte production for each of the lines, and the dose-response of the lines to virus exposure. We areanalyzing the associated data for these experiments and presented preliminary results at CRWAD 2023. 5. We are also conducting a series ofexperiments looking at population-level transmission at the varying temperature lines under which each of the populations have been reared at. We are in the process of analyzing the data associated with theseexperiments. The experiments are on-going and we will be collecting additional data in subsequent generations. 6. As in the previous year, we have continued to develop Bayesian models and methods related to this objective. Some of this work includes examining computational and theoretical aspects of multiscale ecological state space models. In general, all ofthis work has led to the publication of three journal articles and one book chapter. The research was also presented at two conferences and at an invited departmental seminar. Additionally, a graduate student in PI Elderd's lab is conducting research on neural networks and machine learning related to the virus and hemocyte data being collected. The graduate student is currently preparing a manuscript based on his research. Additional publications are close to completion and will be submitted soon. ? 7. During the past year, a number of individuals have been trained on the grant. This includes onepost-doctoral researcher, three graduate students, twopost-graduate students, and eightundergraduate students.Pramod Pantha in Co-PDDassanayake's lab was trained in evolutionary genomics analysis methods. A graduate student in Co-PD Dukic's lab successfully defended her thesis and is currently employed in industry. Additionally, an undergraduate student in PD Elderd's lab is starting work on a thesis related to the research that she helped with over the previous reporting period. Part of the training for the undergraduate, post graduate, and graduate students in PD Elderd's labincluded weekly meetings where the students read and discussed primary literature related to the project.
Publications
- Type:
Book Chapters
Status:
Accepted
Year Published:
2023
Citation:
Arehart C., J. Arehart, M. David, B. DAmico, E. Sozzi, V. Dukic, and F. Pomponi. MONOPOLI: A customizable model using demographics and policy scenarios to predict COVID-19 infections around the world. Handbook of Visual, Experimental and Computational Mathematics - Bridges through Data.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2023
Citation:
Bortz, D., D. Messenger, and V. Dukic. Direct estimation of parameters in ODE models using WENDy: Weak-form estimation of nonlinear dynamics. Bulletin of Mathematical Biology.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Richards, R. L., B. D. Elderd, and M. A. Duffy. Unhealthy herds and the predator-spreader: Understanding when predation increases disease incidence and prevalence. Ecology and Evolution.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Van Allen, B. G., F. P. Dillemuth, V. Dukic, and B. D. Elderd. Viral transmission and infection prevalence in a cannibalistic host-pathogen system. Oecologia.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
Conference of Research Workers in Animal Diseases. Host-pathogen coevolution in a changing environment: Pathogen exposure and host per- formance (B.D. Elderd (presenter), M. Garvey, S. Grimmell, K. Costanza).
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
International Society for BioProcess Technology (ISBioTech). A tale of two transcriptome responses in agricultural pests via host defenses and viral replication. (P. Pantha (presenter), B. Elderd, M. Dassanayake).
|
Progress 09/01/21 to 08/31/22
Outputs
Target Audience:The target audience reached by our efforts during this reportingperiod includes the greater scientific community as well as graduateandundergraduate students. We have shared the research via journalpublications and presentations. We also have a number of publicationsrelated to the research that will soon be submitted. co-PI Dassanayakeconducted a 6-week virtual RNAseq workshop for a group of eightparticipants - six graduate students and two undergraduate students who had not previously worked with high throughput data before. Thishands-on training involved teaching basic principles in a standardRNAseq experiment and command line guidance to a computationalpipeline for user datasets. Participants processed data from rawsequence files to generate visual representations of differentialexpression and conducted associated functional analyses relevant toeachdataset. Additionally, a post-doctoral researcher, graduatestudents, post-graduate students, and undergraduate students have beentrained in a variety of experimental and computational techniquesneeded to complete the research. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Over the course of the last reporting period, two post-doctoralresearchers, onepost-graduate students, three graduate students, andseven undergraduate have been mentored on multiple aspects of thisproject. Two graduate students and one undergraduate student were trained in DNA extraction methods and analyzing RNAseq data in the Dassanayake lab in preparation of dual RNAseq (insect-virus) and compataive RNAseq analyses planned for the current year. The undergraduate student is incorporating these methods into his Honors Thesis. Additionally, co-PI Dassanayake conducted a 6-week virtualRNAseqworkshop for a group of eightparticipants - six graduate students and two undergraduate students, who had not previously worked with high throughput data before. This hands-on training involved teachingbasicprinciples in a standard RNAseq experiment and command lineguidance to a computational pipeline for user datasets. Participantsprocesseddata from raw sequence files to generate visualrepresentations of differential expression and conducted associatedfunctional analysesrelevant to each dataset. As previouslymentioned, training in the PI Elderd's lab, besides that directlyassociated with the research, includedreading and discussion of theprimary literature related to the projected. How have the results been disseminated to communities of interest?During this reporting period, three journal articles have beenpublished and one presentation at an international conference wasgiven.Individuals involved in this research also have a number ofother manuscripts near submission. Additionally, PI Elderd organized,edited, andsaw through to publication a special features section inthe American Naturalist on looking across scales in disease ecology. What do you plan to do during the next reporting period to accomplish the goals?Over the course of the next reporting period as in the previousreporting period, we will continue to develop Bayesian hierarchicalapproacheswhile also moving forward with evolving/co-evolving hostand pathogen. We will also analyze the data collected associatedindividual risk ofpathogen exposure via the dose-response experimentsand population level risk via the experimental epizootics to examinehowcoevolutionary processes under varying temperature regimes affectdisease susceptibility and transmission. Additionally, we will beginsequencing the host and pathogen in both control and coevolutionarylines and start to analyze that associated data as well.
Impacts
What was accomplished under these goals?
Objectives: 1. We have been focusing our efforts over the past year on the fallarmyworm line that we collected near Purdue University in Lafayette,Indiana. We are currently on the 10th-12th generation of the linedepending on the temperatures at which we are rearing the insects. Wehavebeen rearing them under three different temperature regimes and havedivided the populations at each temperature into lines that we areexposing to virus (co-evolved lines) and to lines that we are keepingfree of virus exposure (control lines). The line established at anaverageday time temperature of 34 C collapsed around the 10thgeneration. This collapse occurred in both the co-evolved and controllines. Thus, thecollapse was likely due to heat stress associatedwith the relatively high temperature at which the lines were beingreared. It should be notedthat this relatively high temperature iswell within the bounds of forecasted average day time temperatures in theSoutheast under climatechange. In the upcoming year, we will beestablishing a second line fall armyworm collected further south inthe Southern United States. 2. During the past year, we have been using our established lines toevolve the pathogen alone and co-evolve the host and the pathogen ateach of the selected temperatures. For the co-evolved host population,we have been exposing the population to doses that would result inthemortality of 50% of the population. These doses are based ondose-response experiments conducted on the previous generation. Fortheevolved virus line, we have been feeding lethal doses of the virusto the control population, which hasn't been previously exposed to virus, andcollecting the subsequently produced virus. 3. Over the course of the last year, we have collected numeroussamples of the host and the virus and will be using those samples tocomplete genome and transcriptome analyses. We are waiting toprocess the samples in order to process them in bulk. 4. Besides evolving and co-evolving the populations, we have also beenconducting additional experiments examining thermal performanceforthe lines, hemocyte production for each of the lines, and thedose-response of the lines to virus exposure. We are in the process ofanalyzing the associated data for these experiments. 5. We have begun the experiments looking at population-leveltransmission at the varying temperature lines under which each of thepopulations have been reared at. We are in the process of analyzingthe data associated with the first rounds of the experiments. Theexperiments are on-going and we will be collecting additional data insubsequent generations. 6. As in the previous year, we have continued to develop Bayesianmodels and methods related to this objective. Some of this workincludes examining computational and theoretical aspects of multiscaleecological state space models. In general, all of this work has led tothepublication of three papers and one presentation during the previousyear. Additional publications are close to completion and will besubmitted soon. One of the papers published was part of co-editedseries of papers in the focused topics section of the AmericanNaturalistentitled "Looking across scales in disease ecology andevolution". The section, which involved manuscripts from a number ofindividualsacross academia, addressed questions of scaling that formspart of this research. Additionally, a graduate student in PI Elderd'slab is conducting research on neural networks and machine learningrelated to the virus and hemocyte data being collected. 7. During the past year, a number of individuals have been trained onthe grant. This includes twopost-doctoral researchers, co-PI MichaelGarvey and Pramod Pantha at LSU, threegraduate students, onepost-graduate student, andsevenundergraduate students. The post-doctoral researcher Michael Garvey has sincemoved on to a permanent position with the USDA inArizona. Pramod Pantha in Co-PI Dassanayake's lab was trained in evolutionary genomics analysis methods. Additionally, an undergraduate student completed work on herHonors Thesisrelated to the research that she helped with over theprevious reporting period. Part of the summer training for theundergraduate, postgraduate, and graduate students included weeklymeetings where the students read primary literature related to theproject, and, then,discussed the literature with the post-doctoralresearcher and the PI Elderd.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Elderd, B. D., N. Mideo, and M. A. Duffy (2022). Looking across scales in disease ecology and evolution. The American Naturalist 199, 5158.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Garvey, M., K. Costanza, S. Grimmell, and B. D. Elderd (2022). Examining the effects of induced plant defenses on Spodoptera frugiperda performance. Applied Sciences 12.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Issa, P. P., M. Garvey, S. Grimmell, P. Pantha, M. Dassanayake, and B. D. Elderd (2021). Hitching a ride: Examining the ability of a specialist baculovirus to translocate through its insect hosts food plant. Pathogens 10.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Conference of Research Workers in Animal Diseases. Abiotic effects of temperature and biotic effects of pathogen exposure on host performance and susceptibility (B.D. Elderd (presenter), M. Garvey, S. Grimmell, J. Senn).
|
Progress 09/01/20 to 08/31/21
Outputs
Target Audience:The target audience reached by our efforts during this reporting period includes the greater scientific community as well as graduate and undergraduate students. We have shared the research via journal publications and presentations. We also have a number of publications related to the research that were submitted and others that will soon be submitted. co-PI Dassanayake conducted a 6-week virtual RNAseq workshop for a group of 15 participants - graduate students and post-doctoral researchers. This hands-on training involved teaching basic principles in a standard RNAseq experiment and command line guidance to a computational pipeline for user datasets. Participants processed data from raw sequence files to generate visual representations of differential expression and conducted associated functional analyses relevant to each dataset. Additionally, a post-doctoral researcher, graduate students, and undergraduate students have been trained in a variety of experimental and computational techniques needed to complete the research. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Over the course of the last reporting period, one post-doctoral researcher, three post graduate students, three graduate students, and one undergraduate have been mentored on multiple aspects of this project. Additionally, co-PI Dassanayake conducted a 6-week virtual RNAseq workshop for a group of 15 participants - graduate students and post-doctoral researchers. This hands-on training involved teaching basic principles in a standard RNAseq experiment and command line guidance to acomputational pipeline for user datasets. Participants processed data from raw sequence files to generate visual representations of differential expression and conducted associated functional analyses relevant to each dataset. How have the results been disseminated to communities of interest?During this reporting period, one journal article has been published, two journal articles has been submitted, and one presentation at an international conference was given. Individuals involved in this research also have a number of other manuscripts near submission. Additionally, PI Elderd has organized an edited special features section in the American Naturalist on looking across scales in disease ecology. What do you plan to do during the next reporting period to accomplish the goals?Over the course of the next reporting period, we will continue to develop Bayesian hierarchical approaches while also moving forward with evolving/co-evolving host and pathogen.
Impacts
What was accomplished under these goals?
Objectives: 1. Establish host-pathogen lines drawn from populations across the geographic range of the host and pathogen distribution. After much delay due to the COVID-19 pandemic and its impact on manufacturing, the growth chambers finally arrived at LSU. Over the past year, we established colonies from populations in the United States -- Louisiana and Indiana, specifically. The populations from South America have not been collected due to COVID-19 travel restrictions, government offices closing during the COVID-19 outbreak, and government unrest in parts of South America. Currently, we are collecting additional individuals from established populations in Louisiana and Indiana. For the former, we are collecting to add some genetic diversity to the colony and, for the latter, to reestablish the population due to population collapse over the past year. We used established colonies from North America to examine thermal performance metrics of fall armyworm larvae (Spodoptera frugiperda), using the recently delivered growth chambers, developed and are constructing OTCs, and establishing dose-response protocols to be used for future experiments. 2. Evolve and co-evolve these lines through differential exposure to hosts and pathogens under various temperatures. This objective is dependent on the establishment of host populations and will be the focus of future research efforts in the coming years. 3. Quantify how evolved and co-evolved lines differ in terms of their genomes and transcriptomes. This objective is dependent upon the establishment of host and pathogen populations and will be the focus of future research efforts in the coming years. An initial effort on this objective included the analysis of transcriptome data for the fall armyworm, Spodoptera frugiperda along with the cabbage looper, Trichoplusia ni. The transcriptome analysis included individuals that had been exposed to virus and a control group that had not been exposed to the virus. The associated manuscript, which will help move future efforts forward, has been published in MDPI: International Journal of Molecular Sciences. 4. Quantify how evolved and co-evolved host lines differ in terms of their individual susceptibility to the virus. This objective is dependent on the establishment of host populations and will be the focus of future research efforts in the coming years. We have completed an initial set of dose-response experiments associated with this objective, which will serve as a stepping stone for future research efforts. 5. Quantify how evolved and co-evolved lines differ in terms of population-level disease transmission dynamics. This objective is dependent on the establishment of host populations and will be the focus of future research efforts in the coming years. We have completed an initial effort to develop and test the necessary open-top chambers (OTCs) to conduct these experiments. We are currently constructing these OTCs. 6. Develop Bayesian hierarchical models to analyze the data collected. We have continued to develop Bayesian models and methods related to this objective. Some of this work includes examining computational and theoretical aspects of multiscale ecological state space models. In general, all of this work has led to the publication of one paper, the submission of two other papers, and one presentation. Additional publications are close to completion and will be submitted soon. The PI Elderd organized and co-edited a focused topics section entitled "Looking across scales in disease ecology and evolution" for the American Naturalist. The section, which involves manuscripts from a number of individuals across academia, addresses questions of scaling that forms part of this research. The focus topic is expected to be published within the next reporting period. Additionally, a new graduate student in PI Elderd's lab will be conducting research on Bayesian neural networks. 7. Train students and post-doctoral researchers in a cross-disciplinary manner via exposure to mathematical model building, lab and field ecology, and transcriptomics. During the past year, a number of individuals have been trained on the grant. This includes a post-doctoral researcher, co-PI Michael Garvey at LSU, three graduate students, and three post-graduate students. One graduate student in Biological Sciences at LSU defended their PhD thesis. His thesis research incorporated comparative transcriptomics methods developed during data analyses of the insect-viral transcriptome analyses supported by the current grant. Additionally, an undergraduate student was trained over the summer and academic year to carry out both field and laboratory experiments related to the project. The undergraduate has started working on her Honors Thesis related to the research that she helped with over the last summer and previous academic year. Part of the summer training for the undergraduate, post-graduate, and graduate students included weekly meetings where the students read primary literature related to the project, and, then, discussed the literature with the post-doctoral researcher and the PI Elderd.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2021
Citation:
Pantha, P., S. Chalivendra, D. Oh, B. D. Elderd, and M. Dassanayake (2021). A tale of two transcriptomic responses in agricultural pests via host defenses and viral replication. MDPI: International Journal of Molecular Sciences 22, 3568.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2021
Citation:
Garvey, M., S. Grimmell, and B. D. Elderd (In Review). Examining the effects of induced plant defenses on Spodoptera frugiperda performance. Journal of Economic Entomology.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2021
Citation:
Elderd, B. D., N. Mideo, and M. A. Duffy (In Review). Looking across scales in disease ecology and evolution. The American Naturalist
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Conference of Research Workers in Animal Diseases (CRWAD). Host-pathogen coevolution in a changing environment: the fall armyworm (Spodoptera frugiperda) and its baculovirus. (B.D. Elderd (presenter), M. Dassanayake, V. Dukic, and M. Garvey).
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Progress 09/01/19 to 08/31/20
Outputs
Target Audience:The target audience reached by our efforts during this reporting period includes the greater scientific community as well as graduate and undergraduate students. We have shared the research via journal publications and presentations. We also have a number of publications related to the research that will soon be submitted. Additionally, a post-doctoral researcher, graduate students, and undergraduate students have been trained in a variety of experimental and computational techniques needed to complete the research. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Over the course of the last reporting period, one post-doctoral researcher, five graduate students, and four undergraduates have been mentored on multiple aspects of this project. How have the results been disseminated to communities of interest?During this reporting period, one journal article has been published, one journal article has been submitted, and one presentation at an international conference was given. Individuals involved in this research also have six manuscripts near submission. Additionally, PI Elderd has organized an edited special features section in the American Naturalist on linking across scales in disease ecology. Co-PI Dukic also organized an invited mini-symposium at SIAM Life Sciences that would feature the grant's work. Unfortunately, due to COVID19, the conference was cancelled but co-PI Dukic plans to organize the symposium again for the 2021 meeting. What do you plan to do during the next reporting period to accomplish the goals?Over the course of the next reporting period, we will continue to develop Bayesian hierarchical approaches while also moving forward with evolving/co-evolving host and pathogen.
Impacts
What was accomplished under these goals?
Objectives: 1. Establish host-pathogen lines drawn from populations across the geographic range of the host and pathogen distribution. To establish host-pathogen lines, we need to acquire additional growth chambers as outlined in the proposal. The growth chambers were originally scheduled to arrive at LSU in late winter. However, due to the COVID-19 pandemic, the delivery of the chambers has been delayed until late summer of 2020. We are currently working on finding outbreaks of fall armyworm for collection in the United States at a sub-tropical northern latitude (e.g., Louisiana) and a northern mid-latitude (e.g., Indiana) site. Given that it is early in the summer, outbreaks haven't occurred but we have been in contact with appropriate personnel at both locations and are ready to collect. The South American populations will be collected during the South American summer of 2020 in December. This assumes no international travel restrictions due to the COVID-19 pandemic. During this reporting period, we have also established firm protocols for quantifying thermal performance curves and for conducting the open-top chamber experiments. 2. Evolve and co-evolve these lines through differential exposure to hosts and pathogens under various temperatures. This objective is dependent upon the establishment of host and pathogen populations and will be the focus of future research efforts in the coming years. 3. Quantify how evolved and co-evolved lines differ in terms of their genomes and transcriptomes. This objective is dependent upon the establishment of host and pathogen populations and will be the focus of future research efforts in the coming years. An initial effort on this objective included the analysis of transcriptome data for the fall armyworm, Spodoptera frugiperda along with the cabbage looper, Trichoplusia ni. The transcriptome analysis included individuals that had been exposed to virus and a control group that had not been exposed to the virus. The analysis has been completed and the associated manuscript will be submitted to BMC Genomics relatively soon. 4. Quantify how evolved and co-evolved host lines differ in terms of their individuals susceptibility to the virus. This objective is dependent upon the establishment of host and pathogen populations and will be the focus of future research efforts in the coming years. 5. Quantify how evolved and co-evolved lines differ in terms of population-level disease transmission dynamics. This objective is dependent upon the establishment of host and pathogen populations and will be the focus of future research efforts in the coming years. 6. Develop Bayesian hierarchical models to analyze the data collected. During the past reporting period, we have begun to work on the development of Bayesian models related to this objective. This has led to the publication of one paper, the submission of one paper, and one presentation. An additional four publications are close to completion and will be submitted soon. The PI Elderd is also organizing and editing a focused topics section entitled ''Looking across scales in disease ecology and evolution'' for the American Naturalist. The section, which involves manuscripts from a number of individuals across academia, directly addresses the scaling questions that forms part of this research. 7. Train students and post-doctoral researchers in a cross-disciplinary manner via exposure to mathematical model building, lab and field ecology, and transcriptomics. During the past year, a number of individuals have been trained on the grant. This includes a post-doctoral researcher, co-PI Michael Garvey at LSU, and three graduate students. One graduate student successfully defended their PhD thesis. Additionally, four undergraduates students are being trained over the summer to carry out both field and laboratory experiments related to the project. Part of the summer training for the undergraduate students includes weekly meetings where the students read primary literature related to the project and, then, discuss the literature with graduates students, the post-doctoral researcher, and the PI Elderd.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Shaffery, P., B. D. Elderd, and V. Dukic. 2020. A Note on Species Richness and the Variance of Epidemic Severity. Journal of Mathematical Biology. 80:20552074.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2020
Citation:
Van Allen, B., F. Dillemuth, and B.D. Elderd. In Review. Cannibalism during a disease outbreak: Just what the doctor ordered. The American Naturalist
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Dukic, V. 2019. Bayesian inference in structured epidemics. CM Statistics Conference.
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Progress 07/01/19 to 06/30/20
Outputs
Target Audience:The target audience reached by our efforts during this reporting period includes the greater scientific community as well as graduate and undergraduate students. We have shared the research via journal publications and presentations. We also have a number of publications related to the research that will soon be submitted. Additionally, a post-doctoral researcher, graduate students, and undergraduate students have been trained in a variety of experimental and computational techniques needed to complete the research. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Over the course of the last reporting period, one post-doctoral researcher, five graduate students, and four undergraduates have been mentored on multiple aspects of this project. How have the results been disseminated to communities of interest?During this reporting period, one journal article has been published, one journal article has been submitted, and one presentation at an international conference was given. Individuals involved in this research also have six manuscripts near submission. Additionally, PI Elderd has organized an edited special features section in the American Naturalist on linking across scales in disease ecology. Co-PI Dukic also organized an invited mini-symposium at SIAM Life Sciences that would feature the grant's work. Unfortunately, due to COVID19, the conference was cancelled but co-PI Dukic plans to organize the symposium again for the 2021 meeting. What do you plan to do during the next reporting period to accomplish the goals?Over the course of the next reporting period, we will continue to develop Bayesian hierarchical approaches while also moving forward with evolving/co-evolving host and pathogen.
Impacts
What was accomplished under these goals?
Objectives: 1. Establish host-pathogen lines drawn from populations across the geographic range of the host and pathogen distribution. To establish host-pathogen lines, we need to acquire additional growth chambers as outlined in the proposal. The growth chambers were originally scheduled to arrive at LSU in late winter. However, due to the COVID-19 pandemic, the delivery of the chambers has been delayed until late summer of 2020. We are currently working on finding outbreaks of fall armyworm for collection in the United States at a sub-tropical northern latitude (e.g., Louisiana) and a northern mid-latitude (e.g., Indiana) site. Given that it is early in the summer, outbreaks haven't occurred but we have been in contact with appropriate personnel at both locations and are ready to collect. The South American populations will be collected during the South American summer of 2020 in December. This assumes no international travel restrictions due to the COVID-19 pandemic. During this reporting period, we have also established firm protocols for quantifying thermal performance curves and for conducting the open-top chamber experiments. 2. Evolve and co-evolve these lines through differential exposure to hosts and pathogens under various temperatures. This objective is dependent upon the establishment of host and pathogen populations and will be the focus of future research efforts in the coming years. 3. Quantify how evolved and co-evolved lines differ in terms of their genomes and transcriptomes. This objective is dependent upon the establishment of host and pathogen populations and will be the focus of future research efforts in the coming years. An initial effort on this objective included the analysis of transcriptome data for the fall armyworm, Spodoptera frugiperda along with the cabbage looper, Trichoplusia ni. The transcriptome analysis included individuals that had been exposed to virus and a control group that had not been exposed to the virus. The analysis has been completed and the associated manuscript will be submitted to BMC Genomics relatively soon. 4. Quantify how evolved and co-evolved host lines differ in terms of their individuals susceptibility to the virus. This objective is dependent upon the establishment of host and pathogen populations and will be the focus of future research efforts in the coming years. 5. Quantify how evolved and co-evolved lines differ in terms of population-level disease transmission dynamics. This objective is dependent upon the establishment of host and pathogen populations and will be the focus of future research efforts in the coming years. 6. Develop Bayesian hierarchical models to analyze the data collected. During the past reporting period, we have begun to work on the development of Bayesian models related to this objective. This has led to the publication of one paper, the submission of one paper, and one presentation. An additional four publications are close to completion and will be submitted soon. The PI Elderd is also organizing and editing a focused topics section entitled ''Looking across scales in disease ecology and evolution'' for the American Naturalist. The section, which involves manuscripts from a number of individuals across academia, directly addresses the scaling questions that forms part of this research. 7. Train students and post-doctoral researchers in a cross-disciplinary manner via exposure to mathematical model building, lab and field ecology, and transcriptomics. During the past year, a number of individuals have been trained on the grant. This includes a post-doctoral researcher, co-PI Michael Garvey at LSU, and three graduate students. One graduate student successfully defended their PhD thesis. Additionally, four undergraduates students are being trained over the summer to carry out both field and laboratory experiments related to the project. Part of the summer training for the undergraduate students includes weekly meetings where the students read primary literature related to the project and, then, discuss the literature with graduates students, the post-doctoral researcher, and the PI Elderd.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Shaffery, P., B. D. Elderd, and V. Dukic. 2020. A Note on Species Richness and the Variance of Epidemic Severity. Journal of Mathematical Biology. 80:20552074.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2020
Citation:
Van Allen, B., F. Dillemuth, and B.D. Elderd. In Review. Cannibalism during a disease outbreak: Just what the doctor ordered. The American Naturalist
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Dukic, V. 2019. Bayesian inference in structured epidemics. CM Statistics Conference.
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