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MAPS REU Student Studies the Effectiveness of Disease Control Measures in Pathosystems

   

Martin presenting his research at the
2019 KU Undergraduate Research Poster Session in July

    Aiming to apply his mathematical skills to a science-related research project, Martin Pollack found an opportunity to study computational biology and biological modeling through a 2019 MAPS Summer Research Experience for Undergraduate Students (REU) at the University of Kansas (KU). The KU MAPS REU program is just one of the many educational outreach initiatives outlined in the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas (MAPS). Martin's REU mentor was Dr. Folashade Agusto, Assistant Professor of Ecology & Evolutionary Biology at KU and MAPS Synthesis Team Leader.

Martin working with Dr. Agusto

     Math has always been easy for Martin, so he chose the MAPS research experience because "I wanted to use my problem solving and quantitative skills in an applied sense, rather than just writing proofs all day for theoretical math sub-disciplines." He added, "I was amazed by the plethora of ways math can be used in biology, which also happens to be my second favorite discipline.” The MAPS REU project he selected matched his research goals perfectly. 
    The title of Martin's study is Effectiveness of Disease Control Measures in Pathosystems with Co-Infection and Vector Preference. He said, “I chose to model plant diseases because understanding how to control them is extremely significant for agriculture and for the conservation of biodiversity." He described his research as follows: "Most plant-vector-virus diseases found in nature are caused by the presence and interaction of multiple viruses in organisms. This interaction is called co-infection. The three main types of co-infection are helper-dependence, cross-protection, and synergism. Organisms such as aphids or other insects are called Vectors. Vectors can carry the diseases in these pathosystems, and they tend to prefer certain categories of host plants over others. In this study, we attempted to make a general compartmental disease model that incorporated co-infection, vector preference, and the transmission of disease to hosts. I tested three common disease control strategies that are utilized in agriculture: 1. increasing the planting of healthy plant hosts; 2. roguing (removal of diseased plant hosts); and 3. the use of pesticides. I hypothesized that using pesticides would be the most effective control measure, with the other two measures being less effective. I also did not think there would be significant differences when testing different types of co-infection or vector preference. I found that when Vectors preferred healthy hosts and all types of co-infection were considered, none of the control measures fully eliminated the disease. When Vectors did not prefer healthy hosts, applying pesticides was the most effective control. The control strategy of increasing the planting of healthy hosts was consistent across all considerations but rarely lowered disease incidence significantly. This was not expected. However, planting hosts with cross-protection present did lower disease occurrence. Roguing, on the other hand, completely eliminated the disease with the presence of helper-dependence and cross-protection, but was largely ineffective against pathosystems with synergism. Rouging’s effectiveness was highly variable depending on the type of co-infection present in the system, which was not expected. Overall, the use of pesticides tended to be the most effective control strategy for each situation.” Even though Martin's model found pesticides to be the most effective control measure, he warned, "applying this measure could prove dangerous and possibly lead to pesticide resistance." 

Martin's poster illustrating his methods and results

     When asked what he learned from his summer research experience, Martin said “I learned how to plan a research project, how to encapsulate my project into a research question, and how to decide what techniques and methods to use to answer it. I also learned how non-linear the scientific process is and found it to be more circular. I was always tweaking my research question or writing new computer code each time I got new results.” He went on to add, “My favorite part of my REU experience was being able to fully commit my focus to a single project. Usually, I am busy taking multiple classes and my extracurricular activities occupy any free time. This summer, I was able to learn a lot about a very specific field and learn how to carry out a research project from start to finish.”     
     Martin is from the San Francisco Bay Area and is currently a sophomore at Grinnell College in Grinnell, IA. He is pursuing a double major in Mathematics and German. During the academic year, Martin is a calculus tutor for his college, and he serves as a German Lab Instructor teaching vocabulary, grammar, and culture to students enrolled in the Intermediate German course. Being a serious musician, Martin plays the violin, viola, and piano and is also a member of a String Quartet. When asked about his hobbies, Martin responded, “My biggest hobby is soccer, and I am a 'regular' in my college’s club soccer scene. I can also be found watching international soccer on my phone regularly.”  
     After earning his bachelor’s degree, Martin plans to attend graduate school and study “a quantitative discipline that utilizes my math skills in applied ways.” Once he completes his education, he will pursue a career as “a data scientist, using numbers and data to learn more about the world” around him.

Workforce Development, Education and Outreach funding for the KU MAPS Summer REU is provided by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas. The grant's workforce development and educational objectives are designed to enhance STEM education in Kansas by supporting activities that will lead to an expanded STEM workforce or prepare a new generation for STEM careers in the areas of aquatic, plant and soil microbiome environments and ecological systems.

Kansas NSF EPSCoR New Funding Opportunity for Early Career Faculty

     Kansas NSF EPSCoR is announcing a new funding opportunity for First Awards in the area of microbiome research. The First Award program helps early-career faculty become competitive for funding from the research directorates at the National Science Foundation by 1) encouraging early-career faculty to submit proposals to the NSF (or other federal funding agency) as soon as possible after their first faculty appointment, and 2) by accelerating the pace of their research and the quality of their subsequent proposals.

    Eligible to apply is any individual tenure track faculty member who is currently untenured
at the assistant professor rank at Kansas State University, University of Kansas, Wichita
State University, Emporia State University, Fort Hays State University, Pittsburg State
University or Washburn University and who:

• is within the first three years of his/her faculty appointment,1
• has not previously received a First Award or similar funding from another EPSCoR or EPSCoR‐like (Centers of Biomedical Research Excellence, COBRE) program in Kansas, and is not currently nor has previously been a lead Principal Investigator of a research grant funded by a federal agency.

First Awards are intended to be single‐investigator awards to support the PI’s research program at their institution.

Download the Request for Proposal Information at: 

2019 First Awards in Microbiome Research

Submission Deadlines:

• White Papers due by 5:00 pm Wednesday, 9/25/2019

Download the First Award

Letter of Intent Information Form 

at LOI Form

• Final Proposals are due by 5:00 pm Monday, 11/25/2019

Workforce Development, Education and Outreach funding for First Awards is provided by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas. The grant's workforce development and educational objectives are designed to enhance STEM education in Kansas by supporting activities that will lead to an expanded STEM workforce or prepare a new generation for STEM careers in the areas of aquatic, plant and soil microbiome environments and ecological systems.

KS-LSAMP Student Studies Groundwater Discharge across Kansas

Gonzalo Alcantar

    An intro-geology class “as well as the instructor’s enthusiasm for teaching the subject” led to Gonzalo Alcantar’s curiosity for “agriculture/farming and aquaponics/vertical farming.” Looking for an opportunity to do further research on the subject, the 2019 Pathways to STEM: Kansas Louis Stokes Alliance for Minority Participation (KS-LSAMP) program at Kanas State University (KSU) presented a great opportunity to explore his interests. The KS-LSAMP program is funded by the National Science Foundation (NSF LSAMP) and "promotes recruitment and retention programs throughout Kansas in support of increasing the success of underrepresented minority students in science, technology, engineering and math (STEM) fields. "The summer portion of KS-LSAMP is called Research Immersion: Pathways to STEM (RiPS) and is an 8-week summer research program that "aims to introduce students to the process of research and assist in their academic and professional success." Gonzalo was one of three students in the KS-LSAMP program sponsored by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas (MAPS). His mentor was Dr. Matthew Kirk, Associate Professor of Geology at Kansas State University (KSU) and MAPS Soils Team leader.

Gonzalo Alcantar working in the Kirk Lab
Photo provided by Matt Kirk

     The title of Gonzalo’s research project is Variation in contribution of groundwater discharge to streams across the Kansas precipitation gradient. He said that he picked this particular topic because “I am interested in everything that goes into agriculture/farming and aquaponics/vertical farming, hence the water research.” Gonzalo explained his project as follows “Groundwater discharge affects the coupling between terrestrial and aquatic habitats and ultimately the biogeochemistry and water quality of streams. To better understand the contribution of groundwater discharge to streams in Kansas, this project tests the following hypotheses: (1) the proportion of groundwater discharge in streamflow decreases with distance east across the Kansas precipitation gradient and (2) the proportion of discharge has increased over the past 60 years. To test these hypotheses, we used the U.S. Geological Survey program PART to carry out hydrograph separation analysis on groundwater discharge data from seven gage stations located across the Kansas precipitation gradient. Our analysis uses stream baseflow as an estimate of groundwater discharge. We also examined precipitation data collected at Hays, Salina, and Topeka, Kansas. The results indicated that the amount of groundwater discharge and runoff both increase eastward across the precipitation gradient but the increase is greater for runoff. Therefore, the proportion of groundwater discharge in streamflow decreases slightly across the precipitation gradient. Over the past 60 years, the proportion of groundwater discharge in streamflow has increased in western Kansas but remained fairly stable in eastern Kansas. Potential reasons for the change in the contribution of groundwater discharge in western Kansas over time include changes in the rate of precipitation and land management changes. The average annual precipitation in western and eastern Kansas has remained largely stable suggesting land management changes could be responsible for variation in the proportion of groundwater discharge over time in western Kansas. These findings suggest that the potential influence of groundwater discharge on stream habitats is greatest in western Kansas. Future research will evaluate the biogeochemical impact of spatial and temporal variation in groundwater discharge in Kansas.” Gonzalo presented his research at the RiPS Summer Program Final Poster Session on July 24, 2019.

Gonzalo Alcantar presenting his research at
the RiPs Summer Program Final
Poster Session

     When asked what his favorite part of his KS-LSAMP experience was, Gonzalo responded, “My favorite part of LSAMP was being able to get some research experience as well as gain better connections with a K-State faculty member.” He continued, “I learned an abundant amount of information about not only my research but also other graduate students’ research in which I was able to help with over the summer. I learned how to work in a lab environment and how to better communicate with my mentor as well as understand my responsibilities and role in a lab.”
     Gonzalo is from Garden City KS and is currently a sophomore at KSU studying Industrial Engineering. He is involved with the Society of Hispanic Engineers (SHPE), the Hispanic and Latino Organization (HALO), and the Multicultural Business Student Association (MBSA) on-campus student organizations. In addition, he is a Teaching Assistant (TA) for Dr. Bailey Sullivan, a Residential Learning Assistant for a Cat Community, a Building Operations Assistant for the K-State Student Union and a Berney Family Welcome Center Ambassador. As for his future plans, Gonzalo wants to pursue a master’s degree in industrial engineering. But for now, he hopes to work closely with his professors during his sophomore year.

Workforce Development, Education and Outreach funding for KS-LAMP is provided by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas. The grant's workforce development and educational objectives are designed to enhance STEM education in Kansas by supporting activities that will lead to an expanded STEM workforce or prepare a new generation for STEM careers in the areas of aquatic, plant and soil microbiome environments and ecological systems.

MAPS Researcher Receives Three New NSF Awards

     

Dr. Jesse Nippert

      Dr. Jesse Nippert, Professor of Biology at Kansas State University (KSU) and research team member working with the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas (MAPS), has received three new National Science Foundations (NSF) Awards to study the impacts of global change on grassland ecosystems. The first award is a three-year grant funded by NSF Hydrological Sciences and is titled Digging deeper: Do deeper roots enhance deeper water and carbon fluxes and alter the trajectory of chemical weathering in woody-encroached grasslands? The goal of this research is to study "how deeper roots associated with woody plant encroachment enhances transport of water and carbon to greater depths, increases the water residence time in the subsurface, and enhances the potential for weathering at depth." The second award is also a three-year award supported by NSF-Macrosystems Biology and NEON-Enabled Science program and is titled Collaborative Research: MRA: A lineage-based framework to advance grassland macroecology and Earth System Modeling. This project seeks to advance the "predictability of grassy ecosystem responses to global change by measuring many grass species traits. The new data will be incorporated into new modeling approaches. The project will enhance understanding of grass ecology, with many applications in agriculture and natural resource management."  The third award comes from the Population and Community Ecology Cluster within the NSF-Division of Environmental Biology  This three-year award is titled Collaborative Research: Rainfall variability and the axes of tree-grass niche differentiation. The scope of this project is to study the savanna biome and combine experimental, observational and modeling approaches to "(1) identify the rainfall regimes that favor trees over grasses, (2) identify the functional traits and tradeoffs that differentiate savanna trees and grasses, and (3) develop and test a mechanistic model of tree and grass dynamics as a function of rainfall."  In addition, the project will examine"functional differences (e.g., drought tolerance, water use efficiency and functional rooting depth) between six tree and six grass species using a greenhouse, growth chamber and field experiments." The first two projects will use the experimental infrastructure of the Konza Prairie Biological Station and the third project's fieldwork will take place in Limpopo Province of South Africa.

HERS Student Studies the Impact Warming Waters of the Blackfoot River has on Westslope Cutthroat Trout

 

Joseph Zupan

     Although Joseph Zupan grew up in West Point, New York, it was the summer vacations fishing and camping with his family on the Blackfoot River in Montana that led to his interest in the environment, animals, and plants. Joseph is a member of the Chippewa Cree Tribe from the Rocky Boys Indian Reservation in Montana, and he participated in the 2019 Haskell Environmental Research Studies (HERS) Institute supported by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas (MAPS) research project. The HERS Institute is an 8-week paid summer internship program where student interns spend six weeks on the Haskell Indian Nations University campus during June and July, learn about climate change and develop individual research projects. Dr. Jay Johnson, Professor and Associate Chair of Geography & Atmospheric Science, Director of The Center for Indigenous Research, Science, and Technology (C-FIRST) at the University of Kansas (KU), and member of the MAPS Workforce Development and Education team, supervises the HERS Institute.
     During his summer vacations to Montana, Joseph said, “We would always catch trout, particularly Westslope Cutthroat Trout (WCT),” and he thought this was “such a beautiful species of fish, it needed to be preserved so that other people are able to enjoy them.” His fishing experiences along with being raised “to respect and love the lands we live in” led to his desire to investigate the WCT for his HERS project. He titled his research project, Trout in Hot Water: Warming Waters Impact on Westslope Cutthroat Trout (WCT) in the Blackfoot River, Montana. Joseph explained his study as follows: “Climate change is negatively impacting trout populations in the Blackfoot River system in Montana. Increasing temperatures are considered to be the most damaging factor impacting a myriad of factors including the hydrological regime, habitat structure, runoff, and snow-pack. An increase in water temperature is of particular concern as it directly impacts nearly all of the WCT physiological functions at each stage of its life cycle. The focus of my research addresses how warming waters of the Blackfoot River are effecting the reproductive cycle of the WCT.” As part of his research process, Joseph analyzed “stream-flow data to compare water and air temperatures during normal and extreme temperatures and studied how warm water impacts the Blackfoot River water regime.” He then compared “dissolved oxygen levels of the river during drought and normal conditions,” and the influence “precipitation during drought versus normal conditions” had on the river. Next, he examined the data that outlined the “WCT needs for survival,” and analyzed the biological and physiological requirements of the WCT reproductive cycle in order to compare" its reproductive needs to those of other trout species. Joseph found that changing temperatures are "a significant factor in the decline of WCT reproduction.” He further concluded that because WCT are “an important species for tribal and state economies, and historically, are a primary food source for Northwestern Native Americans” efforts such as “actively securing cutthroat populations, habitat distributions, and preventing invasive species interactions” need to continue. These recommendations are outlined in more detail as part of the Blackfoot River Restoration project. In addition, Joseph found that after “using existing physiological data on adult WCT temperature tolerance, it became apparent that temperature change may have a detrimental impact on the size of the WCT roe, and if adult WCT populations decrease, there might be no roe.” At the end of his study, Joseph recommended that “future research focus on spawning sites in cold, clear head water streams, and additional WCT physiological roe data should be collected. Specifically, data addressing how temperature effects the viability and gestation needs of the WCT roe.”
 

Joseph working on weather instruments and presenting his research at UCAR

     When asked about his HERS experience, Joseph said, “the HERS program was amazing!” His favorite part of the institute was “how the mentors and program managers genuinely cared about us (the interns). I felt like I was part of a big family and that was really important to me!” Joseph’s HERS mentor was Kate Ingenloff, a doctoral candidate in the Department of Ecology & Evolutionary Biology at KU. As for what he learned from his HERS experience, Joseph stated, “I learned so much in such a small amount of time that I feel like I learned more at the HERS institute than I would during a normal school semester. Specifically, I learned how to refine my research and writing skills as well as manage time, organize a research product, and analyze results. He then added, "when we went to the University Corporation for Atmospheric Research (UCAR) in Boulder, Colorado, I learned about the phenomenon of bomb cyclones and the methods associated with water quality research as well as how to set up weather instruments." Joseph also presented his WCT research during a UCAR poster session.
     Joseph graduated from Haskell Indian Nations University with a Bachelor of Science Degree in Environmental Science last spring. While attending Haskell, he “participated in numerous projects for the Haskell Eco-ambassadors, a student-run environmental organization specializing in wetland remediation.” As an Eco-ambassador he was involved with projects such as “butterfly tagging for the Monarch Watch program at KU, trail cultivation and development, compost development, and habitat restoration.” In addition, Joseph coached children’s ice hockey, taught a women's self-defense class, and was the captain of the First City Cavalry, a semi-professional football team out of Leavenworth, Kansas. This fall, he will pursue a Masters Degree in Geography at KU with a plan to continue his education and earn a Ph.D. Once Joseph finishes his graduate work, he wants to “work on tribal lands as a scientist or tribal college instructor.”

Workforce Development, Education and Outreach funding for the HERS Institute is provided by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas. The grant's workforce development and educational objectives are designed to enhance STEM education in Kansas by supporting activities that will lead to an expanded STEM workforce or prepare a new generation for STEM careers in the areas of aquatic, plant and soil microbiome environments and ecological systems.

KS-LSAMP Student Studies Interference Competition Among Biovar 1 Agrobacteria

Natalie Melendez-Velador
Presenting at the 2019 KS-LSAMP
 Research Immersion: Pathways to STEM Poster Session

     Animals and plants have always been of interest to Natalie Melendez-Velador, and being good in science helped to solidify her pursuit of a biology focus in her Bridges Program at Seward County Community College. This summer, Natalie participated in the 2019 Pathways to STEM: Kansas Louis Stokes Alliance for Minority Participation (KS-LSAMP) program and was sponsored by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas (MAPS). KS-LSAMP is funded by the National Science Foundation and "promotes recruitment and retention programs throughout Kansas in support of increasing the success of underrepresented minority students in science, technology, engineering and math (STEM) fields. The summer portion of KS-LSAMP is called Research Immersion: Pathways to STEM (RiPS) and is an 8-week summer research program that "aims to introduce students to the process of research and assist in their academic and professional success."

Dr. Thomas Platt and Natalie Melendez-Velador
with members of the Platt Lab Team

   Natalie worked with Dr. Thomas Platt, Synthesis Team Leader for the MAPS project and Assistant Professor of Biology at Kansas State University. She also worked with Ashlee Herken, a graduate student with the Platt Lab.  She titled her project, Interference Competition Among Biovar 1 Agrobacteria from Helianthus annuus Roots. According to Natalie, her summer research was very similar to the research she was already doing in her Bridges program. She specified the summer "research focused on methicillin resistant staphylococcus aureus and multi-drug resistant bacteria.” Natalie explained her project as follows: “In this study, we aimed to determine whether a sample of biovar 1 agrobacteria produce bacteriocins inhibiting the growth of several pathogenic strains, including strains with whom they co-occur. This work has the potential to lead to the discovery of noval biocontrol agents for crown gall disease. Root samples of common sunflowers, Helianthus annuus, were collected from Konza Prairie. Isolates were grown on semi-selective media that supports the growth of biovar 1 agrobacteria but excludes the growth of most fungi and bacteria present in the microbial communities on plant roots. We used an inhibition assay to determine if agrobacterial isolates produce bacteriocins interfering with the growth of Agrobacterium tumefaciens strains C58, 15955, and K203. Each of these strains is pathogenic with C58 containing a nopaline-type Ti plasmid, 15955 containing an octopine-type Ti plasmid, and K203 being isolated from the same plant as some of the isolates being tested. Experiments are ongoing but preliminary results indicate that several of the environmental isolates inhibit the growth of C58 but not 15955 or K203. This strain-specific inhibition is consistent with prior work with pathogenic agrobacteria, however, we see no evidence for bacteriocin mediated interference competition among co-occurring strains. Future work will aim to determine the mechanisms mediating strain-specific C58 inhibition, including the possibility that inhibition depends on Ti plasmid encoded functions.” And she added, "the research focused on methicillin resistant staphylococcus aureus and multi-drug resistant bacteria."
    The best part of the summer RiPS KS-LSAMP experience for Natalie was “getting to meet a wide variety of people who each have unique skill sets and experiences.” From this summer experience, Natalie added she “learned new scientific techniques, as well as, how to communicate with team members and diverse audiences about my research.” Natalie presented her research poster at the 2019 LSAMP Poster Session held at Kansas State University on July 24, 2019.
    Natalie is originally from Liberal, KS.  This fall, she will be a sophomore at Seward County Community College pursuing an Associate Degree in Biology. As for her future plans, she said “After getting my associate's degree, I plan to transfer to Kansas State University in the fall of 2020 and major in Biology. I also plan on continuing my research next summer with Dr. Platt.”

Workforce Development, Education and Outreach funding for the KS-LSAMP is provided by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: Microbiomes of Aquatic, Plant, and Soil Systems across Kansas. The grant's workforce development and educational objectives are designed to enhance STEM education in Kansas by supporting activities that will lead to an expanded STEM workforce or prepare a new generation for STEM careers in the areas of aquatic, plant and soil microbiome environments and ecological systems.