Dr. Michael Norris demonstrating proper use of Personal Protective Equipment (PPE) in a BSL3 lab

GAINESVILLE, FL – SEER Lab Medical Geographer Dr. Michael Norris has launched a new BSL3 lab specifically to study COVID-19 at the Emerging Pathogens Institute.

When the pandemic initially broke out, Dr. Norris initially offered his time to help with the testing effort, but quickly realized that his skills could be better utilized elsewhere. He has been working hard setting up the SARC-CoV-2 BSL3 lab from the ground up – ensuring that all the regulatory and compliance paperwork is in place, collaborating with PIs across campus at the College of Medicine, College of Veterinary Medicine, the College of Engineering, and even IFAS.

A lab bench inside the BSL3 COVID lab

Dr. John Lednicky from the Department of Environmental and Global Health runs a virology lab that isolated SARS-CoV-2 from the first patient at Shands. This isolate has only 3 base pairs different from the first sequenced SARS-CoV-2 isolate from Wuhan, China. Dr. Norris was brought on to establish a lab to take the experiments to the next level. The proposal entitled, “Identification of host determinants of SARS-CoV-2 infection” was funded by the UF’s Clinical and Translational Science Institute COVID-19 Rapid-Response Research Pilot Fund.

Comparing uninfected cells to SARS-CoV-2 infected cells at 200x magnification

Dr. Norris is a co-Investigator on the grant and will be overseeing if not performing most experiments directly with the virus in the BSL3. He is working closely with the PI Dr. Christopher Vulpe a CRISPR expert in the Department of Physiology and virologist and CRISPR co-Investigator Dr. Stephanie Karst of the Department of Molecular Genetics and Microbiology. Mike will also be training new individuals on BSL3 laboratory skills to increase the workforce capability.

The abstract for the grant:

“Work demonstrated the utility of functional genetic approaches, including genome-wide CRISPR screens, to identify host factors that promote and restrict viral replication. We will carry out genome-wide CRISPR-based knockout and activation screens to identify host components that regulate SARS-CoV-2 infection. In these screens, pooled mutant cell libraries will be infected with SARS-CoV-2 at a high MOI and mutant cells resistant to SARS-CoV-2 infection will be identified. CDC researchers identified human cell lines susceptible to SARS-CoV-2 lines but the infection is not cytopathic (CPE). Previous work with SARS-CoV-1 demonstrated G0/G1 arrest during infection so we will use continued cellular proliferation (escape from G0/G1 arrest) to identify the resistant cells. We will also attempt to enhance CPE in human cells to enable use as a screening endpoint. As a third alternative, we plan to generate genome wide CRISPR libraries for the African Green Monkey Cells (VeroE6) which are lysed by SARS-CoV-2 infection. Together these approaches should allow identification of host factors that regulate SAR-CoV-2 infection which represent candidate druggable targets with a high likelihood of having broad-spectrum activity across the coronavirus family.”

Quantitative Disease Ecology & Conservation Lab
Emerging Pathogens Institute
CDC Southeastern Center of Excellence in Vector Borne Diseases
University of Florida

Adviser: Dr. Sadie Ryan

Focus Area: Medical Geography in Global Health (MGGH)

Research Statement: I am a mathematical ecologist interested in the disease ecology dynamics between wildlife and humans. Thus far, my research has focused on tick ecology and modeling of tick management strategies. In my current work, I explore the spatial ecology of vector-borne diseases.

Lexi flagging for ticks in Virginia

Who is she?
Dr. Alexis (Lexi) White is a postdoctoral researcher in the Geography Department, the Quantitative Disease Ecology & Conservation Lab, the CDC Southeastern Center of Excellence in Vector Borne Diseases, and the Emerging Pathogens Institute. Lexi completed a B.S. in Wildlife Biology at Maine’s Unity College before moving to Virginia’s Old Dominion University where she completed a Graduate Certificate in Modeling and Simulation and her PhD in Ecological Sciences.

TickBot: A novel robotic device for controlling tick populations in the natural environment

How did she get here?
At Old Dominion, Lexi helped develop a mathematical model of the persistence of multiple pathogens in a single tick population and explored tick control strategies including the TickBot, a robotic tool for controlling tick populations in natural environments.

Can you spot the blood sucker in this image?

Lexi also conducted mark recapture studies – a tool to determine population size when it is impossible to count every member of a population – to explore the use of domesticated birds for tick control. Guinea fowl are widely used across the United States to manage ticks, but there is little evidence to support this. In fact, Lexi found that lone star ticks can feed on guinea fowl – the presence of guinea fowl may even exacerbate the tick problem.

Lexi used her field studies from the TickBot and guinea fowl experiments to create agent-based models of these systems. Agent-based models can be used to model individual interactions with an environment. The combination of field studies and mathematical models allows researchers to explore tick control options in a short period of time in the model rather than multiple field seasons.

What’s she been doing at UF?
Since joining the Geography Department in January 2020, Lexi has been expanding her intellectual horizons – learning spatial analysis, critically assessing geography literature and finding ways to apply the tools of medical geography to her expertise in ecology. She gained valuable tools in Dr. Blackburn’s GIS6456C Applications in GIS – exploring zoonoses, disease ecology, and medical geography.

With these new spatial distribution skills and medical geography knowledge, Lexi has been assessing the potential geographic range of ticks (and tick-borne pathogens) with her PhD adviser and QDEC colleagues. The research hasn’t been published yet, but you can read a preprint here.

Lexi has also been working with the CDC Southeastern Center of Excellence in Vector Borne Diseases on outreach and communications – helping communicate findings from the lab to the general population.

How has she been holding up in Quarantine?
Moving to a new city on the cusp of a global pandemic has been isolating, but regular lab meetings and check-ins have helped Lexi make Gainesville and UF her new home. She’s also been getting to know her new neighborhood with lots of dog walking.

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Image courtesy Centro de Investigaciones en Geografía Ambiental (CIGA), Universidad Nacional Autónoma de México (UNAM)

Dr. Cynthia Simmons and Dr. Robert Walker were invited speakers at the Alexander Von Humbolt Seminar 2019 at the Center for Environmental Geography Research (CIGA), National University of Mexico, Michoacan (UNAM).

Small rural producers, forests and globalization in Latin America

In the first part of the conference the socioeconomic and environmental effects of the entry of transnational meat producing corporations in Brazil and Mexico in the last 30 years will be announced. In relation to the first country, it will be explained (i) how agricultural policies extolled a type of agricultural production system far away from that seen by the original Agrarian Reform and (ii) the socio-economic effects on small producers who are the last link in the big chains. The Mexican case illustrates how the FTA has reconfigured corn-cattle production by inserting it into a “telecoupled network” based on feedlots and with negative impacts on the forest and on the production of greenhouse gas emissions both in Mexico but, especially, in Central America as a great producer of calves for fattening. This is a case that illustrates very well how the commitments acquired to reduce deforestation are of no use if made by a single country, independently; This is because there are many countries that make up the large global chain of meat-fattening-processing-distribution of meat.

In the second part, the changes suffered in the mixed corn-livestock systems in the hands of small producers in an area close to two of the largest feedlots in Mexico will be analyzed. Traditional agricultural and livestock productive management schemes will be illustrated, but also the changes that these systems are undergoing. The potential of these systems to be the local and more sustainable counterpart of the meat produced in the large global chains will be discussed. Opportunities and challenges, in terms of sustainability and reducing the negative impact on Climate Change, of livestock systems in the hands of small producers in Mexico and Latin America will be analyzed.

Pequeños productores rurales, bosques y globalización en América Latina

En la primera parte de la conferencia se darán a conocer los efectos socioeconómicos y ambientales de la entrada de corporaciones transnacionales productoras de carne en Brasil y México en los últimos 30 años. En relación al primer país, se explicará (i) cómo las políticas agrarias ensalzaron un tipo de sistema productivo agropecuario muy lejano al visionado por la Reforma Agraria original y (ii) los efectos socio-económicos en los pequeños productores quienes son el último eslabón de las grandes cadenas. El caso mexicano ilustra cómo el TLC ha reconfigurado la producción de maíz-ganado insertándola en una “telecoupled network” basada en feedlots y con impactos negativos en el bosque y en la producción de emisiones de gases efecto invernadero tanto en México pero, especialmente, en Centro América como gran productora de becerros para engorda. Este es un caso que ilustra muy bien cómo los compromisos que se adquieren para reducir la deforestación no sirven de nada si los hace un solo país, de manera independiente; esto se debe a que son muchos los países que conforman la gran cadena global de cría-engorda-procesamiento-distribución de carne.

En la segunda parte se analizarán los cambios sufridos en los sistemas mixtos maíz-ganadería en manos de pequeños productores en una región cercana a dos de los feedlots más grandes de México. Se ilustrarán los esquemas de manejo productivos agro-pecuarios tradicionales pero también los cambios que están sufriendo dichos sistemas. Se discutirá el potencial de estos sistemas para ser la contraparte local y más sustentable de la carne producida en las grandes cadenas globales. Se analizarán las oportunidades y desafíos, en términos de la sustentabilidad y en reducir el impacto negativo en el Cambio Climático, de los sistemas ganaderos en manos de pequeños productores en México y América Latina.

Image courtesy PLoS Neglected Tropical Diseases

Dr. Sadie Ryan‘s paper Global expansion and redistribution of Aedes-borne virus transmission risk with climate change in PLoS Neglected Tropical Diseases, was included as the March entry for the Best of PLOS 2019 list.

From the announcement:

March: Climate change may mean more mosquito-borne diseases worldwide

OK, this paper isn’t particularly calming–but it is timely and relevant. Researchers in PLOS Neglected Tropical Diseases forecast a global expansion and redistribution of mosquito-borne illnesses (especially Zika, dengue, and chikungunya) as climate change ramps up around the world.

Read more on NPRPopular Science, and the Washington Post.

Image courtesy PLoS ONE.

GAINESVILLE, FL – In a new paper published in PLoS ONE today, Dr. Olivier Walther and colleagues produced the first comprehensive mapping of the West African livestock trade network. Their network analysis of more than 42,000 movements from 2013-17 shows that live animals flow through well-defined, long distance trade corridors and that border markets are important hubs in the regional network. The paper was co-authored by Valerie C. Valerio (lead author, UF), Olivier J. Walther (UF), Marjatta Eilittä, Brahima Cissé, Rachata Muneepeerakul (ABE, UF), Gregory A. Kiker (ABE, UF)

Read Network analysis of regional livestock trade in West Africa in PLoS ONE.

Terrestrial Biomes and Significant Woody Vegetation Change at the Municipio level 2000–2010, Mexico. The 4 major biomes in Mexico are: (1) Desert and Xeric Shrubland (DES); (2) tropical and subtropical coniferous forests (CON); (3) tropical and subtropical dry broadleaf forests (TSB); and tropical and subtropical moist broadleaf forests (TSMB). Image courtesy Land Use Policy

New publication in Land Use Policy explores the relationship between demographic and economic changes and forest cover change in Mexico from 2001-2010. In this collaboration between UF Geography’s Sadie J. Ryan and researchers from UCSB and CU Boulder, drivers of sub-national level forest cover change from 2001-2010 – both loss and gain – were explored using landscape modeling. The goal was to understand the roles of environment, economics – e.g. remittances from abroad, (un)employment, education, cattle ownership – and both internal and international migration in forest cover change across the different biomes of Mexico. The influence of sub-national and international migration together are rarely considered in studies of forest cover change, and was found to be important in every biome in Mexico. The relative roles and types of drivers differed by biomes, pointing to the multiple processes involved in forest loss and gain at sub-national levels.

Read Examining the relationship between migration and forest cover change in Mexico from 2001 to 2010 at Land Use Policy.