Categories
Blog Disease Food & Agriculture Global Change Research

Wuhan coronavirus has linkages with wild animals, says GCC affiliate Luis Escobar

[vc_row][vc_column][vc_column_text]From VT News | January 31, 2020

The consumption of wildlife in China may be the main driver of the country’s coronavirus outbreak, says a Virginia Tech expert.

“It’s not surprising that the coronavirus first identified in Wuhan has linkages with animals, especially wildlife,” said wildlife epidemiology expert Luis Escobar. “China has important traditions related to the consumption of wildlife products, which elevates the risks for emerging diseases. While other countries and cities have high population densities and massive amounts of tourists, we do not see epidemics like the SARS or Wuhan coronaviruses that emerged in China.”

Escobar explains that 75 percent of emerging infectious organisms known to be pathogenic to humans have their origin in animals.

Escobar says “a recent study predicts that severe traveler restrictions from and to Wuhan would likely have minor impact on reducing the spread of the epidemic to other regions. Surveillance is very important now for those with and without symptoms to better understand groups at risk.”

As global health authorities work to prevent further spread of the coronavirus, Escobar says this is a great example of how authorities and researchers should respond to epidemics.

“Compared to previous epidemics of emerging illnesses, Chinese authorities and researchers working on the Wuhan coronavirus epidemic have been open. Data associated with the epidemic have been shared broadly and openly, which has allowed for immediate assessments of the plausible origins and potential transmission risks by research teams around the world.”

“For the first time, China shows signs of being serious about banning wildlife trade to reduce emerging disease outbreaks, which is a good indication that authorities are using scientific evidence to prevent new epidemics in the future,” says Escobar.

About Escobar

Luis Escobar is an assistant professor of disease ecology in the Department of Fish and Wildlife Conservation in Virginia Tech’s College of Natural Resources and Environment. His research focuses on the distribution of wildlife diseases and emerging pathogens at global scales. He uses ecological, biogeographic, and modeling approaches for the understanding of diseases spread under diverse land use and climate change conditions. He is particularly interested in global health and One Health. More here.

Interview

To secure an interview with Escobar, contact Shannon Andrea in the media relations office at sandrea@vt.edu or 703-399-9494.

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Categories
Blog Conservation Global Change Research Sustainable Agriculture

GCC affiliate Luis Escobar contributes to international report on health and climate change

[vc_row][vc_column][vc_column_text]From VT News | January 30, 2020

A child born today will experience a world 4 degrees warmer than the pre-industrial average. This seemingly small variable will have significant impacts on global health outcomes in the future.

To understand the scale and breadth of those outcomes and to offer solutions for countries most affected by climate change, The Lancet medical journal has recently published the 2019 Lancet Countdown. This report presents the findings and provides a collaborative perspective from 35 universities, institutions, and agencies on how climate change will influence human health.

Luis Escobar, assistant professor of disease ecology in the College of Natural Resources and Environment and an affiliate of the Global Change Center housed under Virginia Tech’s Fralin Life Sciences Institute, was a contributor to the report.

“The goal of the Lancet Countdown is to have a consortium of universities and institutions tackle a specific problem,” said Escobar, a faculty member in the Department of Fish and Wildlife Conservation. “We want to demonstrate not only the linkages between climate change and human health, but also provide some guidance about what can be done to limit those impacts.”

Escobar’s research focuses on infectious diseases, a human health challenge that is projected to be significantly impacted by climate change. Escobar said that there is a direct correlation between temperature rise and an increase in infectious disease outbreaks. He noted that this year’s Lancet report was able to take a unique approach to considering that correlation for several diseases.

“In previous studies, we’ve worked to see how climate change is going to impact water-borne diseases going forward,” he said. “This time, we looked to the past. We’ve been studying how environmental conditions have changed over the last two decades and how temperature increase is leading to more adverse outcomes.”

The 2019 Lancet Countdown made five key policy recommendations for countries: the reduction of greenhouse gas emissions, a commitment to ending reliance on fossil fuels, investments in infrastructure to support active lifestyles for people, investment in better monitoring of how climate change is impacting health outcomes, and a strengthening of health care systems.

While those solutions represent a global view of the challenges of climate change, Escobar said that it is easy to find local examples of these impacts.

“Virginia is the oyster capital of the Mid-Atlantic region,” he explained. “Oysters filter the water, which makes them potential carriers of water-borne diseases in the food chain. As climate change threatens aquatic ecosystems, there is a risk of an increase in water-borne pathogens that could contaminate oysters, and, in turn, infect people that consume them, which will result in tremendous damage for the oyster industry.”

Escobar said that the Lancet Countdown report reflects the necessity of having a broad vision when it comes to considering the challenges that a warming planet will bring. He also indicated that a goal of the Lancet Countdown is to change the narrative about climate change.

“We should stop talking about whether or not climate change is happening,” he said. “There is overwhelming evidence of climate change and climate change impacts around the world, and it is time to focus our efforts on demanding action from local and federal governments.”

Escobar noted that the Global Change Center plays a crucial role in helping Virginia Tech researchers and students connect local concerns with broader challenges taking place around the world.

“The Global Change Center allows us to develop local research and thinking on a global scale,” he said. “Questions of how climate change can impact the population of salamanders in the Appalachian Mountains, or how rising sea temperatures could affect coastal areas in Virginia can help researchers see the broader picture of climate change. The center, and my department at Virginia Tech, have both been catalysts in helping me position my science on climate change and health in the international discussion.”

— Written by David Fleming

 

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Categories
Accolades News Research Undergraduate Experiential Learning

8 undergraduate students awarded GCC research grants for 2020

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The Global Change Center at Virginia Tech, with support from the Fralin Life Sciences Institute, is proud to sponsor undergraduate students and their research projects that align with our mission for advancing collaborative, interdisciplinary approaches to address critical global changes impacting the environment and society. Supported projects address basic and/or applied aspects of global change science, engineering, social science and the humanities and are sponsored by a GCC Faculty mentor.

This year’s research grant funds total $5,432, spanning 8 projects across 3 departments. Students will present their research findings as a poster at either the VT Experiential Learning Conference (April 2020 or 2021) or the VT Summer Undergraduate Research Symposium (July 2020).

Congratulations to the following students awarded this year’s GCC undergraduate research grants!

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Project Title: Effects of temperature and humidity on the metabolism of nectar in Aedes albopictus and Ae. aegypti mosquitoes

Mosquitoes transmit several pathogens to humans and other animals killing about a million people every year. If females need blood to produce eggs, both females and males feed on plant nectar which enhances their survival and longevity. For this project, we will focus on two invasive mosquito species, Aedes aegypti and Ae. albopictus. These mosquitoes are originally indigenous to the tropics but have now spread around the world (including the US). Global warming has been shown to increase the habitable range of these mosquitoes in part due to raising temperatures. As their geographical range expands it increases their threat to public health. Surprisingly, how environmental factors such as temperature and humidity, in combination with access to nectar sources, affect mosquito population dynamics remain unknown. To fill this knowledge gap, we will first conduct studies on laboratory strains of mosquitoes and quantify their metabolism and digestion on nectar under different environmental conditions using calorimetric assays. Then field work will be conducted in Virginia to assess sugar feeding prevalence in these invasive species. Altogether, these data will shed light on how mosquitoes are utilizing nectar in the field and will inform on the development of new traps to control mosquito populations.

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Project Title: From water chemistry to growth: making sense of the abiotic world of frogs

Many organisms rely on environmental cues to signal when to grow and develop to maximize chances of survival. However, anthropogenic threats, such as climate change, habitat alteration, and water pollution, pose a challenge to many species as it alters their environment. In Spring 2019, we conducted an artificial pond experiment to explore the effects of water temperatures, increased drying rates, and the combination of both on wood frog, ​Lithobates sylvaticus, a​ nd spring peeper, ​Pseudacris crucifer ​tadpoles. We examined how these environmental changes – anticipated to be an effect of climate change – influenced tadpole growth and survival. Analyzing how temperature and drying influence water quality parameters such as pH, dissolved oxygen, temperature, and conductivity may also lead us to a deeper understanding of the mechanistic pathways through which these environmental changes influence tadpole growth and overall survival. This past semester, I examined the significant differences of these parameters between treatments; however, we have yet to analyze chlorophyll-a to determine how algae, the tadpoles food source, is affected. I propose to expand this project by extracting chlorophyll-a from algae samples collected during the experiment. Analyzing this information along with the other water chemistry parameters will provide a detailed understanding of the tadpoles’ abiotic environment under warming and drying conditions and how this ultimately affects their growth and survival.

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Project Title: Wetlands in a Warming World: The Importance of Wetlands in Headwater Carbon Cycling

Wetlands are productive ecosystems that play an important role in carbon cycling. However, wetland contributions to landscape CO2 and CH4 emissions are often overlooked and the role of wetlands in producing carbon emissions remains a critical gap in carbon budgets. To estimate current and future emissions from wetlands at Coweeta, NC and Jefferson National Forest, VA, I will measure CH4 and CO2 emitted from each wetland to the atmosphere and conduct laboratory warming experiments to calculate microbial organic carbon (OC) uptake and CO2 production. I will use a flux chamber attached to a portable greenhouse gas analyzer to get real-time estimates of CO2 and CH4 fluxes across each wetland. I will develop and test an improved flux chamber design to allow for more accurate and abundant flux measurements. To test how microbial uptake of OC (and subsequent CO2 and CH4 production) may change with increasing temperature, I will incubate filtered and microbially-inoculated wetland water at ambient and +3°C in triplicate bioassays with ambient and amended (+CNP) nutrients. I predict that increased temperature increases OC uptake and CH4 and CO2 production. This experiment will provide insight into the current and future role of wetlands in carbon cycling with changes in temperature.

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Project Title: Development of Poison Ivy Clonal Lines Differentiated for High or Low Urushiol Levels: Genetic Resources for Ecological Studies in Urushiol Chemical Ecology

Poison ivy seedlings grown in vitro produce markedly different steady state urushiol accumulation levels, apparently due to underlying genetic factors. I will leverage these findings to develop poison ivy clonal lines with varying urushiol levels. I have developed an experiment to germinate 50 poison ivy seeds collected from each of four states: Michigan, Iowa, Virginia, and Texas. I will harvest the first true leaf pair from each seedling and assay total-urushiol levels by Gas Chromatograph-Mass Spectrometry. From these results, I will choose from each accession the four plants with the highest urushiol levels and the four with the lowest urushiol levels. This subset of plants from each state will be transplanted to pots with potting mix and grown in a Washington Street greenhouse with supplemental lighting and automated watering. There, they will produce stolons with genetically-identical daughter plants. These clones will again be assayed for total urushiol levels to confirm the stability of the high and low urushiol accumulation traits. The long term goal of this experiment is to transfer these plants to Kentland Farm this summer and quantify whether urushiol actually reduces herbivory by extant native fauna.

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Project Title: In Cold Blood: Understanding The Role Mosquitoes Play in Pathogen Transmission to Frogs

Amphibian extinction is now happening at an unprecedented rate in part due to alteration of local ecosystems, climate change and diseases. Among diseases, emerging viral pathogens, Ranaviruses, as well as Batrachochytrium dendrobatidis, a fungus that infects the skin, are greatly affecting amphibian populations, most notably frogs. This combination of habitat loss, rising temperatures and diseases has made this issue complicated and multifaceted. This project focuses on the role that Culex territans, a mosquito that feeds primarily on cold-blooded animals including frogs and snakes, plays in disease transmission in amphibians in Virginia. Cx. territans is a known pathogenic transmission vector, capable of spreading parasitic trypanosomes to various species of amphibians. We hypothesized that Cx. territans may also be capable of spreading the aforementioned viral and fungal diseases. To test for this hypothesis, we will screen blood fed Cx. territans from local areas for pathogens during plaque assays and PCR with specific primers. Data emerging from this project will help us better understand the complex dynamics seen between amphibian extinction, transmission of pathogens, and host-vector relationships.

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Project Title: CRISPR Genome Editing of Hairy Roots to Identify and Confirm Poison Ivy Urushiol Biosynthetic Genes

Urushiol is produced in poison ivy and causes allergic dermatitis in humans. Poison ivy is projected to become more allergenic with higher atmospheric CO2 levels associated with climate change. Urushiol’s primary ecological purpose is currently unknown because it is uninvestigated. Moreover, none of the urushiol biosynthetic genes and enzymes have been previously validated. A previous Jelesko Lab GCC UG Research Awardee Nye Lott successfully developed an Agrobacterium rhizogenes-based poison ivy stable transformation system to produce transgenic poison ivy hairy roots containing CRISPR-Cas9 gene editing plasmids that target poison ivy PolyKetide Sythase-like (PKS-like) genes proposed to be involved in the first step in urushiol biosynthesis. My research project will follow on Nye’s A. rhizogenes strains containing PKS-specific CRISPR-Cas9 T-DNA binary plasmids to produce transgenic poison ivy hairy root lines with mutated PKS genes. The resulting transgenic hairy root lines will be evaluated for urushiol levels using GC-MS. If they show a decrease in urushiol levels, then the hairy roots lines will be sequenced for mutations in the targeted PKS genes. Hairy root lines with mutated specific PKS genes that result in dramatically less urushiol levels will be strong evidence that a specific PKS gene is necessary for urushiol biosynthesis.

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Project Title: Identification of Urushiol Biosynthetic Genes by Differential Gene Expression in Tissues with Different Urushiol Accumulation Levels

Poison Ivy plants produce urushiol, the compound that causes the characteristic allergic contact dermatitis symptoms in humans. The main goal of this project is to identify genes that are likely responsible for producing urushiol in poison ivy. In order to accomplish this goal, we will use a comparative transcriptomics approach between poison ivy tissues that accumulate markedly different amounts of urushiol. Preliminary work by a former GCC Undergraduate Awardee Nye Lott, suggested that poison ivy drupes accumulated between 8 to 45-fold more urushiol than the adjacent leaves. The lab has 20 matched pairs of poison ivy drupes with adjacent leaf material available for my experiments. I will extract total RNA from five pairs of matched poison ivy drupes and their corresponding adjacent leaves showing maximum differential urushiol accumulation levels. These 10 total RNA samples will be sent to NovoGene for library preparation and Illumina NextGen sequencing (RNA-seq). The collaborating Haak laboratory will perform the RNAseq analyses using their unpublished draft poison ivy whole genome to quantify and identify differentially expressed genes. I will subsequently sort through the differentially expressed poison ivy genes to identify specific predicted enzymatic activities involved in urushiol biosynthesis. This informatic resource will be used for many studies.

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Project Title: The Effect of pH and symbiont density on outcomes in a cleaning symbiosis

For over 20 years, the Brown Lab has studied the context-dependent cleaning symbiosis between crayfish and ecosymbiotic branchiobdellidan annelids. These worms act as cleaners for the crayfish, increasing the hosts’ fitness. However, the benefits from the symbiosis for the host are context dependent, and can shift from mutualism to parasitism under some conditions including high symbiont densities. However, what isn’t currently known is whether the symbiotic outcome will change under conditions of host stress. Given that changes in pH are common stressors in aquatic systems, it makes sense to examine how the outcomes of the symbiosis will change with this change in context. I will use varying levels of the branchiobdellidan, Cambarincola ingens crossed with a pH gradient in an aquarium experiment using previously successful methodologies. Response variables will be growth and survivorship of the host crayfish. We have already run preliminary versions of this experiment and produced results that suggest that intermediate densities of C. ingens will increase growth and survivorship at pH levels that depart from known norms. Lessons learned from that preliminary experiment will increase our probability of success with the proposed experiment.

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Categories
Blog Climate Change Conservation Disease Drinking water Evolution Faculty Spotlight Food & Agriculture Global Change Research

The GCC welcomes seven new faculty affiliates

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Meet our newest faculty affiliates:

 

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Dr. Cully Hession

Professor, Department of Biological Systems Engineering

Research focus: His lab focuses stream channel structure and sediment dynamics, influence of human activities on streams, techniques for measuring and improving in-stream habitat, and development of technologies and strategies for successful stream restoration.  Current research focuses on using drones and drone-based lidar to map riverscapes and tracer studies to better understand sediment transport and fate. Dr. Hession is also PI/co-Director of an interdisciplinary research and extension training program called “Training Future Leaders to Solve Resource Challenges at the Confluence of Water and Society.”[/vc_column_text][/vc_column][/vc_row][vc_row][vc_column][vc_separator style=”shadow”][/vc_column][/vc_row][vc_row][vc_column width=”1/2″][vc_single_image image=”47579″ img_size=”275×355″ style=”vc_box_border”][/vc_column][vc_column width=”1/2″][vc_column_text]

Dr. Florian Zach

Assistant Professor, Deparment of Hospitality & Tourism Management

Research interests:  Dr. Zach is interested in strategic issues that support the sustainable development of tourism destinations. He has investigated the inter-organizational collaboration and networks to understand how destination stakeholders collectively develop tourism innovations. Additionally, he works with colleagues to understand human-computer interaction issues stemming from the use of cutting-edge technologies in the context of tourism. Current projects include exploring the effects of summer adventure parks built by ski resorts in the Austrian Alps as a response to shorter winter and longer summer seasons and also the impacts of the 2018 Florida Red Tide on hotel & short-term rentals (Airbnb & similar).[/vc_column_text][/vc_column][/vc_row][vc_row][vc_column][vc_separator style=”shadow”][/vc_column][/vc_row][vc_row][vc_column width=”1/2″][vc_single_image image=”47688″ img_size=”275×355″ style=”vc_box_border”][/vc_column][vc_column width=”1/2″][vc_column_text]

Dr. J. Leighton Reid

Assistant Professor, School of Plant & Environmental Sciences

Research interests: Dr. Reid’s research interests encompass tropical forest restoration in Latin America and Madagascar as well as temperate forest, woodland, and grassland restoration in the eastern United States. Specifically, he investigates how local restoration interventions interact with their surrounding landscape to affect biodiversity recovery, how keystone plant species can be used to catalyze ecological succession, why some restored ecosystems persist much longer than others, and what soil and environmental factors limit the recolonization of rare plants in regenerating ecosystems.[/vc_column_text][/vc_column][/vc_row][vc_row][vc_column][vc_separator style=”shadow”][/vc_column][/vc_row][vc_row][vc_column width=”1/2″][vc_single_image image=”47595″ img_size=”275×355″ style=”vc_box_border”][/vc_column][vc_column width=”1/2″][vc_column_text]

Dr. Rachel Reid

Research Scientist, Department of Geosciences

Research interests: Dr. Reid is a paleoecologist interested in how disturbances, such as climate and environmental change, impact species, ecosystems, and their interactions over a range of timescales. As a Research Scientist at Virginia Tech, Dr. Reid runs the Stable Isotope Laboratory.[/vc_column_text][/vc_column][/vc_row][vc_row][vc_column][vc_separator style=”shadow”][/vc_column][/vc_row][vc_row][vc_column width=”1/2″][vc_single_image image=”47396″ img_size=”275×355″ style=”vc_box_border”][/vc_column][vc_column width=”1/2″][vc_column_text]

Dr. Theo Lim

Assistant Professor, Department of Urban Affairs & Environmental Planning

Research interests: Dr. Lim’s research focuses on the environmental planning of linked land, water, infrastructure, and social systems. His interests include urban hydrology, distributed stormwater practices, community green infrastructure, energy planning in agricultural and rural settings, land development impacts on the hydrological cycle, and applications of data science in urban & environmental planning.[/vc_column_text][/vc_column][/vc_row][vc_row][vc_column][vc_separator style=”shadow”][/vc_column][/vc_row][vc_row][vc_column width=”1/2″][vc_single_image image=”47637″ img_size=”275×355″ style=”vc_box_border”][/vc_column][vc_column width=”1/2″][vc_column_text]

Dr. Ben Gill

Associate Professor, Department of Geosciences

Research interests: Dr. Gill specializes in reconstructing the present and past chemical cycles on our planet. He leads the Biogeochemistry Laboratory Group at Virginia Tech. The main research focus of his group concerns understanding the connections between major changes in the environment (oxygenation/deoxygenation oceans, climatic warming and cooling, etc.) and major events in the history of life (originations, diversifications and mass extinctions).[/vc_column_text][/vc_column][/vc_row][vc_row][vc_column][vc_separator style=”shadow”][/vc_column][/vc_row][vc_row][vc_column width=”1/2″][vc_single_image image=”47465″ img_size=”275×355″ style=”vc_box_border”][/vc_column][vc_column width=”1/2″][vc_column_text]

Dr. James Weger-Lucarelli

Research Assistant Professor, Department of Biomedical Sciences & Pathology

Research interests: Dr. Weger-Lucarelli’s research focuses on understanding viral and host determinants that mediate disease severity, transmission, evolution, and protection against mosquito-borne viruses. The Weger-Lucarelli lab uses molecular, virological, and computational methods to study these interactions, with the goal to recognize and study emerging viral threats before they product massive outbreaks.  He is also working to produce innovative vaccines to prevent mosquito-borne viral disease.[/vc_column_text][/vc_column][/vc_row][vc_row][vc_column][vc_separator style=”shadow” border_width=”5″][/vc_column][/vc_row]

Categories
Accolades News Undergraduate Experiential Learning

2020 GCC Science Policy Fellowship awarded to Kerry Desmond

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January 27, 2020

 

The Global Change Center recently awarded the 2020 Undergraduate Science Policy Fellowship to Kerry Desmond to attend the Washington Semester Program during summer semester this year.  Ms. Desmond is the seventh student to receive this award.

Kerry is a junior majoring in Civil Engineering with a minor in Green Engineering, with aspirations to pursue graduate studies in Environmental Engineering and to become a public health engineer. Through this fellowship and the Washington Semester Program this summer, she intends to intern with the US Environmental Protection Agency, and is eager to gain experience in the policy sphere of this government agency.

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“I’m drawn to public health engineering for the opportunity to work with citizens, policy makers, engineers and scientists to develop solutions to environmental issues.”

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During the winter semester of 2019-20, Kerry traveled to Rwanda as part of the VT international service-learning course Global Design and Construction. She worked as part of an interdisciplinary team and alongside local professionals in Rilima, Rwanda to design parts of a water sanitation system for a community that lacks access to clean water. In addition to her normal coursework, Kerry currently spends additional time as a calculus tutor and a peer mentor for the Center for the Enhancement of Engineering Diversity (CEED) at Virginia Tech.

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The School of Public and International Affairs (SPIA) at Virginia Tech offers the Washington Semester Program to all undergraduate students, regardless of major. The program provides a unique 11-week immersion into work experience within the nation’s capital. Students work on challenging science policy issues that shape communities locally and nationally while obtaining academic credit.

The Global Change Center (GCC) offers competitive fellowships to undergraduate students to cover the cost of in-state tuition, housing and fees to attend the Washington Semester Program. You can read more about this program here.

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Categories
Blog Disease Faculty Spotlight Food & Agriculture Global Change Research

Researchers combine technologies to resolve plant pathogen genomes

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From VT News | January 27, 2020

With the help of new genomic sequencing and assembly tools, plant scientists can learn more about the function and evolution of highly destructive plant pathogens that refuse to be tamed by fungicides, antibacterial, and antivirals.

But using these genomic technologies is not an easy task. The process not only requires time, but also money. In a recent paper published in Molecular Plant-Microbe Interactions, David Haak and John McDowell, from the School of Plant and Environmental Sciences in the College of Agriculture and Life Sciences, proved that these costly processes can be improved by combining two generations of technology.

What used to take a year-and-a-half and $2 million to complete can now be done within nine days for $1,000 – and the technology performs with greater accuracy and field applicability than ever before.

“Think of it as analogous to a library full of books that are two-thirds or three-quarters completely written. What David has developed is a technology through which he could go to the library and finish those books really quickly and really accurately for a really low price point,” said McDowell, the J. B. Stroobants Professor of Biotechnology.

Before this project began, Haak, an assistant professor and affiliate with the Global Change Center, and his team had been trying to prove that it was possible to generate a completed assembly in a relatively short period of time – but they needed a relatively complex genome to test their theory. A few hallway conversations later, Haak and his students joined forces with McDowell and his team to unravel the complex genome of Phytophthora capsici.

“P. capsici is a representative of a really destructive group of pathogens. Its evolutionary cousin is the pathogen that caused the Irish Potato Famine in the 19th century, which killed at least a million people and caused at least a million more to relocate. These pathogens are still causing difficulty today,” said McDowell. “One of the reasons for that is because their genomes are exquisitely configured to enable them to evolve ways around interventions that farmers put in place in the field.”

A microscopic image of a large root, which divides the photo into two diagonal sections. On each side of the root, there are many P. capsici spores, which resemble lollipops.
An image of P. capsici spores that are attached to an Arabidopsis root and initiating the process of penetration. John Herlihy for Virginia Tech.

 

In this species of pathogen, virulence genes are often located in gene-poor regions interspersed with repetitive regions within the genome. These repetitive regions are prone to rapid evolution and are the key to understanding its pathogenicity, or its ability to cause disease.

To better understand the inner workings of P. capsici, scientists must extract a DNA sample from the pathogen and perform genetic sequencing. Genetic sequencing is a process that determines the order of the nitrogenous bases – or the As, Cs, Gs, and Ts – that make up an organism’s DNA.

However, genomic sequencing can read only a certain amount of DNA segments at one time. Scientists must then take these small sequences and re-assemble them so that the DNA is presented in the right order.

“Generating the sequence data, isn’t really the problem. It’s assembling that data. It’s putting together the sequence information in the right order. The repeat-rich regions make us sometimes put two genes together that don’t belong together or separate a full gene into two halves because we think a repeat goes right in the middle,” said Haak.

All in all, resolving the genome of an organism requires powerful technology – and patience. And although bioinformatic technology has made great leaps and bounds over the years, each generation isn’t necessarily better than the last. Each generation of technology has its own forte.

Using first-generation technology, it would take one-and-a-half years and around $2 million to sequence the P. capsici genome. But with Haak’s technology, it will take just nine days from DNA extraction to a polished assembly – and only cost $1,000. To make things even better, this technology will be able to sequence 100,000 times more information in roughly 1.5 percent of the time. And the technology is the size of a thumb drive.

Second-generation technology performs short read assemblies, which are extremely accurate; however, they do not span across repetitive regions well. And when scientists must go back and reassemble the genome, there is a reasonable chance of error.

“What happens with the short reads is that we don’t know where those repeats begin and end, so we don’t know where to put them to arrange them appropriately,” said Haak.

Oxford Nanopore Technologies (ONT) MinION, or long-read sequencing, is the third generation of sequencing technology, but it has the opposite problem: it is far less accurate but it can give them a better overall picture by spanning across these critical repetitive regions.

Haak and his team combined these second- and third-generation technologies to exploit the accuracy of the former with the ability to span the repeated regions of the latter. It’s the best of both worlds.

Upon using this new technology on P. capsici, Haak and McDowell got quite a shock. Haak and his group revealed that the genome is 1.5 times bigger than previously thought.

“That’s 30 percent of the genome that we didn’t even know existed, and that particular fraction of the genome is, undoubtedly, enriched with the sorts of genes that really make a difference in helping us understand what interacts with the plant or responds to fungicides or farmers’ spray,” said McDowell.

For Haak, the most exciting thing about the results of this paper is its proof-of-concept.

“We have something called the sequence archive database, which is full of all sorts of short-read sequences. We can actually leverage all of that existing data with this newer technology to be able to produce more genomes of this quality,” said Haak.

Haak’s new generation of technology is expected to revolutionize the way in which scientists collect genomic data. With their newly acquired, affordable, real-time data, scientists will be able to improve previous assemblies and quickly generate new ones that they can share to the sequence archives database. On a grander scale, this technology will advance the field of plant genomics and the worldwide effort to save the crop industry from destructive pathogens.

Now that Haak and McDowell have an estimated 97 percent of the genome for P. capsici in their grasps, they plan to use this information as supporting data for two new grant proposals. One proposal will focus on tomato and soybean diseases caused by pathogens of the Phytophthora group and the other proposal will focus on lavender, yet another victim of Phytophthora.

For Haak, this project was special because it was supported by a grant from the Fralin Life Sciences Institute at Virginia Tech with funds allocated to support the Global Systems Science Destination Area.

McDowell added, “I think it speaks to the environment here at Virginia Tech, promoted by Fralin, that enables these sorts of collaborations to come together and get some critical support in the early phase.”

– Written by Kendall Daniels

 

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Accolades Blog Faculty Spotlight Global Change Invasive Species Research Science Communication Student Spotlight

Jacob Barney and Vasiliy Lakoba win awards at the Northeastern Weed Science Society conference

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GCC affiliate Jacob Barney was awarded the Outstanding Educator Award from the Northeastern Weed Science Society at their annual meeting on January 7, 2020 in Philadelphia, PA. The Outstanding Educator Award was established to recognize outstanding contributions to outreach education or resident instruction in Weed Science and weed management.

IGC fellow Vasiliy Lakoba, PhD student with Jacob Barney, was awarded Honorable Mention for his presentation Ecotypic stress response differences are driven by home climate and habitat at the Northeastern Weed Science Society at their annual meeting on January 8, 2020 in Philadelphia, PA.

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Blog Conservation Faculty Spotlight Global Change Invasive Species News Research

Scott Salom’s research on biological control of the hemlock wooly adelgid highlighted in Science

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January 20, 2020

GCC affiliate Dr. Scott Salom is a professor in the department of Entomology at Virginia Tech whose research focuses on forest entomology and biological control. For more than two decades, he has studied tactics and strategies to manage the damaging hemlock wooly adelgid.  These tiny insects, native to Japan, suck the sugars from hemlock needles, eventually killing the trees.  Salom has been testing whether a predatory beetle might aid in controlling the wooly adelgid population; his research on this was recently highlighted by Science. 

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Blog Conservation Global Change Research Sustainable Agriculture

New research finds ranchers consider diverse factors in managing their land

[vc_row][vc_column][vc_column_text]From VT News | January 14, 2020

Wetlands in the Intermountain West, a region nestled between the Rocky Mountains, the Cascade Range, and the Sierra Nevada, are home to a diverse range of flora and fauna. Wetlands may only make up two percent of the region, but 80 percent of wildlife rely on the rich habitat they provide. The majority of these wetlands are located on private ranchlands. While the persistence of these “working wetlands” depends on the management decisions of ranchers, their perspectives are often missing from conservation and policy-making discussions.

In a new study published in Rangeland Ecology and Management, Ashley Dayer, an assistant professor in the Department of Fish and Wildlife Conservation in the College of Natural Resources and Environment at Virginia Tech, explores the diverse factors that influence how ranchers manage their land.

In collaboration with the Intermountain West Joint Venture, an organization committed to bird habitat conservation by fostering public-private partnerships, and the University of Montana, Dayer and her graduate student Mary Sketch (M.S. ’18)  hosted two landowner-listening workshops, one in southern Oregon and another in southwestern Wyoming, and invited various landowners and conservation professionals to encourage dialogue between the two parties. Partners for Conservation, a landowner-led conservation organization, played a key role in successful implementation of the workshops.

“In order to have effective conservation in the west, where ranchers own huge tracts of land, the conservation community is keen to work together with them. Ranchers can make choices to manage their land for the benefits of wildlife or they can make choices that don’t prioritize wildlife,” said Dayer, an affiliated faculty member of the Global Change Center, housed within the Fralin Life Sciences Institute. “We aimed to facilitate a better understanding of how conservation professionals could work with ranchers toward conservation and wildlife management goals.”

The relationships between conservationists and ranchers can be complicated. People are quick to assume that ranchers are solely concerned with profit, but Virginia Tech researchers find that ranchers’ decisions are more complex than that. This complexity needs to be taken into consideration when developing programs and policies to foster private lands conservation.

“The workshops created an open, trusting space where there was social learning and social exchange happening. It was important for ranchers to know the researchers and the conservation professionals alike were there to hear them,” said Mary Sketch, who was the lead author on this paper and another previously published in Society and Natural Resources on the method itself.

Dayer and Sketch evaluated the complex decision-making process of how ranchers choose to manage their land, more specifically how they choose to irrigate their land and why. They found that various reasons go into deciding how land is managed — not just money.

“Our project was able to add nuance to that understanding; there is a lot more to it,” said co-author Alex Metcalf, a social scientist and assistant professor in the W.A. Franke College of Forestry and Conservation at the University of Montana. “Yes, ranchers have to meet the bottom line because they have to make sure they have food on the table, but other concerns and considerations are at play in the choices that they make for their lands.”

This study specifically focused on choices about flood irrigation — a traditional method involving complex ditch systems that spread water across a field, recharging areas once sustained by natural flooding. When the water flows from the ditches, saturates the field, and seeps into the groundwater, it provides forage for cattle to graze on while providing rich habitat for migrating and breeding waterbirds, like ducks and cranes, as well as sage-grouse, an iconic ground-dwelling bird in decline.

“Flood irrigation is often vilified for not being water efficient. The numbers don’t always add up when it comes to saving water because there’s so much more in the game of land management and conservation, like creating wildlife habitat. This traditional definition of efficiency doesn’t grasp that social-ecological complexity,” Sketch said. “Our work suggests an expanded definition that considers how flood irrigation provides bird habitat on working wet meadows, recharges the groundwater for communities downstream, creates in-stream flow for fish, and keeps ranchers ranching.”

Local ranchers speak with partners
Local ranchers speak with partners. Photo courtesy of Intermountain West Joint Venture.

Ranchers described the factors that either help or hinder the use of flood irrigation on private lands. The study identified cultural considerations as a key enabler for continuing flood irrigation. “Ranchers have strong ties with the ranching lifestyle, so many choose to continue flood irrigation because of its history and their personal connection to it,” explained Sketch. “It’s something they do every year, the generation of ranchers before them did it, and want to maintain that tradition.”

“What stands out to me in this work is that there are a group of ranchers committed to the future of their land. They rely on that land for their livelihood; they’re closely tied to it; they spend every day outside. It’s something that they’re very passionate about,” Dayer said. “I think that’s just a critical thing for the majority of the U.S. public living far from ranches to keep in mind — our food isn’t just coming from grocery stores. It’s coming from people who are making choices about how land is used and whether to contribute to conservation.”

Despite the commitment of ranchers to their land, nearly half of all U.S. ranches are sold every decade and recruitment of younger generations into the ranching lifestyle has declined. Most of these once-open spaces have been lost to subdivisions and other development. Land conversion not only erodes the sense of community and cultural identity among ranchers, it also eliminates important wildlife habitat.

To keep ranches both environmentally and economically sustainable, both workshops highlighted key areas where conservation professionals can increase rancher engagement and ensure working wetlands continue to benefit both landowners and wildlife. Ranchers identified partnerships and open communications with conservation professionals and policymakers as critical to maintaining successful operations in addition to effective, long-lasting conservation practices. Central to strong partnerships is building trust and “honest people sitting around, getting over their biases, their agendas, and listening to one another,” said one rancher.

The Intermountain West Joint Venture has a long history of working alongside landowners and conservationists and has become trusted in the region. Their connections, experiences, and on-the-ground work proved valuable in executing the research. As a result, Dayer and Sketch were better able to understand ranchers’ experiences and perspectives. The joint venture is also now playing a critical role in ensuring the results of this study are used.

“This research is ground-breaking in that it helps conservation professionals understand the social context of agricultural irrigation decision-making in the West,” said Dave Smith, Intermountain West Joint Venture coordinator. “The findings will enable the conservation community to increasingly support agricultural irrigators in continuing to provide vital habitat for wetland-dependent birds on working lands.”

Listening turned out to be an effective conservation tool, and Dayer and Sketch hope that this work continues to change how conservation professionals and ranchers work together.

—   Written by Rasha Aridi

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Accolades Air Blog Global Change Research

Linsey Marr appointed to National Academies’ Board on Environmental Studies and Toxicology

[vc_row][vc_column][vc_column_text]From VT News | January 14, 2020

Linsey Marr, the Charles P. Lunsford professor in the Charles E. Via Jr. Department of Civil and Environmental Engineering, has been appointed to the National Academies of Sciences, Engineering, and Medicine Board on Environmental Studies and Toxicology. The board advises the government about environmental decision-making and public understanding of environmental issues.

The board is the principal study unit on pollution problems affecting human health and the environment with the mission to provide the nation with “independent, objective advice and dialog on matters related to the impacts of human activities and environmental exposures on environmental quality and human health.”

Linsey Marr outside holding an air quality measuring device.

“I’m passionate about research to protect human and environmental health, so I am honored by this opportunity to serve the country by sharing my interdisciplinary expertise on air pollutants,” said Marr. “Air pollution is recognized as the biggest environmental threat to public health.”

Marr’s research focuses on characterizing the emissions, fate, and transport of air pollutants in order to provide the scientific basis for improving air quality and health.

Lindsey Marr at dawn standing outside on the Virginia Tech running track, wearing a yellow jacket.

Marr has garnered other recognitions over the past year including the Excellence in Teaching Award by the Virginia Tech Center for Excellence in Teaching and Learning and elected Fellow of the International Society for Indoor Air Quality and Climate.

She came to Virginia Tech in 2003 after earning her bachelor’s in engineering science from Harvard and her doctorate from the University of California at Berkeley.

Written by Courtney Sakry

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