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# Maine EPSCoR
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## An Introduction to the Maine Center for Genetics in the Environment
October 5, 2023
*By Evan Bartow, Writing Intern*
Focused on bringing together researchers across multiple disciplines, the Maine Center for Genetics in the Environment (MGCE) has worked to develop and energize Maine’s genetic research community. MCGE was founded in 2019 in order to further advance the type of research being generated by the $20 million NSF EPSCOR RII Track-1 Molecule to Ecosystem: Environmental DNA as a Nexus of Coastal Ecosystem Sustainability for Maine (Maine-eDNA) project.
Director Michael Kinnison’s vision for MGCE is to make Maine, “A national leader in transformative environmental genetic research, innovation, outreach, and training for the sustainability and wellbeing of natural and human ecosystems and the people that depend on them.” While based at the University of Maine (UMaine), MCGE supports environmental DNA (eDNA) research across the state and throughout a wide range of disciplines that links the research conducted on natural resources, agriculture, public health, and environmental systems.
Allison Gardner
Allison Garnder (Associate Professor of Medical Entomology at UMaine) is part of a collaborative research project with MCGE examining the applications of eDNA in mosquito research. As a medical entomologist, the majority of Gardner’s research in Maine focuses on the distribution of disease vector species that are of public health concern, namely mosquitos and ticks.
With MCGE, Garnder focuses on the study of mosquitoes and their larval stages. Gardner explained that “the goal of my current research is to develop an eDNA system to detect mosquitoes in their aquatic habitat.” Mosquitos have a four-stage life cycle which consists of an egg, larvae, pupil, and adult stage. The juvenile stages (the first three stages) occur in an aquatic habitat, while the adult stage takes place in a terrestrial environment. Standing water in artificial containers, rivers, streams, lakes, and ponds, are all examples of aquatic habitats that mosquitoes tend to occupy, and most human interactions will occur in their final adult stage.
To study disease vector species, most entomologists develop methods to conduct surveillance. Gardner explained that, “Mosquito surveillance in general is of interest because there is a strong correlation between the abundance of disease vectors and the likelihood of disease occurring in human populations.” Some invasive species of mosquitoes that occur in New York and southern New England are of particular concern as these species begin to migrate northward, making the process of mosquito surveillance more important than ever. The introduction of new invasive species will elevate the level of public health concern as new diseases and new species are introduced into the northern population.
When conducting surveillance, previous research has focused on trapping adult mosquitoes due to their higher level of human interaction. However, the process of trapping an adult mosquito can be laborious and expensive due to the difficulties in catching and identifying the species of mosquito. Hoping to reduce the challenges associated with mosquito surveillance, Gardner is testing the application of eDNA collection to the study of juvenile mosquitos. If researchers are able to detect the presence of juvenile mosquitos, it would simplify the process of applying insecticides or control interventions to aquatic habitats.
Gardner examines the use of eDNA tools by collecting water samples from artificial containers, which were then infused with a nutrient solution that attracts mosquitoes. To test the effectiveness of eDNA collection, Gardner placed a set amount of mosquito eggs in some containers to see the minimum number of eggs that could be detected. Hoping to determine the density and time of incubation that mosquito eggs need for eDNA detection, the results of Gardner’s research will help determine the best techniques to maximize mosquito eDNA yield.
Currently processing the results of the study, Gardner is already beginning to see the potential future implications of her research. Due to the large public health concern about disease-carrying insects, the development of optimal eDNA collection methodologies will improve future mosquito surveillance and mitigate the spread of disease. Gardner believes that development of eDNA collection techniques can potentially be expanded to other disease carrying insects such as ticks. The application of eDNA research in the study of disease vector species is a new area of research with many future opportunities that will soon be explorable.
Gardner explained that “MCGE has opened her eyes and interest into this field.” By collaborating with MCGE, many potential opportunities for research became available for herself and the students in her lab. The use of eDNA in medical entomology is a relatively new area of research with many future opportunities and pathways that are available through MCGE.
“I have really enjoyed the collaboration with MCGE because I have the freedom to name my crazy ideas and have a realistic conversation about how these might be possible,” Gardner explained. “MCGE is very open-minded about the possibilities of research that can be accomplished using genetic techniques. The directors of MCGE have a huge wealth of knowledge and information about ways that I can think about problems using a different approach.” Looking to the future, Gardner plans to continue to collaborate with MCGE due to their plethora of knowledge on environmental genetics, supportive atmosphere, and desire to develop new research methodologies.
Gardner’s work with MCGE is just one example of how the center is making a difference in environmental research, as MCGE focuses on pushing the boundaries of current genetics research and expanding the capabilities of environmental geneticists. Covering a wide range of topics, MCGE has facilitated research for both marine and terrestrial environments that include species of all kinds.
One of the main goals of MCGE above all else is to ensure the evolution of genetic research in Maine ecosystems to guarantee better health conditions, as well as providing researchers an environment where societal and ecosystem needs are met. Micheal Kinnison stated, “Our goal is to leverage environmental genetics to benefit people from all walks of life, communities, and industries, including those that have historically lacked access to genetics, genomics, and evolutionary resources, or even been disadvantaged by their misapplications.”
As eDNA and genetics research continues to grow throughout the state of Maine, MCGE will continue to lead the way through their new research area. The development of this organization has expanded the opportunities available for researchers, created a national leader in environmental genetic research, and developed a growing number of collaborative partnerships.
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5717 Corbett Hall, Room 444
Orono, ME
04469
Tel: 207.581.3312
Fax: 207.581.9487
maine.epscor@maine.edu
University of Maine |
Orono, ME 04469
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## Genomic Architecture: RNA research of tidal marsh sparrows under the influence of environmental stressors
*By Stefania Irene Marthakis and Colin Gallagher, Media Intern*
In the field of RNA (ribonucleic acid) research, the NSF EPSCoR RII Track-2 grant, GECO (Genomic Ecology of Coastal Organisms: A Systems-Based Research and Training Program in Genome-Phenome Relationships in the Wild) has made significant research progress in understanding the interaction and differences in genotypes and phenotypes. More specifically, GECO’s research has examined similarities and differences in the genes that code for microRNAs (miRNAs), small RNAs that regulate other genes, among various species of sparrows in saltmarsh (a.k.a. tidal marsh) environments. These RNA molecules are isolated and  sequenced (a method used to discover the exact order of the four nucleotides that make up all RNA molecules in a cell) in large quantities and then analyzed.
Kayla Barton is a Ph.D. candidate of Biochemistry and Molecular Biology at the University of Maine (UMaine). Studying under Benjamin King (UMaine Associate Professor of Bioinformatics), Barton’s research role has involved characterizing and annotating miRNAs of tidal marsh sparrows in order to understand differences in genetic structure.
Ben King and Kayla Barton run samples in lab.
Advances in sequencing and bioinformatics allow for rapid characterization of genomes that include both coding and non-coding genes. Coding genes are transcribed into RNA that are then translated in proteins which have important functions in different tissues. Non-coding genes are transcribed into RNA and these RNA molecules go on to regulate the function of other genes. RNAs and miRNAs (endogenous, small non-coding RNA) in the human body are able to regulate the messenger RNAs (mRNAs), which encode protein. MiRNAs are either perfectly or partially complementary to mRNAs. If perfectly complementary, miRNA will cleave the mRNA, rendering it useless. If partially complementary, miRNA will block the translation of the mRNA.
“I like to describe it as a bakery,” Barton said. “Each cell in your body is a bakery; your proteins are all different types of pastries that fill certain needs. You have the recipes for those pastries, which is your genome. Then you have the bakers, who are your messenger RNAs. And finally, you have the bakery managers, who are the microRNAs that tell the bakers (messenger RNAs) what they can and can’t make.”
GECO’s research hopes to address and answer challenges and objectives within the field of genomics, such as studying how variation in gene expression leads to phenotypic plasticity. The non-coding RNA team researches the function of non-protein coding genes and seeks to characterize genetic variation in these regulatory genes across their focal sparrow species (animals that provide an essential ecological function).
Barton explained, “We sequence miRNA from Saltmarsh, Savannah, and Nelson’s Sparrows and then determine how the complements of miRNAs compare across these species. Are miRNAs expressed in tidal marsh sparrows different from more inland species? And if so, which genes do those miRNAs regulate?”
When analyzing the sequence data, Barton utilizes a variety of software tools, most importantly miRDeep2, which can predict miRNAs. This software runs on High Performance Computing (HPC) clusters that allow the team to analyze the sequence data. Barton then uses another software, BLAST, to align these predicted miRNAs to known miRNAs, allowing her to annotate known and potentially novel miRNAs in different sparrow species. “These are complex workflows that require a lot of technical and programming skills combined with biological knowledge,” King stated. “Barton has the right combination of skills for this challenging project.”
Barton has also helped design an important genetic analysis tool for the GECO team that will be used to simultaneously sequence about 1,000 regions in the genomes of hundreds of individual sparrows. GECO is creating a “Genotyping by Thousands sequencing” (GT-seq) panel that will allow the team to inexpensively find differences in about 1,000 genes that the team has carefully selected. These genes include the miRNAs that Barton has annotated in the sparrows. Barton has assisted King with building the pipeline that designs the specific regions within the genes featured in the GT-seq panel. The GT-seq panel is an important tool for the GECO team to test whether specific sequence variants in the selected genes can be associated with different tidal marsh sparrow phenotypes. “Everyone on the project has picked a set of genes they are interested in that have been shown to affect their various projects,” Barton said. For example, Alice Hotopp (UMaine Ph.D. Candidate in Ecology and Environmental Sciences) is studying genes associated with pigmentation as tidal marsh sparrows have different melanism patterns in their feathers.
While on track to receive her Ph.D. in Biochemistry and Molecular Biology, Barton believes that research into miRNAs has huge potential, as it can be useful to understand how genes are regulated in a variety of organisms, including tidal marsh sparrows. “MiRNAs may be some of the genes that contain particular sequence variants that enable these sparrows to tolerate living in high stress, salty environments,” Barton explained. “By being able to understand that better, maybe we can apply that knowledge to helping to treat human disease. For example, miRNA therapeutics may someday help people with kidney disease where defective osmoregulation leads to water retention and cardiovascular disease.”
As part of her dissertation, Barton is looking at miRNAs that target a specific gene that is potentially involved in osmoregulation (the process of maintaining salt and water balance). Barton concluded, “There are a lot of potential studies that could come from this if we have an annotation of these miRNAs because they are essentially the regulators.” Using her research and analytical skills, Barton plans to continue on to postdoctoral studies after graduation with the goal of working as a bioinformatics expert in industry.