Focused on gathering, analyzing, and utilizing data collected from the Northern Forest Region, the NSF EPSCoR Track-2 INSPIRES project invested heavily in the creation of new environmental sensors. The development of these sensors is led by the WiSe-Net Lab under the direction of Ali Abedi, Associate Vice President for Research and Professor of Electrical and Computer Engineering at the 91±ŹÁÏ (91±ŹÁÏ). Expanding the current sensing capabilities of forestry researchers, the INSPIRES team developed wireless environmental sensor modules equipped with networking and AI capabilities. 

INSPIRES researchers set out to create new devices that fit the needs of forestry researchers and improve upon current sensor technology. These new devices provide “low power and low cost sensor nodes that outshine the current market,” Thayer Whitney, a 91±ŹÁÏ graduate student, explained. This new technology helps forestry researchers measure soil moisture, humidity, temperature, and the diameter of trees. Through the creation of these devices, the INSPIRES project has helped forestry researchers quickly and efficiently collect data from the environment.

Throughout their project, the INSPIRES team helped create more than just new sensory technologies. During a process of collaboration between Alabama Agricultural and Mechanical University (AAMU) and the members of WiSe-Net Lab, both groups helped facilitate student educational opportunities and new relationships for their respective universities. 

Education is at the heart of Maine EPSCoR projects because of how scholarship, mentorship, and collaboration drive innovation and growth of research capacity. In collaboration, the INSPIRES team exemplified the mission of NSF EPSCoR through the development of wireless sensor technologies, new relationships, and student learning.

Raziq Yaqub (Associate Professor of Electrical Engineering and Computer Science at AAMU) began this collaboration while acting as a mentor for electrical engineering students at AAMU, Mphande Phiri, Howard Harris, and Femi Olateru-Olagbegi, who worked with him on their senior design projects. With an extensive background in wireless technology, Yaqub was drawn to INSPIRES due to its function and design. To begin their project, seniors at AAMU studied current sensor technology by reviewing scientific literature, learning about the development process, and exploring alternative use cases for the technology. Yaqub and his students traveled to 91±ŹÁÏ in January 2023, where the INSPIRES team introduced them to the 91±ŹÁÏ WiSe-Net Lab and wireless sensor devices. 

At the WiSe-Net Lab, Whitney and Kenneth Bundy, 91±ŹÁÏ Research Consultant, provided the AAMU students with essential step-by-step directions regarding the development of these devices. Whitney assisted students in the building of the sensors, leveraging his previous experience in assembling the hardware for the INSPIRES. With a strong background in machine learning, computer science, and mathematics, Bundy provided knowledge on the software associated with the devices. After their visit to 91±ŹÁÏ, the AAMU seniors gained valuable hands-on experience that assisted them in their development of similar devices with the specifications necessary for research conducted in Alabama.

This partnership was facilitated by Yaqub and Abedi with the goal to provide benefits to both universities. Yaqub explained that this project brought “essential interdisciplinary research skills” to his students and was especially appreciative of both Abedi and the INSPIRES team’s hospitality and time. By visiting 91±ŹÁÏ, the students received an essential learning experience driven by the Maine researchers. This experience further demonstrated the interconnectedness of research areas and illustrated the importance of collaborative research to the AAMU students.

While the direct goal of this collaboration was to benefit the students, Abedi sees how this partnership and others benefit INSPIRES. “Collaborations like this helped the 91±ŹÁÏ team expand the applications of the research and develop devices to cover new environments and new applications,” Abedi explained. These types of collaborations help facilitate greater learning and the development of new communication and teaching skills for INSPIRES team members. 

Partnerships like the one between 91±ŹÁÏ and AAMU are also essential for the development of new technologies. By bringing together individuals with diverse thoughts and backgrounds, projects can be pushed forward and taken in new directions. Throughout the development of these wireless sensor modules, INSPIRES was not only able to create market-leading environmental sensors, but was also able to expand research capabilities nation-wide.

Maine EPSCoR partner Wabanaki Youth in Science (WaYS) is committed to providing Indigenous youth and communities with hands-on learning opportunities about Indigenous Knowledge and western scientific methods. Fusing western science practices with Indigenous Knowledge allows Wabanaki communities to reclaim spaces in the scientific community.Ìę

Jason Brough, a Ph.D. student in Anthropology and Environmental Policy at the 91±ŹÁÏ (91±ŹÁÏ) and a member of the Northwestern Band of Shoshone Nation, leads an afterschool program for children 6 to 10 years of age focused on getting these students interested in science through a cultural lens. “The Shoshone and the Wabanaki are two different entities, but there are lots of similarities and spiritual beliefs that make sense. I was taught by my Elders,” Brough said. 

The Penobscot Nation Traditional Ecological Knowledge (TEK) Program, a program within WaYS, allows the students to honor the past while framing scientific information in a culturally relevant way, using oral traditions and hands-on learning. 

“The goal for both the WaYS program and the TEK program has been to give Indigenous students, particularly Wabanaki students, a solid foundation culturally. They [our ancestors] already had a solid foundation of what we call sciences, or at least the western sciences,” Brough explained. “If we can give the students that solid foundation culturally, that can eventually help lead to a solid foundation with their identity. It gives them the confidence they need as they progress in school, to be able to go on and get that higher education, to go on to college and start becoming these professionals.”

During the program, students have the opportunity to participate in experiential learning activities. For example, Brough has one lesson plan that allows the children to get involved in maintaining a community garden. Through this experience, they learn what foods are edible to humans, differences in soil types, and how their ancestors interacted with the land. Similarly, the kids will go on nature walks to learn about various plants. Students also learn about water quality, and the living connection they have to the water, which makes it that much more vital to protect it and test the water for contaminants and pollutants.

Brough also dives into storytelling. “One of the things the kids like is when I do stories. We bring in storytellers. Sometimes we’ll have [Penobscot Language Master] Carol Dana or other elders will come and tell stories, but when we don’t have them, I tell them to the best of my knowledge,” Brough stated. “It adds a level of creativity too, and I think that’s something that we need to have in the sciences and culturally it’s always been important.” The students also meet Indigenous researchers at places like the Aquaculture Research Institute to learn about salmon research. Collaborations with various community partners, discussions and stories about their ancestors, and the opportunity to participate in hands-on learning gives the students confidence in their Traditional Knowledge systems and western science methodologies. 

“These things are real to our culture, and the knowledge that their ancestors have is very much so valid, whether they’re passed on through oral tradition or if they’re things that they’re currently learning. Also, [it allows us to] let them know the culture is dynamic. It’s not static. It’s not stuck in the past. We definitely honor the ancestors, and we can honor the spirit of traditions,” Brough said.

Establishing a space where students feel comfortable with western science while learning about past connections and ways of knowing allows students to navigate their way in higher education confidently. While the TEK program is well established within the Penobscot Nation, Brough hopes that the program will expand to more Wabanaki Nation communities, and federal funding will increase to support it. 

“There’s been a lot of assimilation attempts. There’s been a lot of linguistic and cultural genocide, and those are really hard for these types of communities. We see those effects still today in a lot of families. For a lot of those students, this is really one of their main opportunities to experience it in a way they haven’t before,” Brough reflected. 

The many applications of environmental DNA (eDNA) in research and conservation has inspired educators to find ways to implement such topics into their various curricula. As an emerging appliance, eDNA can allow researchers and stakeholders to track population fluctuations of keystone species in order better understand the impacts of climate change on natural environments, as well as to assist with the detection of harmful pathogens. The aid of Maine-eDNA Undergraduate Curriculum Innovation Seed grants has allowed educators across the state of Maine to develop eDNA based curriculum to engage their students with these new scientific techniques. Two educators developing integrated eDNA courses are Judith Roe, at the 91±ŹÁÏ Presque Isle (UMPI), and Yi Jin Gorske at Saint Joseph’s College.Ìę

Judith Roe, Associate Professor of Biology at UMPI, developed a project-based eDNA curriculum for undergraduate genetics, ecology, and environmental science classes. With 10 years experience at UMPI, Roe specializes in medicinal plant barcoding and the genetic identification of snails and birds. Roe works with David Putnam, a UMPI associate professor of science, and Jason Johnston, a UMPI Associate Professor of Ecology, to develop course content.

The course modules are designed for General Biology Laboratory 1 and 2, as well as Genetics, Ecology, and an independent study. Roe is developing an inclusive, cross-skill-level curriculum to engage students from multiple backgrounds to be implemented in classroom, field, and laboratory settings. “At the introductory level, some students don’t even know what taxonomy is. It gives you opportunities to provide context for introductory concepts.” Roe explained, “In upper level classes, you can get into the depth of topics and learning outcomes.”

eDNA is used in a multitude of ecologically, environmentally, and economically important ways, as Roe explained,  “I started using eDNA in research projects, characterizing species of snails and bird feces. Then I realized that eDNA is something that could be accessible for students,” and undergraduate exposure to these new techniques is an important way to ensure a strong basis in genetic skills and knowledge.  “eDNA allows us to determine past species presence without having to see them, only using genetics,” Roe said. With ideas to use eDNA approaches for several marine and microbial projects, Roe began developing eDNA course modules.

In the fall of 2022, Roe conducted the first implementation of eDNA techniques in General Biology Labs (BIO 112) on the topic of soil microbiomes. Starting in the 1920s, arsenical pesticides and herbicides were used to treat pests such as apple moth caterpillars and various insects. Lead, copper, and sodium arsenate were used liberally for the farming of apples, blueberries, and potatoes in New England. Long-term exposure to these chemicals result in elevated cancer risks, which are associated with the historical use of arsenical pesticides and the use of dug wells for drinking water. “We want to know more about where the pesticides were used during the 1920s through the 1950s. Unlike our water, there aren’t any arsenic standards for soil in Maine.” Roe remarked, describing the goals for the BIO 112 lab.

The beginning of the course covered rudimentary topics like the definition of a microbiome and a discussion of what makes soil healthy. “This is a place where you can bring in different perspectives.” Roe expanded. “You can have someone from a soil science class, or from someone involved in plant growth research.” Students investigated questions regarding the importance of soil health, species of bacteria and fungi present in soil samples, arsenic levels across sampling locations, and the effects of arsenical pesticides on the soil microbiome.

Students collected small samples in Aroostook County with locations at a farm owned by Randy Martin, UMPI’s community garden, and Houlton High School’s orchard. Once collected, each was tested to determine respective arsenic levels. With the use of Qiagen PowerSoil Kits, students used centrifugation techniques in eDNA extraction for each sample, which were then sent to CosmosID for species identification. “Many students were surprised by how many fungi were in their 0.25 gram sample of soil.” Roe said. “Many guessed there would be two or three species but when they saw the data, they were astonished by the immense number of species of bacteria and fungi.” Through the use of data visualization, a highly emphasized topic in BIO 112, students studied the presence of Glomeromycota at each sample site. Glomeromycota is an integral monophyletic group, meaning descended from a single ancestor, of fungi that form mutualistic relationships with the roots of many plant species. When analyzed, their presence was low in potato fields and 66 percent of the orchard samples. Nearing the end of the semester, students were asked to pick a bacterial or fungal species present in the samples, conduct literary research, and give a presentation on their respective findings.

Roe continues to develop curriculum modules with plans to introduce eDNA approaches into an introductory environmental science course at UMPI as well as develop a wood turtle eDNA project. Roe stated, “The most rewarding part of developing these course modules is using genetics in a new way to study environmental problems. I am very fortunate to be able to share my discoveries with students and with the broader scientific community.” With goals to further the dissemination of these eDNA course modules, Roe hopes to introduce more undergraduate students to the capabilities of these novel techniques with the aid of Maine-eDNA Curriculum Seed Grant Funding.

Yin Jin Gorske at Saint Joseph’s College in Standish, Maine, works under a Maine-eDNA Education Seed grant to develop undergraduate curriculum for a Course-based Undergraduate Research Experience (CURE) class. Gorske, an assistant professor in the Department of Natural Science, teaches organic and medicinal chemistry, with research interests in drug discovery projects. Working with other faculty, Gorske developed Biology (BIO) 309: “Culture-independent methods to discover natural products produced by soil bacteria,” a multi-disciplinary CURE class that aimed, as Gorske explained, “to model an authentic research team environment, reflective of how research happens in real life. While we have some opportunities to do faculty-student research, there is a limit.” With the knowledge that some students do not have the ability to otherwise participate in research, Gorske wanted to provide a transformative experience that would allow them to think deeply about their level of interest and curiosity with science.  

Utilizing a team-based structure, members of the class worked together in most elements of the course, from soil sample collection to the creation of a scientific podcast. Each of the five undergraduates enrolled has different backgrounds, interests, and skill sets in biology, chemistry, or ecology, as they worked together to create a space to conduct scientific research on the microbiome of Maine’s soil. With one lecture and two labs per week, the class was heavily experience based, lending itself to opportunities for learning and building experimentation and skill sets in a lab environment. “With a class of five students, the ability to explore and utilize the different strengths present in laboratory settings and other components of the course was valuable.” Gorske added. 

Students obtained aseptic, contaminant-free soil samples from four separate locations on the Saint Joseph’s College campus with two replicates per location to ensure more accurate test results. The samples were brought to the lab for testing and analysis. Once the samples were safely in the lab, observably thriving colonies of microorganisms were extracted and allowed to grow in SMS media, a nutrient dense broth ideally suited for the promotion of colony replication. Students then observed the fermented test tubes for signs of colony growth and the consequential presence of metabolites, which govern soil bacteria’s production and ecological function.“We wanted access to those metabolites to see whether those compounds would be active against bacterial species,” Gorske explained. With the use of eDNA, the students were able to genetically characterize microorganisms in the soil samples that produce antimicrobial growth inhibitors for harmful bacteria. Through the process of working with these microorganisms, students investigated questions such as “Are the compounds we’re isolating toxic across the board or perform a specific function?” and “Are these compounds active against other strains of bacteria?” The colonies were then tested against E. coli, M. smegmatis, and S. aureus, of which the latter two are bacteria that cause skin infections. Although some strains of E. coli are necessary for our body to digest food, other strains cause harmful contagious infections. Through their lab work, students discovered that one microbial colony had the ability to inhibit S. aureus, while another could inhibit both E. coli and S. aureus. 

Over the course of the semester, students were assessed in a variety of ways that focused on collaborative demonstrations of knowledge. Students were asked to write manuscripts, create podcasts, turn in their final individual lab notebooks, and engage in feedback and editorial processes. As a multidisciplinary method of showcasing their research, students were asked to create a podcast with seven episodes on relevant topics related to their research experience in BIO 309. Through conducting interviews, writing episode scripts, and learning audio production processes, students were able to explore a new method of scientific communication. “Listening to the students’ podcasts was the most rewarding aspect of teaching this course. There was editing and music, and it was wonderful to see the way they were able to engage in a different way of describing their research,” Gorske remarked. Several scientists from NovaBiotics working on closely related research topics agreed to be interviewed. Amy Spoering, Director of Biological Research at NovaBiotics, participated in the final podcast. “She was the lead microbiologist for the paper that we adapted for the project.” Gorske explained, “For this podcast, she gave a fantastic overview on drug discovery using natural products and focused specifically on her work at Novabiotics.” Once the podcasts were done, they were shared with members of the Saint Joseph’s community. “Creating and sharing their podcasts showed the students that what they were working on is real, it matters, and that there is a whole company devoted to it.”

Gorske plans to further develop the partnership with NovaBiotics and extend the scope and duration of the course. “Because this course laid such a good foundation for the future of BIO 309, I expect to pick up the pace of the data collection and analysis process.” With more time to focus on the analysis of their results, the students would be able to ask more questions, push their projects, and be able to present their findings to the greater scientific community. “Seeing how the students dealt with challenges and confusing results was inspiring,” Gorske said, emphasizing the importance of undergraduate research experiences. Creating spaces for students to engage in eDNA exploration is an essential aspect of developing the future STEM workforce. With the help of seed grants, educators are able to expose budding researchers to the capabilities of these essential tools made possible with the use of eDNA.

In any scientific and humanistic discipline, ethical collection of samples is a vital step in the research process. With a field like environmental DNA (eDNA), researchers sample soil, water, and organisms from the physical environments. The knowledge derived from them is collected on the land of Indigenous tribal nations, which comes with the responsibility to maintain both discussions with the local communities and care for the data collected.  To help address this, the NSF EPSCoR RII Track-1 Maine-eDNA project, along with Maine EPSCoR and the Maine Center for Genetics in the Environment (MCGE) at the 91±ŹÁÏ (91±ŹÁÏ), announced an Open to Collaborate Notice in fall 2022. This signals the project’s commitment to working with and learning from the Wabanaki Nations (the Miꞌkmaq, Maliseet, Passamaquoddy, and Penobscot) and other partners. This commitment is paired with the implementation of Biocultural Notices in the Maine-eDNA database, which are attached with each and every sample from when it is collected in the field, through the lab process, and into the database. 

In the summer of 2021, Darren Ranco, 91±ŹÁÏ Associate Professor of Anthropology and Coordinator of Native American Research, offered an ethics workshop that sparked the interest of multiple graduate students committed to ensure that data collection and storage practices were done in dialogue with local Indigenous groups. Later that fall, during a Maine-eDNA graduate course, Team Science for Maine’s Coastal Macrosystem, Erin Grey (91±ŹÁÏ Assistant Professor of Aquatic Genetics) and Andy Rominger (91±ŹÁÏ Assistant Professor of Ecological Bioinformatics) focused on introducing students to team-based eDNA research. Students collaborated with Local Contexts and Equity for Indigenous Research and Innovation (ENRICH), who facilitate Traditional Knowledge and Biocultural Labels and Notices. Maine-eDNA Ph.D. candidate Jennifer Smith-Mayo and graduate student Beth Y. Davis, along with Melissa Kimble and Laura Jackson from 91±ŹÁÏ Advanced Research Computing, Security and Information Management (ARCSIM) who were developing Maine-eDNA’s database, worked with Ranco and Rominger to maintain discussions around eDNA data that contains cultural rights information. The team continued to work with Local Contexts and ENRICH following the graduate course to implement Biocultural Labels and Notices into the Maine-eDNA dataflow. 

“This work is new and challenging and reflects a deep engagement with research. It is a responsibility and requires more training for faculty and students,” Ranco remarked. “That said, it also opens up so many opportunities for win-win scenarios for both researchers (Indigenous and non-Indigenous) and Tribal Nation citizens. I also want to point out—at least since the MOU in 2018—the 91±ŹÁÏ has become a leader in this work.” Ranco began working with Local Contexts roughly seven years ago to develop Traditional Knowledge Labels in his own research and as a citizen of the Penobscot Nation. 

An international collaborative, Local Contexts aims to create conversations and methods that focus on protecting intellectual property and digital data of Indigenous groups within research spaces. Smith-Mayo explained, “The Local Context Hub is a digital hub and repository. It allows Indigenous communities to adapt Traditional Knowledge and Biocultural Labels to their needs and share them safely with institutions, researchers, and data repositories.” Institutions and researchers create Notices and generate conversations around Indigenous interest with the data. Notices signal that the institution is committed to open dialogue with Indigenous communities and recognize Indigenous interests in data collection and their rights to share in the governance and derived benefits of those data. When institutions and researchers apply for a Notice to the project, local Indigenous groups will decide how and when a Label is assigned. The application of a Label may indicate that the data is only for research or outreach, but a different Label may indicate something is open to commercial use as decided by Indigenous communities. 

Davis explained that the scientific process does not have to be entirely one ideology or another but rather a more nuanced, developed approach to these ethical topics. Modern data practices push to share information and make it easily accessible, but it also ignores the potentially harmful effects that this mindset has on communities. Local Contexts raises the awareness of harm that extractive practices have on people.

“Scientists are connected to the rest of our communities, animals, plants, and humans. We are not isolated,” Davis said. “The pathway that this opens up to us is just a better way of communicating and collaborating, and bringing awareness with ourselves and communities with the work we are doing and the context in which it lies.” 

Engaging in this work does not mean inequalities and injustices are remedied, but it is a step in the right direction. 

 â€œThey signal the right of Indigenous communities to define the use of information, collections, and data, including digital sequence information
generated from biodiversity and genetic resources that are associated with Indigenous traditional lands or waters,” Smith-Mayo said.

In recognizing that DNA is a living organism, there is a level of respect and responsibility that comes with collecting and analyzing it. Development of conversations, building relationships with Indigenous communities, and sharing data in an ethical way are steps in giving authority back to Indigenous people. “This work has made me think about what we are doing as researchers, how we are conducting it, and what kind of relationships we have with the people and the non-humans we coexist and live with,” Smith-Mayo said. 

While this is only a step in the right direction, the Maine-eDNA project can help serve as an example to others and introduce this data approach to  Maine-eDNA participants’ other work.

“It is a clear expression that these parts of the 91±ŹÁÏ take seriously the ethics and responsibility of doing research in Indigenous homelands, in collaboration with Indigenous Tribal Nations and Citizens,” Ranco said.

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 91±ŹÁÏ (91±ŹÁÏ), 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.Ìę

Allison Garnder (Associate Professor of Medical Entomology at 91±ŹÁÏ) 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.Ìę

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. 

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 andÌę 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 91±ŹÁÏ (91±ŹÁÏ). Studying under Benjamin King (91±ŹÁÏ 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. 

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 (91±ŹÁÏ 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.

The Frontier Institute for Research in Sensor Technologies (FIRST), formerly known as the Laboratory for Surface Science and Technology (LASST), is an interdisciplinary research institute at the 91±ŹÁÏ (91±ŹÁÏ), with the vision of becoming a leader in materials, devices, and systems research. The institute, established in 1980, prides itself as a platform where individuals from a variety of scientific backgrounds can work together in order to solve problems that make real economic and societal differences. Through establishment of research infrastructure, spinoff companies, and local and international collaborations, FIRST continues to grow research and development capacity in Maine. 

FIRST, like many research institutes and centers at the 91±ŹÁÏ, was helped by the National Science Foundation’s Established Program to Stimulate Competitive Research (NSF EPSCoR). Awarded in 2000, the six million dollar NSF EPSCoR RII Track-1 grant set out to improve research infrastructure, particularly in the realm of materials and sensors , in order to enhance Maine’s technology industries. This funding allowed FIRST to bring on new faculty, invest in research infrastructure and facilities, and connect a diverse team of researchers. While this grant has long since ended, the impact of  the funding is clearly visible today not only in FIRST’s research but also in its philosophy and mission. 

FIRST Director Sharmila Mukhopadhyay joined the institute in 2020 and was initially attracted by the prospect of nurturing larger collaborative teams. “The whole idea is that we have people from different disciplines collaborate on addressing a larger societal challenge. We currently  have faculty from mechanical, electrical, chemical, and environmental engineering, as well as physics and  chemistry, working together,” said Mukhopadhyay. “So this would be a powerful platform for interdisciplinary advances in high-tech areas that  are  relevant to society today.”

Research in Maine relies on instruments and other electronic tools due to the state’s vast wilderness and rural areas. “If you think of Maine, being well known for environmental and climate sciences, forest research, sustainable energy and rural infrastructure, all of those advances depend on advanced electronic devices and sensors driven by new materials.” Mukhopadhyay stressed. FIRST sees itself as integral to the continuation of these research areas in the state. “The big challenge down the road would be getting these new sensors and new electronic devices which would serve specific functions for the end user.” One research area that FIRST is interested in is materials, or more specifically, nanomaterials. Nanomaterials can be found in almost every piece of technology people use in their daily lives. Researchers study and develop these nanomaterials and their tiny eccentricities in order to package them into sensors and devices built to meet a specific need. 

This can be seen in practice through FIRST’s work with the U.S. Department of Energy (DOE). FIRST is currently developing high temperature sensor systems under DOE EPSCoR funding. These devices will find themselves inside of power plants and need to be accurate and reliable while withstanding hundreds  of degrees of heat.  For these to work, the whole system needs to be built to withstand harsh conditions. In order to power these sensor systems, researchers are utilizing thermo-electric generators to improve their energy efficiency. Mukhopadhyay explained, “You want to put them into packages where they can be more efficient and more robust in order to operate in different service environments.” These systems can also be utilized in energy conversion. 

Another priority area at FIRST is research into technologies for detection and mitigation of contaminants in the environment. One current research project involves using nanomaterials to create sensory devices that can detect traces of polyfluoroalkyl substances (PFAS). PFAS, oft-referred to as a forever chemicals_, can leach into the food supply through plants and animals that are grown or raised in contaminated areas, and can have widespread negative effects on humans. Research at FIRST is not only focused on detecting PFAS but also on converting PFAS into harmless products once detected. Doing this requires a diverse team of scientists from academia, government, and industry, and FIRST is continuing to expand such partnerships. 

FIRST has had a long history of active collaboration with outside partners. Mukhopadhyay explained, “Collaboration is the key ingredient that can take the ideas of brilliant scientists to the next level and make use of their work. This day and age, it’s very difficult to work in isolation. How strategically you collaborate, how carefully you pick your collaborators, and how synergistically you develop the collaborative relationship, I think, are extremely important for success.” 

FIRST provides a platform for collaborations to foster over time, allowing researchers to benefit from one another’s scientific expertise. The institute also allows for individuals in any specific field to pick up knowledge from other fields that can be used for viable research applications. The ability to facilitate collaborations involving different disciplinary cultures will only become more important for the next generation of researchers and students. 

Undergraduate research at FIRST has been active and aims to provide students with hands-on experience in cutting-edge areas. While working on their projects, a majority of students are advised by at least two FIRST faculty members in order to achieve high quality interdisciplinary training. Undergraduates, graduate students, and postdoctoral fellows who work with FIRST come out of the experience with a deep understanding of interdisciplinary research, and are prepared to take on our world’s evermore multifaceted challenges. Some students like Henry Carfagno, who initially joined FIRST as an undergraduate research assistant, returned to FIRST as the institute’s Research Facilities Operations Specialist as a full time professional. 

FIRST plays an important role in student development, while expanding the possibilities of materials and sensor technologies, as well as providing scientists of many different disciplines with the opportunity to learn and collaborate in a high tech environment. The institute has changed significantly from its inception in 1980 to what it is today, and it is still growing in new directions with the addition of new faculty members. FIRST continues to drive research and position Maine as a leader in advanced materials and sensor technologies.

Maine EPSCoR Newsletter March 2023:

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Maine-eDNA Research Learning Experience

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Meet Maine-eDNA’s Research Coordinator, Karen James

Climate Change Adaptation: The Bill Morphology of Tidal Marsh Sparrows Through Thermography

Saltmarshes (a.k.a. tidal marshes) are one of the most productive eco-systems on earth. As protectors of coastal landscapes and communities—that absorb flood waters as well as carbon—saltmarshes can also provide insight into climate change adaptation. Among this dynamic habitat that is full of bugs, not a lot of predators, and plenty of places to nest, you will find the Seaside Sparrow, Saltmarsh Sparrow, and Nelson’s SparrowÌę — each representing a different colonization from 2 million years ago, half-a-million years ago, and 5,000 years ago, respectively.

Mackenzie Roeder, a Ph.D. candidate in Ecology & Environmental Sciences at the 91±ŹÁÏ, studies genome-to-phenome linkages in tidal marsh adaptation, specifically from the unique perspective of the bill morphology of Seaside, Saltmarsh, and Nelson’s Sparrows. As part of 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), Roeder brings a comprehensive approach to understanding this phenotype (this trait).Ìę

The sparrow’s bill, with its large surface area—as compared to non-tidal sparrows—is the main tool it uses to interact with the environment. According to Allen’s rule, warm climate-adapted animals have larger appendages than cold climate-adapted animals, which allows them to maximize or minimize heat loss, respectively. A corollary to Allen’s rule known as the Greenburg-Tattersall Corollary suggests this pattern is also true along saline gradients. Roeder investigates whether larger bill size of these sparrows allows for increased levels of radiative heat loss rather than evaporative heat loss (which conserves water). This is especially critical in saltmarshes where freshwater is limited.

“This is a newly understood phenomenon in general,” Roeder stated, “so it’s not understood how common this is across avian taxa yet.”

The bill of the bird—like the legs—is filled with blood vessels. Because heat flows from areas of high temperature to areas of low temperature, Roeder hypothesizes that if blood flow is increased to these areas, which raises the sparrow’s body surface temperature (relative to ambient temperature), this allows the sparrow to lower its core body temperature without evaporation (i.e., no freshwater loss) as heat flows from the warm bill to the cooler air around it.

“These three birds represent independent colonization events of tidal saltmarsh habitat,” Roeder stated,” and, potentially, a degree of specialization to this habitat correlated with the time since colonization, which we refer to as an adaptive gradient. If these birds do phenotypically represent an adaptive gradient, then we would firstly anticipate that they would use their bills to dissipated heat—to some extent at a minimum—probably to a greater extent than other non-tidal taxa, and that this bill ‘use’ would increase proportionally with the time since colonization.”

Roeder further explained, “This means we anticipate that Seaside Sparrows, who colonized first and have the largest bills, would use their bills more-so in a thermoregulatory capacity than Saltmarsh and Nelson’s Sparrows, suggesting that their thermoregulatory strategies may be optimized to reduce freshwater loss.”

Thermography (the use of thermal imaging cameras to monitor changes in heat patterns and blood flow) of wild animals can be complicated in a laboratory setting, because it requires capturing live animals and housing them for extended periods of time. To address this challenge, Roeder has built a portable temperature-controlled thermal chamber (electrical cooler box) that allows her to capture birds in tidal marshes and place them within the box in a safe and calm (dark) environment. Here the birds experience the same thermal gradient (a range from 10°C – 35°C), over the course of one hour while being monitored with a thermal imaging camera, before they are released back into the marsh. Roeder explained, “This standardized gradient exposure is essential for comparing the bird’s physiological responses and mimics a common range of temperatures experienced by the birds during the breeding season.”

Currently, Roeder is focused on thermography as part of her summer 2022 work in Maine, New Hampshire, and New Jersey. With the thermal chamber, Roeder can see what the sparrows do physiologically as the temperature increases. Already, these three sparrows are exhibiting different physiological behaviors.

Roeder’s research has shown “Seaside Sparrows regularly dissipating 20% of their overall radiative heat from their bill. As temperatures increase beyond Ìę25°C, Seaside Sparrows have increased blood flow to the bill such that 50-60% of all heat lost from the bird is from its bill, which is phenomenal!”

Next, Roeder compares her early results with other researchers’ work on Song Sparrows along salient gradients, which inspired her current work. Though the methods are different, their Ìęresults showed that tidally adapted Song Sparrows dissipated more heat from their bills than non-tidally adapted ones, and that the maximum percentage of total heat loss from the bill of these sparrows was ~15%, with an average of 10%. The much larger percentage of overall heat loss in these tidal marsh obligate birds is exactly what Roeder and her team would expect following our adaptive gradient hypothesis.Ìę

Since physiology is a behavior that is affected by the environment, Roeder contemplates whether she is capturing some local phenomenon of climatic acclimation. To address this question, she replicated sites for each species along a natural thermal gradient (from New Jersey to the north-eastern tip of Maine) during the breeding season. She repeated this work on their wintering grounds, where all three species co-occur in the same marshes and are adapted to the same climate.

This led Roeder to ask these critical, comparative questions: “Is the use of the bill, as a thermal window, to lose heat associated with their colonization order? Can we use this system to test hypotheses on the way evolution shapes traits—and helps in adaptation? And finally — what else is affected by this increase in bill size? Does this morphological difference affect their fitness? Does a larger bill mean they’re better able to dissipate heat and compete for mates and territories, does it increase their ability to forage and provide food for their young when it’s hot, does it affect their ability to sing and attract mates?”

Roeder and the GECO team run demographic sites where they monitor the breeding activity of these birds. By finding their nests, monitoring their success, conducting paternity analyses, and monitoring the growth rates of their chicks, they can determine levels of fitness (individual male reproductive success) that they can compare with bill morphology to look for correlations. She is also conducting research studying the songs the males sing to determine if bill morphology impacts song production, and in-turn if abiotic forces (e.g., heat) impact their song quality.

“These ideas are all interconnected and an attempt to comprehensively view the bill and the ways in which it is important to the birds,” Roeder explained. “Finally, I will be using genetic data collected from these birds to determine the heritability (the level of variation in the trait that is due to variation in the genes) of bill morphology and will be conducting a genome-wide association study (GWAS) linking regions of the genome to bill size differences.”

While Roeder studies tidal saltmarsh birds , her thermoregulation research has broad implications for all kinds of taxa, even freshwater-limited environments such as arid habitats and high mountain habitats. And applicable questions on whether the role of a phenotype in thermoregulation, in this case the bill, is different between species, within individuals, and at the level of within-population genomic variation, which can lead to further genome-to-phenome linkages in the study of climate adaptation.

“This is a newer phenomenon to us,” Roeder stated, “a newer way of understanding the trait that is the bill. For a long time, people have just studied it as the way the bird gets food. Thinking of this trait as an integral part of a whole body, not a separate part of the bird, is important. It is the bird. And it takes part in all the things the bird does, so we must understand it from more than one context.”

In early 2022, Maine-eDNA brought on new research coordinator Karen James. This inclusion to the project will help Maine-eDNA coordinate the grant’s vast amount of work happening across the state. James brings with her a deep knowledge of genetics, environmental DNA (eDNA), and its application in marine and terrestrial habitats. While James is new to this position, she is not new to Maine-eDNA. James originally joined the RII Track-1 grant as a research scientist in 2020 after having worked closely with Jacquelyn Gill at the 91±ŹÁÏ’s Climate Change Institute, helping build a DNA reference library for the Beringian flora in Siberia.

While earning her Ph.D. in genetics at the University of Washington, James worked primarily in biomedical research. During this time, James developed an interest in evolutionary developmental biology and, while unrelated to her area of study, botany. After graduating, James started a postdoctoral position at the Natural History Museum in London, England. James explained, “The postdoc at the museum was a way for me to move into botany, evolutionary biology, and natural history generally.” During James’ time at the Natural History Museum, the institution hosted the first conference for the International Barcode of Life, an important predecessor and underpinning of eDNA, and James was part of the working group that selected the “barcode” loci for plants (the pieces of DNA by which plants would be identified in DNA barcoding applications). When James came to Maine, she worked as a staff scientist at the Mount Desert Island Biological Laboratory and later the Climate Change Institute at the 91±ŹÁÏ.

As Maine-eDNA’s research coordinator, James helps bring together the efforts of researchers across the state, which can be difficult on a grant as large and geographically diverse as Maine-eDNA. “On a project this big, where we have concerted and simultaneous parallel efforts like index site sampling, it is important to try and maintain consistency among different people and locations,” explained James. Maine-eDNA’s index site sampling involves researchers collecting data up and down Maine’s coastline and into the interior. All of these samples need to be collected and treated in the same way as they make their way to the Environmental DNA Lab at the 91±ŹÁÏ in Orono for DNA extraction and processing. This is in addition to other coordinating efforts such as equipment and infrastructure deployment and installation and facilitating communications between research teams. She also coordinates the weekly Maine-eDNA research forum during the academic year and All-Hands meetings.Ìę

James acts as a point person for everyone on the grant, ensuring they have what they need to do their research. And while James has moved into this role, she also continues to serve as a research scientist in support of the Maine Center for Genetics in the Environment (MCGE). James works on a range of research projects like one with Allison Gardner (91±ŹÁÏ Assistant Professor of Arthropod Vector Biology) that explores the use of eDNA as a means for monitoring mosquitoes, specifically ones that pose a potential public health risk, and another to develop a method for detecting ancient DNA in mixed-age environmental samples.

Maine-eDNA benefits greatly from the depth of experience that James brings to the grant, being someone who has been involved deeply with the eDNA field and its development for the past two decades. James explained why working in this capacity is important to her, saying, “I am really excited to be able to, with my background in DNA barcoding, continue in this trajectory using genetics to study natural history and the environment because I didn’t necessarily know I would have an opportunity to do that with my background and training.”