Dr. Benildo de los Reyes, Professor of Molecular Genetics and cooperating faculty member of the Department of Molecular and Biomedical Sciences, arrived at the University of Maine in 2004. He runs a functional genomics lab, in which he uses plants as a model system to understand genetic regulatory networks that allow plants to adapt to various environmental conditions. Specifically, his lab looks at effects of low temperature stress and dehydration as well as disease causing microorganisms and insect herbivores.
With an interest in molecular plant genetics and the tools to effectively explore them, this lab is motivated and well equipped to contribute to the growing pool of knowledge in the world of molecular genetics. While advancing his own research, Dr. de los Reyes is currently advising four graduate students, and hosting an international researcher from the Philippines.
“An emerging paradigm within agricultural breeding practices is actually going back to wild species to obtain some of the genetic background that has been lost through the centuries of breeding practices.” -Myles Butler
Myles Butler, currently pursuing a master’s degree in Botany and Plant Pathology, is working in Dr. de los Reyes’ lab. He was inspired to pursue a graduate degree after taking Dr. de los Reyes’ Principles of Genetics course during his undergraduate studies.
Butlers project intends to reveal cellular mechanisms that provide resistance within potatoes to both the disease late blight and infestation of a common pest, the aphid. He describes his approach as “a no stone left unturned” approach, trying to identify key genetic signatures within the potato that could contribute to resistance or an absence of signatures that could be associated with susceptibility.
In order to do so, Butler is exploring regulatory networks that modulate a cell’s activity in response to a pathogen. A technique utilized for this project is RNA-seq, which enables him to generate genetic sequences, allowing for the identification of unique genes. This technique allows for scientists to see every gene that is being expressed within a plant at a given point, which is important for comparing between time periods and conditions.
“A common theme in Dr. de los Reyes’ research is to characterize the wild species that show these traits of resistance to abiotic or biotic stresses and trying to integrate these traits into the cultivars so we can have much stronger resistance and stress tolerant plants in agriculture.” –Myles Butler
Ai Kitazumi, a PhD student also working under Dr. de los Reyes, started her undergraduate degree program at the College of the Atlantic in Bar Harbor before coming to the University of Maine where she is pursuing her graduate degree.
understand the evolution of regulatory networks during domestication. Using wild species of common crop plants, mainly rice and potatoes, she is looking at what kinds of genes were left behind during domestication that are responsible for dealing with environmental stress responses.
Although the study of molecular genetics is highly specific, it can be translated into our everyday lives through agriculture. Rice is an excellent model system for scientists to use for research because of its small and well-categorized genome, which makes genetic modification easier.
“What I like about my research is that I’m trained for many purposes…I used to just look at one gene…what the function of it is, how the gene responds, what does its sequence mean. Now I have been trained to profile 30,000 genes at the same time…I have fun trying to keep each genes specific story intact when looking at a large number of genes.” –Ai Kitazumi.
During domestication of common crop species, genes are selected for a variety of purposes, such as palatability and shape, and by doing so, genes are left behind that are useful in other ways. A focus in Dr. de los Reyes’ lab is looking at genes that facilitate resistance to stress and disease. Wild species are stronger in this aspect; the cultivated plants need pesticides and the use of fertilizers. If these genes that were left in the past were reintroduced into the genome of these species, there could be a lesser need for pesticides and fertilizers in our cultivation process.
Kitazumi recently completed a highly competitive two-month long International Collaborative Research Fellowship Award at the National Institute of Genetics at Mishima, Shizuoka, Japan.
Jasper Alpuerto came to the University of Maine from the Philippines after meeting Dr. de los Reyes, who at the time was on his sabbatical leave from UMaine. Majoring in agronomy with a focus in plant breeding in his undergraduate studies, Jasper was intrigued by Dr. de los Reyes research which inspired him to apply to graduate school at UMaine.
His current research is a follow-up of a previous project done by Ananya Mukherjee involving a gene, vacuolar-processing enzyme (VPE), which is found to be involved in a plants defense response during aphid feeding and late blight infection. He is using a reverse genetic approach to study Arabidopsis thaliana, a common model species, in order to clarify the role of VPE in response to aphid feeding. Alpuerto plans on using his knowledge in molecular biology and genomics in order to continue his work in applied breeding practices.
“I think we are in need of another Green revolution… the population is increasing and the land is decreasing, we need food everyday, and I want to be a part of the community that produces food for everyone…” –Jasper Alpuerto
His research is exploring the effect of mutations in calcium regulatory proteins on cardiac rhythmicity in Drosophila, fruit flies. His project involves a variety of techniques including culture maintenance, fly heartbeat monitoring using microscope-phototransistor system, RNAi, and cardiac rhythmicity data analysis.
Jay is a high achieving academic student in the School of Biology & Ecology, and has received a wide range of awards throughout his time at UMaine including highest GPA for a third year student in the School of Biology & Ecology. Recently, he was awarded the INBRE Functional Genomics Fellowship, an extremely competitive fellowship awarded to a forth year Honors student working on a thesis related to biomedical research in comparative functional genomics.
In May, Jay will be defending his Honors Thesis and is currently deciphering what his academic future has in store for him. He is in the process of applying to graduate schools around the country, where he hopes to study molecular biology or stem cell research. Both topics of interest are related to the research he has been conducting. “I just find those topics fascinating…there is a huge world out there” Jay explained with a spark of excitement in his eyes.
After scrolling though the faculty profiles on the SBE website, Jay became interested in Dr. Dusty Dowse’s lab and his research on cardiac rhythmicity. He became a volunteer during the summer after his freshmen year at UMaine, and has continued to conduct research there for the past two years. Dr. Dowse has had the pleasure of working with Jay for three and a half years now, and during this time was able to see Jay transform from a volunteer in his lab, to an independent researcher.
“Jay has gone from saying, “How do I do this?” to “Why am I doing this?” Jay has taken an active role in planning his project and doing the background research. He has become more of a leader in his own research” says Dowse.
Working in a lab is a great way for students to gain hands on experience and prepare themselves for their future careers. It also gives students the opportunity to form a connection with their professors, which is often difficult due to class size.
“A lot of the science classes are really big, so it’s hard to have a more personal interaction with your professor. But working in the lab you get to know the professor better, and they get to know you better. Whenever I have questions, I can bring it to Dusty. I believe that personal interactions are very important for academic achievement,” explains Jay.
Dr. Dowse had similar advice to give to undergraduate students hoping to enhance their undergraduate academic experience.
“Generally speaking, in any level, including the professional level, doing something that is directly related to where the information you are absorbing comes from is important. If all you are doing is reading from textbooks, you are not getting a good idea for why these things are happening…. Science is not a belief, you don’t believe in science. If you are actually out there in the real world doing the work…you begin to get a real feel for what 1,000 years of science has led to.”
Congratulations to Jinlun Bai on his academic excellence, and we wish him the best of luck with the remainder of his time at the University of Maine.
Congratulations to SBE graduate student Krista Slemmons on receiving a faculty position! Slemmons accepted a position at the University of Wisconsin-Stevens Point this fall semester where she is teaching biology courses, as well as conducting research and supervising biology student teachers during their teaching experience.
Slemmons received her undergraduate degree at Denison University with a B.S in Biology, and received her master’s degree from Miami University in environmental science as well as Wright State University. Slemmons studied at the University of Maine to receive her Ph.D. in Ecology & Environmental Science.
During her time at the University of Maine, Slemmons research focused on artic & alpine lakes that were fed by glaciers using pale- ecological and modern techniques to do so. Her research focused on diatoms, an extremely temperature sensitive species of algae, and how they were affected through time as glaciers continue to recede. During a research project her first summer at the University of Maine, she preformed a lake experiment in the Bear tooth mountains located in Southern Montana. Using modern techniques, she used carbon-14 uptake experiments to measure the productivity of the algae in a glacier fed lakes and a “snow fed” lake. She also preformed nutrient enrichment experiments, in which she would add nutrients to both the glacier fed lakes and the snow fed lakes to see how the algae would respond. In order to compare changes that occur to the algae communities before and after, and how they change as the glaciers change, they looked at a core dated as far back as 3,000 years ago. She also had the opportunity to look at a 9,000-year-old core from East Greenland, a project that was in collaboration with the department of earth sciences.
Slemmons explained the monumental influences Umaine had on her career, and expressed a great appreciation for the climate change institute as well as the School of Biology and Ecology for giving her an interdisciplinary approach to science, as well as a broader interpretation of the world around her. “These programs opened up my mind and gave me new insight into how the world really works,” says Slemmons.
During Slemmons’ time here, she was a teaching assistant for Biology 100 & 200, received the Chase distinguished Research Assistantship, the Correll Fellowship, and a National Park Service Fellowship.
We wish Krista Slemmons and her family the best of luck in Wisconsin!
The Schoodic Experience is part of the SBE biological science orientation course, NFA 117, offered to freshmen Biology, Ecology, Zoology, and Clinical Laboratory Science majors. But as the students of this trip found, the three day trip to the Schoodic Education and Research Center in Acadia National Park was much more than just an orientation course. Students had the opportunity to explore their major in an out of classroom experience, where they were able to meet their professors, fellow peers, and graduate students that many will have as a TA for a variety of laboratory classes.
Every year SBE faculty lead different workshops and lectures, giving students the opportunity to see a variety of different areas of study. Field excursions went for 90-120 minutes, and students were given the choice of which excursions they would like to attend.
Brian Olsen, assistant professor of Biology & Ecology, led a field excursion titled “Birds of Schoodic”. Students were taught how to identify birds using a field guide, as well as the thought process required to identify a hypothesis using the scientific method in a real applicable situation. Ann Dieffenbacher, Assistant director for Administration, led a field excursion to a near by bog to study the climate and ecological history of Schoodic using samples from the soil. Clarissa Henry, associate professor of biological sciences, gave a demonstration on zebra fish, showing her students how to identify mutant zebra fish embryos using dissecting microscopes. Seth Tyler, professor of Zoology, led an intertidal pool walk titled “Life in the Intertidal Zone”, where students collected many organisms for identification. During down time, students had the oppurtunity to play sports, participate in activities and games, and enjoy evening movies.
“The idea behind taking students to Schoodic as part of their NFA 117 experience…is to give them a better chance of bonding with each other and meeting a few more faculty as well as their advisor. Students who choose to take this version of NFA 117 usually score better on academic work. We think this is because they have formed a tight group with other first year students on whom they can rely on for help and support. Schoodic students hit the academic treadmill quicker and more prepared.”
Researchers in SBE as well as the Engineering Department are taking advantage of radio-controlled planes to solve the mysteries of bird migration. Brian Barainca, a mechanical engineering student, has been building radio-controlled (RC) planes ever since he was in high school. When SBE Professor Rebecca Holberton saw him flying his RC planes on campus, she called upon him to help with bird migration research, and it has been an adventure ever since.Ani Varjabedian, a student in SBE’s Zoology program, was working in Professor Holberton’s acoustics lab and started working on the RC plane project in order to bring a biological perspective to it. “I’m interested in using the plane to test different altitudes of bird flight and where we can see the most birds,” explained Varjabedian. The goal of using a plane to observe bird migration is to view birds without disturbance and at a closer proximity. “You have to get pretty close to birds when you view them on the ground, which could disturb them,” explained Barainca, “but with the plane you can step back and get to where you need to go.” In this way, the plane reduces error by eliminating human presence from observation.
The plane works via a remote control by someone on the ground. A camera on the front of the plane sends live video footage to the controller in order for the controller to see exactly where the plane is going. Although the current camera on the plane is great for live viewing, Barainca hopes to get a new camera that is higher quality for recording. Also, the camera is not equipped to see if there are birds right below the plane, which Barainca hopes to also improve.
The researchers ideally want to survey shorebird populations and find migration patterns. The plane will hopefully be able to track birds with radio frequency signals. Tagging birds with radio tags has not been successful in the past because researchers don’t necessarily know where the birds go. If the plane can detect tagged birds it will be monumental for migration research.
Barainca is obsessed with aircraft. Although he already knew how to build planes, his engineering education has helped him apply what he has learned to biology. “Airplanes brought me to mechanical engineering, and my major has helped me analyze stress on the plane,” he said. Best of luck to Professor Holberton, Ani Varjabedian and Brian Barainca as they soar to a new level of bird research.
The purpose of the course is to be able to identify species of birds by sight and sound, and to be able to understand how specific birds are related to each other and how they are adapted to the environment. “I like the lectures because they are a lot of fun. I love learning about birds. They are unlike any other species on earth…I had heard that this class was the most sought after undergraduate ecology class at UMaine. I knew that it would be interesting, because I had Brian Olsen as a professor in BIO 100 & 200” explains Dana Freshley, a student studying communication with a minor in biology. This course allows students to see how all the interdisciplinary aspects of an organism’s environment play a role in the interaction of all living organisms.
“Biology is often taught through reductionism. Students learn about each system and biological mechanism isolated from all of the other things going on at the same time…The beauty of organismal sciences is that we get to talk about the nexus among the biological sub disciplines using a single organism as a semester long case study…I think that adds a needed flavor to how a student then interprets their other classes” explains Olsen.
In the lab, which is not a requirement, Olsen gives his students exposure to some of the major methods currently used by avian biologists. These methods provide students with pertinent skills by teaching his students identification skills without relying on a guidebook, or an iPhone, though these things are great resources for ecologist currently. Along with knowledge of general fieldwork procedure, the course exposes students to Program R (a very common program used by biologists), mist netting and capturing techniques, and how to use the necessary technology for ornithology, such as radio telemetry. These necessary skills provide students with building blocks for future work with birds in the eastern North America.
Olsen assigns his students a semester long project that will help improve their ability to construct a formal research paper. Students are able to design a field project, and analyze the data using the Program R mentioned above. Throughout the semester, students present on their research project, giving them multiple opportunities to receive input from their professor as well as their classmates. Dana Freshley and India Stewart, both current students in Avian Biology& Ecology, decided to do their research on the American Crow. Their project involves fieldwork in which they visit 6 birding spots a week, testing population habitat as a function of temperature. They will be presenting their results in a few weeks.
Olsen’s love for Avian Studies was sparked during a summer field job he acquired in the summer before his sophomore year college. He became a field site surveyor in the White Mountains, and from this experience his love for avian studies began to emerge. Olsen described his passion for Avian Studies as “A slow growing love.”
“Brian always keeps you alert, attentive, and he uses his sense of humor to teach his class. He always looks at the broader picture of ecology which makes him a great ecologist,” says Dana, a student of Olsen.
Olsen has been a valued member of our SBE Faculty since 2008. He has been teaching this course for five years, and he is still surprised and delighted by the diverse ways students handle difficult questions. “I really enjoy watching students grapple with open ended scenarios…when we work on hypothetical applications of biological theory, especially when students construct and defend answers that were far removed from what I expected” said Olsen. Olsen runs a research lab called “The Olsen Lab” with help from several undergraduate and graduate students. The research he focuses on in his Avian Biology course is not directly correlated to his personal research, though he does recruit potential students for his research in the Olsen Lab.
“In terms of research, I find a deep abiding joy by indulging my own intellectual curiosity and working with graduate students is deeply rewarding…to work with some of the best students form the undergraduate pool …allows for both the teaching relationship and the abilities of the students to grow. It is a pretty awesome experience.”
Good luck to Professor Olsen and his students as they finish up the rest of their semester.
Graduate student Jenny Shrum is as excited as ever to start her new project on maple trees this spring. She is interested in the role of sugar maples in the Northeast and is examining how climate change may shape this role. The first part of her study explores the plausibility of using traits expressed at the edge of a species’ range to help cope with climate change. In the case of sugar maples, she is interested in finding out if trees from other regions might actually be better suited to the conditions Maine will be experiencing in fifty years. If so, foresters and syrup producers may be able to plan sugar maple seeds from those regions here. Many people think that tree species exist here because they are best adapted to this environment, but that’s not always the case. “We might be able to utilize specific characteristics adapted by a certain subpopulation to help a forest or sugar bush to thrive despite climate change.” The second part of her study will try to draw correlations between sap flow and weather conditions to better understand how the sugaring season is likely to be affected as the severity, length, and timing of winter changes in the decades to come.
Shrum is a Ph.D. candidate in the Graduate Program in Ecology and Environmental Sciences and is working under SBE professor Brian McGill. Her dissertation will include planting different populations of sugar maple seeds from across the range in a common garden and comparing the rate of germination and seedling growth success. With a little luck, she hopes to find a successful tree that perhaps can be tapped for syrup in later years. Unfortunately Shrum won’t be able to tap the trees before her Ph.D. program is over. “It takes 20 years before you can tap a tree,” she said. However there may be people able to continue the study.
Shrum has found several citizens that have been tapping trees for many years, and they may be able to give insight into maple syrup production in the past and future. “One man said he doesn’t see sugar maples reproducing like he used to, and now he has to plant them himself,” she said. “Another man has been collecting soil temperature in his yard at two feet deep for the last 20 years. I can use this data to correlate temperature and snow cover to sap flow.” After talking to citizens it is clear to Shrum that maple trees provide a certain role in New England culture and are very important to the people of Maine.
Before coming to UMaine, Shrum was working on numerous wildlife ecology projects over a span of fifteen years, but she is enjoying working with maple trees even more. “I wanted to study something that had ecological, economic and social importance. This is something that families have been doing for years and I hope this research will be meaningful and help someone along the way,” she said. Best of luck to Jenny Shrum as she continues her research. Shrum is producing a short video about her research that will be available on the SBE website by mid summer.
The University of Maine Herbarium is the most comprehensive collection of plants, fungi, lichens, and mosses in Maine. Records concerning the establishment of the herbarium are unclear, but it is likely that it began when UMaine was created as the Maine College of Agriculture and the Mechanic Arts. One of the earliest contributors of specimens to the herbarium was Merritt Lyndon Fernald, the son of the third president of UMaine, Merritt Caldwell Fernald. Starting at age 13 Fernald collected plants, and the herbarium now has over 600 of his specimens that he collected throughout his lifetime. Fernald became a world-renowned botanist at Harvard. The Herbarium now houses about 70,000 specimens in Hannibal Hamlin Hall. Information about most of these specimens is also kept in a digital database that anyone can access by visiting the herbarium website (herbaria.umaine.edu).
The purpose of the Herbarium is to document the flora of Maine and to provide a repository for specimens. The Herbarium is also a teaching facility and a resource for the broader community. It is used in at least five biology classes ranging in topics from fungi to the taxonomy of vascular plants. Workers at the Herbarium, such as SBE graduate students Eric Doucette and Garth Holman, and Professor Chris Campbell, identify plants for citizens, farmers, land-trusts, people conducting conservation easements and others. Scientists interested in a group of plants that occurs in Maine can borrow UMaine specimens.
The UMaine Herbarium Friends Group, which meets monthly, focuses on caring for the specimens and usually works on one plant group that is native to Maine during each meeting. The specimens are kept in cases that are airtight. Periodically, the specimens are frozen for one week, which provides a non-toxic alternative to pesticides suppression of insect pests like dermestid beetles that can damage the specimens.
In addition to its primary mission of documenting the flora of Maine, the Herbarium is also used in other areas of research, such as climate change. Data from the timing of the opening of overwintering tree buds on Herbarium specimens, combined with other data, can be used to see if bud-break has shifted over the past 150 years. Scientists can also obtain samples of pollen from herbarium specimens and extract DNA from specimens are over 100 years old. Because of its significance in research, the herbarium is highly valuable to the research community.
The Herbarium is supported by members of the Josselyn Botanical Society of Maine.
The photo shows a University of Maine Herbarium specimen of northern white cedar (also called arborvitae). This conifer tree is common in Maine, often used as an ornamental, and its wood is important for log homes and shingles. As the label in the lower-right hand corner indicates, this specimen was collected in Lincolnville. In addition to the leaves, the specimen has cones (about 1 cm long) and a piece of the fibrous bark characteristic of this species.