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  • Funding Opportunity Announcement (FOA): Research / Pilot Projects at Undergraduate Institutions

    Funding is available for Research Projects, Pilot Projects, and Collaborative Pilot Projects in Maine through Maine INBRE.

    FOA is open for applications starting 11/13/2023; Applications Due 2/2/2024; Potential Start Date: 5/1/2024

    See FOA details here.

    Apply for project funding here.

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  • Newsletter: Maine INBRE News – August 2023

  • Summer Courses Wrap Up with Microscopy in Focus for Maine INBRE Students

    Students and young science faculty from all around Maine converged on MDI Bio Lab’s campus this month for an intensive 10-day course in the use of the most modern microscopy of the day.

     “When I started out I thought I knew all about microscopes: you adjust the lens, you look through light. And you see,” says Seth Ashby, a rising junior studying microbiology at UMaine Orono. “But what I didn’t realize, and almost every student I think would agree with this, is how little we actually knew about microscopy.”

    That knowledge gap was amply filled, Ashby says, by the daily lectures and hands-on experience provided by a roster of faculty and others who work with the array of advanced imaging instruments and software in MDI Bio Lab’s Light Microscopy Facility, directed by Frederic Bonnet, Ph.D.

    “We use microscopy as a tool that’s essential to microbiology, but we were severely underutilizing it,” Ashby says. “And I think that was the best part; every lecture without fail introduced that to me. And I loved it.”

    Ashby was one of 12 students and young faculty who applied for and won coveted seats in the course, which is offered free thanks to the federally funded Maine INBRE network. INBRE stands for IDeA Network of Biomedical Research Excellence. Led by MDI Bio Lab, the program is funded by a grant from the National Institutes of Health’s National Institute of General Medical Sciences. Over the last decade it has sent $87 million in direct support to 14 research and higher education institutions in Maine. Working collaboratively, they’ve leveraged those funds to provide-hands on research experience for undergraduates, support early career faculty as they build labs and seek research grants, and modernize scientific infrastructure, such as state-of-the-art microscopy. INBRE was created by Congress to steer federal research dollars to 23 rural and other small states (and Puerto Rico) with historically low levels of NIH funding. For students from economically challenging backgrounds, such as Seth Ashby, the support is vital.

    Read More

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  • Omics Training Available Now Through Maine INBRE-NIGMS (NIH)

    The NIGMS is offering free access to their new Sandbox platform through Maine INBRE. Access includes 12 analysis training modules in different -omics areas, image analysis and data science, as well as access to the computational infrastructure to complete the training.

    Contact Bioinformatics Core Co-Director Joel Graber (gro.lbidmnull@rebargj) ASAP to apply for a slot!

    NIH/NIGMS Cloud Learning Modules. This repository aims to teach students, researchers, and clinicians, among others, how to utilize the power of cloud technology for the benefit of life sciences applications and research. Types of data used across the modules include but are not limited to genomics, methylomics, transcriptomics, proteomics, and medical imaging data across formats such as FASTA/FASTQ, SAM, BAM, CSV, PNG, and DICOM. Learning modules range in areas from introductory material to single-omics approaches, multi-omics techniques, single cell analysis, metagenomics, and AI/ML imaging applications.


    • Fundamentals of Bioinformatics

    • Single-omics:
    — RNAseq
    — DNA Methylation Analysis
    — Transcriptome Assembly
    — Genomic Annotation and
    Pathway Analysis
    — ATACseq and sc-ATACseq

    • Multi-omics and Metagenomics:
    — Metagenomics of Biofilm
    — Multi-omics Analysis

    • Machine Learning:
    — Biomedical Image Analysis
    — Biomarker Discovery with ML/AI

    • Data Science Methodology:
    — Biomedical Data Science

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  • Dr. Timothy Breton Awarded $551,000 NSF Grant

    Former Maine INBRE project leader Dr. Timothy Breton (University of Maine at Farmington) has been awarded a National Science Foundation (NSF) grant to support studies that are a continuation of his INBRE-funded research. The $551,559  project is jointly funded by the Physiological Mechanisms and Biomechanics Program of BIO-Integrative Organismal Systems and the Established Program to Support Competitive Research (EPSCoR) at NSF.

    “This work directly stemmed from my prior INBRE award and is a continuation of the project”, said Dr. Breton. “(The award) is in no small part thanks to the INBRE awards and support for UMaine Farmington that served as the foundation. In addition to the science, the project also has a large role in growing bioinformatics education in four western Maine high schools.”

    Read more from UMF here.

    Details on the research program:

    SREBs (Super-conserved Receptors Expressed in Brain) are a group of hormone receptor proteins in vertebrate animals whose function is poorly understood. This knowledge gap stems from a lack of verified hormones that bind to SREBs on the surface of cells. Previous studies have supported functional roles for SREBs in the brain, gut, and gonads that may be conserved in animals. This project applies novel, artificially synthesized molecules that are known to bind to SREB receptors in ovaries of three fish species to assess SREB function in reproduction. The species were chosen based on previously identified genetic differences resulting in different profiles of SREB subtypes across these species. Results will be compared among the fish species to identify unique and shared functions. The resulting improved understanding of SREB functions may provide a foundation for future commercial applications in animal reproduction and in aquaculture. The research will generate databases that will foster undergraduate and high-school student research experiences in bioinformatics in rural western Maine, which has a high proportion of first-generation college students. Local high-school teachers will be trained to use these databases in their classes and to develop independent bioinformatics modules for sustainable use. These educational activities serve as a scalable model to bring bioinformatics training to under-served student populations, contributing to biotechnology workforce development. In addition, through a collaboration with two researchers at the University of Florida, the project will contribute to training of a graduate student and post-doctoral fellow.

    The project starts on September 1, 2023.

    Related articles about Dr. Breton’s research:

    Student Authors at UMaine Farmington

    Sharing Core Facilities Vital to Research at UMaine Farmington

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  • Former Colby INBRE Student Authors Paper in Scientific Reports Journal

    Colby College graduate Laura Drepanos (B.A., 2023, Computational Biology) is the first author of a paper recently published in the journal Scientific Reports, describing findings from her undergraduate research. The article, Loss of Krüppel-like factor 9 deregulates both physiological gene expression and development, presents research related to the function of a biomedically important, stress responsive transcription factor, Krüppel-like factor 9 (Klf9). Drepanos’ participation in Colby’s January 2021 INBRE short course on RNA-seq data analysis sparked an interest in independent research. She was awarded an INBRE undergraduate research fellowship during the summer of 2021, during which she was co-mentored by Drs. Joel Graber and James Coffman, analyzing data from an RNA-seq experiment that had been performed by graduate student Ian Gans in the Coffman lab to determine how gene expression and Klf9 function vary with time of day in zebrafish larvae. She continued this work under the mentorship of Dr. Andrea Tilden at Colby and the Bioinfomatics Core through the Maine INBRE Bioinformatics Scholars program during the academic year. That work, together with follow up experiments carried out in the Coffman lab, culminated in the published paper.

    Drepanos also held academic year fellowships at the Jackson Laboratory, working in the lab of Dr. Gregory Carter to study genetic factors that alter neurological pathways and potentially lead to human diseases like Alzheimer’s and lupus. She is currently employed as a Computational Associate at the Broad Institute of Harvard & MIT, working in research and development on their functional genomics Genetic Perturbation Platform.

    Additional authors on the paper include Ian Gans, a former University of Maine graduate student who was awarded his Ph.D. in 2022 and is now a postdoctoral research fellow in the Myocardial Biology and Heart Failure lab at the MaineHealth Institute for Research; Janelle Grendler, a University of Maine Machias graduate and alum of the ME-INBRE student research program who is a Research Assistant in the Coffman Lab at MDI Biological Laboratory; Sophia Guitar, a student at Lafayette College who worked as an undergraduate research fellow in the Coffman lab in 2022, as well as Drs. Tilden, Graber, and Coffman, and INBRE Bioinformatics Core staff.

    Drepanos L, Gans IM, Grendler J, Guitar S, Fuqua JH, Maki NJ, Tilden AR, Graber JH, Coffman JA. Loss of Krüppel-like factor 9 deregulates both physiological gene expression and development. Sci Rep. 2023 Jul 28;13(1):12239. doi: 10.1038/s41598-023-39453-3. PMID: 37507475; PMCID: PMC10382561.

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  • Summer Symposium Features Research from Undergraduate Fellows


    University of Maine-Farmington student William Harriman, who was mentored by by Dr. Geoffrey Ganter at the University of New England, presents his research findings at the Student Summer Symposium earlier this month.

    The annual Student Summer Symposium was hosted at MDI Biological Laboratory on Friday, August 4th and featured the research findings of undergraduate student fellows from colleges and universities across Maine through  short talks and poster presentations.

    The 17 undergraduate students highlighted below were awarded 10-week mentored research fellowships at various academic and research institutions in Maine through INBRE. In addition to mentored lab research, the students participated in bioinformatics workshops, translational medicine lectures, a Communicating Science course, as well as responsible conduct of research training.

    Student Fellow Home Institution Mentor/s Research Site
    Katelyn Amero UMaine Honors College Dr. Sally Molloy University of Maine
    Kaitlyn Armstrong UMaine Machias Dr. Jane Disney MDI Biological Lab
    Katherine Buetens Bates College Dr. James Godwin MDI Biological Lab
    Katrina Carrier Bowdoin College Dr. Daniel Powell Bowdoin College
    Eleftheria-Sofia Dragoti College of the Atlantic Dr. Reuben Hudson College of the Atlantic
    Elijah Dumdie Bowdoin College Dr. Hadley Horch Bowdoin College
    Toby Dunne So.Me.Comm College Dr. Dustin Updike MDI Biological Lab
    Lucas Girard So.Me.Comm College Drs. Joel Graber & Andrea Tilden MDI Biological Lab
    William Harriman UMaine Farmington Dr. Geoffrey Ganter University of New England
    HaoWen Huang Colby College Dr. David Angelini Colby College
    Raheem Khadour College of the Atlantic Dr. Nadia Rosenthal Jackson Laboratory
    Hayden Kittell UMaine Machias Dr. Lori Banks Bates College
    Sebastian Leon Fallas Bates College Dr. Prayag Murawala MDI Biological Lab
    Michael Patnaude UMaine Farmington Dr. Romain Madelaine MDI Biological Lab
    Carla Rodriguez Medina UMaine Fort Kent Dr. Jared Talbot University of Maine
    Katherine Stevens UMaine Honors College Dr. Robert Wheeler University of Maine
    Abigail Wick Colby College Dr. James Coffman MDI Biological Lab

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  • Former INBRE Fellow Nishad Jayasundara Awarded a Named Chair at Duke

    Former INBRE fellow and College of the Atlantic grad Nishad Jayasundara has been named the Juli Plant Grainger Assistant Professor of Global Environmental Health at Duke University, where his research focuses on exploring the adverse ecological and human health impacts of chemical pollution and climate change.

    Nishad Jayasundara in 2006 as a then recent graduate of the College of the Atlantic.

    Known for his innovative studies using fish species as sentinels to measure the biochemical and physiological consequences of exposure to chemical and physical stressors, Dr. Jayasundara recently has been working with an interdisciplinary team of environmental and health researchers to unravel how climate change and water contamination may be driving a rise in kidney disease among rice farmers in Sri Lanka.

    “The quality of Nishad’s research speaks for itself. Though still in the early stage of his career, he’s already tackling complex challenges and doing work that could have far-reaching beneficial impacts on the health of people and our planet,” said Toddi Steelman, Stanback Dean of the Nicholas School at Duke.

    Read full article from Duke University here.

    While studying at the College of the Atlantic in 2002, Nishad signed up for a short course on molecular biology offered through the INBRE program. This sparked an interest in hands-on scientific research that led to a BRIN (precursor of INBRE) research fellowship during that summer in which he studied the toxicology of hexavalent chromium in marine animals. These experiences, as well as staff research assistant positions at both the Jackson Laboratory and MDI Biological Laboratory, paved the path for him to pursue a Ph.D., which he received in 2012 from Stanford University.

    Jayasundara pursued these passions for 4 years as an assistant professor in the School of Marine Sciences at the University of Maine, and joined the faculty as an assistant professor of environmental toxicology and health at Duke University’s Nicholas School of the Environment, where he had received his postdoctoral training. During that time and in recognition of his early-career work on the consequences of exposures to polycyclic aromatic hydrocarbons (PAHs), he received the prestigious Karen Wetterhahn Memorial Award from the National Institute of Environmental Health Sciences in 2015.

    “During my undergraduate years in Maine, I benefited immensely from the research opportunities that were available for students and I am excited about creating a research platform for students who are curious about how changes in the environment are affecting the biological systems around us,” he said.

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  • INBRE Course Sparks Interest in Biotech Tools

    Freeport resident Samuel Broadbent’s first exposure to the advanced gene-editing technology called “CRISPR” came during an INBRE short course for College of the Atlantic undergraduates. That fired an ongoing interest in the science of developmental biology.

    “I find development to be particularly fascinating, how we go from a single cell to an entire organism,” he says. Today Broadbent continues to pursue his passion at the MDI Biological Lab, where most recently he has been training to use a truly state-of-the-art 3D “light sheet” microscope that the Lab just constructed – one of only 20 like it in the world. “The Lab has an amazing variety of tools which are really unique, like this microscope,” Broadbent says. “There are a lot of techniques and technologies at this institution that you can’t necessarily get working at other labs. I think that’s a big advantage for me, going forward as a young scientist, an aspiring scientist.”

    And those tools are at the service of science-hungry learners all over Maine, from high schoolers to senior researchers, thanks to the collaborative network of 14 educational and research institutions that comprise INBRE in Maine. The network provides them the advanced tools, training, and research experience they need to fully participate in today’s biotech revolution.  Over the last decade, INBRE has trained and provided research experiences to thousands of Mainers. Ninety percent of them have pursued post-graduate degrees or careers in health-related fields, and 21% are earning advanced degrees here in Maine.

    Students participate in the 2023 summer undergraduate research fellowship program.

    Read more here.

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  • Core Access Grants Available

    The Maine INBRE Core Access voucher program offers grants (up to $5000) to researchers affiliated with institutions involved in biomedical research and research training in Maine. These awards support research conducted at any Core facility in a northeast IDeA state (Maine, Vermont, New Hampshire, Rhode Island, and Delaware) or other IDeA states if local services are unavailable. Funding is provided on a rolling basis and is determined by the scientific merit, availability of core services, and relevance of the proposal to biomedical research. For detailed information, please refer to the Funding Opportunity Announcement (FOA) and the Maine INBRE website application instructions. Please note that scientists directly funded by a COBRE or other INBRE award are not eligible for funding through this program.

    Example of projects recently funded through this program include:

    • Xuehui Yang, Ph.D., MaineHealth Institute for Research (faculty). $5000 to fund “Molecular Identity of Perivascular Adipose Tissue from Human Abdominal Aortic Aneurysm” to be used at the Dartmouth Genomics and Molecular Biology Shared Resource (GMBSR).
    • David Carlon, Ph.D., Bowdoin College (faculty). $5000 to fund “Mitogenomic mediated changes in gene expression in response to temperature stress” to be used at the Jackson Laboratory Sequencing Core.
    • Timothy Breton, Ph.D., University of Maine Farmington (faculty). $4900 to fund “Comparative profiles of the super-conserved receptors expressed in brain (SREB) in non-mammalian vertebrates” to be used at the MDI Biological Laboratory’s Animal, Microscopy, and Bioinformatics Core.
    • Ada Olins, Ph.D., University of New England (faculty). $2600 to fund “The resilience of in situ nuclear chromatin architecture” to be used at MMCRI’s Microscopy Core.

    There is a rolling application process and if awarded, funds can support services through April 30, 2024.

    Contact:  Dustin Updike, Program Coordinator, gro.lbidmnull@ekidpud

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