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COPY OF Events

  • INBRE Offers a new Data Science Workshop

    We are excited to share information about a new, one-day Data Science workshop for our INBRE network in which participants will learn to implement robust, reproducible, and cost-effective high-performance bioinformatics pipelines in the Cloud: https://mdibl.org/course/workflows-in-the-cloud-2024/. This workshop will be held on the MDI Bio Lab campus on Thursday, April 25, and is geared toward senior undergraduate and graduate students, post-docs, and both research and teaching faculty. Apply today – space is limited!

    Apply Here

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  • Maine Science Symposium (MBMSS) Will Take Place on April 26-27, 2024

    The Maine Biological & Medical Sciences Symposium (MBMSS) is a statewide gathering of scientists and students; an opportunity to share research results, exchange ideas, promote collaboration, and network with Maine scientists in a variety of disciplines. This promises to be another wonderful event, and will feature new Maine faculty as well as student research. Our keynote speaker will be Dr. Martha Muñoz, an evolutionary biologist from Yale University. If you haven’t registered already, don’t wait! The abstract deadline for this year is Monday, April 8.

    Register Here

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  • Former Maine INBRE Director Patricia Hand Honored

    Patricia Hand, Ph.D., was presented with the 2024 W. Fred Taylor Award on February 26, 2024 for outstanding contributions to the National Institutes of Health’s Institutional Development Award program (IDeA). The award, presented by the independent EPSCor/IDeA Foundation, honors the commitment and service of W. Fred Taylor, Ph.D., a founding director of the IDeA program, which is administered by the NIH’s National Institute of General Medical Sciences (NIGMS).

    Hand was instrumental in the success of the program’s mission to expand opportunities for students, young faculty and institutions in states and territories that had historically seen low levels of biomedical research funding. Hand, an immunologist and longtime senior staffer at MDI Bio Lab, proved to be a talented and dedicated partner for such efforts in Maine.

    “I’m honored to receive this award, as I have the utmost respect and admiration for what Dr. Taylor and his NIGMS colleagues have done to strengthen biomedical research capacity in IDeA states,” Hand said. “It was the highlight of my career to work with my colleagues at MDI Biological Laboratory, and other institutions in Maine, regionally and nationally on this significant initiative.”

    Hand received the award during a luncheon held in the Intercontinental Hotel. Also on hand were MDI Bio Lab’s president, Herman Haller, M.D., Chief of Staff Jeri Bowers and James Coffman, Ph.D., the current director of the Maine INBRE, an IDeA-funded network of state research and academic institutions that Hand established and led for 15 years.

    “Thousands of Maine students and young faculty have benefited from Dr. Hand’s scientific vision and administrative brilliance,” Haller said. “Thanks to her high standards and hard work, the Maine INBRE is a shining example of how well-placed federal investments can unlock a rural state’s potential for scientific achievement and competitiveness in the biomedical economy.”

    In 2001, Maine was among the first states to be tapped for a new IDeA initiative, now called the IDeA Network of Biomedical Research Excellence, or INBRE. MDI Bio Lab was chosen to lead the Maine INBRE; Hand was its Principal Investigator from its inception until 2016.

    The Maine INBRE started out as a consortium of six research and academic that collaborated to provide students with firsthand research experience, support early-career faculty and build more robust research infrastructure. Some two decades later, the resource-sharing network now embraces 14 institutions in Maine and is poised for more growth.

    Since it began, the Maine INBRE has provided hands-on research experience to more than 2,600 students, created and sustained more than 100 jobs in the state, provided $87 million in direct funding to state institutions, and provided resources to early career faculty that helped them win more than $110 million in other federal research grants.

    Ninety percent of Maine INBRE graduates have gone on to  advanced degrees or careers in scientific and medical fields; 21% have pursued those goals here in Maine.

    “Patricia was the driving force for establishing and growing the Maine INBRE program and network of institutions,” said MDI Bio Lab’s James Coffman, Ph.D., who now directs the Maine INBRE. “This was no small feat, as there was no precedent to provide a model for the undertaking. Patricia took up the challenge, recognizing the exceptional opportunity the program afforded for developing Maine’s largely disconnected collection of research and academic institutions into a cohesive collaborative network, to the benefit of all.”

    MDI Bio Lab press release

     

     

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  • Open FOA: Funding Available for Research / Pilot Projects in Maine

    The Maine INBRE currently invites applications for three types of project awards: Research Projects; stand-alone Pilot Projects; and Collaborative Pilot Projects. Investigator and institutional eligibility, duration, and scope for each of the three types of awards are described in the Funding Opportunity Announcement (FOA). Funding decisions will be based on the scientific merit of the proposed research and the ability to involve students in significant, innovative biomedical and data science research.

    Applications Due 2/2/2024; Potential Start Date: 5/1/2024

    These funding opportunities are available to qualified faculty at the following undergraduate institutions in Maine: Bates, Bowdoin, and Colby Colleges; College of the Atlantic; Universities of Maine at Orono, Farmington, Machias, Augusta, Presque Isle, Fort Kent, and the University of Southern Maine; Southern Maine Community College; The University of New England.

    Qualified faculty at the following research institutions in Maine are eligible for funding as part of a Collaborative Pilot Project: University of Maine at Orono; MaineHealth Institute for Research; The Jackson Laboratory; and the MDI Biological Laboratory.

    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.

    TRAINING MODULES

    • 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.

    Citation:
    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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