Courses
Course Overview
As this is a foundations course for the GSBSE Ph.D. program, students may have a broad range of background experience and training in molecular biology and/or genetics – from very little to advanced. The goal of this course is to provide a common foundation for students in the major principles of molecular genetics from which students can base more advanced studies.
It is expected that by the end of this course you will understand the major principles of molecular genetics and the underlying processes by which cells and organisms replicate, repair, read, and translate their genetic codes. You should achieve an advanced understanding of these topics that will allow you to read the primary research literature, understand the biological processes examined, and interpret the results in the larger context of molecular genetics.
This class is offered in the Fall.
Topics Covered
- Mendelian inheritance, DNA as
genetic material & classic molecular
biology techniques - Genome structure, chromatin & the
nucleosome, DNA replication - DNA mutation & repair, homologous
recombination - Transcription & RNA splicing
- Translation, the genetic code
- Prokaryotic transcriptional regulation
- Eukaryotic transcriptional regulation
- Regulatory RNAs
- Gene regulation in development &
evolution - Site-specific recombination and
transposition - Systems biology, model organisms and
genetic disease
Instructor
Gregory A. Cox
Director, GSBSE
gregory.a.cox@maine.edu
(207) 581-3071
Course Overview
This course is the fourth and last half-semester module in the GSBSE BMS 625: Foundations sequence.
This course is a graduate-level introduction to Animal Physiology, with a special emphasis on building skills and knowledge relevant for a successful graduate and professional career. Students will take part in preparing and presenting content curriculum around a specific physiological system with relevance to their own ongoing or future research. A significant portion of the grade comes from class participation, including in critical thinking and analytical exercises as well as article discussions.
Special topics and scientific themes in the study of physiology will be presented in order to help students gain the skills and abilities needed to confront any physiological topic in the future.
This class is offered in the Fall.
Learning Objectives
- Be able to vet and acquire reputable scientific resources in physiology that span textbooks, review and primary research articles in peer-reviewed journals, and lay science articles.
- Think critically about experiments, data, and what knowledge is missing and can be pursued by research in fields of physiological research
- Present curriculum to peers in order to present an up-to-date view of a topic in physiology; spur discussion; create opportunities for analytical thinking.
- Build pedagogical skills relevant for a future career
- Understand the basics of several physiological systems, including: Metabolic, Immune, Nervous, Endocrine/Circulatory
- Appreciate the scientific themes that underlie physiological systems
- Gain skills and knowledge relevant for a successful graduate and professional career in the biomedical sciences; including team work
Instructor
Karissa Tilbury
Associate Professor of Bioengineering; Cooperating Associate Professor of Physics
karissa.tilbury@maine.edu
(207) 581-2460
Course Overview
This course is part of the foundations class and will survey selected advanced aspects of basic biochemistry that are both fundamental and relevant to GSBSE areas of investigational focus. Generally, this class will cover central principles of macromolecular structure and catalysis, intermediary metabolism, and aspects of macromolecular information flow (e.g., signaling).
Students will participate in class discussion or a research paper highlighting the topic at hand. Generally, the students will confer amongst themselves to provide an introduction/overview of the paper on hand, then split up presentation of the results by data figures, and then a summary, followed by further discussion by all. (Depending on the number of attendees, we may alternate responsibility for conducting the paper presentation to preassigned teams. However, in this case, everyone is still expected to participate in the overall discussion.)
This class is offered in the Spring.
Topics Covered
- Protein and enzyme pH behavior); protein tertiary and quaternary structures
- Enzymes
- Biosignaling: Receptor tyrosine kinases
- Intermediary metabolism I-Glycolysis
- Intermediary metabolism II-Gluconeogenesis, Pentose phosphate shunt
- Lipids
- Principles of Metabolic regulation-I Thermogenesis
- Principles of metabolic regulation-II
- Fatty acid catabolism
- Lipid biosynthesis
- Metabolic integration: tissues, hormones, and obesity
- Protein synthesis
- Targeting and degradation
- Regulation of gene expression in eukaryotes
- RNA-mediated gene regulation
- Developmental cascades
Instructor
Course Overview
This class is an introduction to biostatistics with application to the biomedical sciences and genetics, and introduction to computational biology.
The goal this course is for students to understand and apply the principles of statistics to appropriately design research studies, analyze the collected data, draw appropriate conclusions, and test assumptions. Students will learn basic modeling techniques such as linear regression, analysis of variance (ANOVA), and basic categorical data analysis. Students will be introduced to a sampling of advanced techniques and topics such as multivariate data analysis, missing data, multiple testing, survival analysis, and nonparametric methods. The overall goal is for students to have a broad understanding of good research design as well as understand some of the basic statistical methods available for the analysis of different types of data sets.
This class is offered in the Spring.
Topics Covered
- Introduction to Statistics: sampling theory, distributions, summary statistics, types of variables, hypothesis testing, confidence intervals
- Introduction to the R language, using Excel and R for basic statistical analysis, summary of graphing capabilities
- Regression and Correlation
- T-tests and ANOVA
- Categorical data analysis, Multivariate Analysis
- Study design and power analysis; Advanced topics: survival analysis, nonparametric methods, mixed models, missing data, multiple testing
- Introduction to genome-scale data: types of experiments, current technologies, experimental output
- Analysis of genome-scale data: quality assessment and correction methods
- Analysis of genome-scale data: dimensional reduction by data clustering
- Analysis of genome-scale data: functional assessment by integrating annotation data
- Basics of genetic association mapping and quantitative trait loci: data types and regression models
- Advanced topics in genetic association studies: linkage disequilibrium, population stratification, and model systems.
- Advanced topics in genetic association studies: epistasis and pleiotropy
Instructor
Matthew Dube
Associate Professor of Data Science, Computer Information Systems, and Applied Mathematics
(207) 621-3212
Course Overview
Reading, critiquing, and discussion of primary literature related to a biological question.
This class is offered in the Fall and Spring.
Topics Covered
- Varies
Instructor
Matthew Lynes
Faculty Scientist I
matthew.lynes@mainehealth.org
Course Overview
Students will become familiar with concepts of complex traits, gene mapping resources and computational approaches to analysis of genomic information.
The course will utilize Canvas course management capabilities to provide assignments, outlines, lecture material, stimulate discussion, etc. All students will be provided with access.
This class is offered in the Spring.
Topics Covered
- Accessing genome databases (Browsers, MODs)
- Modeling complex genetic disorders (DO, CC etc)
- Epistasis and Pleiotropy
- Beyond the sequence part 1: The proteome
- Beyond the sequence part 2: The epigenome
Instructor
Gregory A. Cox
Director, GSBSE
gregory.a.cox@maine.edu
(207)581-3071
Course Overview
Successful biomedical research requires proposing and testing a novel hypothesis, and the ability to apply the scientific method and implement the appropriate scientific methods to address the biological question. This course focuses on common techniques used in cell and molecular biology. By the end of the course, students will be expected to understand principals, assays, methods, and interpretation of data generated using these techniques. This course is designed for first and second year Ph.D. students or M.S. students. The format of this course will be student-led presentations and discussion of weekly topics, including analysis of published data from the literature. In addition, students will complete short problem sets during the semester. There will be a final written assignment to test the students’ mastery of the principles covered during the semester.
This class is offered in the Fall.
Topics Covered
- Orientation, Scientific Method and Lab Fundamentals of experimental design
- DNA methods I (DNA extraction, gels and restriction enzymes and mapping, Southern blots, sequencing, next gen)
- DNA methods II (Primer design, DNA polymerases, real time quantitative PCR, cDNA methods, nucleotide BLAST)
- DNA methods III (Bacterial transformation and plasmid purification, vectors for recombinant protein production, vectors for eukaryotic gene expression, viral expression vectors, DNA cloning
- RNA methods (Total RNA extraction, polyA RNA purification, Northern blot analysis)
- RNA methods II (siRNA, shRNA, microRNAs, RNA-seq)
- Gene regulation and expression methods (RNase protection assay, promoter reporter assay, gene chip microarray)
- Cell cycle analysis (flow cytometry, measurement of DNA synthesis, senescence, and apoptosis)
- Protein methods I (Protein extraction, SDS-PAGE, antibodies, western blotting, immunoprecipitation)
- Proteins methods II (translational assays, posttranslational modification, subcellular protein trafficking, secretion)
- Protein methods III (immunofluorescence/confocal microscopy, mass spec, proteomics)
- Cell signaling pathway methods (ligand-receptor interactions, detecting activation of receptors, detecting activation of signaling pathways)
- DNA-protein interaction methods (EMSA, ChIP, DNA reporter assays)
- Tissue culture methods (normal and transformed cell characteristics, tissue culture, gene delivery – lentivirus, adenovirus, retrovirus, and plasmid transfection)
- Mouse genetic models overview
Instructors
Course Overview
This course is intended to teach you the basics about writing a grant to secure funding for your scientific and/or engineering research. Throughout the semester, you will write a full grant and participate in a mock grant review process. The grant you write should encompass the work that one PhD student could accomplish, with their current resources, in 4-‐5 years of work. In addition to the nuts and bolts of grantwriting, this course will also cover some of the more bureaucratic aspects of writing (what organizations fund competitive grants, how do you find them, how do you tailor your proposal for them, how do you write a budget and biographical sketch). Writing a fundable grant requires imagination, knowledge of the scientific literature, time spent writing and rewriting to make your point crystal clear, and quite a bit of optimism. Are you ready for the challenge?
This class is offered in the Fall
Topics Covered
- Keys to writing a fundable grant
- Writing process overview video (online only)
- Developing your question
- Organization of the Research Strategy Section
- Key aspects of writing for the NIH: NRSA Graduate Fellowship
- Pre- and Post-award Management
- Organization of the Biosketch, Budget and Mentoring Plan
- Keys to writing for a private foundation
- Key aspects of writing for the NSF
- The review process
- Study section etiquette and training
- Mock Study Section
- Responding to critiques
Instructors
Prerequisite
This is a course for second year of PhD program or above, or with instructor permission. We highly recommend taking this course after successful completion of fall semester “Introduction to Experimental Design and Grant Writing”
Course Overview
This course follows up on the BMS 650 Grant Writing topics (a prerequisite for BMS 651) by focusing on preparing a fellowship research plan in the style of an NIH F31 predoctoral fellowship application based on your own thesis research to form the foundation for submission to a funding agency. The expertise of multiple faculty members will help to guide the crafting of your research ideas into a competitive fellowship application, with a strong and logical series of specific aims, experimental designs, predicted and alternative outcomes as well as future directions. The course culminates with your ability to experience a mock study section with course faculty and guest faculty across the GSBSE program reviewing and discussing each proposal and following NIH scoring conventions.
This class is offered in the Spring.
To be successful in this course, you are expected to:
- Have a dissertation research project that you can use to write a research plan
- Be willing to read and critique (with written comments) other students’ materials on a weekly basis
- Revise and improve your proposal throughout the semester
- Be willing for your proposal to undergo faculty review in a mock study section
Instructors
