Reverse Ecology:
Computational Integration of Genomes, Organisms, and Environments

IGERT Curriculum







Curriculum

Education and Training

Overview.  Brown/MBL IGERT fellows will spend their first two years engaged in a stimulating framework for education and research that sponsors a dialogue at the interface of molecular biology, environmental science and computational biology.  A new Core Curriculum will focus on explicit training in how to approach integrative biological and environmental questions with training in field work, experimental design, next generation genomic analyses, and computational and statistical tools that are applied to a practical problem spanning traditional disciplinary boundaries. This will be achieved through a year-long immersion course, foundation course work in specific disciplines, research rotations, and training in grant writing, professional skills, and global perspectives on research that teach integration as a discipline on par with traditional courses (e.g., ecology, genetics, or computer programming). 

Components of this Core Curriculum include four modules that will be completed in the first two years: 1) A flagship year long immersion course on Reverse Ecology co-taught by Brown and MBL faculty incorporating hands on training in field work, experimental design, next generation genomic analysis, and computational and statistical training focused on an integrative question at Long Term Ecological Research (LTER) sites; 2) core courses in each of four distribution areas (see Figure 1) to ensure depth of training in the foundations of reverse ecology; 3) Team-based research rotations where students and faculty from across disciplinary boundaries engage in specific research projects sponsored by participating Brown and MBL faculty; and 4) A skills and professionalism course where expertise in grant writing, seminar presentation, ethics, international perspective on science, and outreach to non academic partners are developed.

Reverse Ecology Immersion Course.

IGERT fellows will take this course in their first year of support.  Students and faculty will tackle an integrative problem in environmental and organismal genomics centered around research at participating Long Term Ecological Research (LTER) sites with which many MBL faculty have been involved. We will focus on field sites that are within driving distance of Brown and MBL to enable repeated access and to stay within budgets, such as the Plum Island and Harvard Forest LTER Sites, and the Great Sippewissett Salt Marsh site near MBL.  Each field site is a nexus of researchers from all over the world and will provide a broad context for fellows to become familiar with a diverse body of research carried out by researchers from many countries.  These sites provide ideal experimental contexts for the application of Reverse Ecological approaches 

Field Biology.  The course will begin in late August with a retreat at the focal LTER site where a review of ongoing research will be provided by faculty. Field trips to important microhabitats within each site will be conducted and critical ecological, environmental and organismal characteristics that are amenable to genomic analyses will be presented.  This will provide a working knowledge of the patterns in nature unique to the focal LTER site, and will develop camaraderie among the IGERT fellows for a sense of common mission. 

Project and Experimental Design. The course will run for both semesters of the academic year and will meet twice a week.  Meetings will involve the analysis of primary literature related to the day’s topic, and an open round table discussion to address the question at hand, or a laboratory session.  In the first section of the course, the team will formulate testable hypotheses that address specific questions about ecological function and organismal adaptations at the LTER sites.  The next section will focus on experimental design and statistical analysis for powerful, ecologically and genomically informed sampling regimes to address these questions.  For example: How should one sample salt marsh estuaries to test the hypothesis that microbial ‘species’ track this salinity gradient?  How should one sample the genome or transcriptome of Impatiens test the hypothesis distinct morphologies are locally adapted when a reference genome is not available? 

Wet Lab Methods. Samples will be processed for nucleic acid extraction as well as other phenotypic and environmental metrics needed for the question at hand.  Wet lab skills will be developed in a molecular biology module as needed for all fellows, using either Brown or MBL laboratory facilities. A major theme of this section will be to deconstruct the commonly used (and highly effective) kits and methods that are now a staple of wet lab analyses.  Soil DNA Kits, gel extraction kits, DNA concentration columns, etc. provide mysterious buffers and columns with cook book instructions. Mail-order primers, adapters and sequence analysis result in little tubes coming back in the mail or an email with a link to sequence reads.  Most users never take the time to understand how these things work, and many don’t care.  A critical component of the analysis and discussion during this section will be researching the origin and composition of these kits, and the chemistry, biochemistry, and molecular biology underlying their efficacy.  This will be a hands-on way of teaching the critical foundation material in an efficient and targeted manner.  The end result of this section will be samples of nucleic acid that are ready for next generation sequence analysis. 

Computational and Statistical Analysis. This section of the course will provide the instruction to enable fellows to manipulate and analyze short-read DNA sequence data sets using Perl and Python scripts and the R statistical package.  High throughput DNA reads will be processed, using either the MBL’s W. M. Keck Ecological and Evolutionary Genetics Facility, or outsources as needed.  The resulting files are very large and are not amenable for typical laptop software package analysis.  While some software is coming on line, the types of questions motivating the research often dictate what kinds of information needs to be extracted from short read data sets.  Faculty at MBL and Brown (e.g., Sogin, Dunn, Mark Welch, Huber) have considerable experience with these analyses and will guide this section of the course.   

Data Presentation and Manuscript Preparation. The final section of the course will involve instruction in data presentation and manuscript preparation based on the results and analyses performed in the earlier sections.  This will begin with a mini symposium where fellows will give short talks on their specific projects. Each presentation will require independent intellectual contribution, but also state the clear collaborative nature of the effort, as the two main themes (environmental and organismal genomics) will involve 3-5 fellows each year.  The presentations will be critiqued on their presentations to obtain formal instruction in public speaking. Ultimately, the project(s) will be written up for submission of one or more manuscript(s) at the end of the semester, with fair and balanced distribution of analysis and writing efforts. 

Core Curriculum Distribution Requirements

To complement this immersion course, all fellows will be required to take one additional course in each of the four areas listed below that span the intellectual breadth of Reverse Ecology: 1) Ecology and Evolutionary Biology, 2) Molecular and Cellular Biology, 3) Computational Biology and 4) Applied Math & Statistics.  All fellows will have an Advisory Committee that will recommend courses based on each fellow’s previous undergraduate training, current interests and professional goals, and recommend courses that fit these needs.  Note that many of these courses can also apply as credit in the core curriculum of a student’s home department.  This will allow students to complete both the IGERT requirements, and their graduate program requirements without undue course burden in the first two years.  Below is a partial listing of relevant courses in each area.

Ecology & Evolutionary Biology (EEB) Ecology, Evolution, Evolutionary Genetics, Evolutionary Ecology, Evolutionary Medicine, Experimental Design in Ecology, Environmental Science, Plant Diversity, Plant Ecology, Plant Ecological Physiology, Marine Biology, Microbial Diversity in the Environment, Microbial Diversity (MBL Summer Course), Workshop in Molecular Evolution (MBL summer course), Quantitative Approaches in Biology, Terrestrial Biogeochemistry and the Functioning of Ecosystems

Molecular & Cellular Biology & Biochemistry (MCB) Biochemistry, Cell and Molecular Biology, Microbiology, Genetics, Embryology (MBL summer course), Environmental and Genetic Toxicology, Introduction to Genomics and Bioinformatics, Molecular Genetics, Molecular Biology of Microbes, Physiology, Plant Physiology, Comparative Animal Physiology, Synthetic Biological Systems, Techniques in Molecular and Cell Science, Virology

Computer Science (CS)  Introduction to Computing, Algorithms and Data Structures, Programming with Data Structures and Algorithms, Discrete Structures and Probability, Systems Programming, Modules of Computation, Database Management Systems, Distributed Computer Systems, Probabilistic Methods in Computer Science, Computational Molecular Biology, Computational Theory of Molecular Evolution, Algorithmic Foundations of Computational Biology, Computational Methods for Biology

Applied Mathematics and Statistics  (AM) Introduction to Mathematical Modeling, Methods in Applied Mathematics, Quantitative Models in Biological Systems, Inference in Genomics and Molecular Biology, Statistical Inference I & II, Computational Probability and Statistics, Mathematical Models in Computational Biology, Partial Differential Equations, Discrete High-Dimension Inferences in Genomics, Applied Regression and ANOVA.

Research Rotations

Each fellow will participate in a team-based research rotation with Brown or MBL faculty.  The participating IGERT faculty are spread among four Departments at Brown and two Centers at MBL, and span a wide range of topics related to the Reverse Ecology theme.  Rotations will be conducted as integrative projects among collaborating faculty.  Students with biological and computational expertise will be paired with faculty with complementary expertise to focus on the details of ongoing research of these faculty.