Graduate Courses

BIOL 51600 - Molecular Biology of Cancer - Session Offered: Spring

The course begins with a review of the current research techniques used to examine the biology of eukaryotic cells and then covers seminal discoveries in the areas of cell cycle regulation, DNA, and RNA tumor virology, growth factors and their receptors, signal transduction and oncogenes.  For all topics, an emphasis is placed on the molecular mechanisms governing growth regulation and how alterations in these mechanisms can give rise to disease states such as cancer.  Reading of both historical and current primary literature is required as a supplement to a course textbook.

This course is designed primarily for students interested in professional careers in which a knowledge of molecular biology, as it pertains to growth control and human cancer, would be useful.  There are three scheduled guest lecturers, each of whom presents a seminar on a current cancer research topic in their laboratory.

BIOL 51700 - Molecular Biology: Proteins - Session Offered: Spring

The principles of protein three-dimensional structure are examined.  The course is divided into "theoretical" and "application" sections.  In the theoretical section, general principles of protein structure are discussed in detail.  In the application section, the structural principles learned in the first part of the course are applied to particular protein systems.  Topics covered in the theoretical section of the course include:  covalent structure of proteins; protein secondary, tertiary and quaternary structure; physical forces influencing protein structure; protein surface areas and internal packing; internal motion in protein molecules; protein folding; comparison of protein primary and prediction of tertiary structures; and structural features of integral membrane proteins.

Students use computer graphics to visualize the principles of protein architecture that are described in class, to take quizzes, and to do homework assignments.

BIOL 52900 - Bacterial Physiology - Session Offered: Spring

 

A detailed consideration of several of the following topics from the primary literature:  function and regulation of central metabolic routes; mechanisms controlling intercellular signaling and differentiation; transport and secretion; specialized metabolism, including photosynthesis, methanogenesis and microbial alternative energy production; evolution and interaction of regulatory systems. 

The course emphasizes metabolic features that are common for all bacteria or for large groups of organisms and is intended for students in many different departments who need an understanding of bacterial physiology.  A major section of the course revolves around genomics and high-throughput techniques such as transcriptomics, proteomics and next-generation sequencing.  As part of this section, students are taught how to use free, web-based computer software that is available for finding and analyzing such information.

BIOL 53300 - Medical Microbiology - Session Offered: Fall

This is an advanced undergraduate course on bacterial pathogenesis. Topics will include basic principles of the infectious process, infectious agents, mechanisms of pathogenesis, technologies for studying bacterial pathogens, and genomics of human bacterial pathogens. Reading assignments will be from course textbook and scientific literature.

BIOL 53601 - Biological & Structural Aspects of Drug Design & Action - Session Offered: Spring

This course will provide an overview of the modern day drug discovery pipeline process and an in-depth look at the basic biology, structure, and mechanisms-of actions behind currently marketed therapeutics.  The course will start with a historical account of the discovery of natural product drugs such as aspirin and penicillin and will then venture into the modern day era of the drug discovery pipeline with an emphasis on the principles of target selection, assay development, high-throughput screening and structure-based drug design.  We will explore different classes of antibiotics, antiviral, and anti-cancer drugs and their targets including small molecule drugs and modern biologics-based drugs.

BIOL 53700 - Immunobiology - Session Offered: Fall

BIOL 53700 is an introductory course intended for graduate and senior undergraduate students interested to learn why we do not die from a common cold and why you cannot always give a kidney to your best friend.  This course will define the role of the immune system in fighting infection, its potential to prevent cancer, and describe how through the use vaccines people can avoid these illnesses.  We will also discuss the other side of the immune system, the one causing problems, such as autoimmunity, allergy, and transplant rejection.

BIOL 53800 - Molecular, Cellular and Developmental Neurobiology - Session Offered: Spring

From Alzheimers and Parkinsons disease to stroke and neurotrauma, neurological disease and injury present some of the most debilitating and intractable medical problems.  Recent progress in molecular neuroscience has begun to reveal the mechanisms of several human neurological diseases and to suggest potential therapies.  Biology 538 explores topics in basic cellular, molecular and developmental neuroscience and their connections to neural disease and injury.  Readings are derived from the current literature.

BIOL 54100 - Molecular Genetics of Bacteria - Session Offered: Fall

Advanced bacterial genetics, with emphasis on the use of genetics as a powerful and creative intellectual activity that enables us to discover biological functions and to construct new organisms by the manipulation of DNA. Major topics include mutations, genetic selections, recombination, regulatory mechanisms, genomic evolution.

BIOL 54200 - Lab in Neurophysiology - Session Offered: Fall

In this five-week module, students will study laboratory methods in electrophysiology by focusing on membrane potential, action potentials and their propagation, and neuromuscular transmission. Students will be introduced to the theory and use of amplifiers, electrodes, data collection and analysis.

BIOL 54900 - Microbial Ecology - Session Offered: Spring

The course will cover a small number of topics in which there has been extensive recent research and emphasizes the physiological responses made by microorganisms to their environment.  The topics include the adaptations made to nutrient limitation and starvation, microbial utilization of xenobiotic compounds, techniques to measure microbial activities in natural environments, metabolic interactions between microbes and other organisms, and the interdependence of microbial, physical, and chemical factors in aquatic ecosystems. Bacteriophage and their role in the environment will also be addressed.  Reading assignments will be made from review articles and primary research articles relevant to the topics.  There will be several class projects that will use molecular methods for evaluating bacterial community structure and the use of bioluminescent organisms for in situ monitoring of microbial physiology and nutrient bioavailability.

BIOL 55001 - Eukaryotic Molecular Biology - Session Offered: Spring

Eukaryotic Molecular Biology will be a general survey course intended for advanced undergrads and beginning grad students.  The course will draw upon examples from the plant, animal, and fungal kingdoms, and will familiarize students with the basic principles of molecular biology analyses as they apply to eukaryotic organisms.  By the end of the course students should have knowledge of these molecular processes and should be able to design and analyze experiments dealing with these topics.  This is not a first course in molecular biology.  Recommended BIOL 41500

BIOL 56200 - Neural Systems - Session Offered: Spring

Overview of the structure and function of neural systems including those involved with motor, somatosensory, visual, auditory, learning, memory, and higher cortical processes. Molecular and cellular aspects of neural function are integrated with discussion of relevant neuroanatomy. Background in cell biology, psychobiology, physiology or anatomy is recommended. Typically offered Spring.
3.000 Credit hours

BIOL 56310 - Protein Bioinformatics - Session Offered: Spring

Accumulation of biological data, such as genome sequences, protein structures and sequences, metabolic pathways, opened up a new way of research in biology - bioinformatics.  Through the survey of the various active research topics in bioinformatics, in this course we will learn bioinformatics databases, tools, and algorithms behind these tools.  Special emphasis is placed on protein sequence and structure analyses.  Covered topics will include methods for protein sequence comparison, protein structure comparison, protein structure prediction/modeling, protein docking prediction, protein function prediction, and protein network analysis.

BIOL 58000 - Evolution - Session Offered: Spring

The course explores evolution as a basic concept of the biological sciences and examines current methods of experimentation within the area, as well as evidences for and possible mechanisms of evolutionary change.

BIOL 58210 - Ecological Statistics - Session Offered: Fall

This course covers topics that are useful for successfully designing and analyzing statistically observational and experimental studies in ecology, animal behavior, evolutionary biology, forestry, wildlife sciences, fisheries, etc. Some topics are: differences between hypotheses and predictions, design of an ecological study, general linear models, assumptions, different types of designs (factorial, nested, repeated measures, blocks, split-plots, etc.), fitting models to data, etc. The course will focus on the conceptual understanding of these topics (e.g., interpreting the results of statistical tests) and practice with statistical programs and real datasets.

BIOL 58705 - Animal Communication - Session Offered: Fall

This is an alternating year course, next offered Fall 2020, Fall 2022,Fall 2024.

  BIOL 58705 will be a broad-scaled analysis of animal communication. Topics will include the physics of sound- and light-signal production, propagation and reception of signals, the use of communication as a means of information transfer, and the evolution of signaling systems. Comments:  Some mathematical principles will be covered (e.g. in the evolution of signals), so some background in mathematics (e.g. calculus or algebra and introductory physics) would be helpful.

BIOL 59100 - Field Ecology - Session Offered: Fall

This is an alternate odd year course. Next offering Fall 2019, Fall 2021. 

A field course in ecology that stresses natural history and testing ecological theory under natural conditions. Group and individual projects include observational and experimental approaches. Emphasis is on the study of plant and animal species interactions in terrestrial (including montane and coastal) and aquatic habitats. Issues in community, population, behavioral, and conservation biology are addressed. Several all-day Saturday and two weekend field trips. 

BIOL 59200 - Evolution of Behavior - Session Offered: Spring

This is an alternating year course. Next offered Spring 2021, Spring 2023. 

An investigation of behaviors as adaptations: specializations of sensory and motor mechanisms involved in behavior; animal communication systems; behavioral ecology; patterns of social behavior as solutions to ecological problems, such as predator avoidance and resource exploitation. Emphasis will be on theoretical principles; examples will be broadly comparative, ranging from microorganisms to mammals. 

BIOL 59500 - Special Assignments - Session Offered: Fall Spring Summer

59500 (Seniors/Graduate). Reading, discussions, written reports, seminar presentations, and field or laboratory work provided for enrichment in special areas of the biological sciences.

BIOL 59500AM - Neurobiol Of Learning & Memory - Session Offered: Fall

How does our brain learn? How are our memories created? We will discuss a range of learning processes from cellular and molecular mechanisms to perception and behavior. We will look at the history of the key concepts and discoveries, including the technological advances, which made these discoveries possible. Most of the research discussed will be from animal experiments with some human studies.

BIOL 59500B - Water Supply In Dev Countries - Session Offered: Fall Spring

Sustainable solutions to water supply and sanitation problems in developing countries require a multidisciplinary, holistic approach.  To address this issue, a multidisciplinary service-learning class will be initiated beginning in the Fall 2012 semester.  Enrollment in the class will be limited to 12-15 students and is limited to undergraduate and graduate students in the academic units listed below.  Students selected for enrollment in the class will be identified by application, which will include a copy of the student’s academic transcripts a document (statement of purpose) of no more than 2 pages in length describing your interest in this class and your motivations for participating in it.  Interested students should submit an application by email to Professor Blatchley (blatch@purdue.edu)

The objective for this service learning class will be to define feasibility of community-scale water treatment systems for use in the Dominican Republic.  Feasibility will be characterized based on issues relating to scientific and engineering principles of the proposed systems, as well as the effects of these systems on public health and economic/entrepreneurial issues.  Work on this project will involve coordination with Aqua Clara International (Holland, MI), a non-profit organization who work to provide affordable safe water solutions for communities in developing countries.

 

BIOL 59500BN - Data Analysis In Neuroscience - Session Offered: Spring

During this five-week module students will learn how to use python, a widely used free open-source programming language, to analyze real-life neuroscience data and perform basic statistical analyses. Students will learn to use the latest high-level data analysis and plotting libraries such as pandas, scipy, matplotlib, seaborn. All programming and analysis will be done using Ipython/Jupiter notebook, a web-based interactive computational environment, which promotes reproducibility of data analysis in science.

BIOL 59500BTL - Building the Tree of Life - Session Offered: Spring

The Tree of Life represents Earth’s biodiversity and its history, and forms the basis of all biological knowledge. Phylogenetic methods allow us to reconstruct the Tree of Life and infer the evolutionary history and relationships of genes and organisms. This knowledge, in turn, can be used to address questions of organismal classification, biogeography, community assembly, and macroevolution. This jointly taught course introduces tree thinking and its underlying algorithms of inferring phylogenies, with an emphasis on the various applications of phylogenetic methods to such topics as those listed above. Through a combination of lectures, computer labs, and discussion of primary literature, the course will provide hands-on experience with commonly-used tools and their applications in research for senior undergraduate and graduate students from relevant science backgrounds.

BIOL 59500CMA - CRISPR Mechanisms & Applications - Session Offered: Spring

This course aims for upper-level undergraduate and graduate students interested in the CRISPR technology, one of the most important scientific developments thus far in this century. It covers the fundamental principles and mechanisms of bacterial immune systems, the CRISPR-Cas systems, and the applications based on these systems, such as genome editing and molecular diagnostics. The course will be taught based on current primary literatures, and students will learn how to read and interpret scientific data through lectures and in-class presentations and discussions.  

BIOL 59500CR - X-Ray Crystallography - Session Offered: Spring

This course will provide an introduction to structure determination of macromolecules using X-ray crystallography and will attempt to balance theory and practice, consisting of ~60% lectures and ~40% lab modules. The course is divided into five 3-week modules covering (i) Crystallization, (ii) Data Collection, (iii) Molecular Replacement, (iv) Experimental Phasing, and (v) Model Building and Refinement, Validation, and Visualization. The goal of the course is to equip students with the necessary tools to develop and execute an X-ray crystallography project, starting from construct design to publication. By the end of the course, students should be familiar with the (i) structure determination pipeline, (ii) theory behind X-ray diffraction methods, (iii) methods for crystallization, (iv) phasing options for solving a crystal structure, and (v) contemporary crystallography software.

BIOL 59500CRYO - CryoEM 3D Reconstruction - Session Offered: Fall

Cryo-electron microscopy (Cryo-EM) is a revolutionary structural bio logy method that allows the determination of the atomic structures of viruses and protein complexes to elucidate the structural basis of their functions. The atomic structures will deepen the understanding of biological processes such as metabolism, signaling, cell cycles, etc., and help the development of vaccines and drugs to combat viral infections, cancers, neurodegenerative diseases, etc. The Bio595 Cryo-EM 3D Reconstruction course will introduce cryo-EM principles, including instruments, sample preparation, data collection, and data analysis. The students will also learn how to determine a protein complex or virus structure to 2-3 Angstrom resolutions using a GPU-accelerated Linux workstation or cluster. 

BIOL 59500DE - Disease Ecology - Session Offered: Spring

This course is designed to provide upper level undergraduate and graduate students with an understanding of the ecological and evolutionary complexity inherent to host-pathogen interactions.

BIOL 59500DIST - Experimental Design & Quantitative Analysis in Life Sciences - Session Offered: Summer

This course is aimed at preparing our students in experimental design and quantitative analysis specifically applied to the Life Sciences in order to read the scientific literature critically, generate scientific questions, hypotheses and predictions, design research studies, analyze the data statistically, and communicate results. The course will use R and RStudio, which are open-source platforms that are increasingly used in the scientific community to analyze data quantitatively. 

BIOL 59500EC - Ecology - Session Offered: Fall

A lecture-based course that examines the abiotic and biotic factors mediating and predicting abundance and distribution of species. It focuses on ecological processes and population dynamics integrating individual, population, community and ecosystem levels to provide a broad overview of ecology as a field. By integrating classic work with recent studies, and using mathematical models as a foundation, this course addresses they main overarching concepts and processes mediating species distributions and interactions.

BIOL 59500EL - Laboratory in Ecology - Session Offered: Fall

Companion Lab to 59500EC

BIOL 59500ETS - Energy Transduction in Society - Session Offered: Spring

Description: Application of Basic Concepts in the Biological and Biomedical Sciences, Centered on Mechanisms of Biological Energy Transduction, to Problems in Medicine, Agriculture, and Society.

This course is intended for students in biology, physics, chemistry, and engineering to obtain insight into interdisciplinary collaborative approaches by biologists, physicists, and physicians who are concerned with improved understanding and the solution of major problems in medicine, and problems and solutions associated with the changing solar environment of the Earth. The subjects of cellular energy and energy transduction will be a paradigm, starting with discussion of the salient features of the energy-transduction centered in transport complexes of biological cellular membrane. The course will progress to case studies where students will apply this knowledge to problems involving mitochondrial dysfunction in cancer and neuropathology, the crossroads of mitochondrial metabolism and the biology of aging, mechanisms of virus infection and influenza virus translocation. The chloroplast will be the second cellular organelle whose structure and function are discussed, the latter in the context of the principles of photosynthetic solar energy conversion and the problems of global warming and agricultural productivity. Through the exploration of these subjects, the course in general will discuss a range of issues important not just for an understanding of the science, but also in the context of societal problems which include infectious disease, global warming, agricultural productivity, and radiation exposure in possible space travel. The broad goal of the course is to develop skills in thinking critically beyond one’s primary discipline, considering problems of ethics and the consequences to individuals and society in the utilization and application of modern medicine and technology.

BIOL 59500ICI - Immunology of Cancer & Infectious Disease - Session Offered: Spring

Immunology of Cancer and Infectious disease is for advanced undergraduate and graduate students interested in pursuing a deeper understanding of immune mechanisms in health and disease.  We will largely use primary literature to understand concepts in infection immunology (vaccination, anti-viral/anti-bacterial responses) and in cancer immunity (cold vs hot tumors, tumor microenvironment and immunotherapy). Class will contain lectures, student presentation of primary literature and expert panel discussions.

BIOL 59500JJ - Genetics Omics Host Microbe - Session Offered: Spring

This is a 500 level course for graduate students and senior undergraduates (outstanding junior
undergraduates can take it upon approval by the instructor). The course will cover the genetic
basis of virulence factors from pathogens such as bacteria, viruses, fungi and parasites, with an
emphasis on bacterial pathogens. Genetic and –omics methods including genomics and proteomics in the analysis of host-­microbe interactions will be discussed. We will also cover the
role of microbiota in the development of infection and/or immune diseases. On the host side, the
genetic basis of host defense against infection will be covered. Several commonly used model host
systems, including mice, Caenorhabditis elegans, Drosophila, zebra fish, and some protozoan hosts will be introduced and discussed.

This course will allow the students to understand the genetic basis of infections and infectious diseases. They will also learn the genetic methods for study host microbe interactions from the
prospective of both the pathogen and host.

BIOL 59500M - Practical Biocomputing - Session Offered: Spring

Electronic resources and high-throughput technologies are transforming biology; becoming a "power use" of these resources is essential for all graduate students in biology today.  Unfortunately, these resources are often incomplete (requiring various sources to be combined), massive (making it difficult to find the specific information one is seeking) or in the wrong format (making them difficult to use).  This course will teach how to use the Perl programming language to find and retrieve information, to develop user-agents to process information using new and existing programs, how to create relational databases for storing information, and how to make information available via dynamic websites.
This course is designed for beginning graduate students in the life sciences, but would be a useful addition of most biology undergraduate majors.  Prior computer programming experience is not required.

BIOL 59500O - Biology Teaching Methods Secondary School - Session Offered: Fall

BIOL 59500PD - Pathways in Human Health and Disease - Session Offered: Fall

This course is intended for both upper-level undergraduate and graduate students. It will cover major intracellular signaling pathways in eukaryotes and their roles in human disease, with an emphasis on cancer but also touching on other major modern diseases such as COVID-19. We will explore avenues being pursued to target signaling mechanisms for therapeutic benefit. Topics include G protein-coupled receptors, receptor tyrosine kinases, nuclear hormone receptors, protein kinases and phosphatases, mTOR, the Wnt/β-catenin pathway, cell cycle control, DNA damage checkpoint control, regulated proteolysis, and programmed cell death. The course will be taught from current primary literature using a textbook as a background resource. Students will learn how to read and interpret scientific data through regular lectures, extramural seminars, in-class presentations, and take-home assignments.

BIOL 59500Q - Introduction to Bioinformatics - Session Offered: Fall

This course is designed for graduate students to be taken in conjunction with the BIOL 47800 (Introduction to Bioinformatics) lecture course. It provides additional background in bioinformatics by focusing on reading and critical analysis of classic and current papers from the bioinformatics literature. While intended primarily for graduate students, this course would be appropriate for well-prepared undergraduates, especially those contemplating graduate studies in computational biology or bioinformatics. This course is not a programming course and would be beneficial for graduate students in any area of molecular or cellular biology in which computational analysis is important. This course covers the same topics as BIOL 47800, including sequence comparisons, database searching, genomics, microarrays, protein structure, etc.

BIOL 59500QE - Neural Mechanisms In Health And Disease - Session Offered: Spring

An examination of the mechanisms by which nervous systems process information in normal and pathologic states. Cellular and systems-level information processing will be studied with a focus on sensory and motor systems.  Students will gain some hands-on experience in the analysis of neural data. Some neuroanatomy will be included to understand how nervous systems are organized. Pathological states such as Alzheimer’s, autism, and aging will be studied, both in terms of understanding the systems and cellular deficits as well as examining potential solutions to improve the outcomes for these neural disorders.

 

BIOL 59500SBL - Structural Biology Lab - Session Offered: Spring

This five-week lab module is designed for upper-level undergraduate and graduate students to learn the structure and function of macromolecular including protein, DNA and RNA. Students will attend weekly lectures followed by lab practices to explore the molecular structure and interactions. Students will learn tools for structural visualization and analysis and complete a structural biology project in the lab. At the end of the course, students will understand how the structure of macromolecules is related to their function.  

BIOL 59500TMM - Theory Of Molecular Methods - Session Offered: Spring

Theory of molecular methods will introduce upper level undergraduate students and graduate students to the theory and practice of many commonly used molecular biology methods.  Emphasis will be placed on understanding the theoretical basis for these techniques, their utility in various circumstances, and their limitations.  Although taught as a lecture, students should be able to take this knowledge back to the laboratory to help them in their research efforts.  The course will be as close as possible to a laboratory experience without being in an actual laboratory setting.  This course is designed to prepare students for other in-depth scientific courses, for graduate rotations, and for future laboratory work.  Exams will be experimental in nature (e.g., design an experiment to do something or in this type of situation, which technique/vector/etc. would best be used, and why).

BIOL 59500U - Cell Biology of Plants - Session Offered: Fall

This lecture course, aimed at upper division undergraduates and graduate students, will cover aspects of cellular biology which are fundamental to our understanding of plant growth, differentiation and development.  The course content assumes that the student will have a strong background in the cell biology of eukaryotes, and some exposure to basic problems in plant biology.  Topics to include:  techniques of modern cell biology; cell division and cell cycle regulation; cytoplasmic streaming and intracellular motility; structure and function of peroxisomes, vacuoles, cell walls, and plastids; protein import, cell-cell communication and plasmodesmata.

BIOL 59500X - Methods & Measurements in Biophysical Chemistry - Session Offered: Fall

This course is intended as an introduction to physical methods in biochemistry and aims to provide an understanding of the techniques of spectroscopy, diffraction, magnetic resonance and other physical methods.  The purpose of the course is to expose students to the application of these techniques to specific problems in biological systems, the interpretation of the resulting data, and analysis of the strengths and limitations of each technique.  Examples from research articles will be discussed that illustrate how these methods are used in modern biochemistry.  Given the scope of the course, each topic will be treated only at the level of an introduction to the method.  Students interested in studying these techniques in-depth could then take more specialized or advanced courses such as BIOL 51100/51400/61100 (x-ray crystallography), CHEM 61500/61600 (Nuclear magnetic resonance spectroscopy), BIOL 59500 (Electron microscopy and 3D reconstruction), or other special topics courses to be offered by the faculty.  Analysis of techniques used in physical measurements of biological systems.  Application of these techniques to studies of structure and dynamic behavior of biological macromolecules, composition and orientation of structural elements and cofactors, ligand binding and conformational change in biological interactions and detailed probes of local changes in structure, solvent accessibility and specific bonds formed in biological reactions. Specific techniques to be covered are:  UV/Vis spectroscopy, circular dichroism, IR and Raman spectroscopy, fluorescence and single particle methods, analytical ultracentrifugation, surface plasmon resonance, scattering, x-ray crystallography, NMR and ESR spectroscopy, electron microscopy, mass spectroscopy.   Comments:  Although designed for students in biochemistry and biophysics, this course is also appropriate for upper level undergraduates and graduate students in the areas of chemistry and physics who are interested in the applications of physical methods to biological problems.

BIOL 60000 - Bioenergetics - Session Offered: Fall

Energy transduction in biological membranes: physical chemical foundations; electron-proton transfer; active transport. Atomic structures of integral membrane protein complexes responsible for respiratory, photosynthetic generation of electrochemical potential; ATPase motor; structure-based mechanisms. Mitochondria-related diseases. Experimental, particularly spectroscopic, methods.

BIOL 60200 - Cellular Neurobiology - Session Offered: Fall

This course is intended as a first course in cellular and molecular neurobiology for graduate students from a wide range of disciplines. Topics will include neuronal and glial structure, axonal transport, electrical properties of neurons, the ionic basis of the action potential, ion channel structure and function, synaptic release, neurotransmitters and neurohormones, neurotransmitter receptors and transduction mechanisms, sensory receptors, neural induction, patterning of the embryonic nervous system, neural growth and trophic factors, neural stem cells, axon guidance, and synaptic plasticity during development. Class meetings are 75% lectures and 25% small-group discussions of the primary literature or computer-based tutorials.  Grading is based on tests of lecture material and assigned textbook readings (40%), homework problems based on paper readings and tutorials (35%), and participation in discussions (25%). Pre-requisites are an undergraduate major in Science or Engineering that included a college level course in Physics as well as a course in Cell Biology or Biochemistry. Students lacking this basic background may be admitted with the permission of the instructor, if they are willing to backfill some basic material with extra readings.

BIOL 62000 - Advanced Topics in Eukaryotic Cell Biology - Session Offered: Spring

A study of current areas of cell biological research, including the cytoskeleton, the regulation of the cell cycle, and the functions and dynamics of membrane-bound organelles.

BIOL 64700 - Membrane Proteins - Session Offered: Spring

This course will focus on the structural basis of the functions and dys-functions of diverse membrane proteins, analyzed by x-ray, electron microscopy, and spectroscopy.  The functions will include biogenesis, ion channels, transport, energy transduction, and trans-membrane signaling.  Unique problems associated with the structure analysis of integral membrane proteins will be discussed.

BIOL 65200 - Advanced Ecology Discussion - Session Offered: Fall

Weekly meetings to discuss and evaluate seminal papers in the fields of evolutionary, population, and community ecology. During the last week, students will critically evaluate a contemporary paper on a topic related to the "classic" papers discussed during the semester. Students will have a choice among papers submitted by participating faculty members; their critique will be assessed on content, originality, rigor, and clarity. 

BIOL 65300 - Advanced Evolution Discussion - Session Offered: Spring

Weekly meetings to discuss and evaluate seminal papers in the fields of evolution and population biology.  Each participating member is responsible for two meetings, chooses the papers and guides discussion.  As in any graduate discussion class, students must participate rather than just attend for experience.  During the last week, students will critically evaluate a contemporary paper on a topic related to the "classic" papers discussed during the semester.  Students will have a choice among papers submitted by participating faculty members; their critique will be assessed on content, originality, rigor, and clarity.

BIOL 66200 - Seminar Methods in Professional Development I - Session Offered: Fall

An introduction for incoming graduate students to methods of seminar presentation and critique and to various guidelines for professional development during their graduate school experience. Topics include research laboratory safety (REM), how to give a talk, acclimating to graduate studies (especially time management), how to select a major professor and an advisory committee, how to prepare for qualifying exams, Purdue University guidelines for responsible conduct of research, how to organize a poster presentation, how to negotiate with mentors, and expectations for success. The course also serves to socialize the incoming cohort of students among themselves and with more senior students in the broad range of research disciplines available.

BIOL 66300 - Seminar Methods & Professional Development II - Session Offered: Spring

This course is a continuation of BIOL 66200 and expands the introduction for incoming graduate students to methods of seminar presentation and critique and to various guidelines for professional development during their graduate school experience.  Topics include seminar topic selection and 20-minute seminar design. Tutorials on electronic services at the P. U., Library and Citation Management Programs, and evaluating classmate presentations.  Using the skills learned the previous semester, each student is required to make a 20-minute PowerPoint presentation to the class based on a pre-approved topic of their choice.  The speaker is asked questions and the presentation receives written evaluations by all members of the class.  Each student practices with Prof. Levy prior to the public presentation.  The course also continues to socialize the incoming cohort of students among themselves and with more senior students in the braod range of research disciplines available.

BIOL 69100 - Biological Research Methods - Session Offered: Fall Spring

Open to graduate students in the Department of Biological Sciences and designed primarily for students in their first year of graduate study. The course consists of two laboratory assignments, each of which lasts about two months. Students may take one or two of these per semester. During each laboratory assignment, the student will be exposed to methods, equipment, and experimental procedures currently in use in a particular departmental research laboratory selected by the student and through arrangement with the professor in charge of that laboratory. This course may be repeated for credit.

BIOL 69500 - Structural Biology Seminar - Session Offered: Fall

Each semester there are several separate seminar offerings. In this seminar students will present, and we will critically discuss, foundational classic papers and cutting-edge manuscripts in pathogenesis of bacterial, viral, fungal, and parasitic infections.  The student record will indicate the specific seminar(s) in which he/she has participated. Oral presentations required. At least two credits are required of Ph.D. candidates.

BIOL 69500 - Special Assignments - Session Offered: Fall Spring Summer

69500 (Graduate). Reading, discussions, written reports, seminar presentations, and field or laboratory work provided for enrichment in special areas of the biological sciences.

BIOL 69500 - Microsopy For Life Scientists - Session Offered: Spring

Purpose of the course:

 

Many life scientists are using advanced imaging techniques without fully understanding the underlying principles of sample preparation, imaging formation, and data analysis. The goal of this course is to provide graduate students with a fundamental knowledge in various aspects of light microscopy, including modern fluorescence imaging techniques, digital image processing and analysis with emphasis on how to optimally image and analyze biological samples. Completing this course will help students to make better use of available techniques and design new experiments.

Major topics include:

1.  How light travels through a light microscope to form an image

2.  Image formation in bright-field, phase contrast, DIC, epifluorescence, and confocal microscopy

3.  How to use Image J (http://rsbweb.nih.gov/ij/) for automated image processing and analysis

 

Additional topics include how to handle and adjust common hardware components, how to recognize and correct common image artifacts, and how to prepare biological samples for best imaging.  Concept-based lectures are complemented with hands-on laboratories.  Coverage is from a non-mathematical perspective, and no knowledge of math of physics is expected.

BIOL 69500 - Popular Science Communication - Session Offered: Spring

Students will be introduced to popular science communication in a broad context, and this course will be focus on communicating in particular scientific knowledge in ecology and evolution. Students will be immersed in discussions about the role of communication in science and the cultural, practical and policy-related role of science communication in society. This will be a student-lead seminar in which they will be given relevant supplementary material and will be expected to actively participate leading class discussions on those topics. Throughout the semester, however, experts on different aspects of sci comm will be invited as speakers to share their experience disseminating scientific knowledge to non-scientists.Over the course of the semester, students will develop their own science communication project springing from a scientific research topic of their choice. Projects can include articles for magazines intended for the general public, blogs, podcasts, videos or talks in our community, among other venues. The course will be focus on communicating science in particular of ecology and evolution.

BIOL 69500 - Advanced Molecular Virology - Session Offered: Spring

This course is an in-depth study of viral replication strategies, viral evolution, and virus-animal host interactions.  Lectures will cover the structure of virions and viral genomes, genome replication and transcription, viral RNA processing and translation, and virion assembly.  The viral life cycle, the origins of virus-associated disease, including transformation, and the host response to viral infections will be explored.  Methods for the prevention and treatment of viral diseases, including AIDS, will be investigated.  Discussion of recent articles from the primary literature will promote the understanding of cutting-edge research in virology.

BIOL 69500PW - Professional Writing in Bio Ed - Session Offered: Spring

This course is designed to help graduate students in the Biology Education program to increase their academic writing skills. Academic writing is challenging for many students thus providing writing support to them is critical. Students in this course will learn how to write conference proposals, research articles, and grant proposals. Furthermore, students will learn elements of successful writing in science and social studies. Finally, throughout the course, students will give and receive feedback on their proposal or research article drafts from each other and the instructor. 

BIOL 69600 - Development & Disease Seminar - Session Offered: Spring

It is well established that vesicle trafficking and signaling are functionally linked. For example, endocytosis can contribute to the regulation of ligand availability and receptor levels at the cell surface. It is through this mechanism that endocytosis leads to receptor downregulation  and shapes extracellular morphogen gradients. However, endocytosis is also required for signaling activation; it is now recognized that localization of ligand-receptor complexes at endosomal compartments (‘signaling endosomes’) is required for the initiation of specific signaling events. Although the exact mechanism is unknown, endocytosis also plays a crucial role in the activation of the Notch-DSL developmental pathway.

In this class, we will cover a series of topic that illustrate the link between vesicle trafficking & signaling and its potential applications.

 

The seminar will be run as a journal club, with students making a 45 min. presentation of a recent paper from the literature.   The paper will be selected by the instructor and provided to the student at least 2 weeks prior to the seminar.

 

BIOL 69600 - Structural Biology Seminar - Session Offered: Spring

Each semester there are several separate seminar offerings. They will likely be on the following topics: biochemistry, crystallography, ecology and population biology, genetics, mechanisms of development, microbiology, neurobiology, and plant physiology. The student record will indicate the specific seminars in which he/she has participated. Oral presentations required. At least two credits are required of Ph.D. candidates.

BIOL 69600 - Structural Biology Seminar - Session Offered: Fall

BIOL 69600 - Ecology And Evolution Seminar - Session Offered: Fall

TBA

BIOL 69600 - Stem Cells and Disease - Session Offered: Spring

Course Description - For many years cell, molecular and developmental biologists have studied how embryonic cells commit to a particular cell lineage and terminally differentiate into a specialized cell type.  A wealth of information has been obtained by identifying genes that define the differentiated cell and how these genes are transcriptionally regulated.  Having "conquered" this important biological problem, investigators have now begun to focus on manipulating differentiated cells to reverse their developmental history and regain their original pluripotent state or to directly transdifferentiate into a different cell type.  For example, it is now possible to reprogram terminally differentiated cells directly to an alternative differentiated state or to a stem cell state where the cells can be induced to form other cell types.  In both cases, wholesale alterations in gene expression patterns occur, revealing the complexity of these molecular changes. 

During the semester students will be asked to research a particular topic in stem cell biology, cancer stem cell biology, animal disease models, and transgenic mouse strategies for addressing key issues on how altering the phenotype of adult cells may be used to treat human diseases.  Each student will be assigned a single topic to research and to present to the class.  For each topic the lead student is to provide the class with several articles to read in advance and also lead a discussion on their specific topic.  Participation in discussions is an essential component of this class and attendance is mandatory.  A final course grade will be determined by attendance, active participation and presentation of specific topics. 

BIOL 69600 - Seminar in Neuroscience - Session Offered: Fall

Seminar in Neuroscience

Spinal cord and traumatic brain injury:

Mechanisms and treatments

In the United States, more than 5.5 million people suffer from different forms of traumatic brain injury (TBI) or spinal cord injury (SCI). The combined health care costs for TBI and SCI in the US alone amount to over $70 billion annually. TBI is the leading cause of death and disability in children and young adults in the United States. Thus, these mechanical injuries provide a significant health care, economic, and personal challenge for the people affected by them. Although significant progress has been made in recent decades in understanding the underlying mechanisms and developing new treatments, we are still far away from reliable methods that would allow full repair of injured nerves. This is largely due the fact that the adult mammalian central nervous system has a very limited regeneration capacity. This seminar course is targeted at graduate students in the life sciences, biomedical engineering, and health sciences with an interest in basic and translational neuroscience. We will discuss key papers on the underlying mechanisms, treatments, and diagnostics of SCI and TBI. Besides classical papers we will also focus on the most recent developments in this field. 

BIOL 69800 - Research MS Thesis - Session Offered: Fall Spring Summer

Research MS Thesis. Permission of instructor required.

BIOL 69900 - Research PH.D. Thesis - Session Offered: Fall Spring Summer

Research PhD Thesis. Permission of instructor required.