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Course Descriptions

Biology Courses

BIOL 11000 - Fundamentals of Biology I - Session Offered: Fall Spring Summer

BIOL 11000/11100 is a two-semester principles of biology sequence that introduces students to the major concepts of the discipline, with emphasis on the experimental and logical basis of the information presented.  BIOL 11000/11100 includes lectures and laboratories that begin with atoms and build to the diversity of life.  Topics include chemistry, biochemistry of macromolecules, cell structure and function, photosynthesis, respiration, evolution, the diversity of life and DNA structure and replication.  This course is intended as the first semester of two semesters.  These courses are NOT independent and should be taken in sequence.


BIOL 11100 - Fundamentals of Biology II - Session Offered: Fall Spring

BIOL 11100 focuses on genetics, molecular biology, physiology and development.


BIOL 11200 - Fundamentals of Biology I - Session Offered: Fall Spring Summer

BIOL 11200/11300 is a two-semester principles of biology sequence that introduces students to the major concepts of the discipline, with emphasis on the experimental and logical basis of the information presented.  BIOL 11200/11300 includes lectures that begin with atoms and build to the diversity of life.  Topics include chemistry, biochemistry of macromolecules, cell structure and function, photosynthesis, respiration, evolution, the diversity of life and DNA structure and replication.   This course is intended as the first semester of two semesters.  These courses are NOT independent and should be taken in sequence.


BIOL 11300 - Fundamentals of Biology II - Session Offered: Fall Spring

BIOL 11300  focuses on genetics, molecular biology, physiology and development.


BIOL 11500 - Biology Resource Seminar - Session Offered: Fall

The Biology Resource Seminar is a one-credit course for freshman biology majors. The course is designed to help integrate new biology students into the Department of Biological Sciences, to help them adjust to university life, and to assist them in developing academic and intellectual survival skills using the medium of introductory Biology courses. Each presentation section of this course is led by an academic advisor and an undergraduate teaching intern. The course meets twice a week in groups of approximately 20 students.


BIOL 12100 - Biology I: Diversity, Ecology, and Behavior - Session Offered: Summer Fall

Overview of the unity and diversity of life. We attempt to construct a framework for ordering biology by studying both the shared and specialized modifications of organisms that allow them to adapt to their environment. We also apply biological principles to social, medical and environmental issues. Topics include: diversity of life, respiration, photosynthesis, mitosis/meiosis, Mendelian genetics and complications, natural selection, Hardy-Weinberg equilibrium, population growth (including humans), interactions among populations (competition, predation, parasitism), behavior, and conservation biology.


BIOL 13100 - Biology II: Development, Structure and Function of Organisms - Session Offered: Spring

Introduces embryonic development and examines the functioning of physiological systems of both plants and animals. The underlying cellular and molecular basis for these processes will be emphasized. In particular, the transport of molecules and small ions through biological membranes will be studied. This will require an understanding of membrane structure, diffusion, electrical potentials and other physical and chemical principles. In addition to the specific topics covered, an important objective of this course will be to connect what is covered to both current and historical research endeavors, to prepare Biology majors for further study in the curriculum of the Department of Biological Sciences. While students other than Biology majors are welcome, they should be aware that the rigorous approach taken in this course will require considerable time and effort. A number of problem sets will be posed and students will write and peer review several essays to explain how experimental and quantitative aspects of biology have changed along a historical continuum. Regular weekly help sessions (run by both the professor and student aids) will be arranged to provide the chance to ask questions and discuss particular points in greater depth than the large lecture format permits.


BIOL 13500 - First Year Biology Laboratory - Session Offered: Fall Spring

Laboratory exercises emphasizing student mastery of basic laboratory skills needed to succeed in the biological sciences; intended for beginning (first-year) biology majors.

 

 


BIOL 14503 - Year 1 BIO Lab:Disease Ecology - Session Offered: Fall

The course will engage students in authentic research while acquiring the necessary skills and concepts to be a successful biology major. Our research topic will be disease ecology in freshwater systems. Disease ecology is a growing field investigating the causes and effects of pathogen transmission and epidemics, primarily in natural populations. We will begin with a series of skill and knowledge building laboratories, and then transition into independent research projects that culminate in presentation of the data in a poster session. Students will learn the fundamentals of disease ecology, basic laboratory techniques, how to perform scientific experiments, and gain experience communicating findings to other scientists and the public. 


BIOL 14504 - Year 1 BIO Lab: Diet, Disease, and Immune Systems - Honors - Session Offered: Spring

We are what we eat! The food we put into our bodies not only gives us the nutrients, vitamins and minerals we need to live, but it can also influence other ways in which our bodies function, right down to how well our immune system works. The immune system plays a critical role in defending our body from infection, but can also contribute to autoimmune disease when the immune response becomes dysregulated. Importantly, autoimmune disease is currently skyrocketing in countries that consume a “Western Diet” (i.e., high salt, high sugar, low fiber), suggesting that these dietary components, or lack thereof, may contribute to dysregulation of the immune response. CD4+ T cells, a kind of immune cell, play an important role in the immune system as they control the balance between protective immunity and autoimmune disease. Recent evidence indicates a strong correlation between “Western Diet” and dysfunction of this important immune cell type. Therefore, our goal is to examine the effects of these dietary components on CD4+ T cell function and how this might contribute to autoimmune disease. Students will work in teams and cover a distinct subset of microbial or dietary components. As such, each student will learn the necessary skills to perform scientific experiments starting from the literature search, experimental design, carrying out controlled experiments, interpreting results and conveying the results to the greater scientific community.


BIOL 14505 - Year 1 Biology Lab:Phages to Folds - Session Offered: Fall

Students will learn how to use bioinformatics to study a gene sequence of their choice from the local SEA-PHAGES program. Students will then use molecular biology and biophysical techniques to characterize their gene product. The goal of each project will be to gain insight into the 3-dimensional fold of each of these mysterious novel phage genes. Students will work in teams but will have their own individual project such that each student will learn the necessary skills to perform scientific experiments starting from the bioinformatics to cloning to purification to structural characterization to communicating their findings to others.


BIOL 19700 - Biology Freshman Honors Seminar - Session Offered: Fall

This class includes discussion of topics related to futures and careers in biology, and current research opportunities in biology.Various faculty members present ongoing research projects being conducted in different areas of biology in Biological Sciences.Students will have an opportunity to visit a research lab.Some in-class projects designed to introduce students how to think as a researcher will also be conducted.Open only to students in the Biological Sciences Honors Program.The credit may be used only toward free electives.


BIOL 20300 - Human Anatomy and Physiology (Nursing Nexus Learning Community) - Session Offered: Fall

BIOL 20300/20400 is a two-semester 8-credit course designed to give the student a basic understanding of the anatomy, organization and function of the human body. There will be introductory lectures on the basic concepts of biochemistry and cell biology before the major topics of the course are dealt with. For the two semesters, these topics include the organization of the human body; muscle and bone; the nervous system (including the special senses); the cardiovascular system; respiration; digestion; metabolism, excretion, fluid; electrolyte and acid-base balance; the endocrine system; reproduction and genetics. The subject matter will be related to clinical and health-related issues.The laboratory is a hands-on experience designed to complement the lectures. Many labs will use computer assisted data acquisition equipment to carry out experiments on muscle, heart and brain.  This is the first semester of a two-semester sequence. BIOL 20300 is a prerequisite for BIOL 20400. This section of the course is for Nursing Learning Community students only.


BIOL 20300 - Human Anatomy and Physiology - Session Offered: Fall Summer

BIOL 20300/20400 is a two-semester 8-credit course designed to give the student a basic understanding of the anatomy, organization and function of the human body. There will be introductory lectures on the basic concepts of biochemistry and cell biology before the major topics of the course are dealt with. For the two semesters, these topics include the organization of the human body; muscle and bone; the nervous system (including the special senses); the cardiovascular system; respiration; digestion; metabolism, excretion, fluid; electrolyte and acid-base balance; the endocrine system; reproduction and genetics. The subject matter will be related to clinical and health-related issues.The laboratory is a hands-on experience designed to complement the lectures. Many labs will use computer assisted data acquisition equipment to carry out experiments on muscle, heart and brain. This is the first semester of a two-semester sequence. BIOL 20300 is a prerequisite for BIOL 20400. NOTE:  Not available for credit toward graduation for majors in the Department of Biological Sciences.


BIOL 20400 - Human Anatomy and Physiology - Session Offered: Spring

BIOL 20400 is the second semester of a two-semester course that includes two 50-minute lectures, one recitation in preparation for the laboratory, and one two-hour lab. This course is designed to give the student a basic understanding of the anatomy, organization and function of the human body.  To assist the student in mastering the subject matter, the introductory lectures in BIO 20300 cover the basic concepts of biochemistry and cell biology.  The topics covered in BIO 20400 include respiration; digestion; metabolism; excretion; fluid, electrolyte, and acid-base balance; the endocrine system; reproduction and genetics. The subject matter will be related to relevant questions of clinical or health-related importance.  This is the second semester of a two-semester sequence.  BIOL 20200/20400 should NOT be taken out of sequence.  Any student wishing to do so must obtain the instructors permission.  NOTE:  Not available for credit toward graduation for majors in the Department of Biological Sciences.


BIOL 20500 - Biology for Elementary School Teachers - Session Offered: Fall

Unifying concepts of biology taught with materials appropriate for future elementary school teachers.  Does not satisfy requirements for College of Science majors. A major objective of this course is to help students develop the ability to identify, pursue and resolve a scientific problem. This includes making careful observations, accurately recording, organizing, and analyzing data and formulating reasonable databased conclusions. The activities in the course will focus on the topics of ecosystems, biological energy (i.e. photosynthesis and cellular respiration), and cell structure and function.  NOTE:  Not available for credit toward graduation for majors in the Department of Biological Sciences.


BIOL 20600 - Biology for Elementary School Teachers - Session Offered: Spring

Continuation of BIOL 20500.  (However, BIOL 20500 is not a pre-requisite for BIOL 20600).  Unifying concepts of biology taught with materials appropriate for future elementary school teachers.  Content areas to be covered this semester include meiosis, genetics, diversity, evolution, and human body systems. Emphasis is put on learning biology through collaborative problem solving and inquiry. Formal lab write-up will be required for one of the laboratory experiments conducted.  NOTE:  Does not satisfy requirements for College of Science majors- Students who are not elementary education majors should contact the instructor before enrolling in this course.  NOTE:  Not available for credit toward graduation for majors in the Department of Biological Sciences.


BIOL 22100 - Introduction to Microbiology - Session Offered: Fall Spring Summer

Microbiology is a rapidly expanding field of study, currently drawing information from and contributing information to nearly all the sciences from cellular chemistry to global climate change.  Microbiologists are called upon to address issues in medicine, food science, agriculture and biotechnology.  A thorough introduction to the subject is important for students in many disciplines.  Although Bio 22100 is an introduction, most students will find it a challenging course due to the breadth of science that even basic microbiology encompasses.  We will cover the following topics: biochemistry; microscopy; bacterial physiology; growth and metabolism; growth control ; genetics and its modern applications; immunology; pathogenesis, including specific microorganisms of medical importance; agricultural and environmental microbiology; and food microbiology.  After successfully completing Bio 22100, a student will have the background in microbiology necessary for further study in medicine or allied health sciences, microbial ecology, antimicrobial pharmacology and related disciplines.  He or she will also have an understanding of the microbiological diversity in the biosphere, and be better prepared to appreciate the extent to which microbiology shapes our daily lives. NOTE:  Not available for credit toward graduation for majors in the Department of Biological Sciences.


BIOL 23000 - The Biology of the Living Cell - Session Offered: Fall

Cells are amazing, multifunctional machines that are subject to the same physical constraints as machines made by humans. This is an exciting time to learn biology because the ability to understand and manipulate cellular machinery can lead to major improvements in the global quality of life, including health, food production and energy use! An introduction to cell biology builds on a foundation of the physical sciences and explores the complexity of life. The course is divided into five main subject areas:

1. First Principles. We will review the relevant physical principles of thermodynamics and biological chemistry. The macromolecules that form a cell - proteins, membrane lipids, nucleic acids, and carbohydrates - will be discussed.

2. Bioenergetics. We will discuss how the living cell transduces energy into useful currency. Topics include oxidation, reduction, glycolysis, ATP synthesis, and the harnessing of potential energy across biological membranes to do useful work.

3. Information flow in cells (the Central Dogma). DNA is transcribed to RNA. Messenger RNA is translated to protein. Proteins are often modified post-translationally and targeted to specific locations in the cell.

4. Responding to the Environment. How do cells respond to their environment? We will discuss the different strategies that have evolved in prokaryotes and eukaryotes. Topics include gene regulation and cellular signaling.

5. Cellular Systems. We will discuss a few examples that illustrate biological complexity. Topics may include cell division, cell motility, and intercellular communication.


BIOL 23100 - BIOL III: Cell Structure & Function - Session Offered: Fall Summer

BIOL 23100 introduces students to cell biology through 3 over-arching themes:  First, the shape and organization of molecules, organelles and cells underlie their function.  Second, cellular organization and function require energy, and cells are in part energy-transducing machines.  Third, the cell is constantly changing -- its shape, activity and molecular composition are dynamic and transient.  Cell biology builds on a foundation of math, chemistry and physics, so we begin by discussing the structure and function of macromolecules and the most relevant principles of chemistry, kinetics and thermodynamics.

We continue with treatments of bioenergetics and biosynthesis, and then spend the second half of the course on signal transduction, intercellular communication, cell division and the cell cycle, the cytoskeleton, and cell motility.  We will draw on examples from many cell types, including neurons, fertilized eggs, muscle, and epithelia, and issues of human health and disease, including cancer, endocrine disorders, infectious disease, and nerve gas.


BIOL 23200 - Laboratory BIOL III Cell Structure and Function - Session Offered: Fall

Students are introduced to the molecular biology of the eukaryotic cell. In the first section students study topics in protein biology and biochemistry such as protein structure, function, isolation, molecular evolution, and the detection and molecular basis of human disease. Techniques used for these experiments include electrophoresis, chromatography, and the Western blot procedure. In the second section students localize enzymes in plant and animal cells, perform cell fractionation procedures, and study the properties of specific cell-surface receptor. Experiments on the properties and structure of DNA are presented in the final section of the course. These exercises stress the organization and complexity of the genome, gene function and regulation, and the structure of the eukaryotic chromosome. Techniques include restriction nuclease mapping and basic DNA cloning techniques. Students also carry out an independent research project of their own design.


BIOL 24100 - Biology IV: Genetics and Molecular Biology - Session Offered: Spring

This course covers basic principles of classical genetics, molecular biology, and population genetics. The classical genetics section includes discussions on Mendelian genetics, linkage and meiotic mapping, sex determination, cytoplasmic inheritance, and chromosomal aberrations.  The molecular biology section continues with discussions on DNA structure and replication, chromosomal organization, transcription, translation, the genetic code, mutations, DNA repair, and transposable elements.  Basic regulatory mechanisms in prokaryotic and eukaryotic gene expression, as well as current developments (recombinant DNA technology, cancer-causing genes, imprinting, developmental genetics) are also presented.


BIOL 24200 - Laboratory Biology IV: Genetics and Molecular Biology - Session Offered: Spring

Experiments performed range from exercises in classical transmission genetics to molecular genetics and recombinant DNA techniques.


BIOL 28600 - Introduction to Ecology and Evolution - Session Offered: Spring

Evolutionary processes and ecological principles associated with individuals, populations, communities, and ecosystems.  Topics include genetic drift, natural selection, adaptation, life tables, population dynamics, competition, predation, biodiversity, and ecological stability, with emphasis on natural systems.


BIOL 28600 - Introduction to Ecology and Evolution (Distance) - Session Offered: Fall Summer

Evolutionary processes and ecological principles associated with individuals, populations, communities, and ecosystems.  Topics include genetic drift, natural selection, adaptation, life tables, population dynamics, competition, predation, biodiversity, and ecological stability, with emphasis on natural systems.


BIOL 29300 - Planning Your Future in Biology - Session Offered: Spring

Biology 29300 is a one-credit course designed for sophomores in the Department of Biological Sciences.  This course will help students maximize the remainder of their undergraduate career.  The course will cover biology career information and suggestions for professional development.  Students will learn about the various disciplines that make up modern Biological Sciences.  Students will learn about opportunities in undergraduate research and tour two research laboratories.  In-depth presentations from biology alumni from a variety of fields are featured.  Assignments include a Plan of Study, a resume, and one written paper evaluating the career path of one alumni speaker and describing the students response to the presentation.


BIOL 29400 - Biology Research - Session Offered: Fall Spring Summer

BIOL 29400- For Freshman and Sophomores.  Supervised individual research. Project must be approved by the Honors Committee, Department of Biological Sciences. Honors Research program students should register for BIOL 49900.

Please note:  A biology major can earn research credit under BIOL 29400 for working with faculty in Biological Sciences or any other department on campus.  This research must be approved on an Application for Credit in Undergraduate Research form, available in the Biology Counseling Office.

Any other major can earn credit under BIOL 29400 for working with faculty in Biological Sciences ONLY.  This research must be approved on an Application for Credit in Undergraduate Research form, available in the Biology Counseling Office.  If the student wants to earn research credit with other faculty, the student should seek credit under the course/number of the faculty members home department.


BIOL 29500 - Special Assignments - Session Offered: Fall Spring

BIOL 29500 (Sophomores) Reading, discussions, written reports, seminar presentations, and field or laboratory work provided for enrichment in special areas of the biological sciences.


BIOL 29500 - Teaching Biology - Session Offered: Spring

This course focuses on teaching and learning strategies and combines theoretical approaches to university teaching and learning with practical hands-on teaching experience.  Class activities include discussions of current issues in the classroom, presentation practice, as well as a self-assessment of the student instructors. This course is required for first time teaching interns in Biological Sciences, and the successful completion of the course is necessary for additional teaching assignments in the department.


BIOL 31800 - The COVID-19 Pandemic - Session Offered: Fall

The course will cover the COVID-19 pandemic caused by the SARS-CoV-2. It will provide a window onto the intersection of science and society and the challenges created when leaders and the populace are inadequately informed. We will explore the biology of the virus and the disease caused by it. The primary literature will be reviewed with the aim of critically evaluating data and understanding the basis of inferences or lack thereof. Vaccine and antiviral approaches will be discussed. Historical approaches to pandemics, comparative analyses of responses by countries and states, investigations into the origins of SARS-CoV-2, and various conspiracy theories will be topics of deliberation.  We will see how achieving scientific understanding is a dynamic process. The COVID-19 scientific literature will be dissected with a focus on publication ethics. Students will each make an oral presentation and write an essay on a relevant topic thereby allowing them to fulfill graduation requirements. These assignments will require the demonstration of the capacity to report data, organize the material, and convey it using formal English. All sources will need to be documented and assessed for credibility. The initial tranche of classes will be lectures by the Professor with discussion. Most of the remaining classes will be student presentations on assigned topics with moderation by the Professor. Guest lectures by appropriate experts will also be included. 


BIOL 32101 - 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 32800 - Principles of Physiology - Session Offered: Spring

This course is designed to provide students with an introduction to physiology with an emphasis on cellular mechanisms that underlie anatomical and physiological adaptations used by animals to survive in their habitat.  Topics covered will range from cellular respiration to the physical limits of animal performance as we deconstruct and then reconstruct the body to examine how animals can live in extreme environments. Goals for this course are for students to gain a foundation in basic physiological principles, to learn about the integrative nature of the systems of animals, and to appreciate how and why animals have evolved the strategies to help them survive in their unique environments!


BIOL 36700 - Principles of Development - Session Offered: Fall

This course introduces the core concepts in developmental biology. The emphasis is on the early development of a fertilized egg, how it lays down the basic body plan and generates different major organs. The core concepts will be introduced through examples from various vertebrate and invertebrate models, including fly, sea urchins, planarian, axolotl, frog, zebrafish, bird, mouse and human. The course will also show students how to apply the core concepts to think critically about practical subjects including medicine, stem cells, regeneration, and evolution. Typically offered Spring.


BIOL 38700 - Macromolecules - Session Offered: Fall

The goal is to expose students to the world of macromolecules, their physicochemical properties, the influence of these properties on function and structure, and how these properties are determined and exploited. Permission of department required.


BIOL 39300 - Preparing For Your Future in Biology - Session Offered: Spring

The objective of BIOL 393 is to assist students in beginning to prepare for life after Purdue.  Students will learn about interviewing, networking, professional etiquette, job searching, graduate and professional school searching, resumes, personal statements, industrial practices, and how to formulate a career development plan.  You will have the opportunity to interact with amazing alumni from around the country who have utilized their Bachelor of Science degrees in extraordinary ways.  Our goal is for you to be able to construct a polished image on top of your already solid biology background!


BIOL 39500 - Special Assignments - Session Offered: Fall Spring

39500 (Juniors). Reading, discussions, written reports, seminar presentations, and field or laboratory work provided for enrichment in special areas of the biological sciences.


BIOL 39600 - Premed Planning Seminar - Session Offered: Fall Spring

Recommended for Sophomore or Junior year, this course offers information and advice on application processes, aptitude tests, writing personal statements, professional school interviews, and letters of recommendation.  Students in the course will also formulate an alternative career plan.  The class is open to all pre-health students.


BIOL 39699 - Professional Practice Internship - Session Offered: Fall Spring Summer

To obtain professional practice with qualified employers within industry, government, or small business.  Permission of department required.  Typically offerend Fall, Spring, and Summer.


BIOL 41500 - Introduction to Molecular Biology - Session Offered: Spring

An introduction to modern molecular biology techniques and how they are utilized to address current topics in eukaryotic gene expression. Emphasis will be placed on experimental procedures and model systems, such as site-directed mutagenesis of isolated genes and their subsequent introduction into mammalian cells. Topics will include the molecular control mechanisms associated with RNA transcription and processing, protein-DNA interactions, gene regulation in development and growth control.

 


BIOL 41600 - Viruses and Viral Disease - Session Offered: Spring

The objective of this course is to provide students with an introductory understanding of viruses and their impact on human health.  The course will be divided into two sections.  During the first section, we will discuss the cellular and organismal events that occur following virus infection, including viral entry, replication, modulation of cell biology by viral proteins, the host immune response to infection, evasion of the immune response by viruses, and resulting virus-induced disease.  The emphasis of this first section will be on the general strategies used by viruses to establish and maintain infection in a population.  In the second section, we will discuss in relative detail our current understanding of select important human viruses including poliovirus, dengue virus,  influenza, SV40, and HIV.  The objective of this section will be to understand how the unique aspects of each virus-s biology affect the outcome of infection with these pathogens.  In addition to virus-associated diseases, we will discuss potential ways that viruses may provide symbiotic benefits to their hosts and thereby shape the course of human evolution.  Throughout the course, we will emphasize societal and political aspects of virology and virus-derived technologies, including vaccine development, the use of viruses as gene therapy vectors, and the threat of viral bioterror or bio-error.


BIOL 42000 - Eukaryotic Cell Biology - Session Offered: Fall Summer

The course covers specific topics on the structure and function of eukaryotic cells. The first half of the course includes an analysis of the function of membrane bound organelles (especially the endoplasmic reticulum, Golgi apparatus, and lysosomes). Protein targeting to these organelles is examined in detail. The second half covers muscle and actin-based non-muscle motility, cilia and other microtubule-based movements, and ends with the regulation of the cell cycle and growth control. The course emphasizes the experimental basis for our understanding of organelle function and regulatory events.


BIOL 43600 - Neurobiology - Session Offered: Fall Summer

This course covers key aspects in molecular, cellular, and developmental neurobiology. Topics include: Cell biology of neurons and glial cells, electrophysiological properties of neurons, electrical and chemical signaling between neurons, synaptic integration and plasticity, development and regeneration of the nervous system, nervous system diseases. Up-to-date research findings and techniques will be included. A basic knowledge of cell biology and protein structure and function is strongly recommended.


BIOL 43800 - General Microbiology - Session Offered: Fall

Basic concepts specific to microbial structure/function, nutrition, regulation and growth constitute the first section of the course. The next section involves discussions of microbial diversity centering on mechanisms for generating energy and synthesizing essential cell components. The importance of these mechanisms to environmental cycling of key elements is included. The last section deals with the interaction of bacteria with their environments and includes the role of plasmids and viruses, interactions with plants and pathogenicity.


BIOL 43900 - Laboratory in General Microbiology - Session Offered: Fall

Students will learn how to safely manipulate microorganisms without contamination, how to grow bacteria from laboratory or environmental samples and measure their growth, and how to differentiate species based on the physiological properties of their cells.  They will also learn how to design experiments and interpret experimental results.  Experiments investigate topics including media and plating techniques, bacterial growth measurements, microbial diagnostics, enzyme kinetics and cell physiology.  The course concludes with a short (5 lab periods) independent design project, which students plan and carry out based on literature research. 


BIOL 44100 - Biology Senior Seminar in Genetics - Session Offered: Fall

Students are required to give a half hour talk based on journal articles chosen from a list on current developments in eukaryotic and microbial genetics or a related topic of the students choice.


BIOL 44212 - Microscopy and Cell Biology - Session Offered: Spring

In this five-week module, students will learn how to prepare specimens for viewing by fluorescence microscopy.  Specimens include mammalian tissue culture cells and zebrafish embryos.  The emphasis will be on the staining of the cytoskeleton in these preparations, utilizing antibodies and fluorescent probes.  The specimens will be viewed by wide-field and confocal laser scanning fluorescence microscopy.  Images will be acquired, processed and analyzed by modern computational methods.  Students will learn the basics of cell culture, immunocytochemistry, fluorescence microscopy, digital image processing and data analysis. At the end of the course, students prepare a PowerPoint presentation of their images and data.


BIOL 44400 - Human Medical Genetics - Session Offered: Spring

An intermediate-level survey course of human genetics with a balanced review of both Mendelian and molecular aspects. Review of current development and application of DNA technology emphasized.


BIOL 44600 - Molecular Bacterial Pathogenesis - Session Offered: Spring

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

This course will focus on the interface of classical cell biology and microbiology, with emphasis on the exploitation of mammalian host cell by medically relevant pathogens, such as Yersinia, Salmonella, and Listeria. This course will cover the molecular mechanisms of infectious diseases. It will introduce modern cellular microbial strategies for studying the complex interaction between pathogens and their host cells. Topics and readings will be prepared from the most current literature.


BIOL 47800 - Introduction to Bioinformatics - Session Offered: Fall

The unveiling of the map of the human genome signals the dawning of the post-genomics age. New technologies and information are rapidly converging to change the way we do science and the way science will impact our culture. Some of these developments include the sequencing of the chromosomal content in an entire organism, high through-put strategies to identify genes whose patterns of expression change in response to the needs of the organism, and advances in the visualization of the structures of the proteins that are encoded by the genes.The course will focus on genome analysis and microarray strategies, and will include a presentation of the context of bioinformatics, the methods of data acquisition, the strategies by which the data are analyzed including the use of appropriate analysis software, and the ways the data are interpreted.


BIOL 48100 - Eukaryotic Genetics - Session Offered: Spring

A study of the processes of genetic continuity in eukaryotes and of the roles of genes in development.  Principles of gene transmission, mutation, organization, and regulation will be discussed using examples from animals, plants, and fungi.  Emphasis will be placed on the power of the molecular and classical genetic approaches to illuminate complex biological phenomena.


BIOL 48300 - Environmental & Conservation Biology - Session Offered: Spring

Intended for mid-level undergraduate biology majors, this course will provide an introduction to the application of ecological principles to environmental issues.  It will introduce fundamental ecological theory and empiricism, and demonstrate their application to practical issues concerning effects of environmental change, at each level of organization from the individual to the ecosystem.  Whole-biosphere issues, such as global warming and global patterns of productivity, will form the umbrella issues for more focused integrations of ecological knowledge centered at the population level to understand the viability of small and threatened populations. The global extinction crisis and the geography of biodiversity will be covered, and the course will focus on particular case studies of threatened ecosystems and analyses of the genetic and demographic stability of populations.  The history and prognosis for the coexistence of human civilizations with the rest of natural ecosystems form the background for applying ecology to policy.


BIOL 49400 - Biology Research - Session Offered: Fall Spring Summer

BIOL 49400- For Juniors and Seniors. Supervised individual research. Project must be approved by the Honors Committee, Department of Biological Sciences. Honors Research program students should register for BIOL 49900.

Please Note:  A biology major can earn research credit under BIOL 49400 for working with faculty in Biological Sciences or any other department on campus.  This research must be approved on an Application for Credit in Undergraduate Research form, available in the Biology Counseling Office.

Any other major can earn credit under BIOL 49400 for working with faculty in Biological Sciences ONLY.  This research must be approved on an Application for Credit in Undergraduate Research form, available in the Biology Counseling Office.  If the student wants to earn research credit with other faculty, the student should seek credit under the course/number of the faculty members home department.


BIOL 49500 - Special Assignments - Session Offered: Fall Spring Summer

49500 (Seniors). Reading, discussions, written reports, seminar presentations, and field or laboratory work provided for enrichment in special areas of the biological sciences.


BIOL 49500 - The RNA World, CRISPR, and Coronavirus - Session Offered: Spring

The RNA World, the hypothesis that ribonucleic acid (RNA) was the first of the three central biological macromolecules (RNA, DNA, and protein) to function as a genetic material and preceded the others in terrestrial evolutionary history, is a core concept in modern biology.  The evidence for the existence of the RNA world is strong and includes the facts that RNAs can and do function as catalysts and provide the critical components for protein production and even for DNA replication.  This course will reexamine biology from the perspective of evolution from an RNA World. 

Two central examples of the manifestation of the persistence of the RNA World will be explored. 

  1.    1.  The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is in fact an RNA-dependent antibacteriophage immunity machinery that is being used as a gene-editing technology. 
  2.   2.  Coronaviruses are positive-sense RNA viruses, which may be descended from early RNA life forms.

The course will explore not only chemical origin-of-life scenarios and RNA biology but also how modern biology reflects its RNA origins.  We will also explore the medical, social and ethical implications of RNA-derived technologies and how viruses with RNA as their genetic material cast their influence upon our lives at manifold levels.


BIOL 49500BMR - Biodiversity & Museum Research - Session Offered: Fall

Increasing human alteration of the global environment has greatly impacted the biodiversity of our planet. Natural history collections, which form the basis of our knowledge of Earth’s biodiversity, are invaluable resources for addressing the conserviation of biodiversity and understanding how it is responding to global change. Public displays at natural history museums represent only a tiny fraction of the preserved organisms and immense information these collections comprise. These collections have been used to address diverse questions about the effects of climate change and pollution, conservation, public health, toxicology, invasive species, wildlife forensics, and food security. In this course, students will explore the uses of both physical and digitized biodiversity collections and apply ecological and evolutionary theory to experimental design and execution. Semester-long projects will incorporate digitized natural history collections and other data, integrating student conceptual knowledge with application to original research questions, including those pertaining to shifts in the timing of biological events and variation in phenotypes. The course will also provide an introduction to basic data science skills and coding in R.


BIOL 49500DSB - Data Science for Biologists - Session Offered: Fall

All of us are drawn to real-world biological questions. Nevertheless, we might underestimate the hidden demand for computing skills to conduct the actual research. By nature, biological data is versatile, vast, complex, and noisy. Therefore, customized scripts are often needed for data processing, analyses, and visualization. Tools for data management and version control function as virtual lab books to ensure that the studies are 100% reproducible. This course is designed to equip students with practical programming skills via an array of biological case studies. Through hands-on computer labs, students will learn how to translate a biological question into logical thinking and write good code in python and R, perform scientific computing and visualization in R, and manage projects in an organized fashion.


BIOL 49500TEC - Topics in Endocrinology & Cancer - Session Offered: Spring

Description: The goals of the course are to expanded student’s knowledge base in an area of research of their interest.  The course will consist of lectures that establish the topic framework, which includes the research areas of Endocrinology, Cancer, Diet and Obesity.  Students will develop skills to effectively analyze, critically evaluate, and depict data while strengthening scientific communication skills through delivering information orally and in writing.  To accomplish these goals, students will conduct a proper literature review and produce an associated written document for a specific scientific topic, give formal presentations on research articles and generate a written and oral research proposal. 


BIOL 49700 - Biology Honors Seminar - Session Offered: Spring

Required of all Juniors and Seniors in the Honors Research Program.  Optional for other honors research students.  Relevant research seminars and discussions.  Informal presentation and discussion of your ongoing research.  Participation in the Undergraduate Research Day.


BIOL 49800 - Biology Teaching - Session Offered: Fall Spring

Supervised teaching experience for Juniors and Seniors.  Must have approval of course instructor in advance. 


BIOL 49900 - Biology Honors Thesis Research - Session Offered: Fall Spring Summer

Research under the guidance of a scientist. Department approval is required.


BIOL 51099 - 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 51101 - 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 51202 - Methods & Measurements in Biophysical Chemistry - Session Offered: Fall

Biological applications of physical methods including absorption spectroscopy (UV-Vis, FTIR and Raman and CD spectroscopy), fluorescence spectroscopy and super high-resolution imaging, spin resonance methods (NMR and ESR spectroscopy), mass and thermodynamic based methods (thermophoresis, analytical ultracentrifugation, ITC and surface plasmon resonance) and diffraction/structural methods using NMR, cryo-EM and X-ray scattering/crystallography. Each topic is treated at an introductory level with examples from the literature. The course objective for students is to obtain a general understanding of the physical principles underlying each of the techniques, as well as the basic ability to apply the technique to biological systems of interest.  


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 51606 - 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 52101 - 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 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 52905 - Disease Ecology - Session Offered: Spring

Study of the ecological and evolutionary complexity inherent to host-pathogen interactions. Includes case studies from a diverse array of systems, including plants, animals, aquatic and terrestrial systems. Emphasis is on the interactions between multiple hosts and pathogens within complex, dynamic environments. Introduction to parasite and pathogen diversity, host-pathogen coevolution, community ecology and the importance of pathogens in conservation and management.


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 55101 - Theory Of Molecular Methods - Session Offered: Spring

This course 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). Permission of instructor required. 

 

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 58601 - Ecology - Session Offered: Fall

This is an advanced ecology course that examines the ecological process and dynamics of populations, communities, and ecosystems. Topics include the physical, physiological, behavioral, and population genetic factors that influence how organisms interact with one another and their environment, the nature of population growth, and attributes of community structure. Course material integrates case studies from field and laboratory experiments, simulations, and theoretical models to understand life histories, species interactions, and community and ecosystem processes. 


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 2023 

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 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 59500EL - Laboratory in Ecology - Session Offered: Fall

Companion Lab to BIOL 58601


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 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 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 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 59500V - 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 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 - 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 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: 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.


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