[bioundgrd] Biology Advanced Undergraduate Seminars Spring 2015

[Jordan King]

Please see the message below from Professor Horvitz regarding Advanced Undergraduate Seminars for the upcoming academic year. You can find course information here: https://biology.mit.edu/undergraduate/course_listings/advanced_undergraduate_seminars

December 4, 2014

TO:     Biology Majors
FROM:   H. Robert Horvitz, Professor of Biology


        I am writing to inform you of an exciting course offering from the Department of Biology for Spring 2015:  a set of 6 very current seminar courses, 7.34x, Advanced Undergraduate Seminars. These courses are similar in nature to the Advanced Undergraduate Seminars offered this past semester. A complete listing of the courses, instructors, and brief course descriptions is enclosed. The topics are highly varied and encompass areas of genetics, genomics, biochemistry, molecular biology, microbiology, cell biology, developmental biology, cancer biology, immunology, reproductive biology, epigenetics, stem cells, synthetic biology, bioengineering, biotechnology and human disease.



A student can take any number of these courses.  The courses, which generally involve four to eight students, are for 6 units, graded pass/fail, and meet two hours each week. The focus is on reading and discussing the primary research literature.  Most courses have two short written assignments.  Some include field trips to MIT research laboratories or to commercial sites using technologies discussed in the courses. The level of each course will be tailored to the students who enroll. Because of the small size of these courses, we expect students not to drop these courses once they have begun.


        These courses offer a number of special features:  small class size, a high degree of personal contact with the instructor, a focus on the primary research literature, and an opportunity to discuss current problems in biology interactively.  I believe these courses greatly enrich an undergraduate’s experience.  There are limited alternative opportunities available to undergraduates to interact closely with instructors who are experienced full-time researchers; to learn to read, understand, and analyze primary research papers; and to engage in the type of stimulating discussions and debates that characterize how science is really done.  Most advanced MIT undergraduates (generally juniors and seniors) have been sufficiently exposed to the basics of biology to be able to read the primary literature and appreciate both methodologies and cutting-edge advances.  These courses have two goals:  first, to expose students to the kind of thinking that is central to contemporary biological research; and second, to impart specific knowledge in particular areas of biology.  These courses are designed to be intellectually stimulating and also to provide excellent preparation for a variety of future careers that require an understanding both of what modern biology is and of how it is done.  Students who have taken Advanced Undergraduate Seminars in the past (different specific courses, same general design) have been enormously enthusiastic about their experiences.

         I am writing to you before Registration Day to encourage you to consider enrolling in one of these seminar courses.  Please feel free to contact any of the instructors to learn more about their courses and in particular to discuss possible meeting days and times if those listed are not possible for you.

            To learn more about the Advanced Undergraduate Seminars to be offered during the Spring 2015 semester, please check our website (https://biology.mit.edu/undergraduate/course_listings/advanced_undergraduate_seminars) and/or contact the instructors.






Advanced Undergraduate Seminars
2014-2015

Spring 2015

7.341  Of Mice and Men: Humanized Mice in Cancer Research
Instructor: Mandeep Kaur (mkaur at mit.edu<mailto:mkaur at mit.edu>, 4-5100, laboratory of Jianzhu Chen)
Spring 2015. Wednesdays 11 am – 1 pm (Class date and time are flexible.) Room 68-150.

Almost everyone knows someone whose life has been affected by cancer. This devastating disease, which still carries a social stigma in certain parts of the world, generally remains unbeatable despite numerous efforts to curb and curtail it since the inception of the War On Cancer in the 1970s. Why is cancer such a difficult disease to treat? Despite all the effort and money poured into developing new cancer treatments, why are there so few cancer therapies that specifically target tumor cells? What is the best system to model the development of a human tumor? How can novel therapies be tested in a system that mimics the human body by modeling the interaction between human tumor cells and a human immune system, which plays a role in the detection and elimination of tumor cells? Cancer is thought to develop and spread by escaping surveillance from human immune cells, which would otherwise eliminate it. How can new treatment modalities, especially immune-based therapies that harness the natural ability of immune cells to kill target cells, be developed to treat cancer? These and other questions will be addressed in this course. We will explore the concepts of mouse models for human cancer, humanized cancer mice and cancer immunotherapy by reading recent and classic research articles. Humanized mice, like Mouse Man from the comic world, are essentially mice on the outside and human in the inside because of the presence of an intact and functional human immune system after engraftment with human stem cells. In humanized cancer mice the development of a human tumor occurs alongside a normal human immune system. We will focus on analyzing and critiquing research papers describing the development of human cancer models using humanized mice, thus hopefully mirroring the situation in patients. A review of the literature and a dissection of experimental designs will serve as a framework to guide discussions about the strengths and weaknesses of humanized mice (also referred to as humice) in cancer research and their unique position as a platform for the testing of new therapies prior to use in the clinic. The course will end with the exploration of a tantalizing new concept: the development of “personalized mice” or mouse “avatars” for individual cancer patients to test drug toxicities prior to dosing the patient as an effort to improve therapeutic efficacy and minimize undesired side effects. Many believe that immunotherapies represent the future of cancer therapy and humanized mice are a recent addition to the cancer biologist’s tool-kit for modeling human cancer, and this course will act as an introduction to the latest developments in the fields of cancer biology and immunotherapy. We will use the humice cancer field as a vehicle to fulfill the primary objective of this course -- the art and science of reading, analyzing and critiquing research articles. We will also have the opportunity to attend one or more seminars by experts in the field and visit a research laboratory actively involved in the generation of cancer humice.



7.342  Pluripotent Stem Cells and Genome Engineering for Modeling Human Diseases

Instructors: Malkiel Cohen (malkiel at wi.mit.edu<mailto:malkiel at wi.mit.edu>, 617-852-5860, laboratory of Rudolf Jaenisch)

                   Katherine Wert (wert at wi.mit.edu<mailto:wert at wi.mit.edu>, 425-922-9055, laboratory of Rudolf Jaenisch)

Spring 2015. Wednesdays, 1 pm – 3 pm. (Class day and time are flexible.) Room 68-150.


One of the major priorities in biomedical research is understanding the molecular events that establish the complex processes involved in human development and the relationships of these processes to human disease and disease progression. The role of stem cells as a tool to help reveal these processes has long been appreciated.  During the 20th century, Mario Capecchi, Martin Evans, and Olivier Smithies made ground-breaking discoveries using mouse embryonic stem cells for gene targeting in mammals. Their efforts made it possible to modify DNA of specific genes within the genomes of living and fertile mice, allowing scientists to determine the roles of individual genes in health and disease. This approach of genome engineering has produced numerous non-human vertebrate models of human disorders, including diabetes, cancer, cardiovascular and neurodegenerative diseases. For their discoveries, Capecchi, Evans, and Smithies shared the 2007 Nobel Prize in Physiology or Medicine. In 2012, the Nobel Prize in Physiology or Medicine was received by Shinya Yamanaka and John Gurdon for their discovery that cells of mature humans and other animals can be reprogrammed to an early embryonic stage, known as pluripotency, which can then lead to various cell types of the adult organism. This work and many other studies have stimulated the stem cell field into generating pluripotent stem cells from human patients, and these patient-specific stem cells have been used to better model human diseases by reflecting the disorder in a cell culture system. In many cases, scientists can now induce patient-specific stem cells to become the cell type that is affected by the disease and can then study the diseased cells to understand the mechanisms underlying disease progression and to use these cells to test potential treatment options. In this class, we will explore stem cell biology and the ways in which this field has developed to shape our ability to study complex human disease. We will introduce the fields of stem cell biology and genome engineering through critical reading of both the classical and newest primary research literature. This course will focus on the methods used to study embryonic and induced pluripotent stem cells, genome editing to create transgenic animal models of human diseases, regenerative medicine such as the transplantation of stem cell-derived cell types to replace diseased tissues, and current hot topics in genome engineering, such as CRISPR/cas9, a novel method that can be used within living organisms or cells to delete or insert genes of interest. In addition, we will discuss specific disease model systems and their benefits and limitations for understanding the disease and treating human patients. Students will learn the principles of experimental design and the main concepts and questions concerning stem cell biology, become familiar with current research techniques used to model complex human diseases, and become able to critically evaluate the claims in this field.


7.343  Molecular Mechanisms of Cell Identity: Epigenetics
Instructors:     Maja Klosinska (mklosins at wi.mit.edu<mailto:mklosins at wi.mit.edu>, 8-6765; laboratory of Mary Gehring)
                    Brian Abraham (abraham at wi.mit.edu<mailto:abraham at wi.mit.edu>, 8-5236; laboratory of Richard Young)
Spring 2014.  Thursdays, 11 am – 1 pm. (Class time is flexible.) Room 68-150.

Almost every one of the trillions of cells in a plant or animal inherits the same DNA sequence, which can be traced back to the original fertilized egg.  Yet plants and animals can have hundreds of specialized cell types with widely ranging jobs.  How can individual cells specialize if they all have the same set of DNA instructions that are passed down during cell division?  The short answer is that not all DNA instructions are followed in all cells. Join us for the long answer, which involves exploring the molecular mechanisms that govern cell identity, its establishment and maintenance, and its inheritance.  Epigenetic inheritance plays a major role in these processes. Epigenetics is a fast-moving field with boundaries that are debated and are evolving. We will begin by discussing the definition of “epigenetics” and its importance in controlling the wheres and whens of gene transcription.  We will cover a list of proposed epigenetic processes, including chemical modifications to DNA, DNA-packaging proteins, and the transcription apparatus, and show how all act together to specify gene expression profiles that dictate cell identity.  The two daughter cells of a parent often share elements of the parent’s identity, and at least some epigenetic factors are heritable across cell divisions, and perhaps across generations.  Each cell division necessitates maintenance or reconstitution of epigenetic marks, sometimes at the scale of whole chromosomes.  For instance, since, for many animals, female genomes inherit two X chromosomes, one must be silenced, lest expression of genes on this chromosome be twice as high as in males with only a single X chromosome.  We will cover the elegant mechanisms by which this silencing is carried out and how it is maintained across cell lifetimes and divisions.  Studies of mice (e.g., cells of Agouti mice share identical genomes but manifest in diet-dependent coat colors) as well as of humans (e.g., the offspring conceived during the Dutch Hongerwinter themselves produce fatter-than-average offspring, linked to epigenetic marks on specific metabolic genes) indicate that non-DNA-sequence information can be transmitted through generations, while molecular studies show how epigenetic profiles can be reestablished after cell division. Epigenetic mechanisms also have been implicated in memory formation and learning. Our discussions will extend to diseases in which disruption of factors involved in DNA packaging, chromatin modification, or transcription has been implicated, such as in cancer, diabetes, and numerous mental disorders. This incipient field of epigenetics has uncovered central principles of regulation of gene transcription, which establishes cell identity, and is involved in development, disease, and even —very possibly—how we think.  This course will explore the primary research literature in the field of epigenetics, with a special focus on experimental design and the critical interpretation of data.


7.344  Treating Infertility – From Bench to Bedside and Bedside to Bench
Instructors: Michelle Carmell (carmell at wi.mit.edu<mailto:carmell at wi.mit.edu>, 617-258-5174; laboratory of David Page)
                   Jana Hersch (jhersch at alum.mit.edu<mailto:jhersch at alum.mit.edu>, 617-710-3496<file://localhost/tel/617-710-3496>, laboratory of Peter Reddien)
Spring 2015. Thursdays, 1 pm – 3 pm (Class date and time are flexible). Room 68-150.

In the western world, approximately 10-15% of couples suffer from subfertility. Consequently, over 5 million babies have been born thanks to assisted reproductive technologies, and more than half of those have been born in the past six years alone.  In some countries, 3-5% of births are achieved with assisted reproductive technologies, and this number is projected to grow as societies are increasingly interested in beating the biological clock.  This class will cover the basic biology behind fertility and explore the etiology of infertility.  We will cover the latest developments in reproductive science and discuss the clinical challenges of translating research findings into medical treatments.  We will discuss recent studies of gonadal stem cells and their use for rejuvenation of fertility, oocyte and embryo cryopreservation studies and usage, current diagnostic tools for common causes of male infertility, and key mouse models with reproductive phenotypes.  This class will highlight open questions in reproductive biology, familiarize students with both tried-and-true and emerging reproductive technologies, and explore the advantages and pitfalls of each.  Students will have the opportunity to visit a Boston-area IVF clinic and speak with researchers who are on the front lines of reproductive technologies.


7.345  Synthetic Biology and Metabolic Engineering: How We Design Bacteria To Make Products of Societal Importance
Instructor:  Jens Plassmeier (jplassme at mit.edu<mailto:jplassme at mit.edu>, 617-253-5106; laboratory of Tony Sinskey)
Spring 2015. Fridays, 11 am - 1 pm. (Class time is flexible.) Room 68-150.

Biotechnology is a rapidly growing field that offers alternative ways to produce substances that previously were either made by complex chemical syntheses or impossible to produce. What do the organisms of the biosphere, specifically microorganisms, have to offer to biotechnological endeavors? The advantages of using microbes include the use of carbonic waste streams (e.g. food and crop waste) or CO2 for the production of products that are useful to us (biofuels, amino acids, etc.), fewer toxic waste byproducts than in chemical syntheses, and the possibility of producing highly complex molecules economically. Our ever-increasing repertoire of controllable biological functions (encoded by the genes present in an organism) allows for the efficient production of a broad variety of biomolecules. The number of possibilities grows as synthetic biology (the ability to synthesize DNA and design genes at will) progresses in its ability to alter microorganisms and enzymes to make chemical structures that have never existed. In this course we will focus on the production of biomolecules using microbial systems. We will discuss potential growth substrates (such as agricultural waste and CO2) that can be used and learn about both established and cutting-edge manipulation techniques in the field of synthetic biology. This course will include the production of biofuels, amino acids (e.g. lysine), food additives (e.g. monosodium glutamate, MSG), specialty chemicals (e.g. succinate), and biopharmaceuticals (e.g. plasmids for gene therapy). We will learn how microbes have been used for several millennia to produce flavorings and alcoholic beverages (e.g. wine and beer) and discuss how biotechnology has been used to enhance the production capabilities of such microbial strains. We also will discuss the production of enzymes that can be purified and used in various applications: have you ever wondered why you can wash your clothes at low temperatures? In addition, we will consider the production of medically relevant substances, such as antibiotics and biocompatible materials (e.g. polymers for tissue implants and tissue-engineering scaffolds). A field trip to a biotech company in the Cambridge area should be part of this course to show how molecular biology and microbiology research can directly lead to the production of marketable compounds like plastics, medicines, and food additives.  In this literature-based course, students will learn to read and critically evaluate primary research articles published in the field of microbial biotechnology.


7.346  Peptides as Biological Signaling Molecules and Novel Drugs
Instructor: Mohammed Shabab (shabab at mit.edu<mailto:shabab at mit.edu>, 617-253-3745, laboratory of Graham Walker)
Spring 2015. Fridays, 1 pm- 3 pm. (Class date and time are flexible.) Room 68-150.

All living cells possess machinery for peptide synthesis, secretion, and posttranslational modifications. An enormous structural and functional diversity of peptides is generated by use of this cellular machinery. Peptides are broadly used as signal molecules for intercellular communication in prokaryotes, plants, fungi, and animals. Peptide signals in animals include vast numbers of peptide hormones, growth factors and neuropeptides. Some of the best known examples are enkephalins (which help us sense pain) somatotropin (which helps us grow), and insulin and glucagon (both of which regulate our blood glucose levels). Similarly, in plants peptide signals such as CLAVATA3 play important roles in development. Peptides are also used by living organisms as components of their host defense systems. What determines the functional specificity of each peptide? How do these small polymers of amino acids survive hostile protein-digesting enzymes? How are they able to communicate with their specific peptide receptors or interacting proteins for proper functioning?  In this course, we will learn about molecular bases of peptide signaling. In addition, peptides potentially can be used as potent broad-spectrum antibiotics and hence might define novel therapeutic agents.  For example, antimicrobial peptides (AMPs) are low molecular weight proteins with broad spectrum antimicrobial activity against bacteria, viruses, and fungi and are found among all classes of life. The ability of these natural molecules to kill multidrug-resistant microorganisms has gained them considerable attention and clinical interest, since multidrug-resistant microorganisms have developed resistance to multiple antimicrobial agents and are difficult to treat with available antibiotics. One of most notorious examples is deadly strains of methicillin-resistant Staphylococcus aureus. Infections from these pathogenic bacteria are untreatable with known antibiotics like gentamicin, streptomycin and kanamycin. Some antimicrobial peptides can kill methicillin-resistant Staphylococcus aureus strains, making them as promising future drugs. In this class, we will discuss AMPs, their biological functions, mechanisms of action, and applicability as therapeutic agents. Students will learn about various human defense peptides, such as defensins, and about plant peptides involved in symbiosis, such as nodule-specific cysteine-rich peptides. We will consider techniques to detect, quantify and modify peptides. We will also discuss experimental methods such as high-performance liquid chromatography (HPLC) and liquid chromatography coupled with mass spectroscopy (LC-MS) used for quantification of small molecules such as peptides. We will focus on the primary research literature, and students will learn how to read and critique research papers. Additionally, we will visit Cubist Pharmaceuticals, a pharmaceutical company based in Lexington, which is developing peptides as drugs for various pathological conditions, such as complicated urinary tract infections.



Jordan King
Biology Education Office 68-120
Massachusetts Institute of Technology
31 Ames Street, Cambridge, MA 02139
ph: 617-252-1783 / f: 617-258-9329 / e: kingj at mit.edu<mailto:kingj at mit.edu>
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