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BIO. 372/572 ADVANCED MOLECULAR AND CELL BIOLOGY (3 cr) LECTURER: Drs. Lisa Dorn and Bea Holton Spring 2010 OFFICE: LD: HS45, BH: HS42, PHONE: LD: 3064, BH: 7087 E-MAIL: [email protected]; [email protected]. OFFICE HOURS: LD:. Posted on the announcements page of D2L BH: W1:50-4pm; Th 1:50pm-3:00pm, or by appointment. I usually arrive on campus between 8 am and 4:00pm. LECTURE HOURS: 11:30am-12:30pm MWF in Halsey Science HS208. TEXT: Lodish, et. al. (2007) Molecular Cell Biology, 6th edition, W.H. Freeman and Company, OBJECTIVES: Molecular and cell biology concerns the anatomy, physiology and biochemistry of animal and plant cells. This course will be theme-based, meaning that we will cover about 5-6 topics of current interest to cell and molecular biologists. We will use these topics to learn about general processes such as receptor/ligand interactions, signal transduction, cytoskeleton (and control of its distribution), gene regulation, cell cycle and protein translocation. For the sections on molecular biology, we will cover topics concerned with the molecular mechanisms that generate variation at the phenotypic level and the consequences for the evolution of that phenotype. Throughout this course, we will read and discuss original papers from the literature so that students will also become familiar with the methods and the logic that scientists use to test their hypotheses. Due Dates and Exam Dates Date Significant events 19 Feb Presentations 2 groups 22 Feb Writing Assignment Handout#1 1 March Presentations 2 groups 5-March EXAM 1 10 March Presentations 1 groups 17-March Paper 1 Due 22-28 March SPRING BREAK 29 March Switch instructors 12 Apr EXAM 2 Writing Assignment #2 Handout 19 Apr Presentations 2 Groups 30 April Hand in 2nd writing assignment 5 May Presentations (2 groups) 16 May EXAM 3 Instructor Dorn Dorn Dorn Holton/Dorn Holton Holton Outline of Lecture Topics* MOLECULAR BIOLOGY/GENETICS HALF: Molecular structure of genes & chromosomes – Gene expression is indirectly driven by the structure of chromosomes and the distribution of regulatory elements in the sequence of nucleotides. Here we will briefly review how sequences of nucleotides are arranged in semi-discrete regions (depending on who is arguing) of the chromosomes to encode the information in a gene that will be expressed. Ch. 10 Parts of Chapter 9 (I will refer back to chapter 9 several times in the semester to review experimental techniques) Transcriptional Regulation -- Most gene expression is regulated at the level of production of mRNA. Here we will study the various mechanisms by which that is accomplished. Here we will begin our discussion of the techniques that have evolved out of genomics and their implications for investigating disease. Ch. 11 Post-Transcriptional Regulation -- This is where we will study epigenetic molecular mechanisms of gene expression: such as hypermethylation, RNA interference and other mechanisms of post-translational gene silencing. Ch. 12 Potential topics if there’s time Molecular evolution -- Here we will try to bring together what we know about gene expression to the study of how DNA sequences inside and outside of the gene regions of a chromosome have evolved and to some extent the influence of gene expression on speciation and phenotypic evolution. The literature CELL BIOLOGY HALF: The chapters listed will serve as useful background to the papers we will discuss. We will discuss some of the relevant parts of the chapters as we read articles. Techniques in cell biology – One of the most important parts of being a scientist is to know how we know what we know! Throughout the semester we will discuss various specific topics and read papers from the literature so that we will understand how the authors drew the conclusions that they did. To read papers productively, one has to understand basic techniques in cell biology. Ch. 9 Memory – Long term potentiation is the process by which neurons “store” information that allows for memory. What is the cellular/molecular basis of memory? Ch. 23 How cells receive signals Ch. 15 How cells transduce signals so that cell behavior and gene expression alter Ch. 16 How cells integrate signals and gene controls Ch. 16 Aging and Lysozomal Activity – Ch 14 Potential topics if there is time: Stem Cell Research – This discussion will focus on past papers that show whether there is potential to use stem cells to repair damaged or defective tissues and on recent papers showing progress in making pluripotent human stem cells. *This is an advanced class that covers current, interesting topics. If you have topics that YOU would like to see covered, please give them to us and we will try to work them in. GRADING: 40% of the grade will be based on three in-class short essay exams (each exam will include some comprehensive questions), 30% on two short, research-style papers, and 10% will be based on one oral presentation, 10% on critiques of oral presentations and 10% on problem sets. 92-100% = A, 89-91 = AB, 82-88 = B, 79-81 = BC, 72-78 = C, 68-71 = CD, 60-67 = D, below 60% = F. Grades will only be “curved”, if necessary and not until the final total has been calculated. GRADING SCALE:. A = 93-100%, A- = 90-92 B+ = 87-89, B = 83-86, B- = 80-82, C+ = 77-79, C = 73-76, C- = 70-72, D+ = 67 - 69, D = 63-66, D- = 60-62 F (Failure) < 60 ORAL PRESENTATION: Undergraduate students will work in pairs; graduate students will work as individuals. Undergraduates will report, in 20 min., the results of one research paper from the literature. You may choose any topic that interests you as long as it is relevant to cell or molecular biology, and as long as the paper comes from a journal that reports primary research (do not use Scientific American, Discovery, Trends in Cell Biology, etc.). Much of your talk will involve explaining the data to the audience so that the audience can determine the validity of the work. Graduate students must report on 3 papers and may take up to 25 min. GRADUATE STUDENTS: Graduate students will be graded by a higher standard than undergraduates. Graduate students are expected to be proficient in writing. At this point, they should have a good command of scientific vocabulary and use it appropriately. They should understand commonly used scientific techniques and knowledgeably discuss data gleaned from such methods. Their data interpretations should show insight into the larger, more general problems being addressed. Additional assignments: 1) As mentioned above, graduate students must give an oral presentation by themselves; and 2) they must prepare a short (2pg) mini-review of the literature surrounding the topic of the presentation (due at the time of the presentation). WRITING ASSIGNMENTS: General Instructions We will provide students with selected data from the literature that are relevant to theories discussed in class. Students are to treat the data as though they were their own and as though they wanted to present them to others in their field. Consequently, you must first capture the interest of the reader by explaining the significance of the hypothesis tested in your paper; second, explain clearly the results so that the reader understands their meaning and draws the same conclusions as you and, finally, discuss how your results expand upon knowledge published to date. Each paper will have: - Introduction that gives some background information but mostly outlines questions in the field (that will be addressed by your data) and significance of the work presented. A rationale statement is often useful. - Results section that explains the data. What do the data show? (To answer this question, you may also have to explain a bit about the techniques used and the rationale for doing specific experiments.) Why were certain controls done? - Discussion section in which a reasonable hypothesis is formulated from the data. This sounds like a lot of writing, but, in fact, the maximum page length will be two typewritten, singlespaced page (font no less than 12). The key is to think clearly, write concisely and say exactly what you mean…no more, no less. Students may discuss the data (and interpretations of the data) among themselves. However, and they can ask us questions, preferably in class where all can profit from the questions and answers.