Assignments

This page presents the major assignments for each module, plus information for the Journal Club presentations associated with modules 1 and 2. Note that other daily homework assignments are contained at the end of the description for lab description.

Class Guidelines

Guidelines for Oral Presentations

Guidelines for Writing a Lab Report

Module Assignments

For each module, students are to complete a major assignment. Staff from the MIT Writing and Communications Center introduce each assignment with a tutorial session, and offer personalized help for the students. In the following table, examples of student work are presented courtesy of the student authors and used with permission.

MODULE #	ASSIGNMENTS	SUPPORTING FILES	STUDENT WORK EXAMPLES
1	Genome engineering portfolio	From Atissa Banuazizi Lecture slides on creating 20.109 presentations (PDF)
2	Expression engineering written report	From Neal Lerner Lecture slides on writing research reports (PDF) A guide to scientific writing (PDF) (Courtesy of Marilee Ogren-Balkema. Used with permission.) Techniques for responding to a peer’s writing (PDF)	“Experimental siRNA targeting the 469-624bp region of Renilla Luciferase is ineffective in reducing expression in mouse embryonic stem cells” (PDF) (Courtesy of Jessica Keenan and Augusto Tentori. Used with permission.)
3	Biomaterials engineering oral presentation	From Atissa Banuazizi Lecture slides on creating research proposal presentations (PDF)	“Expression of dsRNA in Spirogyna algae to inhibit development of malaria carrying mosquitoes” (PDF) (Courtesy of Kat Pak and Matthew Loper. Used with permission.)

MODULE #

ASSIGNMENTS

SUPPORTING FILES

STUDENT WORK EXAMPLES

Genome engineering portfolio

From Atissa Banuazizi

Lecture slides on creating 20.109 presentations (PDF)

Expression engineering written report

From Neal Lerner

Lecture slides on writing research reports (PDF)

A guide to scientific writing (PDF) (Courtesy of Marilee Ogren-Balkema. Used with permission.)

Techniques for responding to a peer’s writing (PDF)

“Experimental siRNA targeting the 469-624bp region of Renilla Luciferase is ineffective in reducing expression in mouse embryonic stem cells” (PDF) (Courtesy of Jessica Keenan and Augusto Tentori. Used with permission.)

Biomaterials engineering oral presentation

From Atissa Banuazizi

Lecture slides on creating research proposal presentations (PDF)

“Expression of dsRNA in Spirogyna algae to inhibit development of malaria carrying mosquitoes” (PDF) (Courtesy of Kat Pak and Matthew Loper. Used with permission.)

Journal Club

The following lists are provided as a guideline for the types of papers that might be relevant for your presentation. You are not limited to these primary research articles. The list is provided simply to give you an idea of the kinds of subjects that could make suitable presentations for the class. Search PubMed yourself to find articles of interest to you. Once you have decided on a paper for your presentation, please email the instructors. As you prepare your talk be sure to follow our guidelines for oral presentations.

List of Papers for Module 1 Presentations

List of Papers for Module 2 Presentations

Scientific data is communicated in many ways. Data can be shared informally through email with a collaborator or in lab group meetings. Data can also be formally communicated as publications in peer-reviewed journals or as hour-long seminars at international meetings. Successful scientific careers require both written and oral presentations, and scientific reputations are based on BOTH. It is important to know that every presentation, no matter how informal, will build or hurt your reputation.

Seminars, group meetings, ten-minute talks, and journal clubs are all ways scientists share data orally. While the content, length and purpose of each talk varies, they share certain common elements, including organization, clarity, and proper attribution for the work.

The oral presentations you will give in this class will be ten-minute talks. Your talks will include an introduction to the topic, a presentation of data, a summary and a time to answer questions from your classmates. Realistically, only two or three ideas can be effectively conveyed in so short a time, and even that will require that you carefully plan what you will say and then practice saying it. You will not be allowed to talk for more than ten minutes.

Things to Remember About Giving Your Talk

A 10’ talk is not a 30’ talk given very fast
It will help if you memorize at least the first few sentences of your talk
Think of ways to transition from one slide to the next (“In the next slide I’ll show you some data that identifies the protein detected”)
Figure out how to work the lights, slide projector, curtains etc before you begin
Keep the lights as bright as possible. If you have to turn the lights off for some image to be properly seen, then remember to turn the lights back on. People can and do fall asleep during dark seminars
Laser pointers or sticks should be used to direct attention to images on the screen. Don’t point to your transparency on the overhead projector since your finger will look gigantic on the screen. Don’t aim your laser pointer at anyone since it can damage a person’s eyes

How to Deal with Nerves

Consider it excitement and turn it into enthusiasm
Remember that even the most experienced speakers get nervous right before a talk
Speak in a louder voice
Don’t speak in a monotone
Do practice your talk, which will help eliminate crutch words such as “so,” “um,” and “like”

Format

SECTION	MINUTES	NUMBER OF SLIDES	DO	DONT’S
Introduction	1-2	1-2	Set the scene for the data you will present, justifying the study and your interest in presenting it Try to summarize background material with a model slide End your introduction by stating the question you will address and what the audience will see	Assume you are addressing experts Give more information than is absolutely needed to understand the rest of your talk Put too much information on each slide. You can bring in a few details as you speak if you are using Microsoft® PowerPoint®
Data	7-8	3-4	Present the data in a logical sequence, letting each slide build upon the last Include a title for each slide. The title should be the conclusion to be drawn Make every element of your slide visible to the entire room. This means 20 point font or greater Interpret each slide thoroughly and carefully Point out strengths and weaknesses of the data along the way	Read your talk. Similarly, don’t read lists from slides Put too much information on each slide. Each slide should make only one point Ever say, “I know you can’t read this, but…” Everything on each slide should be legible Be afraid to remind audience how the data fits into the overall question
Summary	1	1	Review each of your main “messages” Say what the study contributed to the field	Forget to acknowledge all contributors
Question and answer		0	Answer the question being asked. If you are unclear about the question, ask for clarification Respect every question and questioner	Take too long with one question. If the topic is involved, suggest you meet after the talk to discuss it more

Rehearse Your Talk Several Times

Find examples of talks at MIT Video

A formal lab report is the principle way scientific data are conveyed to the rest of the scientific community and preserved for future examination. Each scientific journal has its own idiosyncrasies regarding particulars of the format, but the most common elements of a scientific report, in order of presentation, are:

Title
List of Authors
Abstract
Introduction
Materials and Methods
Results, including figures and tables
Discussion
References

The requirements for each section are outlined below. This information is given in the order that you might actually write your report rather than the order in which the parts are presented in the final report. If you want more information, you can find parts of this text in an on-line collection of instructional materials used in the Purdue University Writing Lab. Other parts are inspired by Robert A. Day’s book, How to Write and Publish a Scientific Paper from Oryx Press, a copy of which is available in the teaching lab.

Authors

This is often the subject of many heated discussions and hurt feelings when only one report can be submitted to describe many people work. Since each of you will submit your own report, questions about who the authors will be, in what order, and what responsibilities each will have are moot. However you should list the name of your partner on your report since she contributed to the work.

Figures and Tables

Some readers begin by scanning the figures first. The figures, with the legends, should provide a self-explanatory overview of your data. Decide what the data show, then create figures which highlight the most important points of your paper.

Tables are used to present repetitive data that is numerical. Graphs or illustrations, collectively called figures, are used to present numerical trends, raw data (like a picture of a gel), or a model that explains your work.

When you prepare your figures and tables, keep in mind that it is significantly more expensive for journals to publish figures and tables than text, so try to present the data in a way that is worthy of such added expense. The table below is an example of an ineffective table.

TEMPERATURE	REPEATS	CORTICAL CELLS	ION FLOW
24°C	5	+	-
24°C	5	-	+

The information in Table 1 could be presented in one sentence, such as: “In ten experiments carried out at 24°C, ion flow was detected only in the presence of cortical cells.” This is a clearer and more concise way to present the information. In addition, all tables and figures must have numbers, titles and legends.

Figure and Table Legends

Legends to the figures and tables explain the elements that appear in the illustration. Conclusions about the data are NOT included in the legends. As you write your first draft, state in a short simple sentence, what the point of the figure or table is. In later drafts, make sure each element of the figure or table is explained. Your figure legends should be written in the present tense since you are explaining elements that still exist at the time that you are writing the paper.

Results

To write the results section, use the figures and tables as a guide. Start by outlining, in point form, what you found, going slowly through each part of the figures. Then take the points and group them into paragraphs, and finally order the points within each paragraph. Present the data as fully as possible, including stuff that at the moment does not quite make sense.

Verbs in the results section are usually in the past tense. Only established scientific knowledge is written about in the present tense, “the world is round,” for example. You cannot presume that your own data are part of the body of established scientific knowledge, and so when you describe your own results, use the past tense, “a band of 1.3 KB was seen,” for example. There are, however, exceptions to this general rule. It is acceptable to say, “Table 3 shows the sizes of the DNA fragments in our preparation.” It is also acceptable to say, “In a 1991 paper, Ebright and coworkers used PCR to mutagenize DNA.”

Materials and Methods

This is like a cooking recipe. Include enough detail so that someone can repeat the experiment. It is important that the reader be able to interpret the results knowing the context in which they were obtained.

The Materials and Methods section should be written in the past tense, since your experiments are completed at the time you are writing your paper.

Discussion

This is the section of the paper for you to show off your understanding of the data. You should summarize what you found. Explain how this relates to what others have found. Explain the implications.

Introduction

Introduce what your question is. Explain why someone should find this interesting. Summarize what is currently known about the question. Introduce a little of what you found and how you found it. You should explain any ideas or techniques that are necessary for someone to understand your results section.

Abstract

The abstract is a very short summary (usually around 150-250 words) of what the question is, what you found, and why it may be important.

The importance of abstracts is increasing as more scientists are using computers to keep up with the literature. Since computers can only search for words in a paper’s title and abstract, these may be the only parts that many people read. The abstract may also be the way a journal’s editor decides whether to send your paper out for peer review or reject it as uninteresting and not generally relevant. Consequently, a well written abstract is extraordinarily important.

Title

The title should be short (about 10 words), interesting, and it should describe what you found.

References

Include only those references that pertain to the question at hand. Journals vary considerably in their preferred format for the reference list. For this class, you should list the references alphabetically by the first author’s last name. Include all the authors, the paper’s title, the name of the journal in which it was published, its year of publication, the volume number, and page numbers. Please carefully follow the punctuation and format requirements. A typical reference should look like

Pavletich N. P., C. O. Pabo. “Zinc Finger-DNA Recognition: Crystal Structure of a Zif268-DNA Complex at 2.1 A.” Science 252 (1991):809-817.

In the body of your report, this article would be cited as follows: “The crystal structure of the Zif268-DNA complex has been solved (Pavletich 1991).”

If two or more articles can be cited for this finding, then they are listed alphabetically, separated by a comma.

Evaluation

Content

SECTION	GOAL	EVALUATION
Title	To give content information to reader	Engaging	Appropriate	Not enough content information or too much
Abstract	To concisely summarize the experimental question, general methods, major findings, and implications of the experiments in relation to what is known or expected	Key information is presented completely and in a clear, concise way All information is correct Organization is logical Captures any reader’s interest	Sufficient information is presented in proper format Would benefit from some reorganization Understandable with some prior knowledge of experiment	Some key information is omitted or tangential information is included Some information is misrepresented Some implications are omitted Incorrect format is used
Introduction	To identify central experimental questions, and appropriate background information. To present a plausible hypothesis and a means of testing it	Relevant background information is presented in balanced, engaging way Your experimental goals and predictions are clear and seem a logical extension of existing knowledge Writing is easy to read All background information is correctly referenced	Relevant background information is presented but could benefit from reorganization Your experiment is well described and a plausible hypothesis is given With some effort, reader can connect your experiments to background information Writing is understandable Background information is correctly referenced	Background information is too general, too specific, missing and/or misrepresented Experimental question is incorrectly or not identified No plausible hypothesis is given Writing style is not clear, correct or concise References are not given or properly formatted
Materials and methods	To describe procedures correctly, clearly, and succinctly. Included a correctly formatted citation of the lab manual	Sufficient for another researcher to repeat your experiment Lab manual cited	Procedures could be pieced together with some effort Lab manual cited	Procedures incorrectly or unclearly described or omitted Lab manual not cited
Results	To present your data using text AND figures/tables	Text tells story of your major findings in logical and engaging way Figures and tables are formatted for maximum clarity and ease of interpretation All figures and tables have numbers, titles and legends that are easy for the reader to follow	Text presents data but could benefit from reorganization or editing to make story easier for reader Text includes interpretation of results that is better suited for discussion section Figures and tables are formatted to be clear and interpretable All figures and tables have numbers, titles and legends	Text omits key findings, inaccurately describes data, or includes irrelevant information Text difficult to read due to style or mechanics of writing Text difficult to read due to logic or organization Figures and tables missing information, improperly formatted or poorly designed Figures and tables have inadequate or missing titles or legends
Discussion	To evaluate meaning and importance of major findings	Appropriate conclusions drawn from findings Connections made between experimental findings Connections made between findings and background information Future directions considered Writing is compelling	Appropriate conclusions drawn from findings Experimental limitations considered Writing is clear	Conclusions omitted, incorrectly drawn or not related to hypothesis Relationship between experimental findings and background information is missing or incorrectly drawn Writing style and mechanics make argument difficult to follow
References	To give credit work on which your own is based	Complete list of reliable sources, including peer-reviewed journal article(s) Properly formatted in body of report and in reference section	Adequate list or reliable sources With minor exceptions, properly formatted in body of report and in reference section	List is incomplete or includes sources not cited in body of report List includes inappropriate sources List not properly formatted References not properly cited in body of report

Style

WRITING STYLE AND MECHANICS	EVALUATION
Voice	Appropriate for audience Consistent passive or active voice	Too simple or too advanced Irregular use of passive and active voice
Word choice	Concise Says what you mean Scientific vocabulary used correctly	Verbose Ambiguous or incorrect Scientific vocabulary misused
Fluency	Sentences and paragraphs well structured Punctuation correct or only minor errors Grammar correct or minor errors Spelling correct	Sentences repetitive or awkward Paragraphs not logical Periods, commas, colons and semicolons misused Significant number of run-on sentences, sentence fragments, misplaced modifiers, subject/verb disagreements Significant number of spelling errors
Scientific format	Past tense for describing new findings Present tense used for accepted scientific knowledge and figure legends All sections included and properly formatted	Misleading verb tenses Some sections missing Abstract not single spaced Figures missing legends References not properly formatted

WRITING STYLE AND MECHANICS

EVALUATION

Voice

Appropriate for audience

Consistent passive or active voice

Too simple or too advanced

Irregular use of passive and active voice

Word choice

Concise

Says what you mean

Scientific vocabulary used correctly

Verbose

Ambiguous or incorrect

Scientific vocabulary misused

Fluency

Sentences and paragraphs well structured

Punctuation correct or only minor errors

Grammar correct or minor errors

Spelling correct

Sentences repetitive or awkward

Paragraphs not logical

Periods, commas, colons and semicolons misused

Significant number of run-on sentences, sentence fragments, misplaced modifiers, subject/verb disagreements

Significant number of spelling errors

Scientific format

Past tense for describing new findings

Present tense used for accepted scientific knowledge and figure legends

All sections included and properly formatted

Misleading verb tenses

Some sections missing

Abstract not single spaced

Figures missing legends

References not properly formatted

Parts

Dwyer, M. A., L. L. Looger, and H. W. Hellinga. “Computational Design of a Biologically Active Enzyme.” Science 304 (2004): 1967-1971.

Knight, T. “Idempotent Vector Design for Standard Assembly of Biobricks.” Massachussetts Institute of Technology Artificial Intelligence Laboratory, MIT Synthetic Biology Working Group, 2004.

Phillips, I., and P. A. Silver. “A New Biobrick Assembly Strategy Designed for Facile Protein Engineering.” Massachussetts Institute of Technology Artificial Intelligence Laboratory, MIT Synthetic Biology Working Group, 2003.

Devices

Fields, S., and O. K. Song. “A Novel Genetic System to Detect Protein-Protein Interactions.” Nature 340 (1989): 245-246.

Hasty, J., D. McMillen, and J. J. Collins. “Engineered Gene Circuits.” Nature 420 (2002): 224-230.

Elowitz, M. B., and S. Leibler. “A Synthetic Oscillatory Network of Transcriptional Regulators.” Nature 403 (2000): 335-338.

Bayer, T. S., and C. D. Smolke. “Programmable Ligand-controlled Riboregulators of Eukaryotic Gene Expression.” Nat Biotechnol 23 (2005): 337-343.

Atsumi, S., and J. W. Little. “Regulatory Circuit Design and Evolution Using Phage {Lambda}.” Genes & Dev 18 (2004): 2086-2094.

Gardner, T. S., C. R. Cantor, and J. J. Collins. “Construction of a Genetic Toggle Switch in Escherichia coli.” Nature 403 (2000): 339-342.

Anderson, J. C., C. Voigt, and A. P. Arkin. “Environmental Signal Integration by a Modular AND Gate.” Molecular Systems Biology 3 (2007): 133.

Win, M. N., and C. D. Smolke. “A Modular and Extensible RNA-based Gene-regulatory Platform for Engineering Cellular Function.” Proc Natl Acad Sci USA (August 20, 2007).

Systems

Basu, S., Y. Gerchman, C. H. Collins, F. H. Arnold, and R. Weiss. “A Synthetic Multicellular System for Programmed Pattern Formation.” Nature 434 (2005): 1130-1134.

Anderson, J. C., E. J. Clarke, A. P. Arkin, and C. A. Voigt. “Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria.” J Mol Biol 355 (2006): 619-627.

Dejong, J. M., Y. Liu, A. P. Bollon, R. M. Long, S. Jennewein, D. Williams, and R. B. Croteau. “Genetic Engineering of Taxol Biosynthetic Genes in Saccharomyces Cerevisiae.” Biotechnol Bioeng 93 (2006): 212-224.

Levskaya, A., A. A. Chevalier, J. J. Tabor, Z. B. Simpson, L. A. Lavery, M. Levy, E. A. Davidson, A. Scouras, A. D. Ellington, and E. M. Marcotte, et al. “Synthetic Biology: Engineering Escherichia coli to See Light.” Nature 438 (2005): 441-442.

Martin, V. J., D. J. Pitera, S. T. Withers, J. D. Newman, and J. D. Keasling. “Engineering a Mevalonate Pathway in Escherichia coli for Production of Terpenoids.” Nat Biotechnol 21 (2003): 796-802.

Noireaux, V., and A. Libchaber. “A Vesicle Bioreactor as a Step Toward an Artificial Cell Assembly.” Proc Natl Acad Sci USA 101 (2004): 17669-17674.

Wang, L., J. Xie, and P. G. Schultz. “Expanding the Genetic Code.” Annu Rev Biophys Biomol Struct 35 (2006): 225-249.

Yeh, B. J., R. J. Rutigliano, A. Deb, D. Bar-Sagi, and W. A. Lim. “Rewiring Cellular Morphology Pathways with Synthetic Guanine Nucleotide Exchange Factors.” Nature 447, no. 7144 (2007): 596-600.

Dueber, J. E., E. A. Mirsky, and W. A. Lim. “Engineering Synthetic Signaling Proteins with Ultrasensitive Input/Output Control.” Nat Biotechnol 25, no. 6 (2007): 660-662.

Artificial Life

Glass, J. I., N. Assad-Garcia, N. Alperovich, S. Yooseph, M. R. Lewis, M. Maruf, C. A. Hutchison III, H. O. Smith, and J. C. Venter. “Essential Genes of a Minimal Bacterium.” Proc Natl Acad Sci 103 (2006): 425-430.

Ishikawa, K., K. Sato, Y. Shima, I. Urabe, and T. Yomo. “Expression of a Cascading Genetic Network within Liposomes.” FEBS Lett 576 (2004): 387-390.

Smith, H. O., C. A. Hutchison III, C. Pfannkoch, and J. C. Venter. “Generating a Synthetic Genome by Whole Genome Assembly: {Phi}X174 Bacteriophage from Synthetic Oligonucleotides.” Proc Natl Acad Sci USA 100 (2003): 15440-15445.

Tumpey, T. M., C. F. Basler, P. V. Aguilar, H. Zeng, A. Solorzano, D. E. Swayne, N. J. Cox, J. M. Katz, J. K. Taubenberger, and P. Palese, et al. “Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus.” Science 310 (2005): 77-80.

Itaya, M., K. Tsuge, M. Koizumi, and K. Fujita. “Combining Two Genomes in One Cell: Stable Cloning of the Synechocystis PCC6803 Genome in the Bacillus Subtilis 168 Genome.” Proc Natl Acad Sci USA 102, no. 44 (November 1, 2005): 15971-6.

Lartigue, C., J. I. Glass, N. Alperovich, R. Pieper, P. P. Parmar, C. A. Hutchison 3rd, H. O. Smith, and J. C. Venter. “Genome Transplantation in Bacteria: Changing One Species to Another.” Science 317, no. 5838: 632-8.

Other

Haywood, Annika F. M., and Brian E. Staveley. “Parkin Counteracts Symptoms in a Drosophila Model of Parkinson’s Disease.” BMC Neuroscience. 5 (2004): 14.

RNAi in Other Different Cell Types

Sharma, S. K., and M. Nirenberg. “Silencing of Genes in Cultured Drosophila Neurons by RNA Interference.” Proc Natl Acad Sci USA 104, no. 31 (July 23, 2007): 12925-12930.

Nakatsuka, T., Y. Abe, Y. Kakizaki, S. Yamamura, and M. Nishihara. “Production of Red-flowered Plants by Genetic Engineering of Multiple Flavonoid Biosynthetic Genes.” Plant Cell Rep 26, no. 11 (November, 2006): 1951-1959.

Galliot, B., M. Miljkovic-Licina, L. Ghila, and S. Chera. “RNAi Gene Silencing Affects Cell and Developmental Plasticity in Hydra.” C R Biol 330, no. 6-7 (June-July 2007): 491-497.

Gary, D. S., A. Davidson, O. Milhavet, H. Slunt, and D. R. Borchelt. “Investigation of RNA Interference to Suppress Expression of Full-length and Fragment Human Huntingtin.” Neuromolecular Med 9, no. 2 (2007): 145-155.

Brandao, P. E., J. G. Castilho, W. Fahl, P. Carnieli Jr., Rde N. Oliveira, C. I. Macedo, M. L. Carrieri, and I. Kotait. “Short-interfering RNAs as Antivirals Against Rabies.” Braz J Infect Dis 11, no. 2 (April 2007): 224-225.

Wang, N., Y. H. Sun, J. Liu, G. Wu, J. G. Su, Y. P. Wang, and Z. Y. Zhu. “Knock Down of gfp and No Tail Expression in Zebrafish Embryo by in vivo-transcribed Short Hairpin RNA with T7 Plasmid System.” J Biomed Sci 14, no. 6 (November 2007): 767-776.

Otani, M., T. Hamada, K. Katayama, K. Kitahara, S. H. Kim, Y. Takahata, T. Suganuma, and T. Shimada. “Inhibition of the Gene Expression for Granule-bound Starch Synthase I by RNA Interference in Sweet Potato Plants.” Plant Cell Rep 26, no. 10 (October 2007): 1801-1807.

Serman, A., F. Le Roy, C. Aigueperse, M. Kress, F. Dautry, and D. Weil. “GW Body Disassembly Triggered by siRNAs Independently of their Silencing Activity.” Nucleic Acids Res 35, no. 14 (2007): 4715-4727.

Kaushik, Deb, Mayandi Sivaguru, Hwan Yul Yong, and R. Michael Roberts. “Cdx2 Gene Expression and Trophectoderm Lineage Specification in Mouse Embryos.” Science 311 no. 5763 (2006): 992-996. Retraction .

Kim, Jongpil, Keiichi Inoue, Jennifer Ishii, William B. Vanti, Sergey V. Voronov, Elizabeth Murchison, Gregory Hannon, Asa Abeliovich. “A MicroRNA Feedback Circuit in Midbrain Dopamine Neurons.” Science 317, no. 5842 (August 31, 2007): 1220-1224.

Zimmermann, T. S., A. C. Lee, A. Akinc, B. Bramlage, D. Bumcrot, M. N. Fedoruk, J. Harborth, J. A. Heyes, L. B. Jeffs, M. John, A. D. Judge, K. Lam, K. McClintock, L. V. Nechev, L. R. Palmer, T. Racie, I. Röhl, S. Seiffert, S. Shanmugam, V. Sood, J. Soutschek, I. Toudjarska, A. J. Wheat, E. Yaworski, W. Zedalis, V. Koteliansky, M. Manoharan, H. P. Vornlocher, and I. MacLachlan. “RNAi-Mediated Gene Silencing in Non-human Primates.” Nature 441, no. 7089 (May 4, 2006): 111-114.

Nakamura, Hiroshi, Shahid S. Siddiqui, Xiang Shen, Asrar B. Malik, Jose S. Pulido, Nalin M. Kumar, and Beatrice Y. J. T. Yue. “RNA Interference Targeting Transforming Growth Factor-ß Type II Receptor Suppresses Ocular Inflammation and Fibrosis.” Molecular Vision 10 (2004): 703-711.

siRNA Validation and Applications

Qiu, S., C. M. Adema, and T. Lane. “A Computational Study of Off-target Effects of RNA Interference .” Nucleic Acids Res 33, no. 6 (March 30, 2005): 1834-1847.

Zhang, J., C. Wang, N. Ke, J. Bliesath, J. Chionis, Q. S. He, Q. X. Li, J. E. Chatterton, F. Wong-Staal, and D. Zhou. “A More Efficient RNAi Inducible System for Tight Regulation of Gene Expression in Mammalian Cells and Xenograft Animals .” RNA 13, no. 8 (August 2007): 1375-1383.

Gonzalez-Alegre, P., and H. L. Paulson. “Technology Insight: Therapeutic RNA Interference–How Far from the Neurology Clinic ?” Nat Clin Pract Neurol 3, no. 7 (July 2007): 394-404.

Natt, F. “siRNAs in Drug Discovery: Target Validation and Beyond .” Curr Opin Mol Ther 9, no. 3 (June 2007): 242-247.

Scherer, L., J. J. Rossi, and M. S. Weinberg. “Progress and Prospects: RNA-based Therapies for Treatment of HIV Infection .” Gene Ther 14, no. 14 (July 2007):1057-1064.

Wood, M., H. Yin, and G. McClorey. “Modulating the Expression of Disease Genes with RNA-Based Therapy .” PLoS Genet 3, no. 6 (June 29, 2007): e109

Krueger, U., T. Bergauer, B. Kaufmann, I. Wolter, S. Pilk, M. Heider-Fabian, S. Kirch, C. Artz-Oppitz, M. Isselhorst, and J. Konrad. “Insights into Effective RNAi Gained from Large-Scale siRNA Validation Screening .” Oligonucleotides 17, no. 2 (Summer 2007 ): 237-250.

Tschaharganeh, D., V. Ehemann, T. Nussbaum, P. Schirmacher, and K. Breuhahn. “Non-specific Effects of siRNAs on Tumor Cells with Implications on Therapeutic Applicability Using RNA Interference .” Pathol Oncol Res 13, no. 2 (2007): 84-90.

Baigude, H., J. McCarroll, C. S. Yang, P. M. Swain, and T. M. Rana. “Design and Creation of New Nanomaterials for Therapeutic RNAi .” ACS Chem Biol 2, no. 4 (April 24, 2007): 237-241.

Schiffelers, R. M., J. Xu, G. Storm, M. C. Woodle, and P. V. Scaria. “Effects of Treatment with Small Interfering RNA on Joint Inflammation in Mice with Collagen-induced Arthritis .” Arthritis Rheum 52, no. 4 (April 2005):1314-1318.

Mikat, V., and A. Heckel. “Light-dependent RNA Interference with Nucleobase-caged siRNAs .” RNA 13, no. 12 (December 2007): 2341-2347.

Portfolio components:

Part 1: Rebuttal to Editorial

This will be written as a homework assignment associated with lab module 1.4 (Examine candidate clones), exchanged with your lab partner for peer review, then submitted to the teaching faculty as part of your portfolio. This portion of the assignment accounts for up to 15% of your grade.

Essay 1: Choose one of the following quotes to address. Both come from Andrew Pollack in the New York Times, Tuesday, Jan 17, 2006, Custom-Made Microbes, at Your Service which quotes Professor Arnold of Caltech as saying:

“(Synthetic Biology) has a catchy new name, but anybody over 40 will recognize it as good old genetic engineering applied to more complex problems.”

and

“There is no such thing as a standard component, because even a standard component works differently depending on the environment. The expectation that you can type in a sequence and can predict what a circuit will do is far from reality and always will be.”

Essay 2: “Editorial: Meaning of Life.” In Nature (2007) 447: 1031-1032:

“it would be a service…to dismiss the idea that life is a precise scientific concept”

Part 2: M13.1 Redesign Description and Parts

Submit your annotated sequence as well as a human-readable text to describe your refactoring. What do you need to do exactly? First, choose a section of the M13.1 scaffold in which you will do your refactoring work (you should choose what you want to refactor based on what seems interesting or important to you). Do not try to refactor all of M13. Only one section between two unique restriction endonuclease sites. Second, design the sequence of DNA for your refactored section of the M13 genome (Note: your DNA sequence must start and end with two of the available unique restriction endonuclease sites across the M13 genome). Third, provide the annotated sequence for your refactored section (follow the color scheme suggested, or a better, clearly defined scheme of your own). Don’t do anything fancy. A rich text file, word document, or powerpoint file should be good enough. Fourth, provide a one paragraph description of what the purpose or goal of your refactored section is (e.g., what will it test? or, what new function will it provide?). Also, include a cost estimate for your refactored section ($1.35 per bp) and tell us whether or not you think we should have the section synthesized (GO or NO GO). We will quickly check your designs (regardless of GO/NO GO), follow-up w/ any questions, and then order them for DNA synthesis (if you or we say GO). Because we are trying to do this v. quickly this term, it is very important that your clearly annotate your designed sequence (so that we can check it), and provide a good written paragraph describing what your design goals are (so that we can more readily understand what you are hoping to do). This portion of the assignment accounts for up to 40% of your grade.

Redesign Ideas from 20.109 (S07)

GENE	IDEAS
II	Make p2 sensitive to and perhaps degraded by any one of various stimuli (e.g. heat, light, pH, chemical input) so replication can be regulated Encode so that p2 can be switched on and off based on the environment which it’s in, for example: stops replication of phage genome when in a certain concentration of Ca²⁺ enters the cell Make p2 require a cofactor that must be added before replication of the phage begins Make p2 count the number of times it nicks DNA Modify p2 in a way that helps p5 sequester the + strands more effectively, perhaps making p5 work more efficiently by reducing competition Modify such that it not only nicks the double stranded form of the genome to initiate replication of the + strand, but also nicks the - strand to impede the formation of dsDNA (this would also help p5) Separate g2 and g10 by inserting entire sequence of g10 after transcription end of g2/g10 (essentially repeating g10 twice in succession), so that the two genes are independent Alter the gene to make it more active and thus replicate DNA more frequently — see how increased DNA production affects phage growth Modify so it can nick foreign DNA (e.g. the E. coli’s) and the phage can replicate and package a portion of the host DNA Remove p2 and p5 to see if the bacteria still make the phage gene products without replicating the phage DNA
X	Make p10 sensitive to a different stimulus than p2 to again regulate replication Perhaps a dual control mechanism for p2 and p10 expression Increase the number of p10 so that the phage can produce more double strands Modify such that the + strands of DNA are not soley dependent on the presence of p10. This modification works together with our modification of p2 Put a tag on p10 to see what it binds at various parts of replication. This will help elucidate how it controls the amount of double stranded M13 genomes Modify to add another level of regulation for phage propagation. This, coupled with control of II, could allow complex control of the life cycle behavior of the virus Make pX more active so that more + strands will accumulate, allowing the host cell to produce even more phages Extract from gene II
V	Add a tag different from p8 (e.g. RFP) to determine what stage of the phage life cycle it is in or to monitor levels of p5-ssDNA complex Alter interaction with p9/p7 so that a limited number of ssDNA may be surrounded by p8 at a time Make it sensitive to mechanism that allows for assay of DNA amount and location, change its assembly mechanism to influence phage size Modify protein so that similar proteins, other than p8 can bind to the surface Remove overlap of p5 gene with start codon of gene for p7. An activation site could be added in prior to start codon in gene for p7 that could be used to allow only limited amounts of pV ( and pVII) to be expressed. This could give control over the the quantity of fully assembled phage to be produced by the host Modify such that p5 can sequester the + stranded DNA more effectively so that there is less competition with the formation of double stranded Vary the activity of the protein and thus the competition between dsDNA formation and the sequestering of ssDNA- compare the results to find the optimum level of phage production possible Modify expression so that we can control the amount of time the virus DNA spends inside the host (as opposed to actively being packaged and spreading to other bacteria) Allow it to sequester double stranded DNA also, then it can be used as a vector for infecting cells with desired DNA fragments Add more DNA binding sites to see if more DNA can be packaged into phage Add some base pairs between V and VII to allow for a restriction site
VII	Alter gene so protein adopts different/more flexible conformation. A change in conformation might expand the different residues that can be attatched to its N-terminal portion Change the way p7 interacts with p9 Modify to increase rate host will shed phage, i.e. decrease the phage-host interaction time Modify the last few codons to remove overlap with the gene encoding p9 Add sequence to the 5’ end of gene so protein could build nanowires or long filaments or other useful materials Delete to learn more about its function Increase it’s expression to learn more about its function Tag protein to monitor interaction with p5/DNA complex
IX	Modify p9 to bind to p3 to create long filaments of phage lined up end to end Modify to express different reactive chains on the phage surface Change the function so that p9 will now lyse the bacteria Modify to make the phage secretion occur at a faster rate so that interaction time with the host is reduced Modify beginning and end sequences so that g9 does not overlap with g7 and g8 Modify the p9 so that it can bind to bacterial surface proteins (the way p3 does) — see if this allows the phage to interact with other bacteria (now that both ends of the phage can bind and perhaps bridge the two bacterial cells)
VIII	Add epitope or other tags, e.g. x-ray sensitive, UV sensitive, flourescent Alter gene so p8 has an affinity for certain residues or salts. This can vastly increase the function of m13 as a whole. It can be used to transport different things into bacteria Change p8 interactions with p5 to regulate size of phage or influence shape of phage by changing how it assembles into a coat Alter gene so fewer copies of p8 fit on phage coat allowing a more flexible packing structure Insert sequence between genes for p5 and p8 to isolate production of these proteins and control their expression levels via activation or repression sites Change amino acid sequence to allow p8 (and thus the entire virus) to bind to certain materials, like metals Add a small protein to the gene for p8 to amplify because p8 is synthesized so many times uncoupled gene for p8 from the gene for p9
III	Add epitope or other tags, e.g. X-ray sensitive, UV sensitive, flourescent Modify portion of p3 that normally interacts with TolA on bacterial pilus to vary phage selectivity to different or only certain bacteria Make p3 bigger so that the phage can bind to objects easier and so that they might bind to bigger objects Selective degredation of p3 to control the maximum amount of DNA allowable on the phage sequence Modify to monitor the timing of the phage escape from host Add sequence to make the tail protein longer Make series of changes to explore the mechanism by which p3 enters and exits the cell. For example: exchange charged amino acids for neutral, acidic for neutral or basic, etc. Delay the time at which the p3/p6 cap is added by making p3 expression a function of environmental cues such as ionic strength or pH. Could also study the effect this would have on the infection process since p3 is also the protein which binds to the TolA protein on the bacterial pilus Change the GTG to ATG start

Part 3: Data Summary for p3-Modifications You Performed in Lab

Consult the Guidelines for writing a lab report. Additionally, many of the “for next time” assignments can get you started on this part of the portfolio. Including but not limited to:

Table: Oligonucleotide design, sequence consequences for phage when inserted and sequence data
Table: Ligation results
Figure: Agarose gel examining candidate clones
Figure: Western results
Table: Plaque assay
Short paragraph for each table and figure describing and interpreting what’s shown
One or two sentence summary of your experimental results
One or two sentence proposal for what you’d do next if we had one more month to spend on this project

This portion of the assignment accounts for up to 20% of your grade.

Part 4: Mini-business Plan for the Registry of Standard Biological Parts

Put yourself 5 years in the future and imagine that the Registry is floundering. Though the number of useful parts has grown through the hard work and dedication of its volunteer workforce in the iGEM program, there is a notable lack of standards:

around the parts themselves (some work always, some in rare conditions, some not at all)
around the assembly process (alternative biobricks and registries have gained popularity)
and around documentation for the parts (some have great spec sheets and some have nothing)

Decide that you will direct the Registry into a manufacturing, service, high tech, or retail business and then devise a plan to grow and stabilize that business. This portion of the assignment accounts for up to 25% of your grade.

In no more than three pages provide a business plan that includes:

1. An Executive Summary

In 250 words or fewer, explain:
- What is your product
- Who are your customers
- What the future holds for the registry in particular and synthetic biololgy more generally
- What you see as the key to success
This summary should sound enthusiastic, professional and be more readable than most “mission statements.”
Consider writing this section after you’ve written the rest of the plan.
Describe what the Registry is, including products, services, customers, ownership, history, location, facilities.
Include strengths and core competencies of the Registry.
Segue into the next section by mentioning the significant challenges faced in the near and long term.
This section should be no longer than 2 paragraphs.

2. Summary of the Current Registry

Describe what the Registry is, including products, services, customers, ownership, history, location, facilities.
Include strengths and core competencies of the Registry.
Segue into the next section by mentioning the significant challenges faced in the near and long term.
This section should be no longer than 2 paragraphs.

3. Market Analysis

Dedicate one paragraph to a description of the market. You might consider including information like:

Who makes up your market?
What is it’s size now? how fast is it growing? how do you know?
What percentage of the market do you expect the Registry to have now and 5 years from now?
How could changes in technology, government, and the economy affect your business?

4. Business Plan

Specify your strategy for continued growth of the Registry. The emphasis of this section will differ depending on the kind of business model you have chosen (retail, manufacturing, service or high tech)

Here are some questions you might consider as you formulate your business plan:

How will you promote the use of the Registry?
How will you advertise?
How will you price your product/services?
Where will you locate the Registry (or BioBrick franchises) and how you will distribute parts/services?
How you will keep the Registry competitive?
How/if you will protect intellectual property while also promoting sharing and community?
Does your plan emphasize increased production, diversification, or eventual sale of franchises?
How long will your strategy take to be partially or fully realized?
Are there start-up costs associated with your business model? How much and where will the capital come from?
Will your registry require insurance coverage or litigation insurance?
Are there trademarks, copyrights, or patents (pending, existing, or purchased) considerations?
How many and what kind (skilled, unskilled, and professional) of employees to you anticipate?
Where will you recruit employees?
Will top notch employees advance? To what?
How will you training employees?
What kind of inventory will you keep: raw materials, supplies, finished goods?
Will there be seasonal fluctuations to demand for parts?
Will you need lead-time for ordering?
Do you expect shortages or delivery problems?
Are supply costs steady? Reliable?
Will you sell parts on credit?
How will you set prices?
What kind of guarantees and privacy protects will you offer?

This section has no defined length or format but should end on an enthusiastic note that might lead some venture capital firm or a funding agency to stay interested.

You are asked to write a formal lab report detailing your work in this module. Specifics for each section of this report are detailed below. Be sure to re-read the Guidelines for writing a lab report.

Abstract

Please keep the number of words under 250.
Do not include references in the abstract.
Try drafting this section after you’ve written the rest of the report.
If you’re truly stuck, start by modifying one crystallizing sentence from each of the sections of your report.
Please do not plagiarize (accidentally or other) the class wiki. This applies to your entire report.

Introduction

The homework you wrote after the first day of this new module will serve at the heart of your introduction. You should add (at least) one final paragraph to narrow the information “funnel,” ending your introduction with a clear description of the problem you’re studying and the method you are using. If you would like to preview for the reader your key results and conclusions in the last sentence of your introduction, you may.

Materials and Methods

If you used any kits for any of the manipulations, it is sufficient to cite the manufacturer’s directions, e.g. “RNA was prepared with the Qiagen RNeasy kit” Subdivide this section into the following

DNA and RNA
- siRNA design
- psiCHECK2
Mouse embryonic cell culture and transfection
Luciferase assays
Mouse whole genome microarray
- mention kits as relevant, including any deviation from published protocol if any
- mention how much RNA was used
- describe array analytical methods in results section rather than in Materials and Methods

Results

Figures

You should include but are not limited to the following figures and tables

Table
- include siRNA you designed, plus scrambled, and positive control sequences
Table or figure
- luciferase data
Figure
- images of your transfected cells
Figure
- microarray analytics
Figure
- microarray conclusions

Each figure should be numbered, and should have a title and legend

Results Text

In paragraph form, describe each figure and the observations you made.
As much as possible, reserve conclusions about your data for the discussion section.

Discussion

You should include but are not limited to

Conclusions you can draw from your work, including any uncertainties
Other data (published or personal communications) that support or contradict your conclusions. For example, you’ll want to look at
- The data collected by the other lab for your same siRNA
- And also what your labmates found for their siRNA
Limitations of your work, e.g. what kinds of experiments/controls/samples would have been great to include
- Luciferase activity from microarray data?
- Off-target effects from microRNA activity?
Next experiments you would like to try to extend your findings and strengthen your conclusions

References

Carefully format these, including a wiki citation like: “20.109 F'07 lab wiki: URL accessed on January 1, 2020.”
Do not include encyclopedias (including Wikipedia) in your reference list since these sources are insufficiently scholarly. You should find the primary references that support those summaries.

Guidelines for Your 20.109 Research Proposal

Writing a research proposal requires that you identify an interesting topic, spend lots of time learning about it, and then design some clever experiments to advance the field. It also requires that you articulate your ideas so any reader is convinced of your expertise, your creativity and the significance of your findings, should you have the opportunity to carry out the experiments you’ve proposed. To begin you must identify your research question. This may be the hardest part and the most fun. You can start by finding a handful of topics to share with your lab partner. Together you should discuss and evaluate the topics you’ve gathered. Consider them based on:

your interest in the topic
the availability of good background information
your likelihood of successfully advancing current understanding
the possibility of advancing foundational technologies or finding practical applications
if your proposal could be carried out in a reasonable amount of time and with non-infinite resources

It might be that not one of the topics you’ve identified is really suitable, in which case you should find some new ideas. It’s also possible that through discussion with your lab partner, you’ve found something new to consider. Both of these outcomes are fine but relatively quickly you and your partner should settle on a general topic or two so you can begin the next step in your proposal writing, namely background reading and critical thinking about the topic.

A few ground rules that are 20.109 specific:

you should not propose any research question that has been the subject of your UROP or research experience outside of 20.109. This proposal must be original.
you should keep in mind that this proposal will be presented to the class, so try to limit your scope to an idea that can be convincingly presented in a ten minute oral presentation.

Once you and your partner have decided on a suitable research problem, it’s time to become an expert on the topic. This will mean searching the literature, talking with people, generating some ideas and critically evaluating them. To keep track of your efforts, you should start a wiki catalog on your OpenWetWare user page. How you format the page is up to you but check out the OpenWetWare yeast rebuild or the T7.2 wiki pages for examples of research ideas in process.

As you become more expert on your research topic, you’ll read a lot about it and you may feel

like there’s too much to read
like you have too many ideas and no way to map or prioritize them
like you don’t understand what you’re reading
all of the above

One of the best ways to help frame the problem for yourself is to discuss it with someone new. You will have an opportunity during lab to talk with a person from another lab group. This person will offer you a fresh ear to consider your proposal. You can rework your proposal based on the conversations you’ve had.

Prepare a 10 minute Microsoft® Powerpoint® talk that describes the research question you have identified, how you propose to study the question and what you hope to learn. A general outline your research proposal presentation is:

a brief project overview
sufficient background information for everyone to understand your proposal
a statement of the research problem and goals
project details and methods
predicted outcomes if everything goes according to plan and if nothing does
needed resources to complete the work
societal impact if all goes well

On the day you present your team should print out and bring three copies of your Microsoft® Powerpoint® slides. Black and white is fine and you can print more than one slide per page if you like. You should also write and print out your “talking points” into the comments box of each of the slides you’ll present. These are speaking notes for your presentation. They should include the words you’ll use to describe each slide and the transitions you’ve planned between them. For example from last year’s presentations, one slide’s talking points were:

“Slide shows normalized data (we took logs)
- Red color used for down-regulated genes
- Lime green for up-regulated
- Olive green used when nothing changed

We dictated what would be considered “Nothing” by putting them into bins Arbitrarily assigned ‘nothing’ as anything between -1 and 1, because it could just have to do with background and the such

Note many open reading frames and hypothetical proteins

Now let’s look at each component individually!”

You will be graded on the integrated success of your presentation: concepts, slides, talking points, and presentation.

Browse Course Material

Course Info

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As Taught In

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Laboratory Fundamentals in Biological Engineering

Class Guidelines

Module Assignments

From Atissa Banuazizi

From Neal Lerner

From Atissa Banuazizi

Journal Club

Things to Remember About Giving Your Talk

How to Deal with Nerves

Format

Rehearse Your Talk Several Times

Authors

Figures and Tables

Figure and Table Legends

Results

Materials and Methods

Discussion

Introduction

Abstract

Title

References

Evaluation

Content

Style

Parts

Devices

Systems

Artificial Life

Other

RNAi in Other Different Cell Types

siRNA Validation and Applications

Part 1: Rebuttal to Editorial

Part 2: M13.1 Redesign Description and Parts

Redesign Ideas from 20.109 (S07)

Part 3: Data Summary for p3-Modifications You Performed in Lab

Part 4: Mini-business Plan for the Registry of Standard Biological Parts

1. An Executive Summary

2. Summary of the Current Registry

3. Market Analysis

4. Business Plan

Introduction

Materials and Methods

Results

Figures

Results Text

Discussion

References

Guidelines for Your 20.109 Research Proposal

Course Info

Instructors

Departments

As Taught In

Level

Topics

Learning Resource Types