Search results

Create the page "Needs Work" on this wiki!

• 20.109(F09): System engineering research article
  *conclusions you can draw from your work, including any uncertainties *limitations of your work, e.g. what kinds of experiments/controls/samples would have been great to i
  7 KB (1,101 words) - 19:38, 28 July 2015
• 20.109(F09):Guidelines for oral presentations
  ... elements, including organization, clarity, and proper attribution for the work. *Figure out how to work the lights, slide projector, curtains etc before you begin.
  5 KB (777 words) - 19:38, 28 July 2015
• 20.109(F09):Guidelines for writing up your research
  ... list the name of your partner on your report since she contributed to the work. ... trends, raw data (like a picture of a gel), or a model that explains your work.
  13 KB (1,951 words) - 19:38, 28 July 2015
• 20.109(F09): Mod 3 Day 6 Oral presentations
  * needed resources to complete the work
  5 KB (879 words) - 19:38, 28 July 2015
• 20.109(F09): Mod 2 Day 6 Readouts of DNA, Protein
  ...): System engineering research article| research article]] describing this work is due in just over one week. This assignment is due by 11:00 a.m. on the d
  13 KB (2,115 words) - 19:38, 28 July 2015
• 20.109(F09):Guidelines for working in the tissue culture facility
  ...ut most are common practice and will be good habits for any tissue culture work you do. ...y with 70% ethanol. Start from the back and proceed forward. Swab during work if necessary.
  6 KB (1,084 words) - 19:38, 28 July 2015
• 20.109(F09): Mod 3 Day 1 Growth of phage materials
  ...ientists who can tolerate a mix of p8 proteins on the phage coat for their work, there are phage-display variations that mix and match fusion and wild-type ... oxide, gold, iridium and indium tin oxide are all in-hand thanks to their work (e.g see reference [http://www.sciencemag.org/cgi/content/abstract/312/5775
  16 KB (2,666 words) - 19:38, 28 July 2015
• 20.109(F09): Mod 2 Day 1 Testing an engineered biological system
  ...eral scheme for Two Component Signaling]] Fortunately evolution appears to work with motifs and many of these motifs behave in a reasonably modular fashion
  13 KB (2,163 words) - 19:38, 28 July 2015
• 20.109(F09): Mod 2 Day 2 Measuring system performance
  ... to make accessory pigments needed for the light-sensing fusion protein to work. These phycobillins are shown in the box at the left of the signaling pathw ...ortant to think about effective figures that summarize and anticipate your work. [[Image:BlackBox details.png|thumb|center|400px]]
  11 KB (1,859 words) - 19:39, 28 July 2015
• 20.109(S10):Protein-level analysis (Day6)
  ...lets return to thinking about the structure of cartilage for a bit. Our work in this module has focused on chondrocytes themselves (viability and morpho ... diluted antibody per well. Incubate for 90 min (at room temperature), and work on Parts 2 and 3 of today's protocol.
  9 KB (1,466 words) - 19:49, 28 July 2015
• 20.109(S10):Wrap-up analysis (Day7)
  ...nce they will undergo partly different manipulations. You may also want to work on two separate worksheets, one for each collagen type.
  5 KB (919 words) - 19:49, 28 July 2015
• 20.109(F10)
  ...ts at the bench, ones that will increase the likelihood of success in your work and ensure the health and safety of you and those around you. By the end of
  3 KB (445 words) - 21:00, 28 July 2015
• 20.109(F10):Module 2
  ...---have lagged behind in the design and construction of novel systems that work in reliable, scalable, intuitive ways. Biology simply does not always perfo
  3 KB (443 words) - 21:00, 28 July 2015
• 20.109(F10): Mod 2 Day 7 Readout of Protein
  ...k on your report, ask questions of each other or the teaching faculty, and work on your oral presentation if that's coming up too. ...): System engineering research article| research article]] describing this work is due in just over one week. This assignment is due by 11:00 a.m. on the d
  10 KB (1,613 words) - 21:00, 28 July 2015
• 20.109(F10):Module 3
  ...9863670 CNN videotape of Angie Belcher teaching President Obama about this work]
  2 KB (313 words) - 21:00, 28 July 2015
• 20.109(F10):DNA engineering "Progress Report"
  ...figures, but if you do so, you must include the reference to the published work. Reference format requirements are described in [[20.109(F10):Guidelines fo ... be used to detect homologous recombination in mammalian cells. The reader needs to know what the goal is: which plasmid did you set out to create? Part B o
  7 KB (1,131 words) - 21:00, 28 July 2015
• 20.109(F10):Guidelines for editing OpenWetWare
  ==Sign your work==
  3 KB (461 words) - 21:00, 28 July 2015
• 20.109(F10):Lab basics
  *Procedures for doing tissue culture work =Communicating your work=
  1 KB (184 words) - 21:00, 28 July 2015
• 20.109(F10): Mod 2 Day 1 Testing an engineered biological system
  ...eral scheme for Two Component Signaling]] Fortunately evolution appears to work with motifs and many of these motifs behave in a reasonably modular fashion
  14 KB (2,180 words) - 21:00, 28 July 2015
• 20.109(F10):General lab policy
  ... your partner and to others in the lab if you are not up to speed when the work begins. ... have cut yourself (even if you consider it minor), if something broke and needs cleaning up, or if you are on fire.
  2 KB (429 words) - 21:00, 28 July 2015
• 20.109(F10):Guidelines for working in the tissue culture facility
  ...ut most are common practice and will be good habits for any tissue culture work you do. ...y with 70% ethanol. Start from the back and proceed forward. Swab during work if necessary.
  6 KB (1,084 words) - 21:00, 28 July 2015
• 20.109(F10):Guidelines for writing up your research
  ...ist the name of your partner on your report since (s)he contributed to the work. Indicate that you are the primary author of the report by underlining your ... trends, raw data (like a picture of a gel), or a model that explains your work.
  18 KB (2,793 words) - 21:00, 28 July 2015
• 20.109(F10):Guidelines for oral presentations
  ... elements, including organization, clarity, and proper attribution for the work. *Figure out how to work the lights, slide projector, curtains etc before you begin.
  5 KB (815 words) - 21:00, 28 July 2015
• 20.109(F10): System engineering research article
  *conclusions you can draw from your work, including any uncertainties *limitations of your work, e.g. what kinds of experiments/controls/samples would have been great to i
  7 KB (1,095 words) - 21:00, 28 July 2015
• 20.109(F10): Mod 1 Day 1 DNA engineering using PCR
  ... establish good habits for documentation of your work. By documenting your work according to the exercises done today, you will ...re there are no spaces between or after the letters or your search wont work. Change the color of the start codon to blue. Repeat the Find proc
  22 KB (3,783 words) - 21:00, 28 July 2015
• 20.109(F10): Mod 3 Day 6 Oral presentations
  * needed resources to complete the work
  5 KB (880 words) - 21:00, 28 July 2015
• 20.109(F10): Mod 1 Day 3 Agarose gel electrophoresis
  Ligations generally work best when there is a 1:4 ratio of backbone to insert. You will ligate your
  10 KB (1,744 words) - 21:00, 28 July 2015
• 20.109(F10): Mod 1 Day 5 Examine candidate clones
  *work best in the same buffer and at the same temperature.<br> ...faculty has set up four overnight LB + AMP cultures of bacteria for you to work with. Three of these cultures have colonies from the ligation reactions you
  11 KB (1,830 words) - 21:00, 28 July 2015
• 20.109(S11)
  ...ts at the bench, ones that will increase the likelihood of success in your work and ensure the health and safety of you and those around you. By the end of
  3 KB (555 words) - 21:05, 28 July 2015
• 20.109(S11):Lab basics
  *Procedures for doing tissue culture work. ==Communicating your Work==
  1 KB (172 words) - 21:05, 28 July 2015
• 20.109(S11):General lab policy
  ... your partner and to others in the lab if you are not up to speed when the work begins. ... have cut yourself (even if you consider it minor), if something broke and needs cleaning up, or if you are on fire.
  2 KB (434 words) - 21:05, 28 July 2015
• 20.109(S11):Amplify aptamer-encoding DNA (Day1)
  You and your partner may work together on the lab practical. (Note: this will not be the case for future Before starting today's wet lab work, you may want to wipe down your pipettes and your benchtop with 70% ethanol
  10 KB (1,688 words) - 21:05, 28 July 2015
• 20.109(S11):Purify aptamer-encoding DNA (Day2)
  ...ts low viscosity means that high weight percent solutions are tractable to work with, and that the solidified gel remains pliable rather than brittle. HR a ... the work you do in Module 1 in a formal lab report. To help you pace your work, as well as give you feedback early on, you will be required to draft small
  11 KB (1,852 words) - 21:05, 28 July 2015
• 20.109(S11):Prepare RNA by IVT (Day3)
  ... different from DNA in its stability. Consequently it is more difficult to work with RNA in the lab. It is not the techniques themselves that are difficult *Before you begin your experiment, clean your work area: (1) remove all clutter, (2) wipe down the benchtop with warm water an
  16 KB (2,632 words) - 21:05, 28 July 2015
• 20.109(S11):RNA to DNA by RT-PCR (Day5)
  ...anscription reaction to make more of the RNA mixture. For this process to work, the 6-5 and 8-12 sequences must amplify at the same rate, a fact that has ...d compete with this interaction seems to work. In Prof. Niless original work, he used a different RT-PCR kit that did not face this inhibition issue, wh
  8 KB (1,243 words) - 21:05, 28 July 2015
• 20.109(S11):Complete DNA design (Day2)
  ...e &lambda; and Higher Organisms''. Despite having only 50,000 bp of DNA to work with, &lambda; is able to exist in two distinct states &mdash; lytic or lys
  14 KB (2,340 words) - 21:05, 28 July 2015
• 20.109(S11):Post-selection IVT and journal club (Day6)
  ...mework will be due. However, it is strongly suggested that you continue to work on your report, particularly the RT-PCR figure and experimental schematic. ...f your own strengths and weaknesses can often help you improve your future work. After you give your presentation today, write a brief self-evaluation. Spe
  2 KB (251 words) - 21:05, 28 July 2015
• 20.109(S11):Aptamer binding assay (Day7)
  ...f your own strengths and weaknesses can often help you improve your future work. After you give your presentation next time, write a brief self-evaluation.
  10 KB (1,596 words) - 21:05, 28 July 2015
• 20.109(S11):Journal club (Day8)
  ...at 1:30 pm sharp in room 16-336. (Day 6 presentations will begin after lab work is finished, b/w 1:30 and 2 pm.)
  8 KB (1,210 words) - 21:05, 28 July 2015
• 20.109(S11):Module 2
  ...ronment might substantially affect their function. In this module, we will work on understanding and improving an edge detection system effected by bacteri ...pful discussions during early module development, as well as for her prior work in developing a [http://openwetware.org/wiki/20.109(F10):Module_2 related m
  3 KB (437 words) - 21:05, 28 July 2015
• 20.109(S11):Prepare DNA for cloning (Day3)
  ...While the gel runs, you will set up control digests to understand how they work and why we had to do this one for you in the interests of time. ...te the IPTG- and light-sensitive systems to each other. For the mapping to work well, you should treat all the different cell strains as consistently as po
  17 KB (2,967 words) - 21:05, 28 July 2015
• 20.109(F11)
  ...ts at the bench, ones that will increase the likelihood of success in your work and ensure the health and safety of you and those around you. By the end of
  4 KB (629 words) - 21:07, 28 July 2015
• 20.109(F11): Mod 1 Day 3 Agarose gel electrophoresis
  Ligations generally work best when there is a 1:4 ratio of backbone to insert. You will ligate your
  10 KB (1,802 words) - 21:07, 28 July 2015
• 20.109(F11): Assignments
  ...in the "for next time" section of each lab day. <font color = red> You can work with your lab partner, friends and teaching assistants on these assignments <font color= red><b>Late work will be penalized 1/3 of a letter grade for each day late and will not be a
  4 KB (549 words) - 21:07, 28 July 2015
• 20.109(F11):DNA engineering lab practical
  *You will work alone on this lab practical, not with your lab partner.
  1 KB (179 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 1 Day 1 DNA engineering using PCR
  ... establish good habits for documentation of your work. By documenting your work according to the exercises done today, you will ...re there are no spaces between or after the letters or your search wont work. Change the color of the start codon to blue. Repeat the Find proc
  22 KB (3,809 words) - 21:08, 28 July 2015
• 20.109(F11):DNA engineering powerpoint summary
  ...r this assignment, though you will receive feedback on the quality of your work. ...nt summary all along, through the "For Next Time" assignments or other lab work. This is your chance to show off your understanding of all you've done. As
  3 KB (528 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 3 Day 6 Oral presentations
  * needed resources to complete the work
  5 KB (879 words) - 21:08, 28 July 2015
• 20.109(F11):Guidelines for working in the tissue culture facility
  ...ut most are common practice and will be good habits for any tissue culture work you do. ...y with 70% ethanol. Start from the back and proceed forward. Swab during work if necessary.
  10 KB (1,639 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 1 Day 4 DNA ligations and bacterial transformations
  ...t.edu/environment/ehs/about_ehs.html (EHS)] come to discuss tissue culture work with you. ...y| guidelines for mammalian cell culture.]] Next time, you will begin your work in the tissue culture facility. <br>
  12 KB (1,904 words) - 21:08, 28 July 2015
• 20.109(F11):Lab basics
  *Procedures for doing tissue culture work =Communicating your work=
  2 KB (204 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 1 Day 6 Lipofection & lab practical
  ...o far and improve the content accordingly. If you have questions about the work, you have numerous [[20.109(F11):People| resources available to help you.]]
  10 KB (1,541 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 1 Day 5 Examine candidate clones & tissue culture
  ...faculty has set up four overnight LB + AMP cultures of bacteria for you to work with. Three of these cultures have colonies from the ligation reactions you ... enzymes youll use. The following table may be helpful as you plan your work.
  13 KB (2,328 words) - 21:08, 28 July 2015
• 20.109(F11): System engineering research article
  *conclusions you can draw from your work, including any uncertainties *limitations of your work, e.g. what kinds of experiments/controls/samples would have been great to i
  7 KB (1,159 words) - 21:08, 28 July 2015
• 20.109(F11):Module 2
  ...---have lagged behind in the design and construction of novel systems that work in reliable, scalable, intuitive ways. Biology simply does not always perfo
  3 KB (445 words) - 21:08, 28 July 2015
• 20.109(F11):Blogging and summary thoughts
  ...9 blog] and you, as students in 20.109, are being asked to reflect on your work in this lab class and then share your impressions. *Future directions you can imagine for the work
  2 KB (400 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 2 Day 1 Testing an engineered biological system
  ...eral scheme for Two Component Signaling]] Fortunately evolution appears to work with motifs and many of these motifs behave in a reasonably modular fashion ...gal assays you ran (best to include your experimental values and show your work for at least one calculation), then answer the following questions:
  14 KB (2,184 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 2 Day 2 Measuring system performance
  ... to make accessory pigments needed for the light-sensing fusion protein to work. These phycobillins are shown in the box at the left of the signaling pathw ...ortant to think about effective figures that summarize and anticipate your work. [[Image:BlackBox details.png|thumb|center|400px]]
  21 KB (3,476 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 3 Day 4 Solar cell assembly
  The groups not visiting the Belcher lab should use the extra time to work on their research proposals. These will be presented in just one week!!
  5 KB (811 words) - 21:08, 28 July 2015
• 20.109(F11):Guidelines for editing OpenWetWare
  ==Sign your work==
  3 KB (461 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 2 Day 3 Tools for system engineering
  ...en defined through traditional scientific studies of EnvZ, for example the work from Tom Silhavy's lab( [http://openwetware.org/wiki/PMID:_9721293 ] and [[ ...ld examine the bacterial photograph you set up last time and document your work and your ideas about the experiment.
  30 KB (4,934 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 2 Day 6 Readouts of DNA, Protein
  ...el should take approximately one hour to run. During that hour, you should work on part two of today's protocol.<br>
  16 KB (2,610 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 2 Day 7 Readout of Protein
  ...k on your report, ask questions of each other or the teaching faculty, and work on your oral presentation if that's coming up too. ...ts of your choosing, to talk with other groups about their results, and to work on your research article.
  10 KB (1,644 words) - 21:08, 28 July 2015
• 20.109(F12): Mod 3 Day 1 Growth of phage materials
  ...ientists who can tolerate a mix of p8 proteins on the phage coat for their work, there are phage-display variations that mix and match fusion and wild-type ... oxide, gold, iridium and indium tin oxide are all in-hand thanks to their work (e.g see reference [http://www.sciencemag.org/cgi/content/abstract/312/5775
  18 KB (3,015 words) - 13:43, 29 July 2015
• 20.109(F12):Module 3
  ...9863670 CNN videotape of Angie Belcher teaching President Obama about this work]
  3 KB (362 words) - 13:43, 29 July 2015
• 20.109(F12): Written research pre-proposal
  ... and then submit or present a proposal, as if you were seeking to fund the work. ...og this proposal development is up to you but be active in organizing your work or you'll find it much harder to pull all the content into a cohesive propo
  4 KB (640 words) - 13:43, 29 July 2015
• 20.109(F12): Written research proposal
  ...dea and then submit a written proposal, as if you were seeking to fund the work for the next '''3 years'''!
  2 KB (372 words) - 13:43, 29 July 2015
• 20.109(F12): Mod 3 Day 6 Oral presentations
  * needed resources to complete the work
  2 KB (345 words) - 13:43, 29 July 2015
• 20.109(F12) Pre-proposal: Inducing Apoptosis with Sound
  ... inducing lysis), and also without contact using ultrasound[5], but little work has been done in using a sound input in an engineered system to initiate pr
  6 KB (833 words) - 13:43, 29 July 2015
• 20.109(S13):OWW in 20.109
  ===Sign your work===
  9 KB (1,512 words) - 13:48, 29 July 2015
• 20.109(S13):Site-directed mutagenesis (Day2)
  ...al of information in order to design mutagenized inverse pericams – nice work! Today you will put your designs into practice. ...reaction, to ensure that all the reagents are working properly. You should work quickly but carefully, and keep your tube in a chilled container at all tim
  13 KB (2,152 words) - 13:48, 29 July 2015
• 20.109(S13):Testing cell viability (Day3)
  ...of your labmates time.''' Reading the protocol in advance will help you work more quickly, and is strongly recommended. When observing your cells under fluorescence excitation, you should work with the room lights off for best results. A member of the teaching faculty
  15 KB (2,447 words) - 13:48, 29 July 2015
• 20.109(S13):Bacterial amplification of DNA (Day3)
  ...work on Parts 3 and (optional) 5, label the tubes you will need in Part 4, work on your notebooks, start the FNT assignment (it's a little long for a weekd '''Please clearly show all your work and reasoning throughout this assignment. Parts A through C should be compl
  13 KB (2,181 words) - 13:48, 29 July 2015
• 20.109(S13):Design mutant (Day1)
  ...s wasting a month of your time repeating experiments already proven not to work or reinventing the wheel. ...As you work, you can ask yourself why these stretches of the protein might work the way that they do, and how they might be changed.
  26 KB (4,387 words) - 13:48, 29 July 2015
• 20.109(S13):Prepare expression system (Day4)
  #Incubate on ice for 1 hour. You can work on parts 2, 4, and 5 of today's protocols now, as well as assemble the mate ...ein_engineering_report | research article]] describing your protein design work. For this assignment, you will write start outlining and drafting the intro
  20 KB (3,344 words) - 13:48, 29 July 2015
• 20.109(S13):Induce protein and evaluate DNA (Day5)
  As evidenced by Nagai’s work, wild-type inverse pericam is not toxic to BL21(DE3) cells. Although it is ...our cells with IPTG, you will let the resultant protein factories do their work for 2-3 hours. During this time, you will evaluate the DNA from your two X#
  15 KB (2,584 words) - 13:48, 29 July 2015
• 20.109(S13):Purify protein (Day6)
  ... has 15 &mu;L of liquid in it. You might use the table below to guide your work. #*The timing function on this centrifuge does not work! Bring your timer and manually turn the centrifuge off after 2 min. Start t
  13 KB (2,134 words) - 13:48, 29 July 2015
• 20.109(S13):Design experiment (Day1)
  ... of the surrounding environment on cell phenotype. In particular, you will work with primary chondrocytes and/or mesenchymal stem cells in 3D gel culture. ...er time. We will also have some mesenchymal stem cells for a few groups to work with in order to investigate conditions that promote chondrogenesis. Please
  18 KB (2,946 words) - 13:48, 29 July 2015
• 20.109(S13): Cell-biomaterial engineering report
  ...did in previous reports. You can assume a reader highly familiar with your work, such as a graduate school advisor to whom you are providing an update. Summarize your findings and briefly suggest future work in about 2-3 pages, not counting figures. What we usually call Results and
  3 KB (415 words) - 13:48, 29 July 2015
• 20.109(S13):Preparing cells for analysis (Day4)
  Before (second TC cohort) or after (first TC cohort) your wet-lab work today, take some time to discuss the five research results you wrote up for ...trix dissolution for better protein or proteoglycan recovery. Split up the work with your partner whatever way is most convenient. '''Remember to label you
  25 KB (4,196 words) - 13:48, 29 July 2015
• 20.109(S13):Initiating transcript and protein assays (Day5)
  ... Buffer to the plate. Wait another 60-90 minutes. In the meantime, you can work on cell viability analysis (first listed on Day 4 Part 4). ...of RNA in your cDNA reaction, a 5-10x further dilution of your cDNA should work well.
  15 KB (2,467 words) - 13:48, 29 July 2015
• 20.109(S13):Assess protein function (Day8)
  ...got last time. Begin by analyzing the wild-type protein as a check on your work (your curve should resemble Nagai's Figure 3L), and then move on to your mu ...t be discouraged if your wild-type values do not exactly match Nagai’s work, or if there is variation between Parts 1, 2, and 3.
  16 KB (2,718 words) - 13:48, 29 July 2015
• 20.109(S13):Protein-level and wrap-up analysis (Day7)
  ...nce they will undergo partly different manipulations. You may also want to work on two separate worksheets, one for each collagen type.
  6 KB (932 words) - 13:48, 29 July 2015
• 20.109(S13): DNA engineering report
  ... of technical information, and consequently should strive to present your work in a logical, step-by-step fashion. ...intrigue your reader. Keep in mind, you have little space to motivate your work and you need to catch the reader’s attention.
  8 KB (1,267 words) - 13:48, 29 July 2015
• 20.109(S13):Guidelines for oral presentations
  ... elements, including organization, clarity, and proper attribution for the work. *Generally speaking, you should figure out how to work the lights, slide projector, curtains, etc. before you begin. In this class
  5 KB (895 words) - 13:48, 29 July 2015
• 20.109(S13):Module 3 oral presentations
  * needed resources to complete the work
  6 KB (923 words) - 13:48, 29 July 2015
• 20.109(S13):Reflection assignments summary page
  ...f your own strengths and weaknesses can often help you improve your future work. After you give your presentation, write a brief self-evaluation (200 words ... this revision that you think are generalizable and will translate to your work on the second report? Again, 200-250 words should suffice.
  5 KB (806 words) - 13:48, 29 July 2015
• 20.109(S13):Guidelines for writing up your research
  ...ort by underlining your name. Others who substantially contributed to your work, such as your lab partner, should also be listed. ...motivate the audience to keep reading! How? Reveal the significance of the work through connections to both prior scientific accomplishments and interestin
  22 KB (3,317 words) - 13:48, 29 July 2015
• 20.109(S13):Guidelines for working in the tissue culture facility
  ...ut most are common practice and will be good habits for any tissue culture work you do. ...y with 70% ethanol. Start from the back and proceed forward. Swab during work if necessary.
  7 KB (1,175 words) - 13:48, 29 July 2015
• 20.109(S14):Preparing cells for analysis (Day4)
  ... you are in the second group, you may use the time that you are waiting to work on your FNT or the optional data analysis, but also be sure to prepare your ...trix dissolution for better protein or proteoglycan recovery. Split up the work with your partner whatever way is most convenient. '''Remember to label you
  24 KB (4,100 words) - 13:59, 29 July 2015
• 20.109(S14):Transcript-level analysis (Day6)
  ...let’s return to thinking about the structure of cartilage for a bit. Our work in this module so far has focused on on the cells themselves (viability and ... diluted antibody per well. Incubate for 90 min (at room temperature), and work on Parts 2 and 3 of today's protocol.
  16 KB (2,528 words) - 13:59, 29 July 2015
• 20.109(S14):Guidelines for working in the tissue culture facility
  ...ut most are common practice and will be good habits for any tissue culture work you do. ...y with 70% ethanol. Start from the back and proceed forward. Swab during work if necessary.
  7 KB (1,207 words) - 13:59, 29 July 2015
• 20.109(S14):Guidelines for writing up your research
  ...ort by underlining your name. Others who substantially contributed to your work, such as your lab partner, should also be listed. ... to keep reading! How do you do the latter? Reveal the significance of the work through connections to both prior scientific accomplishments and interestin
  22 KB (3,344 words) - 13:59, 29 July 2015
• 20.109(S14): Cell engineering mini-report
  ...did in previous reports. You can assume a reader highly familiar with your work, such as a graduate school advising committee to whom you are providing an Summarize your findings and briefly suggest future work in ~ 4 pages, give or take, not counting figures. What we usually call Resu
  3 KB (411 words) - 13:59, 29 July 2015
• 20.109(S14):Module 3 oral presentations
  * needed resources to complete the work ...n this proposal. For example, if you propose molecular and/or ''in vitro'' work, you would want to be able to say a few words about ''in vivo'' experiments
  14 KB (2,342 words) - 13:59, 29 July 2015
• 20.109(S14): TA notes for module 3
  #None: all work today is computer work. Get passing familiarity with the faculty-selected journal articles. #150 mM NaCl in autoclaved water--needs to be sterile filtered
  11 KB (1,791 words) - 13:59, 29 July 2015
• 20.109(F13): TA notes for module 1
  * Make a plan for preparing the high volume TC work we do. Lab also needs you to:
  16 KB (2,601 words) - 14:02, 29 July 2015
• 20.109(F14)
  ...ts at the bench, ones that will increase the likelihood of success in your work and ensure the health and safety of you and those around you. By the end of
  3 KB (481 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 3 Agarose gel electrophoresis
  Ligations generally work best when there is a 1:4 '''molar''' ratio of backbone to insert. You will ...ngineering_summary | '''formal written summary''']]. To help you pace your work, as well as give you feedback early on, you will be required to draft small
  13 KB (2,248 words) - 14:02, 29 July 2015
• 20.109(F14):20.109 Class Blog summary page
  ...first, as it refreshes my memory and reminds me how exciting it was do the work. Next, I take this ‘writers high’ to the data section, which I find the
  6 KB (1,018 words) - 14:02, 29 July 2015
• 20.109(F14): Assignments
  Although your lab work will be done in pairs, <font color = CC0000>'''most assignments will be sub ...</font color> We strongly recommend that you plan ahead and space out your work when possible. For assignments that may be revised, be sure to read the lat
  9 KB (1,248 words) - 14:02, 29 July 2015
• 20.109(F14): DNA engineering summary
  ...in figures and supporting text – including context for understanding the work’s broader implications. ... of technical information, and consequently should strive to present your work in a logical, step-by-step fashion. To aid in educating the audience, an In
  9 KB (1,410 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 1 DNA engineering using PCR
  ... establish good habits for documentation of your work. By documenting your work according to the exercises done today, you will ...re there are no spaces between or after the letters or your search won’t work. Change the color of the start codon to blue. Repeat the “Find…” proc
  23 KB (3,882 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 4 DNA ligations and bacterial transformations
  ... will confirm the presence of the PCR insert. Please clearly show all your work and reasoning, and be sure that your assignment explicitly includes * work best in the same buffer and at the same temperature
  11 KB (1,836 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 5 Examine candidate clones & tissue culture
  ...faculty has set up four overnight LB + AMP cultures of bacteria for you to work with. Three of these cultures have colonies from the ligation reactions you ... enzymes you’ll use. The following table may be helpful as you plan your work. As an example, ''XbaI'' is 20,000 U/mL; therefore one reaction will requir
  20 KB (3,455 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 6 Lipofection and paper discussion
  While you were out, there was a significant amount of work done to complete your CometChip assay (Thank you, Isaak!). Below is a summa
  11 KB (1,850 words) - 14:02, 29 July 2015
• 20.109(F14):Lab tour
  ...ur computer versus operating from the web based application (although both work). You can also download Evernote to your smart phone for ease of uploading
  29 KB (4,864 words) - 14:02, 29 July 2015
• 20.109(F14):Module 2
  ...---have lagged behind in the design and construction of novel systems that work in reliable, scalable, intuitive ways. Biology simply does not always perfo
  3 KB (506 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 1 Testing an engineered biological system
  ...eral scheme for Two Component Signaling]] Fortunately evolution appears to work with motifs and many of these motifs behave in a reasonably modular fashion
  15 KB (2,383 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 4 DNA ligations, bacterial transformations and CometChip
  ... will confirm the presence of the PCR insert. Please clearly show all your work and reasoning in your lab notebook, and be sure that your plan explicitly i * work best in the same buffer and at the same temperature
  12 KB (2,060 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 2 Measuring system performance
  ... to make accessory pigments needed for the light-sensing fusion protein to work. These phycobilins are shown in the box at the left of the signaling pathwa
  21 KB (3,387 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 3 Tools for system engineering
  ...en defined through traditional scientific studies of EnvZ, for example the work from Tom Silhavy's lab( [http://openwetware.org/wiki/PMID:_9721293 ] and [[ ...ld examine the bacterial photograph you set up last time and document your work and your ideas about the experiment.
  28 KB (4,560 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 6 Readouts of DNA, Protein
  ...el should take approximately one hour to run. During that hour, you should work on part two of today's protocol.<br>
  15 KB (2,449 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 7 Readout of Protein
  ...k on your report, ask questions of each other or the teaching faculty, and work on your oral presentation if that's coming up too. ...ts of your choosing, to talk with other groups about their results, and to work on your research article.
  11 KB (1,712 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 3 Day 1 Growth of phage materials
  ... oxide, gold, iridium and indium tin oxide are all in-hand thanks to their work (e.g see reference [http://www.sciencemag.org/cgi/content/abstract/312/5775 Pre-lab work:
  16 KB (2,583 words) - 14:02, 29 July 2015
• 20.109(F14): TA notes for module 1
  * Make a plan for preparing the high volume TC work we do. Lab also needs you to:
  16 KB (2,511 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 3 Day 2 Phage nanowires
  ...ith ethanol, and then with water. You will have time during these steps to work on the FNW, a first step toward developing a research proposal idea. Next t <font color = red>'''Today's lab has some safety hazards and you must work extremely carefully.'''</font color> Lab coats, gloves and goggles are a mu
  13 KB (2,165 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 3 Day 3 TEM
  ===How does a TEM work?=== * needed resources to complete the work
  10 KB (1,709 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 3 Day 4 Solar cell assembly
  The groups not visiting the Belcher lab should use the extra time to work on their research proposals and get some peer feedback. Last time, you star
  11 KB (1,798 words) - 14:02, 29 July 2015
• 20.109(F14):OWW basics
  ===Sign your work===
  9 KB (1,539 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 3 Day 6 Wrap-up and data summary
  Working with your partner, write a short report describing the Module 3 work according to the [[20.109%28F14%29:_Biomaterial_engineering_report | linked
  4 KB (620 words) - 14:02, 29 July 2015
• 20.109(F14): DNA engineering methods
  ... for this assignment, but you will receive substantive feedback about your work from a laboratory instructor. ...e, not the DNA repair assay phase. In other words, you should describe the work from M1D1-D5, NOT including tissue culture.
  3 KB (408 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 4 DNA Ligation & Transformation
  ... will confirm the presence of the PCR insert. Please clearly show all your work and reasoning in your lab notebook, and be sure that your plan explicitly i * work best in the same buffer and at the same temperature
  12 KB (2,028 words) - 14:02, 29 July 2015
• 20.109(F14):Statement on collaboration and integrity
  ... but also lets others independently assess the merits of both the original work and the conclusions you have drawn from it.
  2 KB (319 words) - 14:02, 29 July 2015
• 20.109(F14):Guidelines for writing up your research
  ...ort by underlining your name. Others who substantially contributed to your work, such as your lab partner, should also be listed. ...motivate the audience to keep reading! How? Reveal the significance of the work through connections to both prior scientific accomplishments and interestin
  22 KB (3,322 words) - 14:02, 29 July 2015
• 20.109(F14):Guidelines for oral presentations
  ... elements, including organization, clarity, and proper attribution for the work. *Generally speaking, you should figure out how to work the lights, slide projector, curtains, etc. before you begin. In this class
  5 KB (895 words) - 14:02, 29 July 2015
• 20.109(F14):Guidelines for working in the tissue culture facility
  ...ut most are common practice and will be good habits for any tissue culture work you do. ...y with 70% ethanol. Start from the back and proceed forward. Swab during work if necessary.
  7 KB (1,163 words) - 14:02, 29 July 2015
• 20.109(F14): Slides for Journal Club Presentation
  ...what the study contributed to the field. Maybe there's been some follow up work worth noting?
  3 KB (513 words) - 14:02, 29 July 2015
• 20.109(F14):Lab basics
  *Procedures for doing tissue culture work =Communicating your work=
  1 KB (185 words) - 14:02, 29 July 2015
• 20.109(F14):General lab policy
  ==Late Work== ...ade each day late and will not be accepted after a week.</font color> Only work turned in on time is guaranteed timely or extensive feedback.
  3 KB (479 words) - 14:02, 29 July 2015
• 20.109(F14): TA notes for module 2
  *front bench needs transparencies for printing. *Each pair needs ice bucket, electroporation cuvette, 2 MacLacMUG+Cam34+Amp25+Kan10
  15 KB (2,438 words) - 14:02, 29 July 2015
• 20.109(F14):Guidelines for editing OpenWetWare
  ==Sign your work==
  3 KB (462 words) - 14:02, 29 July 2015
• 20.109(F14):Module 3
  ...nn.html CNN videotape of Angie Belcher teaching President Obama about this work]<br>
  4 KB (612 words) - 14:02, 29 July 2015
• 20.109(F14):Module 3 oral presentations
  * needed resources to complete the work ...n this proposal. For example, if you propose molecular and/or ''in vitro'' work, you would want to be able to say a few words about ''in vivo'' experiments
  14 KB (2,324 words) - 14:02, 29 July 2015
• 20.109(F14): Biomaterial engineering report
  ...summarize and interpret the class-wide findings and briefly suggest future work. What we usually call Results and Discussion should be combined. The Method |Contextualizing Results and Suggestions for Future Work
  4 KB (577 words) - 14:02, 29 July 2015
• 20.109(F14): System engineering report
  *conclusions you can draw from your work, including any uncertainties *limitations of your work, e.g. what kinds of experiments/controls/samples would have been great to i
  7 KB (1,144 words) - 14:02, 29 July 2015
• 20.109(F14): System engineering research article
  ...ort by underlining your name. Others who substantially contributed to your work, such as your lab partner, should also be listed. *conclusions you can draw from your work, including any uncertainties
  8 KB (1,258 words) - 14:02, 29 July 2015
• 20.109(F14):OWW in 20.109
  ===Sign your work===
  9 KB (1,523 words) - 14:02, 29 July 2015
• 20.109(S15)
  ...ts at the bench, ones that will increase the likelihood of success in your work and ensure the health and safety of you and those around you. By the end of
  3 KB (482 words) - 17:15, 29 July 2015
• 20.109(S15): Assignments
  Although your lab work will be done in pairs, <font color = CC0000>'''most assignments will be sub ...</font color> We strongly recommend that you plan ahead and space out your work when possible. For assignments that may be revised, be sure to read the lat
  9 KB (1,366 words) - 17:15, 29 July 2015
• 20.109(S15): Biomaterial engineering report
  ...summarize and interpret the class-wide findings and briefly suggest future work. What we usually call Results and Discussion should be combined. The Method |Contextualizing Results and Suggestions for Future Work
  4 KB (570 words) - 17:15, 29 July 2015
• 20.109(S15): Complete Western and prepare damaged DNA (Day3)
  ...don't need to measure out this volume. Keep in mind that the washing steps work by dilution, so it is a balance between adding enough to create a sink for
  18 KB (2,985 words) - 17:15, 29 July 2015
• 20.109(S15): Mod 3 Day 1 Growth of phage materials
  ... oxide, gold, iridium and indium tin oxide are all in-hand thanks to their work (e.g see reference [http://www.sciencemag.org/cgi/content/abstract/312/5775 Pre-lab work:
  16 KB (2,583 words) - 17:15, 29 July 2015
• 20.109(S15): Mod 3 Day 1 Growth of phage materials (Day 1)
  ... oxide, gold, iridium and indium tin oxide are all in-hand thanks to their work (e.g see reference [http://www.sciencemag.org/cgi/content/abstract/312/5775 Pre-lab work:
  16 KB (2,577 words) - 17:15, 29 July 2015
• 20.109(S15): TEM (Day 3)
  ===How does a TEM work?===
  8 KB (1,323 words) - 17:15, 29 July 2015
• 20.109(S15):16S PCR and paper discussion (Day3)
  ...crobiome data summary | abstract and data summary]]. To help you pace your work, as well as give you feedback early on, you will be required to draft small ...2-10x, with higher generally being better and at least 3-4x being known to work in our system.'''
  22 KB (3,588 words) - 17:15, 29 July 2015
• 20.109(S15):20.109 Class Blog summary page
  ...first, as it refreshes my memory and reminds me how exciting it was do the work. Next, I take this ‘writers high’ to the data section, which I find the
  6 KB (1,017 words) - 17:15, 29 July 2015
• 20.109(S15):AIV detection assay and analysis (Day7)
  ...l of the 16S rRNA sequencing data for their final report.''' Please try to work through this entire protocol today so that you are familiar with the steps #*''Why is it more convenient to work with the reverse complement when sequencing from the reverse direction?''
  24 KB (3,931 words) - 17:15, 29 July 2015
• 20.109(S15):Biotemplating on phage nanowires (Day 2)
  ...ith ethanol, and then with water. You will have time during these steps to work on the FNW, a first step toward developing a research proposal idea. Next t <font color = red>'''Today's lab has some safety hazards and you must work extremely carefully.'''</font color> Lab coats, gloves and goggles are a mu
  14 KB (2,281 words) - 17:15, 29 July 2015
• 20.109(S15):Cell preparation for DNA repair assays (Day4)
  ...nhibitors that had been used in human cells with success, but they did not work in our CHO cell system either. Therefore, we are calling on you -- the Spri ...to your fellow 109er about what they have done well and what needs further work. Complete this activity using the "golden rule" -- offer the type of feedba
  18 KB (2,885 words) - 17:15, 29 July 2015
• 20.109(S15):DNA cloning (Day4)
  ...ke your teaching faculty very happy if you contribute to their preparatory work.
  16 KB (2,696 words) - 17:15, 29 July 2015
• 20.109(S15):DNA repair assays (Day5)
  #*As you work, tip the plate down a little to pool the media at the bottom of each well.
  14 KB (2,396 words) - 17:15, 29 July 2015
• 20.109(S15):DNA sequencing (Day5)
  ... many colonies, today we will use a commercially available kit so that the work can go more quickly. The principle is the same as that of our "quick and di In another week you will finally get to see the results of all your hard work!
  16 KB (2,688 words) - 17:15, 29 July 2015
• 20.109(S15):Diagnostic primer design (Day2)
  ...se primer bind to ''different'' strands of DNA. You may find it easiest to work with only the coding strand sequence at first, and then take the complement
  13 KB (2,073 words) - 17:15, 29 July 2015
• 20.109(S15):Flow cytometry and paper discussion (Day6)
  ...your perspective &ndash; it turns out in scientific research that the hard work is just beginning once the data is quantified! Interpreting the data and dr The one piece of wet lab work that you will do next time is complete your NHEJ inhibitor validation assay
  15 KB (2,568 words) - 17:15, 29 July 2015
• 20.109(S15):General lab policy
  ==Late Work== ...ade each day late and will not be accepted after a week.</font color> Only work turned in on time is guaranteed timely or extensive feedback.
  3 KB (478 words) - 17:15, 29 July 2015
• 20.109(S15):Growth of phage nanowires (Day 1)
  ... oxide, gold, iridium and indium tin oxide are all in-hand thanks to their work (e.g see reference [http://www.sciencemag.org/cgi/content/abstract/312/5775 Pre-lab work:
  16 KB (2,579 words) - 17:15, 29 July 2015
• 20.109(S15):Guidelines for oral presentations
  ... elements, including organization, clarity, and proper attribution for the work. *Generally speaking, you should figure out how to work the lights, slide projector, curtains, etc. before you begin. In this class
  5 KB (894 words) - 17:15, 29 July 2015
• 20.109(S15):Guidelines for working in the tissue culture facility
  ...ut most are common practice and will be good habits for any tissue culture work you do. ...y with 70% ethanol. Start from the back and proceed forward. Swab during work if necessary.
  7 KB (1,162 words) - 17:15, 29 July 2015
• 20.109(S15):Guidelines for writing up your research
  ...ort by underlining your name. Others who substantially contributed to your work, such as your lab partner, should also be listed. ...motivate the audience to keep reading! How? Reveal the significance of the work through connections to both prior scientific accomplishments and interestin
  21 KB (3,275 words) - 17:15, 29 July 2015
• 20.109(S15):Introduction to cell strains and plating (Day1)
  ...ross which you will compare repair: cell type and damage topology. We will work exclusively with Chinese hamster ovary (CHO) cells; wild-type cells are cal ...e. Be sure to keep the conical tube containing your cells capped while you work at the microscope.
  18 KB (3,046 words) - 17:15, 29 July 2015
• 20.109(S15):Lab basics
  *Procedures for doing tissue culture work =Communicating your work=
  1 KB (184 words) - 17:15, 29 July 2015
• 20.109(S15):Lab tour
  ...ur computer versus operating from the web based application (although both work). You can also download Evernote to your smart phone for ease of uploading
  25 KB (4,176 words) - 17:15, 29 July 2015
• 20.109(S15):Microbial DNA extraction (Day1)
  ...s transmission) is the flu virus. For your safety, all the samples we will work with today have been screened to exclude those carrying human–pathogenic Returning to today's specific work, each of you will extract a DNA pool from a single bird cloacal sample usin
  15 KB (2,507 words) - 17:15, 29 July 2015
• 20.109(S15):Microbiome data summary
  ...igures and supporting text &ndash; including context for understanding the work’s broader implications. ...; of technical information, and consequently should strive to present your work in a logical, step-by-step fashion.
  14 KB (2,270 words) - 17:15, 29 July 2015
• 20.109(S15):OWW basics
  ===Sign your work===
  9 KB (1,538 words) - 17:15, 29 July 2015
• 20.109(S15):Phylogenetic analysis (Day7)
  #*''Why is it more convenient to work with the reverse complement when sequencing from the reverse direction?''
  15 KB (2,410 words) - 17:15, 29 July 2015
• 20.109(S15):Research proposal presentation
  * needed resources to complete the work ...n this proposal. For example, if you propose molecular and/or ''in vitro'' work, you would want to be able to say a few words about ''in vivo'' experiments
  14 KB (2,323 words) - 17:15, 29 July 2015
• 20.109(S15):Solar cell assembly (Day 4)
  The groups not visiting the Belcher lab should use the extra time to work on their research proposals and get some peer feedback. Last time, you star #*needed resources to complete the work
  13 KB (2,017 words) - 17:15, 29 July 2015
• 20.109(S15):Statement on collaboration and integrity
  ... but also lets others independently assess the merits of both the original work and the conclusions you have drawn from it.
  2 KB (319 words) - 17:15, 29 July 2015
• 20.109(S15):Student registration and questionnaire
  ...T. I learned basic cognition tests and how to edit fMRI scans. I currently work at the Jasanoff Lab. I'm working on a PAG/MFB study in rats. I've learned h
  3 KB (433 words) - 17:15, 29 July 2015
• 20.109(S15):Wrap-up and data summary (Day 6)
  Working with your partner, write a short report describing the Module 3 work according to the [[20.109%28S15%29:_Biomaterial_engineering_report | linked
  4 KB (617 words) - 17:15, 29 July 2015
• 20.109(S12)
  ...ts at the bench, ones that will increase the likelihood of success in your work and ensure the health and safety of you and those around you. By the end of
  4 KB (660 words) - 17:30, 29 July 2015
• 20.109(S12): Assignments
  ... done in pairs, <font color = CC0000>'''you must submit individual written work (for both daily homeworks and major assignments) and give individual journa ...</font color> We strongly recommend that you plan ahead and space out your work when possible.
  8 KB (1,121 words) - 17:30, 29 July 2015
• 20.109(S12):General lab policy
  ...mdash; especially your partner &mdash; if you are not up to speed when the work begins. #Do not work with chemicals until you are sure of their safe handling. Be aware of their
  2 KB (431 words) - 17:30, 29 July 2015
• 20.109(S12):OWW in 20.109
  ===Sign your work===
  7 KB (1,136 words) - 17:30, 29 July 2015
• 20.109(S12):Aptamer binding assay (Day7)
  ...f your own strengths and weaknesses can often help you improve your future work. After you give your presentation, write a brief self-evaluation (200 words
  11 KB (1,870 words) - 17:30, 29 July 2015
• 20.109(S12):Amplify aptamer-encoding DNA (Day1)
  You and your partner may work together on the lab practical. (Note: this will not be the case for future Before starting today's wet lab work, you may want to wipe down your pipettes and your benchtop with 70% ethanol
  10 KB (1,682 words) - 17:30, 29 July 2015
• 20.109(S12):Purify aptamer-encoding DNA (Day2)
  ...ts low viscosity means that high weight percent solutions are tractable to work with, and that the solidified gel remains pliable rather than brittle. HR a ... the work you do in Module 1 in a formal lab report. To help you pace your work, as well as give you feedback early on, you will be required to draft small
  11 KB (1,844 words) - 17:30, 29 July 2015
• 20.109(S12):Prepare RNA by IVT (Day3)
  ... different from DNA in its stability. Consequently it is more difficult to work with RNA in the lab. It is not the techniques themselves that are difficult *Before you begin your experiment, clean your work area: (1) remove all clutter, (2) wipe down the benchtop with warm water an
  16 KB (2,671 words) - 17:30, 29 July 2015
• 20.109(S12):RNA to DNA by RT-PCR (Day5)
  ...anscription reaction to make more of the RNA mixture. For this process to work, the 6-5 and 8-12 sequences must amplify at the same rate, a fact that has ...d compete with this interaction seems to work. In Prof. Niles’s original work, he used a different RT-PCR kit that did not face this inhibition issue, wh
  8 KB (1,365 words) - 17:30, 29 July 2015
• 20.109(S12):Post-selection IVT and journal club (Day6)
  ...f your own strengths and weaknesses can often help you improve your future work. After you give your presentation, write a brief self-evaluation (200 words
  2 KB (252 words) - 17:30, 29 July 2015
• 20.109(S12):Journal club (Day8)
  ...at 1:30 pm sharp in room 16-336. (Day 6 presentations will begin after lab work is finished, b/w 1:30 and 2 pm.)
  7 KB (1,085 words) - 17:30, 29 July 2015
• 20.109(S12):Testing cell viability (Day3)
  ...of your labmates time.''' Reading the protocol in advance will help you work more quickly, and is strongly recommended. ...performing the viability assay, and/or during incubation steps, you should work on Part 3 of today's protocol.
  17 KB (2,877 words) - 17:30, 29 July 2015
• 20.109(S12):Module 2
  ...iscussions during the development of this module, as well as for her prior work in developing a [http://openwetware.org/wiki/20.109:Module_2 related module
  4 KB (535 words) - 17:30, 29 July 2015
• 20.109(S12):Start-up protein engineering (Day1)
  ...s wasting a month of your time repeating experiments already proven not to work or reinventing the wheel. ...As you work, you can ask yourself why these stretches of the protein might work the way that they do, and how they might be changed.
  26 KB (4,263 words) - 17:30, 29 July 2015
• 20.109(S12):Site-directed mutagenesis (Day2)
  ...al of information in order to design mutagenized inverse pericams – nice work! Today you will put your designs into practice. ...reaction, to ensure that all the reagents are working properly. You should work quickly but carefully, and keep your tube in a chilled container at all tim
  13 KB (2,109 words) - 17:30, 29 July 2015
• 20.109(S12):Bacterial amplification of DNA (Day3)
  ...work on Parts 3 and (optional) 5, label the tubes you will need in Part 4, work on your notebooks, start the FNT assignment, etc. '''Be sure to pre-chill y ...ke your teaching faculty very happy if you contribute to their preparatory work. Please label 2 large glass test tubes with your team color and sample name
  17 KB (2,889 words) - 17:30, 29 July 2015
• 20.109(S12):Prepare expression system (Day4)
  #Incubate on ice for 1 hour. You can work on parts 2, 4, and 5 of today's protocols now, as well as assemble the mate ===Microbial work===
  19 KB (3,278 words) - 17:30, 29 July 2015
• 20.109(S12):Induce protein and evaluate DNA (Day5)
  As evidenced by Nagai’s work, wild-type inverse pericam is not toxic to BL21(DE3) cells. Although it is ...our cells with IPTG, you will let the resultant protein factories do their work for 2-3 hours. During this time, you will evaluate the DNA from your two X#
  17 KB (2,911 words) - 17:30, 29 July 2015
• 20.109(S12):Characterize protein expression (Day6)
  ... has 15 &mu;L of liquid in it. You might use the table below to guide your work. #*The timing function on this centrifuge does not work! Bring your timer and manually turn the centrifuge off after 2 min. Start t
  13 KB (2,041 words) - 17:30, 29 July 2015
• 20.109(S12):Assess protein function (Day7)
  ...people can compare their own mutants to those of other teams doing similar work. #Now work your way from reservoirs #2 to #12 (highest calcium concentration), and fro
  23 KB (3,809 words) - 17:30, 29 July 2015
• 20.109(S12):Transcript-level analysis (Day6)
  ...lets return to thinking about the structure of cartilage for a bit. Our work in this module so far has focused on on the cells themselves (viability and ... diluted antibody per well. Incubate for 90 min (at room temperature), and work on Parts 2 and 3 of today's protocol.
  17 KB (2,752 words) - 17:30, 29 July 2015
• 20.109(S12):Guidelines for oral presentations
  ... elements, including organization, clarity, and proper attribution for the work. *Generally, figure out how to work the lights, slide projector, curtains, etc. before you begin. In this class
  5 KB (893 words) - 17:30, 29 July 2015
• 20.109(S12): RNA engineering report
  ... of technical information, and consequently should strive to present your work in a logical, step-by-step fashion.
  5 KB (796 words) - 17:30, 29 July 2015
• 20.109(S12): RNA computational analysis
  ...f 20.109, we do not expect you to know the details of how these algorithms work.
  12 KB (1,846 words) - 17:30, 29 July 2015
• 20.109(S12):Start-up biomaterials engineering (Day1)
  ...o you should decide who will seed at 1:10 and who will seed at 1:2. As you work, try to put into practice what you learned about sterile technique in the d ... of the surrounding environment on cell phenotype. In particular, you will work with primary chondrocytes and/or mesenchymal stem cells in 3D gel culture.
  16 KB (2,574 words) - 17:30, 29 July 2015
• 20.109(S12):Module 3 oral presentations
  * needed resources to complete the work
  5 KB (905 words) - 17:30, 29 July 2015
• 20.109(S12):Initiate cell culture (Day2)
  ...eir knee joints is more similar to that of humans. In this module, we will work with an ''in vitro'' culture model of cartilage-forming cells. Half the class at a time will work in the tissue culture room today. Today will be physically and mentally lab
  10 KB (1,708 words) - 17:30, 29 July 2015
• 20.109(S12):Preparing cells for analysis (Day4)
  ...trix dissolution for better protein or proteoglycan recovery. Split up the work with your partner whatever way is most convenient. '''Remember to label you ...did when washing your freshly synthesized beads. A 10 mL pipet size should work well for most beads, while for very delicate beads, you should use a 2 mL s
  19 KB (3,261 words) - 17:30, 29 July 2015
• 20.109(S12):Initiating transcript and protein assays (Day5)
  ... Buffer to the plate. Wait another 60-90 minutes. In the meantime, you can work on cell viability analysis (first listed on Day 4 Part 4). ...of RNA in your cDNA reaction, a 5-10x further dilution of your cDNA should work well.
  13 KB (2,192 words) - 17:30, 29 July 2015
• 20.109(S12):Protein-level and wrap-up analysis (Day7)
  ...nce they will undergo partly different manipulations. You may also want to work on two separate worksheets, one for each collagen type.
  6 KB (929 words) - 17:30, 29 July 2015
• 20.109(S12):Guidelines for writing up your research
  ...ort by underlining your name. Others who substantially contributed to your work, such as your lab partner, should also be listed. ...motivate the audience to keep reading! How? Reveal the significance of the work through connections to both prior scientific accomplishments and interestin
  21 KB (3,191 words) - 17:30, 29 July 2015
• 20.109(S12):Guidelines for working in the tissue culture facility
  ...ut most are common practice and will be good habits for any tissue culture work you do. ...y with 70% ethanol. Start from the back and proceed forward. Swab during work if necessary.
  7 KB (1,163 words) - 17:30, 29 July 2015
• 20.109(S12):Reflection assignments summary page
  ...f your own strengths and weaknesses can often help you improve your future work. After you give your presentation, write a brief self-evaluation (200 words ... this revision that you think are generalizable and will translate to your work on the second report? Again, 200-250 words should suffice.
  5 KB (799 words) - 17:30, 29 July 2015
• 20.109(F13)
  ...ts at the bench, ones that will increase the likelihood of success in your work and ensure the health and safety of you and those around you. By the end of ...is semester and get to know each other well. Everyone in the 20.109 family needs the support of their peers and instructors. If you find yourself in a situa
  7 KB (1,152 words) - 17:33, 29 July 2015
• 20.109(F13):Module 3 oral presentations
  * needed resources to complete the work ...n this proposal. For example, if you propose molecular and/or ''in vitro'' work, you would want to be able to say a few words about ''in vivo'' experiments
  14 KB (2,304 words) - 17:33, 29 July 2015
• 20.109(F13): Assignments
  Although your lab work will be done in pairs, <font color = CC0000>'''most assignments will be sub ...</font color> We strongly recommend that you plan ahead and space out your work when possible. For assignments that may be revised, be sure to read the lat
  8 KB (1,188 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 1 Day 1 DNA engineering using PCR
  ... establish good habits for documentation of your work. By documenting your work according to the exercises done today, you will ...re there are no spaces between or after the letters or your search won’t work. Change the color of the start codon to blue. Repeat the “Find…” proc
  21 KB (3,687 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 2 Day 6 Analysis & Planning 2
  ...ut you don't need to measure this out. Keep in mind that the washing steps work by dilution, so it is a balance between adding enough to create a sink for Scanning your Western blot is only the first step! You just did ''a lot'' of work to obtain what appears to be observational data. However, we can use densit
  17 KB (2,799 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 1 Day 2 Clean and cut DNA
  ... fragment sizes expected for each double digest below. '''Please show your work.''' ...ngineering_methods | '''formal methods section''']]. To help you pace your work, as well as give you feedback early on, you will be required to draft and/o
  11 KB (1,881 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 2 Day 1 System Design
  ...th and 2. The authors of the original model are '''always''' cited in your work.
  26 KB (4,292 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 1 Day 4 DNA ligations and bacterial transformations
  ...y| guidelines for working in the tissue culture facility]], where you will work next time. You can also peek ahead at steps 1 and 2 in Part 4 and start pre ... will confirm the presence of the PCR insert. Please clearly show all your work and reasoning, and be sure that your assignment explicitly includes
  11 KB (1,914 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 1 Day 3 Agarose gel electrophoresis
  Ligations generally work best when there is a 1:4 '''molar''' ratio of backbone to insert. You will ...ngineering_summary | '''formal written summary''']]. To help you pace your work, as well as give you feedback early on, you will be required to draft small
  13 KB (2,222 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 1 Day 5 Examine candidate clones & tissue culture
  ...faculty has set up four overnight LB + AMP cultures of bacteria for you to work with. Three of these cultures have colonies from the ligation reactions you ... enzymes you’ll use. The following table may be helpful as you plan your work. As an example, ''XbaI'' is 20,000 U/mL; therefore one reaction will requir
  17 KB (2,866 words) - 17:33, 29 July 2015
• 20.109(F13):Module 3
  ...nn.html CNN videotape of Angie Belcher teaching President Obama about this work]<br>
  4 KB (557 words) - 17:33, 29 July 2015
• 20.109(F13):Guidelines for working in the tissue culture facility
  ...ut most are common practice and will be good habits for any tissue culture work you do. ...y with 70% ethanol. Start from the back and proceed forward. Swab during work if necessary.
  7 KB (1,163 words) - 17:33, 29 July 2015
• 20.109(F13):OWW in 20.109
  ===Sign your work===
  9 KB (1,523 words) - 17:33, 29 July 2015
• 20.109(F13):General lab policy
  ...mdash; especially your partner &mdash; if you are not up to speed when the work begins. #Do not work with chemicals until you are sure of their safe handling. Be aware of their
  3 KB (500 words) - 17:33, 29 July 2015
• 20.109(F13):Statement on collaboration and integrity
  ... but also lets others independently assess the merits of both the original work and the conclusions you have drawn from it.
  2 KB (319 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 2 Day 7 HTS and Analysis
  ...ill employ a 96-well multichannel pipette to significantly cut down on our work -- giving us a different method to minimize our pipetting steps.
  9 KB (1,414 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 3 Day 4 Solar cell assembly
  The groups not visiting the Belcher lab should use the extra time to work on their research proposals and get some peer feedback. Last time, you star * needed resources to complete the work
  13 KB (2,096 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 3 Day 1 Growth of phage materials
  ... oxide, gold, iridium and indium tin oxide are all in-hand thanks to their work (e.g see reference [http://www.sciencemag.org/cgi/content/abstract/312/5775 Pre-lab work:
  18 KB (2,861 words) - 17:33, 29 July 2015
• 20.109(F13):Guidelines for oral presentations
  ... elements, including organization, clarity, and proper attribution for the work. *Generally speaking, you should figure out how to work the lights, slide projector, curtains, etc. before you begin. In this class
  5 KB (895 words) - 17:33, 29 July 2015
• 20.109(F13): System engineering report
  ...rigue your reader. '''Keep in mind, you have little space to motivate your work and you need to catch the reader’s attention.''' ...stance might be overcome in the clinic? Are human studies relevant to this work? Studies in other organisms (cell lines, mice, etc)?
  10 KB (1,586 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 3 Day 2 Phage nanowires
  ...ith ethanol, and then with water. You will have time during these steps to work on the FNT, a first step toward developing a research proposal idea. Next t Today's lab has some safety hazards and you must work extremely carefully. Lab coats, gloves and goggles are a must when you're a
  15 KB (2,422 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 3 Day 3 TEM
  ===How does a TEM work?===
  8 KB (1,330 words) - 17:33, 29 July 2015
• 20.109(F13): Biomaterial engineering report
  ...summarize and interpret the class-wide findings and briefly suggest future work. What we usually call Results and Discussion should be combined. The Method |Contextualizing Results and Suggestions for Future Work
  4 KB (650 words) - 17:33, 29 July 2015
• 20.109(F13):Guidelines for writing up your research
  ...ort by underlining your name. Others who substantially contributed to your work, such as your lab partner, should also be listed. ...motivate the audience to keep reading! How? Reveal the significance of the work through connections to both prior scientific accomplishments and interestin
  22 KB (3,319 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 3 Day 6 Wrap-up and data summary
  Working with your partner, write a short report describing the Module 3 work according to the [[20.109%28F13%29:_Biomaterial_engineering_report | linked
  4 KB (638 words) - 17:33, 29 July 2015
• 20.109(F13): DNA engineering methods
  ... for this assignment, but you will receive substantive feedback about your work from a laboratory instructor. ...e, not the DNA repair assay phase. In other words, you should describe the work from M1D1-D5.
  3 KB (433 words) - 17:33, 29 July 2015
• 20.109(F13): DNA engineering summary
  ...in figures and supporting text – including context for understanding the work’s broader implications. ... of technical information, and consequently should strive to present your work in a logical, step-by-step fashion.
  10 KB (1,548 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 2 Day 2 Mutation Analysis
  ... different from DNA in its stability. Consequently it is more difficult to work with RNA in the lab. It is not the techniques themselves that are difficult *Before you begin your experiment, clean and prepare your work area: (1) remove all clutter, (2) wipe down the benchtop with warm water an
  18 KB (2,944 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 2 Day 6 Transfection of SH2 Domains
  ...ut you don't need to measure this out. Keep in mind that the washing steps work by dilution, so it is a balance between adding enough to create a sink for Scanning your Western blot is only the first step! You just did ''a lot'' of work to obtain what appears to be observational data. However, we can use densit
  16 KB (2,673 words) - 17:33, 29 July 2015
• 20.109(F13):Reflection assignments summary page
  ...first, as it refreshes my memory and reminds me how exciting it was do the work. Next, I take this ‘writers high’ to the data section, which I find the
  6 KB (916 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 2 Day 3 Prepare for LTS
  *(1) How do MM-111 and Lapatinib work? (You may need to read ahead to the Ligand-receptor interactions section to ... be changed if the assumptions experimentally verified in S9 & S10 did not work out?
  23 KB (3,661 words) - 17:42, 29 July 2015
• 20.109(F13):S3 and SDS offices announcement
  ...verify your situation, and then discuss with you how to address the missed work. Students will not be excused from coursework without verification from St ...for accommodations, please contact me early in the semester so that we can work together to get your accommodation logistics in place.
  1 KB (217 words) - 17:33, 29 July 2015
• 20.109(S10)
  ...ts at the bench, ones that will increase the likelihood of success in your work and ensure the health and safety of you and those around you. By the end of
  3 KB (459 words) - 19:48, 28 July 2015
• 20.109(S10):Characterize protein expression (Day6)
  ... has 15 &mu;L of liquid in it. You might use the table below to guide your work. #Measure the absorbance of each sample at 595 nm. Work as quickly as you can, because the absorbance will continue to slowly chang
  14 KB (2,165 words) - 19:48, 28 July 2015
• 20.109(S10):Post-selection IVT and journal club (Day6)
  ...mework will be due. However, it is strongly suggested that you continue to work on your report, particularly the RT-PCR figure and experimental schematic. **You should work on Part III of the computational assignment, and hand in a picture of the f
  2 KB (267 words) - 19:49, 28 July 2015
• 20.109(S10):Lab basics
  *Procedures for doing tissue culture work. ==Communicating your Work==
  1 KB (162 words) - 19:49, 28 July 2015
• 20.109(S10):General lab policy
  ... your partner and to others in the lab if you are not up to speed when the work begins. ... have cut yourself (even if you consider it minor), if something broke and needs cleaning up, or if you are on fire.
  2 KB (386 words) - 19:49, 28 July 2015
• 20.109(S10):Aptamer binding assay (Day7)
  ...f your own strengths and weaknesses can often help you improve your future work. After you give your presentation next time, write a brief self-evaluation.
  9 KB (1,560 words) - 19:49, 28 July 2015
• 20.109(S10):Guidelines for working in the tissue culture facility
  ...ut most are common practice and will be good habits for any tissue culture work you do. ...y with 70% ethanol. Start from the back and proceed forward. Swab during work if necessary.
  7 KB (1,148 words) - 19:49, 28 July 2015
• 20.109(S10):Guidelines for editing OpenWetWare
  ==Sign your work==
  3 KB (494 words) - 19:49, 28 July 2015
• 20.109(S10):Module 2
  ...iscussions during the development of this module, as well as for her prior work in developing a [http://openwetware.org/wiki/20.109:Module_2 related module
  3 KB (497 words) - 19:49, 28 July 2015
• 20.109(S10):Amplify aptamer-encoding DNA (Day1)
  You and your partner may work together on the lab practical. (Note: this will not be the case for future Before starting today's wet lab work, you may want to wipe down your pipettes and your benchtop with 70% ethanol
  10 KB (1,656 words) - 19:49, 28 July 2015
• 20.109(S10):Purify aptamer-encoding DNA (Day2)
  ...ts low viscosity means that high weight percent solutions are tractable to work with, and that the solidified gel remains pliable rather than brittle. HR a ... the work you do in Module 1 in a formal lab report. To help you pace your work, as well as give you feedback early on, you will be required to draft small
  11 KB (1,764 words) - 19:49, 28 July 2015
• 20.109(S10):Prepare RNA by IVT (Day3)
  ... different from DNA in its stability. Consequently it is more difficult to work with RNA in the lab. It is not the techniques themselves that are difficult *Before you begin your experiment clean your work area, removing all clutter. Wipe down the benchtop with warm water then “
  15 KB (2,450 words) - 19:49, 28 July 2015
• 20.109(S10):RNA to DNA by RT-PCR (Day5)
  ...anscription reaction to make more of the RNA aptamer. For this process to work, the 6-5 and 8-12 aptamers must amplify at the same rate, a fact that has b ...o compete with this interaction seems to work. If Prof. Niles’s original work, he used a different RT-PCR kit that did not face this inhibition issue, wh
  7 KB (1,218 words) - 19:49, 28 July 2015