Search results

Create the page "Assignment 10 navigation" on this wiki!

• Assignment 8, Part 2: lock-in amplifier and temperature control
  This is Part 2 of [[Assignment 8 Overview| Assignment 8]]. ... transimpedance amplifier: an LM741. A good value for R_sense is 10 Ω.
  17 KB (2,813 words) - 22:56, 7 November 2017
• 20.109(S14):Preparing cells for analysis (Day4)
  ...easure protein content: move these to an eppendorf tube. The goal is about 10-15 (2-3 mm) beads per tube. #*For large beads (4-5 mm), you might use only 5-10 beads, and for very small beads (<1 mm), you might use 20 or more.
  24 KB (4,100 words) - 13:59, 29 July 2015
• 20.109(F14): Mod 1 Day 3 Agarose gel electrophoresis
  | 10 &mu;L'''^''' #Incubate in the 50&deg;C water bath for 10 minutes, until the agarose is completely dissolved. Every few minutes, you
  13 KB (2,248 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 1 DNA engineering using PCR
  ...0.6 inches (top, bottom, left and right) and you should change the text to 10 point Courier font. Courier font has a fixed letter width so all the lines ... ATGs you’re likely to find in 5700 bases. Do you think there will be 1? 10? 100? If there is more than one, how will you decide which ATG starts EGFP?
  23 KB (3,882 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 2 Clean and cut DNA
  ...the membrane. '''EB''' is one solution we do know everything about. It’s 10 mM Tris pH 8.5. Since the DNA will solubilize at low salt and high pH, it e ... this assignment within ApE. Other program features may help you solve the assignment, but be sure not to "black box" any steps that you aren't sure you also und
  11 KB (1,780 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 5 Examine candidate clones & tissue culture
  ...50 &mu;l of Solution III to each tube and immediately vortex each tube for 10 seconds with your vortex set at the highest setting. White clumps should ap ...rate the trypsin off the cells. Incubate the cells (“dry”) at 37° for 10 minutes, again using your timer to precisely time this incubation.
  20 KB (3,455 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 1 Testing an engineered biological system
  |0:10 | 1:10 dilution
  15 KB (2,383 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 4 DNA ligations, bacterial transformations and CometChip
  ... realize that even with high efficiency cells only 1 DNA molecule in about 10,000 is successfully transformed. ...droplets, and then incubate the reactions at room temperature for at least 10 minutes.
  12 KB (2,060 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 3 Tools for system engineering
  *EXTRA CREDIT: you can get 2 points of extra credit on this FNW assignment by doing 2 small things in addition to your outline: **Strain NB462 (genotype: MC4100 ara+ (OmpC-lacZ) 10-25 envZ::KanR +pPL-PCBamp)
  28 KB (4,560 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 5 Assessing re-tuned system
  #* 10 ul of sequencing primer NO296 (seq = TCG TCA ACC TCA TTT TGC GCC AG, this h ...d>'''Please note: this FNW assignment is due on Thursday, 10/30 or Friday, 10/31'''</font color>
  8 KB (1,382 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 7 Readout of Protein
  ...apacity for each lane is usually 100 to 200 ug (that would be 20 ul of a 5-10 ug/ul protein preparation). Thus 1 ng represents a protein that is approxim ...ence of specific antibodies. Even the very best antisera have no more than 10% of their antibodies directed against a particular antigen. The quality of
  11 KB (1,712 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 3 Day 1 Growth of phage materials
  ...ched by a second, third, fourth round of panning. Ultimately anywhere from 10 to 1000 candidate sequences may remain from a starting pool of 1 billion [h ...d single-walled carbon nanotubes (SWNTs) ([http://openwetware.org/wiki/Doi:10.1038/nnano.2011.50 ]) by incorporating the DSPHTELP peptide into p8. They w
  16 KB (2,583 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 3 Day 3 TEM
  ...nWetWare for examples of research ideas in process. As part of a later FNT assignment, you will have to print out your wiki page specifying your topic, your rese <font color = blue>'''The written portions of this assignment are due on T/W, Dec 2nd & 3rd. Please pay special attention to the bolded b
  10 KB (1,709 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 3 Day 5 Solar cell testing
  ... this "sandwich" of materials you've made into a 100&deg;C drying oven for 10 minutes. (This step melts the Surlyn to the surface of the anode.) ..._module_of_a_different_color_is_still_biological_engineering. | reflection assignment]], either.
  6 KB (1,016 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 4 DNA Ligation & Transformation
  ... realize that even with high efficiency cells only 1 DNA molecule in about 10,000 is successfully transformed. ...droplets, and then incubate the reactions at room temperature for at least 10 minutes.
  12 KB (2,028 words) - 14:02, 29 July 2015
• 20.109(S15): Complete Western and prepare damaged DNA (Day3)
  ...ing costs $6-8 per reaction, which can add up if you need to examine, say, 10 or more candidates. Agarose gel electrophoresis, by comparison, costs perha #Add enough TBS-T to cover your membranes &ndash; between 10-15 mL should work, but you don't need to measure out this volume. Keep in m
  18 KB (2,985 words) - 17:15, 29 July 2015
• 20.109(S15): Mod 3 Day 1 Growth of phage materials
  ...ched by a second, third, fourth round of panning. Ultimately anywhere from 10 to 1000 candidate sequences may remain from a starting pool of 1 billion [h ...d single-walled carbon nanotubes (SWNTs) ([http://openwetware.org/wiki/Doi:10.1038/nnano.2011.50 ]) by incorporating the DSPHTELP peptide into p8. They w
  16 KB (2,583 words) - 17:15, 29 July 2015
• 20.109(S15): Mod 3 Day 1 Growth of phage materials (Day 1)
  ...ched by a second, third, fourth round of panning. Ultimately anywhere from 10 to 1000 candidate sequences may remain from a starting pool of 1 billion [h ...d single-walled carbon nanotubes (SWNTs) ([http://openwetware.org/wiki/Doi:10.1038/nnano.2011.50 ]) by incorporating the DSPHTELP peptide into p8. They w
  16 KB (2,577 words) - 17:15, 29 July 2015
• 20.109(S15): TEM (Day 3)
  ...nWetWare for examples of research ideas in process. As part of a later FNT assignment, you will have to print out your wiki page specifying your topic, your rese ... a smaller diameter than those in the Y condition. The X wires had about a 10 nm? diameter, and the Y wires were about 2?-fold larger." Feel free to incl
  8 KB (1,323 words) - 17:15, 29 July 2015
• 20.109(S15):16S PCR and paper discussion (Day3)
  ...are enough for the number of reactions you need to run, plus an additional 10%. In addition to the two DNA-containing reactions, you should prepare a no- ! Amount for 3 reactions + 10%
  22 KB (3,588 words) - 17:15, 29 July 2015
• 20.109(S15):AIV detection assay and analysis (Day7)
  | 95&deg;C for 10 min ...etween 2/2/14 and 3/2/14. Click the link labeled with the tracking number 10-256046007.
  24 KB (3,931 words) - 17:15, 29 July 2015
• 20.109(S15):Begin Western protein analysis and choose system conditions (Day2)
  ...ence of specific antibodies. Even the very best antisera have no more than 10% of their antibodies directed against a particular antigen. The quality of ...apacity for each lane is usually 100 to 200 ug (that would be 20 ul of a 5-10 ug/ul protein preparation). Thus 1 ng represents a protein that is approxim
  27 KB (4,480 words) - 17:15, 29 July 2015
• 20.109(S15):Biotemplating on phage nanowires (Day 2)
  ...mplating, you may want to consult this review article: [http://dx.doi.org/10.1021/cm702152a] Sotiropoulou, Sofia, et al. "Biotemplated Nanostructured Ma #* Add ~10 dry ice chunks to the evaporation dish and let sit for 15 min. You can mea
  14 KB (2,281 words) - 17:15, 29 July 2015
• 20.109(S15):Cell preparation for DNA repair assays (Day4)
  ...diluted in OptiMEM (hereafter OM) as needed for all 12 transfections, plus 10%. ...ne experimental (B) &ndash; diluted in OM, enough for 6 transfections plus 10%, each.
  18 KB (2,885 words) - 17:15, 29 July 2015
• 20.109(S15):DNA cloning (Day4)
  ... realize that even with high efficiency cells only 1 DNA molecule in about 10,000 is successfully transformed. | 10
  16 KB (2,696 words) - 17:15, 29 July 2015
• 20.109(S15):DNA sequencing (Day5)
  ...penwetware.org/wiki/20.109%28S15%29:Primer_design_memo primer design memo] assignment. ...e A group; finally, start adding Soln. I to the B group when you reach the 10 min spin step for the A group. As one partner wraps up the B group, the oth
  16 KB (2,688 words) - 17:15, 29 July 2015
• 20.109(S15):Diagnostic primer design (Day2)
  [[Image:Screen Shot 2015-01-10 at 11.04.00 AM.png|thumb|450px|right|'''Schematic of avian influenza virus ...etware.org/wiki/20.109%28S15%29:Primer_design_memo#Content_Guidelines memo assignment] for details. Note that you are not yet required to write up the "overall s
  13 KB (2,073 words) - 17:15, 29 July 2015
• 20.109(S15):Growth of phage nanowires (Day 1)
  ...ched by a second, third, fourth round of panning. Ultimately anywhere from 10 to 1000 candidate sequences may remain from a starting pool of 1 billion [h ...d single-walled carbon nanotubes (SWNTs) ([http://openwetware.org/wiki/Doi:10.1038/nnano.2011.50 ]) by incorporating the DSPHTELP peptide into p8. They w
  16 KB (2,579 words) - 17:15, 29 July 2015
• 20.109(S15):Solar cell assembly (Day 4)
  ...recombined with the sensitizer or redox mediator (which occurs on a 10^-2, 10^-3second time frame). If instead, the electrons entered a metal, recombina ...ages on OpenWetWare for examples of research ideas in process. '''For this assignment, please submit a printed copy of your research page, making sure it defines
  13 KB (2,017 words) - 17:15, 29 July 2015
• 20.109(S15):Solar cell testing (Day 5)
  ... this "sandwich" of materials you've made into a 100&deg;C drying oven for 10 minutes. (This step melts the Surlyn to the surface of the anode.) #Don't forget your final [[20.109(S15):20.109 Class Blog summary page | blog assignment]], either. Remember, you are required to complete a total of four blog post
  6 KB (985 words) - 17:15, 29 July 2015
• 20.109(F13): Mod 2 Day 6 Analysis & Planning 2
  ...ions into the sink and add enough TBS-T to cover your membranes -- between 10-15 mL should work, but you don't need to measure this out. Keep in mind tha #Shake your container for 10 min.
  17 KB (2,799 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 2 Day 1 System Design
  In 2012, [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048004 Bidkhori et al.] employed an ordinary differentia ...CLC and Intrinsic Resistance to TKI in Loss of PTEN Expression. PLoS ONE 7(10)]''']]
  26 KB (4,292 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 3 Day 1 Growth of phage materials
  ...ched by a second, third, fourth round of panning. Ultimately anywhere from 10 to 1000 candidate sequences may remain from a starting pool of 1 billion [h ...d single-walled carbon nanotubes (SWNTs) ([http://openwetware.org/wiki/Doi:10.1038/nnano.2011.50 ]) while the p8#9 phage can bind thin gold films ([http:
  18 KB (2,861 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 3 Day 2 Phage nanowires
  ...may want to consult this review article: [http://cdn-pubs.acs.org/doi/abs/10.1021/cm702152a?journalCode=cmatex Sotiropoulou, Sofia, et al. "Biotemplated #* Add ~10 dry ice chunks to the evaporation dish and let sit for 10 min. You can measure the temperature of this mixture, which should be ~ ne
  15 KB (2,422 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 3 Day 3 TEM
  ...nWetWare for examples of research ideas in process. As part of a later FNT assignment, you will have to print out your wiki page specifying your topic, your rese ... a smaller diameter than those in the Y condition. The X wires had about a 10 nm? diameter, and the Y wires were about 2?-fold larger." Feel free to incl
  8 KB (1,330 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 3 Day 5 Solar cell testing
  ... this "sandwich" of materials you've made into a 100&deg;C drying oven for 10 minutes. (This step melts the Surlyn to the surface of the anode.) ..._module_of_a_different_color_is_still_biological_engineering. | reflection assignment]], either.
  6 KB (1,007 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 2 Day 2 Mutation Analysis
  ##95° 10 min ##repeat steps 2-4 10 times
  18 KB (2,944 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 2 Day 3 Prepare for LTS
  #Remove one 10 cm² plate of SKOV3 cells from the TC incubator. ...port | research article]] describing your Systems Biology study. For this assignment, you will start outlining and drafting the introduction to your report. Rec
  23 KB (3,661 words) - 17:42, 29 July 2015
• 20.109(S14):16S PCR and paper discussion (Day3)
  ...are enough for the number of reactions you need to run, plus an additional 10%. In addition to the two DNA-containing reactions, you should prepare a no- ! Amount for 3 reactions + 10%
  19 KB (3,108 words) - 13:58, 29 July 2015
• 20.109(S14):Phylogenetic and primer analyses (Day7)
  ...ass comparisons, along with composite trees for each bird population. (See assignment description for further guidance.) Most of the guidance about your data analysis is found in the assignment description [[20.109%28S14%29:Microbiome_summary |'''linked here'''.]]
  17 KB (2,730 words) - 13:58, 29 July 2015
• 20.109(S14):DNA cloning (Day4)
  ... realize that even with high efficiency cells only 1 DNA molecule in about 10,000 is successfully transformed. | [http://www.neb.com/nebecomm/products/productN3231.asp DNA ladder] (load 10 &mu;L)
  15 KB (2,521 words) - 13:58, 29 July 2015
• 20.109(S14):Initiate cell culture (Day2)
  ... rest of the afternoon however you see fit. (Whether that involves the FNT assignment, notebook prep, or a walk in the sunshine - are we still expecting sunshine ...ot shared, one per person), and the large are for temporary waste in steps 10-12 below (shared, one per hood).
  9 KB (1,550 words) - 13:59, 29 July 2015
• 20.109(S14):Lab tour
  ...ay. Afterward, you may have some time remaining to begin the For Next Time assignment, and are strongly encouraged to do so. We'll re-group at 4:15 pm for a BioS #Using your P20, measure 10, 15 and 20 l of the 0.01% XC stock solution into the bottom of three cuve
  28 KB (4,689 words) - 13:59, 29 July 2015
• 20.109(S14):Begin Western protein analysis (Day2)
  ...ence of specific antibodies. Even the very best antisera have no more than 10% of their antibodies directed against a particular antigen. The quality of ...apacity for each lane is usually 100 to 200 ug (that would be 20 ul of a 5-10 ug/ul protein preparation). Thus 1 ng represents a protein that is approxim
  16 KB (2,680 words) - 13:59, 29 July 2015
• 20.109(S14):Complete Western and prepare damaged DNA (Day4)
  ...ing costs $6-8 per reaction, which can add up if you need to examine, say, 10 or more candidates. Agarose gel electrophoresis, by comparison, costs perha #Add enough TBS-T to cover your membranes &ndash; between 10-15 mL should work, but you don't need to measure out this volume. Keep in m
  17 KB (2,797 words) - 13:59, 29 July 2015
• 20.109(S14):DNA repair assays(Day6)
  | 10-21 ...e class, please prepare six 15 mL conicals, labeled 0, 0.1, 0.5, 1, 5, and 10 &mu;M, and six similarly labeled eppendorf tubes.
  17 KB (2,912 words) - 13:59, 29 July 2015
• 20.109(S14):Testing cell viability (Day3)
  ...both live and dead cells; it emits fluorescence in the green channel. SYTO 10 has lower affinity for nucleic acids than does ethidium, and thus is exclud ...orescent dyes such as the fluorescein derivative CFDA-SE are used: about 6-10 divisions can be seen by flow cytometry (see figure at right).
  15 KB (2,507 words) - 13:59, 29 July 2015
• 20.309 Main Page
  |style="width: 10%;"|'''Important dates''' |style="width: 15%;"|'''Assignment due'''
  8 KB (887 words) - 20:47, 16 October 2020
• 20.109(F15):Bacterial amplification of DNA (Day3)
  ... of DNA, but even with highly competent cells only 1 DNA molecule in about 10,000 is successfully transformed. Moreover, the process is somewhat less eff #In an eppendorf tube, combine 10 &mu;L of of your ''DpnI''-digested product with 2.5 &mu;L of loading dye. '
  13 KB (2,207 words) - 11:40, 4 September 2015
• 20.109(F15):Clean and cut DNA (Day2)
  ...the membrane. '''EB''' is one solution we do know everything about. It’s 10 mM Tris, pH 8.5. Since the DNA will solubilize at low salt and high pH, it ... this assignment within ApE. Other program features may help you solve the assignment, but be sure not to "black box" any steps that you aren't sure you also und
  11 KB (1,805 words) - 19:52, 18 September 2015