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  • 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<sub>sense</sub> is 10 &Omega;.
    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 cm<sup>2</sup> 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
  • 20.109(F15):Journal Club II (Day8)
    ...d a mini-presentation that was focused on your research project. For this assignment, you will present work completed by other scientists that has been peer-rev '''''You will complete this assignment individually.'''''
    12 KB (1,779 words) - 04:42, 3 November 2015
  • 20.109(S16):Journal Club II (Day8)
    ...d a mini-presentation that was focused on your research project. For this assignment, you will present work completed by other scientists that has been peer-rev '''''You will complete this assignment individually.'''''
    10 KB (1,596 words) - 18:50, 2 April 2016
  • 20.109(S16):Cell preparation for DNA repair assays (Day5)
    ...hematic above. To account for pipetting error, you will add an additional 10% of each component to the mixture. ...hematic above. To account for pipetting error, you will add an additional 10% of each component to the mixture.
    16 KB (2,542 words) - 18:34, 28 March 2016
  • 20.109(F16):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) - 15:11, 18 May 2016
  • 20.109(F16):Journal club II (Day 6)
    '''You will complete this assignment individually.''' Please review the 20.109 [http://engineerbiology.org/wiki/ ...d a mini-presentation that was focused on your research project. For this assignment, you will present work completed by other scientists that has been peer-rev
    10 KB (1,515 words) - 16:52, 2 November 2016
  • 20.109(F16):Data analysis (Day7)
    .... Note: This will be counted in your homework grade and is due tonight at 10 pm (Thursday, October 6 or Friday, October 7, according to your laboratory ... data slide.''' Use this as a guide to complete the M1D7 in-class homework assignment and for the data slides that within the M1 Data Summary.]]
    5 KB (901 words) - 16:39, 6 October 2016
  • 20.109(S17):Journal Club II (Day8)
    '''You will complete this assignment individually.''' Please review the 20.109 [http://engineerbiology.org/wiki/ ...d a mini-presentation that was focused on your research project. For this assignment, you will present work completed by other scientists that has been peer-rev
    12 KB (1,818 words) - 20:50, 6 April 2017
  • Assignment 3, Part 1: visualizing actin with fluorescence contrast
    This is Part 1 of [[Assignment 3 Overview| Assignment 3]]. # Add 1 mL of pre-warmed 10 μM CytoD solution and incubate at 37 &deg;C for 15 minutes. Watch the time
    15 KB (2,365 words) - 20:25, 25 February 2020
  • Assignment 2: fluorescence microscopy
    [[Category:20.309 assignment 1]] This assignment has 3 parts.
    3 KB (531 words) - 18:23, 14 February 2020
  • Assignment 7 Overview
    Short strands of DNA from about 10-50 base pairs in length are called "oligonucleotides" or just "oligos." In ==How to do this lab (assignments 7 through 10)==
    13 KB (1,864 words) - 21:49, 3 April 2018
  • Assignment 1, Part 4: Measuring magnification and bead size
    #* The microruler calibration slide has tick marks that are 10 &mu;m apart. Every 100 &mu;m, there is a longer tick mark. {{Template:Assignment Turn In|message=<br />
    8 KB (1,209 words) - 04:16, 14 February 2020
  • Assignment 1, Part 2: Optics bootcamp
    This is Part 2 of [[Assignment 1 Overview: Transillumination microscopy| Assignment 1]]. {{Template:Assignment Turn In|message=Report the focal length you measured for each lens A throug
    20 KB (3,371 words) - 06:40, 31 January 2020
  • Assignment 1, Part 1: Pre-lab questions
    This is Part 1 of [[Assignment 1 Overview: Transillumination microscopy| Assignment 1]]. ...\theta^4 \over {4!}} - ...</math> and are accurate to 1% if <math>\theta < 10^o</math>.)
    20 KB (3,312 words) - 20:00, 5 September 2019
  • Assignment 1, Part 3: Building your transillumination microscope
    [[Category:20.309 assignment 1]] In the remaining parts of this assignment, you will build a compound microscope, determine its magnification, and att
    38 KB (6,482 words) - 19:23, 6 September 2019
  • Assignment 5, Part 2: live cell particle tracking of endocytosed beads
    This is Part 2 of [[Assignment 5 Overview| Assignment 5]]. ...g CytoD: Pipet out remaining medium, add 1 mL pre-warmed CytoD solution at 10 μM (pre-mixed for you) to the dish, and incubate for 15 minutes at 37&deg;
    4 KB (742 words) - 18:01, 30 March 2020
  • Assignment 7, Part 2: measure temperature and fluorescence
    This is Part 2 of [[Assignment 7 Overview| Assignment 7]]. ==Overview of the lab portion of this assignment==
    22 KB (3,650 words) - 17:42, 6 April 2018
  • Assignment 3, Part 2: experimental design with fluorescence
    This is Part 2 of [[Assignment 3 Overview| Assignment 3]].<br/> You are trying to image a 10 micron thick cell that expresses Enhanced Green Fluorescent Protein (EGFP)
    2 KB (380 words) - 17:51, 26 September 2018
  • Assignment 6 Overview
    ...d debug several electronic circuits to measure melting curves of DNA. This assignment will introduce you to the electronic components and test equipment you will ... of the instructors about doing a stimulating mini-project instead of this assignment.
    3 KB (432 words) - 12:51, 14 October 2018
  • Assignment 6, Part 1: Pre-lab questions
    This is Part 1 of [[Assignment 6 Overview| Assignment 6]]. {{Template:Assignment Turn In|message=
    2 KB (327 words) - 20:28, 3 April 2018
  • Assignment 6, Part 2: Electronics bootcamp
    This is Part 2 of [[Assignment 6 Overview| Assignment 6]]. ...cal constraints. The resistors in the lab range in value from 1 &Omega; to 10 M&Omega;. Within that range, manufacturers only produce certain standard va
    27 KB (4,589 words) - 11:31, 15 October 2018
  • Assignment 9, Part 3: Fitting your data
    {{Template:Assignment Turn In|message = <br/> {{Template:Assignment Turn In|message= Plot the residuals vs.
    5 KB (760 words) - 22:39, 27 April 2018
  • Assignment 7, Part 1: op amp golden rules questions
    This is Part 1 of [[Assignment 7 Overview| Assignment 7]]. {{Template:Assignment Turn In|message=Turn in your answers to the following questions}}
    6 KB (955 words) - 21:44, 3 April 2018
  • Assignment 7, Part 3: testing your instrument and measuring a DNA melting curve
    This is Part 3 of [[Assignment 7 Overview| Assignment 7]]. ==Assignment 7 measurements==
    5 KB (836 words) - 18:17, 27 October 2017
  • Assignment 10 Overview
    =Assignment 10= ...A_Sequences This page] lists the DNA sequences of your known samples. This assignment has 3 main parts:
    8 KB (1,286 words) - 16:37, 8 May 2018
  • Assignment 8, Part 1: convolution
    This is Part 1 of [[Assignment 8 Overview| Assignment 8]]. {{Template:Assignment Turn In|message=Turn in your answers to the following questions}}
    5 KB (753 words) - 17:40, 5 November 2017
  • Assignment 9 Overview
    ... melting instrument, and (hopefully) collected some spectacular data. This assignment will focus on extracting useful information from the data in order to make The goal for Assignment 9 is to write a model for ''V<sub>f,measured</sub>'' that takes these effec
    6 KB (872 words) - 00:20, 25 January 2018
  • Assignment 9, Part 1: model function
    ...ped element model. The Biot number for the glass vial is about 0.03 (''h''=10.5 <sup>W</sup>/<sub>m</sub>2<sub> K</sub>, ''l''=3 mm, and ''k''=1.05 <sup> TimeVector = (0:(length(InputData)-1))/10;
    12 KB (1,969 words) - 15:29, 14 November 2017
  • 20.109(F17):Journal club II (Day 6)
    '''You will complete this assignment individually.''' Please review the 20.109 [http://engineerbiology.org/wiki/ ...d a mini-presentation that was focused on your research project. For this assignment, you will present work completed by other scientists that has been peer-rev
    10 KB (1,586 words) - 05:39, 20 October 2017
  • Assignment 2 Part 1: Noise in images
    [[Category:20.309 assignment 1]] ...imizing noise is a key challenge in many applications. In this part of the assignment, you will use MATLAB or another computing environment of your choice to sim
    24 KB (3,859 words) - 20:38, 18 February 2020
  • Assignment 2 Part 2: Fluorescence microscopy
    [[Category:20.309 assignment 1]] ...h and ''h'' is the Planck constant approximately equal to 6.626070040(81)×10<sup>−34</sup> J⋅s. In Section 7 of Einstein's paper, he offered a persu
    18 KB (2,752 words) - 18:39, 12 September 2019
  • Assignment 2 Part 3: Build an epi-illuminator for your microscope
    ...rection to adjust for non-uniform illumination. Once you've completed this assignment, you should be ready for next week when you'll make beautiful images of sta ** "OD" is an abbreviation for "optical density," which is log<sub>10</sub> of the power transmitted by the filter divided by the incident power.
    13 KB (2,282 words) - 19:21, 21 February 2020
  • Assignment 4 part 1: Make a fake image
    This is part 1 of [[Assignment 4: finding and measuring things| Assignment 4]]. ...m positions, radius of 5 pixels, and an intensity (total photon number) of 10<sup>5</sup>. (Note that all the units are in pixels.)
    10 KB (1,374 words) - 22:31, 4 March 2020
  • Assignment 4 part 2: Measure resolution
    This is part 2 of [[Assignment 4: finding and measuring things| Assignment 4]]. ... generated a synthetic image of 90 nm radius spheres in the part 1 of this assignment.
    24 KB (3,552 words) - 19:42, 28 February 2020
  • Assignment 4 part 3: Track microspheres over time
    This is Part 3 of [[Assignment 4: finding and measuring things| Assignment 4]]. In this part of the assignment, you will write code to follow microscopic objects throughout a series of m
    10 KB (1,344 words) - 19:58, 28 February 2020
  • 20.109(S18):Laboratory tour
    ...oday. Afterward, you should have some time remaining to begin the Homework assignment, and are strongly encouraged to do so. <font color = CC0000>'''Your lab pra #Using your P20, measure 10, 15 and 20 μL of the 0.01% XC stock solution into the bottom of three cuve
    26 KB (4,362 words) - 21:39, 6 February 2018
  • 20.109(S18):Journal club presentations (Day6 and 7)
    <font color=#0404B4>'''You will complete this assignment individually.'''</font color> Please review the 20.109 [http://engineerbiol ...d a mini-presentation that was focused on your research project. For this assignment, you will present work completed by other scientists that has been peer-rev
    15 KB (2,395 words) - 15:10, 28 June 2018
  • 20.109(F18):Lab tour
    ...oday. Afterward, you should have some time remaining to begin the Homework assignment, and are strongly encouraged to do so. <font color = CC0000>'''Your lab pra #Using your P20, measure 10, 15 and 20 μL of the 0.1% food coloring stock solution into the bottom of
    27 KB (4,435 words) - 19:28, 6 September 2018
  • Assignment 5, Part 1: MSD difference tracking and microscope stability
    This is Part 1 of [[Assignment 5 Overview| Assignment 5]]. ...docytosis]. They are the same kind of cells you took pretty pictures of in assignment 3 (NIH 3T3). Trapped inside of the cells, the particles inside of cells wil
    9 KB (1,018 words) - 19:38, 1 April 2020
  • Electronics boot camp lab part 1
    ...t 2 of [[Electronics boot camp I: passive circuits and transfer functions| Assignment 7]]. ...cal constraints. The resistors in the lab range in value from 1 &Omega; to 10 M&Omega;. Within that range, manufacturers only produce certain standard va
    31 KB (5,193 words) - 17:21, 23 January 2020
  • Electronics written problems
    ...t 1 of [[Electronics boot camp I: passive circuits and transfer functions| Assignment 6]]. {{Template:Assignment Turn In|message=
    6 KB (975 words) - 18:45, 15 April 2019
  • Assignment 8, Part 2: fabricate a microfluidic device
    In this part of the assignment, you will make a microfluidic device that will allow you to switch the flow * This protocol has two steps with 15-60 minute wait times. Part 2 of this assignment can be completed in parallel with Part 1, if you want to keep making progre
    7 KB (1,150 words) - 15:50, 26 March 2020
  • Assignment 8, Part 2: build a two-color microscope
    In Assignment 10, we'll be imaging the nuclear response of the Hog1 protein to osmotic shock In Assignment 3, you chose filters to measure two colors ''simultaneously''. Since the ye
    4 KB (644 words) - 16:20, 4 November 2019
  • Assignment 8, Part 3: add flow control and test your device
    ...gage the solenoid valve), then switch on and off the power to the valve at 10 kHz with a 17% duty cycle (to keep the solenoid engaged, but with lower pow <li> Record a step response movie ("low salt" first for 10 s, then "high salt" for 60 s) using the following commands:
    14 KB (2,339 words) - 22:11, 7 November 2019
  • Electronics written problems II
    ...rt 1 of [[Electronics boot camp I: passive circuits and transfer functions|Assignment 7]]. ...andom, additive, normally distributed voltage with a standard deviation of 10<sup>-3</sup> V.
    5 KB (776 words) - 17:26, 23 January 2020
  • Assignment 8, Part 0: convolution practice
    {{Template:Assignment Turn In|message= ...signals numbered 1-10. For each time domain signal A-H, write the number 1-10 in the empty column of the matching frequency-domain signal. You may use a
    2 KB (358 words) - 17:44, 13 October 2022
  • Assignment 9 Overview: Analyzing yeast images
    ...witch the flow through the device from two fluid reservoirs. In Assignment 10, we'll use this new setup to replicate part of the experiment described in {{Template:Assignment Turn In|message = Our goal for assignment 10 is to reproduce the bode plot in the paper (Figure 2 B and C), and fit it t
    3 KB (385 words) - 21:03, 14 November 2019
  • Assignment 9, Part 1: Analyze two-color yeast images
    {{Template:Assignment Turn In|message = Read the paper and answer the written questions in [[Assignment 9 Overview: Analyzing yeast images]].
    10 KB (1,426 words) - 16:08, 12 November 2019
  • 20.109(S19):Laboratory tour
    ...oday. Afterward, you should have some time remaining to begin the Homework assignment, and are strongly encouraged to do so. <font color = CC0000>'''Your lab pra #Using your P20, measure 10, 15 and 20 μL of the 0.1% food coloring stock solution into the bottom of
    27 KB (4,454 words) - 15:43, 6 February 2019
  • 20.109(S19):Journal club presentations (Day7 and 8)
    <font color=#0404B4>'''You will complete this assignment individually.'''</font color> Please review the 20.109 [http://engineerbiol ...d a mini-presentation that was focused on your research project. For this assignment, you will present work completed by other scientists that has been peer-rev
    15 KB (2,407 words) - 00:58, 4 April 2019
  • 20.109(F19):Lab tour
    ...oday. Afterward, you should have some time remaining to begin the Homework assignment, and are strongly encouraged to do so. <font color = CC0000>'''Your lab pra #Using your P20, measure 10, 15 and 20 μL of the 0.1% food coloring stock solution into the bottom of
    27 KB (4,413 words) - 20:37, 30 August 2019
  • 20.109(F19):Image CometChip (Day6)
    ...on the Data summary! To assist you in the preparation of your first major assignment, we will review the main concepts covered in this module. Remember, DNA da ...rmation provided by your Instructor to edit your Figure / Caption homework assignment. Also, the teaching faculty will meet with each team to provide specific f
    10 KB (1,633 words) - 14:08, 1 October 2019
  • 20.109(F19):Complete antibody staining for Western blot analysis (Day4)
    #*Dilute the primary antibodies in 10 mL of blocking buffer. #*Dilute the secondary antibodies in 10 mL of blocking buffer.
    8 KB (1,322 words) - 22:58, 9 September 2019
  • Assignment 6 Overview: two color microscope
    ...wly-formed optics skills from the first half of the semester for Part 1 of Assignment 6 to upgrade your microscope. Many of the following assignments will be building towards Assignment 10, where we will measure the osmotic shock response of ''S. cerevisiae''. The
    3 KB (480 words) - 01:11, 9 April 2020
  • 20.109(S20):Laboratory tour
    ...oday. Afterward, you should have some time remaining to begin the Homework assignment, and are strongly encouraged to do so. <font color = CC0000>'''Your lab pra #Using your P20, measure 10, 15 and 20 μL of the 0.1% food coloring stock solution into the bottom of
    27 KB (4,434 words) - 14:55, 5 February 2020
  • 20.109(S20):Journal club presentations (Day4 and 5)
    <font color=#0404B4>'''You will complete this assignment individually.'''</font color> Please review the 20.109 [http://engineerbiol For this assignment, you will present work completed by other scientists that has been peer-rev
    18 KB (2,824 words) - 21:51, 7 April 2020
  • 20.109(F20):Lab tour
    ...or figures when completing individual assignments, if you are unsure if an assignment should be completed individually or in partners, just ask! Please do not pl ....edu/S/course/20/fa20/20.109/ Stellar] for the 'Orientation questionnaire' assignment.<br>
    27 KB (4,406 words) - 17:48, 31 August 2020
  • 20.109(F20):M1D5
    #Prepare 2 &mu;M and 10 &mu;M As treatment concentrations in media. ...f a well (of diameter 6.35 mm) and compare this to the size of the cells (~10 &mu;m).
    15 KB (2,489 words) - 22:13, 17 September 2020
  • 20.109(F20):M2D5
    ===Part 4: Edit homework assignment=== ...or the homework assignment due today. You can submit the updated slide by 10 pm tonight for grading. You will get a grade for submitting the original s
    7 KB (1,070 words) - 22:12, 13 October 2020
  • 20.109(F20):M3D4
    ...the holoenzyme is formed. B. The holoenzyme binds to DNA promoters at the -10 / -35 sites that are specific to the &sigma; factor. C. When bound to DNA, ...ing to DNA as it is responsible for promoter recognition and binds to the -10 / -35 sites, thereby recruiting RNAP to the promoter. In bacterial cells &
    16 KB (2,633 words) - 15:58, 4 December 2020
  • 20.109(S21):M1D3
    ... realize that even with high efficiency cells only 1 DNA molecule in about 10,000 is successfully transformed. In our transformation protocol we will adj ...fer the supernatant to a blue DNA binding, silica column and centrifuge at 10,000g for 30sec. Discard the flow through into a tube labeled ''''zymo waste
    11 KB (1,745 words) - 15:37, 1 March 2021
  • 20.109(S21):Laboratory tour
    ...or figures when completing individual assignments, if you are unsure if an assignment should be completed individually or in partners, just ask! Please do not pl ....edu/S/course/20/sp21/20.109/ Stellar] for the 'Orientation questionnaire' assignment.<br>
    28 KB (4,443 words) - 16:02, 16 February 2021
  • 20.109(S21):M2D3
    #Complete Steps #8 - 10 a total of 3 times. ===Part 5: Edit homework assignment===
    14 KB (2,241 words) - 18:42, 26 January 2021
  • 20.109(S21):M3D4
    Now we must keep >10 bp of sequence on each side in a way that meets all our requirements. To qu ===Part 4: Start Mini-report assignment===
    11 KB (1,857 words) - 18:30, 11 May 2021
  • 20.109(F21):Laboratory tour
    ...or figures when completing individual assignments, if you are unsure if an assignment should be completed individually or in partners, just ask! Please do not pl ....edu/S/course/20/fa21/20.109/ Stellar] for the 'Orientation questionnaire' assignment.<br>
    34 KB (5,598 words) - 20:50, 9 September 2021
  • 20.109(F21):M1D4
    ...f a well (of diameter 6.35 mm) and compare this to the size of the cells (~10 &mu;m). #Wash your CometChip by adding enough neutralization buffer to cover (~10-12 mL) and incubate for 5 min at room temperature.
    15 KB (2,480 words) - 15:38, 23 September 2021
  • 20.109(F21):M1D6
    #*The information for the As concentration exposure (0 &mu;M, 2 &mu;M, and 10 &mu;M) is down the left side. ==Navigation links==
    12 KB (2,055 words) - 19:24, 30 September 2021
  • 20.109(S22):Laboratory tour
    ...or figures when completing individual assignments, if you are unsure if an assignment should be completed individually or in partners, just ask! Please do not pl ....edu/S/course/20/sp22/20.109/ Stellar] for the 'Orientation questionnaire' assignment.<br>
    34 KB (5,639 words) - 21:02, 1 February 2022
  • 20.109(F22):Laboratory tour
    ...or figures when completing individual assignments, if you are unsure if an assignment should be completed individually or in partners, just ask! Please do not pl ...rs, and upload your document to Canvas for the 'Orientation questionnaire' assignment.<br>
    34 KB (5,645 words) - 20:34, 8 September 2022
  • 20.109(S23):Laboratory tour
    ...or figures when completing individual assignments, if you are unsure if an assignment should be completed individually or in partners, just ask! Please do not pl ...rs, and upload your document to Canvas for the 'Orientation questionnaire' assignment.<br>
    34 KB (5,644 words) - 21:01, 8 February 2023
  • 20.109(F23):Laboratory tour
    ...or figures when completing individual assignments, if you are unsure if an assignment should be completed individually or in partners, just ask! Please do not pl ...rs, and upload your document to Canvas for the 'Orientation questionnaire' assignment.<br>
    34 KB (5,582 words) - 16:04, 6 September 2023
  • 20.109(F23):M1D7
    ...example, if the ''t''<sub>calculated</sub> for a data set with ''n'' - 1 = 10 is 3 (given that the ''t''<sub>tabulated</sub> is 2.228), then the data set ...ributed evenly you will first assess what needs to be done to complete the assignment and then decide who will be responsible for which parts.
    9 KB (1,498 words) - 19:14, 5 October 2023
  • 20.109(S24):Laboratory tour
    ...or figures when completing individual assignments, if you are unsure if an assignment should be completed individually or in partners, just ask! Please do not pl ...rs, and upload your document to Canvas for the 'Orientation questionnaire' assignment.<br>
    34 KB (5,582 words) - 20:30, 18 April 2024
  • 20.109(S24):M1D4
    ...rams - Finding the Z score threshold" you will use the preset threshold of 10 for the data analysis. #*The default value of 10 will be present, simply delete and enter your value.
    15 KB (2,431 words) - 19:46, 21 February 2024
  • 20.109(S24):M1D8
    ...s any questions you may have about the material covered, data analyzed, or assignment details. #Wash the membrane with 5 mL of 1X Detection Wash Buffer for 10 minutes at room temperature at 50 rpm.
    5 KB (749 words) - 17:35, 7 March 2024

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