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• Assignment 8, Part 2: lock-in amplifier and temperature control
  This is Part 2 of [[Assignment 8 Overview| Assignment 8]]. ...rates. You will also use a computer model to compensate for the difference in temperature between the heating block and sample, photobleaching, and therm
  17 KB (2,813 words) - 22:56, 7 November 2017
• 20.309:Course Information
  ...system] to reserve a place in the lab. Most lab exercises can be completed in about 6 hours per week. Some students find the lab work significantly more ...ours before coming to the lab. If there are no scholars signed up 24 hours in advance, the lab may be closed without notice.
  5 KB (714 words) - 16:37, 7 February 2020
• Electronics Mini-Lab
  ...instructors about doing a stimulating mini-project instead of the mini-lab assignment. '''a)''' Combining resistance values in parallel and in series, draw a simplified version of the circuit containing the given volta
  35 KB (5,891 words) - 18:46, 7 April 2017
• 20.109(S08):Testing cell viability (Day3)
  ... to depletion by cells on the outer rim, even when at a high concentration in the bulk fluid. Finally, note that most cells require certain soluble and/o ...r in their cell permeance and nucleic acid affinity. Fluorescence emission in the green (left) and red (right) channels is shown for the same field of ce
  18 KB (3,087 words) - 16:04, 15 June 2015
• 20.109(S08):Initiate cell culture (Day2)
  ... is more similar to that of humans. In this module, we will work with an ''in vitro'' culture model of cartilage-forming cells. ...mple, high molecular weights correlate with increased viscosity. Alginates in general are shear-thinning, which is to say their viscosity decreases as sh
  12 KB (2,006 words) - 16:04, 15 June 2015
• 20.109(S08):Site-directed mutagenesis (Day2)
  Last time you navigated a great deal of information in order to design mutagenized inverse pericams nice work! Today you will ...hole until it is transformed into competent bacteria and repaired by them. In order to propagate only the mutant plasmid, the parental DNA is specificall
  12 KB (1,954 words) - 14:24, 5 June 2015
• 20.109(S08):Prepare expression system (Day3)
  ... colonies were picked the next day for liquid overnight cultures, which in turn were miniprepped to purify mutant plasmid DNA. However, the inverse pericam ...ide). To further reduce ‘leaky’ expression of the protein of interest (in our case, inverse pericam), the pLysS version of BL21(DE3) contains T7 lyso
  13 KB (2,221 words) - 14:24, 5 June 2015
• 20.109(S07): Yeast transformation
  ... if...?"</i>. And oddly, spending some time being negative before you jump in is likely to improve your chances of a successful outcome since some of the ...If the controls in an experiment haven't worked there is very little point in considering the data you have collected. Even experienced researchers often
  19 KB (3,251 words) - 15:32, 15 June 2015
• 20.109(S07): Start-up expression engineering
  ...getically speaking, quite wasteful. Why make a protein if it's not useful? In this experimental module we'll see how nature has refined the genetic progr ... of the activity. We'll study one chromatin-remodeling complex called SAGA in this experimental module.
  28 KB (4,311 words) - 15:32, 15 June 2015
• Bryan Hernandez/20.109/Lab notebook/Module 1/Day 5
  ... strain. These will be run in duplicate on the gel, so we can cut the blot in half and you will have two blots to probe next time. ...ter, please ask the teaching faculty to help. The cells will scatter light in proportion to their density, at least within a certain range of densities,
  11 KB (1,756 words) - 15:32, 15 June 2015
• 20.109(S07): Western analysis
  ...ts that contribute to the overall behavior of the system may be understood in great detail. As you've seen, however, reassembly of the component level un ... tolerated by the phage, specifically, if the tagged protein is detectable in bacteria that are infected by your manipulated phage and if the phage life
  13 KB (2,004 words) - 15:31, 15 June 2015
• 20.109(S07): Start-up signal measurement
  ...unt an SOS response within minutes. Stress response genes are up-regulated in an effort to protect the bacterial host from far more severe consequences o ...on between a cell’s outer membrane and its internal processors. Messages in eukaryotic cells also travel between the nucleus and the cytoplasm, plus be
  21 KB (3,477 words) - 15:31, 15 June 2015
• 20.109(S07): Bio-material engineering/Optimizing panning
  Thanks to recent advances in DNA synthesis chemistry, high quality pools of oligonucleotides are availab ... the junction of the Aga2 sequence with the 36-base pair oligo is the same in every plasmid but the 12 amino acid sequence fused to each Aga2 protein can
  10 KB (1,637 words) - 15:31, 15 June 2015
• 20.109(F07): siRNA design
  In the previous experimental module, your work has focused on DNA. In this experimental module, RNA gets the spotlight. While DNA has one job, to ...term used to describe how much of a gene product is synthesized by a cell. In liver cells, expression of genes for liver-specific proteins is high and br
  21 KB (3,532 words) - 15:54, 15 June 2015
• 20.109(F07): DNA ligation and bacterial transformation
  ...earized M13K07 backbone with your oligonucleotide insert by mixing the two in the presence of ATP and an enzyme, T4 DNA ligase. During the ligation react ...ired construct, namely the M13K07 backbone carrying a short added sequence in the gene for p3. Alternative ligation products may arise, including a simpl
  16 KB (2,748 words) - 15:54, 15 June 2015
• 20.109(F07): M13.1
  ...ts that contribute to the overall behavior of the system may be understood in great detail. As you've seen, however, there isn't always a straightforward ...step example is provided here. It's inspired by the T7 algorithm described in the [http://www.nature.com/doifinder/10.1038/msb4100025 Chan et al paper.]
  19 KB (3,059 words) - 16:00, 15 June 2015
• 20.109(F07): Western analysis
  ...olerated by the phage, specifically, if the modified protein is detectable in bacteria that are infected by your manipulated phage and if the phage life ...sequently, proteins are coated with a detergent ("SDS"---same thing that's in many shampoos) to allow them to be drawn through the electrophoresis matrix
  11 KB (1,724 words) - 15:54, 15 June 2015
• 20.109(F07): Transmission electron microscopy
  ...ral size (250X magnification). Compound microscopes, like the ones we have in lab, use a second lens to magnify the image from the first and can increase ...” then strikes a fluorescent screen, giving rise to an image that varies in darkness according to the sample's density. For samples that are amenable t
  7 KB (1,172 words) - 15:55, 15 June 2015
• 20.109(F07): ECD assembly
  ...ntil the stock is replenished to see all the aspects of this “revolution in book reading.” The promotional material for this handheld book-sized pro ...module), you note how their workings rely on excitation of a material held in tiny cells between panels of glass. The excited materials emit light of par
  13 KB (2,320 words) - 15:55, 15 June 2015
• 20.109(F08): Start-up expression engineering
  ...getically speaking, quite wasteful. Why make a protein if it's not useful? In this experimental module we'll see how nature has refined the genetic progr ... of the activity. We'll study one chromatin-remodeling complex called SAGA in this experimental module.
  29 KB (4,451 words) - 19:05, 28 July 2015
• 20.109(F08): Yeast transformation
  ... if...?"</i>. And oddly, spending some time being negative before you jump in is likely to improve your chances of a successful outcome since some of the ...If the controls in an experiment haven't worked there is very little point in considering the data you have collected. Even experienced researchers often
  19 KB (3,254 words) - 19:05, 28 July 2015
• 20.109(F08): Phage nanowires
  ...way to find out from the dinosaurs themselves how the iridium came to rest in this clay layer. ...osive, unmachinable, dinosaur killing metal thats relevant for our work in this module. Iridium, when oxidized to IrO2, has a d-orbital conductance ba
  13 KB (2,275 words) - 19:05, 28 July 2015
• 20.109(F08): Western Analysis
  ...olerated by the phage, specifically, if the modified protein is detectable in bacteria that are infected by your manipulated phage and if the phage life ...sequently, proteins are coated with a detergent ("SDS"---same thing that's in many shampoos) to allow them to be drawn through the electrophoresis matrix
  11 KB (1,723 words) - 19:05, 28 July 2015
• 20.109(F08): Transmission electron microscopy
  ...ral size (250X magnification). Compound microscopes, like the ones we have in lab, use a second lens to magnify the image from the first and can increase ...” then strikes a fluorescent screen, giving rise to an image that varies in darkness according to the sample's density. For samples that are amenable t
  7 KB (1,172 words) - 19:05, 28 July 2015
• 20.109(F08): ECD assembly
  ...ntil the stock is replenished to see all the aspects of this “revolution in book reading.” The promotional material for this handheld book-sized pro ...module), you note how their workings rely on excitation of a material held in tiny cells between panels of glass. The excited materials emit light of par
  13 KB (2,320 words) - 19:05, 28 July 2015
• 20.109(F08): Mod 2 Day 4 SDS-PAGE, screen for phenotypes
  ...ogy has given us the ability to read the 4 letter genetic program of cells in their entirety. Molecular techniques like the ones you've learned so far th Instead of rewriting the DNA in response to every change in its surroundings, a cell will vary the output of its genes, varying their a
  25 KB (4,068 words) - 19:05, 28 July 2015
• 20.109(F08): Mod 1 Day 7 Lipofection
  ...ld be transcribed by RNA polymerase. The polyadenylation sequence assists in the export and stability of the mRNA so that it gets translated by the ribo ...s introduced into a cell). For stable transfection, the DNA is introduced in such a way that it is maintained indefinitely. Today you will be transient
  10 KB (1,701 words) - 19:05, 28 July 2015
• 20.109(F08): Mod 3 Day 2 Phage nanowires
  ...way to find out from the dinosaurs themselves how the iridium came to rest in this clay layer. ...osive, unmachinable, dinosaur killing metal thats relevant for our work in this module. Iridium, when oxidized to IrO2, has a d-orbital conductance ba
  13 KB (2,079 words) - 19:05, 28 July 2015
• 20.109(F08): Mod 2 Day 1 Protein engineering with PCR
  ...omatin remodeling is required for appropriate gene expression which is, in turn, required for healthy cell behaviors. <br> ... first few days of this module, we'll add a protein tag to some SAGA genes in yeast or some sequences that are regulated by SAGA. If we wanted to genetic
  30 KB (4,904 words) - 19:06, 28 July 2015
• 20.109(F08): Mod 2 Day 2 Yeast transformation
  ... if...?"</i>. And oddly, spending some time being negative before you jump in is likely to improve your chances of a successful outcome since some of the ...If the controls in an experiment haven't worked there is very little point in considering the data you have collected. Even experienced researchers often
  18 KB (3,152 words) - 19:06, 28 July 2015
• 20.109(F08): Mod 2 Day 5 Probe western, isolate RNA
  ...ex. Assuming the protein we're interested in is expressed and intact, then in general, the quality of Western results depends on the quality of the antib ...recognize multiple epitopes. We will be using a polyclonal antibody raised in rabbits against the Protein A from <i>Staphylococcus aureus</i>, but for th
  20 KB (3,266 words) - 19:06, 28 July 2015
• 20.109(F08): Mod 3 Day 6 ECD assembly
  ...mazon's Kindle]][[Image:Epaper.png|thumb|right| Epaper microcapsules]]Just in time for the 2007 holiday shopping season, Amazon.com came out with a wirel ...module), you note how their workings rely on excitation of a material held in tiny cells between panels of glass. The excited materials emit light of par
  12 KB (2,111 words) - 19:06, 28 July 2015
• 20.109(F08):DNA engineering powerpoint pitch guidelines
  *This assignment is due by 11:00 a.m. on the day you have lab. Please turn in your "P3" electronically by emailing it to bevin, nlerner, myapoe, nkuldell *This assignment is submitted as a powerpoint file but you will _not_ have the opportunity t
  2 KB (319 words) - 19:06, 28 July 2015
• 20.109(S09): Luciferase assays and RNA prep (Day6)
  ...sed on what was observable. And amazingly this completely wrong theory was in place for nearly 2000 years. Rudolph Virchow didnt state that where a Coupled with data collection is instrumentation and technology. Advances in technology often lead to scientific progress. (e.g., microscopes that heral
  14 KB (2,345 words) - 19:34, 28 July 2015
• 20.109(F09): Mod 2 Day 3 Tools for system engineering
  ...increase the phosphatase activity of the sensor when the cells are growing in the light. The first class of mutants (we'll call them K+) should make the ...Cph1 to EnvZ, called Cph8, changes the numbering of the residues, as shown in the figure below. It's hoped, however, that the local environment of the re
  24 KB (3,897 words) - 19:39, 28 July 2015
• 20.109(F09): Mod 3 Day 2 Phage nanowires
  [[Image:CoinBattery.jpg|thumb|Coin-type battery]]The materials prepared in this lab have activity as battery electrodes. The redox properties of the ...into a coin type battery and tested. Groups will vary the amount of silver in the gold phage nanowires to see how these variations affect the charge/disc
  7 KB (1,146 words) - 19:39, 28 July 2015
• 20.109(S09):Prepare expression system (Day4)
  ... your oh-so devoted teaching staff picked two colonies per mutant to grow in liquid culture. The XL1-Blue cell line, although it now carries the inverse ...ide). To further reduce leaky expression of the protein of interest (in our case, inverse pericam), the pLysS version of BL21(DE3) contains T7 lyso
  21 KB (3,468 words) - 19:33, 28 July 2015
• 20.109(S09): siRNA design (Day1)
  ...on proteins, and to implement protein modifications, you manipulated DNA. In this experimental module, RNA gets the spotlight. While DNA almost exclusiv ...term used to describe how much of a gene product is synthesized by a cell. In liver cells, expression of genes for liver-specific proteins is high and th
  22 KB (3,613 words) - 19:33, 28 July 2015
• 20.109(F09): Mod 1 Day 6 Restriction map and tissue culture
  ...ause people were doing exactly that, extracting tissue and letting it live in a dish for a short time. Today, most tissue culture experiments are done us ...an divide indefinitely. (Some inherent cell-to-cell variation still exists in such cells.)
  11 KB (1,830 words) - 19:38, 28 July 2015
• 20.109(F09): Mod 1 Day 7 Lipofection
  ...ld be transcribed by RNA polymerase. The polyadenylation sequence assists in the export and stability of the mRNA so that it gets translated by the ribo ...s introduced into a cell). For stable transfection, the DNA is introduced in such a way that it is maintained indefinitely. Today you will be transient
  10 KB (1,594 words) - 19:38, 28 July 2015
• 20.109(F09): Mod 1 Day 8 FACS analysis
  ... sample of this cell type from a complex mixture by using a FACS machine. In addition to purification, the FACS machine can count the number of cells th ...rged droplets, each containing a single cell. The stream of droplets pass in front of a laser beam, and the scattered light is analyzed by a series of f
  5 KB (804 words) - 19:38, 28 July 2015
• 20.109(F09):DNA engineering "Progress Report"
  ...ualifying exams, but now they would like to hear what progress you've made in the lab over the last few months. The following guidelines have been adapte This assignment is due by 11:00 a.m. on the day you have lab. Please turn in your progress reports electronically by uploading them to the [http://stell
  7 KB (1,083 words) - 19:38, 28 July 2015
• 20.109(F09):DNA engineering "Memo"
  ...in which you argue either FOR or AGAINST taking the delta5/delta3 research in your division forward. This assignment is due by 11:00 a.m. on the day you have lab. Please turn in your memos electronically by uploading them to the [http://stellar.mit.edu/
  5 KB (747 words) - 19:38, 28 July 2015
• 20.109(F09):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> ...ence ones. If time permits, you will read the absorbance of your dilutions in the spectrophotometer so transfer the volumes to cuvettes and do not throw
  27 KB (4,508 words) - 19:38, 28 July 2015
• 20.109(F09): Mod 2 Day 6 Readouts of DNA, Protein
  ...ression of the light sensing protein, Cph8, and the mutant versions of it. In general, detection depends on which antibody you choose, and the quality of ...ize one epitope, while other antibodies, called polyclonal antibodies, are in fact antibody pools that recognize multiple epitopes. We will be using a mo
  13 KB (2,115 words) - 19:38, 28 July 2015
• 20.109(F09): Mod 2 Day 2 Measuring system performance
  ...e output...then the cells might swim to the light rather than turn a color in response. ...nderstanding of the system we're working with is obviously needed. To look in the black box that senses light, we'll have to learn more about the two com
  11 KB (1,859 words) - 19:39, 28 July 2015
• 20.109(F10): Mod 2 Day 7 Readout of Protein
  ...ression of the light sensing protein, Cph8, and the mutant versions of it. In general, detection depends on which antibody you choose, and the quality of ...ize one epitope, while other antibodies, called polyclonal antibodies, are in fact antibody pools that recognize multiple epitopes.
  10 KB (1,613 words) - 21:00, 28 July 2015
• 20.109(F10):DNA engineering "Progress Report"
  ...ualifying exams, but now they would like to hear what progress you've made in the lab over the last few months. The following guidelines have been adapte This assignment is due by 11:00 a.m. Please turn in your progress reports electronically by uploading them to the [http://stell
  7 KB (1,131 words) - 21:00, 28 July 2015
• 20.109(F10):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> ...ence ones. If time permits, you will read the absorbance of your dilutions in the spectrophotometer so transfer the volumes to cuvettes and do not throw
  27 KB (4,538 words) - 21:00, 28 July 2015
• 20.109(S11):Amplify aptamer-encoding DNA (Day1)
  ... screening, and has a heme binding affinity of 220 nM. Both were described in [http://www.ncbi.nlm.nih.gov/pubmed/17168539 this] 2006 paper. ...rage capabilities. We will make use of these capabilities more extensively in Module 2.
  10 KB (1,688 words) - 21:05, 28 July 2015
• 20.109(S11):Prepare DNA for cloning (Day3)
  ...etting it slowly cool - very similar to how we denatured RNA and cooled it in Module 1, except this time we want two strands to anneal rather than to for ... digests to understand how they work and why we had to do this one for you in the interests of time.
  17 KB (2,967 words) - 21:05, 28 July 2015
• 20.109(F11)
  ...ng, notebook keeping and publicly presenting your data. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an excitin *Agi's Monday office hour is cancelled. I'm in no shape to be breathing near anyone; I'm happy to discuss research proposa
  4 KB (629 words) - 21:07, 28 July 2015
• 20.109(F11):DNA engineering powerpoint summary
  *This assignment is due by 1PM. *This assignment can be '''no more than 10 slides total.'''
  3 KB (528 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 1 Day 6 Lipofection & lab practical
  ...ld be transcribed by RNA polymerase. The polyadenylation sequence assists in the export and stability of the mRNA so that it gets translated by the ribo ...s introduced into a cell). For stable transfection, the DNA is introduced in such a way that it is maintained indefinitely. Today you will be transient
  10 KB (1,541 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 1 Day 7 FACS analysis
  ... sample of this cell type from a complex mixture by using a FACS machine. In addition to purification, the FACS machine can count the number of cells th ...rged droplets, each containing a single cell. The stream of droplets pass in front of a laser beam, and the scattered light is analyzed by a series of f
  5 KB (840 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 2 Day 2 Measuring system performance
  ...e output...then the cells might swim to the light rather than turn a color in response. ...nderstanding of the system we're working with is obviously needed. To look in the black box that senses light, we'll have to learn more about the two com
  21 KB (3,476 words) - 21:08, 28 July 2015
• 20.109(F11): Mod 2 Day 7 Readout of Protein
  ...ression of the light sensing protein, Cph8, and the mutant versions of it. In general, detection depends on which antibody you choose, and the quality of ...ize one epitope, while other antibodies, called polyclonal antibodies, are in fact antibody pools that recognize multiple epitopes.
  10 KB (1,644 words) - 21:08, 28 July 2015
• 20.109(F12): Mod 3 Day 1 Growth of phage materials
  ...rganisms themselves. Humans have a lot to learn from natures successes. In the upcoming weeks well use a virus that infects bacteria, namely the ba ...Esther Bullitt, Boston University School of Medicine), where the black bar in each image is 50 nm long. And what about the upper limit to the length of t
  18 KB (3,015 words) - 13:43, 29 July 2015
• 20.109(S13):Testing cell viability (Day3)
  ... to depletion by cells on the outer rim, even when at a high concentration in the bulk fluid. Finally, note that most cells require certain soluble and/o ...r in their cell permeance and nucleic acid affinity. Fluorescence emission in the green and red (left) and red alone (right) channels is shown for the sa
  15 KB (2,447 words) - 13:48, 29 July 2015
• 20.109(S13):Prepare expression system (Day4)
  ... your oh-so devoted teaching staff picked two colonies per mutant to grow in liquid culture. The XL1-Blue cell line, although it now carries the inverse ...galactoside). To reduce ‘leaky’ expression of the protein of interest (in our case, inverse pericam), the pLysS version of BL21(DE3) contains T7 lyso
  20 KB (3,344 words) - 13:48, 29 July 2015
• 20.109(S13):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> #Below, be sure to use the pipet specified in each step in order to test the calibration of all three.
  27 KB (4,582 words) - 13:48, 29 July 2015
• 20.109(S13):Assess protein function (Day8)
  ...imple case of a receptor-ligand pair that are exclusive to each other, and in which the receptor is monovalent. The ligand (L) and receptor (R) form a co ...tion was derived by algebraic substitution. If the ligand concentration is in excess of that of the receptor, ''[L]'' may be approximated as a constant,
  16 KB (2,718 words) - 13:48, 29 July 2015
• 20.109(F14): Mod 1 Day 3 Agarose gel electrophoresis
  ...rix when a current is applied across it. The larger molecules get entwined in the matrix and retarded; the smaller molecules wind through the matrix more ...ith three agarose concentrations. The 1000 base pair fragment is indicated in each. <br>
  13 KB (2,248 words) - 14:02, 29 July 2015
• 20.109(F14):20.109 Class Blog summary page
  ...ent may be used to replace this score. However, no FNW bonus will be given in addition, and the maximum of three such assignments still holds. ...receive feedback on your blog posts from your instructors (and anyone else in the class that chooses to comment on the blog). Below are some suggested to
  6 KB (1,018 words) - 14:02, 29 July 2015
• 20.109(F14):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> #Below, be sure to use the pipet specified in each step in order to test the calibration of all three.
  29 KB (4,864 words) - 14:02, 29 July 2015
• 20.109(F14):Module 2
  ...to improve and extend the performance of the bacterial photography system. In the process we may also learn something new about the natural systems upon *[[20.109(F14): System engineering research article| Guidelines for this assignment]]<br>
  3 KB (506 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 1 Testing an engineered biological system
  ...jects, or exquisitely control responses to the world changing around them. In this experimental module we will consider the possibilities and limitations ...amilies of proteins that behave in predictable ways, both individually and in combination with other protein families and sequence motifs.
  15 KB (2,383 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 4 DNA ligations, bacterial transformations and CometChip
  ...epair the phosphate backbone, creating a stable circular plasmid (as shown in the figure below). ...ortant to realize that even with high efficiency cells only 1 DNA molecule in about 10,000 is successfully transformed.
  12 KB (2,060 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 2 Measuring system performance
  ...e output...then the cells might swim to the light rather than turn a color in response. ...nderstanding of the system we're working with is obviously needed. To look in the black box that senses light, we'll have to learn more about the two com
  21 KB (3,387 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 3 Tools for system engineering
  ...at increase the kinasing activity of the sensor when the cells are growing in the dark. The mutants (we'll call them K+) should make the "dark" color of ...Cph1 to EnvZ, called Cph8, changes the numbering of the residues, as shown in the figure below. It's hoped, however, that the local environment of the re
  28 KB (4,560 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 5 Assessing re-tuned system
  #the β-gal activity of the mutant photography strains grown in the light and dark ...otype but rather there has been some random change in the cell's genome or in the pPCB plasmid that is responsible. As a class, though, we'll hope that t
  8 KB (1,382 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 2 Day 7 Readout of Protein
  ...ression of the light sensing protein, Cph8, and the mutant versions of it. In general, detection depends on which antibody you choose, and the quality of ...ize one epitope, while other antibodies, called polyclonal antibodies, are in fact antibody pools that recognize multiple epitopes.
  11 KB (1,712 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 3 Day 3 TEM
  ... EDX, enables identification of the atomic composition of heavier elements in the material. EDX has limited detection of elements below sodium (Na) on t ...e must be sufficiently thin and sufficiently sturdy to be hit by electrons in a vacuum. Rather than imaging single atoms, biological samples display con
  10 KB (1,709 words) - 14:02, 29 July 2015
• 20.109(F14): Mod 1 Day 4 DNA Ligation & Transformation
  ...epair the phosphate backbone, creating a stable circular plasmid (as shown in the figure below). ...ortant to realize that even with high efficiency cells only 1 DNA molecule in about 10,000 is successfully transformed.
  12 KB (2,028 words) - 14:02, 29 July 2015
• 20.109(S15):16S PCR and paper discussion (Day3)
  ...arly products themselves become templates that produce the correct product in abundance.]] ...rounds of PCR will not produce the desired product &ndash; we will see why in today's pre-lab lecture.)
  22 KB (3,588 words) - 17:15, 29 July 2015
• 20.109(S15):20.109 Class Blog summary page
  ...ent may be used to replace this score. However, no FNW bonus will be given in addition, and the maximum of three such assignments still holds. ...receive feedback on your blog posts from your instructors (and anyone else in the class that chooses to comment on the blog). Below are some suggested to
  6 KB (1,017 words) - 17:15, 29 July 2015
• 20.109(S15):Begin Western protein analysis and choose system conditions (Day2)
  ...ll be using during Module 2, and plated a known quantity of each cell type in preparation for protein analysis. Today you will lyse the cells, isolate th ...ize one epitope, while other antibodies, called polyclonal antibodies, are in fact antibody pools that recognize multiple epitopes. Antibodies can be rai
  27 KB (4,480 words) - 17:15, 29 July 2015
• 20.109(S15):Biotemplating on phage nanowires (Day 2)
  In an effort to optimize efficiency in our solar cells, we will test and compare three sets of nano-composites of ...in the infected cell (either from a separate plasmid or an additional gene in the phage genome) such that the resulting phage have both types of p8, and
  14 KB (2,281 words) - 17:15, 29 July 2015
• 20.109(S15):Cell preparation for DNA repair assays (Day4)
  ===DNA repair inhibitors -- let's find one that works in CHO cells!=== ...od to perturb the NHEJ pathway. And 2) chemical inhibitors are used widely in biological engineering, so it is useful to think about their strengths and
  18 KB (2,885 words) - 17:15, 29 July 2015
• 20.109(S15):DNA cloning (Day4)
  ... an antibiotic resistance marker on the backbone, and growing the bacteria in said antibiotic. (We’ll say more about that procedure below.) This method ...uct, and a backbone, such as a commercially available vector, are depicted in black and blue, respectively. These are digested with the same restriction
  16 KB (2,696 words) - 17:15, 29 July 2015
• 20.109(S15):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> #Below, be sure to use the pipet specified in each step in order to test the calibration of all three.
  25 KB (4,176 words) - 17:15, 29 July 2015
• 20.109(S15):Solar cell assembly (Day 4)
  ===Solar cells in society=== ...products as they are lightweight, flexible, and exhibit better performance in diffuse light than competitors.
  13 KB (2,017 words) - 17:15, 29 July 2015
• 20.109(S12):Amplify aptamer-encoding DNA (Day1)
  ... screening, and has a heme binding affinity of 220 nM. Both were described in [http://www.ncbi.nlm.nih.gov/pubmed/17168539 this] 2006 paper. ...rage capabilities. We will make use of these capabilities more extensively in Module 2.
  10 KB (1,682 words) - 17:30, 29 July 2015
• 20.109(S12):Purify aptamer-encoding DNA (Day2)
  ...your two aptamer-encoding DNA fragments in preparation for performing an ''in vitro'' transcription (IVT) reaction that will copy the DNA into RNA. IVT r ...ield and appropriate sieving matrix. DNA fragments are typically separated in gels composed of agarose, a seaweed-derived polymer (see figure, below left
  11 KB (1,844 words) - 17:30, 29 July 2015
• 20.109(S12):Testing cell viability (Day3)
  ... to depletion by cells on the outer rim, even when at a high concentration in the bulk fluid. Finally, note that most cells require certain soluble and/o ...r in their cell permeance and nucleic acid affinity. Fluorescence emission in the green and red (left) and red alone (right) channels is shown for the sa
  17 KB (2,877 words) - 17:30, 29 July 2015
• 20.109(S12):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> #Below, be sure to use the pipet specified in each step in order to test the calibration of all three.
  27 KB (4,554 words) - 17:30, 29 July 2015
• 20.109(S12):Bacterial amplification of DNA (Day3)
  ...kely present at a low concentration, and moreover it is nicked rather than in intact circular form. What we would like to do now is repair and further am ...microgram of DNA, but even with highly competent cells only 1 DNA molecule in about 10,000 is successfully transformed. Thus we need a way to identify tr
  17 KB (2,889 words) - 17:30, 29 July 2015
• 20.109(S12):Initiate cell culture (Day2)
  ... is more similar to that of humans. In this module, we will work with an ''in vitro'' culture model of cartilage-forming cells. ...mple, high molecular weights correlate with increased viscosity. Alginates in general are shear-thinning, which is to say their viscosity decreases as sh
  10 KB (1,708 words) - 17:30, 29 July 2015
• 20.109(F13):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> #Below, be sure to use the pipet specified in each step in order to test the calibration of all three.
  28 KB (4,787 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 2 Day 1 System Design
  ...FR) signaling network with the goal of overcoming a growing common problem in the treatment of disease -- drug resistance. ...to overcome the resistance to EGFR inhibition in the SKOV3 cell line later in the module.
  26 KB (4,292 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 1 Day 3 Agarose gel electrophoresis
  ...rix when a current is applied across it. The larger molecules get entwined in the matrix and retarded; the smaller molecules wind through the matrix more ...ith three agarose concentrations. The 1000 base pair fragment is indicated in each. <br>
  13 KB (2,222 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 3 Day 2 Phage nanowires
  In an effort to optimize efficiency in our solar cells, we will test and compare test two sets of nano-composites ...in the infected cell (either from a separate plasmid or an additional gene in the phage genome) such that the resulting phage have both types of p8, and
  15 KB (2,422 words) - 17:33, 29 July 2015
• 20.109(F13): Mod 2 Day 3 Prepare for LTS
  ...ed your SKOV3 cells from [http://www.atcc.org/ ATCC], a repository started in 1925 to provide a source of common reagents for scientists. If you investig ...s. For your reference, the total cell growth surface area of a single well in a 6-well plate is 9.5 cm².
  23 KB (3,661 words) - 17:42, 29 July 2015
• 20.109(S10):Amplify aptamer-encoding DNA (Day1)
  ... screening, and has a heme binding affinity of 220 nM. Both were described in [http://www.ncbi.nlm.nih.gov/pubmed/17168539 this] 2006 paper. ...rage capabilities. We will make use of these capabilities more extensively in Module 2.
  10 KB (1,656 words) - 19:49, 28 July 2015
• 20.109(S10):Prepare expression system (Day4)
  ... your oh-so devoted teaching staff picked two colonies per mutant to grow in liquid culture. The XL1-Blue cell line, although it now carries the inverse ...ide). To further reduce ‘leaky’ expression of the protein of interest (in our case, inverse pericam), the pLysS version of BL21(DE3) contains T7 lyso
  22 KB (3,701 words) - 19:49, 28 July 2015
• 20.109(S10):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> ...ence ones. If time permits, you will read the absorbance of your dilutions in the spectrophotometer so do not throw them away.
  26 KB (4,410 words) - 19:49, 28 July 2015
• 20.109(S10):Initiate cell culture (Day2)
  ... is more similar to that of humans. In this module, we will work with an ''in vitro'' culture model of cartilage-forming cells. ...mple, high molecular weights correlate with increased viscosity. Alginates in general are shear-thinning, which is to say their viscosity decreases as sh
  12 KB (1,957 words) - 19:49, 28 July 2015
• 20.109(S10):Testing cell viability (Day3)
  ... to depletion by cells on the outer rim, even when at a high concentration in the bulk fluid. Finally, note that most cells require certain soluble and/o ...r in their cell permeance and nucleic acid affinity. Fluorescence emission in the green and red (left) and red alone (right) channels is shown for the sa
  16 KB (2,677 words) - 22:02, 28 August 2016
• 20.109(S11):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> ...ence ones. If time permits, you will read the absorbance of your dilutions in the spectrophotometer so do not throw them away.
  26 KB (4,424 words) - 21:05, 28 July 2015
• 20.109(F12): Mod 1 Day 7 FACS analysis
  ... sample of this cell type from a complex mixture by using a FACS machine. In addition to purification, the FACS machine can count the number of cells th ...rged droplets, each containing a single cell. The stream of droplets pass in front of a laser beam, and the scattered light is analyzed by a series of f
  5 KB (842 words) - 13:41, 29 July 2015
• 20.109(F12):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> ...ence ones. If time permits, you will read the absorbance of your dilutions in the spectrophotometer so transfer the volumes to cuvettes and do not throw
  27 KB (4,585 words) - 13:41, 29 July 2015
• 20.109(F12): Mod 3 Day 2 Phage nanowires
  ... how the p8 proteins allow the SWNTs to associate in parallel to the phage in the photo), but the viruses also position parts of the SWNTs to the surroun Today in lab you will react your SWNT:phage with titanium isopropoxide, harvest a sm
  10 KB (1,590 words) - 13:41, 29 July 2015
• 20.109(F12): M1 ppt summary and notes
  *This assignment is due by 11AM. *This assignment can be '''no more than 12 slides total.'''
  6 KB (922 words) - 13:41, 29 July 2015
• 20.109(F12): FACS data analysis and defense
  *The slides for this assignment are due by 11AM. *The oral defense for this assignment will take place during lab on M2D1, either 10.11.12 or 10.12.12.
  3 KB (584 words) - 13:41, 29 July 2015
• 20.109(F12): Online cloning lab and defense
  ... need, rather than have them done for you by the teaching faculty...and so in that sense this is a more "real" view to the work you'll do when you leave Sign in (upper right, blue button), then "Launch Your Labs" (center of screen, blue
  4 KB (767 words) - 13:41, 29 July 2015
• 20.109(F12):Module 2
  ...to improve and extend the performance of the bacterial photography system. In the process we may also learn something new about the natural systems upon ...F12): System engineering research article| Guidelines for research article assignment]]<br>
  4 KB (506 words) - 13:41, 29 July 2015
• 20.109(F12): Mod 2 Day 2 Measuring system performance
  ...e output...then the cells might swim to the light rather than turn a color in response. ...nderstanding of the system we're working with is obviously needed. To look in the black box that senses light, we'll have to learn more about the two com
  22 KB (3,562 words) - 13:41, 29 July 2015
• 20.109(F12): Mod 2 Day 1 Testing an engineered biological system
  ...jects, or exquisitely control responses to the world changing around them. In this experimental module we will consider the possibilities and limitations ...amilies of proteins that behave in predictable ways, both individually and in combination with other protein families and sequence motifs.
  15 KB (2,366 words) - 13:41, 29 July 2015
• 20.109(F12): Mod 2 Day 5 Assessing re-tuned system
  #the β-gal activity of the mutant photography strains grown in the light and dark ...otype but rather there has been some random change in the cell's genome or in the pPCB plasmid that is responsible. As a class, though, we'll hope that t
  8 KB (1,334 words) - 13:41, 29 July 2015
• 20.109(F12): Mod 2 Day 6 Readouts of DNA, Protein
  ... reaction rates. Thus it's important to show that the protein still exists in the cell (at a minimum) and that its expression is about the same as the wi ...that is later probed with an antibody specific to the protein of interest. In our case we will use a polyclonal antibody to detect the EnvZ portion of Cp
  15 KB (2,536 words) - 13:41, 29 July 2015
• 20.109(F12): Mod 2 Day 7 Readout of Protein
  ...ression of the light sensing protein, Cph8, and the mutant versions of it. In general, detection depends on which antibody you choose, and the quality of ...ize one epitope, while other antibodies, called polyclonal antibodies, are in fact antibody pools that recognize multiple epitopes.
  11 KB (1,673 words) - 13:41, 29 July 2015
• 20.109(S13):PCR and paper discussion (Day3)
  ...low concentration compared to the DNA in the sample as a whole, especially in complex mixtures, thus increasing opportunities for non-specific binding. ...it a great non-specific binder of proteins that we will use time and again in 20.109.
  17 KB (2,771 words) - 13:47, 29 July 2015
• 20.109(S13):Initiate cell culture (Day2)
  ... is more similar to that of humans. In this module, we will work with an ''in vitro'' culture model of cartilage-forming cells. ...mple, high molecular weights correlate with increased viscosity. Alginates in general are shear-thinning, which is to say their viscosity decreases as sh
  9 KB (1,562 words) - 13:48, 29 July 2015
• 20.109(S14):16S PCR and paper discussion (Day3)
  ...nt at a low concentration compared to the DNA in the sample as a whole, as in a complex mixture. Note that only engineered polymerases, such as those bou ...it a great non-specific binder of proteins that we will use time and again in 20.109.
  19 KB (3,108 words) - 13:58, 29 July 2015
• 20.109(S14):DNA cloning (Day4)
  ... an antibiotic resistance marker on the backbone, and growing the bacteria in said antibiotic. (We’ll say more about that procedure below.) This method ...uct, and a backbone, such as a commercially available vector, are depicted in black and blue, respectively. These are digested with the same restriction
  15 KB (2,521 words) - 13:58, 29 July 2015
• 20.109(S14):Initiate cell culture (Day2)
  ... is more similar to that of humans. In this module, we will work with an ''in vitro'' culture model of cartilage-forming cells. ...mple, high molecular weights correlate with increased viscosity. Alginates in general are shear-thinning, which is to say their viscosity decreases as sh
  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 ...e stations below: all are fair game, as is the lab safety material covered in the orientation pre-lab lecture.'''</font color>
  28 KB (4,689 words) - 13:59, 29 July 2015
• 20.109(S14):Begin Western protein analysis (Day2)
  ...ll be using during Module 2, and plated a known quantity of each cell type in preparation for protein analysis. Today you will lyse the cells, isolate th ...We'll learn more about the structure of antibodies, and different contexts in which they are used, during Module 3. For now, we'll discuss where they com
  16 KB (2,680 words) - 13:59, 29 July 2015
• 20.109(S14):Complete Western and prepare damaged DNA (Day4)
  ... and cells) our system for investigating NHEJ. In fact, it's quite typical in scientific research that a long development phase is required just to get t ...ty amazing if you think about it! Several of the enzymes that will be used in class are “high fidelity” variants, designed for more specific activity
  17 KB (2,797 words) - 13:59, 29 July 2015
• 20.109(S14):DNA repair assays(Day6)
  ... that cannot pass through viable membranes and thus identifies dead cells. In addition to purification, the flow cytometer can count the number of cells ...trical charge deflects the cell to make it fall into a collection chamber. In FC, each cells is interrogated, and documented as fluorescent or not, but t
  17 KB (2,912 words) - 13:59, 29 July 2015
• 20.109(S14):Testing cell viability (Day3)
  ... to depletion by cells on the outer rim, even when at a high concentration in the bulk fluid. Finally, note that most cells require certain soluble and/o ...r in their cell permeance and nucleic acid affinity. Fluorescence emission in the green and red (left) and red alone (right) channels is shown for the sa
  15 KB (2,507 words) - 13:59, 29 July 2015
• 20.109(F15):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> #Below, be sure to use the pipet specified in each step in order to test the calibration of all three.
  23 KB (3,828 words) - 19:49, 11 September 2015
• 20.109(F15):20.109 Class Blog summary page
  ...ay be used to replace this score. However, no homework bonus will be given in addition, and the maximum of three such assignments still holds. ...receive feedback on your blog posts from your instructors (and anyone else in the class that chooses to comment on the blog). Below are some suggested to
  6 KB (1,007 words) - 13:06, 15 October 2015
• 20.109(F15):Homework
  ...eat the training but you do need to print out your training record to hand in.</b> ...es as you need to complete them; the software keeps track of your progress in the course.
  28 KB (4,514 words) - 20:04, 2 December 2015
• 20.109(S16):20.109 Class Blog summary page
  ...ay be used to replace this score. However, no homework bonus will be given in addition, and the maximum of three such assignments still holds. ...receive feedback on your blog posts from your instructors (and anyone else in the class that chooses to comment on the blog). Below are some suggested to
  6 KB (1,008 words) - 19:24, 28 March 2016
• 20.109(S16):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> #Below, be sure to use the pipet specified in each step in order to test the calibration of all three.
  23 KB (3,828 words) - 13:50, 4 February 2016
• 20.109(S16):Cell preparation for DNA repair assays (Day5)
  ...m NHEJ and will, therefore, be the negative control for your experiments. In your experimental setup today you will transfect M059K cells with damaged p ...to discuss how you will get the reporter DNA into the glioblastoma cells. In Module 1, we used transformation to move DNA into bacterial cells, here we'
  16 KB (2,542 words) - 18:34, 28 March 2016
• 20.109(S16):Homework
  ...eat the training but you do need to print out your training record to hand in.</b> ...es as you need to complete them; the software keeps track of your progress in the course.
  25 KB (3,974 words) - 17:41, 5 May 2016
• 20.109(F16):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> Please paste this section into a word editor, fill in the answers, and leave a print-out copy with your instructor.<br>
  27 KB (4,439 words) - 21:13, 9 September 2016
• 20.109(F16):Homework
  ...urses as many times as you need; the software keeps track of your progress in the course. #*If you have completed EHS training in a UROP or in another lab class, you do not need to repeat the training but you do need t
  21 KB (3,289 words) - 21:26, 30 November 2016
• 20.109(S17):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> Please paste this section into a word editor, fill in the answers, and leave a print-out copy with your instructor.<br>
  24 KB (3,951 words) - 21:35, 31 January 2017
• 20.109(S17):Homework
  ...urses as many times as you need; the software keeps track of your progress in the course. #*If you have completed EHS training in a UROP or in another lab class, you do not need to repeat the training but you do need t
  22 KB (3,470 words) - 18:41, 3 May 2018
• Assignment 3, Part 1: visualizing actin with fluorescence contrast
  This is Part 1 of [[Assignment 3 Overview| Assignment 3]]. [[File: 3T3.PNG|thumb|right|3T3 Swiss Albino cells in phase contrast.]]
  15 KB (2,365 words) - 20:25, 25 February 2020
• 20.109(F17):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> ...get to know each other! Please paste this section into a word editor, fill in the answers, and leave a print-out copy with your instructor.<br>
  24 KB (3,974 words) - 13:25, 14 September 2017
• 20.109(F17):Homework
  ...urses as many times as you need; the software keeps track of your progress in the course. #*If you have completed EHS training in a UROP or in another lab class, you do not need to repeat the training but you do need t
  21 KB (3,308 words) - 19:34, 27 October 2017
• Assignment 1 Overview: Transillumination microscopy
  ... of the items you are expected to turn in are indicated by a pencil symbol in the lab manual. ...ignment Turn In|message =This symbol means that you have to turn something in.}}
  5 KB (825 words) - 17:05, 11 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 2: epi illuminator for fluorescence microscopy
  In this part of the lab, you will use a 5mW, 532 nm laser with focusing optics When you work with lasers, keep these laser safety best practices in mind:
  8 KB (1,447 words) - 14:06, 25 August 2017
• Assignment 7 Overview
  ...ure-dependent equilibrium between single-stranded and double-stranded DNA in solution. Several web-based tools are available to predict melting melting ...e-stranded helicies and single-stranded random coils. The forward reaction in which two complementary, single stranded DNA (ssDNA) molecules combine to f
  13 KB (1,864 words) - 21:49, 3 April 2018
• Assignment 5 Overview
  ==Assignment details == This assignment has 2 parts:
  3 KB (426 words) - 13:34, 23 March 2020
• Assignment 1, Part 4: Measuring magnification and bead size
  ...ieldExampleImages.png|right|thumb|Example images included by past students in their Week 1 report: (top) Air Force target, (center) Silica spheres and du ...ill use to make quantitative measurements of size). Use the measured value in your calculations, not the number printed on the objective.
  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]]. ''[https://www.youtube.com/watch?v=O7oD_oX-Gio You got your ''mens'' in my ''manus.]''
  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]]. ...he concepts of light and lenses, and ends with problems that you will turn in.
  20 KB (3,312 words) - 20:00, 5 September 2019
• Assignment 1, Part 3: Building your transillumination microscope
  [[Category:20.309 assignment 1]] ... that the pores of it were not regular; yet it was not unlike a Honey-comb in these particulars.''
  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]]. * <u>Dish 1</u> will be used to monitor particles in untreated cells, while
  4 KB (742 words) - 18:01, 30 March 2020
• Assignment 5, Part 1: viscosity and diffusivity in glycerol-water mixtures
  This is Part 1 of [[Assignment 5 Overview| Assignment 5]]. ...g|right|thumb|200px|Imaging chamber for fluorescent microspheres diffusing in water:glycerol mixtures]]
  3 KB (542 words) - 17:18, 3 March 2020
• Assignment 7, Part 2: measure temperature and fluorescence
  This is Part 2 of [[Assignment 7 Overview| Assignment 7]]. ''In theory, there is no difference between theory and practice. But, in practice, there is.''
  22 KB (3,650 words) - 17:42, 6 April 2018
• Assignment 3 Overview
  ==Assignment details == This assignment has 2 parts:
  3 KB (377 words) - 14:08, 1 October 2018
• Assignment 3, Part 2: experimental design with fluorescence
  This is Part 2 of [[Assignment 3 Overview| Assignment 3]].<br/> Let's explore fluorescence in contexts beyond your 20.309 specific design.
  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]]. ...The divider circuit comprises two resistors and a voltage source, as shown in the schematic diagram. You will select the values for ''R₁'' and
  27 KB (4,589 words) - 11:31, 15 October 2018
• Assignment 6, Part 3: Identifying unknown filter circuits
  In this part of the lab, you will measure the transfer function of four filter ...een 10 Hz and 1 MHz. You may want to measure choose additional frequencies in transition regions. The transfer function consists of two plots: one that s
  2 KB (330 words) - 17:07, 2 October 2018
• Assignment 9, Part 3: Fitting your data
  ...ng this type of operation many times for many different DNA melting curves in the next couple weeks. It may be helpful to write a function to make this t {{Template:Assignment Turn In|message = <br/>
  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 8 Overview
  ==Assignment details == This assignment has 2 parts:
  4 KB (615 words) - 18:43, 29 January 2018
• 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
  ... This assignment will focus on extracting useful information from the data in order to make some quantitative conclusions. ...fluorescence voltage, ''V_f,measured''(''t''), that you measured in lab depends not only on the parameters of interest, ''&Delta;H<sup>&deg;</s
  6 KB (872 words) - 00:20, 25 January 2018
• Assignment 9, Part 1: model function
  ... are modeling have a nearly uniform temperature. Components that are small in size, have high thermal conductivity, and have low heat transfer coefficien ...rcuit is a first-order, low-pass filter. In this circuit, a step increase in block temperature causes the sample temperature to rise exponentially to a
  12 KB (1,969 words) - 15:29, 14 November 2017
• Assignment 9, Part 2: Simulating DNA melting data and testing the model function
  This is Part 2 of [[Assignment 9 Overview| Assignment 9]]. ...tional form, run the code, then see whether the outputs match what you put in.
  9 KB (1,403 words) - 21:02, 17 April 2018
• Assignment 2 Part 1: Noise in images
  [[Category:20.309 assignment 1]] ... array of tiny solar cells with a bucket underneath each one. (The cameras in the lab have about 400,000 solar cell/buckets, called ''pixels'', which is
  24 KB (3,859 words) - 20:38, 18 February 2020
• Assignment 2 Part 2: Fluorescence microscopy
  [[Category:20.309 assignment 1]] ...e light is conceived into the stone, and is given back after some time, as in childbirth''
  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 ...s. You must attend the safety lecture before you work with high power LEDs in lab. See an instructor if you missed the lecture. Do not begin working with
  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]]. ...you know exactly. The drawback of synthetic images is that they may differ in some important way from the actual images that come out of your microscope.
  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]]. ...th>R</math> of an optical system is the distance between two point sources in the sample plane such that the ''peak'' of one source’s ''image'' falls o
  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]]. ...sing in purely viscous solutions of glycerol-water, and (next week) moving in fibroblast cells after endocytosis.
  10 KB (1,344 words) - 19:58, 28 February 2020
• 20.109(S18):Laboratory tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> Please paste this section into a word editor, fill in the answers, and leave a print-out copy with your instructor.<br>
  26 KB (4,362 words) - 21:39, 6 February 2018
• 20.109(S18):Homework
  ...urses as many times as you need; the software keeps track of your progress in the course. #*If you have completed EHS training in a UROP or in another lab class, you do not need to repeat the training but you do need t
  23 KB (3,594 words) - 18:41, 3 May 2018
• 20.109(F18):Homework
  ...urses as many times as you need; the software keeps track of your progress in the course. #*If you have completed EHS training in a UROP or in another lab class, you do not need to repeat the training but you do need t
  22 KB (3,505 words) - 21:06, 21 August 2019
• 20.109(F18):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> Please paste this section into a word editor, fill in the answers, and leave a print-out copy with your instructor.<br>
  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]]. ...efinitely moving &mdash; albeit on a scale much smaller than the particles in glycerin solutions you measured previously.
  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]]. ...The divider circuit comprises two resistors and a voltage source, as shown in the schematic diagram. You will select the values for ''R₁'' and
  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
  ...ribe, and A. van Oudenaarden, "The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae," Science, vol. 319, no. 5862, pp. 482–484, 2008 ...le-sided tape and then sandwiched between a slab of PDMS and a cover slip. In the new version of the microfluidic device, the PDMS is poured over a 3-D p
  7 KB (1,150 words) - 15:50, 26 March 2020
• Assignment 8, Part 2: build a two-color microscope
  ...we'll be imaging the nuclear response of the Hog1 protein to osmotic shock in ''S. cerevisiae''. To quantify nuclear localization, we will need to locate ...etly using this dual band filter all along. It should already be installed in your microscope.
  4 KB (644 words) - 16:20, 4 November 2019
• Electronics bootcamp II: feedback systems
  In the second part of the boot camp, you will build the circuit below and char [[Image:Third order low-pass filter in feedback.png|center]]
  3 KB (390 words) - 19:08, 1 November 2019
• Assignment 8, Part 3: add flow control and test your device
  ...valves with a lab computer. While we're at it, wouldn't it also be nice to turn on and off your LEDs using a computer signal? A data acquisition or (DAQ) c ...tion if you're interested]. For our purposes, we'll implement a transistor in the following way, where it will act like a voltage controlled switch:
  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]]. ... ones). In this problem you will consider a simple model of the distortion in a patch clamp measurement.
  5 KB (776 words) - 17:26, 23 January 2020
• Assignment 8, Part 0: convolution practice
  ...eful because you can combine functions in table 8.0.2 using the properties in table 8.0.1 to figure out the transforms of an endless number of functions Note: there is an error in the table below. The transform of <math>u(t)</math> is: <math>\frac{1}{2}\l
  2 KB (358 words) - 17:44, 13 October 2022
• Assignment 9 Overview: Analyzing yeast images
  ...10, we'll use this new setup to replicate part of the experiment described in the following paper: ...ribe, and A. van Oudenaarden, "The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae," Science, vol. 319, no. 5862, pp. 482–484, 2008
  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
• Assignment 10, Part 1: Measuring the osmotic shock response of yeast
  Assignment 10 is the culmination of a lot of hard work. You've built a two-color epi-f ...y to do something, try it! Then tell us what you did when you turn in your assignment.
  16 KB (2,644 words) - 21:39, 21 November 2019
• 20.109(S19):Laboratory tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> Please paste this section into a word editor, fill in the answers, and upload your document to Stellar.<br>
  27 KB (4,454 words) - 15:43, 6 February 2019
• 20.109(S19):Homework
  ...urses as many times as you need; the software keeps track of your progress in the course. #*If you have completed EHS training in a UROP or in another lab class, you do not need to repeat the training but you do need t
  24 KB (3,715 words) - 01:02, 30 April 2019
• 20.109(F19):Lab tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> Please paste this section into a word editor, fill in the answers, and upload your document to Stellar.<br>
  27 KB (4,413 words) - 20:37, 30 August 2019
• 20.109(F19):Homework
  ...urses as many times as you need; the software keeps track of your progress in the course. #*If you have completed EHS training in a UROP or in another lab class, you do not need to repeat the training but you do need t
  22 KB (3,438 words) - 17:37, 16 October 2019
• Assignment 6, Part 1: build a two-color microscope
  This is Part 1 of [[Assignment 6 Overview: two color microscope| Assignment 6]]. ...etly using this dual band filter all along. It should already be installed in your microscope.
  3 KB (510 words) - 17:06, 23 January 2020
• Assignment 6, Part 2: electronics written problems
  This is Part 2 of [[Assignment 6 Overview: two color microscope| Assignment 6]]. {{Template:Assignment Turn In|message=
  1 KB (217 words) - 05:20, 5 April 2020
• 20.109(S20):Laboratory tour
  ... these stations - all are fair game, as is the lab safety material covered in today's pre-lab lecture.'''</font color> Before you begin work in the lab, please put on the proper PPE.
  27 KB (4,434 words) - 14:55, 5 February 2020
• 20.109(S20):Homework
  #Before you can conduct experiments in the teaching laboratory you will need to complete the following online trai #*If you have completed EHS training in a UROP or in another lab class, you do not need to repeat the training but will need to
  24 KB (3,726 words) - 16:31, 25 April 2020
• Spring 2020 Assignment 6
  This is Part 2 of [[Assignment 6 Overview: two color microscope| Assignment 6]]. {{Template:Assignment Turn In|message=
  2 KB (263 words) - 19:16, 9 April 2020
• Spring 2020 Assignment 7
  ... ones). In this problem you will consider a simple model of the distortion in a patch clamp measurement. ...ut 100 mV in amplitude and about 1 ms in duration. You can model the noise in the system as a random, additive, normally distributed voltage with a stand
  5 KB (771 words) - 22:50, 14 April 2020
• Spring 2020 Assignment 8
  {{Template:Assignment Turn In|message= File:Thermal System Analogy Problem.png |Thermal system:Coffee in a thermos
  2 KB (355 words) - 19:09, 27 April 2020
• Spring 2020 Assignment 9
  {{Template:Assignment Turn In|message = ...response, and pole zero diagram. (Write one letter A-E in each box below.) In the row labeled “Description,” write a descriptive name of each system,
  11 KB (1,616 words) - 16:42, 30 April 2020
• Spring 2020 assignment 10
  ...FP). It had a 40x objective and a 125 mm tube lens - remember that results in a 25x magnification. ...medium provided to the yeast cells contains a high salt concentration, and in the experiment we oscillate between a high and low salt medium at a fixed r
  8 KB (1,160 words) - 18:43, 26 April 2020
• Spring 2020 Assignment 10
  ...L, and completing it will give you +2 points of extra credit on a previous assignment. ... the [https://www.dropbox.com/sh/33d8t5a7yhhlv77/AAAerwjGLrE_sr6TjaXS764Ga/Assignment%2010?dl=0&subfolder_nav_tracking=1 course dropbox], and load the data into
  4 KB (653 words) - 13:57, 6 May 2020
• 20.109(F20):Lab tour
  ... goal is to familiarize everyone with common techniques and equipment used in scientific research. The Instructors will provide demonstrations for common ...stration in the community who tries to build upon those results. Integrity in citing sources not only gives credit to those who have earned it, but also
  27 KB (4,406 words) - 17:48, 31 August 2020
• 20.109(S21):Laboratory tour
  ... goal is to familiarize everyone with common techniques and equipment used in scientific research. The Instructors will provide demonstrations for common ...stration in the community who tries to build upon those results. Integrity in citing sources not only gives credit to those who have earned it, but also
  28 KB (4,443 words) - 16:02, 16 February 2021
• 20.109(F21):Laboratory tour
  ...tructors will provide demonstrations and other are self-guided. The order in which you complete the stations does not matter. <font color = CC0000>'''T ...stration in the community who tries to build upon those results. Integrity in citing sources not only gives credit to those who have earned it, but also
  34 KB (5,598 words) - 20:50, 9 September 2021
• 20.109(S22):Laboratory tour
  ...tructors will provide demonstrations and other are self-guided. The order in which you complete the stations does not matter. <font color = CC0000>'''T ...stration in the community who tries to build upon those results. Integrity in citing sources not only gives credit to those who have earned it, but also
  34 KB (5,639 words) - 21:02, 1 February 2022
• 20.109(F22):Laboratory tour
  ...tructors will provide demonstrations and other are self-guided. The order in which you complete the stations does not matter. <font color = CC0000>'''T ...stration in the community who tries to build upon those results. Integrity in citing sources not only gives credit to those who have earned it, but also
  34 KB (5,645 words) - 20:34, 8 September 2022
• 20.109(S23):Laboratory tour
  ...tructors will provide demonstrations and other are self-guided. The order in which you complete the stations does not matter. <font color = CC0000>'''T ...stration in the community who tries to build upon those results. Integrity in citing sources not only gives credit to those who have earned it, but also
  34 KB (5,644 words) - 21:01, 8 February 2023