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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