Search results

Create the page "Assignment Turn In" on this wiki!

• 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