Team:ETHZ Basel/Internal

From 2010.igem.org

(Difference between revisions)
(→Achievements)
(→Mathematical Modeling)
Line 160: Line 160:
** Proofreading: Simona
** Proofreading: Simona
** Status: 80%
** Status: 80%
-
** ToDo:
+
** ToDo:  
 +
***Simona: add one figure about Barkai & Leibler, send George MATLAB files, complete number of Che species for Barkai & Leibler
** Suggestions:
** Suggestions:
***Simona: Evaluation of the model based on this approach was conducted by changing the concentration of the selected Che species according to a series of time steps reflecting light pulses. '''This assumes total removal of the species'''. (unclear, please elaborate with one or two more sentences)
***Simona: Evaluation of the model based on this approach was conducted by changing the concentration of the selected Che species according to a series of time steps reflecting light pulses. '''This assumes total removal of the species'''. (unclear, please elaborate with one or two more sentences)
***Simona: For CheR and Y, the difference in concentration of CheYp drops more than '''Delta (initial value - threshold)''' (unclear, please define the threshold, how it is determined and why it is useful. for an outsider, it is not easily understandable)
***Simona: For CheR and Y, the difference in concentration of CheYp drops more than '''Delta (initial value - threshold)''' (unclear, please define the threshold, how it is determined and why it is useful. for an outsider, it is not easily understandable)
 +
***Simona: rephrased here and there, revert if don't like/don't agree
 +
***Simona: added paragraph on Barkai & Leibler, also added Barkai & Leibler in the parameter table
 +
***Simona: added information that the other two receptor models can be found in the Toolbox as well
 +
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Movement
* https://2010.igem.org/Team:ETHZ_Basel/Modeling/Movement

Revision as of 19:20, 26 October 2010

Internal

This section will be removed before wiki-freeze!

README

  1. Check the teaser and animations until Tuesday, 12.00am. TOP PRIORITY
  2. Embarrassing mistake - some links are not working!! proof readers please check all the links!
  3. Read the general remarks (you can add your own)
  4. Responsibility: Update status of your pages (0% - 100%)
  5. Responsibility: Check suggestions. If you agree and changed the point, remove it!
  6. Responsibility: When your part on a page is finished (or you think so) add a (finished) after your name
  7. Proofreading: Do proofreading of the other sections. When finished, add (finished) after your name
  8. Suggestions: If you have suggestions, enter it in the same way as the other suggestions are written. Gather all information on the page below "Suggestions:".
  9. Problems: If you are not finished by Tuesday, 23.59pm, make status bold.

General remarks

  • OMG there're links that takes u no where!!!
  • Try to use the word E. lemming instead of bacterium or cell, whenever appropriate.
  • Whenever appropriate, mention that the implementation of this particular algorithm is available with the matlab tool box - and give the link
  • Protein names: normally written
  • gene names: italic
  • Directed movement NOT running, please correct!
  • chemotaxis pathway NOT Chemotaxis nor chemotactic
  • E. lemming with space
    • E. lemming vs THE E. lemming: E. lemming: Project name (whole assay), The E. lemming: One single genetically modified E. coli
  • far-red light, not far red light, please correct!
  • internal links - we should refer to other internal pages (hyperlinks) where appropriate, inside the paragraphs.
  • in silico & in vivo, not in-silico & in-vivo
  • ETH Zurich iGEM Team 2010 not ETHZ Basel
  • is E. colis a good plural for E. coli? George: No, use E. coli cells

Teaser & Animations

  • Drafts of teaser & animation text

Responsibilities, Tasks & Suggestions

Introduction

  • https://2010.igem.org/Team:ETHZ_Basel/Introduction/Movie
    • Responsibility: George
    • Proofreading: Elsa
    • Status: 50%
    • ToDo: improve text, add speech
    • Suggestions:
      • Elsa: change background to other color
      • Jörg: add automated microscope image
      • Vincent: make chapters, different effect for highlighting of parts
      • Sven: it is confusing to read the text and watch the movie at the same time. I suggest to “disentangle” this.

Biology & Wet Laboratory

  • https://2010.igem.org/Team:ETHZ_Basel/Biology
    • Responsibility: Elsa
    • Proofreading: Katharina
    • Status:
    • ToDo:
    • Suggestions:
      • Someone: first paragraph, define 'anchor' and 'tumbling' and 'directed movement' before using the terms, second paragraph: quite unclear, if possible, add more details & explain more
      • Someone: add a few sentences (and link them) regarding ARL & Safety
  • https://2010.igem.org/Team:ETHZ_Basel/Biology/Molecular_Mechanism
    • Responsibility: Elsa
    • Proofreading: Sonja
    • Status:
    • ToDo:
    • Suggestions:
      • Sven: There are two mayor types of phytochromes, type.... major / For the design of a light-activated system in Bacteria, one has... bacteria / starting from Haem.... heme phyotochromes in their Prf state in plants can form sequesters in the timescale of seconds.... I don´t know what a “sequester” is – complex? Aggregates? Use another word here
      • Sven: Picture series: Spatial localization in a bacterial cell: Anchor proteins TrigA, MreB and tetR.... TetR / Then in the pictures: it is not clear what is the situation with light and which without – please make clear. Is the “light” word next to the arrows on the right side? Be explicit about “with light” and “without light”
      • Sven: signal transduction (theintracellular concentration.... the intracellular / Watch TrigA, MreB and tetR getting naked!.... TetR
  • https://2010.igem.org/Team:ETHZ_Basel/Biology/Cloning
    • Responsibility: Sonja
    • Proofreading: Elsa
    • Status:
    • ToDo:
    • Suggestions:
      • Sven: I am missing an introductory sentence why we have so many constructs (we did not know which combination.... linker... therefore...)
      • Sven: Also, I am missing a section on the general working of AarI – why is it special.
      • Sven: It would be great to have a “mock”-cloning scheme, so that people can “see” how the strategy with the different ends actually works.
      • Sven: Text below pictures: Those Parts were generated by PCR.... What is “Those”? parts, not Parts
      • Sven: Is “Expression vecotrs” the same as “working vectors”? If so, please reduce to one “name” to avoid confusing. If not, make clear difference.
      • Sven: Picture: From the Brickbox to fusion protein: Text and details in pictrure too small, I could not read it on my (lap top) screen.
      • Sven: Constitutive expression of(the ones the reporter is very convenient as adding an inducer to the selection plates is no longer necessary.... Sentence does not make sense to me.
      • Sven: This gives total freedom of choice for the fusion protein expression system. An existing biobrick - the GFP generator XXXXX - has therefore been investigated and characterized. This is the result: When the GFP generator is introduced into a high copy vector, GFP is expressed in high amounts even in the absence of an inducer (eg IPTG) although its promotor contains a lac operator site. .... I do not understand what the connection between the assembly strategy and the investigation is – please be more specific.
      • Sven: Pictures: general scheme... Text and details in pictrure too small, I could not read it on my (lap top) screen. (Suggestion: not two pictures next to each other, but full page for one picture and then 4 pictures, one below the other.
  • https://2010.igem.org/Team:ETHZ_Basel/Biology/Implementation
    • Responsibility: Sonja
    • Proofreading: Katharina
    • Status:
    • ToDo:
    • Suggestions:
      • Someone: added reference [2]. would be good if a biologist can check if it's the right one. Looks like the page ends abruptly. something like a conclusion perhaps?
      • Sven: Experimental design section: I miss a clearer reference on how this was inspired from the computational part! This is essential because otherwise the reader will not understand why he/she should read the following paragraphs, such as Plasmid copy number
      • Sven: ... the plasmid copy number was determined by the normalization of cell number via optical density measurement followed by plasmid concentration measurements (using a commercial Miniprep kit).
      • Sven: Change to: .... we decided to experimentally verify the estimates from literature. For this, we prepared plasmid DNA from a known number of cells (METHOD?), measured the obtained mount of DNA (Method), and calculated the number of plasmids per cell. The results can be seen in Fig. .....
      • Sven: Figure legend: you have error bars on the columns. Mention how many times you repeated the experiment.
      • Sven: Here in this section, you have the entire reasoning about teO binding sites and whether we need more, like TrigA. Therefore, the heading “plasmid copy number” is misleading. This is more a experimentally validated reasoning of how to implement the requirements about which you learned from modelling. Please make sure that this is transparent form the section-heading
      • Sven: Functionality assays – section
      • Sven: Adopt tense to status of hte project: Were tested? (Results). Will be tested?
  • https://2010.igem.org/Team:ETHZ_Basel/Biology/Archeal_Light_Receptor
    • Responsibility: Elsa
    • Proofreading: Sonja
    • Status:
    • ToDo:
    • Suggestions: Elsa, I added some experimental data. I don't think there need to be more theory, it looks really good. I did not know about the pictures, I would like them to fit to the text, but there is not enough text. Do you think we should remove the Rhodopsin picture? Let me know what you think about this version. And we should adapt the references. Cheers Katharina

Mathematical Modeling

  • https://2010.igem.org/Team:ETHZ_Basel/Modeling
    • Responsibility: Christoph
    • Proofreading: Moritz
    • Status:
    • ToDo:
    • Suggestions:
      • Christoph: improve language
      • Christoph: Model implementation: tab and text order should be equal; implementation and adaption of literature described ones, movement by our own!
      • Christoph: Combined mathematical models: shouldn't light-switch-chemo-movement be the complete?
      • Sven: biology can interwork to gain new... interact?
  • https://2010.igem.org/Team:ETHZ_Basel/Modeling/Light_Switch
    • Responsibility: Moritz
    • Proofreading: Luzi
    • Status:
    • ToDo:
    • Suggestions:
      • Christoph: To model the relocation, we decided to adapt a model recently published by Sorokina et al [1]. As a first step we reimplemented the model as published in the paper." make one good sentence
      • Sven: Sorokina-pictures: Impossible to read what is on the axes… What does RLU stand for?
  • https://2010.igem.org/Team:ETHZ_Basel/Modeling/Chemotaxis
    • Responsibility: George (finished)
    • Proofreading: Simona
    • Status: 80%
    • ToDo:
      • Simona: add one figure about Barkai & Leibler, send George MATLAB files, complete number of Che species for Barkai & Leibler
    • Suggestions:
      • Simona: Evaluation of the model based on this approach was conducted by changing the concentration of the selected Che species according to a series of time steps reflecting light pulses. This assumes total removal of the species. (unclear, please elaborate with one or two more sentences)
      • Simona: For CheR and Y, the difference in concentration of CheYp drops more than Delta (initial value - threshold) (unclear, please define the threshold, how it is determined and why it is useful. for an outsider, it is not easily understandable)
      • Simona: rephrased here and there, revert if don't like/don't agree
      • Simona: added paragraph on Barkai & Leibler, also added Barkai & Leibler in the parameter table
      • Simona: added information that the other two receptor models can be found in the Toolbox as well


Information Processing


Achievements

Team

Retrieved from "http://2010.igem.org/Team:ETHZ_Basel/Internal"