Team:ETHZ Basel/Internal

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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

  • 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

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?

Mathematical Modeling

  • https://2010.igem.org/Team:ETHZ_Basel/Modeling
    • Responsibility: Christoph
    • Proofreading: Moritz
    • Status:
    • ToDo:
    • Suggestions:
      • Christoph: improve language
      • Christoph: first box: E. lemming, these aren't the devices we used for modeling, that is what we model, anchor not necessarily the plasmid
      • Christoph: please rearrange: 1. WHAT complex model set up, consisting of chemotaxis, light, move, implemented and coupled 2. WHY explain support a little bit more
      • 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
    • Proofreading: Simona
    • Status: 60%
    • ToDo:
    • Suggestions:
      • Elsa: link to chemotaxis
      • Moritz: state that models are based on published models and adapted by us.
      • Someone: add picture from chemotaxis pathway
      • Christoph: give an idea about the complexity, e.g. high number of proteins and interactions;
      • Christoph: why did we use only Spiro and Mello?;
      • Christoph: models: text first as it explains the plots;
      • Christoph: please gibe a clearer description of the plots, for an external person it's almost not understandable
      • Sven: Pictures for Spiro-model: It is not clear why the model behaves like this – are there any inputs or why do you have peaks and valleys? Does it describe system behavior in response to something….?? Unclear
      • Sven: Actually true for all the model pictures.
      • Sven: Make sure the reviewer knows at the end of the page which of the two was selected for what!
  • https://2010.igem.org/Team:ETHZ_Basel/Modeling/Experimental_Design
    • Responsibility: George
    • Proofreading: Simona
    • Status: 90%
    • ToDo:
    • Suggestions:
      • Sven: I think the name is misleading – I had no idea what this was about – but this is a great page! Think of a different name? Be sure to link it to all other relevant pages!
      • Sven: Pictures on this page: difficult to read the axes legends!
      • Sven: “Both plots show knicks (especially...” .... what is a “knick”??

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