Difference between revisions of "CSB Assignment Week 4"

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Assignments for Week 4
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Assignments for Week 3<br/>
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<span style="font-size: 70%">Collaboration tools, initializing our project.</span>
 
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<td style="height:30px; vertical-align:middle; text-align:left; font-size:80%;">[[CSB_Assignment_Week_3|&lt;&nbsp;Assignment&nbsp;3]]</td>
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<td style="height:30px; vertical-align:middle; text-align:right; font-size:80%;">[[CSB_Assignment_Week_5|Assignment&nbsp;5&nbsp;&gt;]]</td>
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Assigned material - concepts, exercises and reading - will be reflected in next week's evaluation and feedback session. Please remember to contribute to [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/BCB420_self-evaluation_questions '''self-evaluation questions'''] by Tuesday at noon.
  
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Exercises for this week relate to this week's lecture.<br />
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Pre-reading for this week will prepare next week's lecture.<br />
 
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Exercises and pre-reading will be topics on next week's quiz.
 
  
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==Warm up==
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In many London Underground tube stations there are two escalators going up but only one going down.
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'''Why?''' <span class="mw-customtoggle-01" style="background:#F2F2FF;padding:5px;font-size:80%;margin-left:50px">[''I&nbsp;don't&nbsp;know...'']</span>
  
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Seriously?<br />
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Could it have something to do with the required capacity?<br />
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Then just model the expected flow. Is it symmetric?<br />
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If you think so, you might need a hint... <span class="mw-customtoggle-02" style="background:#EAEAFF;padding:5px;font-size:80%;margin-left:50px">[''Ok.&nbsp;A&nbsp;hint&nbsp;please...'']</span>
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When do people arrive at the escalator?<span class="mw-customtoggle-03" style="background:#E2E2FF;padding:5px;font-size:80%;margin-left:50px">[''Sorry.&nbsp;I&nbsp;still&nbsp;don't&nbsp;get&nbsp;it:&nbsp;aren't&nbsp;there&nbsp;as&nbsp;many&nbsp;going&nbsp;down&nbsp;as&nbsp;coming&nbsp;up?'']</span>
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We'll we'd hope that the number of people going down is the same as coming up. If there were twice as many people coming up, they must have been produced in the underground - an army of tube zombies, bred in the tunnels, spreading through town to do their evil deeds...<br/>
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No: the answer has to do with how the streams of passengers distribute over time. Passengers trickle into the station at more or less a constant rate, but when a train arrives, there's a mad scramble by an impatient horde to exit the station, and for that rush the escalators need greater capacity.
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...TBD
  
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==Exercises==
 
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January 30 2014 saw the publication of what may be the most important scientific advance published in our lifetimes. In two ''nature'' papers, Haruko Obokata described the creation of so-called '''STAP''' (stimulus-triggered acquisition of pluripotency) cells. These cells can be generated by simple stress-protocols applied to leukocytes, but also to brain-, skin-, muscle-, fat-, bone marrow, lung- and liver-derived cells. Successful protocols include bathing the cells in moderately acidic medium for half an hour, mechanically perturbing the cells, or inducing plasma cell membrane pores with streptolysin. Post stress, cells shrink, stop proliferating, downregulate their differentiation gene markers and begin expressing markers of pluripotent stem cells that include our friends OCT4, Nanog, and Sox-2, and others. Cell clusters that form after this apparent transformation can be propagated. '''Strikingly, not only are these clusters able to grow into entire embryos after blastocyst injection, and further into normal, adult mice, but these mice are fertile and demonstrate germline transmission of their genetic markers into their offspring.'''
 
January 30 2014 saw the publication of what may be the most important scientific advance published in our lifetimes. In two ''nature'' papers, Haruko Obokata described the creation of so-called '''STAP''' (stimulus-triggered acquisition of pluripotency) cells. These cells can be generated by simple stress-protocols applied to leukocytes, but also to brain-, skin-, muscle-, fat-, bone marrow, lung- and liver-derived cells. Successful protocols include bathing the cells in moderately acidic medium for half an hour, mechanically perturbing the cells, or inducing plasma cell membrane pores with streptolysin. Post stress, cells shrink, stop proliferating, downregulate their differentiation gene markers and begin expressing markers of pluripotent stem cells that include our friends OCT4, Nanog, and Sox-2, and others. Cell clusters that form after this apparent transformation can be propagated. '''Strikingly, not only are these clusters able to grow into entire embryos after blastocyst injection, and further into normal, adult mice, but these mice are fertile and demonstrate germline transmission of their genetic markers into their offspring.'''
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<td style="height:30px; vertical-align:middle; text-align:left; font-size:80%;">[[CSB_Assignment_Week_3|&lt;&nbsp;Assignment&nbsp;3]]</td>
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<td style="height:30px; vertical-align:middle; text-align:right; font-size:80%;">[[CSB_Assignment_Week_5|Assignment&nbsp;5&nbsp;&gt;]]</td>
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[[Category:Computational_Systems_Biology]]
 
[[Category:Computational_Systems_Biology]]
  
 
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Revision as of 17:01, 2 February 2016

Assignments for Week 3
Collaboration tools, initializing our project.

< Assignment 3 Assignment 5 >

Note! This assignment is currently active. All significant changes will be announced on the mailing list.

 
 

Assigned material - concepts, exercises and reading - will be reflected in next week's evaluation and feedback session. Please remember to contribute to self-evaluation questions by Tuesday at noon.


 


 



 

...TBD



 


 
That is all.


 

Footnotes and references

 



 


 
Ask, if things don't work for you!
If anything about the assignment is not clear to you, please ask on the mailing list. You can be certain that others will have had similar problems. Success comes from joining the conversation.
... are required reading.


 



< Assignment 3 Assignment 5 >
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