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Final five topic for brainstomring

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Posted at 2014-2-27 23:38:15 | All floors |Read mode
Last edited by zhiyuanli In 2014-2-28 01:02 Editor

Dear all,

After some intense discussion, the voted five topics and their PKU participants are:

Tingting Li@ltt ,  Jian Shu@偶尔的小愤青: Multiple cell fates landscape: how do cell choose fates during development and differentiation
this topic links to these posts: http://cqb.pku.edu.cn/bbs/forum. ... =206&extra=page%3D1, http://cqb.pku.edu.cn/bbs/forum. ... =208&extra=page%3D1

Shuobing Chen@robinbin ,  Jiajia Yuan@jyuan: Use systems biology to interpret Traditional Chinese Medicine: What is "jingluo"
relating to these posts: http://cqb.pku.edu.cn/bbs/forum. ... =187&extra=page%3D1http://cqb.pku.edu.cn/bbs/forum. ... =181&extra=page%3D1

Huanjie Sheng @david190810  , Yaofang Xu @FishHead: Synthetic analysis of leadership in biological systems
relating to these posts:http://cqb.pku.edu.cn/bbs/forum. ... =231&extra=page%3D1

Jiawei Yan @Jiawei , Shanshan Qin: How cell measures during regeneration

Zhiyuan Li @zhiyuanli, Yifei Cai @faychoi: Transmissible tumor and epidemic evolution: how to train tumor cell to be nicer
relating links: http://cqb.pku.edu.cn/bbs/forum.php?mod=viewthread&tid=237

a backup topic is:Complex network simplification and structure inferrence by a few tests

Let's roll~

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Posted at 2014-2-28 09:03:04 | All floors
Huanjie Sheng @david190810  , Yaofang Xu @FishHead: Synthetic analysis of leadership in biological systems
relating to these posts:http://cqb.pku.edu.cn/bbs/forum. ... =231&extra=page%3D1

In a heterogenous group of individuals, the role of leader is critical to the behavior of the whole group and each group member.  By Cellular Automaton and Synthetic Biology, it is possible to simulate the interaction of leaders and trailers and the dynamic process of their actions at different scales both experimentally and theoretically.  The study of schools of fish and neural crest cells are serving as examples of the leadership in biological systems.
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 Author| Posted at 2014-2-28 01:08:01 | All floors
Hi, I'm glad to play the transmissible tumor project. A summary of the idea is: one kinds of dog tumor can directly transmit between individuals. It has been persisted for 10k years and become much less lethal than normal tumors. We want to use all kinds of method to understand the cellular pathways that enables the “nicer” behavior of transmissible tumor cells.
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Posted at 2014-2-28 22:11:49 | All floors
Hi~ Our project is about how cell measures during regeneration process. Here's our idea:

The location information is one of the most significant information for development. In most developmental process, most cells reach their right positions then differentiate, such as in Drosophila segmentation and fingers' development. However, the regeneration process is fundamentally different from development. Regeneration is like building a house when each brick is piled on the top, it knows exactly what role it will play. So there may be another strategy for cell to make decision in the  regeneration process other than development, which is what we want to ask.

Besides, we are also interested in whether there are some general methods for cell to sense its spacial location, and how the whole structure information is coded in an organ development or regeneration.

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Posted at 2014-3-9 10:38:01 | All floors
Last edited by ltt In 2014-3-9 10:43 Editor

We kown that during development process there are two common conditions:
1、One mother cell divides into two daughter cells that differentaite into two distinct fates
2、One mother cell divides into two daughter cells, after that, one daughter cell differentiate while another remains to be a undifferentiated cell.

what are we interested in is among various development process(such as embryonic stem cell differentiation,tissue stem cell differentiation...etc), which belong to the case 1?which belong to the case 2? Is there any intrinsic law within the two cases? Can we simulate these two differentiation types in silico or in experiment?


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Posted at 2014-3-9 11:46:07 | All floors
Our project wants using systematic approach to understand Traditional Chinese Medicine. In TCM theory, patient is viewed as a system with different statuses, and it has many theory about "Yingyang", "Wuxing" to describe the physical state. Expect for the pharmacology of TCM, witch aways using the mixture of natural medicine, acupuncture and moxibustion also popular in traditional treatment. This treatment is based on the jingluo and acupoint theory. Many methods, such as IR or NMR, have been used to distinguish the acupoint,  however it is difficult to find the solid evidence to proof the existing of jingluo  and acupoint.
Here we want to use the view of development to understand the relationship of different acupoints, and the view of network to understand the function of acupionts.

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 Author| Posted at 2014-3-10 09:27:58 | All floors
robinbin Posted at 2014-3-9 11:46
Our project wants using systematic approach to understand Traditional Chinese Medicine. In TCM theor ...

This is by far my favorate topic
I don't believe in fire breathing dragon, but some special points in jingmai  is something I can really fell -- when putting pressures on these spots, it feels more sore numb than nearby areas. Muscule feels easier after massaging these special spoints.

Till now, no solid explanation about what these special points are. I don't care if stimulating these points have health benefits. I'm just curious on what they are.

http://en.wikipedia.org/wiki/Meridian_%28Chinese_medicine%29


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Posted at 2014-3-13 15:16:05 | All floors
ltt Posted at 2014-3-9 10:38
We kown that during development process there are two common conditions:
1、One mother cell divides ...

I don't know of any other work, but i heard this guy talk about his, maybe the references from this paper can help find more relevant stuff:
http://www.weizmann.ac.il/weizsi ... ypt_optimality1.pdf

Alon (HUJI)

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Posted at 2014-3-13 15:20:34 | All floors
david190810 Posted at 2014-2-28 09:03
Huanjie Sheng @david190810  , Yaofang Xu @FishHead: Synthetic analysis of leadership in biological s ...

I have no background in this at all, but cell-2-cell communication is a facsinating topic (in the context of leadership, or otherwise). Specifically, i think it would be nice to think of experimental systems that can simulate "real" communication networks with cell, and then measure information output somehow, compare it with real information flow, etc. I have no idea, but i would think that a distributed system model is more appropriate than a hierarchial model, isn't it?

Alon (HUJI)

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 Author| Posted at 2014-3-13 18:50:47 | All floors
alonapple Posted at 2014-3-13 15:20
I have no background in this at all, but cell-2-cell communication is a facsinating topic (in the  ...

For simulating signals for cell, I remember an interesting talk in this qbio from Allyson Sgro in Princeton about the collective movement of discoideum. They used microfluidics to measure the I/O of single discoideum in detail, especially the excitable oscillator of cAMP, then put the measured single-cell parameter into the population model and get nice predictions.
If I remembered correctly, she mentioned that in their observed collective motion of discoideum, there is no “pacemakers” for the spreading waves of cAMP in the population – in other words, no “leader”.
I’m very curious on how did they found it out. Are there some dynamic signatures about “pace makers” one can identify in the collective oscillatory behavior of cell populations?

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Posted at 2014-3-14 20:46:42 | All floors
alonapple Posted at 2014-3-13 15:16
I don't know of any other work, but i heard this guy talk about his, maybe the references from thi ...

THX~It is really helpful!

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Posted at 2014-3-15 13:08:47 | All floors
alonapple Posted at 2014-3-13 15:20
I have no background in this at all, but cell-2-cell communication is a facsinating topic (in the  ...

neural crest cell is one of the most studied example of cell-cell communication, and immunology could be another one.
I am not very familiar with this topic but when I had the interview with PIs in Stowers Institute and Rice U, we came up with this interesting ideas.

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