Lecture 20 – Observing
Goal:
To understand techniques for obtaining information from the human genome.
Objectives: Students should be able to...
Describe how a SNP chip works and the information obtained from performing a SNP chip.
Define polygenic disease and list examples of polygenic diseases.
Explain how different types of human cells function differently despite the cells having the same DNA.
Describe methods of measuring genome-wide gene expression.
Explain how identifying differences in genome-wide gene expression can be a diagnostic tool.
Outline the experimental steps for determining the genomic loci specific that a protein binds (ChIP-seq)
ChIP-seq, or Chromatin Immunoprecipitation - sequencing.
Obtain cells with estrogen receptor bound to the genome.
Add a chemical that cross-links proteins to DNA.
Randomly cut the DNA.
Add an antibody that specifically recognizes the estrogen receptor protein.
Using one of many biochemical techniques, purify the antibody attached to the estrogen receptor protein with the attached DNA.
Isolate the bound DNA from the protein and sequence the DNA.
Map those sequences to your reference genome sequence to determine their locations.
Lecture 21 – Completing the triangle: Perturbing the genome to probe function
Goals:
To understand how to use the 7.00x triangle that shows how a gene relates to function or protein using biochemistry, genetics, recombinant DNA, and genomics.
To identify how molecular biology and current research tools link genetics and genes to biochemistry and proteins and help to determine the function of genes and proteins.
Objectives: Students should be able to…
Describe how to add an extra copy of a gene to add back a function of a protein.
Explain how to make a transgenic mouse to test the phenotype of a mutation.
Explain how to constitutively knock out a gene by homologous recombination.
Explain how to conditionally knock out a gene with the Cre-lox system.
Describe the mechanism of RNA interference (RNAi) and how RNAi affects gene expression.
Identify the natural function of the RNAi system in eukaryotic cells.
Describe how to use TALEN proteins to regulate gene expression and edit the genome.
Describe how to use CRISPR/Cas9 to edit the genome.
Identify the natural function of the CRISPR/Cas9 system in bacteria.
Choose which genome-altering experimental tool to use to solve a given question.
昨天做PSet之前又把這兩周視頻回顧了一遍，超激動。。題目設(shè)置思路也很好（不行，要劇透的感覺。。過了DDL再來寫好了。。） 2014-08-24
這兩周的內(nèi)容與疾病認(rèn)識的關(guān)聯(lián)性比較大，有為最后的application打基礎(chǔ)的意思，其實內(nèi)容不算很復(fù)雜（如下表），但是整個思路我超愛的。。。。。
雖然個人覺得Lecture18稍有拖沓，但是之后火速恢復(fù)了節(jié)奏。。。
1 mutation-allele-disease
通過強(qiáng)勁的HGP （因為原來的方法太pain才會有那么多人參加人類基因組計劃？Lander君無意間泄露了懶人改變世界的秘密2333），可以測序患者家族Pedigree里的個體，我們就可以知道具體哪個位點的堿基不是跟大眾一樣的了。。。所謂HGP后的美好世界，各種mutation被發(fā)現(xiàn)啊。。。這么多突變，哪個才是致?。ㄔ谀臣易澹┑哪?？
STEP1 根據(jù)突變的位置，堿基改變對編碼蛋白的影響，保守性（能長存的東西還是有價值的，所謂要看名著?。﹣沓醪秸J(rèn)定是不是會consequential也就是會不會致病吧。。。
STEP2 之后就是對雙鏈里每個allele的判斷，所謂upper strand和lower strand，雜合子和純合子，顯性遺傳和隱性遺傳會不一樣的。每個allele里可以有數(shù)個mutation，有的mutation會consequential，有的不會，從而判斷allele的致病性。。。
STEP3 把每個allele對應(yīng)到個人，以分析出致病的突變。。。PSet里給出的表格真的很貼心，很方便做題的。。。（這個DDL之后我可以開心的貼了）
但是，但是。。?！癐n the complex real world of human genetics, sometimes, mutations that appear likely to be consequential turn out not to cause disease while others which appear unlikely to be consequential are found to cause disease.”現(xiàn)實還是復(fù)雜的（哪里有二次元的世界簡單安全。。。）
以上，有思路構(gòu)建的感覺，從Lecture里提到的“HD，雙向”到聯(lián)系里的“Noonan’s syndrome和先天聽力障礙 ”都可以走這條線。。。
2 追尋祖先的歷程
所謂的走出非洲事件。。那個跟尼爾德（特）人有過affair的非洲祖祖祖祖祖祖母的后代是亞裔跟高加索人的共同祖先？ （我怎么看那個非洲同學(xué)的表情都好好笑偶，泥垢了）。。。
關(guān)于自然選擇，個人覺得不是說那么混了就是基因好了-適應(yīng)環(huán)境了-把其他人都PK掉了。。。是后代夠多，活到了現(xiàn)在吧（照這個意思，咱大中華絕對可以是優(yōu)勢人群，都不用鼓勵生育的唉） 。。。不過要是再來個物種滅絕啥的就不好說了。。。。
線粒體是侵入人體細(xì)胞共生的某古早生物，真心推薦香檳校的Emergence of Life。。。從最早的核酸“混居”到各種“共生”，常覺得兩課有印證。。對了，推薦過這倆聯(lián)合的http://mooc.guokr.com/post/608104/ 。。。整個思路會寬很多。。
3 大波Noble prize技術(shù)襲來
【General strategy for gene targeting in mice】
圖片來源http://www.nobelprize.org/nobel_prizes/medicine/laureates/2007/press.html
各種基因?qū)?，基因沉默技術(shù)。。。ES什么的，Lander娓娓道來，然后一句“這個得了某某年諾貝爾獎偶（你們想不到也是可以理解的嗎）”，直接跪了。。
（基因knock in，諾獎）
之前某人跟我吹噓的loxP,Gre什么的也褪去了光環(huán)，明白是怎么回事了，雖說建模什么的還是很不容易的。。。RNAi（諾獎）的發(fā)現(xiàn)故事還是很有趣的，這個技術(shù)還是比較普及的低門檻dirty trick。。。。TALEN和CRSPR之前看文獻(xiàn)的時候見過，沒有細(xì)看，原來也是這樣nice的東東，從植物到“前病毒”，果然各種被鉆空子，各種dll被破解。。。。
PS 這兩周視頻可以直接看唉。。。不過，WEEK 11又掛在YOUTUBE了，翻啊翻啊翻啊翻。。。
