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Added transcription and epigenetics giants.
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42 changes: 33 additions & 9 deletions content/resource/biochemistrytools.md
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![randyschekman1](/img/randy_cell_enzymes_bag.jpg)

---
## Foudamental techniques
- Western blot
## Foundational techniques

- **Protein quantification**\
[ ] Western blot

- **Protein purification**\
[ ] Purifying Challenging Proteins, Principles and Methods [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ERJk71FTHSNElA3GMam-l3IBX6v_i_oCQeLQLG1Hb6bBiA?e=mAkBNn)]

---
## Vendor companies
Expand All @@ -42,24 +47,43 @@ thumbnailImagePosition: left
#### **Signaling pathway and basic science**
1. [Zhijian-James Chen lab, UTSW](https://www.james-zhijian-chen-lab.org/)\
[ ] **Discovery of cGAS-cGAMP pathway and its role in immune defense**
- Sun, Lijun, et al. "Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway." Science 339.6121 (2013): 786-791. [ [DOI Link](https://www.doi.org/10.1126/science.1232458)]
- Sun, Lijun, et al. "Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway." Science 339.6121 (2013): 786-791. [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EWZWjSjbymdFsI777Dv2EYsBAlzY_hKLXIg1JZQzN8XxeQ?e=y4CBrs) | [PMID: 23258413](https://pubmed.ncbi.nlm.nih.gov/23258413/) | [DOI Link](https://www.doi.org/10.1126/science.1232458)]
- Wu, Jiaxi, et al. "Cyclic GMP-AMP is an endogenous second messenger in innate immune signaling by cytosolic DNA." Science 339.6121 (2013): 826-830. [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EcEtj2d-iKlGuWeCOcAUFisBiju-HRGaphC-v8jjZmznkA?e=SsslUO) | [DOI Link](https://www.doi.org/10.1126/science.1229963)]

2. [David M. Sabatini lab, WIBR, MIT](https://www.davidmsabatini.com/)\
[ ] **The discovery of mTOR**\
Sabatini et al. "RAFT1: a mammalian protein that binds to FKBP12 in a rapamycin-dependent fashion and is homologous to yeast TORs." Cell 78.1 (1994): 35-43. [[PDF]() | [DOI Link](https://doi.org/10.1016/0092-8674(94)90570-3)]\
[ ] Systematic characterzation of basic mechanisms that regulate growth including nutrient sensing pathways. [[CASTOR](https://doi.org/10.1016/j.cell.2016.02.035) | [Sestrin2](https://doi.org/10.1126/science.aad2087) | [SAMTOR](https://doi.org/10.1126/science.aao3265)]



[ ] **The discovery of mTOR**
- Sabatini et al. "RAFT1: a mammalian protein that binds to FKBP12 in a rapamycin-dependent fashion and is homologous to yeast TORs." Cell 78.1 (1994): 35-43. [[PDF]() | [DOI Link](https://doi.org/10.1016/0092-8674(94)90570-3)]\
[ ] **Systematic characterzation of basic mechanisms that regulate growth including nutrient sensing pathways** [[CASTOR](https://doi.org/10.1016/j.cell.2016.02.035) | [Sestrin2](https://doi.org/10.1126/science.aad2087) | [SAMTOR](https://doi.org/10.1126/science.aao3265)]

3. [Xiaodong Wang lab, UTSW, NIBS](http://www.nibs.ac.cn/en/yjsjyimgshow.php?cid=5&sid=6&id=779)\
[ ] The discovery of mitochondria CytoC mediated apoptosis pathway
- Zou, Hua, et al. "Apaf-1, a human protein homologous to C. elegans CED-4, participates in cytochrome c–dependent activation of caspase-3." Cell 90.3 (1997): 405-413.
[[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ERv446uXYcxCuPrmRHgWvgYBgN04_ogoRRKU8jTIB-WTEw?e=JvdhVY) | [PMID: 9267021](https://pubmed.ncbi.nlm.nih.gov/9267021/) | [DOI Link](https://doi.org/10.1016/s0092-8674(00)80501-2)]

4. [Feng Shao lab, NIBS](http://www.nibs.ac.cn/en/yjsjyimgshow.php?cid=5&sid=6&id=777)\
[ ] **The discovery of GSDMD mediated pyroptosis pathway**
- Shi, Jianjin, et al. "Cleavage of GSDMD by inflammatory caspases determines pyroptotic cell death." Nature 526.7575 (2015): 660-665. [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ER85jPeKCyVIj24uQEX75W4BDUoOxtQY5Ap89wOXnDH6pw?e=8pOlMx) | [DOI Link](https://doi.org/10.1038/nature15514)]


#### **Transcriptional regulation and epigenetics**
1. [Robert Tjian, University of California, Berkeley/HHMI](https://www.tjian-darzacq.mcb.berkeley.edu/tjian/)\
[ ] **The discovery of the SV40 large T antigen**
- Tjian, Robert. "The binding site on SV40 DNA for a T antigen-related protein." Cell 13.1 (1978): 165-179. [[PMID: 202398](https://pubmed.ncbi.nlm.nih.gov/202398/) | [DOI Link](https://doi.org/10.1016/0092-8674(78)90147-2)]

2. [Yi Zhang lab, University of North Carolina at Chapel Hill/HMS/HHMI](https://www.zhanglab.tch.harvard.edu/)


3. [Yang Shi lab, HMS/HHMI/University of Oxford](https://www.harvardshilab.org/)\
[ ] **The discovery of first histone demethylase, LSD1**
- Shi, Yujiang, et al. "Histone demethylation mediated by the nuclear amine oxidase homolog LSD1." Cell 119.7 (2004): 941-953. [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EYPS2hk_U1VCm-bMyCGIu-QBg92LUK47Nw4J3vIEapyRCQ?e=EF25wj) | [DOI Link](https://doi.org/10.1016/j.cell.2004.12.012)]


4. [Chuan He lab, University of Chicago/HHMI](https://he-group.uchicago.edu/He%20research.html)\
[ ] **The discovery of first RNA demethylase that oxidatively reverses N6-methyladenosine (m6A) methylation in mammalian messenger RNA**
- Jia, Guifang, et al. "N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO." Nature chemical biology 7.12 (2011): 885-887. [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ETNp772T_4VNnY3909X_7lUB_8CJ36WsacqULe7ApUAzSA?e=QWFN4P) | [DOI Link](https://doi.org/10.1038/nchembio.687)]



#### **Tool development**
1. [Alice Ting lab, Stanford](http://www.tinglab.org/)

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27 changes: 18 additions & 9 deletions content/resource/geneticstools.md
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---
### Ref. public websites
1. [The Jackson Laborary](https://www.jax.org/): The laboratory is also the world's source for more than 8,000 strains of genetically defined mice, and serves as a worldwide center for scientific courses, conferences, training, and education.
2. [Mouse Genome Informatics](http://www.informatics.jax.org/): MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.



---
### Ref Labs
1. [Allen Institute for Brain Research](http://connectivity.brain-map.org/transgenic/):
2. [Susumu Tonegawa Lab](https://tonegawalab.mit.edu/susumu-tonegawa/), MIT
Expand All @@ -126,29 +124,40 @@ Park, Yongmin Mason, et al. "Astrocyte specificity and coverage of hGFAP-CreERT2






---
# Drosophila melanogaster
![seymour_benzer1](/img/Seymour_and_thefly.png)
Seymour Benzer with mega-Drosophila, 1974.



### Ref. Websites
1. [FlyBase](https://flybase.org/): A Database of Drosophila Genes & Genomes

---
# Zebrafish



### Ref. Websites
1. [ZFIN](https://zfin.org/): The Zebrafish Information Network (ZFIN) is the database of genetic and genomic data for the zebrafish (Danio rerio) as a model organism. ZFIN provides a wide array of expertly curated, organized and cross-referenced zebrafish research data.


---
## Nobel laureates
- Sydney Brenner(1927-2019), The Molecular Sciences Institute, Berkeley, CA\
- **Michael W. Young**, Rockefeller University, New York, NY, USA\
Leading pioneer: **Seymour Benzer(1921-2007)**, California Institute of Technology [[Public Interview](https://pkueducn-my.sharepoint.com/:v:/g/personal/lijun0705_pku_edu_cn/ESTLH4bQeIVEobzIprKewX0BtTvgmcitTEOq1JAt_DVJBw?e=peh8MA) | [Read the Interview](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EZVmcpluPh9Pkayf_EYVUugB8Q9QW5Y5qCPsVW00Of3z7w?e=faAcdk)]\
The Nobel Prize in Physiology or Medicine 2017\
**Time Travels: A 40 Year Journey from Drosophila’s Clock Mutants to Human Circadian Disorders** [[Nobel Lecture video](https://www.youtube.com/watch?v=Blm3QwT-rRk&ab_channel=NobelPrize) | [Lecture Slides](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EQ3Lh8WjagRFoiNVbUsIbk0BbkzwPzSe2gswYWApBQQSoA?e=70flib) | [Read the Lecture](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ERsnFw1YSGpKmK-x6I-OcY8B_SnYvmbc9TuU_qTaM_bA4Q?e=GYkHk2) | [Source](https://www.nobelprize.org/prizes/medicine/2017/young/facts/)]

- **Sydney Brenner(1927-2019)**, The Molecular Sciences Institute, Berkeley, CA\
The Nobel Prize in Physiology or Medicine 2002\
**Nature's Gift to Science** [[Nobel Lecture video](https://pkueducn-my.sharepoint.com/:v:/g/personal/lijun0705_pku_edu_cn/Ec3SUiYnkIZAnC5VfbVEuQcBCIB9298kRxmK85J5uhUt0Q?e=Lh7u48) | [Read the Lecture](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ERaf-DRSrGVOkrs3delRx44B9TsHkEVqe2q1iZhgTmUdgg?e=8xBNmp) | [Source](https://www.nobelprize.org/prizes/medicine/2002/brenner/biographical/)]

- Barbara McClintock(1902-1992), Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA\
- **Barbara McClintock(1902-1992)**, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA\
The Nobel Prize in Physiology or Medicine 1983\
**The Significance of Responses of the Genome to Challenge** [[Nobel Lecture video](https://pkueducn-my.sharepoint.com/:v:/g/personal/lijun0705_pku_edu_cn/Ec3SUiYnkIZAnC5VfbVEuQcBCIB9298kRxmK85J5uhUt0Q?e=Lh7u48) | [Read the Lecture](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ERsnFw1YSGpKmK-x6I-OcY8B_SnYvmbc9TuU_qTaM_bA4Q?e=GYkHk2) | [Source](https://www.nobelprize.org/prizes/medicine/1983/mcclintock/facts/)]

- Michael W. Young, Rockefeller University, New York, NY, USA\
Leading pioneer [Seymour Benzer](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EZVmcpluPh9Pkayf_EYVUugB8Q9QW5Y5qCPsVW00Of3z7w?e=faAcdk)\
The Nobel Prize in Physiology or Medicine 2017\
**Time Travels: A 40 Year Journey from Drosophila’s Clock Mutants to Human Circadian Disorders** [[Nobel Lecture video](https://www.youtube.com/watch?v=Blm3QwT-rRk&ab_channel=NobelPrize) | [Lecture Slides](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EQ3Lh8WjagRFoiNVbUsIbk0BbkzwPzSe2gswYWApBQQSoA?e=70flib) | [Read the Lecture](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ERsnFw1YSGpKmK-x6I-OcY8B_SnYvmbc9TuU_qTaM_bA4Q?e=GYkHk2) | [Source](https://www.nobelprize.org/prizes/medicine/2017/young/facts/)]

18 changes: 13 additions & 5 deletions content/resource/molecularbiology.md
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>
---

Brain organ specific: BR1\
Brain organ specific: AAV-BR1[PDF | PMID: | DOI Link]\
Liver specific:

Brain endothelial cell specific: AAV-BI30
Brain endothelial cell specific: AAV-BI30[PDF | PMID: | DOI Link]



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## Ref Labs
1. [Feng Zhang lab, MIT](https://zlab.bio/)
2. [Karl Deisseroth lab, Stanford](https://web.stanford.edu/group/dlab/about_pi.html)
3. [Yulong Li lab, PKU](http://www.yulonglilab.org/)
4. [David Liu lab, Harvard](https://www.liugroup.us/)
2. [David Liu lab, Harvard](https://www.liugroup.us/)
3. [Karl Deisseroth lab, Stanford](https://web.stanford.edu/group/dlab/about_pi.html)
4. [Yulong Li lab, PKU](http://www.yulonglilab.org/)
5. [Jin Zhang lab, UCSD](http://jinzhanglab.ucsd.edu/)

---
## Nobel laureates
Expand All @@ -165,6 +166,13 @@ The Nobel Prize in Chemistry 2008\
The Nobel Prize in Chemistry 2008\
**Constructing and Exploiting the Fluorescent Protein Paintbox** [[Nobel Lecture video](https://pkueducn-my.sharepoint.com/:v:/g/personal/lijun0705_pku_edu_cn/EX_KX-KLPsFBhgk9pOovOzIBqp8mjNiJMFrchuwG72LKxg?e=9C9yCR) | [Lecture Slides](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EbXNqpxXkjpIrhgjOkKCvzAB_K3sN2tHir1mLW5t61ea4w?e=q1npQ2) | [Read the Lecture](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EVZYQT1jreBBrSaWJ-MMmU8Bja7PbbZo16NCLwFhcSoJRg?e=QwVmgh) | [Source](https://www.nobelprize.org/prizes/chemistry/2008/tsien/facts/)]

- Craig C. Mello, University of Massachusetts Medical School, Worcester, MA, USA\
The Nobel Prize in Physiology or Medicine 2006\
**Return to the RNAi World: Rethinking Gene Expression and Evolution** [[Nobel Lecture video](https://pkueducn-my.sharepoint.com/:v:/g/personal/lijun0705_pku_edu_cn/ERJCKx_Rxm5DqAj_FwjVRQoB514JTZqibAK96j2bjrkALg?e=z9fTmu) | [Lecture Slides](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/Eao2Yc7A65xEkWg53nQmKd8B-cRBCjfUSdwCn0yOD2cEZg?e=JcBHKl) | [Read the Lecture](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EXIuNu-X9aFBmESlD6lhERcBVK6IZ-6J-OKB5-nAM0OJfQ?e=ekQ3KO) | [Source](https://www.nobelprize.org/prizes/medicine/2006/mello/facts/)]

- Andrew Z. Fire, Stanford University School of Medicine, Stanford, CA, USA\
The Nobel Prize in Physiology or Medicine 2006\
**Gene Silencing by Double Stranded RNA** [[Nobel Lecture video](https://pkueducn-my.sharepoint.com/:v:/g/personal/lijun0705_pku_edu_cn/ERJCKx_Rxm5DqAj_FwjVRQoB514JTZqibAK96j2bjrkALg?e=z9fTmu) | [Lecture Slides](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/Eao2Yc7A65xEkWg53nQmKd8B-cRBCjfUSdwCn0yOD2cEZg?e=JcBHKl) | [Read the Lecture](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EXIuNu-X9aFBmESlD6lhERcBVK6IZ-6J-OKB5-nAM0OJfQ?e=ekQ3KO) | [Source](https://www.nobelprize.org/prizes/medicine/2006/fire/facts/)]

- Phillip A. Sharp, Massachusetts Institute of Technology (MIT), Center for Cancer Research, Cambridge, MA, USA\
The Nobel Prize in Physiology or Medicine 1993\
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16 changes: 6 additions & 10 deletions public/categories/category/index.html
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Expand Up @@ -365,7 +365,9 @@ <h1 class="postShorten-title">
</div>
<div class="postShorten-excerpt">

Vendor companies Abcam ThermoFisher R&amp;D Systems BioRad Ref Labs Signaling pathway and basic science Zhijian-James Chen lab, UTSW David M. Sabatini lab, MIT Xiaodong Wang lab, UTSW, NIBS Feng Shao lab, NIBS Tool development Alice Ting lab, Stanford Ref. Protocols Bio-protocol Protocol Exchange
<blockquote>
<p>Our cells engage in protein production, and many of those proteins are enzymes responsible for the chemistry of life. &mdash; Randy Schekman</p>
</blockquote>

<p>

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</div>
<div class="postShorten-excerpt">

Fluorescence Proteins -iRFP: miRFPnano670
RFPs: mRuby3, mCherry
GFPs: mGreenLantern, EGFP
BFPs: TagBFP2, TagBFP
Reference FPbase: FPbase is a moderated, user-editable fluorescent protein database designed by microscopists. Tissue/Cell type specific AAVs Brain organ specific: BR1
Liver specific:
Brain endothelial cell specific: AAV-BI30
Tissue/Cell type specific promoter Pan-neuron: hSyn
Kügler, S., E. Kilic, and M. Bähr. &ldquo;Human synapsin 1 gene promoter confers highly neuron-specific long-term transgene expression from an adenoviral vector in the adult rat brain depending on the transduced area.
<blockquote>
<p>Progress in science depends on new techniques, new discoveries and new ideas, probably in that order. &mdash; Sydney Brenner</p>
</blockquote>

<p>

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<pubDate>Thu, 25 Aug 2022 17:16:39 +0800</pubDate>

<guid>https://leoj.xyz/resource/biochemistrytools/</guid>
<description>Vendor companies Abcam ThermoFisher R&amp;amp;D Systems BioRad Ref Labs Signaling pathway and basic science Zhijian-James Chen lab, UTSW David M. Sabatini lab, MIT Xiaodong Wang lab, UTSW, NIBS Feng Shao lab, NIBS Tool development Alice Ting lab, Stanford Ref. Protocols Bio-protocol Protocol Exchange </description>
<description>&lt;blockquote&gt;
&lt;p&gt;Our cells engage in protein production, and many of those proteins are enzymes responsible for the chemistry of life. &amp;mdash; Randy Schekman&lt;/p&gt;
&lt;/blockquote&gt;</description>
</item>

<item>
Expand All @@ -32,15 +34,9 @@ Mouse genetics tools in brain vasculature system field NG2DsRedBAC: NG2DsRedBAC
<pubDate>Sun, 21 Aug 2022 20:27:51 +0800</pubDate>

<guid>https://leoj.xyz/resource/molecularbiology/</guid>
<description>Fluorescence Proteins -iRFP: miRFPnano670
RFPs: mRuby3, mCherry
GFPs: mGreenLantern, EGFP
BFPs: TagBFP2, TagBFP
Reference FPbase: FPbase is a moderated, user-editable fluorescent protein database designed by microscopists. Tissue/Cell type specific AAVs Brain organ specific: BR1
Liver specific:
Brain endothelial cell specific: AAV-BI30
Tissue/Cell type specific promoter Pan-neuron: hSyn
Kügler, S., E. Kilic, and M. Bähr. &amp;ldquo;Human synapsin 1 gene promoter confers highly neuron-specific long-term transgene expression from an adenoviral vector in the adult rat brain depending on the transduced area.</description>
<description>&lt;blockquote&gt;
&lt;p&gt;Progress in science depends on new techniques, new discoveries and new ideas, probably in that order. &amp;mdash; Sydney Brenner&lt;/p&gt;
&lt;/blockquote&gt;</description>
</item>

<item>
Expand Down Expand Up @@ -146,9 +142,8 @@ Samuel Lundt#, Nannan Zhang#, Jun-Liszt Li, Zhe Zhang, Xiaowan Wang, Ruisi Bao,
<pubDate>Mon, 15 Aug 2022 15:15:42 +0800</pubDate>

<guid>https://leoj.xyz/page/about/</guid>
<description>Hello, My name is Jun-Liszt Li. Currently, I am a graduate student in PKU-CIBR joint program of Peking University. I ask questions in the cutting-edge field of brain vasculature system and brain metabolic system, working on Next-generation omics (scRNAseq; Spatial metabolomics) technology, and next-generation microscopy (Lightsheet, Confocal, 2p), in order to understand the fundamental basis of brain metabolism and brain vasculature system.
Interest Areas Biological Question
Brain vasculature system</description>
<description>Hello, My name is Jun-Liszt Li. Currently, I am a graduate student in PKU-CIBR joint program of Peking University. My long-term goal is to discover and characterize basic mechanisms underlying brain aging and neuron growth. In addition, I working on Next-generation omics (scRNAseq; Spatial metabolomics) technology, next-generation microscopy (Lightsheet, Confocal, 2p), and next-generation gene therapy (AAV, promoter) in order to apply these technologies to solve specific problems.
Interest Areas Biological Question</description>
</item>

<item>
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16 changes: 6 additions & 10 deletions public/categories/subcategory/index.html
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Expand Up @@ -365,7 +365,9 @@ <h1 class="postShorten-title">
</div>
<div class="postShorten-excerpt">

Vendor companies Abcam ThermoFisher R&amp;D Systems BioRad Ref Labs Signaling pathway and basic science Zhijian-James Chen lab, UTSW David M. Sabatini lab, MIT Xiaodong Wang lab, UTSW, NIBS Feng Shao lab, NIBS Tool development Alice Ting lab, Stanford Ref. Protocols Bio-protocol Protocol Exchange
<blockquote>
<p>Our cells engage in protein production, and many of those proteins are enzymes responsible for the chemistry of life. &mdash; Randy Schekman</p>
</blockquote>

<p>

Expand Down Expand Up @@ -408,15 +410,9 @@ <h1 class="postShorten-title">
</div>
<div class="postShorten-excerpt">

Fluorescence Proteins -iRFP: miRFPnano670
RFPs: mRuby3, mCherry
GFPs: mGreenLantern, EGFP
BFPs: TagBFP2, TagBFP
Reference FPbase: FPbase is a moderated, user-editable fluorescent protein database designed by microscopists. Tissue/Cell type specific AAVs Brain organ specific: BR1
Liver specific:
Brain endothelial cell specific: AAV-BI30
Tissue/Cell type specific promoter Pan-neuron: hSyn
Kügler, S., E. Kilic, and M. Bähr. &ldquo;Human synapsin 1 gene promoter confers highly neuron-specific long-term transgene expression from an adenoviral vector in the adult rat brain depending on the transduced area.
<blockquote>
<p>Progress in science depends on new techniques, new discoveries and new ideas, probably in that order. &mdash; Sydney Brenner</p>
</blockquote>

<p>

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