2022-08-25_updated

resource updated

content/page/about.md

@@ -101,6 +101,20 @@ Undergraduate Researcher advised by Dr.Gang Cao, Ph.D.
 non-invasive manipulation of neuronal activity.
 - MTB(Mycobacterium tuberculosis) gene overexpression and knockout(CRISPR system)
 
+**HZAU-iGEM team member,**
+Inovation Lab, College of Life science and technology, HZAU\
+FEBRUARY 2015 - OCTOBER 2016\
+2016 HZAU-iGEM team member with instructor Dr.BingGuang Ma, PhD
+- Systems and Synthetic Biology learning: student presentation, case-based learning, and discussion
+- During the Competition and in our project, I am responsible for the Optical control part which uses light switchable circuit (LSC) to control the expression of bacteria movement related gene CheZ.
+- Website of HZAU-iGEM2016: http://2016.igem.org/Team:HZAU-China
+
+2015 HZAU-iGEM team member with instructor Dr.BingGuang Ma, PhD
+- Systems and Synthetic Biology learning: student presentation, case-based learning, and discussion
+- During the Competition and in our project, I am responsible for the interface part. We choose the light and use Optogenetics technique to regulate the synthetic gene oscillator in bacteria.
+- Website of HZAU-iGEM2015: http://2015.igem.org/Team:HZAU-China
+
+
 # Posters & Conferences:
 SEPTEMBER 2015 — PRESENT
 1. Attendee, High-end-Symposium of Metabolomics and exposomics, Dalian 

content/page/publication.md

@@ -22,19 +22,19 @@ showActions:    false
 **✝: corresponding author**
 
 
-1. Lian Liu#, Linzhi Zou#, Kuan Li#, Hanqing Hou, Qun Hu, Shuang Liu, Jie Li, Chenmeng Song, Jiaofeng Chen, Shufeng Wang, Yangzhen Wang, Changri Li, Haibo Du, **Jun-Liszt Li**, Fangyi Chen, Zhigang Xu, Wenzhi Sun, Qianwen Sun, Wei Xiong✝ (2022) Template-independent genome editing in the Pcdh15av−3j mouse, a model of human DFNB23 nonsyndromic deafness. **Cell Reports** [Link](https://www.cell.com/cell-reports/fulltext/S2211-1247(22)00859-2)
+1. Lian Liu#, Linzhi Zou#, Kuan Li#, Hanqing Hou, Qun Hu, Shuang Liu, Jie Li, Chenmeng Song, Jiaofeng Chen, Shufeng Wang, Yangzhen Wang, Changri Li, Haibo Du, **Jun-Liszt Li**, Fangyi Chen, Zhigang Xu, Wenzhi Sun, Qianwen Sun, Wei Xiong✝ (2022) Template-independent genome editing in the Pcdh15av−3j mouse, a model of human DFNB23 nonsyndromic deafness. **Cell Reports** [[DOI Link](https://doi.org/10.1016/j.celrep.2022.111061)]
 
-2. Samuel Lundt#, Nannan Zhang#, **Jun-Liszt Li**, Zhe Zhang, Xiaowan Wang, Ruisi Bao, Feng Cai, Wenzhi Sun, Woo-Ping Ge, Shinghua Ding✝ (2021) NAMPT deletion in project neurons induces bioenergetic stress and activates cell death and inflammatory pathways: **Journal of Cerebral Blood Flow & Metabolism** ([PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EeMdie0AmzVFtF0Ibrj84w8BfCFt-J6ysC9ZgNv4z_yzIA?e=cgKWnC)) [Link](https://journals.sagepub.com/doi/10.1177/0271678X21992625?icid=int.sj-abstract.citing-articles.2)  _**Second author**_
+2. Samuel Lundt#, Nannan Zhang#, **Jun-Liszt Li**, Zhe Zhang, Xiaowan Wang, Ruisi Bao, Feng Cai, Wenzhi Sun, Woo-Ping Ge, Shinghua Ding✝ (2021) NAMPT deletion in project neurons induces bioenergetic stress and activates cell death and inflammatory pathways: **Journal of Cerebral Blood Flow & Metabolism** [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EeMdie0AmzVFtF0Ibrj84w8BfCFt-J6ysC9ZgNv4z_yzIA?e=cgKWnC) |  [DOI Link](https://doi.org/10.1177%2F0271678X21992625)]  _**Second author**_
 
-3. Huanhuan Pang#, **Jun-Liszt Li#**, Xiaoling Hu, Fei Chen, Xiaofei Gao, Lauren Zacharias, Ralph Deberardinis, Wenzhi Sun✝, Zeping Hu✝, Woo-Ping Ge✝ (12/28/2020) Precision mapping of the mouse brain metabolome. **BioRxiv** ([PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EU-xBTRDra9Nq5ii6XGPA1sBb5L2IG1T4OkFt5M27uIAFQ?e=Znk6ct))([Shiny app](https://leoj.shinyapps.io/BSMAv1_updated/)) [Link](https://www.biorxiv.org/content/10.1101/2020.12.28.424544v1.full)  _**Co-first author**_
+3. Huanhuan Pang#, **Jun-Liszt Li#**, Xiaoling Hu, Fei Chen, Xiaofei Gao, Lauren Zacharias, Ralph Deberardinis, Wenzhi Sun✝, Zeping Hu✝, Woo-Ping Ge✝ (12/28/2020) Precision mapping of the mouse brain metabolome. **BioRxiv** [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EU-xBTRDra9Nq5ii6XGPA1sBb5L2IG1T4OkFt5M27uIAFQ?e=Znk6ct) | [Shiny app](https://leoj.shinyapps.io/BSMAv1_updated/) | [Link](https://www.biorxiv.org/content/10.1101/2020.12.28.424544v1.full)]  _**Co-first author**_
 
-4. Lian Liu#, Kuan Li#, Linzhi Zou, Hanqing Hou, Qun Hu, Shuang Liu, Shufeng Wang, Yangzhen Wang, Jie Li, Chenmeng Song, Jiaofeng Chen, Changri Li, Haibo Du, **Jun-Liszt Li**, Fangyi Chen, Zhigang Xu, Wenzhi Sun, Qianwen Sun✝, Wei Xiong✝ (2020) Template-independent genome editing and repairing correct frameshift disease in vivo​. **BioRxiv** [Link](https://www.biorxiv.org/content/10.1101/2020.11.13.381160v1.abstract) 
+4. Lian Liu#, Kuan Li#, Linzhi Zou, Hanqing Hou, Qun Hu, Shuang Liu, Shufeng Wang, Yangzhen Wang, Jie Li, Chenmeng Song, Jiaofeng Chen, Changri Li, Haibo Du, **Jun-Liszt Li**, Fangyi Chen, Zhigang Xu, Wenzhi Sun, Qianwen Sun✝, Wei Xiong✝ (2020) Template-independent genome editing and repairing correct frameshift disease in vivo​. **BioRxiv** [[Link](https://www.biorxiv.org/content/10.1101/2020.11.13.381160v1.abstract)] 
 
-5. Gao X#, **Li JL**, Chen X, Ci B, Chen F, Lu N, Shen B, Zheng L, Jia J, Yi Y, Zhang S, Shi Y, Shi K, Propson NE, Huang Y, Poinsatte K, Zhang Z, Yue Y, Bosco DB, Lu YM, Yang SB, Adams RF, Lindner V, Huang F, Wu LJ, Zheng H, Han F, Hippenmeyer S, Stowe AM, Peng B, Margeta M, Wang X, Liu Q, Korbelin J, Trepel M, Lu H, Zhou BO, Zhao H, Sun W, Bachoo RM, Ge WP✝ (9/15/2020) Reduction of neuronal activity mediated by blood-vessel regression in the brain. **BioRxiv** ([PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/Ea0s6AgGlzBDoblX9nWAbdwBi4bpGu9EKgGhQD86-8ellQ?e=cvfbuL)) [Link](https://www.biorxiv.org/content/10.1101/2020.09.15.262782v1) _**Second author**_
+5. Gao X#, **Li JL**, Chen X, Ci B, Chen F, Lu N, Shen B, Zheng L, Jia J, Yi Y, Zhang S, Shi Y, Shi K, Propson NE, Huang Y, Poinsatte K, Zhang Z, Yue Y, Bosco DB, Lu YM, Yang SB, Adams RF, Lindner V, Huang F, Wu LJ, Zheng H, Han F, Hippenmeyer S, Stowe AM, Peng B, Margeta M, Wang X, Liu Q, Korbelin J, Trepel M, Lu H, Zhou BO, Zhao H, Sun W, Bachoo RM, Ge WP✝ (9/15/2020) Reduction of neuronal activity mediated by blood-vessel regression in the brain. **BioRxiv** [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/Ea0s6AgGlzBDoblX9nWAbdwBi4bpGu9EKgGhQD86-8ellQ?e=cvfbuL) |  [Link](https://www.biorxiv.org/content/10.1101/2020.09.15.262782v1)] _**Second author**_
 
 6. Wentong Hong# , Zhonggan Ren# , Pifang Gong# , **Jun-Liszt Li**. Wenzhi Sun, Woo-PingGe, Chun-Li Zhang, Shumin Duan, Song Qin✝ (2020) Temporal-spatial generation of astrocytes in the developing diencephalon; **J. Neurosci**, under review; _**Second author**_
 
-7. Beal J, Haddock-Angelli T, Gershater M, de Mora K, Lizarazo M, Hollenhorst J, Randy Rettberg✝,**iGEM interlab Study Contributors** (2016) Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli. PLoS 7NE 11(3): e0150182. doiV10.13•1vjournal.pone.0150182 2015 iGEM Interlab Study Contributors: HZAU-China: Pan Chu, **Jun Li(Jun-Liszt Li)**, Keji Yan [Link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150182)
+7. Beal J, Haddock-Angelli T, Gershater M, de Mora K, Lizarazo M, Hollenhorst J, Randy Rettberg✝,**iGEM interlab Study Contributors** (2016) Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli. PLoS 7NE 11(3): e0150182. doiV10.13•1vjournal.pone.0150182 2015 iGEM Interlab Study Contributors: HZAU-China: Pan Chu, **Jun Li(Jun-Liszt Li)**, Keji Yan [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EVM1XjiQzAJOj8TVxIzUkE4BJvN91iF9-FyCBOcOmA4pHw?e=5UQ2De) | [DOI Link](https://doi.org/10.1371/journal.pone.0150182)]
 
 
 # Academic Publications

content/resource/Imagingtools.md

@@ -56,11 +56,18 @@ In this talk, two-photon microscopy-which uses strong pulsed infrared lasers to
 
 #### Lab DIY
 Thorlabs: \
-**Tiling Light-Sheet Microscope(TLSM)**: Liang Gao lab, Westlake University\
-Open-top Light-Sheet Microscopy:\
+**Tiling Light-Sheet Microscopy(TLSM)**: Liang Gao lab, Westlake University\
+**Open-top Light-Sheet Microscopy**: Jonathan T. C. Liu Lab, University of Washington
+- Glaser, Adam K., et al. "A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues." Nature Methods 19.5 (2022): 613-619.
+[[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EWZRt6YMg-FDpu3Y4RThzl4BaRAPnXxKCt2HzW-yC_KiNA?e=skvgl1) |  [Link](https://doi.org/10.1038/s41592-022-01468-5)]
+
 **Axial-Sweeping technology**: Fiolka Reto lab, 
-- Dean, Kevin M., et al. "Deconvolution-free subcellular imaging with axially swept light sheet microscopy." Biophysical journal 108.12 (2015): 2807-2815. ([Link](https://www.cell.com/biophysj/fulltext/S0006-3495(15)00498-1)) ([PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ESykLKp0h4BFnzsJWAcaWFsBtPWYHDmxnvw4WFWgxvRpSQ?e=ujhNPB))
+- Dean, Kevin M., et al. "Deconvolution-free subcellular imaging with axially swept light sheet microscopy." Biophysical journal 108.12 (2015): 2807-2815. [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ESykLKp0h4BFnzsJWAcaWFsBtPWYHDmxnvw4WFWgxvRpSQ?e=ujhNPB) |  [Link](https://www.cell.com/biophysj/fulltext/S0006-3495(15)00498-1)]
+
+**Mesoscale selective plane illumination microscopy(mesoSPIM)**: [Official website](www.mesospim.org)
+- Voigt, Fabian F., et al. "The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue." Nature methods 16.11 (2019): 1105-1108. [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ESykLKp0h4BFnzsJWAcaWFsBtPWYHDmxnvw4WFWgxvRpSQ?e=ujhNPB) |  [Link](https://doi.org/10.1038/s41592-019-0554-0)]
 
+---
 #### Commercial
 Lavision BioTec Inc:
 [UltraMicroscope Light Sheet Microscope](https://www.lavisionbiotec.com/)\

content/resource/biochemistrytools.md

@@ -0,0 +1,42 @@
+---
+title: "Biochemistry tools"
+date: 2022-08-25T17:16:39+08:00
+categories:
+- category
+- subcategory
+tags:
+- PEGASOS
+- CUBIC
+- Clarity
+keywords:
+- tech
+comments:       false
+showMeta:       false
+showActions:    false
+thumbnailImage: /img/MnS-Total-Protein-Prestain-CF680T-BSA-gel.png
+thumbnailImagePosition: left
+#thumbnailImage: //example.com/image.jpg
+---
+
+
+
+
+## Vendor companies
+1. [Abcam](https://www.abcam.com/)
+2. [ThermoFisher](https://www.thermofisher.cn/cn/zh/home/life-science/antibodies/primary-antibodies.html?icid=ab-search-primary-icons)
+3. [R&D Systems](https://www.rndsystems.com/products)
+4. [BioRad](https://www.bio-rad.com/)
+
+
+### Ref Labs
+
+- **Signaling pathway and basic science**
+1. [Zhijian-James Chen lab, UTSW](https://www.james-zhijian-chen-lab.org/)
+
+2. [David M. Sabatini lab, MIT](https://www.davidmsabatini.com/)
+
+3. [Xiaodong Wang lab, UTSW, NIBS](http://www.nibs.ac.cn/en/yjsjyimgshow.php?cid=5&sid=6&id=779)
+
+- **Tool development**
+1. [Alice Ting lab, Stanford](http://www.tinglab.org/)
+

content/resource/clearingmethod.md

@@ -7,7 +7,7 @@ categories:
 tags:
 - PEGASOS
 - CUBIC
-- Clarity
+- ClARITY
 keywords:
 - tech
 comments:       false
@@ -29,17 +29,26 @@ This webinar will explain tissue clearing, how it functions, and the three main
 ---
 
 ### PEGASOS (Using in our lab, recommended):
-1. Jing, Dian, et al. "Tissue clearing of both hard and soft tissue organs with the PEGASOS method." Cell research 28.8 (2018): 803-818. ([Link](https://www.nature.com/articles/s41422-018-0049-z))
-([PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EcRC9PmbyA9BrlgLKSaS3bIB9E8yuXrCHZV1DNa0FvrtzA?e=cCFpYf))
-
-2. **PEGASOSv2**
+1. **PEGASOS version 1:** Jing, Dian, et al. "Tissue clearing of both hard and soft tissue organs with the PEGASOS method." Cell research 28.8 (2018): 803-818. [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EcRC9PmbyA9BrlgLKSaS3bIB9E8yuXrCHZV1DNa0FvrtzA?e=cCFpYf) |  [DOI Link](https://doi.org/10.1038/s41422-018-0049-z)]
 
+2. **TESOS system:** Yi, Yating, et al. "Mapping of individual sensory nerve axons from digits to spinal cord with the Transparent Embedding Solvent System." bioRxiv (2021).
+[[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EcRC9PmbyA9BrlgLKSaS3bIB9E8yuXrCHZV1DNa0FvrtzA?e=cCFpYf) |  [DOI Link](https://doi.org/10.1101/2021.11.13.467610)]
 
 ### CUBIC 
-1. Matsumoto, Katsuhiko, et al. "Advanced CUBIC tissue clearing for whole-organ cell profiling." Nature protocols 14.12 (2019): 3506-3537. ([Link](https://doi.org/10.1038/s41596-019-0240-9)) ([PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EWJ98QI4jH9EilElkpcsP_YBHCZWy2BbVRPylE8RaoM48w?e=1hmNwM))
+1. Matsumoto, Katsuhiko, et al. "Advanced CUBIC tissue clearing for whole-organ cell profiling." Nature protocols 14.12 (2019): 3506-3537. [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EWJ98QI4jH9EilElkpcsP_YBHCZWy2BbVRPylE8RaoM48w?e=1hmNwM) | [DOI Link](https://doi.org/10.1038/s41596-019-0240-9)] 
+
+
+
+### CLARITY
+1. Chung, Kwanghun, et al. "Structural and molecular interrogation of intact biological systems." Nature 497.7449 (2013): 332-337.
+[[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EeRWa1y-2KRAkXVZSb9BWCEBxPE4tILssQiVjyazDavKYw?e=Zz1x8K) | [DOI Link](https://doi.org/10.1038/nature12107)] 
 
 
 ### **Ref labs**
 1. Ali Erturk lab,
 2. Hiroki R Ueda lab, RIKEN
-3. Hu Zhao lab, CIBR
+3. Hu Zhao lab, CIBR
+
+
+### Reference
+1. Vieites-Prado, Alba, and Nicolas Renier. "Tissue clearing and 3D imaging in developmental biology." Development 148.18 (2021): dev199369. [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EXtq7XqWdAVGooPpTW88xVIB1XXXNMJYIeGLrT8l9AUt-w?e=UV26jB) | [DOI Link](https://doi.org/10.1242/dev.199369)]

content/resource/molecularbiology.md

@@ -39,53 +39,80 @@ thumbnailImagePosition: left
 
 
 ## 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
+Excitatory neuron: CaMKIIa
+Inhibitory neuron: pGAD1. mDlx
 
 
+Constitutive expression: EF1a, CAG
 
+Drug induced: Tet-on system
 
-
+activity depedent: c-Fos promoter
 
 
 ## Genetically encoded indicators
 Calcium: GCaMP series (GCaMP8, GCaMP7, GCaMP6)\
 Potassium:
-Dopaine:
+Dopamine:
 Histamine:
 eCB:
 
 
 ## CRISPR systems
+> The CRISPR-Cas system is a natural immune system for prokaryotes. Some bacteria, after being invaded by a virus, can store a small segment of the virus gene in a storage space called CRISPR in their own genome. When a virus invades again, the bacteria can recognize the virus based on the stored fragment and disable it by cutting off the virus' DNA.
+---
 
-- DNA target Cas9 based:
-Knock out: SpCas9, SaCas9
-DNA base editor: dCas9-xxx
+### DNA target Cas9 based
+**Knock out**: SpCas9, SaCas9\
+DNA base editor: dCas9-xxx\
 Transcriptional activator:
 
 
-- RNA target Cas13
-RNA knockdown: Cas13d(RfxCas13d or CasRx, Cas13d from Ruminococcus flavefaciens XPD3002)
+### RNA target Cas13 based
+> Compared to Cas9-mediated DNA editing, Cas13-based RNA editing tools target dynamically transcribed RNA without permanent alteration of the genome, and the effect of RNA editing can be controlled by means of dose adjustment, etc., which is reversible and quite safer.
+---
 
-- DNA base editor
+- RNA knockdown: Cas13d(RfxCas13d or CasRx, Cas13d from Ruminococcus flavefaciens XPD3002) [[DOI Link](https://doi.org/10.1016/j.cell.2018.02.033) | PMID:[29551272](https://pubmed.ncbi.nlm.nih.gov/29551272/)]
+
+
+- RNA base editor: **REPAIR**(RNA Editing for Programmable A to I Replacement, dCas13-ADAR2): Using catalytically inactive Cas13 (dCas13) to direct adenosine-to-inosine deaminase activity by ADAR2. [[DOI Link](https://doi.org/10.1126/science.aaq0180) | PMID:[ 29070703](https://pubmed.ncbi.nlm.nih.gov/29070703/)]
+
+
+### DNA base editor
 
 
 ## Optogenetics tools
 
-Neuronal activity activation: [ChR2]()
+- Neuronal activity activation: 
+ChR2(Channelrhodopsin-2)[hChR2(H134R) | ChR2(C128A/C128S)]
+
+
+- Neuronal activity scilence: NpHR(Halorhodopsin)
 
-Neuronal activity scilence: 
+- Light-activated Cyclases: PAC & Cyclop
 
 
+# Reference
+1. [Resource website of Optogenetics in neuroscience](https://web.stanford.edu/group/dlab/optogenetics/), Karl Deisseroth lab
+2. [Georg Nagel lab, University of Würzburg](https://www.biozentrum.uni-wuerzburg.de/en/bot1/research/prof-dr-georg-nagel/)
+3. [Peter Hegemann lab, Humboldt-University of Berlin](https://www.unisyscat.de/people/current-group-leaders/hegemann-peter.html)
 
 
 ## Open Source & Commercial Softwares

public/archives/index.html

@@ -304,6 +304,10 @@ <h4 class="archive-title" style="text-decoration: none;">2022</h4>
         <ul class="archive-posts archive-month" data-date="202208">
           <h5 class="archive-title" style="text-decoration: none;">August</h5>
 
+            <li class="archive-post archive-day" data-date="20220825">
+              <a class="archive-post-title" href="https://leoj.xyz/resource/biochemistrytools/">Biochemistry tools</a>
+            </li>
+
             <li class="archive-post archive-day" data-date="20220821">
               <a class="archive-post-title" href="https://leoj.xyz/resource/molecularbiology/">Molecular biology tools</a>
             </li>