2022-09-06-stashed_file_restore

stashed_file_restore and conflict attention.

content/page/research.md

@@ -31,6 +31,10 @@ Metabolism is physiologically fundamental to a biological system. Understanding
 
 **One the road of discovering new metabolic machinery......**
 
+<<<<<<< Updated upstream
+=======
+
+>>>>>>> Stashed changes
 ---
 ## Molecular engineering
 ![5](/img/homepage_aav.jpg)

content/resource/Imagingtools.md

@@ -69,7 +69,8 @@ In this talk, two-photon microscopy-which uses strong pulsed infrared lasers to
 ---
 
 # Light-sheet Microscopy
-![lightsheet001](/img/536fbb_e905706e774b47b19e8802138342a844_mv2.webp)
+![lightsheet001](/img/536fbb_e905706e774b47b19e8802138342a844_mv2.webp)\
+![tlsm002](/img/Dingtalk_20220903141016.jpg)
 
 #### Lab DIY
 Thorlabs: \
@@ -136,17 +137,23 @@ During 20 years of friendship, Betzig and Hess collaborated to create the first
 
 # Electron Microscopy
 
+<<<<<<< Updated upstream
 **Ref labs**: 
 1. [Thomas Reese, National Institutes of Health]() and [John Heuser, Washington University in St. Louis]()
 Thomas Reese studies synaptic structure and function using advanced light and electron microscopy techniques. John Heuser developed and spent his career using quick-freeze, deep-etch electron microscopy to study all aspects of cell biology.\
     - **Imaging Synaptic Vesicle Transmission**: Two pioneering electron microscopists, John Heuser and Tom Reese, reminisce about their early attempts to image synaptic vesicle transmission. (**iBiology interview**, recorded in July 2015: [[Part 1: Imaging synaptic vesicle transmission](https://pkueducn-my.sharepoint.com/:v:/g/personal/lijun0705_pku_edu_cn/EQITWJRLtSFKg5tqfCGYYC0BWzaz7CQK-HwYTtVZLXM9QA?e=I3wBVq) | [Part 2: The Future of Electron Microscopy](https://pkueducn-my.sharepoint.com/:v:/g/personal/lijun0705_pku_edu_cn/EVsGt6E9HN5Cuvfk9zGInF0BCLrcb1P8cZMgwN9UZDU_Xw?e=bm14gg) | [Part 3: Why Collaborate?](https://pkueducn-my.sharepoint.com/:v:/g/personal/lijun0705_pku_edu_cn/ES-O26Hl429Ilc5a9L6KqAUB7F86M2nlDTxsq1KlX6qNqw?e=OcweNL) | [Source](https://www.ibiology.org/neuroscience/imaging-synaptic-vesicle-transmission/#part-1)])
 
+=======
+**Ref labs**: [Thomas Reese Lab, National Institutes of Health]()\
+[John Heuser Lab, Washington University in St. Louis]()\
+>>>>>>> Stashed changes
 
 
 
 # Croy-Electron Microscopy(cryo-EM)
 
 
+<<<<<<< Updated upstream
 **Ref labs**: 
 1. [Yifan Cheng Lab, UCSF](https://cryoem.ucsf.edu/)\
 **Atomic structures of TRPV1**: With David Julius’s laboratory at UCSF\
@@ -163,12 +170,21 @@ Thomas Reese studies synaptic structure and function using advanced light and el
     - Part 6: Single-particle analysis [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EbhLC2uJvGFGhHV2UEnibG0BCTDZaas8XJVuTgZf-MD8vw?e=hgCiGb)]
     - Part 7: 2-D crystallography [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/Edo3stS6v9hCrD7fTZ-Gx-cBHfhmwsP_y9zOurIfAVz3xg?e=iBYBXl)]
 
+=======
+**Ref labs**: [Yifan Cheng Lab, UCSF](https://cryoem.ucsf.edu/)\
+**Atomic structures of TRPV1**: With David Julius’s laboratory at UCSF\
+[Liao, et al. 2016, Nature; Cao et al. 2013 Nature and Gao et al. 2016, Nature]
+>>>>>>> Stashed changes
 
 **Ref softwares**:
 1. **MotionCorr**: This program corrects whole frame image motion recordded with dose fractionated image stack. [MotionCor2](https://emcore.ucsf.edu/ucsf-motioncor2)
     - Xueming Li, Paul Mooney, Shawn Zheng, Chris Booth, Michael B. Braunfeld, Sander Gubbens, David A. Agard and Yifan Cheng (2013) Electron counting and beam-induced motion correction enables near atomic resolution single particle cryoEM. Nature Methods, 10, 584-590. PMID: 23644547 
 2. **GeFREALIGN**: FREALIGN is a program developed by Niko Grigorieff laboratory for high-resolution refinement of 3D reconstruction from cryoEM of single particles. 
+<<<<<<< Updated upstream
     - Xueming Li, Nikolaus Grigorieff and Yifan Cheng (2010) GPU-enabled FREALIGN: Accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors. Journal of Structural Biology, advanced publication online June 14 2010. PMID: 20558298
+=======
+- Xueming Li, Nikolaus Grigorieff and Yifan Cheng (2010) GPU-enabled FREALIGN: Accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors. Journal of Structural Biology, advanced publication online June 14 2010. PMID: 20558298
+>>>>>>> Stashed changes
 
 **Ref database**:
 1. EMDB: https://www.ebi.ac.uk/pdbe/emdb/

content/resource/biochemistrytools.md

@@ -36,6 +36,7 @@ thumbnailImagePosition: left
 
 - **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)]
+<<<<<<< Updated upstream
 
 
 
@@ -50,6 +51,8 @@ thumbnailImagePosition: left
     - Guideline of Cell biology experiment, Part II (In Chinese, 细胞实验指南(下)) [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/Ee5Qbs939yFMvdbCV3iSbD0BdbhidwjLXTkoyxSk9M6TmA?e=fAVeeC)]
     - Gibco Cell Culture Basics Handbook(In Chinese) [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/EViSuQ_uP71Fqy3SHpHozhUBbA1xmaOYom-gIrwEW4-2sQ?e=UfLvlT)]
 
+=======
+>>>>>>> Stashed changes
 
 ---
 ## Vendor companies
@@ -77,9 +80,13 @@ thumbnailImagePosition: left
 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)]
+<<<<<<< Updated upstream
     - **iBiology Talk** [[PartI: Introduction to mTOR and the regulation of growth](https://pkueducn-my.sharepoint.com/:v:/g/personal/lijun0705_pku_edu_cn/Eb3JB4rNE2tMllUhPjex9CgBILDuE3oh47e37JY2pfzBlw?e=sUbxRS)]
 - **Systematic characterization 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)]
     - **iBiology Talks** [[PartII: Regulation of mTORC1 by nutrients](https://pkueducn-my.sharepoint.com/:v:/g/personal/lijun0705_pku_edu_cn/EXIwSNNwJgNAiO7RrVcJgtwBSTARmHylcl-SLXGBUIXDuQ?e=92ZqTV) | [PartIII: Ribophagy and nucleotide recycling](https://pkueducn-my.sharepoint.com/:v:/g/personal/lijun0705_pku_edu_cn/ESKOpuClGHFHn8BlERrknlwBHenie_CticrKRads96R1Mw?e=7d9oQA)]
+=======
+- **Systematic characterization 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)]
+>>>>>>> Stashed changes
 
 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**
@@ -101,25 +108,39 @@ thumbnailImagePosition: left
 
 
 #### **Transcriptional regulation and epigenetics**
+<<<<<<< Updated upstream
 1. [Robert Tjian, University of California, Berkeley/HHMI](https://www.tjian-darzacq.mcb.berkeley.edu/tjian/)
 - **The discovery of the SV40 large T antigen**
+=======
+1. [Robert Tjian, University of California, Berkeley/HHMI](https://www.tjian-darzacq.mcb.berkeley.edu/tjian/)\
+[ ] **The discovery of the SV40 large T antigen**
+>>>>>>> Stashed changes
     - 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/)\
+<<<<<<< Updated upstream
 - **The discovery of first histone demethylase, LSD1** 
+=======
+[ ] **The discovery of first histone demethylase, LSD1** 
+>>>>>>> Stashed changes
     - 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)\
+<<<<<<< Updated upstream
 - **The discovery of first RNA demethylase that oxidatively reverses N6-methyladenosine (m6A) methylation in mammalian messenger RNA**
+=======
+[ ] **The discovery of first RNA demethylase that oxidatively reverses N6-methyladenosine (m6A) methylation in mammalian messenger RNA**
+>>>>>>> Stashed changes
     - 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)]
 
 
 #### **Structural Biology**
+<<<<<<< Updated upstream
 1. [Yigong Shi lab, Princeton University/Tsinghua University/Westlake University](https://ygshi.org/)
 - **Structural basis of pre-mRNA splicing**
 - **Structural basis of Apoptosis (Programmed Cell Death)**
@@ -146,6 +167,23 @@ thumbnailImagePosition: left
 
 <iframe src="//player.bilibili.com/player.html?aid=466289085&bvid=BV1n5411f7jm&cid=503902575&page=1" scrolling="no" border="0" frameborder="yes" framespacing="0" allowfullscreen="true"> </iframe>
 
+=======
+1. [Yigong Shi lab, Princeton University/Tsinghua University/Westlake University](https://ygshi.org/)\
+[ ] **Structural basis of pre-mRNA splicing**\
+[ ] **Structural basis of Apoptosis (Programmed Cell Death)**\
+[ ] **Alzheimer's Disease (AD) and Regulated Intramembrane Proteolysis (RIP)**
+
+3. [Hao Wu lab, Harvard Medical School](https://www.wulab.tch.harvard.edu/)\
+[ ] **The discoverer of signalosomes**, which are large macromolecular complexes involved in cell death and in innate and adaptive immune pathways.
+    - Wu, Hao. "Higher-order assemblies in a new paradigm of signal transduction." Cell 153.2 (2013): 287-292. [[PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/ES4S-RQx0FFEsL1XMYEsweQBeAjiV5qHw0yrYIDRkcZmMQ?e=8L9mMo) | [DOI Link](https://doi.org/10.1016/j.cell.2013.03.013)]
+
+2. [Nieng Yan lab, Tsinghua University/Princeton University](https://scholar.princeton.edu/yanlab)\
+[ ] **Structural basis of Membrane transport**\
+[ ] **Structural and mechanistic investigation of sterol homeostasis**
+
+
+
+>>>>>>> Stashed changes
 
 
 

content/resource/clearingmethod.md

@@ -50,6 +50,7 @@ This webinar will explain tissue clearing, how it functions, and the three main
 ### **HYBRiD**
 1. Nudell, Victoria, et al. "HYBRiD: hydrogel-reinforced DISCO for clearing mammalian bodies." Nature Methods 19.4 (2022): 479-485. [[HYBRiD Protocol](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/Ebg4JFincUFEuKS9YgpUKPMBzZK74iKDo1ZKjsGY7h-YvA?e=metnlq) |  [PDF](https://pkueducn-my.sharepoint.com/:b:/g/personal/lijun0705_pku_edu_cn/Ebq6ijWvJd5JvViypRDJ_MEBIDvp5nk4LBZKgMUlrut8Eg?e=IkTZVR) | [PMID: 35347322](https://pubmed.ncbi.nlm.nih.gov/35347322/) | [DOI Link](https://doi.org/10.1038/s41592-022-01427-0)] 
 
+<<<<<<< Updated upstream
 
 ### **Expansion Microscopy**
 1. Expansion Revealing (ExR)
@@ -72,6 +73,20 @@ Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
 1. [Sigma-Aldrich](https://www.sigmaaldrich.com/US/en): Sigma-Aldrich is an American chemical, life science, and biotechnology company that is owned by the German chemical conglomerate Merck Group. Sigma-Aldrich was created in 1975 by the merger of Sigma Chemical Company and Aldrich Chemical Company.
 2. [Aladdin, 阿拉丁](http://api.aladdin-e.com/)： This company covers reagents and R & D materials in high-end chemistry, life sciences, analytical chromatography and materials science.
 
+=======
+
+### Expansion Microscopy
+
+
+
+---
+### **Ref labs**
+1. Ali Erturk Lab, MIT
+2. Edward Boyden Lab, MIT
+3. Hiroki R Ueda Lab, RIKEN
+4. [Ye Li Lab](https://www.ye-lab.org/team), The Scripps Research Institute
+5. Hu Zhao Lab, CIBR
+>>>>>>> Stashed changes
 
 
 ### Reference

content/resource/massspectrometry.md

@@ -51,17 +51,28 @@ thumbnailImagePosition: left
 
 
 
+<<<<<<< Updated upstream
 ## Vendor companies
 1. [ThermoFisher](https://www.thermofisher.cn/cn/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms.html)
 2. [SCIEX](https://sciex.com/products/mass-spectrometers)
 3. [Agilent](https://www.agilent.com.cn/zh-cn/product/liquid-chromatography)
 4. [Waters](https://www.waters.com/nextgen/us/en/products/columns.html)
 5. [Shimadzu Corporation](https://support.shimadzu.com.cn/an/resource/index.html#105)
+=======
+---
+## Vendor companies
+1. ThermoFisher
+2. SCIEX
+3. Agilent
+
+
+>>>>>>> Stashed changes
 
 
 
 ---
 # MALDI system
+<<<<<<< Updated upstream
 1. MALDI
     - Rapiflex, MALDI-TOF/TOF, Bruker  
     - TimsTOF, Bruker
@@ -71,6 +82,12 @@ thumbnailImagePosition: left
     - MassTech
     - TransMIT
 
+=======
+
+
+
+---
+>>>>>>> Stashed changes
 ## Vendor companies
 1. [Bruker](https://www.bruker.com/en.html)
 2. [MassTech™](https://www.apmaldi.com/main/)
@@ -88,6 +105,7 @@ thumbnailImagePosition: left
 
 
 ### Metabolomics analysis softwares
+<<<<<<< Updated upstream
 1. [MetaboAnalyst](https://www.metaboanalyst.ca/MetaboAnalyst/home.xhtml): v5.0
 2. [MZmine3](http://mzmine.github.io/)
 3. [MS-DIAL](http://prime.psc.riken.jp/compms/msdial/main.html)
@@ -131,3 +149,8 @@ thumbnailImagePosition: left
     Panelists: John A. Bowden, Ben Garcia, Jessica Prenni, Edward Huttlin, Lingjun Li, Rachel Loo, David Geffen, Vicki Wysocki
 
 
+=======
+1. MetaboAnalyst
+2. MZmine3
+3.
+>>>>>>> Stashed changes