...ARHGAP35 Rho GTPase activating protein 35 ARHGEF2 Rho/Rac guanine nucleotide exchange factor 2 CCND CCND1...enriched in brain RHO RHOA RHOB RHOC Ras homolog family member ROCK ROCK1 ROCK2 Rho associated coiled-...Neurofibromin 1 NFE2L2 Nuclear factor, erythroid 2 like 2 NFKB1 Nuclear factor of kappa light polypeptide...RAC2 RAC3 Ras-related C3 botulinum toxin substrate (rho family, small GTP binding protein Rac) RAF AFAF BRAF...leucine-rich repeat scaffold protein SOS SOS1 SOS2 SOS Ras/Rho guanine nucleotide exchange factor SPRED SPRED1 SPRED2...enhancer of kinase suppressor of Ras CYTH2 Cytohesin 2 DUSP DUSP1 DUSP2 DUSP3 DUSP4 DUSP5 DUSP6 Dual specificity...transcription factor ECT2 Epithelial cell transforming 2 EGFR Epidermal growth factor receptor EIF4EBP EIF4EBP1...

...fall under two general categories: rho-dependent and rho-independent. Rho factor is a helicase which assists...polymerase in the termination of the transcript. Rho-dependent terminators are not usually employed in...Nearly all common bacterial expression plasmids use Rho-independent terminators, which include naturally ...engineered high-efficiency terminators such as T0. Rho-independent termination is also known as intrinsic...conserved secondary structure and sequence conserved Rho-independent termination annotation for 90 bacterial...structure to induce transcript cleavage, similar to the Rho-independent termination found in prokaryotes. This...Polymerase I uses a process similar to the prokaryotic Rho-dependent mechanism, whereas Polymerase II termination...

....    Figure 2: Opto-RhoGEFs to control Rho GTPase activity. A) Schematic of Opto-RhoGEF design and activity...movement, and more, often driven by Rho family signaling pathways. Rho guanine-nucleotide exchange factors...GEFs ITSN1, TIAM1, or p63RhoGEF (which activate the Rho GTPases Cdc42, Rac1, and RhoA, respectively) using...depending on the specific Rho GTPase/GEF pair (Ridley, 2016). Taking control of a RhoGEF is a great way to stimulate... J. (2023). Opto-RhoGEFs, an optimized optogenetic toolbox to reversibly control Rho GTPase activity on...factors (GEFs) activate their partner Rho GTPase, leading to behaviors like lamellipodia or filopodia formation...membrane-recruitment optogenetic tools for manipulating Rho GTPases based on BcLOV4. These single-component systems...

...target sites for editing. PAM sequences can be from 2-6 base pairs in length and follow the DNA sequence... Eric Perkins Mammalian genomic DNA is not just a 2-D linear molecule snaking through our cells’ nuclei...PubMed PMID: 30166441. MerMAIDs - marine channelrhodopsins for the optogenetic toolbox Article contributed...contributed by Susanna Bachle Anion-conducting channelrhodopsins (ChR) are ion channels that can be used to...

...still depolarize neurons at lower MOIs. Figure 2: ChRgers are delivered by intravenous injection into... shines on excitatory channelrhodopsin-expressing neurons, the channelrhodopsins respond by opening and...deliver channelrhodopsins to the brain. This delivery route concentrates lots of channelrhodopsins in one...since current channelrhodopsins tools have low conductance, but also confines channelrhodopsin activation...conductance compared to current channelrhodopsins. Their new channelrhodopsins, called ChRgers, make the brain...engineering channelrhodopsins There are three main challenges to engineering channelrhodopsins to have improved...to predict if a channelrhodopsin sequence would result in a functional channelrhodopsin, as well as predict...

...immunoglobulin heavy diversity 2-15 D2, IGHD215 IGHD2-2 immunoglobulin heavy diversity 2-2 IGHD22 IGHD2-21 immunoglobulin...heat shock 70kDa protein 2 HSP70-2, HSP70-3 HSPA4 heat shock 70kDa protein 4 APG-2, HS24/P52, MGC131852, ...variable 2-33 (non-functional) IGLV233, V1-9 IGLV2-8 immunoglobulin lambda variable 2-8 IGLV28, V1-2 IGLV3...beta 4 DEFB-2, DEFB102, DEFB2, HBD-2, SAP1 EDN1 endothelin 1 ET1, HDLCQ7 EDN2 endothelin 2 ET2, PPET2 ...receptor subfamily 2, group C, member 1 TR2 NR2C2 nuclear receptor subfamily 2, group C, member 2 TAK1, TR2R1...suppression of tumorigenicity 2 - STC1 stanniocalcin 1 STC STC2 stanniocalcin 2 STC-2, STCRP TAC1 tachykinin,...Rac1 RAC2 ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) EN-7, Gx...

... L. Direct multiplex imaging and optogenetics of Rho GTPases enabled by near-infrared FRET. Nat Chem Biol... iRFP713, % Oligomeric state Photo-stabilityc, t1/2, s pKa Brightness in HeLa cells vs. iRFP713, % d ...blue-light controlled optogenetics, such as channelrhodopsins and tools based on light-oxygen-voltage (LOV...

...of basal H 2 O 2 levels with peroxiredoxin-based probes Real-time monitoring of basal H 2 O 2 levels with...Belousov Hydrogen Peroxide (H 2 O 2 ) Cytosolic or mitochondrial sensor for H 2 O 2 oxidation (roGFP2-Orp1) ...peroxiredoxin-2-based probe. Nat Commun. 2018 Aug 7;9(1):3145. Hadley Sikes Hydrogen Peroxide (H 2 O 2 ) Monitoring...Calcium Red fluorescent calcium sensors (fRCaMP1/2, GECO1/2) The kinetic mechanisms of fast-decay red-fluorescent...intracellular Zn(2+) homeostasis. Nat Methods. 2009 Oct;6(10):737-40. Maarten Merkx Zinc eZinCh-2 Zn2+ FRET ... eZinCh-2: A Versatile, Genetically Encoded FRET Sensor for Cytosolic and Intraorganelle Zn(2+) Imaging...(6):e38591. Sakiko Okumoto Hydrogen Peroxide (H 2 O 2 ) Fluorescent reporter of cytosolic hydrogen peroxide...

...subset of cells under a more specific promoter (e.g. Rho-Cre is expressed in the retina). Fluorescent Cre:...Cre-ERT2 CAG Mammalian Heller 112622 pVHC_PGKneoLox2DTA.2 Venus, Cre-ERT2, targeting vector with MCS for homology...homology arms Mammalian Heller 112623 pEHC_PGKneoLox2DTA.2 Emerald, Cre-ERT2, targeting vector with MCS for homology... arms Mammalian Heller 112624 pmTHC_PGKneoLox2DTA.2 TFP, Cre-ERT2, targeting vector with MCS for homology...arms Mammalian Heller 112625 ptdTHC_PGKneoLox2DTA.2 tdTomato, Cre-ERT2, targeting vector with MCS for ...25;1504(4):467-86. doi:10.1016/0022-2836(81)90375-2. PubMed . Ventura A, Meissner A, Jaenisch R, Jacks...Tamoxifen inducible CAG Mammalian Cepko 13779 pRho-Cre Cre-Myc rhodopsin Mammalian Cepko 13780 pNrl-Cre Cre-Myc...

...as an optogenetic tool is the widely used Channelrhodopsin-2 (ChR2) from Chlamydomonas reinhardtii . ChR2...opsins, such as the Halorhodopsins, Archaerhodopsins and Leptosphaeria rhodopsins, are pumps that can ...cations to flow into the cell. Variants of channelrhodopsin have been engineered or identified to increase...

...AAV vectors for trial purposes in serotypes AAV1, 2, 5, 8, 9 and retrograde Engineered Serotypes Retrograde...DREADDs PSAMs Optogenetics Channelrhodopsins Halorhodopsins Archaerhodopsins Recombinases Cre Flp Dre Biosensors...

... mutations in the gene methyl-CpG binding protein 2 ( MECP2 ). MECP2 Rett syndrome is an X-linked disorder...X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet . 23, 185–188. (Link opens in a new window... Cuddapah et al. 2014. Methyl-CpG-binding protein 2 (MECP2) mutation type is associated with disease severity... Specific mutations in methyl-CpG-binding protein 2 confer different severity in Rett syndrome. Neurology...males with mutations in Methyl-CpG binding protein 2. Am J Med Genet B Neuropsychiatr Genet . 180, 55–67...neurodevelopmental disorder that presents in early toddlerhood primarily affecting females at an incidence of...

...GEVIs (called ASAP 1 and 2), they found an indicator that is optimized for 2-photon imaging of voltages...resultant JEDI-2P sensors overcome many challenges in 2-photon in-vivo imaging of voltage fluctuations. Image...suitable for in vivo optogenetic use.   Fig. 2: A) HcKCR1 is highly selective for K+ over other Na...slice of HcKCR1-EYFP and tdTomato expressed layer 2/3 neurons in mouse. C) Action potential frequencies... of light-gated potassium channelrhodopsins, named Kalium channelrhodopsins (KCRs), from a fungus-like...-2P Novel class of light-gated potassium channelrhodopsins Myc-tag antibody anti-c-Myc [9E10] now available...   Novel class of light-gated potassium channelrhodopsins by: Mike Lacy New work from the labs of Mingshan...

...stimulation         In the video above, Channelrhodopsin 2 (Chr2) has been expressed in the motor cortex... example, the light-gated cation channel, Channelrhodopsin 2 (ChR2), exists in several states: closed/...different steps and materials required for each [1, 2]. This protocol [3] provides, in exquisite detail,...lasers are relatively cheap and will run you about $2-3,000/laser. However, an important caveat is that ...PMID: 21628464; PubMed Central PMCID: PMC3138296. 2. Sparta DR, et al. Construction of implantable optical...board, Jacqueline N Crawley  [et al]. 2012;Chapter 2:Unit2 16. doi: 10.1002/0471142301.ns0216s58. PubMed...coordination by Gi/o protein-coupled vertebrate rhodopsin in cerebellar Purkinje cells. The Journal of biological...

...light-activated tool for controlling neuronal activity, channelrhodopsin-2 (ChR2), a blue light-activated cation channel..., D., Hegemann, P., & Bamberg, E. (2003). Channelrhodopsin-2, a directly light-gated cation-selective ...used in tandem with the opsin.      Figure 2: Diagram of excitatory (ChR2) activation by light ...) domains, phytochrome B (PhyB), and cryptochrome 2 (CRY2) (Zhang & Cui, 2015). When stimulated with light...comparative analysis of microbial opsins. Nature Methods, 9(2), 159–172. https://doi.org/10.1038/nmeth.1808 References...comparative analysis of microbial opsins. Nature Methods, 9(2), 159–172. https://doi.org/10.1038/nmeth.1808 Nagel...intracellular signaling pathways. Trends in Biotechnology, 33(2), 92–100. https://doi.org/10.1016/j.tibtech.2014.11.007...

...PMC3337962. 8. Zhao S, et al. Cell type-specific channelrhodopsin-2 transgenic mice for optogenetic dissection...commonly used in optogenetics: 1) electrophysiology and 2) behavioral experiments. I’m not an electrophysiologist...choice in the brain region you wish to stimulate 2) Fabrication and implantation of the optical fiber...thoroughly elsewhere (here and here for instance) [2], [3]. Karl Deisseroth of Stanford University , one...reviews for a discussion of the different variants [1, 2, 4]. And, of course, the best way to learn about the...monitor expression at various time points (e.g. every 1-2 weeks over 8 weeks) in order to determine the optimal...(4):251-66. doi: 10.1038/nrn3171. PMID: 22430017. 2. Fenno L, et al. The development and application of...

...H134R)-EYFP CaMKII ChR2/H134R EYFP Constitutive 1, 2, 5, 9 Deisseroth 26973 pAAV-hSyn-hChR2(H134R)-EYFP....WPRE.SV40 CAG ChR2/H134R mCherry Constitutive 1, 2, 5, 9 Deisseroth 127090 pAAV-CAG-DIO-ChR2(H134R)-eYFP...optogenetics AAV collection, including channelrhodopsins, halorhodopsins, and more. Viral...

...Currently available from the Kim lab are 2 presynaptic and 2 postsynaptic targeting mGRASP plasmids. Additionally... cells were pulsed with 2µg/ml of Doxycycline for 2 hours, and imaged on the Keyence BZ-9000 fluorescence...work! Robinson et al., Dev Cell 2010 Feb 16;18(2):324-31. Cheeseman et al., J Cell Sci 2013 May 1...promotes the formation of an isopeptide bond between 2 peptide tags, SpyTag and KTag. The group demonstrated... of three sets of cloning vectors (Level 0, 1, or 2) which can be utilized in three successive assembly...1 modules can be similarly assembled into a Level 2 vector, thus forming a functional genetic circuit....circuit. Flexibility has been built into the Level 2 vectors to allow for additional iterations of Level 1 assembly...

...promoter upstream of an opsin gene (e.g., channelrhodopsin-2, ChR2) fused to a reporter gene (e.g., mCherry...Atasoy, Deniz, et al. "A FLEX switch targets Channelrhodopsin-2 to multiple cell types for imaging and long-range...the correct orientation to be transcribed (Figure 2) (Sharma and Zhu, 2014). How does FLEx enable strong... Abdallah, Khaled, et al. "Adeno-associated virus 2/9 delivery of Cre recombinase in mouse primary afferents...Microbial rhodopsins are encoded by opsin genes, and include bacteriorhodopsins, halorhodopsins, and channelrhodopsins... 50 years ago with the discovery of microbial rhodopsins, light-sensitive proteins that absorb photons...light (Zhang et al., 2011). What do microbial rhodopsins and neurons have in common? Neuronal stimulations...

...Gordon Fishell 83899-AAV1 pAAV-mDlx-GCaMP6f-Fishell-2 GCaMP6f expression in forebrain GABA-ergic interneurons...Gordon Fishell 83899-AAV9 pAAV-mDlx-GCaMP6f-Fishell-2 GCaMP6f expression in forebrain GABA-ergic interneurons...Gordon Fishell 83899-AAVrg pAAV-mDlx-GCaMP6f-Fishell-2 GCaMP6f expression in forebrain GABA-ergic interneurons...AAV9 pAAV-hSyn-DIO-ChrimsonR-mRuby2-ST Cation channelrhodopsin ChrimsonR fused to mRuby2 fluorophore and ...pAAV-CAG-DIO-ChroME-ST-P2A-H2B-mRuby3 Cation channelrhodopsin ChroME targeted to the neuronal soma and proximal...