News and Updates

This month we dive into the world of optogenetically induced condensates and their application possibilities.

Paper of the Month October: Light-induced targeting enables proteomics on endogenous condensates.

Featured Paper: Optogenetic control of condensates: principles and applications.

Job Offer of the Month:

Scientist in Molecular Optogenetics at Prolific Machines

If you have job openings in molecular optogenetics, we will be happy to post them here. Please contact us at hello@optobase.org.

Dear OptoBase Users,

We are excited to announce that OptoBase has undergone a design refresh!
You’ll still find all the information, publications, and your favorite switches - including some brand new switches and tools - right where you expect them.
We hope you enjoy the new look and wish you continued success in your research.

Best regards,
The OptoBase Team

Paper of the Month September: Notch1 Phase Separation Coupled Percolation facilitates target gene expression and enhancer looping.

Featured Paper: OptoAssay—Light-controlled dynamic bioassay using optogenetic switches.

Paper of the Month August: Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag.

Featured Paper: Optogenetic control of kinesin-1, -2, -3 and dynein reveals their specific roles in vesicular transport.

Paper of the Month July: Reshaping tumor microenvironment by regulating local cytokines expression with a portable smart blue-light controlled device.

Featured Paper: A Self-Powered Optogenetic System for Implantable Blood Glucose Control.

Optogenetic switches responding to different wavelengths can be combined to construct multiplexed optogenetic circuits. Such applications can be found on OptoBase using the search term "Multichromatic".

Paper of the Month June: Exploring plant-derived phytochrome chaperone proteins for light-switchable transcriptional regulation in mammals.

Featured Paper: Leveraging the histidine kinase-phosphatase duality to sculpt two-component signaling.

Paper of the Month May: Red-Light-Induced Genetic System for Control of Extracellular Electron Transfer.

Featured Paper: Optogenetics Illuminates Applications in Microbial Engineering.

Paper of the Month April: Spatial organization and functions of Chk1 activation by TopBP1 biomolecular condensates.

Featured Paper: Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells.

New Release in March: An optogenetic method for the controlled release of single molecules.

Featured Paper: NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop.

Paper of the Month February: Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility.

Featured Paper: A platform to induce and mature biomolecular condensates using chemicals and light.

Optogenetics is a powerful technique to manipulate biomolecular condensates. All related publications are tagged with the application "Organelle Manipulation".

Paper of the Month January: Programmable RNA base editing with photoactivatable CRISPR-Cas13.

Featured Paper: Optogenetic control of RNA function and metabolism using engineered light-switchable RNA-binding proteins

Paper of the Month August: Optogenetic clustering and membrane translocation of the BcLOV4 photoreceptor.

Featured Paper: Directly light-regulated binding of RGS-LOV photoreceptors to anionic membrane phospholipids.

Fascinating research in combination with a little bit of fun:

Paper of the Month July: "A biological camera that captures and stores images directly into DNA."

Featured Paper: "Designer Condensates: A Toolkit for the Biomolecular Architect."

Optogenetics is a excellent method to control cell signaling!

Paper of the Month June: An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells.

Featured Paper: Optogenetic manipulation identifies the roles of ERK and AKT dynamics in controlling mouse embryonic stem cell exit from pluripotency.

Paper of the Month May:  Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells.

Featured Paper: How to use optogenetics in engineered living materials (ELMs): Light-Regulated Pro-Angiogenic Engineered Living Materials.

Paper of the Month April: A light-inactivated degron: Controlling protein stability with SULI, a highly sensitive tag for stabilization upon light induction.

Featured Papers: Learn more about light-activated degrons for mammalian cells and yeast.

Paper of the Month March: Optogenetic closed-loop feedback control of the unfolded protein response optimizes protein production.

Featured Paper: Learn more about the optimization of protein/chemical production using optogenetics: Optogenetic regulation of engineered cellular metabolism for microbial chemical production.

Paper of the Month February: Engineering of bidirectional, cyanobacteriochrome-based light-inducible dimers (BICYCL).

Featured Paper: First publication of the switches Am1_c0023g2/BAm_red and Am1_c0023g2/BAm_green.

Paper of the Month December: Rapid and reversible optogenetic silencing of synaptic transmission by clustering of synaptic vesicles.

Featured Paper: Learn more about optogenetic inactivation of proteins with the "LARIAT" tool. 

Paper of the Month November:  Patterned mechanical feedback establishes a global myosin gradient.

Featured Paper: First published application of an optogentic switch in Drosophila: Fast manipulation of cellular cAMP level by light in vivo.

Paper of the Month October:  Optogenetic-controlled immunotherapeutic designer cells for post-surgical cancer immunotherapy.

Featured Paper: Another strategy to use Optogenetics for cancer immunotherapy: Near-Infrared Nano-Optogenetic Activation of Cancer Immunotherapy via Engineered Bacteria.

Paper of the Month September: Spatiotemporal control of ERK pulse frequency coordinates fate decisions during mammary acinar morphogenesis.

Paper of the Month August: Review about Shedding light on current trends in molecular optogenetics.

Featured Paper: Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease, highlighted in the review above.

Paper of the Month July: A new sophisticated illumination device called "LITOS".  Check out other illumination devices in our Materials section.

Featured Paper: Learn more about Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine.

Paper of the Month June: Development of the MagRed (DrBphP/Aff6_V18FΔN) switch: A red light-responsive photoswitch for deep tissue optogenetics.

Featured Paper: First application of the DrBphP switch: Neurotrophin receptor tyrosine kinases regulated with near-infrared light.

Using bioluminescence to activate optogenetic switches and for communication between cells: 

Paper of the Month April: Synthetic cells with self-activating optogenetic proteins communicate with natural cells.

Featured Paper: Cell to Cell Signaling through Light in Artificial Cell Communities: Glowing Predator Lures Prey.

Paper of the Month March: A background paper on PhyB: Plant phytochrome B is an asymmetric dimer with unique signalling potential.

Featured Paper: An "Extracellular Optogenetics" application of PhyB/PIF6: Light-Induced Printing of Protein Structures on Membranes in Vitro.

We constantly adapt optoBase for the latest molecular optogenetic trends. Thus, the new application tag Extracellular optogenetics includes all publications in our database that

• apply photoreceptors in vitro beyond characterization studies and
• systems where photoreceptors are expressed on the outer cell surface.

We hope that this new tag streamlines your search on optoBase and welcome suggestions for future tags. Your optoBase-team

PHYB/PIF-mediated gene transfer. Spatiotemporally confined red light-controlled gene delivery at single-cell resolution using adeno-associated viral vectors.

Paper of the Month November: Two-input protein logic gate for computation in living cells.

Featured Paper: Learn more about logic gates in optogenetics: High-performance chemical- and light-inducible recombinases in mammalian cells and mice.

Paper of the Month October: A light tunable differentiation system for the creation and control of consortia in yeast.

Featured Paper: Learn more about optogenetics in yeast: The rise and shine of yeast optogenetics.

Paper of the Month September: NIR light-responsive bacteria with live bio-glue coatings for precise colonization in the gut.

Featured Paper: Learn more about optogenetics in bacteria: Synthetic Biological Approaches for Optogenetics and Tools for Transcriptional Light-Control in Bacteria.

Paper of the month August: A guide to the optogenetic regulation of endogenous molecules.

Featured Paper: Learn more about RNA editing with the photoactivatable CRISPR-Cas13: Photoactivatable RNA N6-Methyladenosine Editing with CRISPR-Cas13.

• Paper of the Month July: Review on the Clinical Applicability of Optogenetic Gene Regulation.
• Featured Paper: Learn more about optogenetic tools for controlling intracellular signaling. Optogenetic Approaches for the Spatiotemporal Control of Signal Transduction Pathways.
• Try out our search options to include only reviews.

• Paper of the Month June: Development of the red light optogenetic switch iLight. Single-component near-infrared optogenetic systems for gene transcription regulation.
• Featured Paper: Development of another red light optogenetic switch: DrBphP. Neurotrophin receptor tyrosine kinases regulated with near-infrared light.

Paper of the month May: Circularly permuted LOV2 as a modular photoswitch for optogenetic engineering.

Featured Paper: Learn more about optogenetic tools based on LOV domains: LOVTRAP: an optogenetic system for photoinduced protein dissociation.

Paper of the month April: Optogenetic-based Localization of Talin to the Plasma Membrane Promotes Activation of β3 Integrins.

Featured Paper: Optogenetic interrogation of integrin αVβ3 function in endothelial cells. Try out our filter options to search for more integrin research papers.

Paper of the month March: For a broad overview over the field of Molecular Optogenetics: Steering Molecular Activity with Optogenetics: Recent Advances and Perspectives.

Featured Paper: Optogenetics sheds new light on tissue engineering and regenerative medicine.

• Paper of the Month February: Optogenetic manipulation of cellular communication using engineered myosin motors.
• Featured Paper: Development of the blue-light optogenetic switch CRY2olig. An optimized optogenetic clustering tool for probing protein interaction and function.

• Paper of the Month January: Liquid-liquid phase separation of light-inducible transcription factors increases transcription activation in mammalian cells and mice.
• Featured Paper: Learn more about optogenetically-controlled phase separation. Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets.

Research Highlights in December

• Paper of the Month December: Engineering an Optogenetic CRISPRi Platform for Improved Chemical Production.
• Featured Paper: Learn more about optogenetically-controlled chemical production. Optogenetic regulation of engineered cellular metabolism for microbial chemical production.

• Paper of the Month November: Structural insights into the photoactivation of Arabidopsis CRY2.
• Featured Paper: Learn more about the background of CRY2. Structural insights into BIC-mediated inactivation of Arabidopsis cryptochrome 2.

• Paper of the Month October: Orthogonal control of the RAF/ERK and the AKT signaling pathway: Multichromatic Control of Signaling Pathways in Mammalian Cells.
• Featured Paper: Multi-chromatic control of mammalian gene expression and signaling (2013-04). Try out our filter options to search for more multichromatic publications.
  

• Paper of the Month September: Optoribogenetic control of regulatory RNA molecules.
• Featured Paper: The first application of AsLOV2. A genetically encoded photoactivatable Rac controls the motility of living cells.
  

• Paper of the Month August: Development of light-responsive protein binding in the monobody non-immunoglobulin scaffold.
• Featured Paper: Development of the red-light optogenetic switch PhyB/PIF. Spatiotemporal control of cell signalling using a light-switchable protein interaction.

• Paper of the Month July: "optoConfig-96" — A graphical user interface for the optoPlate-96.

• Featured Paper: Optogenetic control of gene expression in plants in the presence of ambient white light.

We are happy to introduce the “Paper of the Month”, which highlights one outstanding research paper of the previous month. Furthermore, the OptoBase team chooses one additional, groundbreaking paper from our extensive, weekly updated database.

• Paper of the Month June: “LAVA” illumination device. Engineered Illumination Devices for Optogenetic Control of Cellular Signaling Dynamics.
• Featured Paper: Development of the blue-light optogenetic switch CRY2/CIBN. Rapid blue-light-mediated induction of protein interactions inliving cells (2010-10).

• Enhanced plant growth by using the light-gated potassium channel BLINK1 based on AsLOV2. "Optogenetic manipulation of stomatal kinetics improves carbon assimilation, water use, and growth."
• Development of a low-cost illumination device for 96 well plates. "High-throughput multicolor optogenetics in microwell plates."
• Elucidating bacterial two-component systems by employing CcaS/CcaR and Cph1. "Rewiring bacterial two-component systems by modular DNA-binding domain swapping."
• Development of the optogenetic switch PAL. "A blue light receptor that mediates RNA binding and translational regulation."
• Optogenetic control of antibodies/nanobodies. "Optogenetic activation of intracellular antibodies for direct modulation of endogenous proteins" and "Optogenetic control of protein binding using light-switchable nanobodies."

Use the new OptoBase syntax option — journal:”name of your journal of interest” — to search for papers by journal name, be it a full name or its ISO abbreviation. Extra tip: use partial queries, such as journal:"ACS" or journal:”Nature”, to retrieve papers from whole journal collections. 

OptoBase has been upgraded with a new tool — Glossary. There you will find brief definitions of various terms and abbreviations commonly used in optogenetics. P.s.: You are most welcome to suggest new terms via our submission form! 

We are proud to announce that the paper presenting OptoBase got last week successfully published in ACS Synthetic Biology. If you refer to OptoBase in your work, please cite it as this publication!

Improve your publication search experience by getting to know our database and learning about the OptoBase-specific syntax, now further explained with a set of helpful examples.

Looking for optogenetic publications presenting a particular type of biological application(s)? The new tool, Find The Application, helps you find them instantly.

A FAQ section was added to improve the OptoBase usability.

Check out our new tool that helps you find the most suitable optogenetic switches for your upcoming project.  

The set of switches with a predefined function was added to complete our collection of optogenetic switches.

Launch Version 1.0