Curated Optogenetic Publication Database

Search precisely and efficiently by using the advantage of the hand-assigned publication tags that allow you to search for papers involving a specific trait, e.g. a particular optogenetic switch or a host organism.

Showing 1 - 5 of 5 results
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Changes in tongue-palatal contact during swallowing in patients with skeletal mandibular prognathism after orthognathic surgery.

near-infrared red BphP1/Q-PAS1 DrBphP HEK293T HeLa Neuro-2a Transgene expression Endogenous gene expression
PLoS ONE, 19 May 2021 DOI: 10.21203/ Link to full text
Abstract: This study aimed to evaluate improvement of tongue-palatal contact patterns during swallowing after orthognathic surgery in mandibular prognathism patients. Thirty patients with mandibular prognathism treated by orthognathic surgery (average age of 27 years, 3 months) and 10 controls (average age 29 years, 6 months) participated in this study. Tongue-palatal contact patterns of patients before and three months after surgery were evaluated by electropalatography (EPG) as well as controls. Whole total of tongue-palatal contact at 0.3, 0.2, and 0.1 sec before complete tongue-palatal contact during swallowing were evaluated. The duration of swallowing phases was also examined. Complete contact of tongue-tip in the alveolar part of individual artificial EPG plate were shown at 0.3, 0.2, and 0.1 sec before complete tongue-palatal contact in the controls, although incomplete contact in the alveolar part were shown at 0.3 sec in mandibular prognathism patients. Whole total of tongue-palatal contact at 0.3 and 0.2 sec before complete tongue-palatal contact was significantly lower in the patients before surgery than in the controls (p<0.05). However, these values increased after surgery. The duration of oral and pharyngeal phase was significantly longer in the patients before surgery than in the controls and the patients after surgery (p<0.01). This study demonstrated that the tongue-palatal contact pattern improved and the duration of oral and pharyngeal phase was shortened in mandibular prognathism patients during swallowing after orthognathic surgery. It is suggested that changes in maxillofacial morphology by orthognathic surgery can induce normal tongue movement during swallowing. (The data underlying this study have been uploaded to figshare and are accessible using the following DOI:

Creating Red Light-Switchable Protein Dimerization Systems as Genetically Encoded Actuators with High Specificity.

near-infrared red BphP1/PpsR2 DrBphP HEK293T HeLa mouse in vivo S. cerevisiae
ACS Synth Biol, 12 Nov 2020 DOI: 10.1021/acssynbio.0c00397 Link to full text
Abstract: Protein dimerization systems controlled by red light with increased tissue penetration depth are a highly needed tool for clinical applications such as cell and gene therapies. However, mammalian applications of existing red light-induced dimerization systems are hampered by limitations of their two components: a photosensory protein (or photoreceptor) which often requires a mammalian exogenous chromophore and a naturally occurring photoreceptor binding protein typically having a complex structure and nonideal binding properties. Here, we introduce an efficient, generalizable method (COMBINES-LID) for creating highly specific, reversible light-induced heterodimerization systems independent of any existing binders to a photoreceptor. It involves a two-step binder screen (phage display and yeast two-hybrid) of a combinatorial nanobody library to obtain binders that selectively engage a light-activated form of a photoswitchable protein or domain not the dark form. Proof-of-principle was provided by engineering nanobody-based, red light-induced dimerization (nanoReD) systems comprising a truncated bacterial phytochrome sensory module using a mammalian endogenous chromophore, biliverdin, and light-form specific nanobodies. Selected nanoReD systems were biochemically characterized, exhibiting low dark activity and high induction specificity, and further demonstrated for the reversible control of protein translocation and activation of gene expression in mice. Overall, COMBINES-LID opens new opportunities for creating genetically encoded actuators for the optical manipulation of biological processes.

Bacterial Phytochrome as a Scaffold for Engineering of Receptor Tyrosine Kinases Controlled with Near-Infrared Light.

red DrBphP HeLa PC6-3 Signaling cascade control
J Mol Biol, 14 Apr 2020 DOI: 10.1016/j.jmb.2020.04.005 Link to full text
Abstract: Optically controlled receptor tyrosine kinases (opto-RTKs) allow regulation of RTK signaling using light. Until recently, the majority of opto-RTKs were activated with blue-green light. Fusing a photosensory core module of Deinococcus radiodurans bacterial phytochrome (DrBphP-PCM) to the kinase domains of neurotrophin receptors resulted in opto-RTKs controlled with light above 650 nm. To expand this engineering approach to RTKs of other families, here we combined the DrBpP-PCM with the cytoplasmic domains of EGFR and FGFR1. The resultant Dr-EGFR and Dr-FGFR1 opto-RTKs are rapidly activated with near-infrared and inactivated with far-red light. The opto-RTKs efficiently trigger ERK1/2, PI3K/Akt, and PLCγ signaling. Absence of spectral crosstalk between the opto-RTKs and green fluorescent protein-based biosensors enables simultaneous Dr-FGFR1 activation and detection of calcium transients. Action mechanism of the DrBphP-PCM-based opto-RTKs is considered using the available RTK structures. DrBphP-PCM represents a versatile scaffold for engineering of opto-RTKs that are reversibly regulated with far-red and near-infrared light.

Revisiting and Redesigning Light-Activated Cyclic-Mononucleotide Phosphodiesterases.

red DrBphP LAPD HEK293 in vitro Immediate control of second messengers
J Mol Biol, 10 Jul 2019 DOI: 10.1016/j.jmb.2019.07.011 Link to full text
Abstract: As diffusible second messengers, cyclic nucleoside monophosphates (cNMPs) relay and amplify molecular signals in myriad cellular pathways. The triggering of downstream physiological responses often requires defined cNMP gradients in time and space, generated through the concerted action of nucleotidyl cyclases and phosphodiesterases (PDEs). In an approach denoted optogenetics, sensory photoreceptors serve as genetically encoded, light-responsive actuators to enable the noninvasive, reversible, and spatiotemporally precise control of manifold cellular processes, including cNMP metabolism. Although nature provides efficient photoactivated nucleotidyl cyclases, light-responsive PDEs are scarce. Through modular recombination of a bacteriophytochrome photosensor and the effector of human PDE2A, we previously generated the light-activated, cNMP-specific PDE LAPD. By pursuing parallel design strategies, we here report a suite of derivative PDEs with enhanced amplitude and reversibility of photoactivation. Opposite to LAPD, far-red light completely reverts prior activation by red light in several PDEs. These improved PDEs thus complement photoactivated nucleotidyl cyclases and extend the sensitivity of optogenetics to red and far-red light. More generally, our study informs future efforts directed at designing bacteriophytochrome photoreceptors.

Neurotrophin receptor tyrosine kinases regulated with near-infrared light.

blue red DrBphP TULIP CHO HeLa mouse in vivo NIH/3T3 PC6-3 SH-SY5Y U-87 MG Signaling cascade control Multichromatic
Nat Commun, 8 Mar 2019 DOI: 10.1038/s41467-019-08988-3 Link to full text
Abstract: Optical control over the activity of receptor tyrosine kinases (RTKs) provides an efficient way to reversibly and non-invasively map their functions. We combined catalytic domains of Trk (tropomyosin receptor kinase) family of RTKs, naturally activated by neurotrophins, with photosensory core module of DrBphP bacterial phytochrome to develop opto-kinases, termed Dr-TrkA and Dr-TrkB, reversibly switchable on and off with near-infrared and far-red light. We validated Dr-Trk ability to reversibly light-control several RTK pathways, calcium level, and demonstrated that their activation triggers canonical Trk signaling. Dr-TrkA induced apoptosis in neuroblastoma and glioblastoma, but not in other cell types. Absence of spectral crosstalk between Dr-Trks and blue-light-activatable LOV-domain-based translocation system enabled intracellular targeting of Dr-TrkA independently of its activation, additionally modulating Trk signaling. Dr-Trks have several superior characteristics that make them the opto-kinases of choice for regulation of RTK signaling: high activation range, fast and reversible photoswitching, and multiplexing with visible-light-controllable optogenetic tools.
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