Genetically encoded epigenetic sensors for visualization of H3K9me3, H3K9ac and H3K4me1 histone modifications in living cells.

Post-translational modifications of histones play a crucial role in chromatin structure maintenance and epigenetic regulation. The LiveMIEL (Live-cell Microscopic Imaging of Epigenetic Landscape) method represents a promising approach for tracking histone modifications. It involves visualization of epigenetic modifications using genetically encoded fluorescent sensors and further analysis of the obtained intranuclear patterns by multiparametric image analysis.

Tracking induced pluripotent stem cell differentiation with a fluorescent genetically encoded epigenetic probe.

Epigenetic modifications (methylation, acetylation, etc.) of core histones play a key role in regulation of gene expression. Thus, the epigenome changes strongly during various biological processes such as cell differentiation and dedifferentiation.

An improved pathway for autonomous bioluminescence imaging in eukaryotes.

The discovery of the bioluminescence pathway in the fungus Neonothopanus nambi enabled engineering of eukaryotes with self-sustained luminescence. However, the brightness of luminescence in heterologous hosts was limited by performance of the native fungal enzymes. Here we report optimized versions of the pathway that enhance bioluminescence by one to two orders of magnitude in plant, fungal and mammalian hosts, and enable longitudinal video-rate imaging.

Post-COVID Neuropsychiatric Complications in Children and Adolescents: a Study Design for Early Diagnosis and Treatment Using Innovative Technologies.

Background: The COVID-19 pandemic has had significant impacts on the child and adolescent population, with long-term consequences for physical health, socio-psychological well-being, and cognitive development, which require further investigation. We herein describe a study design protocol for recognizing neuropsychiatric complications associated with pediatric COVID-19, and for developing effective prevention and treatment strategies grounded on the evidence-based findings.

Methods: The study includes two cohorts, each with 163 participants, aged from 7 to 18 years old, and matched by gender.

Synthesis of New Morphinan Opioids by TBADT-Catalyzed Photochemical Functionalization at the Carbon Skeleton.

The synthesis of new morphinan opioids by the addition of photochemically generated carbon-centered radicals to substrates containing an enone in the morphinan C-ring, is described. Using tetrabutylammonium decatungstate (TBADT) as a hydrogen atom transfer photocatalyst, diverse radical donors can be used to prepare a variety of C8-functionalized morphinan opioids. This work demonstrates the late-stage modification of complex, highly functionalized substrates.

Computational redesign of a fluorogen activating protein with Rosetta.

The use of unnatural fluorogenic molecules widely expands the pallet of available genetically encoded fluorescent imaging tools through the design of fluorogen activating proteins (FAPs). While there is already a handful of such probes available, each of them went through laborious cycles of in vitro screening and selection. Computational modeling approaches are evolving incredibly fast right now and are demonstrating great results in many applications, including de novo protein design.

PDT with genetically encoded photosensitizer miniSOG on a tumor spheroid model: A comparative study of continuous-wave and pulsed irradiation.

Background: Therapeutic effects of PDT depend on many factors, including the amount of singlet oxygen, localization of photosensitizer and irradiation protocol. The present study was aimed to compare the cytotoxic mechanisms of PDT under continuous-wave (CW) and pulsed irradiation using a tumor spheroid model and a genetically encoded photosensitizer miniSOG.

Methods: O detection in miniSOG and flavin mononucleotide (FMN) solutions was performed.

FUCCI-Red: a single-color cell cycle indicator for fluorescence lifetime imaging.

The phase of the cell cycle determines numerous aspects of cancer cell behaviour including invasiveness, ability to migrate and responsiveness to cytotoxic drugs. To non-invasively monitor progression of cell cycle in vivo, a family of genetically encoded fluorescent indicators, FUCCI (fluorescent ubiquitination-based cell cycle indicator), has been developed. Existing versions of FUCCI are based on fluorescent proteins of two or more different colors fused to cell-cycle-dependent degradation motifs.

Genetically Encoded Red Photosensitizers with Enhanced Phototoxicity.

Genetically encoded photosensitizers are increasingly used as optogenetic tools to control cell fate or trigger intracellular processes. A monomeric red fluorescent protein called SuperNova has been recently developed, however, it demonstrates suboptimal characteristics in most phototoxicity-based applications. Here, we applied directed evolution to this protein and identified SuperNova2, a protein with S10R substitution that results in enhanced brightness, chromophore maturation and phototoxicity in bacterial and mammalian cell cultures.

A General Mechanism of Green-to-Red Photoconversions of GFP.

Here we dissect the phenomena of oxidative and reductive green-to-red photoconversion of the Green Fluorescent Protein. We characterize distinct orange- and red-emitting forms (λ/λ = 490/565 nm; λ/λ = 535/600 nm) arising during the Enhanced Green Fluorescent Protein (EGFP) photoconversion under low-oxygen conditions in the presence of reductants. These forms spectroscopically differ from that observed previously in oxidative redding (λ/λ = 575/607 nm).

Genetically Encoded Fluorescent Sensor for Poly-ADP-Ribose.

Poly-(ADP-ribosyl)-ation (PARylation) is a reversible post-translational modification of proteins and DNA that plays an important role in various cellular processes such as DNA damage response, replication, transcription, and cell death. Here we designed a fully genetically encoded fluorescent sensor for poly-(ADP-ribose) (PAR) based on Förster resonance energy transfer (FRET). The WWE domain, which recognizes iso-ADP-ribose internal PAR-specific structural unit, was used as a PAR-targeting module.

Crystal Structure of Phototoxic Orange Fluorescent Proteins with a Tryptophan-Based Chromophore.

Phototoxic fluorescent proteins represent a sparse group of genetically encoded photosensitizers that could be used for precise light-induced inactivation of target proteins, DNA damage, and cell killing. Only two such GFP-based fluorescent proteins (FPs), KillerRed and its monomeric variant SuperNova, were described up to date. Here, we present a crystallographic study of their two orange successors, dimeric KillerOrange and monomeric mKillerOrange, at 1.

KillerOrange, a Genetically Encoded Photosensitizer Activated by Blue and Green Light.

Genetically encoded photosensitizers, proteins that produce reactive oxygen species when illuminated with visible light, are increasingly used as optogenetic tools. Their applications range from ablation of specific cell populations to precise optical inactivation of cellular proteins. Here, we report an orange mutant of red fluorescent protein KillerRed that becomes toxic when illuminated with blue or green light.

Green fluorescent protein with anionic tryptophan-based chromophore and long fluorescence lifetime.

Spectral diversity of fluorescent proteins, crucial for multiparameter imaging, is based mainly on chemical diversity of their chromophores. Recently we have reported, to our knowledge, a new green fluorescent protein WasCFP-the first fluorescent protein with a tryptophan-based chromophore in the anionic state. However, only a small portion of WasCFP molecules exists in the anionic state at physiological conditions.