Optogenetic regulation of site-specific subtelomeric DNA methylation

Telomere length homeostasis, critical for chromosomal integrity and genome stability, is controlled by intricate molecular regulatory machinery that includes epigenetic modifications. Here, we examine site-specific and spatiotemporal alteration of the subtelomeric methylation of CpG islands using optogenetic tools to understand the epigenetic regulatory mechanisms of telomere length maintenance. Human DNA methyltransferase3A (DNMT3A) were assembled selectively at chromosome ends by fusion to cryptochrome 2 protein (CRY2) and its interacting complement, the basic helix loop helix protein-1 (CIB1). CIB1 was fused to the telomere-associated protein telomere repeat binding factor-1 (TRF1), which localized the protein complex DNMT3A-CRY2 at telomeric regions upon excitation by blue-light monitored by single-molecule fluorescence analyses. Increased methylation was achieved selectively at subtelomeric CpG sites on the six examined chromosome ends specifically after blue-light activation, which resulted in progressive increase in telomere length over three generations of HeLa cell replications. The modular design of the fusion constructs presented here allows for the selective substitution of other chromatin modifying enzymes and for loci-specific targeting to regulate the epigenetic pathways at telomeres and other selected genomic regions of interest

Transient vortex dynamics and evolution of Bose metal from a 2D superconductor on MoS2_2

The true character of physical phenomena is thought to be reinforced as the system becomes disorder-free. In contrast, the two-dimensional (2D) superconductor is predicted to turn fragile and resistive away from the limit I -> 0, B -> 0, in the pinning-free regime. It is intriguing to note that the very vortices responsible for achieving superconductivity by pairing, condensation, and, thereby reducing the classical dissipation, render the state resistive driven by quantum fluctuations in the T -> 0. While cleaner systems are being explored for technological improvements, the 2D superconductor turning resistive when influenced by weak electric and magnetic fields has profound consequences for quantum technologies. A metallic ground state in 2D is beyond the consensus of both Bosonic and Fermionic systems, and its origin and nature warrant a comprehensive theoretical understanding supplemented by in-depth experiments. A real-time observation of the influence of vortex dynamics on transport properties so far has been elusive. We explore the nature and fate of a low-viscous, clean, 2D superconducting state formed on an ionic-liquid gated few-layered MoS$_2$ sample. The vortex-core being dissipative, the elastic depinning, intervortex interaction, and the subsequent dynamics of the vortex-lattice cause the system to behave like an overdamped harmonic oscillator, leaving transient signatures in the transport characteristics. The temperature and magnetic field dependence of the transient nature and the noise characteristics of the magnetoresistance confirm that quantum fluctuations are solely responsible for the Bose metal state and the fragility of the superconducting state

Bladder Mucosal Cystitis Cystica Lesions Are Tertiary Lymphoid Tissues That Correlate With Recurrent Urinary Tract Infection Frequency in Postmenopausal Women

PURPOSE: We identify correlates and clinical outcomes of cystitis cystica, a poorly understood chronic inflammatory bladder change, in women with recurrent urinary tract infections. MATERIALS AND METHODS: A retrospective, observational cohort of women with recurrent urinary tract infections who underwent cystoscopy (n=138) from 2015 to 2018 were identified using electronic medical records. Cystitis cystica status was abstracted from cystoscopy reports and correlations were identified by logistic regression. Urinary tract infection-free survival time associated with cystitis cystica was evaluated by Cox proportional hazards regression. Exact logistic regression was used to identify factors associated with changes to cystitis cystica lesions on repeat cystoscopy. Biopsies of cystitis cystica lesions were examined by routine histology and immunofluorescence. RESULTS: Fifty-three patients (38%) had cystitis cystica on cystoscopy. Cystitis cystica was associated with postmenopausal status (OR: 5.53, 95% CI: 1.39-37.21), pelvic floor myofascial pain (6.82, 1.78-45.04), having ≥4 urinary tract infections in the past year (2.28, 1.04-5.09), and a shorter time to next urinary tract infection (HR: 1.54, 95% CI: 1.01-2.35). Forty-two patients (82%) demonstrated improvement or resolution of lesions. Ten/11 (91%) biopsied cystitis cystica lesions were tertiary lymphoid tissue with germinal centers and resembled follicular cystitis. CONCLUSIONS: Cystitis cystica lesions were associated with postmenopausal status, pelvic floor myofascial pain, and number of urinary tract infections in the prior year and predicted worse recurrent urinary tract infection outcomes. Cystitis cystica lesions are tertiary lymphoid tissue/follicular cystitis that may improve or resolve over time with treatment. Identifying cystitis cystica in recurrent urinary tract infection patients may be useful in informing future urinary tract infection risk and tailoring appropriate treatment strategies

Cerebral Venous Thrombosis and Acute Pulmonary Embolism following Varicella Infection

Varicella infection is caused by varicella-zoster virus (VZV) and commonly presents as a self-limiting skin manifestation in children. VZV also causes cerebral arterial vasculopathy and antibody-mediated hypercoagulable states leading to thrombotic complications in children, although there are very few such reports in adults. Postulated causal factors include vasculitis, direct endothelial damage, or acquired protein S deficiency secondary to molecular mimicry. These induced autoantibodies to protein S could lead to acquired protein S deficiency and produce a hypercoagulable state causing venous sinus thrombosis. Here we report the case of a 26-year-old man who presented with cortical venous sinus thrombosis and acute pulmonary embolism following varicella infection. Both conditions responded to anticoagulation treatment

Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay

SARS-CoV-2 proteases Mpro and PLpro are promising targets for antiviral drug development. In this study, we present an antiviral screening strategy involving a novel in-cell protease assay, antiviral and biochemical activity assessments, as well as structural determinations for rapid identification of protease inhibitors with low cytotoxicity. We identified eight compounds with anti-SARS-CoV-2 activity from a library of 64 repurposed drugs and modeled at protease active sites by in silico docking. We demonstrate that Sitagliptin and Daclatasvir inhibit PLpro, and MG-101, Lycorine HCl, and Nelfinavir mesylate inhibit Mpro of SARS-CoV-2. The X-ray crystal structure of Mpro in complex with MG-101 shows a covalent bond formation between the inhibitor and the active site Cys145 residue indicating its mechanism of inhibition is by blocking the substrate binding at the active site. Thus, we provide methods for rapid and effective screening and development of inhibitors for blocking virus polyprotein processing as SARS-CoV-2 antivirals. Additionally, we show that the combined inhibition of Mpro and PLpro is more effective in inhibiting SARS-CoV-2 and the delta variant

A Chemical Strategy for Intracellular Arming of an Endogenous Broad-Spectrum Antiviral Nucleotide

The naturally occurring nucleotide 3′-deoxy-3′,4′-didehydro-cytidine-5′-triphosphate (ddhCTP) was recently found to exert potent and broad-spectrum antiviral activity. However, nucleoside 5′-triphosphates in general are not cell-permeable, which precludes the direct use of ddhCTP as a therapeutic. To harness the therapeutic potential of this endogenous antiviral nucleotide, we synthesized phosphoramidate prodrug HLB-0532247 (1) and found it to result in dramatically elevated levels of ddhCTP in cells. We compared 1 and 3′-deoxy-3′,4′-didehydro-cytidine (ddhC) and found that 1 more effectively reduces titers of Zika and West Nile viruses in cell culture with minimal nonspecific toxicity to host cells. We conclude that 1 is a promising antiviral agent based on a novel strategy of facilitating elevated levels of the endogenous ddhCTP antiviral nucleotide

Structure-Function Studies of DNA Binding Domain of Response Regulator KdpE Reveals Equal Affinity Interactions at DNA Half-Sites

Expression of KdpFABC, a K+ pump that restores osmotic balance, is controlled by binding of the response regulator KdpE to a specific DNA sequence (kdpFABCBS) via the winged helix-turn-helix type DNA binding domain (KdpEDBD). Exploration of E. coli KdpEDBD and kdpFABCBS interaction resulted in the identification of two conserved, AT-rich 6 bp direct repeats that form half-sites. Despite binding to these half-sites, KdpEDBD was incapable of promoting gene expression in vivo. Structure-function studies guided by our 2.5 Å X-ray structure of KdpEDBD revealed the importance of residues R193 and R200 in the α-8 DNA recognition helix and T215 in the wing region for DNA binding. Mutation of these residues renders KdpE incapable of inducing expression of the kdpFABC operon. Detailed biophysical analysis of interactions using analytical ultracentrifugation revealed a 2∶1 stoichiometry of protein to DNA with dissociation constants of 200±100 and 350±100 nM at half-sites. Inactivation of one half-site does not influence binding at the other, indicating that KdpEDBD binds independently to the half-sites with approximately equal affinity and no discernable cooperativity. To our knowledge, these data are the first to describe in quantitative terms the binding at half-sites under equilibrium conditions for a member of the ubiquitous OmpR/PhoB family of proteins