Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP.

7SK is a conserved noncoding RNA that regulates transcription by sequestering the transcription factor P-TEFb. 7SK function entails complex changes in RNA structure, but characterizing RNA dynamics in cells remains an unsolved challenge. We developed a single-molecule chemical probing strategy, DANCE-MaP (deconvolution and annotation of ribonucleic conformational ensembles), that defines per-nucleotide reactivity, direct base pairing interactions, tertiary interactions, and thermodynamic populations for each state in RNA structural ensembles from a single experiment. DANCE-MaP reveals that 7SK RNA encodes a large-scale structural switch that couples dissolution of the P-TEFb binding site to structural remodeling at distal release factor binding sites. The 7SK structural equilibrium shifts in response to cell growth and stress and can be targeted to modulate expression of P-TEFbresponsive genes. Our study reveals that RNA structural dynamics underlie 7SK function as an integrator of diverse cellular signals to control transcription and establishes the power of DANCE-MaP to define RNA dynamics in cells.

Non-Coding Ribonucleic Acids as Diagnostic and Therapeutic Targets in Cardiac Fibrosis.

PURPOSE OF REVIEW: Cardiac fibrosis is a crucial juncture following cardiac injury and a precursor for many clinical heart disease manifestations. Epigenetic modulators, particularly non-coding RNAs (ncRNAs), are gaining prominence as diagnostic and therapeutic tools. RECENT FINDINGS: miRNAs are short linear RNA molecules involved in post-transcriptional regulation; lncRNAs and circRNAs are RNA sequences greater than 200 nucleotides that also play roles in regulating gene expression through a variety of mechanisms including miRNA sponging, direct interaction with mRNA, providing protein scaffolding, and encoding their own products. NcRNAs have the capacity to regulate one another and form sophisticated regulatory networks. The individual roles and disease relevance of miRNAs, lncRNAs, and circRNAs to cardiac fibrosis have been increasingly well described, though the complexity of their interrelationships, regulatory dynamics, and context-specific roles needs further elucidation. This review provides an overview of select ncRNAs relevant in cardiac fibrosis as a surrogate for many cardiac disease states with a focus on crosstalk and regulatory networks, variable actions among different disease states, and the clinical implications thereof. Further, the clinical feasibility of diagnostic and therapeutic applications as well as the strategies underway to advance ncRNA theranostics is explored.

Complete and Immediate Resolution of See-Saw Nystagmus Following Pituitary Macroadenoma Resection: Case Report and Review of the Literature.

See-saw nystagmus (SSN) is a rare form of nystagmus characterised by alternating elevation with incyclotorsion of one eye and concomitant depression with excyclotorsion of the other eye, often due to abnormalities involving the midbrain and parasellar region. Herein, we highlight a rare case of pendular SSN, which demonstrated complete resolution following resection of a pituitary macroadenoma. A patient in their 40s was identified to have SSN and was diagnosed with a pituitary macroadenoma. They underwent an endoscopic endonasal transsellar approach for resection of the pituitary adenoma. Their nystagmus resolved immediately after surgery. From a review of the literature, resolution and/or significant improvement in SSN occurred in 74% of cases following treatment, with 100%, 86% and 50% following treatment for medication-induced, neurological infarcts, and mass-effect aetiologies of SSN, respectively. SSN is a rare entity with a wide array of aetiologies. Identification of the causative aetiology and appropriate treatment can lead to significant improvement or resolution of the nystagmus in most cases.

RNA base-pairing complexity in living cells visualized by correlated chemical probing.

RNA structure and dynamics are critical to biological function. However, strategies for determining RNA structure in vivo are limited, with established chemical probing and newer duplex detection methods each having deficiencies. Here we convert the common reagent dimethyl sulfate into a useful probe of all 4 RNA nucleotides. Building on this advance, we introduce PAIR-MaP, which uses single-molecule correlated chemical probing to directly detect base-pairing interactions in cells. PAIR-MaP has superior resolution compared to alternative experiments, can resolve multiple sets of pairing interactions for structurally dynamic RNAs, and enables highly accurate structure modeling, including of RNAs containing multiple pseudoknots and extensively bound by proteins. Application of PAIR-MaP to human RNase MRP and 2 bacterial messenger RNA 5' untranslated regions reveals functionally important and complex structures undetected by prior analyses. PAIR-MaP is a powerful, experimentally concise, and broadly applicable strategy for directly visualizing RNA base pairs and dynamics in cells.

Loss to follow-up after food impaction among patients with and without eosinophilic esophagitis.

Symptoms of esophageal dysfunction such as food impaction are consistent with, but not diagnostic for eosinophilic esophagitis (EoE) without obtaining histology. We conducted a retrospective study to characterize patients with food impaction at a tertiary center. We hypothesized that many patients with food impaction may be lost to follow-up and that many have features suggestive of EoE. Adult patients presenting to the emergency department with esophageal food impaction were identified from an endoscopic database. Electronic medical records were manually abstracted. We examined associations between demographics, comorbid conditions, and follow-up with biopsy findings. Of 220 patients who presented to the emergency department for food impaction, 74.1% were men. Adequate follow-up was not documented in 120 (54.5%). Those lost to follow-up did not differ significantly by gender, age at symptom onset, or distance from hospital compared to those with follow-up. Esophageal biopsies were obtained in 158 (71.8%), and those with ≥15 eos/HPF were more likely to be lost to follow-up than those with <15 eos/HPF (52.8% vs. 34.8%, P < 0.05). Of those never biopsied, 79.0% were lost to follow-up and had intermediate proportions of males, food allergy, and asthma when compared to those with and without eosinophilic inflammation. Patients with food impaction commonly have EoE but are often lost to follow-up. Among those never biopsied, demographic and clinical features suggest that many may have undiagnosed EoE. Strategies for increasing use of biopsies in patients with food impaction and improving follow-up are needed to diagnose and manage EoE.

Pharmacokinetic optimitzation of CCG-203971: Novel inhibitors of the Rho/MRTF/SRF transcriptional pathway as potential antifibrotic therapeutics for systemic scleroderma.

We recently reported the development of a novel inhibitor of Rho-mediated gene transcription (1, CCG-203971) that is efficacious in multiple animal models of acute fibrosis, including scleroderma, when given intraperitoneally. The modest in vivo potency and poor pharmacokinetics (PK) of this lead, however, make it unsuitable for long term efficacy studies. We therefore undertook a systematic medicinal chemistry effort to improve both the metabolic stability and the solubility of 1, resulting in the identification of two analogs achieving over 10-fold increases in plasma exposures in mice. We subsequently showed that one of these analogs (8f, CCG-232601) could inhibit the development of bleomycin-induced dermal fibrosis in mice when administered orally at 50mg/kg, an effect that was comparable to what we had observed earlier with 1 at a 4-fold higher IP dose.

Ranking United States University-Based General Surgery Programs on the Academic Achievement of Surgery Department Faculty.

OBJECTIVE: Rankings of residency programs are highly influential and utilized by residency applicants. Existing ranking resources often use opaque criteria that may include bias or do not accurately represent the academic achievement of current faculty. This study aims to create an updated general surgery residency ranking list based on the academic achievements of their respective surgery department faculty members. DESIGN: One hundred and six general surgery residency programs were selected from the American Medical Association Residency & Fellowship Programs Database. The names of faculty members affiliated with the departments of surgery were manually obtained. Lifetime and five-year h-indexes, a sum of grant awards from the National Institute of Health and Veterans Affairs, and a tally of journal editorial board positions were collected for the faculty. Metrics were compared among surgical departments, and the corresponding residency programs were ranked accordingly. SETTING: The study evaluated university-based general surgery residency programs in the United States from 2017 to 2019 via assessing their respective institutions' departments of surgery. PARTICIPANTS: A total of 7568 faculty members were evaluated. Faculty were required to be full-time, clinical surgeons to meet inclusion criteria. RESULTS: Based on a composite of all measured criteria, the top overall surgery department was at the University of Michigan. Massachusetts General Hospital had the highest lifetime and five-year h-indexes. Brigham and Women's Hospital had the most National Institute of Health funding, and the University of Pittsburgh Medical Center had the most Veterans Affairs funding. Washington University in St. Louis/Barnes Jewish Hospital had the most editorial board positions in their department. CONCLUSIONS: The academic success of departments of surgery was evaluated to develop a ranking list of general surgery residency programs. Through utilizing standardized methods and several measures of academic achievement, this comprehensive general surgery residency classification system will allow residency applicants to make more informed decisions.

Hitting a Wall: An Ambiguous Case of Wallenberg Syndrome.

Wallenberg syndrome is the most common stroke of the posterior circulation. Diagnosis of Wallenberg syndrome is often overlooked as initial MRI may show no visible lesion. We present an atypical case of Wallenberg syndrome in which the initial MRI of the brain was normal. Our patient is a 65-year-old male who was brought in by emergency medical services complaining of right-sided facial droop, slurred speech, and left-sided weakness for one day. Physical examination showed decreased left arm and leg strength compared to the right side, decreased left facial temperature sensations, decreased left arm and leg temperature sensations, and difficulty sitting upright with an associated leaning towards the left side. An initial magnetic resonance imaging (MRI) of the brain with and without contrast revealed no abnormality. In light of such a high suspicion for stroke based on the patient's neurologic deficits, a repeat MRI of the brain was performed three days later and exposed a small focus of bright signal (hyperintensity) on T2-weighted fluid-attenuated inversion recovery and diffusion-weighted imaging (DWI) in the left posterior medulla. Wallenberg syndrome, also known as lateral medullary syndrome or posterior inferior cerebellar artery syndrome, is a constellation of symptoms caused by posterior vascular accidents. The neurological deficits associated with this disease are due to damage of the lateral medulla, inferior cerebellar peduncle, nucleus of trigeminal nerve, nucleus and fibers of vagus and glossopharyngeal nerves, descending sympathetic tract, spinothalamic tract, and/or vestibular nuclei. MRI with DWI is the gold standard to confirm the diagnosis. Wallenberg syndrome has the potential to leave patients extremely debilitated. Early detection, management, and rehabilitation are critical for improving post-stroke recovery.

Characterization and Manipulation of Carbon Precursor Species during Plasma Enhanced Chemical Vapor Deposition of Graphene.

To develop a synthesis technique providing enhanced control of graphene film quality and uniformity, a systematic characterization and manipulation of hydrocarbon precursors generated during plasma enhanced chemical vapor deposition of graphene is presented. Remote ionization of acetylene is observed to generate a variety of neutral and ionized hydrocarbon precursors, while in situ manipulation of the size and reactivity of carbon species permitted to interact with the growth catalyst enables control of the resultant graphene morphology. Selective screening of high energy hydrocarbon ions coupled with a multistage bias growth regime results in the production of 90% few-to-monolayer graphene on 50 nm Ni/Cu alloy catalysts at 500 °C. Additionally, synthesis with low power secondary ionization processes is performed and reveals further control during the growth, enabling a 50% reduction in average defect densities throughout the film. Mass spectrometry and UV-Vis spectroscopy monitoring of the reaction environment in conjunction with Raman characterization of the synthesized graphene films facilitates correlation of the carbon species permitted to reach the catalyst surface to the ultimate quality, layer number, and uniformity of the graphene film. These findings reveal a robust technique to control graphene synthesis pathways during plasma enhanced chemical vapor deposition.

Plasma-Enhanced Chemical Vapor Deposition of Acetylene on Codeposited Bimetal Catalysts Increasing Graphene Sheet Continuity Under Low-Temperature Growth Conditions.

Here, we report a novel method for low-temperature synthesis of monolayer graphene at 450 °C on a polycrystalline bimetal Ni-Au catalyst. In this study, low-temperature chemical vapor deposition synthesis of graphene was performed at 450 °C on codeposited Ni-Au which shows successful monolayer graphene formation without an extra annealing process. The experimental results suggest that electron beam codeposition of bimetal catalyst is the key procedure that enables the elimination of the pre-growth high-temperature annealing of the catalyst prior to graphene synthesis, an indispensable process, used in previous reports. The formation was further improved by plasma-assisted growth in which the inductively coupled plasma ionizes the carbon precursors that interact with codeposited Ni-Au catalyst of 50 nm in thickness at 450 °C. These combined growth conditions drastically increase the graphene's sheet uniformity and area connectivity from 11.6% to 99%. These fabrication parameters enable the graphene formation that shifts from a bulk diffusion-based growth model towards a surface based reaction. The technique reported here opens the opportunity for the low-temperature growth of graphene for potential use in future CMOS applications.

Regulation of apoptosis-related genes by nitric oxide in cancer.

Nitric oxide (NO) is a simple molecule with a complex and pleiotropic biological activity. NO or related species have been implicated in the regulation of many genes that participate in many diverse biological functions including programmed cell death or apoptosis. Apoptosis is a process that may potentially be disrupted in cancer cells conferring a survival advantage. In addition, malignant tumor cells can develop an intricate system of resistance to apoptotic stimuli. NO or related species have been shown to play a dual role in the regulation of apoptosis in malignant cells either promoting cell death or protecting cells from pro-apoptotic induction. However, the specific role of NO in the regulation of apoptosis/survival-related genes expression seems to tilt the balance toward the promotion of pro-apoptotic and the suppression of anti-apoptotic genes. Herein we have reviewed the most relevant aspects involving NO and/or reactive intermediates in the regulation of apoptosis-related genes--mainly--at the transcriptional level. We described the basic apoptotic molecules that potentially are affected by NO and how NO-mediated signaling gets transmitted to the transcriptional machinery that governs the expression of these genes. In addition, we discussed some of the fundamental functional consequences of the regulation of apoptosis-related genes by NO in cancer biology and its potential therapeutic implications.

Transcription regulator Yin-yang 1: from silence to cancer.

Yin Yang (YY) 1 represents the epitome of what is considered to be a "Swiss army knife" transcription factor and regulator. YY1 is a ubiquitous and multifunctional zinc-finger transcription factor member of the Polycomb group protein family, a group of homeobox gene receptors that can act as activators or repressors of transcriptional activity. Furthermore, YY1 can act as a redox sensor, adaptor molecule, and chromatin structure and function regulator. YYl's characteristic function as transcriptional activator and repressor relies on its C2H2 (x4) zinc-finger structural DNA-binding motifs tangled with 2 specific regulatory domains. This structural conformation will render the activity of YY1 susceptible to changes in cellular redox status. YY1 also has been shown to undergo chromatin remodeling via interactions with histone acetyl transferase and histone deacetylase complexes. Both groups modify histones, resulting in altered chromatin structure. Herein, we will discuss the multiple roles and mechanisms of YY1 in the regulation of gene expression, its genetic factor functions, epigenetic regulatory activity, and its role as a redox sensor in the context of malignant neoplastic diseases.