Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein.

NusG/Spt5 proteins are the only transcription factors utilized by all cellular organisms. In enterobacteria, NusG antagonizes the transcription termination activity of Rho, a hexameric helicase, during the synthesis of ribosomal and actively translated mRNAs. Paradoxically, NusG helps Rho act on untranslated transcripts, including non-canonical antisense RNAs and those arising from translational stress; how NusG fulfills these disparate functions is unknown. Here, we demonstrate that NusG activates Rho by assisting helicase isomerization from an open-ring, RNA-loading state to a closed-ring, catalytically active translocase. A crystal structure of closed-ring Rho in complex with NusG reveals the physical basis for this activation and further explains how Rho is excluded from translationally competent RNAs. This study demonstrates how a universally conserved transcription factor acts to modulate the activity of a ring-shaped ATPase motor and establishes how the innate sequence bias of a termination factor can be modulated to silence pervasive, aberrant transcription.

The Polyanionic Drug Suramin Neutralizes Histones and Prevents Endotheliopathy.

Drugs are needed to protect against the neutrophil-derived histones responsible for endothelial injury in acute inflammatory conditions such as trauma and sepsis. Heparin and other polyanions can neutralize histones but challenges with dosing or side effects such as bleeding limit clinical application. In this study, we demonstrate that suramin, a widely available polyanionic drug, completely neutralizes the toxic effects of individual histones, but not citrullinated histones from neutrophil extracellular traps. The sulfate groups on suramin form stable electrostatic interactions with hydrogen bonds in the histone octamer with a dissociation constant of 250 nM. In cultured endothelial cells (Ea.Hy926), histone-induced thrombin generation was significantly decreased by suramin. In isolated murine blood vessels, suramin abolished aberrant endothelial cell calcium signals and rescued impaired endothelial-dependent vasodilation caused by histones. Suramin significantly decreased pulmonary endothelial cell ICAM-1 expression and neutrophil recruitment caused by infusion of sublethal doses of histones in vivo. Suramin also prevented histone-induced lung endothelial cell cytotoxicity in vitro and lung edema, intra-alveolar hemorrhage, and mortality in mice receiving a lethal dose of histones. Protection of vascular endothelial function from histone-induced damage is a novel mechanism of action for suramin with therapeutic implications for conditions characterized by elevated histone levels.

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH.

Imaging the transcriptome in situ with high accuracy has been a major challenge in single-cell biology, which is particularly hindered by the limits of optical resolution and the density of transcripts in single cells1-5. Here we demonstrate an evolution of sequential fluorescence in situ hybridization (seqFISH+). We show that seqFISH+ can image mRNAs for 10,000 genes in single cells-with high accuracy and sub-diffraction-limit resolution-in the cortex, subventricular zone and olfactory bulb of mouse brain, using a standard confocal microscope. The transcriptome-level profiling of seqFISH+ allows unbiased identification of cell classes and their spatial organization in tissues. In addition, seqFISH+ reveals subcellular mRNA localization patterns in cells and ligand-receptor pairs across neighbouring cells. This technology demonstrates the ability to generate spatial cell atlases and to perform discovery-driven studies of biological processes in situ.

Dynamics of release factor recycling during translation termination in bacteria.

In bacteria, release of newly synthesized proteins from ribosomes during translation termination is catalyzed by class-I release factors (RFs) RF1 or RF2, reading UAA and UAG or UAA and UGA codons, respectively. Class-I RFs are recycled from the post-termination ribosome by a class-II RF, the GTPase RF3, which accelerates ribosome intersubunit rotation and class-I RF dissociation. How conformational states of the ribosome are coupled to the binding and dissociation of the RFs remains unclear and the importance of ribosome-catalyzed guanine nucleotide exchange on RF3 for RF3 recycling in vivo has been disputed. Here, we profile these molecular events using a single-molecule fluorescence assay to clarify the timings of RF3 binding and ribosome intersubunit rotation that trigger class-I RF dissociation, GTP hydrolysis, and RF3 dissociation. These findings in conjunction with quantitative modeling of intracellular termination flows reveal rapid ribosome-dependent guanine nucleotide exchange to be crucial for RF3 action in vivo.

Imaging-based screens of pool-synthesized cell libraries.

Mapping a genetic perturbation to a change in phenotype is at the core of biological research. Advances in microscopy have transformed these studies, but they have largely been confined to examining a few strains or cell lines at a time. In parallel, there has been a revolution in creating synthetic libraries of genetically altered cells with relative ease. Here we describe methods that combine these powerful tools to perform live-cell imaging of pool-generated strain libraries for improved biological discovery.

Analyzing nursing students' mental health profiles at the onset of COVID-19.

The purpose of this descriptive-exploratory study was to identify profiles of mental health among undergraduate nursing students to understand the relationship between student's mental health profiles and relevant risk and protective factors at the onset of COVID-19. Latent Class Analysis (LCA) was employed to cull these students' mental health profiles (yielding 3 profiles) using data collected from 277 participants enrolled in a four-year BSN Program at a large, public institution in the Southeastern United States. Relational analyses of these profiles indicated that students who were the most vulnerable for mental health challenges also had the highest resilience and coping scores.

Time-resolved imaging-based CRISPRi screening.

Our ability to connect genotypic variation to biologically important phenotypes has been seriously limited by the gap between live-cell microscopy and library-scale genomic engineering. Here, we show how in situ genotyping of a library of strains after time-lapse imaging in a microfluidic device overcomes this problem. We determine how 235 different CRISPR interference knockdowns impact the coordination of the replication and division cycles of Escherichia coli by monitoring the location of replication forks throughout on average >500 cell cycles per knockdown. Subsequent in situ genotyping allows us to map each phenotype distribution to a specific genetic perturbation to determine which genes are important for cell cycle control. The single-cell time-resolved assay allows us to determine the distribution of single-cell growth rates, cell division sizes and replication initiation volumes. The technology presented in this study enables genome-scale screens of most live-cell microscopy assays.

Isotopic evidence for quasi-equilibrium chemistry in thermally mature natural gases.

Natural gas is a key energy resource, and understanding how it forms is important for predicting where it forms in economically important volumes. However, the origin of dry thermogenic natural gas is one of the most controversial topics in petroleum geochemistry, with several differing hypotheses proposed, including kinetic processes (such as thermal cleavage, phase partitioning during migration, and demethylation of aromatic rings) and equilibrium processes (such as transition metal catalysis). The dominant paradigm is that it is a product of kinetically controlled cracking of long-chain hydrocarbons. Here we show that C2+n-alkane gases (ethane, propane, butane, and pentane) are initially produced by irreversible cracking chemistry, but, as thermal maturity increases, the isotopic distribution of these species approaches thermodynamic equilibrium, either at the conditions of gas formation or during reservoir storage, becoming indistinguishable from equilibrium in the most thermally mature gases. We also find that the pair of CO2 and C1 (methane) exhibit a separate pattern of mutual isotopic equilibrium (generally at reservoir conditions), suggesting that they form a second, quasi-equilibrated population, separate from the C2 to C5 compounds. This conclusion implies that new approaches should be taken to predicting the compositions of natural gases as functions of time, temperature, and source substrate. Additionally, an isotopically equilibrated state can serve as a reference frame for recognizing many secondary processes that may modify natural gases after their formation, such as biodegradation.

Improvement of Therapeutic Value of Quercetin with Chitosan Nanoparticle Delivery Systems and Potential Applications.

This paper reviews recent studies investigating chitosan nanoparticles as drug delivery systems for quercetin. The therapeutic properties of quercetin include antioxidant, antibacterial and anti-cancer potential, but its therapeutic value is limited by its hydrophobic nature, low bioavailability and fast metabolism. Quercetin may also act synergistically with other stronger drugs for specific disease states. The encapsulation of quercetin in nanoparticles may increase its therapeutic value. Chitosan nanoparticles are a popular candidate in preliminary research, but the complex nature of chitosan makes standardisation difficult. Recent studies have used in-vitro, and in-vivo experiments to study the delivery of quercetin alone or in combination with another active pharmaceutical ingredient encapsulated in chitosan nanoparticles. These studies were compared with the administration of non-encapsulated quercetin formulation. Results suggest that encapsulated nanoparticle formulations are better. In-vivo or animal models simulated the type of disease required to be treated. The types of diseases were breast, lung, liver and colon cancers, mechanical and UVB-induced skin damage, cataracts and general oxidative stress. The reviewed studies included various routes of administration: oral, intravenous and transdermal routes. Although toxicity tests were often included, it is believed that the toxicity of loaded nanoparticles needs to be further researched, especially when not orally administered.

In the SARS-CoV-2 Pandora Pandemic: Can the Stance of Premorbid Intestinal Innate Immune System as Measured by Fecal Adnab-9 Binding of p87:Blood Ferritin, Yielding the FERAD Ratio, Predict COVID-19 Susceptibility and Survival in a Prospective Population Database?

SARS-CoV-2 severity predictions are feasible, though individual susceptibility is not. The latter prediction allows for planning vaccination strategies and the quarantine of vulnerable targets. Ironically, the innate immune response (InImS) is both an antiviral defense and the potential cause of adverse immune outcomes. The competition for iron has been recognized between both the immune system and invading pathogens and expressed in a ratio of ferritin divided by p87 (as defined by the Adnab-9 ELISA stool-binding optical density, minus the background), known as the FERAD ratio. Associations with the FERAD ratio may allow predictive modeling for the susceptibility and severity of disease. We evaluated other potential COVID-19 biomarkers prospectively. Patients with PCR+ COVID-19 tests (Group 1; n = 28) were compared to three other groups. In Group 2 (n = 36), and 13 patients displayed COVID-19-like symptoms but had negative PCR or negative antibody tests. Group 3 (n = 90) had no symptoms and were negative when routinely PCR-tested before medical procedures. Group 4 (n = 2129) comprised a pool of patients who had stool tests and symptoms, but their COVID-19 diagnoses were unknown; therefore, they were chosen to represent the general population. Twenty percent of the Group 4 patients (n = 432) had sufficient data to calculate their FERAD ratios, which were inversely correlated with the risk of COVID-19 in the future. In a case report of a neonate, we studied three biomarkers implicated in COVID-19, including p87, Src (cellular-p60-sarcoma antigen), and Abl (ABL-proto-oncogene 2). The InImS of the first two were positively correlated. An inverse correlation was found between ferritin and lysozyme in serum (p < 0.05), suggesting that iron could have impaired an important innate immune system anti-viral effector and could partially explain future COVID-19 susceptibility.

The Non-Invasive Prediction of Colorectal Neoplasia (NIPCON) Study 1995-2022: A Comparison of Guaiac-Based Fecal Occult Blood Test (FOBT) and an Anti-Adenoma Antibody, Adnab-9.

Given the need to improve the sensitivity of non-invasive methods to detect colorectal neoplasia, particularly adenomas, we compared a fecal test using a monoclonal antibody (Mab) raised against constituents of colonic adenomas designated Adnab-9 (Adenoma Antibody 9), recognizing an N-linked 87 kDa glycoprotein, to gFOBT, which is shown to reduce CRC mortality. p87 immunohistochemistry testing is significantly more sensitive (OR 3.64[CI 2.37-5.58]) than gFOBT (guaiac-based fecal occult blood test) for adenomas (<3 in number), advanced adenomas (OR 4.21[CI 2.47-7.15]), or a combination of the two (OR 3.35[CI 2.47-4.53]). p87 immunohistochemistry shows regional Paneth cell (PC) expression mainly in the right-sided colon and is significantly reduced in the ceca of African Americans (p < 0.0001). In a subset of patients, we obtained other body fluids such as urine, colonic effluent, and saliva. Urine tests (organ-specific neoantigen) showed a significant difference for advanced adenomas (p < 0.047). We conclude that fecal p87 testing is more sensitive than gFOBT and Adnab-9 and could be used to better direct the colonoscopy screening effort.

Comparison of organ and effective dose estimations from different Monte Carlo simulation-based software methods in infant CT and comparison with direct phantom measurements.

PURPOSE: Computational dosimetry software is routinely used to evaluate the organ and effective doses from computed tomography (CT) examinations. Studies have shown a significant variation in dose estimates between software in adult cohorts, and few studies have evaluated software for pediatric dose estimates. This study aims to compare the primary organ and effective doses estimated by four commercially available CT dosimetry software to thermoluminescent dosimeter (TLD) measurements in a 1-year-old phantom. METHODS: One hundred fifteen calibrated LiF (Mg, Cu, P)-TLD 100-H chips were embedded within an anthropomorphic phantom representing a 1-year-old child at positions that matched the approximate location of organs within an infant. The phantom was scanned under three protocols, each with whole-body coverage. The mean absorbed doses from 25 radiosensitive organs and skeletal tissues were determined from the TLD readings. Effective doses for each of the protocols were subsequently calculated using ICRP 103 formalism. Dose estimates by the four Monte Carlo-based dose calculation systems were determined and compared to the directly measured doses. RESULTS: Most organ doses determined by computation dosimetry software aligned to phantom measurements within 20%. Additionally, comparisons between effective doses are calculated using computational and direct measurement methods aligned within 20% across the three protocols. Significant variances were found in bone surface dose estimations among dosimetry methods, likely caused by differences in bone tissue modeling. CONCLUSION: All four-dosimetry software evaluated in this study provide adequate primary organ and effective dose estimations. Users should be aware, however, of the possible estimated uncertainty associated with each of the programs.

Efficacy of the scatter correction algorithm in portable chest radiography.

PURPOSE: Portable chest radiographs (CXRs) continue to be a vital diagnostic tool for emergency and critical care medicine. The scatter correction algorithm (SCA) is a post-processing algorithm aiming to reduce scatter within portable images. This study aimed to assess whether the SCA improved image quality (IQ) in portable CXRs. METHODS: Objective and subjective IQ assessments were undertaken on both phantom and clinical images, respectively. For objective analysis, attenuators were placed on the anterior surface of the patient's thorax to simulate pathologies present within uniform regions of the phantom's lung and heart. Phantom CXRs were acquired with three different tube-current-times (mAs). Phantom images were processed with different SCA strengths. Contrast to noise ratios (CNR) within the attenuator were determined for each algorithm strength and compared to non-SCA images. For subjective analysis, two independent radiologists graded 30 clinical images with and without the SCA activated. The images were graded for IQ in different anatomical structures and overall diagnostic confidence. RESULTS: Objectively, most strengths of the SCA improved the CNR in both regions. However, a detrimental effect was recorded for some algorithm strengths in regions of high contrast. Subjectively, both observers recorded the SCA significantly improved IQ in clinical CXRs in all anatomical regions. Observers indicated the greatest improvement in the lung and hilar regions, and least improvement in the chest wall and bone. All images with and without the SCA were deemed diagnostic. CONCLUSION: This study shows the potential radiation dose neutral IQ improvement when using an SCA in clinical patient CXRs.

Genotypes of rhinovirus detected among children in two communities of South-West Nigeria.

Rhinoviruses (RVs) are the most common etiological agent implicated in respiratory infections among infants and children. There are currently no approved antivirals and vaccine for use against the virus; hence, the need for information on the genotypes of rhinovirus from developing countries of the world with high burden of the infection. This study determined the genotypes of rhinovirus circulating among children in selected cities in Nigeria. Nasopharyngeal and oropharyngeal samples were carefully collected from children showing signs of respiratory infection in two communities in South-west Nigeria. Polymerase Chain Reaction was used to amplify the hypervariable part of the 5'- non-coding region, the entire viral protein gene 4 and the 5' terminus of the VP2 gene of RV. Nucleotide BLAST and phylogenetic analyses were used to genotype the isolates. Of the samples analysed, 12.7% showed rhinovirus positivity. All the three genotypes of rhinovirus were detected with genotype C (71.4%), being the predominant. Multiple strains of rhinovirus were found circulating. We showed for the first time the genotypes and strains of rhinovirus circulating in Nigeria. Further studies are required to highlight transmission patterns and disease severity among rhinovirus species in Nigeria.

Tuning the sequence specificity of a transcription terminator.

The bacterial hexameric helicase known as Rho is an archetypal sequence-specific transcription terminator that typically halts the synthesis of a defined set of transcripts, particularly those bearing cytosine-rich 3'-untranslated regions. However, under conditions of translational stress, Rho can also terminate transcription at cytosine-poor sites when assisted by the transcription factor NusG. Recent structural, biochemical, and computational studies of the Rho·NusG interaction in Escherichia coli have helped establish how NusG reprograms Rho activity. NusG is found to be an allosteric activator of Rho that directly binds to the ATPase motor domain of the helicase and facilitates closure of the Rho ring around non-ideal (purine-rich) target RNAs. The manner in which NusG acts on Rho helps to explain how the transcription terminator is excluded from acting on RNA polymerase by exogenous factors, such as the antitermination protein NusE, the NusG paralog RfaH, and RNA polymerase-coupled ribosomes. Collectively, an understanding of the link between NusG and Rho provides new insights into how transcriptional and translational fidelity are maintained during gene expression in bacteria.

Systemic inflammatory response to inhaled endotoxin does not correlate with airway response.

BACKGROUND: Endotoxin is a component of particulate matter linked to respiratory disease. Our group has shown that experimental endotoxin inhalation challenge reproducibly triggers neutrophilic inflammation in the airways and in peripheral blood. Sputum induction is currently the only available method for assessing airway neutrophilia but is laborious and time-consuming. This analysis examined the correlation between systemic and airway inflammatory responses to endotoxin to determine if peripheral blood could serve as a surrogate marker for neutrophilic airway inflammation. METHODS: We conducted a retrospective study of 124 inhaled endotoxin challenges conducted at our center using 20,000 endotoxin units (EU) of Clinical Center Reference Endotoxin (CCRE). Venipuncture and induced sputum samples were obtained at baseline and 6 hours after completion of endotoxin challenge. The relationship between change in sputum neutrophils (post-challenge - baseline) and change in peripheral blood neutrophils (post-challenge - baseline) was assessed using Spearman's correlation analyses. RESULTS: Inhaled endotoxin induced a significant increase in mean sputum percent neutrophils and peripheral blood absolute neutrophil counts in healthy adults with or without mild asthma, but no significant correlation was found between airway and systemic neutrophilia (r = 0.13, p = 0.18). Stratification by degree of airway neutrophil response and by atopic or asthmatic status did not change the results. CONCLUSIONS: Inhalation challenge with endotoxin safely and effectively induces airway neutrophilic inflammation in most individuals. Increases in endotoxin-induced peripheral blood neutrophils do not correlate well with airway responses and should not be used as a surrogate marker of airway inflammation.

Intravenous Magnesium Sulfate to Treat Acute Headaches in the Emergency Department: A Systematic Review.

INTRODUCTION: Non-traumatic headaches comprise up to 4% of all emergency department (ED) visits. Current practice is moving toward multimodal analgesia regimens that limit narcotic use. OBJECTIVE: The objective of this systematic review is to address the following research question: In patients with non-traumatic headaches (Population), does administration of intravenous magnesium sulfate (Intervention) compared to placebo, corticosteroids, dopamine antagonists, ergot alkaloids, non-steroidal anti-inflammatory drugs (NSAIDs), triptans, or usual care result in better pain control, lower rate of recurrence at 24 hours, lower requirements for rescue analgesia, and less adverse medication effects (Outcomes)? METHODS: Scholarly databases and relevant bibliographies were searched, as were clinical trial registries and relevant conference proceedings to limit publication bias. Studies were not limited by date, language, or publication status. Inclusion criteria were: (1) randomized clinical trial (RCT), (2) patients age ≥18 years, (3) non-traumatic headache, (4) patients treated in ED or an outpatient acute care treatment center, and (5) magnesium sulfate administered intravenously (IV). Eligible comparison groups included: placebo, conventional therapy, dopamine antagonist, NSAID, corticosteroid, ergot alkaloid, or triptans. RESULTS: Out of 4018 identified references, 7 RCTs (545 participants) that treated migraine headaches (n = 6) and benign non-traumatic headaches (n = 1) met inclusion criteria. Pain intensity was improved with magnesium sulfate vs comparators at 60-120 minutes, but not at earlier time points. Result for the endpoint of pain reduction by 50% were conflicting as 3 studies reported that headache was improved, unchanged, and less with magnesium sulfate. Complete pain relief was improved with magnesium sulfate in 1 study, and in the migraine with aura (MA) subgroup in another. The need for rescue analgesia at any point was improved with magnesium sulfate in 1 study, and in the MA subgroup in another. Twenty-four-hour headache recurrence was improved with magnesium sulfate in 1 study, but unchanged in a second. The intended meta-analysis was not performed due to the clinical heterogeneity among studies. CONCLUSION: While we cannot draw a firm conclusion on the efficacy or benefit of intravenous magnesium sulfate in the treatment of acute non-traumatic headaches, the existing evidence indicates potential benefits in pain control beyond 1 hour, aura duration, and need for rescue analgesia.

Ligand-induced and small-molecule control of substrate loading in a hexameric helicase.

Processive, ring-shaped protein and nucleic acid protein translocases control essential biochemical processes throughout biology and are considered high-prospect therapeutic targets. The Escherichia coli Rho factor is an exemplar hexameric RNA translocase that terminates transcription in bacteria. As with many ring-shaped motor proteins, Rho activity is modulated by a variety of poorly understood mechanisms, including small-molecule therapeutics, protein-protein interactions, and the sequence of its translocation substrate. Here, we establish the mechanism of action of two Rho effectors, the antibiotic bicyclomycin and nucleic acids that bind to Rho's primary RNA recruitment site. Using small-angle X-ray scattering and a fluorescence-based assay to monitor the ability of Rho to switch between open-ring (RNA-loading) and closed-ring (RNA-translocation) states, we found bicyclomycin to be a direct antagonist of ring closure. Reciprocally, the binding of nucleic acids to its N-terminal RNA recruitment domains is shown to promote the formation of a closed-ring Rho state, with increasing primary-site occupancy providing additive stimulatory effects. This study establishes bicyclomycin as a conformational inhibitor of Rho ring dynamics, highlighting the utility of developing assays that read out protein conformation as a prospective screening tool for ring-ATPase inhibitors. Our findings further show that the RNA sequence specificity used for guiding Rho-dependent termination derives in part from an intrinsic ability of the motor to couple the recognition of pyrimidine patterns in nascent transcripts to RNA loading and activity.

Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor.

Ring-shaped hexameric helicases and translocases support essential DNA-, RNA-, and protein-dependent transactions in all cells and many viruses. How such systems coordinate ATPase activity between multiple subunits to power conformational changes that drive the engagement and movement of client substrates is a fundamental question. Using the Escherichia coli Rho transcription termination factor as a model system, we have used solution and crystallographic structural methods to delineate the range of conformational changes that accompany distinct substrate and nucleotide cofactor binding events. Small-angle X-ray scattering data show that Rho preferentially adopts an open-ring state in solution and that RNA and ATP are both required to cooperatively promote ring closure. Multiple closed-ring structures with different RNA substrates and nucleotide occupancies capture distinct catalytic intermediates accessed during translocation. Our data reveal how RNA-induced ring closure templates a sequential ATP-hydrolysis mechanism, provide a molecular rationale for how the Rho ATPase domains distinguishes between distinct RNA sequences, and establish structural snapshots of substepping events in a hexameric helicase/translocase.

In situ genotyping of a pooled strain library after characterizing complex phenotypes.

In this work, we present a proof-of-principle experiment that extends advanced live cell microscopy to the scale of pool-generated strain libraries. We achieve this by identifying the genotypes for individual cells in situ after a detailed characterization of the phenotype. The principle is demonstrated by single-molecule fluorescence time-lapse imaging of Escherichia coli strains harboring barcoded plasmids that express a sgRNA which suppresses different genes in the E. coli genome through dCas9 interference. In general, the method solves the problem of characterizing complex dynamic phenotypes for diverse genetic libraries of cell strains. For example, it allows screens of how changes in regulatory or coding sequences impact the temporal expression, location, or function of a gene product, or how the altered expression of a set of genes impacts the intracellular dynamics of a labeled reporter.