Biochemical and genetic dissection of the RNA-binding surface of the FinO domain of Escherichia coli ProQ.

RNA-binding proteins play important roles in bacterial gene regulation through interactions with both coding and noncoding RNAs. ProQ is a FinO-domain protein that binds a large set of RNAs in Escherichia coli, though the details of how ProQ binds these RNAs remain unclear. In this study, we used a combination of in vivo and in vitro binding assays to confirm key structural features of E. coli ProQ's FinO domain and explore its mechanism of RNA interactions. Using a bacterial three-hybrid assay, we performed forward genetic screens to confirm the importance of the concave face of ProQ in RNA binding. Using gel shift assays, we directly probed the contributions of ten amino acids on ProQ binding to seven RNA targets. Certain residues (R58, Y70, and R80) were found to be essential for binding of all seven RNAs, while substitutions of other residues (K54 and R62) caused more moderate binding defects. Interestingly, substitutions of two amino acids (K35, R69), which are evolutionarily variable but adjacent to conserved residues, showed varied effects on the binding of different RNAs; these may arise from the differing sequence context around each RNA's terminator hairpin. Together, this work confirms many of the essential RNA-binding residues in ProQ initially identified in vivo and supports a model in which residues on the conserved concave face of the FinO domain such as R58, Y70, and R80 form the main RNA-binding site of E. coli ProQ, while additional contacts contribute to the binding of certain RNAs.

A highly diastereoselective one-pot Ugi/radical spirocyclization/aza-Michael addition sequence.

We hereby report a highly diastereoselective synthesis of chalcogenated azaspirotricycles via a one-pot Ugi/spirocyclization/aza-Michael addition sequence. The reaction proceeds via a key visible light mediated spirocyclization step under mild, metal-free and energy efficient conditions. A variety of complex sulfenylated and selenylated azaspirotricycles were obtained in good yields. The reaction was found to be scalable and preliminary mechanistic studies indicated that the spirocyclization step proceeds via radical intermediates.

Leaching Approach for ß-Glucosidase Extraction from Fermented Rice Husk in Solid State Cultivation by Aspergillus protuberus.

Environmental problems are caused by the disposal of agrowastes in developing countries. It is imperative to convert such wastes into useful products, which require enzymes such as ß-glucosidase. ß-Glucosidase has variety of applications in biotechnology including food, textile, detergents, pulp and paper, pharmaceutical and biofuel industries. ß-Glucosidase production was performed using the locally isolated Aspergillus protuberus using best growth circumstances on rice husk in solid-state fermentation (SSF). Leaching of ß-glucosidase from fermented rice husk with number of solvents to evaluate their extraction efficacy. Among the different solvents examined, acetate buffer (0.02 M, pH 5.0) proved to be the best solvent. The subsequent parameters were optimized with acetate buffer. Two washes with acetate buffer each by shaking (30 min) in a ratio of 1 g of rice husk: 5 ml of acetate buffer together attained maximum recovery of ß-glucosidase with 41.95 U/g of rice husk.

Optimization of a bacterial three-hybrid assay through in vivo titration of an RNA-DNA adapter protein.

Noncoding RNAs regulate gene expression in every domain of life. In bacteria, small RNAs (sRNAs) regulate gene expression in response to stress and are often assisted by RNA-chaperone proteins, such as Hfq. We have recently developed a bacterial three-hybrid (B3H) assay that detects the strong binding interactions of certain E. coli sRNAs with proteins Hfq and ProQ. Despite the promise of this system, the signal-to-noise has made it challenging to detect weaker interactions. In this work, we use Hfq-sRNA interactions as a model system to optimize the B3H assay, so that weaker RNA-protein interactions can be more reliably detected. We find that the concentration of the RNA-DNA adapter is an important parameter in determining the signal in the system and have modified the plasmid expressing this component to tune its concentration to optimal levels. In addition, we have systematically perturbed the binding affinity of Hfq-RNA interactions to define, for the first time, the relationship between B3H signal and in vitro binding energetics. The new pAdapter construct presented here substantially expands the range of detectable interactions in the B3H assay, broadening its utility. This improved assay will increase the likelihood of identifying novel protein-RNA interactions with the B3H system and will facilitate exploration of the binding mechanisms of these interactions.

α-Carbonyl sulfoxonium ylides in transition metal-catalyzed C-H activation: a safe carbene precursor and a weak directing group.

Transition metal-catalyzed cross-coupling of sp2 C-H bonds with diazo compounds via carbene migratory insertion represents an efficient strategy for the construction of C-C and C-heteroatom bonds in organic synthesis. Despite the popularity of diazo compounds as coupling partners in C-H activation, they pose serious safety and stability issues due to potential exothermic reactions linked with the release of N2 gas. However, compared with diazo compounds, sulfoxonium ylides are generally crystalline solids, more stable, widely used in industrial scales, and easier/safer to prepare. Therefore, recent years have witnessed an upsurge in employing α-carbonyl sulfoxonium ylides as an alternative carbene surrogate in transition metal-catalyzed C-H activation. Unlike diazo compounds, α-carbonyl sulfoxonium ylides contain inherent potential to serve as a coupling partner as well as a weak directing group. This review will summarize the progress made in both categories of reactions.

T405, a New Penem, Exhibits In Vivo Efficacy against M. abscessus and Synergy with ß-Lactams Imipenem and Cefditoren.

Mycobacteroides abscessus (Mab) is an emerging environmental microbe that causes chronic lung disease in patients with compromised lung function such as cystic fibrosis and bronchiectasis. It is intrinsically resistant to most antibiotics, therefore there are only few antibiotics that can be repurposed to treat Mab disease. Although current recommendations require daily intake of multiple antibiotics for more than a year, cure rate is low and often associated with significant adverse events. Here, we describe in vivo efficacy of T405, a recently discovered ß-lactam antibiotic of the penem subclass, in a mouse model of pulmonary Mab infection. Imipenem, one of the standard-of-care drugs to treat Mab disease, and also a ß-lactam antibiotic from a chemical class similar to T405, was included as a comparator. Probenecid was included with both T405 and imipenem to reduce the rate of their renal clearance. T405 exhibited bactericidal activity against Mab from the onset of treatment and reduced Mab lung burden at a rate similar to that exhibited by imipenem. The MIC of T405 against Mab was unaltered after 4 weeks of exposure to T405 in the lungs of mice. Using an in vitro assay, we also demonstrate that T405 in combination with imipenem, cefditoren or avibactam exhibits synergism against Mab. Additionally, we describe a scheme for synthesis and purification of T405 on an industrial scale. These attributes make T405 a promising candidate for further preclinical assessment to treat Mab disease.

Quantum-Critical Resistivity of Strange Metals in a Magnetic Field.

Resistivity in the quantum-critical fluctuation region of several metallic compounds such as the cuprates, the heavy fermions, Fe chalogenides and pnictides, Moiré bilayer graphene, and WSe_{2} is linear in temperature T as well as in the magnetic field H_{z} perpendicular to the planes. Scattering of fermions by the fluctuations of a time-reversal odd polar vector field Ω has been shown to give a linear in T resistivity and other marginal Fermi-liquid properties. An extension of this theory to an applied magnetic field is presented. A magnetic field is shown to generate a density of vortices in the field Ω proportional to H_{z}. The elastic scattering of fermions from the vortices gives a resistivity linear in H_{z} with the coefficient varying as the marginal Fermi-liquid susceptibility ln(ω_{c}/T). Quantitative comparison with experiments is presented for cuprates and Moiré bilayer graphene.

Visible-Light Mediated Arbuzov-Like Reaction with Thiophenols.

We hereby disclose, a visible light mediated addition of sulfenyl radicals to trialkyl phosphites to access functionalized phosphorothioates. The use of cheap and readily available Eosin Y as a photocatalyst under mild energy efficient conditions bypassing the use of external oxidants forms the chief highlight of the work. The protocol is scalable and mechanistic studies indicate that the reaction proceeds through an ionic-Arbuzov like pathway from phosphoranyl radicals.

Regioselective Dichotomy in Ru(II)-Catalyzed C-H Annulation of Aryl Pyrazolidinones with 1,3-Diynes.

Herein, we present a substrate-controlled regiodivergent strategy for the selective synthesis of C3 or C2-alkynylated indoles via ruthenium-catalyzed [3 + 2]-annulation of readily available pyrazolidinones and 1,3-diynes. Remarkably, C3-alkynylated indoles were obtained in good yields when 1,4-diarylbuta-1,3-diynes were employed as the coupling partners. On the other hand, dialkyl-1,3-diynes led to the selective formation of C2-alkynylated indoles. The key features of the strategy are the operationally simple conditions and external-oxidant-free, broad-scope, and substrate-switchable indole synthesis. Scale-up reactions and further transformations expanded the synthetic utility of the protocol.

Determinants of RNA recognition by the FinO domain of the Escherichia coli ProQ protein.

The regulation of gene expression by small RNAs in Escherichia coli depends on RNA binding proteins Hfq and ProQ, which bind mostly distinct RNA pools. To understand how ProQ discriminates between RNA substrates, we compared its binding to six different RNA molecules. Full-length ProQ bound all six RNAs similarly, while the isolated N-terminal FinO domain (NTD) of ProQ specifically recognized RNAs with Rho-independent terminators. Analysis of malM 3'-UTR mutants showed that tight RNA binding by the ProQ NTD required a terminator hairpin of at least 2 bp preceding an 3' oligoU tail of at least four uridine residues. Substitution of an A-rich sequence on the 5' side of the terminator to uridines strengthened the binding of several ProQ-specific RNAs to the Hfq protein, but not to the ProQ NTD. Substitution of the motif in the malM-3' and cspE-3' RNAs also conferred the ability to bind Hfq in E. coli cells, as measured using a three-hybrid assay. In summary, these data suggest that the ProQ NTD specifically recognizes 3' intrinsic terminators of RNA substrates, and that the discrimination between RNA ligands by E. coli ProQ and Hfq depends both on positive determinants for binding to ProQ and negative determinants against binding to Hfq.

Genetic identification of the functional surface for RNA binding by Escherichia coli ProQ.

The FinO-domain-protein ProQ is an RNA-binding protein that has been known to play a role in osmoregulation in proteobacteria. Recently, ProQ has been shown to act as a global RNA-binding protein in Salmonella and Escherichia coli, binding to dozens of small RNAs (sRNAs) and messenger RNAs (mRNAs) to regulate mRNA-expression levels through interactions with both 5' and 3' untranslated regions (UTRs). Despite excitement around ProQ as a novel global RNA-binding protein, and its potential to serve as a matchmaking RNA chaperone, significant gaps remain in our understanding of the molecular mechanisms ProQ uses to interact with RNA. In order to apply the tools of molecular genetics to this question, we have adapted a bacterial three-hybrid (B3H) assay to detect ProQ's interactions with target RNAs. Using domain truncations, site-directed mutagenesis and an unbiased forward genetic screen, we have identified a group of highly conserved residues on ProQ's NTD as the primary face for in vivo recognition of two RNAs, and propose that the NTD structure serves as an electrostatic scaffold to recognize the shape of an RNA duplex.

Dynamic contrast-enhanced MRI and Doppler sonography in patients with squamous cell carcinoma of head and neck treated with induction chemotherapy.

In view of the inherent limitations associated with performing dynamic contrast enhanced-magnetic resonance imaging (DCE-MRI) in clinical settings, current study was designed to provide a proof of principle that Doppler sonography and DCE-MRI derived perfusion parameters yield similar hemodynamic information from metastatic lymph nodes in squamous cell carcinomas of head and neck (HNSCCs). Strong positive correlations between volume fraction of plasma space in tissues (Vp ) and blood volume (r = 0.72, p = 0.02) and between Vp and %area perfused (r = 0.65, p = 0.04) were observed. Additionally, a moderate positive correlation trending towards significance was obtained between volume transfer constant (Ktrans ) and %area perfused (r = 0.49, p = 0.09).

Besdata Video Laryngeal Mask (BD-VLM)- a New Vision-Incorporated 3rd Generation Video Laryngeal Mask Airway : Dear editor.

Since the recent editorial 2, we were approached to evaluate another video laryngeal mask airway - the Besdata Video Laryngeal Mask (BD-VLM) TM, which has a different design concept, specifications and characteristics (Figure 1) compared to the other two.

Features of new vision-incorporated third-generation video laryngeal mask airways.

Numerous studies have shown that blindly inserted supraglottic airway devices (SADs) are sub-optimally placed in 50 to 80% of all cases. Placement under direct vision has been recommended. We describe the very first two new SADs of the third generation that incorporate a videoscope with flexible tip. Both devices are made up of two interlocking components-the SAD and a videoscope. The 3rd generation, direct vision SADs allow vision-guided insertion, corrective manoeuvres, if needed, and correct placement in the hypopharynx and possess additional features which permit insertion of a gastric tube and endotracheal intubation should the need arise. This article describes the two new devices' physical characteristics, features, rationale for use, advantages and limitations in comparison to existing devices. Each of the two new devices-the Video Laryngeal Mask (VLMTM, UE Medical®) and the SafeLM® Video Laryngeal Mask System (SafeLMTM VLMS, Magill Medical Technology®) consist of two parts: (a) a disposable 2nd generation SAD with a silicone cuff and an anatomically curved tube; and (b) a reusable patient-isolated videoscope and monitoring screen, with the flexible scope located into a specially-designed, blind-end channel terminating in the bowl of the SAD, preventing the videoscope from contacting patient body fluids in the SAD bowl. Third generation placement-under-direct-vision supraglottic airway devices possess several theoretical safety and ease of use advantages which now need to be validated in clinical use.

Diagnosing Portal Hypertension with Noninvasive Subharmonic Pressure Estimates from a US Contrast Agent.

Background The current standard for assessing the severity of portal hypertension is the invasive acquisition of hepatic venous pressure gradient (HVPG). A noninvasive US-based technique called subharmonic-aided pressure estimation (SHAPE) could reduce risk and enable routine acquisition of these pressure estimates. Purpose To compare quantitative SHAPE to HVPG measurements to diagnose portal hypertension in participants undergoing a transjugular liver biopsy. Materials and Methods This was a prospective cross-sectional trial conducted at two hospitals between April 2015 and March 2019 (ClinicalTrials.gov identifier, NCT02489045). This trial enrolled participants who were scheduled for transjugular liver biopsy. After standard-of-care transjugular liver biopsy and HVPG pressure measurements, participants received an infusion of a US contrast agent and saline. During infusion, SHAPE data were collected from a portal vein and a hepatic vein, and the difference was compared with HVPG measurements. Correlations between data sets were determined by using the Pearson correlation coefficient, and statistical significance between groups was determined by using the Student t test. Receiver operating characteristic analysis was performed to determine the sensitivity and specificity of SHAPE. Results A total of 125 participants (mean age ± standard deviation, 59 years ± 12; 80 men) with complete data were included. Participants at increased risk for variceal hemorrhage (HVPG ≥12 mm Hg) had a higher mean SHAPE gradient compared with participants with lower HVPGs (0.79 dB ± 2.53 vs -4.95 dB ± 3.44; P < .001), which is equivalent to a sensitivity of 90% (13 of 14; 95% CI: 88, 94) and a specificity of 80% (79 of 99; 95% CI: 76, 84). The SHAPE gradient between the portal and hepatic veins was in good overall agreement with the HVPG measurements (r = 0.68). Conclusion Subharmonic-aided pressure estimation is an accurate noninvasive technique for detecting clinically significant portal hypertension. © RSNA, 2020 Online supplemental material is available for this article. See also the editorial by Kiessling in this issue.

Catalytic Insertion Reactions of α-Imino Carbenoids.

Over the past decade, α-imino carbenoids generated via transition metal (such as rhodium, nickel, copper, palladium, silver) catalyzed denitrogenative ring-opening of N-sulfonyl-1,2,3-triazoles have found an extensive account of applications in synthetic organic chemistry. Particularly, they have been widely utilized as a donor/acceptor carbene complex in a range of transformations leading to diverse nitrogen containing compounds and heterocycles. Along the same direction, 3-diazoindolin-2-imines were successfully applied as an alternative source of α-imino carbenoid precursors for the development of a number of methodologies to access diverse indole derivatives. This review summarizes the insertion reactions of α-imino metal carbenes derived from N-sulfonyl-1,2,3-triazoles and 3-diazoindolin-2-imines.

Rh(III)-Catalyzed Stereoselective C-C Bond Cleavage of ACPs with N-Phenoxyacetamides: The Critical Role of the Nucleophilic Directing Group.

Rh(III)-catalyzed redox-neutral chemodivergent coupling of N-phenoxyacetamides and alkylidenecyclopropanes (ACPs) has been documented. The reaction proceeds via C-H activation, regioselective migratory insertion and stereoselective ß-carbon elimination followed by ß-hydride elimination, resulting in o-dienylation of phenols in nonpolar solvents, whereas [3 + 2]-annulation leading to dihydrobenzofurans was realized in polar fluorinated solvents. It was observed that the nucleophilic directing group controls the elimination of ß-carbon and so plays a vital role for achieving high stereoselectivities. The synthetic utility of the dienylation and annulation was demonstrated by carrying out gram scale reactions and further derivatization.

Hepatic Vein Contrast-Enhanced Ultrasound Subharmonic Imaging Signal as a Screening Test for Portal Hypertension.

BACKGROUND: Portal hypertension is the underlying cause of most complications associated with cirrhosis, with the hepatic venous pressure gradient (HVPG) used for diagnosis and disease progression. Subharmonic imaging (SHI) is a contrast-specific imaging technique receiving at half the transmit frequency resulting in better tissue suppression. AIMS: To determine whether the presence of optimized SHI signals inside the hepatic vein can be used as a screening test for portal hypertension. METHODS: This prospective trial had 131 patients undergoing SHI examination of portal and hepatic veins using a modified Logiq 9 scanner (GE, Waukesha, WI). Images acquired after infusion of the ultrasound contrast agent Sonazoid (GE Healthcare, Oslo, Norway) were assessed for the presence of optimized SHI signals in the hepatic vein and compared to the HVPG values obtained as standard of care. RESULTS: Of 131 cases, 64 had increased HVPG values corresponding to subclinical (n = 31) and clinical (n = 33) portal hypertension (> 5 and > 10 mmHg, respectively), and 67 had normal HVPG values (< 5 mmHg). Two readers performed independent, binary qualitative assessments of the acquired digital clips. Reader one (experienced radiologist) achieved for the subclinical subgroup sensitivity of 98%, specificity of 88%, and ROC area of 0.93 and for the clinical subgroup sensitivity of 100% and specificity of 61%, with an ROC area of 0.74. Reader two (less experienced radiologist) achieved for the subclinical subgroup sensitivity of 77%, specificity of 76%, and ROC area of 0.76 and for the clinical subgroup sensitivity of 88% and specificity of 63%, with an ROC area of 0.70. Readers agreement was of 83% with kappa value of 0.66. CONCLUSION: The presence of optimized SHI signals inside the hepatic vein can be a qualitative screening test for portal hypertension, which could reduce the need for invasive diagnostic procedures.

Association of Obstructive Sleep Apnea With Difficult Intubation: Prospective Multicenter Observational Cohort Study.

BACKGROUND: Obstructive sleep apnea (OSA) has been found to be associated with difficult airway, although there is a paucity of prospective studies investigating thresholds of OSA severity with difficult airway outcomes. The aim of this study was to examine the association between OSA and difficult intubation or difficult mask ventilation. We also explored the utility of the Snoring, Tiredness, Observed apnea, high blood Pressure, Body mass index, Age, Neck circumference, and Gender (STOP-Bang) score for difficult airway prediction. METHODS: The Postoperative Vascular Complications in Unrecognized Obstructive Sleep Apnea (POSA) trial was an international prospective cohort study of surgical patients 45 years or older with one or more cardiac risk factor presenting for noncardiac surgery, with planned secondary analyses of difficult airway outcomes. Multivariable logistic regression analyses tested associations between OSA severity and predictors of difficult airway with difficult intubation or difficult mask ventilation. Overall, 869 patients without prior diagnosis of OSA were screened for OSA risk with the STOP-Bang tool, underwent preoperative sleep study, and had routine perioperative care, including general anesthesia with tracheal intubation. The primary outcome analyzed was difficult intubation, and the secondary outcome was difficult mask ventilation. RESULTS: Based on the sleep studies, 287 (33%), 324 (37%), 169 (20%), and 89 (10%) of the 869 patients had no, mild, moderate, and severe OSA, respectively. One hundred and seventy-two (20%) had a STOP-Bang score of 0-2 (low risk), 483 (55%) had a STOP-Bang score of 3-4 (intermediate risk), and 214 (25%) had a STOP-Bang score 5-8 (high risk). The incidence of difficult intubation was 6.7% (58 of 869), and difficult mask ventilation was 3.7% (32 of 869). Multivariable logistic regression demonstrated that moderate OSA (odds ratio [OR] = 3.26 [95% confidence interval {CI}, 1.37-8.38], adjusted P = .010) and severe OSA (OR = 4.05 [95% CI, 1.51-11.36], adjusted P = .006) but not mild OSA were independently associated with difficult intubation compared to patients without OSA. Relative to scores of 0-2, STOP-Bang scores of 3-4 and 5-8 were associated with increased odds of difficult intubation (OR = 3.01 [95% CI, 1.13-10.40, adjusted P = .046] and 4.38 [95% CI, 1.46-16.36, adjusted P = .014]), respectively. OSA was not associated with difficult mask ventilation, and only increasing neck circumference was found to be associated (adjusted P = .002). CONCLUSIONS: Moderate and severe OSA were associated with difficult intubation, and increasing neck circumference was associated with difficult mask ventilation. A higher STOP-Bang score of 3 or more may be associated with difficult intubation versus STOP-Bang score of 0-2. Anesthesiologists should be vigilant for difficult intubation when managing patients suspected or diagnosed with OSA.

Time to consider supraglottic airway device oropharyngeal leak pressure measurement more objectively.

Oropharyngeal leak pressure (OLP) is considered a measure of successful placement, adequate performance and is a useful comparator between supraglottic airway devices (SADs). OLP measurement is based on the premise that the SAD is sited properly in the hypopharynx after blind placements, but the evidence suggests otherwise. Several limitations and controversies surround OLP. This editorial addresses the uses and pitfalls of OLP, the rationale for and methods of ascertaining OLP, the pros and cons of OLP measurement and newer modalities to improve its accuracy.