Understanding ATP Binding to DosS Catalytic Domain with a Short ATP-Lid.

DosS is a heme-containing histidine kinase that triggers dormancy transformation inMycobacterium tuberculosis. Sequence comparison of the catalytic ATP-binding (CA) domain of DosS to other well-studied histidine kinases reveals a short ATP-lid. This feature has been thought to block binding of ATP to DosS's CA domain in the absence of interactions with DosS's dimerization and histidine phospho-transfer (DHp) domain. Here, we use a combination of computational modeling, structural biology, and biophysical studies to re-examine ATP-binding modalities in DosS. We show that the closed-lid conformation observed in crystal structures of DosS CA is caused by the presence of Zn2+ in the ATP binding pocket that coordinates with Glu537 on the ATP-lid. Furthermore, circular dichroism studies and comparisons of DosS CA's crystal structure with its AlphaFold model and homologous DesK reveal that residues 503-507 that appear as a random coil in the Zn2+-coordinated crystal structure are in fact part of the N-box α helix needed for efficient ATP binding. Such random-coil transformation of an N-box α helix turn and the closed-lid conformation are both artifacts arising from large millimolar Zn2+ concentrations used in DosS CA crystallization buffers. In contrast, in the absence of Zn2+, the short ATP-lid of DosS CA has significant conformational flexibility and can effectively bind AMP-PNP (Kd = 53 ± 13 µM), a non-hydrolyzable ATP analog. Furthermore, the nucleotide affinity remains unchanged when CA is conjugated to the DHp domain (Kd = 51 ± 6 µM). In all, our findings reveal that the short ATP-lid of DosS CA does not hinder ATP binding and provide insights that extend to 2988 homologous bacterial proteins containing such ATP-lids.

Ideation and assessment of a nitric oxide delivery system for spontaneously breathing subjects.

BACKGROUND: There is an increasing interest in safely delivering high dose of inhaled nitric oxide (NO) as an antimicrobial and antiviral therapeutics for spontaneously breathing patients. A novel NO delivery system is described. METHODS: We developed a gas delivery system that utilizes standard respiratory circuit connectors, a reservoir bag, and a scavenging chamber containing calcium hydroxide. The performance of the system was tested using a mechanical lung, assessing the NO concentration delivered at varying inspiratory flows. Safety was assessed in vitro and in vivo by measuring nitrogen dioxide (NO2) levels in the delivered NO gas. Lastly, we measured the inspired and expired NO and NO2 of this system in 5 healthy subjects during a 15-min administration of high dose NO (160 parts-per-million, ppm) using our delivery system. RESULTS: The system demonstrated stable delivery of prescribed NO levels at various inspiratory flow rates (0-50 L/min). The reservoir bag and a high flow of entering air minimized the oscillation of NO concentrations during inspiration on average 4.6 ppm for each 10 L/min increment in lung inspiratory flow. The calcium hydroxide scavenger reduced the inhaled NO2 concentration on average 0.9 ppm (95% CI -1.58, -0.22; p = .01). We performed 49 NO administrations of 160 ppm in 5 subjects. The average concentration of inspired NO was 164.8±10.74 ppm, with inspired NO2 levels of 0.7±0.13 ppm. The subjects did not experience any adverse events; transcutaneous methemoglobin concentrations increased from 1.05±0.58 to 2.26±0.47%. CONCLUSIONS: The system we developed to administer high-dose NO for inhalation is easy to build, reliable, was well tolerated in healthy subjects.

Understanding ATP binding to DosS catalytic domain with a short ATP-lid.

DosS is a heme-sensor histidine kinase that responds to redox-active stimuli in mycobacterial environments by triggering dormancy transformation. Sequence comparison of the catalytic ATP-binding (CA) domain of DosS to other well-studied histidine kinases suggests that it possesses a rather short ATP-lid. This feature has been thought to inhibit DosS kinase activity by blocking ATP binding in the absence of interdomain interactions with the dimerization and histidine phospho-transfer (DHp) domain of full-length DosS. Here, we use a combination of computational modeling, structural biology, and biophysical studies to re-examine ATP-binding modalities in DosS's CA domain. We show that the closed lid conformation observed in protein crystal structures of DosS CA is caused by the presence of a zinc cation in the ATP binding pocket that coordinates with a glutamate residue on the ATP-lid. Furthermore, circular dichroism (CD) studies and comparisons of DosS CA crystal structure with its AlphaFold model and homologous DesK reveal that a key N-box alpha-helix turn of the ATP pocket manifests as a random coil in the zinc-coordinated protein crystal structure. We note that this closed lid conformation and the random-coil transformation of an N-box alpha-helix turn are artifacts arising from the millimolar zinc concentration used in DosS CA crystallization conditions. In contrast, in the absence of zinc, we find that the short ATP-lid of DosS CA has significant conformational flexibility and can bind ATP (Kd = 53 ± 13 µM). We conclude that DosS CA is almost always bound to ATP under physiological conditions (1-5 mM ATP, sub-nanomolar free zinc) in the bacterial environment. Our findings elucidate the conformational adaptability of the short ATP-lid, its relevance to ATP binding in DosS CA and provide insights that extends to 2988 homologous bacterial proteins containing such ATP-lids.

Metalloprotein enabled redox signal transduction in microbes.

Microbes utilize numerous metal cofactor-containing proteins to recognize and respond to constantly fluctuating redox stresses in their environment. Gaining an understanding of how these metalloproteins sense redox events, and how they communicate such information downstream to DNA to modulate microbial metabolism, is a topic of great interest to both chemists and biologists. In this article, we review recently characterized examples of metalloprotein sensors, focusing on the coordination and oxidation state of the metals involved, how these metals are able to recognize redox stimuli, and how the signal is transmitted beyond the metal center. We discuss specific examples of iron, nickel, and manganese-based microbial sensors, and identify gaps in knowledge in the field of metalloprotein-based signal transduction pathways.

Patient hesitancy in perioperative clinical trial enrollment during the COVID-19 pandemic.

The COVID-19 pandemic has caused tremendous disruptions to non-COVID-19 clinical research. However, there has been little investigation on how patients themselves have responded to clinical trial recruitment during the COVID-19 pandemic. To investigate the effect of the COVID-19 pandemic on rates of patient consent to enrollment into non-COVID-19 clinical trials, we carried out a cross-sectional study using data from the Nitric Oxide/Acute Kidney Injury (NO/AKI) and Minimizing ICU Neurological Dysfunction with Dexmedetomidine-Induced Sleep (MINDDS) trials. All patients eligible for the NO/AKI or MINDDS trials who came to the hospital for cardiac surgery and were approached to gain consent to enrollment were included in the current study. We defined "Before COVID-19" as the time between the start of the relevant clinical trial and the date when efforts toward that clinical trial were deescalated by the hospital due to COVID-19. We defined "During COVID-19" as the time between trial de-escalation and trial completion. 5,015 patients were screened for eligibility. 3,851 were excluded, and 1,434 were approached to gain consent to enrollment. The rate of consent to enrollment was 64% in the "Before COVID-19" group and 45% in the "During COVID-19" group (n = 1,334, P<0.001) (RR = 0.70, 95% CI 0.62 to 0.80, P<0.001). Thus, we found that rates of consent to enrollment into the NO/AKI and MINDDS trials dropped significantly with the onset of the COVID-19 pandemic. Patient demographic and socioeconomic status data collected from electronic medical records and patient survey data did not shed light on possible explanations for this observed drop, indicating that there were likely other factors at play that were not directly measured in the current study. Increased patient hesitancy to enroll in clinical trials can have detrimental effects on clinical science, patient health, and patient healthcare experience, so understanding and addressing this issue during the COVID-19 pandemic is crucial.

Individualized Multimodal Physiologic Approach to Mechanical Ventilation in Patients With Obesity and Severe Acute Respiratory Distress Syndrome Reduced Venovenous Extracorporeal Membrane Oxygenation Utilization.

OBJECTIVE: To investigate whether individualized optimization of mechanical ventilation through the implementation of a lung rescue team could reduce the need for venovenous extracorporeal membrane oxygenation in patients with obesity and acute respiratory distress syndrome and decrease ICU and hospital length of stay and mortality. DESIGN: Single-center, retrospective study at the Massachusetts General Hospital from June 2015 to June 2019. PATIENTS: All patients with obesity and acute respiratory distress syndrome who were referred for venovenous extracorporeal membrane oxygenation evaluation due to hypoxemic respiratory failure. INTERVENTION: Evaluation and individualized optimization of mechanical ventilation by the lung rescue team before the decision to proceed with venovenous extracorporeal membrane oxygenation. The control group was those patients managed according to hospital standard of care without lung rescue team evaluation. MEASUREMENT AND MAIN RESULTS: All 20 patients (100%) allocated in the control group received venovenous extracorporeal membrane oxygenation, whereas 10 of 13 patients (77%) evaluated by the lung rescue team did not receive venovenous extracorporeal membrane oxygenation. Patients who underwent lung rescue team evaluation had a shorter duration of mechanical ventilation (p = 0.03) and shorter ICU length of stay (p = 0.03). There were no differences between groups in in-hospital, 30-day, or 1-year mortality. CONCLUSIONS: In this hypothesis-generating study, individualized optimization of mechanical ventilation of patients with acute respiratory distress syndrome and obesity by a lung rescue team was associated with a decrease in the utilization of venovenous extracorporeal membrane oxygenation, duration of mechanical ventilation, and ICU length of stay. Mortality was not modified by the lung rescue team intervention.

High Concentrations of Nitric Oxide Inhalation Therapy in Pregnant Patients With Severe Coronavirus Disease 2019 (COVID-19).

BACKGROUND: Rescue therapies to treat or prevent progression of coronavirus disease 2019 (COVID-19) hypoxic respiratory failure in pregnant patients are lacking. METHOD: To treat pregnant patients meeting criteria for severe or critical COVID-19 with high-dose (160-200 ppm) nitric oxide by mask twice daily and report on their clinical response. EXPERIENCE: Six pregnant patients were admitted with severe or critical COVID-19 at Massachusetts General Hospital from April to June 2020 and received inhalational nitric oxide therapy. All patients tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. A total of 39 treatments was administered. An improvement in cardiopulmonary function was observed after commencing nitric oxide gas, as evidenced by an increase in systemic oxygenation in each administration session among those with evidence of baseline hypoxemia and reduction of tachypnea in all patients in each session. Three patients delivered a total of four neonates during hospitalization. At 28-day follow-up, all three patients were home and their newborns were in good condition. Three of the six patients remain pregnant after hospital discharge. Five patients had two negative test results on nasopharyngeal swab for SARS-CoV-2 within 28 days from admission. CONCLUSION: Nitric oxide at 160-200 ppm is easy to use, appears to be well tolerated, and might be of benefit in pregnant patients with COVID-19 with hypoxic respiratory failure.

Inhaled nitric oxide prevents systemic and pulmonary vasoconstriction due to hemoglobin-based oxygen carrier infusion: A case report.

Hemoglobin-based oxygen carriers (HBOCs) are used in extreme circumstances to increase hemoglobin concentration and improve oxygen delivery when allogenic red blood cell transfusions are contraindicated or not immediately available. However, HBOC-induced severe pulmonary and systemic vasoconstriction due to peripheral nitric oxide (NO) scavenging has stalled its implementation in clinical practice. We present a case of an 87 year-old patient with acute life-threatening anemia who received HBOC while breathing NO gas. This case shows that inhaled NO allows for the safe use of HBOC infusion by preventing HBOC-induced pulmonary and systemic vasoconstriction.

Protocol of a randomised controlled trial in cardiac surgical patients with endothelial dysfunction aimed to prevent postoperative acute kidney injury by administering nitric oxide gas.

INTRODUCTION: Postoperative acute kidney injury (AKI) is a common complication in cardiac surgery. Levels of intravascular haemolysis are strongly associated with postoperative AKI and with prolonged (>90 min) use of cardiopulmonary bypass (CPB). Ferrous plasma haemoglobin released into the circulation acts as a scavenger of nitric oxide (NO) produced by endothelial cells. Consequently, the vascular bioavailability of NO is reduced, leading to vasoconstriction and impaired renal function. In patients with cardiovascular risk factors, the endothelium is dysfunctional and cannot replenish the NO deficit. A previous clinical study in young cardiac surgical patients with rheumatic fever, without evidence of endothelial dysfunction, showed that supplementation of NO gas decreases AKI by converting ferrous plasma haemoglobin to ferric methaemoglobin, thus preserving vascular NO. In this current trial, we hypothesised that 24 hours administration of NO gas will reduce AKI following CPB in patients with endothelial dysfunction. METHODS: This is a single-centre, randomised (1:1) controlled, parallel-arm superiority trial that includes patients with endothelial dysfunction, stable kidney function and who are undergoing cardiac surgery procedures with an expected CPB duration >90 min. After randomisation, 80 parts per million (ppm) NO (intervention group) or 80 ppm nitrogen (N2, control group) are added to the gas mixture. Test gases (N2 or NO) are delivered during CPB and for 24 hours after surgery. The primary study outcome is the occurrence of AKI among study groups. Key secondary outcomes include AKI severity, occurrence of renal replacement therapy, major adverse kidney events at 6 weeks after surgery and mortality. We are recruiting 250 patients, allowing detection of a 35% AKI relative risk reduction, assuming a two-sided error of 0.05. ETHICS AND DISSEMINATION: The Partners Human Research Committee approved this trial. Recruitment began in February 2017. Dissemination plans include presentations at scientific conferences, scientific publications and advertising flyers and posters at Massachusetts General Hospital. TRIAL REGISTRATION NUMBER: NCT02836899.

An interactive contouring module improves engagement and interest in radiation oncology among preclinical medical students: Results of a randomized trial.

PURPOSE: Studies have shown significant gaps in knowledge of radiation therapy among medical students and primary care providers. The goal of this study was to evaluate the effect of an interactive contouring module on knowledge and interest in radiation oncology among preclinical medical students. METHODS AND MATERIALS: Second-year medical students at the University of California, San Diego were randomized to participate in an interactive contouring exercise or watch a traditional didactic lecture on radiation oncology. Participants completed knowledge tests and surveys at baseline, immediately following the exercise, and 3 months later. Statistical analysis included Wilcoxon signed-rank test for pre- and posttest comparisons and Wilcoxon rank sum test for comparison between groups. RESULTS: Forty-three medical students participated in the trial (21 in the didactic group; 22 in the contouring group). Students completing the contouring module demonstrated similar overall knowledge improvement compared with the traditional didactic group (+8.6% vs +6.6%, not significant) but endorsed greater engagement on a 5-point Likert-type scale (3.10 vs 3.76, P = .02). At 3-month follow-up, there was a nonsignificant trend toward improved overall knowledge in the contouring group (43% vs 51%, P = .10), with a significance difference in a subset of questions on knowledge of the process of radiation therapy as well as side effects (51% vs 75%, P = .002). Students in the contouring group demonstrated more interest in pursuing a clinical radiation oncology rotation (2.52 vs 3.27, P = .01). CONCLUSIONS: Use of an interactive contouring module was an effective method to teach preclinical medical students about radiation oncology, with no significant difference in knowledge gained compared with a traditional didactic lecture; however, higher engagement among students completing the contouring module led to improved retention of knowledge of radiation side effects and greater interest in radiation oncology. These data suggest a potential benefit of integrating an interactive radiation oncology module into the preclinical medical school curriculum.

Multi-institutional Randomized Trial Testing the Utility of an Interactive Three-dimensional Contouring Atlas Among Radiation Oncology Residents.

PURPOSE: The delivery of safe and effective radiation therapy relies on accurate target delineation, particularly in the era of highly conformal treatment techniques. Current contouring resources are fragmented and can be cumbersome to use. The present study reports on the efficacy and usability of a web-based contouring atlas compared with those of existing contouring resources in a randomized trial. METHODS AND MATERIALS: We enrolled radiation oncology residents into a 2-phase contouring study. All residents contoured a T1N1 nasopharyngeal cancer case using the currently available resources. The participants were then randomized to recontour the case with access to existing resources or an interactive web-based contouring atlas (eContour.org). Contour analysis was performed using conformation number and simultaneous truth and performance level estimation. At completion of the second contouring session, the residents completed a multiple choice question knowledge test and a 10-item System Usability Scale. RESULTS: Twenty-four residents from 5 institutions completed the study. Compared with the residents using currently available resources, the residents using eContour had improved contour agreement with both the consensus (0.63 vs 0.52; P=.02) and the expert (0.58 vs 0.50; P=.01) contours for the high-risk clinical target volume and greater agreement with the expert contour for the contralateral parotid gland (0.44 ± 0.12 vs 0.56 ± 0.08; P=.003). The residents using eContour demonstrated greater knowledge of contour delineation and radiographic anatomy on a multiple-choice knowledge-based test (89% vs 77%; P=.03). Usability (89 vs 66; P<.0001) and satisfaction (4.1 vs 3.0; P=.002) were greater for eContour than for the existing resources. CONCLUSIONS: This study demonstrates the capacity of an interactive 3-dimensional contouring atlas to improve quality of resident target delineation in radiation oncology. Further research is needed to define the utility of easily accessible interactive educational reference tool to improve adherence to contouring-based guidelines and quality of care in routine clinical practice.

Use of the Modification of Diet in Renal Disease Equation for Estimating Glomerular Filtration Rate in the Urologic Literature.

PURPOSE: To evaluate the use of the modification of diet in renal disease (MDRD) equation in the urologic literature and the degree to which it is used appropriately. METHODS: Medline was queried searching the title, keywords, or abstract of seven urology journals for the exact phrases "MDRD" or "modification of diet in renal disease." Forty-seven articles published between 2004 and 2013 met the inclusion criteria and were reviewed. Each article was reviewed in its entirety and graded on the appropriateness of its use of MDRD to estimate glomerular filtration rate (GFR). Inappropriate use was defined as using the MDRD equation to make comparisons or conclusions about true renal function with the majority of estimated glomerular filtration rate (eGFR) values >60 mL/min per 1.73 m(2). RESULTS: Of the 47 articles reviewed, 17 (36%) were Grade 1 (appropriate use of MDRD), 20 (43%) were Grade 2 (inappropriate use of MDRD but not critical to claims of article), and 10 (21%) were Grade 3 (inappropriate use of MDRD). Of the Grade 3 articles, only 40% (4 of 10) acknowledged the limitations of this equation for estimating GFR. CONCLUSIONS: The majority of articles using the MDRD equation to estimate GFR did so using values where the estimate is quite unstable (eGFR >60 mL/min per 1.73 m(2)), thereby limiting the validity of the claims. Urologists should reconsider the use of MDRD for comparing estimates of GFR in patients with normal renal function in published articles.