Functional Protein Dynamics in a Crystal.

Proteins are molecular machines and to understand how they work, we need to understand how they move. New pump-probe time-resolved X-ray diffraction methods open up ways to initiate and observe protein motions with atomistic detail in crystals on biologically relevant timescales. However, practical limitations of these experiments demands parallel development of effective molecular dynamics approaches to accelerate progress and extract meaning. Here, we establish robust and accurate methods for simulating dynamics in protein crystals, a nontrivial process requiring careful attention to equilibration, environmental composition, and choice of force fields. With more than seven milliseconds of sampling of a single chain, we identify critical factors controlling agreement between simulation and experiments and show that simulated motions recapitulate ligand-induced conformational changes. This work enables a virtuous cycle between simulation and experiments for visualizing and understanding the basic functional motions of proteins.

Unfermented ß-fructan Fibers Fuel Inflammation in Select Inflammatory Bowel Disease Patients.

BACKGROUND & AIMS: Inflammatory bowel diseases (IBD) are affected by dietary factors, including nondigestible carbohydrates (fibers), which are fermented by colonic microbes. Fibers are overall beneficial, but not all fibers are alike, and some patients with IBD report intolerance to fiber consumption. Given reproducible evidence of reduced fiber-fermenting microbes in patients with IBD, we hypothesized that fibers remain intact in select patients with reduced fiber-fermenting microbes and can then bind host cell receptors, subsequently promoting gut inflammation. METHODS: Colonic biopsies cultured ex vivo and cell lines in vitro were incubated with oligofructose (5 g/L), or fermentation supernatants (24-hour anaerobic fermentation) and immune responses (cytokine secretion [enzyme-linked immunosorbent assay/meso scale discovery] and expression [quantitative polymerase chain reaction]) were assessed. Influence of microbiota in mediating host response was examined and taxonomic classification of microbiota was conducted with Kraken2 and metabolic profiling by HUMAnN2, using R software. RESULTS: Unfermented dietary ß-fructan fibers induced proinflammatory cytokines in a subset of IBD intestinal biopsies cultured ex vivo, and immune cells (including peripheral blood mononuclear cells). Results were validated in an adult IBD randomized controlled trial examining ß-fructan supplementation. The proinflammatory response to intact ß-fructan required activation of the NLRP3 and TLR2 pathways. Fermentation of ß-fructans by human gut whole microbiota cultures reduced the proinflammatory response, but only when microbes were collected from patients without IBD or patients with inactive IBD. Fiber-induced immune responses correlated with microbe functions, luminal metabolites, and dietary fiber avoidance. CONCLUSION: Although fibers are typically beneficial in individuals with normal microbial fermentative potential, some dietary fibers have detrimental effects in select patients with active IBD who lack fermentative microbe activities. The study is publicly accessible at the U.S. National Institutes of Health database (clinicaltrials.gov identification number NCT02865707).

Airway obstruction time and outcomes in patients with foreign body airway obstruction: multicenter observational choking investigation.

Aim: Foreign body airway obstruction (FBAO) is a major public health concern worldwide for infants and older adults. This study determines the association between airway obstruction time and neurological outcomes to plan an effective response for patients with FBAO. Methods: This multicenter retrospective observational study was carried out among patients with life-threatening FBAO in Japan over a period of 4 years. The duration of airway obstruction was calculated from the time of the accident to the time of foreign body removal. The study examined the relationship between airway obstruction time and outcome. The primary outcome was vegetative state or death at hospital discharge. Results: Among 119 patients, 68 were in the category of vegetative state or death. Logistic regression analysis showed that longer airway obstruction time (adjusted odds ratio 1.04; 95% confidence interval 1.01-1.07) was associated with vegetative state or death. When the cut-off value was set at 10, the sensitivity was 0.88, the specificity 0.47, with the area under the curve 0.69. Using the other cut-off value of 4 min, the negative predictive value was 1.00. Conclusion: Longer airway obstruction time was associated with vegetative state or death for patients with FBAO. The incidence of vegetative state or death increased when the airway obstruction time exceeded 10 min. Meanwhile, 4 min or less may be set as a target time for foreign body removal in order to prevent vegetative state or death and plan an effective response.

Protocol for a nationwide prospective, observational cohort study of foreign-body airway obstruction in Japan: the MOCHI registry.

INTRODUCTION: Foreign body airway obstruction (FBAO) is a major public health issue worldwide. In 2017, there were more than 5000 fatal choking cases in the USA alone, and it was the fourth leading cause of preventable injury-related death in the home and community. In Japan, FBAO is the leading cause of accidental death and with almost 9000 fatalities annually. However, research on FBAO is limited, particularly on the impact of a foreign body (FB) removal manoeuvres by bystanders. The primary objective of this study is to determine the impact of bystander FB removal manoeuvres on 1 month neurological outcome. Our secondary objectives include (1) evaluating the efficacy of a variety of FB removal manoeuvres; (2) identifying risk factors for unsuccessful removal and (3) evaluating the impact of time intervals from incidents of FBAO to FB removal on neurological outcome. METHODS AND ANALYSIS: We will conduct a nationwide multi-centre prospective cohort study of patients with FBAO who present to approximately 100 emergency departments in both urban and rural areas in Japan. Research personnel at each participating site will collect variables including patient demographics, type of FB and prehospital variables, such as bystander FB removal manoeuvres, medical interventions by prehospital personnel, advanced airway management and diagnostic findings. Our primary outcome is 1 month favourable neurological outcome defined as cerebral performance category 1 or 2. Our secondary outcomes include success of FB removal manoeuvres and complications from the manoeuvres. We hypothesise that bystander FB removal manoeuvres improve patient survival with a favourable neurological outcome. ETHICS AND DISSEMINATION: This study received research ethics approval from Nippon Medical School Hospital (B-2019-019). Research ethics approval will be obtained from all participating sites before entering patients into the registry. The study was registered at the University Hospital Medical Information Network (UMIN) Clinical Trials Registry. TRIAL REGISTRATION NUMBER: UMIN 000039907.

New classifications for Life-threatening foreign body airway obstruction.

INTRODUCTION: Foreign body airway obstruction (FBAO) is a common medical emergency; however, few studies of life-threatening FBAO have been reported and no standard classification system is available. METHODS: We retrospectively evaluated patients who presented to the emergency departments of two hospitals and were diagnosed with FBAO. The primary outcome was cerebral performance category (CPC) score at discharge. To establish a new classification system for FBAO, FBAO was classified into three types based on the anatomical and physiological characteristics of the obstructed airway. RESULTS: A total of 137 patients were enrolled. Median age was 79.0 years. The most common cause of FBAO was meat, followed by bread, rice cake, and rice. Of all patients, 65.7% suffered cardiac arrest and 51.1% died. In contrast, 28.5% had favorable neurological outcomes, defined as CPC 1 and 2. Upper airway obstruction (type 1) was the most common (type 1, 78.1%), while trachea and/or bilateral main bronchus obstruction (type 2, 12.4%) showed significantly higher mortality than type 1 obstruction (82.4% vs 47.7%, P = 0.0078). Patients with unilateral bronchus and/or distal bronchus obstruction (type 3, 9.5%) were significantly more likely to consume a dysphagia diet than type 1 patients (23.1% vs 0%, P < 0.0001). CONCLUSION: The majority of patients with life-threatening FBAO were elderly and had poor neurological outcomes. Our new classification system divides FBAO into three types, and revealed that mortality was significantly higher with type 2 than type 1 obstruction. This classification system may improve the management of patients with FBAO and assessment of patient outcomes.