Draft Genome Sequence of Rhodococcus sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium.

We report here the 4.9-Mb genome sequence of a quinoline-degrading bacterium, Rhodococcus sp. strain ATCC 49988. The draft genome data will enable the identification of genes and future genetic modification to enhance traits relevant to heteroaromatic compound degradation

Laser-induced hierarchical carbon patterns on polyimide substrates for flexible urea sensors

Thermochemical decomposition of organic materials under heat-treatment in the absence of oxygen, known as the pyrolysis process, is often employed to convert micro and nano patterned polymers into carbon structures, which are subsequently used as device components. Pyrolysis is performed at ≥900 °C, which entails substrate materials with a high thermal stability that excludes flexible, polymeric substrates. We use optimized laser radiation to pattern graphitic carbon structures onto commercially available polyimide (Kapton) sheets in the micrometer to millimeter scale by inducing a localized, rapid pyrolysis, for the fabrication of flexible devices. Resulting laser carbon films are electrically conductive and exhibit a high-surface area with a hierarchical porosity distribution along their cross-section. The material is obtained using various combinations of laser parameters and pyrolysis environment (oxygen-containing and inert). Extensive characterization of laser carbon is performed to understand the correlation between the material properties and laser parameters, primarily fluence and power. A photothermal carbonization mechanism based on the plume formation is proposed. Further, laser carbon is used for the fabrication of enzymatic, pH-based urea sensors using two approaches: (i) direct urease enzyme immobilization onto carbon and (ii) electrodeposition of an intermediate chitosan layer prior to urease immobilization. This flexible sensor is tested for quantitative urea detection down to 10−4 M concentrations, while a qualitative, color-indicative test is performed on a folded sensor placed inside a tube to demonstrate its compatibility with catheters. Laser carbon is suitable for a variety of other flexible electronics and sensors, can be conveniently integrated with an external circuitry, heating elements, and with other microfabrication techniques such as fluidic platforms

COVID-19 and Acute Esophageal Obstruction Management in the Emergency Department: An U.S. multicenter research network propensity-matched analysis

Introduction- The Coronavirus Disease-2019 (COVID-19) caused by the novel SARS-CoV-2 led to significant strain on the Emergency Department (ED) visits worldwide. Multiple stay-at-home orders were issued during the pandemic unless medical treatment was urgently needed . Acute esophageal obstruction (AEO) due to food/ foreign body impaction usually present to the ED, given its severe symptoms. Most esophageal foreign bodies pass through the gastrointestinal (GI) tract uneventfully, and related mortality is very low. Still, most of these patients receive endoscopic interventions (up to 76%). The number of non-urgent endoscopies plummeted sharply during the pandemic to reduce exposure and preserve personal protective equipment. It is unclear if ED visits for AEO and their endoscopic management changed due to the COVID-19 pandemic in the United States (US). Methods- We utilized a federated cloud-based network database named TriNetX, which provides access to electronic medical records from 92 healthcare organizations from the US. The AEO adult patients hospitalized from January 1, 2020, to December 1, 2020, were compared to a similar timeline in 2019 from TriNetX. We used ICD-10 codes for food/foreign body in esophagus, causing other injury acute food impaction (T18.128 A, T18.12), foreign body esophagus (T18.198, T18.1, T18.19, T18.108, T18.108A). Outcomes of the study included utilization rates of esophagogastroduodenoscopy (EGD), esophageal perforation, inpatient hospitalization, and mortality. The outcomes were measured before and after 1:1 propensity matching of the groups based on the baseline demographics and comorbidities. Results- Prevalence of AEO among all ED visits in 2020 were 0.12% (5890 AEO ED visits among 4,672,024 total visits), compared to 0.17% (23,478 AEO ED visits among 14,199,648 total visits) in 2019. There was a small but significant decrease (0.05%) in AEO ED visits from pre-pandemic compared to pandemic times (P<0.01). Patient with AEO had higher prevalence of eosinophilic esophagitis (mean 270 [4.6%] vs. 885 [3.8%], p=0.004) and alcohol-related disorders (mean 465 5 [7.9%] vs. 1659 [7.1%], p=0.03) in 2020 group vs. 2019 group. Patients in the 2020-group had a lower EGD utilization (RR 0.63,95%CI:0.58–0.67, p<0.001) but esophageal perforation (RR 0.87,95%CI:0.41–1.82) and inpatient hospitalization rates (RR 0.92,95%CI:0.79-1.05) did not differ between two groups. Interestingly, during the pandemic, the AEO patients had a lower mortality rate (RR 0.23, 95%CI:0.17–0.31, p<0.001) than in 2019. Conclusion With the advent of COVID-19, multiple stay-at-home orders were issued in the US, with widespread healthcare services and utilization disruption. Patients have expressed concerns about visiting healthcare facilities due to the potential of the spread of SARS-CoV-2 . Many GI societies also recommended deferring elective procedures. This was due to a concern for potential transmission of the virus from aerosolization of GI secretions and judicious use of PPE, which resulted in an overall reduction in the number of endoscopies during the pandemic. Our study shows a small reduction (0.05%) of AEO ED visits in 2020 compared to 2019. However, EGD utilization plummeted to 63% for AEO in 2020. If this is due to spontaneous resolution of the food impaction or reduced presentations to the ED needs to be studied prospectively

The Utility of Cervical Spine Bracing As a Postoperative Adjunct to Multilevel Anterior Cervical Spine Surgery

Background: Use of cervical bracing/collar subsequent to anterior cervical spine discectomy and fusion (ACDF) is variable. Outcomes data regarding bracing after ACDF are limited. Here, we study the impact of bracing on short-term outcomes related to safety, quality of care, and direct costs in multilevel ACDF.Methods: Retrospective cohort analyses of all consecutive patients undergoing multilevel ACDF with or without bracing from 2013 to 2017 was undertaken (n = 616). Patient demographics and comorbidities were analyzed. Tests of independence and logistic regressions were used to assess differences in length of stay (LOS), discharge disposition (home, assisted rehabilitation facility [ARF], or skilled nursing facility [SNF]), quality-adjusted life year (QALY), direct cost, readmission within 30 days, and emergency room (ER) visits within 30 days.Results: Amongst the study population, 553 were braced and 63 were not braced. There was no difference in comorbidities (P \u3e .05) such as obesity, smoking, chronic obstructive pulmonary disease, hypertension, coronary artery disease, congestive heart failure, and problem list number. A significant difference in American Society of Anesthesiologists (ASA) score was found, with more ASA 2 patients in the braced cohort and more ASA 3 patients in the unbraced cohort (P = .007). LOS was extended for the unbraced group (median 156.9 +/- 211.4 versus 86.67 +/- 130.6 h, P = .003), and ER visits within 30 days were 0.21 times less likely in the braced group (P = .006). There was no difference in readmission (P = .181), QALY gain (P = .968), and direct costs (P = .689).Conclusion: Bracing following multilevel cervical fixation does not alter short-term postoperative course or reduce the risk for early adverse outcomes in a significant manner

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction

Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5′ ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct

STEAP4 expression in human islets is associated with differences in body mass index, sex, HbA1c, and inflammation

Objective STEAP4 (six-transmembrane epithelial antigen of the prostate 4) is a metalloreductase that has been shown previously to protect cells from inflammatory damage. Genetic variants in STEAP4 have been associated with numerous metabolic disorders related to obesity, including putative defects in the acute insulin response to glucose in type 2 diabetes. Purpose We examined whether obesity and/or type 2 diabetes altered STEAP4 expression in human pancreatic islets. Methods Human islets were isolated from deceased donors at two medical centers and processed for quantitative polymerase chain reaction. Organ donors were selected by status as non-diabetic or having type 2 diabetes. Site 1 (Edmonton): N = 13 type 2 diabetes donors (7M, 6F), N = 20 non-diabetic donors (7M, 13F). Site 2 (Virginia): N = 6 type 2 diabetes donors (6F), N = 6 non-diabetic donors (3M, 3F). Results STEAP4 showed reduced islet expression with increasing body mass index among all donors (P < 0.10) and non-diabetic donors (P < 0.05) from Site 1; STEAP4 showed reduced islet expression among type 2 diabetes donors with increasing hemoglobin A1c. Islet STEAP4 expression was also marginally higher in female donors (P < 0.10). Among type 2 diabetes donors from Site 2, islet insulin expression was reduced, STEAP4 expression was increased, and white blood cell counts were increased compared to non-diabetic donors. Islets from non-diabetic donors that were exposed overnight to 5 ng/ml IL-1β displayed increased STEAP4 expression, consistent with STEAP4 upregulation by inflammatory signaling. Conclusions These findings suggest that increased STEAP4 mRNA expression is associated with inflammatory stimuli, whereas lower STEAP4 expression is associated with obesity in human islets. Given its putative protective role, downregulation of STEAP4 by chronic obesity suggests a mechanism for reduced islet protection against cellular damage

Real-Time Increased Detection of Neoplastic Tissue in Barrett’s Esophagus with Probe-Based Confocal Laser Endomicroscopy: Final Results of an International Multicenter, Prospective, Randomized, Controlled Trial

BACKGROUND: Probe-based confocal laser endomicroscopy (pCLE) allows real-time detection of neoplastic Barrett's esophagus (BE) tissue. However, the accuracy of pCLE in real time has not yet been extensively evaluated. OBJECTIVE: To compare the sensitivity and specificity of pCLE in addition to high-definition white-light endoscopy (HD-WLE) with HD-WLE alone for the detection of high-grade dysplasia (HGD) and early carcinoma (EC) in BE. DESIGN: International, prospective, multicenter, randomized, controlled trial. SETTING: Five tertiary referral centers. PATIENTS: A total of 101 consecutive BE patients presenting for surveillance or endoscopic treatment of HGD/EC. INTERVENTIONS: All patients were examined by HD-WLE, narrow-band imaging (NBI), and pCLE, and the findings were recorded before biopsy samples were obtained. The order of HD-WLE and NBI was randomized and performed by 2 independent, blinded endoscopists. All suspicious lesions on HD-WLE or NBI and 4-quadrant random locations were documented. These locations were examined by pCLE, and a presumptive diagnosis of benign or neoplastic (HGD/EC) tissue was made in real time. Finally, biopsies were taken from all locations and were reviewed by a central pathologist, blinded to endoscopic and pCLE data. MAIN OUTCOME MEASUREMENTS: Diagnostic characteristics of pCLE. RESULTS: The sensitivity and specificity for HD-WLE were 34.2% and 92.7%, respectively, compared with 68.3% and 87.8%, respectively, for HD-WLE or pCLE (P = .002 and P < .001, respectively). The sensitivity and specificity for HD-WLE or NBI were 45.0% and 88.2%, respectively, compared with 75.8% and 84.2%, respectively, for HD-WLE, NBI, or pCLE (P = .01 and P = .02, respectively). Use of pCLE in conjunction with HD-WLE and NBI enabled the identification of 2 and 1 additional HGD/EC patients compared with HD-WLE and HD-WLE or NBI, respectively, resulting in detection of all HGD/EC patients, although not statistically significant. LIMITATIONS: Academic centers with enriched population. CONCLUSIONS: pCLE combined with HD-WLE significantly improved the ability to detect neoplasia in BE patients compared with HD-WLE. This may allow better informed decisions to be made for the management and subsequent treatment of BE patients. (Clinical trial registration number: NCT00795184.)

The Rewiring of Ubiquitination Targets in a Pathogenic Yeast Promotes Metabolic Flexibility, Host Colonization and Virulence

Funding: This work was funded by the European Research Council [http://erc.europa.eu/], AJPB (STRIFE Advanced Grant; C-2009-AdG-249793). The work was also supported by: the Wellcome Trust [www.wellcome.ac.uk], AJPB (080088, 097377); the UK Biotechnology and Biological Research Council [www.bbsrc.ac.uk], AJPB (BB/F00513X/1, BB/K017365/1); the CNPq-Brazil [http://cnpq.br], GMA (Science without Borders fellowship 202976/2014-9); and the National Centre for the Replacement, Refinement and Reduction of Animals in Research [www.nc3rs.org.uk], DMM (NC/K000306/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Acknowledgments We thank Dr. Elizabeth Johnson (Mycology Reference Laboratory, Bristol) for providing strains, and the Aberdeen Proteomics facility for the biotyping of S. cerevisiae clinical isolates, and to Euroscarf for providing S. cerevisiae strains and plasmids. We are grateful to our Microscopy Facility in the Institute of Medical Sciences for their expert help with the electron microscopy, and to our friends in the Aberdeen Fungal Group for insightful discussions.Peer reviewedPublisher PD

New InhA Inhibitors Based on Expanded Triclosan and Di-Triclosan Analogues to Develop a New Treatment for Tuberculosis

The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) has reinforced the need for the development of new anti-TB drugs. The first line drug isoniazid inhibits InhA. This is a prodrug requiring activation by the enzyme KatG. Mutations in KatG have largely contributed to clinical isoniazid resistance. We aimed to design new ‘direct’ InhA inhibitors that obviate the need for activation by KatG, circumventing pre-existing resistance. In silico molecular modelling was used as part of a rational structure-based drug-design approach involving inspection of protein crystal structures of InhA:inhibitor complexes, including the broad spectrum antibiotic triclosan (TCS). One crystal structure exhibited the unusual presence of two triclosan molecules within the Mycobacterium tuberculosis InhA binding site. This became the basis of a strategy for the synthesis of novel inhibitors. A series of new, flexible ligands were designed and synthesised, expanding on the triclosan structure. Low Minimum Inhibitory Concentrations (MICs) were obtained for benzylphenyl compounds (12, 43 and 44) and di-triclosan derivative (39), against Mycobacterium bovis BCG although these may also be inhibiting other enzymes. The ether linked di-triclosan derivative (38) displayed excellent in vitro isolated enzyme inhibition results comparable with triclosan, but at a higher MIC (125 µg mL−1). These compounds offer good opportunities as leads for further optimisation

Pharmacogenomics of GLP-1 Receptor Agonists:a genome-wide analysis of observational data and large randomised controlled trials

Background: In the treatment of type 2 diabetes, GLP-1 receptor agonists lower blood glucose concentrations, body weight, and have cardiovascular benefits. The efficacy and side effects of GLP-1 receptor agonists vary between people. Human pharmacogenomic studies of this inter-individual variation can provide both biological insight into drug action and provide biomarkers to inform clinical decision making. We therefore aimed to identify genetic variants associated with glycaemic response to GLP-1 receptor agonist treatment. Methods: In this genome-wide analysis we included adults (aged &gt;= 18 years) with type 2 diabetes treated with GLP-1 receptor agonists with baseline HbA1c of 7% or more (53 mmol/mol) from four prospective observational cohorts (DIRECT, PRIBA, PROMASTER, and GoDARTS) and two randomised clinical trials (HARMONY phase 3 and AWARD). The primary endpoint was HbA1c reduction at 6 months after starting GLP-1 receptor agonists. We evaluated variants in GLP1R, then did a genome-wide association study and gene-based burden tests. Findings: 4571 adults were included in our analysis, of these, 3339 (73%) were White European, 449 (10%) Hispanic, 312 (7%) American Indian or Alaskan Native, and 471 (10%) were other, and around 2140 (47%) of the participants were women. Variation in HbA1c reduction with GLP-1 receptor agonists treatment was associated with rs6923761G -&gt; A (Gly168Ser) in the GLP1R (0.08% [95% CI 0.04-0.12] or 0.9 mmol/mol lower reduction in HbA1c per serine, p=6.0 x 10(-5)) and low frequency variants in ARRB1 (optimal sequence kernel association test p=6.7 x 10(-8)), largely driven by rs140226575G -&gt; A (Thr370Met; 0.25% [SE 0.06] or 2.7 mmol/mol [SE 0.7] greater HbA1c reduction per methionine, p=5.2 x 10(-6)). A similar effect size for the ARRB1 Thr370Met was seen in Hispanic and American Indian or Alaska Native populations who have a higher frequency of this variant (6-11%) than in White European populations. Combining these two genes identified 4% of the population who had a 30% greater reduction in HbA1c than the 9% of the population with the worse response. Interpretation: This genome-wide pharmacogenomic study of GLP-1 receptor agonists provides novel biological and clinical insights. Clinically, when genotype is routinely available at the point of prescribing, individuals with ARRB1 variants might benefit from earlier initiation of GLP-1 receptor agonists