Publications by authors named "Douglas Young"

270 Publications

Localized Scarlatiniform Rash of the Ears and Antecubital Fossa in COVID-19.

J Am Board Fam Med 2021 Feb;34(Suppl):S183-S185

From 7th Medical Group, Dyess Air Force Base, US Air Force, Abilene TX (TTP, DMY); Abilene Dermatology & Skin Surgery Center, Abilene TX (PBR).

The worldwide spread of the novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a global pandemic since its identification in Wuhan, China in December 2019. Few cases of COVID-19-associated dermatologic manifestations have been reported in the literature to date. This report describes the clinical features of a localized pruritic scarlatiniform rash of the ears and antecubital fossa on defervescence in a 29-year-old patient with COVID-19. Our case stands to further illuminate the dermatologic manifestations of this novel disease.
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http://dx.doi.org/10.3122/jabfm.2021.S1.200152DOI Listing
February 2021

Properties of Thermal Analgesia in a Human Chronic Low Back Pain Model.

J Pain Res 2020 13;13:2083-2092. Epub 2020 Aug 13.

Biology Department, University of Washington, Seattle, WA, USA.

Purpose: For years, heat has been used for comfort and analgesia is recommended as a first-line therapy in many clinical guidelines. Yet, there are questions that remain about the actual effectiveness of heat for a condition as common as chronic low back pain, and factors such as time of onset, optimal temperature, and duration of effect.

Materials And Methods: A randomized double-blinded controlled trial was designed to compare the analgesic response to heat delivered via pulses at 45°C (experimental group, N=49) to steady heat at 37°C (control group, N=51) in subjects with longstanding low back pain. Treatment lasted 30 minutes with follow-up out to four hours. The hypothesis was that the experimental group would experience a higher degree of analgesia compared to the control group. Time of onset and duration of effect were also measured.

Results: Both groups were similar in average duration of pain (10.3 years). The primary outcome measure was pain reduction at 30 minutes after the end of treatment, using a 10-points numeric pain scale. Reduction in pain was greater for the experimental group than the control group (difference in mean reduction = 0.72, 95% CI 0.15-1.29, p = 0.014). Statistically significant differences in pain levels were observed from the first measure at 5 minutes of treatment through 120 minutes after completion of treatment. Reduction in pain associated movement was greater in the active heat group than the placebo group (p = 0.04).

Conclusion: High-level pulsed heat (45°C) produced significantly more analgesia as compared to steady heat at 37°C at the primary end point and for an additional 2 hours after treatment. The onset of analgesia was rapid, <5 minutes of treatment. The results of this trial provide insight into the mechanisms and properties of thermal analgesia that are not well understood in a chronic low back pain model.
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http://dx.doi.org/10.2147/JPR.S260967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7434528PMC
August 2020

The software tool to find greener solvent replacements, PARIS III.

Environ Prog Sustain Energy 2020 Jan;39(1):1-13331

Office of Research and Development, U.S. Environmental Protection Agency, Washington, DC.

PARIS III (Program for Assisting the Replacement of Industrial Solvents III, Version 1.4.0) is a pollution prevention solvent substitution software tool used to find mixtures of solvents that are less harmful to the environment than the industrial solvents to be replaced. By searching extensively though hundreds of millions of possible solvent combinations, mixtures that perform the same as the original solvents may be found. Greener solvent substitutes may then be chosen from those mixtures that behave similarly but have less environmental impact. These extensive searches may be enhanced by fine-tuning impact weighting factors to better reflect regional environmental concerns; and by adjusting how close the properties of the replacement must be to those of the original solvent. Optimal replacements can then be compared again and selected for better performance, but less environmental impact. This method can be a very effective way of finding greener replacements for harmful solvents used by industry.
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http://dx.doi.org/10.1002/ep.13331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7433800PMC
January 2020

Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex.

Nat Commun 2019 09 5;10(1):3994. Epub 2019 Sep 5.

Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, Spain.

The Mycobacterium tuberculosis complex (MTBC) members display different host-specificities and virulence phenotypes. Here, we have performed a comprehensive RNAseq and methylome analysis of the main clades of the MTBC and discovered unique transcriptional profiles. The majority of genes differentially expressed between the clades encode proteins involved in host interaction and metabolic functions. A significant fraction of changes in gene expression can be explained by positive selection on single mutations that either create or disrupt transcriptional start sites (TSS). Furthermore, we show that clinical strains have different methyltransferases inactivated and thus different methylation patterns. Under the tested conditions, differential methylation has a minor direct role on transcriptomic differences between strains. However, disruption of a methyltransferase in one clinical strain revealed important expression differences suggesting indirect mechanisms of expression regulation. Our study demonstrates that variation in transcriptional profiles are mainly due to TSS mutations and have likely evolved due to differences in host characteristics.
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http://dx.doi.org/10.1038/s41467-019-11948-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728331PMC
September 2019

Genetic Encoding of a Bioconjugation Handle for [2+2+2] Cycloaddition Reactions.

Chembiochem 2020 02 17;21(3):310-314. Epub 2019 Oct 17.

Department of Chemistry, College of William & Mary, PO Box 8795, Williamsburg, VA, 23187, USA.

Protein bioconjugates have many critical applications, especially in the development of therapeutics. Consequently, the design of novel methodologies to prepare protein bioconjugates is of great importance. Herein we present the development and optimization of a novel strategy to prepare bioconjugates through a genetically encoded [2+2+2] cycloaddition reaction. To do this, a novel unnatural amino acid (UAA) containing a dipropargyl amine functionality was synthesized and incorporated site specifically. This UAA-containing protein was reacted with an alkyne-containing fluorophore to afford a covalently linked, well-defined protein bioconjugate. This reaction is convenient with an optimized reaction time of just two hours at room temperature and yields a stable, polysubstituted benzene ring. Overall, this work contributes a new bioconjugation strategy to the growing toolbox of reactions to develop protein bioconjugates, which have a myriad of applications.
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http://dx.doi.org/10.1002/cbic.201900391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123993PMC
February 2020

Proteomic and transcriptomic experiments reveal an essential role of RNA degradosome complexes in shaping the transcriptome of Mycobacterium tuberculosis.

Nucleic Acids Res 2019 06;47(11):5892-5905

Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland.

The phenotypic adjustments of Mycobacterium tuberculosis are commonly inferred from the analysis of transcript abundance. While mechanisms of transcriptional regulation have been extensively analysed in mycobacteria, little is known about mechanisms that shape the transcriptome by regulating RNA decay rates. The aim of the present study is to identify the core components of the RNA degradosome of M. tuberculosis and to analyse their function in RNA metabolism. Using an approach involving cross-linking to 4-thiouridine-labelled RNA, we mapped the mycobacterial RNA-bound proteome and identified degradosome-related enzymes polynucleotide phosphorylase (PNPase), ATP-dependent RNA helicase (RhlE), ribonuclease E (RNase E) and ribonuclease J (RNase J) as major components. We then carried out affinity purification of eGFP-tagged recombinant constructs to identify protein-protein interactions. This identified further interactions with cold-shock proteins and novel KH-domain proteins. Engineering and transcriptional profiling of strains with a reduced level of expression of core degradosome ribonucleases provided evidence of important pleiotropic roles of the enzymes in mycobacterial RNA metabolism highlighting their potential vulnerability as drug targets.
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http://dx.doi.org/10.1093/nar/gkz251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582357PMC
June 2019

Dual RNA-Seq of Human Leprosy Lesions Identifies Bacterial Determinants Linked to Host Immune Response.

Cell Rep 2019 03;26(13):3574-3585.e3

Division of Dermatology, David Geffen School of Medicine, Los Angeles, CA, USA. Electronic address:

To understand how the interaction between an intracellular bacterium and the host immune system contributes to outcome at the site of infection, we studied leprosy, a disease that forms a clinical spectrum, in which progressive infection by the intracellular bacterium Mycobacterium leprae is characterized by the production of type I IFNs and antibody production. Dual RNA-seq on patient lesions identifies two independent molecular measures of M. leprae, each of which correlates with distinct aspects of the host immune response. The fraction of bacterial transcripts, reflecting bacterial burden, correlates with a host type I IFN gene signature, known to inhibit antimicrobial responses. Second, the bacterial mRNA:rRNA ratio, reflecting bacterial viability, links bacterial heat shock proteins with the BAFF-BCMA host antibody response pathway. Our findings provide a platform for the interrogation of host and pathogen transcriptomes at the site of infection, allowing insight into mechanisms of inflammation in human disease.
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http://dx.doi.org/10.1016/j.celrep.2019.02.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508871PMC
March 2019

Mechanistic investigation and further optimization of the aqueous Glaser-Hay bioconjugation.

Org Biomol Chem 2019 03;17(13):3396-3402

Department of Chemistry, College of William & Mary, PO Box 8795, Williamsburg, VA, USA 23185.

The Glaser-Hay bioconjugation has recently emerged as an efficient and attractive method to generate stable, useful bioconjugates with numerous applications, specifically in the field of therapeutics. Herein, we investigate the mechanism of the aqueous Glaser-Hay coupling to better understand optimization strategies. In doing so, it was identified that catalase is able to minimize protein oxidation and improve coupling efficiency, suggesting that hydrogen peroxide is produced during the aqueous Glaser-Hay bioconjugation. Further, several new ligands were investigated to minimize protein oxidation and maximize coupling efficiency. Finally, two novel strategies to streamline the Glaser-Hay bioconjugation and eliminate the need for secondary purification have been developed.
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http://dx.doi.org/10.1039/c9ob00327dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6482449PMC
March 2019

B-type natriuretic peptide predicts deterioration in functional capacity following lung resection.

Interact Cardiovasc Thorac Surg 2019 06;28(6):945-952

Academic Unit of Anaesthesia, Pain and Critical Care, University of Glasgow, Glasgow, UK.

Objectives: Following lung resection, there is a decrease in the functional capacity and quality of life, which is not fully explained by changes in pulmonary function. Previous work demonstrates that B-type natriuretic peptide (BNP) is associated with short- and long-term complications following lung resection, leading to the suggestion that cardiac dysfunction may contribute to functional deterioration. Our aim was to investigate any relationship between BNP and subjective and objective indices of functional deterioration following lung resection surgery.

Methods: Twenty-seven patients undergoing lung resection had serum BNP measured preoperatively, on postoperative day (POD)1 and POD2, and at 2 months postoperatively. The functional deterioration was assessed using 6-min walk tests and the Medical Research Council dyspnoea scale. 'Deterioration in functional capacity' was defined as either an increase in the Medical Research Council dyspnoea score or a significant decrease in the 6-min walk test distance.

Results: BNP increased over time (P < 0.01) and was significantly elevated on POD1 and POD2 (P < 0.02 for both). Seventeen patients demonstrated functional deterioration 2 months postoperatively. At all perioperative time points, BNP was significantly higher in patients showing deterioration (P < 0.05 for all). Preoperative BNP was predictive of functional deterioration at 2 months with an area under the receiver-operating characteristic curve of 0.82 (P = 0.01, 95% confidence interval 0.65-0.99).

Conclusions: This study has demonstrated, using subjective and objective measures, that preoperative BNP is a predictor of functional deterioration following lung resection. BNP may have a role in preoperative risk stratification in this population, allowing therapy in future to be targeted towards high-risk patients with the aim of preventing postoperative cardiac dysfunction.

Clinical Trial Registration Number: NCT01892800.
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http://dx.doi.org/10.1093/icvts/ivz016DOI Listing
June 2019

Efficacy of intravaginal dehydroepiandrosterone (DHEA) on moderate to severe dyspareunia and vaginal dryness, symptoms of vulvovaginal atrophy, and of the genitourinary syndrome of menopause.

Menopause 2018 11;25(11):1339-1353

StatLog Consulting Inc, Ottawa, Ontario, Canada.

Objective: The aim of this study is to confirm the local beneficial effects of intravaginal dehydroepiandrosterone (DHEA, Prasterone) on moderate to severe dyspareunia or pain at sexual activity, the most frequent symptom of vulvovaginal atrophy due to menopause or genitourinary syndrome of menopause (GSM).

Methods: In a prospective, randomized, double-blind, and placebo-controlled phase III clinical trial, the effect of daily intravaginal 0.50% DHEA (6.5 mg) (Prasterone, EndoCeutics) was examined on four coprimary objectives, namely percentage of parabasal cells, percentage or superficial cells, vaginal pH, and moderate to severe pain at sexual activity (dyspareunia) identified by the women as their most bothersome vulvovaginal atrophy symptom. The intent-to-treat population included 157 and 325 women in the placebo and DHEA-treated groups, respectively.

Results: After daily intravaginal administration of 0.50% DHEA for 12 weeks, when compared to baseline by the analysis of covariance test, the percentage of parabasal cells decreased by 27.7% over placebo (P < 0.0001), whereas the percentage of superficial cells increased by 8.44% over placebo (P < 0.0001), vaginal pH decreased by 0.66 pH unit over placebo (P < 0.0001), and pain at sexual activity decreased by 1.42 severity score unit from baseline or 0.36 unit over placebo (P = 0.0002). On the other hand, moderate to severe vaginal dryness present in 84.0% of women improved at 12 weeks by 1.44 severity score unit compared to baseline, or 0.27 unit over placebo (P = 0.004). At gynecological evaluation, vaginal secretions, epithelial integrity, epithelial surface thickness, and color all improved by 86% to 121% over the placebo effect (P < 0.0001 for all comparisons with placebo). Serum steroid levels remained well within the normal postmenopausal values according to the involved mechanisms of intracrinology. The only side effect reasonably related to treatment is vaginal discharge due to melting of the vehicle at body temperature and this was reported in about 6% of the participants.

Conclusions: The daily intravaginal administration of 0.50% (6.5 mg) DHEA (Prasterone) has shown clinically and highly statistically significant effects on the four coprimary parameters suggested by the US Food and Drug Administration. The strictly local action of Prasterone is in line with the absence of significant drug-related adverse events, thus showing the high benefit-to-risk ratio of this treatment based upon the novel understanding of the physiology of sex steroids in women.
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http://dx.doi.org/10.1097/GME.0000000000001238DOI Listing
November 2018

Evidence-based clinical practice guideline on nonrestorative treatments for carious lesions: A report from the American Dental Association.

J Am Dent Assoc 2018 Oct;149(10):837-849.e19

Background: An expert panel convened by the American Dental Association Council on Scientific Affairs and the Center for Evidence-Based Dentistry conducted a systematic review and formulated evidence-based clinical recommendations for the arrest or reversal of noncavitated and cavitated dental caries using nonrestorative treatments in children and adults.

Types Of Studies Reviewed: The authors conducted a systematic search of the literature in MEDLINE and Embase via Ovid, Cochrane CENTRAL, and Cochrane database of systematic reviews to identify randomized controlled trials reporting on nonrestorative treatments for noncavitated and cavitated carious lesions. The authors used the Grading of Recommendations Assessment, Development and Evaluation approach to assess the certainty in the evidence and move from the evidence to the decisions.

Results: The expert panel formulated 11 clinical recommendations, each specific to lesion type, tooth surface, and dentition. Of the most effective interventions, the panel provided recommendations for the use of 38% silver diamine fluoride, sealants, 5% sodium fluoride varnish, 1.23% acidulated phosphate fluoride gel, and 5,000 parts per million fluoride (1.1% sodium fluoride) toothpaste or gel, among others. The panel also provided a recommendation against the use of 10% casein phosphopeptide-amorphous calcium phosphate.

Conclusions And Practical Implications: Although the recommended interventions are often used for caries prevention, or in conjunction with restorative treatment options, these approaches have shown to be effective in arresting or reversing carious lesions. Clinicians are encouraged to prioritize use of these interventions based on effectiveness, safety, and feasibility.
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http://dx.doi.org/10.1016/j.adaj.2018.07.002DOI Listing
October 2018

Field Test Performance of Junior Competitive Surf Athletes following a Core Strength Training Program.

Int J Exerc Sci 2018 1;11(6):696-707. Epub 2018 Jun 1.

Department of Kinesiology, California State University-Long Beach, Long Beach, CA, USA.

Lower body and core muscular strength are essential for optimal performance in many sports and competitive surfers have similar strength demands when maneuvering a surfboard to achieve competition success. Presently, the use of unstable surfaces is excessively utilized by surf coaches and trainers and to date, research does not support this as an effective training method for long-term improvements. Therefore, the purpose of this study was to determine the effectiveness of an 8-week Core Strength Training Program (CSTP) on a battery of field tests specific to assessing core musculature and lower body strength for junior competitive surf athletes. Nineteen American junior competitive surf athletes (age:15.7±1.01yrs, height:1.77±0.007m, mass:64.67±9.08kg) completed pre- and post-tests with a transitional pre-season to in-season 8-week CSTP intervention. The battery of tests included: rotational power (RP), time to peak acceleration (TP), maximal acceleration (Ma), maximal countermovement jump (CMJ), estimated peak power (PP), core strength (CS), core endurance (CE), and rotational flexibility (RF). Means, standard deviations, RMANOVA with a significance level of p < 0.05, and effect sizes were computed. Results demonstrated significant improvements in L.RP, TP, CMJ, PP, CS, and RF. Based on the results, the CSTP is an effective training program for surf coaches and strength and conditioning professionals to improve strength in the core musculature and lower body. In addition, we conclude implementation of the CSTP enhances athletic performance measurements which will likely increase competition success.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6033504PMC
June 2018

Secondary Sjögren syndrome: A case report using silver diamine fluoride and glass ionomer cement.

J Am Dent Assoc 2018 Aug 24;149(8):731-741. Epub 2018 May 24.

Background And Overview: The authors describe dental treatment for a patient with a complex medical history of secondary Sjögren syndrome with systemic lupus erythematosus and rheumatoid arthritis.

Case Description: An 18-year-old woman's rheumatology group referred her for oral evaluation; she had secondary Sjögren syndrome, systemic lupus erythematosus, and rheumatoid arthritis. The patient had multiple advanced carious lesions, extreme sensitivity, and hyposalivation. The patient selected a minimally invasive treatment plan that focused on silver diamine fluoride (SDF), partial caries removal, and glass ionomer cement (GIC) restorations. The SDF treatment and GIC restorations were successful in arresting carious lesions and restoring form and function but may not completely prevent new carious lesions from forming in the future.

Conclusions And Practical Implications: The case shows that using less invasive treatments, such as SDF and GIC restorations can be used to manage complex cases involving extreme caries risk and be preferable to endodontic treatment and extractions.
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http://dx.doi.org/10.1016/j.adaj.2018.03.021DOI Listing
August 2018

Dental Care for Geriatric and Special Needs Populations.

Dent Clin North Am 2018 04;62(2):245-267

AEGD Program, Hospital Dentistry Program, University of the Pacific, Arthur A. Dugoni School of Dentistry, 155 5th Street, San Francisco, CA 94103, USA.

This article reviews considerations for oral health care associated with the most common causes of mortality and morbidity in older adults. Many of these diseases result in functional or cognitive impairments that must be considered in treatment planning to ensure appropriate, safe, and effective care for patients. Many of these considerations parallel those of adults who have lived with developmental disabilities over a lifetime and similar principles can be applied. Systemic diseases, conditions, and their treatments can pose significant risks to oral health, which requires prevention, treatment, and advocacy for oral health care as integral to chronic disease management.
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http://dx.doi.org/10.1016/j.cden.2017.11.005DOI Listing
April 2018

Playing with the Molecules of Life.

ACS Chem Biol 2018 04 2;13(4):854-870. Epub 2018 Mar 2.

Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 , United States.

Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
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http://dx.doi.org/10.1021/acschembio.7b00974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061972PMC
April 2018

Investigation of copper-free alkyne/azide 1,3-dipolar cycloadditions using microwave irradiation.

Bioorg Med Chem Lett 2018 01 6;28(2):81-84. Epub 2017 Dec 6.

Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187 USA. Electronic address:

The prevalence of 1,3-dipolar cycloadditions of azides and alkynes within both biology and chemistry highlights the utility of these reactions. However, the use of a copper catalyst can be prohibitive to some applications. Consequently, we have optimized a copper-free microwave-assisted reaction to alleviate the necessity for the copper catalyst. A small array of triazoles was prepared to examine the scope of this approach, and the methodology was translated to a protein context through the use of unnatural amino acids to demonstrate one of the first microwave-mediated bioconjugations involving a full length protein.
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http://dx.doi.org/10.1016/j.bmcl.2017.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5761740PMC
January 2018

Development of optimized conditions for Glaser-Hay bioconjugations.

Bioorg Chem 2018 02 5;76:326-331. Epub 2017 Dec 5.

Department of Chemistry, The College of William & Mary, Williamsburg, VA 23187, USA. Electronic address:

The efficient preparation of protein bioconjugates represents a route to novel materials, diagnostics, and therapeutics. We previously reported a novel bioorthogonal Glaser-Hay reaction for the preparation of covalent linkages between proteins and a reaction partner; however, deleterious protein degradation was observed under extended reaction conditions. Herein, we describe the systematic optimization of the reaction to increase coupling efficiency and decrease protein degradation. Two optimized conditions were identified varying either the pH of the reaction or the bidentate ligand employed, allowing for more rapid conjugations and/or less protein oxidation.
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http://dx.doi.org/10.1016/j.bioorg.2017.11.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5818283PMC
February 2018

Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival.

Sci Rep 2017 08 15;7(1):8208. Epub 2017 Aug 15.

Mycobacterial Systems Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom.

Mycobacterium tuberculosis has succeeded as a human pathogen for tens of thousands of years thanks to its ability to resist and adapt to the adverse conditions it encounters upon infection. Bacterial adaptation to stress is commonly viewed in the context of transcriptional regulation, with the implicit expectation that an initial transcriptomic response is tightly coupled to an ensuing proteomic response. However, after challenging M. tuberculosis with nitric oxide we found that the rapid transcriptional responses, detectable within minutes of nitric oxide exposure, typically took several hours to manifest on the protein level. Furthermore, early proteomic responses were dominated by the degradation of a set of proteins, specifically those containing damaged iron-sulphur clusters. Overall, our findings are consistent with transcriptional responses participating mostly in late-stage recovery rather than in generating an immediate resistance to nitric oxide stress, suggesting that survival of M. tuberculosis under acute stress is contingent on mechanisms other than transcriptional regulation. These findings provide a revised molecular understanding of an important human pathogen.
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http://dx.doi.org/10.1038/s41598-017-08306-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557973PMC
August 2017

Fluorescence Modulation of Green Fluorescent Protein Using Fluorinated Unnatural Amino Acids.

Molecules 2017 Jul 16;22(7). Epub 2017 Jul 16.

Department of Chemistry, The College of William & Mary, Williamsburg, VA 231871, USA.

The ability to modulate protein function through minimal perturbations to amino acid structure represents an ideal mechanism to engineer optimized proteins. Due to the novel spectroscopic properties of green fluorescent protein, it has found widespread application as a reporter protein throughout the fields of biology and chemistry. Using site-specific amino acid mutagenesis, we have incorporated various fluorotyrosine residues directly into the fluorophore of the protein, altering the fluorescence and shifting the pKa of the phenolic proton associated with the fluorophore. Relative to wild type GFP, the fluorescence spectrum of the protein is altered with each additional fluorine atom, and the mutant GFPs have the potential to be employed as pH sensors due to the altered electronic properties of the fluorine atoms.
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http://dx.doi.org/10.3390/molecules22071194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5806519PMC
July 2017

Dental Caries: An Update on Dental Trends and Therapy.

Adv Pediatr 2017 08;64(1):307-330

University of the Pacific- Arthur A. Dugoni School of Dentistry, 155 5th Street, San Francisco, CA 94103, USA.

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http://dx.doi.org/10.1016/j.yapd.2017.03.011DOI Listing
August 2017

The Effect of Calibration on Caries Risk Assessment Performance by Students and Clinical Faculty.

J Dent Educ 2017 Jun;81(6):667-674

Dr. Young is Professor, Department of Dental Practice, Arthur A. Dugoni School of Dentistry, University of the Pacific; Dr. Fa is Assistant Professor, Department of Integrated Reconstructive Dental Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific; Mr. Rogers is Administrative Lead for Personalized Instructional Programs, Department of Academic Affairs, Arthur A. Dugoni School of Dentistry, University of the Pacific; and Dr. Rechmann is Professor and Director of Clinical Sciences Research Group, Department of Preventive and Restorative Dental Sciences, School of Dentistry, University of California, San Francisco.

Caries management requires a complete oral examination and an accurate caries risk assessment (CRA). Performing Caries Management by Risk Assessment (CAMBRA) is inefficient when the caries risk level assignment is incorrect. The aim of this study was to evaluate the ability of faculty members and students at one U.S. dental school to correctly assign caries risk levels for 22 CRA cases, followed by calibration with guidelines on how to use the CRA form and a post-calibration test two months after calibration. Inter-examiner reliability to a gold standard (consensus of three experts) was assessed as poor, fair, moderate, good, and very good. Of the 162 students and 125 faculty members invited to participate, 13 students and 20 faculty members returned pre-calibration tests, for response rates of 8% and 16%, respectively. On the post-calibration test, eight students and 13 faculty members participated for response rates of 5% and 10%, respectively. Without guidelines and calibration, both faculty members and students when evaluated as one group performed only poor to fair in assigning correct caries risk levels. After calibration, levels improved to good and very good agreements with the gold standard. When faculty and students were evaluated separately, in the pre-calibration test they correctly assigned the caries risk level on average in only one-quarter of the cases (students 24.1%±13.3%; faculty 23.6%±17.5%). After calibration, both groups significantly improved their correct assignment rate. Faculty members (73.8% correct assignments) showed even significantly higher correct assignment rates than students (47.7% correct assignments). These findings suggest that calibration with a specific set of guidelines improved CRA outcomes for both the faculty members and students. Improved guidelines on how to use a CRA form should lead to improved caries risk assessment and proper treatment strategy for patients.
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http://dx.doi.org/10.21815/JDE.017.013DOI Listing
June 2017

Synthesis and incorporation of a caged tyrosine amino acid possessing a bioorthogonal handle.

Tetrahedron Lett 2016 Oct 10;57(42):4709-4712. Epub 2016 Sep 10.

Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA.

Reversing a bioconjugation in a spatial and temporal fashion has widespread applications, especially toward targeted drug delivery. We report the synthesis and incorporation of an unnatural amino acid with an alkyne modified dimethoxy--nitrobenzyl caging group. This unnatural amino acid can be utilized in a Glaser-Hay conjugation to generate a bioconjugate, but also is able to disrupt the bioconjugate when irradiated with light. These combined features allow for the preparation of bioconjugates with a high degree of site-specificity and allow for the separation of the two components if necessary.
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http://dx.doi.org/10.1016/j.tetlet.2016.09.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5438197PMC
October 2016

A Rab20-Dependent Membrane Trafficking Pathway Controls M. tuberculosis Replication by Regulating Phagosome Spaciousness and Integrity.

Cell Host Microbe 2017 May;21(5):619-628.e5

Host-Pathogen Interactions In Tuberculosis Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. Electronic address:

The intracellular pathogen Mycobacterium tuberculosis (Mtb) lives within phagosomes and also disrupts these organelles to access the cytosol. The host pathways and mechanisms that contribute to maintaining Mtb phagosome integrity have not been investigated. Here, we examined the spatiotemporal dynamics of Mtb-containing phagosomes and identified an interferon-gamma-stimulated and Rab20-dependent membrane trafficking pathway in macrophages that maintains Mtb in spacious proteolytic phagolysosomes. This pathway functions to promote endosomal membrane influx in infected macrophages, and is required to preserve Mtb phagosome integrity and control Mtb replication. Rab20 is specifically and significantly upregulated in the sputum of human patients with active tuberculosis. Altogether, we uncover an immune-regulated cellular pathway of defense that promotes maintenance of Mtb within intact membrane-bound compartments for efficient elimination.
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http://dx.doi.org/10.1016/j.chom.2017.04.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5432432PMC
May 2017

Application of the Solid-Supported Glaser-Hay Reaction to Natural Product Synthesis.

J Org Chem 2016 12 7;81(24):12520-12524. Epub 2016 Dec 7.

Department of Chemistry, College of William & Mary , P.O. Box 8795, Williamsburg, Virginia 23187, United States.

The Glaser-Hay coupling of terminal alkynes is a useful synthetic reaction for the preparation of polyynes; however, chemoselectivity issues have precluded its widespread utilization. Conducting the reaction on a solid-support provides a mechanism to alleviate the chemoselectivity issues and provide products in high purities and yields. Moreover, the polyyne core is a key component to several natural products. Herein, we describe the application of a solid-supported Glaser-Hay reaction in the preparation of several natural products. These compounds were then screened for antibacterial activity, illustrating the utility of the methodology.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5455993PMC
http://dx.doi.org/10.1021/acs.joc.6b02407DOI Listing
December 2016

Utilization of alkyne bioconjugations to modulate protein function.

Bioorg Med Chem Lett 2017 01 16;27(1):30-33. Epub 2016 Nov 16.

Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA. Electronic address:

The ability to introduce or modify protein function has widespread application to multiple scientific disciplines. The introduction of unique unnatural amino acids represents an excellent mechanism to incorporate new functionality; however, this approach is limited by ability of the translational machinery to recognize and incorporate the chemical moiety. To overcome this potential limitation, we aimed to exploit the functionality of existing unnatural amino acids to perform bioorthogonal reactions to introduce the desired protein modification, altering its function. Specifically, via the introduction of a terminal alkyne containing unnatural amino acid, we demonstrated chemically programmable protein modification through the Glaser-Hay coupling to other terminal alkynes, altering the function of a protein. In a proof-of-concept experiment, this approach has been utilized to modify the fluorescence spectrum of green fluorescent protein.
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http://dx.doi.org/10.1016/j.bmcl.2016.11.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5437974PMC
January 2017

Mortality in intensive care: The impact of bacteremia and the utility of systemic inflammatory response syndrome.

Am J Infect Control 2016 11 20;44(11):1291-1295. Epub 2016 Jun 20.

Royal Infirmary, Glasgow, Scotland, UK.

Background: The purpose of this study was to determine the impact of bacteremia on intensive care unit (ICU) mortality and to develop a bacteremia prediction tool using systemic inflammatory response syndrome (SIRS) criteria.

Methods: Patients included those aged >18 years who had blood cultures taken in the ICU from January 1, 2011-December 31, 2013. Eligible patients were identified from microbiology records of the Glasgow Royal Infirmary, Scotland. Clinical and outcome data were gathered from ICU records. Patients with clinically significant bacteremia were matched to controls using propensity scores. SIRS criteria were gathered and used to create decision rules to predict the absence of bacteremia. The main outcome was mortality at ICU discharge. The utility of the decision tools was measured using sensitivity and specificity.

Results: One hundred patients had a clinically significant positive blood culture and were matched to 100 controls. Patients with bacteremia had higher ICU mortality (odds ratio [OR], 2.35; P = .001) and longer ICU stay (OR, 17.0 vs 7.8 days; P ≤ .001). Of 1,548 blood culture episodes, 1,274 met ≥2 SIRS criteria (106 significant positive cultures and 1,168 negative cultures). There was no association between SIRS criteria and positive blood cultures (P = .11). A decision rule using 3 SIRS criteria had optimal predictive performance (sensitivity, 56%; specificity, 50%) but low accuracy.

Conclusions: ICU patients with bacteremia have increased mortality and length of ICU stay. SIRS criteria cannot be used to identify patients at low risk of bacteremia.
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http://dx.doi.org/10.1016/j.ajic.2016.04.214DOI Listing
November 2016

The Effects of Faculty Calibration on Caries Risk Assessment and Quality Assurance.

J Dent Educ 2016 Nov;80(11):1294-1300

Dr. Goolsby and Dr. Young contributed equally to this study. Dr. Goolsby is Assistant Professor, Department of General Practice and Department of Admissions, School of Dentistry, Virginia Commonwealth University; Dr. Young is Professor, Department of Dental Practice, Arthur A. Dugoni School of Dentistry, University of the Pacific; Dr. Chiang is Assistant Professor, Department of General Practice, School of Dentistry, Virginia Commonwealth University; Dr. Carrico is Assistant Professor, Department of Periodontics, School of Dentistry, Virginia Commonwealth University; Dr. Jackson is Assistant Professor, Department of General Practice and Department of Admissions, School of Dentistry, Virginia Commonwealth University; and Dr. Rechmann is Professor and Director of Clinical Sciences Research Group, Department of Preventive and Restorative Dental Sciences, School of Dentistry, University of California, San Francisco.

Accurate caries risk assessment (CRA) plays a pivotal role in managing the disease of dental caries. The aim of this quality assurance study was to determine if faculty calibration training using a specific set of guidelines in a single session would improve the faculty members' CRA decision making. A calibration seminar was held in December 2014 at the Virginia Commonwealth University School of Dentistry, during which seven completed CRA forms for simulated patients were used to test 55 faculty members' risk assignment level before and after an instructional lecture was given. The results showed a statistically significant increase in the proportion of faculty members responding correctly for five of the seven cases on the pre- and posttests (p<0.01). One case showed no significant increase in correct responses (p=0.07), and on the seventh case, which presented low caries risk, there was a significant decrease in the percentage responding correctly (p<0.0001) due to an increase in the proportion overestimating caries risk. This study's findings were consistent with those in previous studies that, without calibration, faculty members are not necessarily accurate at CRA diagnosis. Since the calibration training improved these faculty members' caries risk assessment scoring, future studies should extend to evaluations for both faculty and students.
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November 2016

Characterization of progressive HIV-associated tuberculosis using 2-deoxy-2-[F]fluoro-D-glucose positron emission and computed tomography.

Nat Med 2016 10 5;22(10):1090-1093. Epub 2016 Sep 5.

Department of Medicine, Imperial College London, London, UK.

Tuberculosis is classically divided into states of latent infection and active disease. Using combined positron emission and computed tomography in 35 asymptomatic, antiretroviral-therapy-naive, HIV-1-infected adults with latent tuberculosis, we identified ten individuals with pulmonary abnormalities suggestive of subclinical, active disease who were substantially more likely to progress to clinical disease. Our findings challenge the conventional two-state paradigm and may aid future identification of biomarkers that are predictive of progression.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5055809PMC
http://dx.doi.org/10.1038/nm.4161DOI Listing
October 2016

Development of a Core Curriculum Framework in Cariology for U.S. Dental Schools.

J Dent Educ 2016 Jun;80(6):705-20

Dr. Fontana is Professor, School of Dentistry, University of Michigan; Dr. Guzmán-Armstrong is Clinical Associate Professor, College of Dentistry and Dental Clinics, University of Iowa; Dr. Schenkel is Clinical Associate Professor, College of Dentistry, New York University; Dr. Allen is Clinical Associate Professor, College of Dentistry, New York University; Dr. Featherstone is Professor and Dean, School of Dentistry, University of California, San Francisco; Dr. Goolsby is Assistant Professor, School of Dentistry, Virginia Commonwealth University; Dr. Kanjirath is Assistant Dean, College of Dentistry, Midwestern University-Illinois; Dr. Kolker is Clinical Associate Professor, College of Dentistry and Dental Clinics, University of Iowa; Dr. Martignon is Professor, Universidad El Bosque, Bogotá, Colombia and Senior Lecturer, King's College, London; Dr. Pitts is Professor, King's College, London; Dr. Schulte is Professor, Department for Special Care Dentistry, Dental School, University of Witten/Herdecke, Witten, Germany; Dr. Slayton is Professor and Chair, Center for Pediatric Dentistry, University of Washington; Dr. Young is Professor, Arthur A. Dugoni School of Dentistry, University of the Pacific; and Dr. Wolff is Professor, College of Dentistry, New York University.

Maintenance of health and preservation of tooth structure through risk-based prevention and patient-centered, evidence-based disease management, reassessed at regular intervals over time, are the cornerstones of present-day caries management. Yet management of caries based on risk assessment that goes beyond restorative care has not had a strong place in curriculum development and competency assessment in U.S. dental schools. The aim of this study was to develop a competency-based core cariology curriculum framework for use in U.S. dental schools. The Section on Cariology of the American Dental Education Association (ADEA) organized a one-day consensus workshop, followed by a meeting program, to adapt the European Core Cariology Curriculum to the needs of U.S. dental education. Participants in the workshop were 73 faculty members from 35 U.S., three Canadian, and four international dental schools. Representatives from all 65 U.S. dental schools were then invited to review and provide feedback on a draft document. A recommended competency statement on caries management was also developed: "Upon graduation, a dentist must be competent in evidence-based detection, diagnosis, risk assessment, prevention, and nonsurgical and surgical management of dental caries, both at the individual and community levels, and be able to reassess the outcomes of interventions over time." This competency statement supports a curriculum framework built around five domains: 1) knowledge base; 2) risk assessment, diagnosis, and synthesis; 3) treatment decision making: preventive strategies and nonsurgical management; 4) treatment decision making: surgical therapy; and 5) evidence-based cariology in clinical and public health practice. Each domain includes objectives and learning outcomes.
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June 2016

Structural characterization of CYP144A1 - a cytochrome P450 enzyme expressed from alternative transcripts in Mycobacterium tuberculosis.

Sci Rep 2016 05 26;6:26628. Epub 2016 May 26.

Manchester Institute of Biotechnology, Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Faculty of Life Sciences, The University of Manchester, Manchester M1 7DN, United Kingdom.

Mycobacterium tuberculosis (Mtb) causes the disease tuberculosis (TB). The virulent Mtb H37Rv strain encodes 20 cytochrome P450 (CYP) enzymes, many of which are implicated in Mtb survival and pathogenicity in the human host. Bioinformatics analysis revealed that CYP144A1 is retained exclusively within the Mycobacterium genus, particularly in species causing human and animal disease. Transcriptomic annotation revealed two possible CYP144A1 start codons, leading to expression of (i) a "full-length" 434 amino acid version (CYP144A1-FLV) and (ii) a "truncated" 404 amino acid version (CYP144A1-TRV). Computational analysis predicted that the extended N-terminal region of CYP144A1-FLV is largely unstructured. CYP144A1 FLV and TRV forms were purified in heme-bound states. Mass spectrometry confirmed production of intact, His6-tagged forms of CYP144A1-FLV and -TRV, with EPR demonstrating cysteine thiolate coordination of heme iron in both cases. Hydrodynamic analysis indicated that both CYP144A1 forms are monomeric. CYP144A1-TRV was crystallized and the first structure of a CYP144 family P450 protein determined. CYP144A1-TRV has an open structure primed for substrate binding, with a large active site cavity. Our data provide the first evidence that Mtb produces two different forms of CYP144A1 from alternative transcripts, with CYP144A1-TRV generated from a leaderless transcript lacking a 5'-untranslated region and Shine-Dalgarno ribosome binding site.
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http://dx.doi.org/10.1038/srep26628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4880925PMC
May 2016