Publications by authors named "Matthew Bush"

145 Publications

A conserved cell division protein directly regulates FtsZ dynamics in filamentous and unicellular actinobacteria.

Elife 2021 Mar 17;10. Epub 2021 Mar 17.

Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom.

Bacterial cell division is driven by the polymerization of the GTPase FtsZ into a contractile structure, the so-called Z-ring. This essential process involves proteins that modulate FtsZ dynamics and hence the overall Z-ring architecture. Actinobacteria like and lack known key FtsZ-regulators. Here we report the identification of SepH, a conserved actinobacterial protein that directly regulates FtsZ dynamics. We show that SepH is crucially involved in cell division in and that it binds FtsZ via a conserved helix-turn-helix motif, stimulating the assembly of FtsZ protofilaments. Comparative studies using the SepH homolog from further reveal that SepH can also bundle FtsZ protofilaments, indicating an additional Z-ring stabilizing function . We propose that SepH plays a crucial role at the onset of cytokinesis in actinobacteria by promoting the assembly of FtsZ filaments into division-competent Z-rings that can go on to mediate septum synthesis.
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http://dx.doi.org/10.7554/eLife.63387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7968930PMC
March 2021

Behavioral and Hemodynamic Changes Following Dichotic Training in Patients with Neurological Deficits of the Auditory Nervous System: A Case Series.

J Am Acad Audiol 2021 Mar 4. Epub 2021 Mar 4.

Department of Otolaryngology - Head and Neck Surgery, University of Kentucky, Lexington, Kentucky.

Background:  Dichotic listening occurs when one attends to different acoustical messages presented simultaneously to both ears. This is important for understanding speech in compromised listening situations, such as background noise. Deficits in dichotic listening can be remediated by participating in auditory training. We present two patients with binaural integration deficits who underwent dichotic interaural intensity difference (DIID) training.

Purpose:  The purpose of this investigation is to demonstrate improvement of dichotic listening deficits following DIID training in neurological patients seen clinically for hearing issues.

Research Design:  This was a case series utilizing a pre- and posttreatment design.

Study Sample:  This case series utilized two female participants who demonstrated binaural integration deficits during an auditory processing evaluation.

Intervention:  The participants underwent a pretraining auditory processing evaluation and functional magnetic resonance imaging (fMRI). Participants then underwent 12, 30-minute DIID training sessions followed by posttreatment auditory processing evaluations and fMRI.

Data Collection And Analysis:  Data was collected at the pretreatment appointment and then immediately following the completion of the training.

Results:  Each patient demonstrated varying degrees of improvement on the posttreatment assessment. Case 1 showed significant improvement on the Speech-in-Noise-Revised (SPIN-R) test. fMRI showed changes in activation patterns following training. Case 2 demonstrated improved scores on the Dichotic Digits Test and SPIN-R and increased activation of the calcarine sulcus following training.

Conclusion:  Dichotic training can be an efficacious treatment for binaural integration deficits and may show evidence of improving speech understanding in noise. This case series demonstrates a promising therapy to help patients improve auditory function by improving dichotic listening skills.
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http://dx.doi.org/10.1055/s-0040-1719095DOI Listing
March 2021

The novel ECF56 SigG1-RsfG system modulates morphological differentiation and metal-ion homeostasis in Streptomyces tsukubaensis.

Sci Rep 2020 12 10;10(1):21728. Epub 2020 Dec 10.

Bioengineering and Synthetic Microbiology Group, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.

Extracytoplasmic function (ECF) sigma factors are key transcriptional regulators that prokaryotes have evolved to respond to environmental challenges. Streptomyces tsukubaensis harbours 42 ECFs to reprogram stress-responsive gene expression. Among them, SigG1 features a minimal conserved ECF σ-σ architecture and an additional C-terminal extension that encodes a SnoaL_2 domain, which is characteristic for ECF σ factors of group ECF56. Although proteins with such domain organisation are widely found among Actinobacteria, the functional role of ECFs with a fused SnoaL_2 domain remains unknown. Our results show that in addition to predicted self-regulatory intramolecular amino acid interactions between the SnoaL_2 domain and the ECF core, SigG1 activity is controlled by the cognate anti-sigma protein RsfG, encoded by a co-transcribed sigG1-neighbouring gene. Characterisation of ∆sigG1 and ∆rsfG strains combined with RNA-seq and ChIP-seq experiments, suggests the involvement of SigG1 in the morphological differentiation programme of S. tsukubaensis. SigG1 regulates the expression of alanine dehydrogenase, ald and the WhiB-like regulator, wblC required for differentiation, in addition to iron and copper trafficking systems. Overall, our work establishes a model in which the activity of a σ factor of group ECF56, regulates morphogenesis and metal-ions homeostasis during development to ensure the timely progression of multicellular differentiation.
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http://dx.doi.org/10.1038/s41598-020-78520-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7730460PMC
December 2020

Association of Subjective Hearing Loss and Apolipoprotein E ε4 Allele on Alzheimer's Disease Neurodegeneration.

Otol Neurotol 2021 Jan;42(1):e15-e21

Department of Otolaryngology-Head and Neck Surgery, University of Kentucky College of Medicine.

Objective: Hearing loss (HL) and apolipoprotein E ε4 (ApoE4) allele are both dementia risk factors. No research has investigated the association of these variables regarding dementia, specifically Alzheimer's disease. Our goal was to evaluate HL and ApoE4 allele positivity toward degree of Alzheimer's neurodegeneration.

Study Design: Retrospective.

Setting: Academic.

Patients: Alzheimer's neuropathology obtained from brain tissue databank. Documented demographics, subjective hearing status, cognition, and ApoE4. Subjects divided into four groups based on hearing status and ApoE4 positivity.

Main Outcome Measures: Differences in cognition (clinical dementia rating, mini mental state examination (MMSE), geriatric depression score) and Alzheimer's neuropathology staging (Braak, CERAD) between groups.

Results: Two-hundred and fifty-nine subjects. No significant difference between groups, with regard to hearing status or ApoE4 positivity, in premorbid cognition, including scores for clinical dementia rating and MMSE (p = 0.2332). HL subjects had less severe neuropathology, as compared with normal hearing subjects. For example, high grade Braak stage was present in 27.1 and 51.0% of HL and normal hearing subjects, respectively (p = 0.0263). This finding was in context of equivocal clinical cognition between groups. ApoE4+ individuals had more severe neurodegeneration; for example, 65.7 and 33.5% with high grade Braak stage for ApoE4+ and ApoE4- subjects, respectively (p < 0.0001).

Conclusion: Subjective HL subjects had less severe neuropathology with no difference in cognition, suggesting an additive effect of HL to cognitive burden of Alzheimer's neuropathology. HL appeared to increase cognitive burden, but wasn't manifested by greater neurodegeneration. This is clinically relevant in that treating HL could slow Alzheimer's disease progression.
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http://dx.doi.org/10.1097/MAO.0000000000002855DOI Listing
January 2021

Systematic review of endoscopic-assisted surgical management for congenital nasolacrimal duct obstruction.

Int J Pediatr Otorhinolaryngol 2020 Dec 15;139:110448. Epub 2020 Oct 15.

Department of Otolaryngology, University of Kentucky Medical Center, Lexington, KY, USA. Electronic address:

Objectives: Epiphora is a common presenting complaint in infants affecting up to 6% of infants in the United States. It is most frequently due to congenital anomalies of the nasolacrimal duct system, termed congenital nasolacrimal duct obstruction (CNLDO). Nasolacrimal duct probing is widely accepted as the primary surgical intervention in cases that fail conservative management. Recently, nasal endoscopy has been combined with traditional probing to improve success rates and outcomes. Several studies have been conducted, but the results have been inconclusive overall. The goal of this systematic review is to examine the existing literature on the role of nasal endoscopy during nasolacrimal duct probing and evaluate patient outcomes.

Methods: A systematic search was performed in PubMed, MEDLINE, The Cochrane Library, ClinicalTrials.gov, LILAC, and EMBASE to identify peer-reviewed research. Eligible studies were those containing original peer-reviewed research in English addressing nasolacrimal duct probing for congenital nasolacrimal duct obstruction in conjunction with nasal endoscopy. Two investigators independently reviewed all articles and extracted data. Bias was assessed using the Cochrane Collaboration's tool, the Newcastle-Ottawa Assessment scale, and the NIH Quality Assessment scale.

Results: A literature review ultimately yielded 11 articles that were selected and included in our analysis. Of the seven case series, the success rate was 92.5% for a total of 492 eyes. Of the four cohort/case-control studies, the success rate in conventional probings was 75.3% for a total of 293 eyes. In probings with nasal endoscopy, the success rate was 95.3% for 162 eyes. Overall, there was a high risk of bias and variation in data reporting amongst studies.

Conclusion: Infants with congenital nasolacrimal duct obstruction that does not resolve with conservative treatment often require surgical intervention. Based on this systematic review of the current literature, nasal endoscopy is a useful adjunct for nasolacrimal duct probing.
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http://dx.doi.org/10.1016/j.ijporl.2020.110448DOI Listing
December 2020

Does Adherence to Early Infant Hearing Detection and Intervention Guidelines Positively Impact Pediatric Speech Outcomes?

Laryngoscope 2020 Aug 4. Epub 2020 Aug 4.

Department of Otolaryngology-Head and Neck Surgery, University of Kentucky Medical Center, Lexington, Kentucky, U.S.A.

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http://dx.doi.org/10.1002/lary.28994DOI Listing
August 2020

A Position Paper on Systematic and Meta-analysis Reviews.

Otol Neurotol 2020 08;41(7):879-882

Department of Otolaryngology-Head and Neck Surgery, University of Kentucky, Lexington, Kentucky.

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http://dx.doi.org/10.1097/MAO.0000000000002737DOI Listing
August 2020

Opioid Prescribing Patterns and Usage Following Cochlear Implantation.

Otol Neurotol 2020 08;41(7):922-928

Department of Otolaryngology-Head and Neck Surgery, University of Kentucky Medical Center, Lexington, Kentucky.

Objective: To evaluate opioid prescribing patterns following cochlear implantation (CI) and assess factors associated with recurrent opioid use.

Study Design: Retrospective cohort study.

Setting: National pharmaceutical database recording opioid fulfillment (Truven Health Marketscan Commercial Claims and Encounters and Medicare Claims and Encounters database) PARTICIPANTS:: CI recipients who filled opioid prescriptions between January 2011 and December 2016. All patients had no previous opioid prescriptions filled 60 days before implantation and filled at least one opioid prescription within 1 week after surgery. Cohort 1 filled only one prescription and cohort 2 filled more than one prescription in the 12 months following CI. Univariate/multivariate analysis was performed to assess for associations with recurrent opioid use.

Main Outcome Measure(s): Opioid prescription details and recurrent opioid use.

Results: The study included 98 patients (cohort 1 = 57, cohort 2 (recurrent opioid use) = 41). Hydrocodone 5 mg was most frequently used. The average duration opioids were prescribed was 5.49 days with an average quantity of tablets of 36.1. Recurrent opioid use in cohort 2 was associated with both total morphine milligram equivalents (MME) prescribed/day in the first postoperative week (OR = 1.03, p = 0.01) and use of stronger MME opioids (OR = 7.20, p = 0.05).

Conclusion: Prescribing patterns following CI can influence recurrent opioid use in patients. Each additional tablet of hydrocodone 5 mg beyond 8 tablets/d or oxycodone 5 mg beyond 5.33 tablets/d, increases the likelihood of recurrent opioid use by 15 or 22.5%, respectively. Limiting opioids prescribed per day to no more than 40 MME could lower the likelihood of patients becoming recurrent opioid users postoperatively.
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http://dx.doi.org/10.1097/MAO.0000000000002674DOI Listing
August 2020

Factors Influencing Aberrant Facial Nerve Stimulation Following Cochlear Implantation: A Systematic Review and Meta-analysis.

Otol Neurotol 2020 09;41(8):1050-1059

Department of Otolaryngology-Head and Neck Surgery, University of Kentucky Medical Center.

Objective: The purpose of this study was to systematically evaluate the literature to evaluate the rate of and associated factors with aberrant facial nerve stimulation (AFNS) following cochlear implantation. Additionally, management strategies for AFNS were assessed.

Data Sources: A systematic search was performed in PubMed, Cochrane Database of Systematic Reviews, and Web of Science to identify peer reviewed research.

Study Selection: Eligible studies were those containing peer-reviewed research in English addressing AFNS following cochlear implantation. Studies with paired data were included in the meta-analysis.

Data Extraction: Three investigators independently reviewed all articles and extracted data. Bias was assessed using the National Institutes of Health Study Quality Assessment Tool.

Data Synthesis: Thirty-seven articles were included, representing 5,694 patients. The overall reported AFNS rate was 5.6% (range, 0.68-43%). Array type demonstrated a significant association with AFNS with lateral wall electrodes having a higher odds ratio than perimodiolar electrodes (odds ratio [OR] = 3.92, 95% confidence interval [CI] 1.46-10.47, p = 0.01). CI recipients with otosclerosis were also more likely to experience AFNS compared with non-otosclerosis pathology (OR = 13.73, 95% CI 3.57-52.78, p < 0.01). Patients with cochlear malformations had an overall AFNS rate of 28% (range, 5.3-43%) and those with otosclerosis had an overall rate of 26% (range, 6.25-75%). Reprogramming with or without electrode deactivation was successful for AFNS elimination. Four patients of 3,015 required explantation.

Conclusion: Array type and underlying cochlear pathology are associated with AFNS and implant reprogramming is an overall successful management strategy. Further research is needed to elucidate mechanism of AFNS and develop management strategies that limit impact on hearing outcomes.
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http://dx.doi.org/10.1097/MAO.0000000000002693DOI Listing
September 2020

Trends in Opioid Usage Following Tympanoplasty and Mastoidectomy.

Otol Neurotol 2020 09;41(8):e1035-e1040

Department of Otolaryngology-Head and Neck Surgery, University of Kentucky Medical Center, Lexington, Kentucky.

Objective: Evaluate opioid prescribing patterns following tympanoplasty/mastoidectomy and assess factors associated to recurrent opioid use.

Study Design: Retrospective cohort study.

Setting: National pharmaceutical database recording opioid fulfillment (Truven Health Marketscan Commercial Claims/Encounters and Medicare Claims/Encounters database).

Participants: Patients who 1) underwent tympanoplasty and/or mastoidectomy, 2) filled postoperative opioid prescriptions between 2011 and 2016, and 3) had no opioid prescriptions filled 60 days before surgery. Cohort 1 filled only one prescription and cohort 2 filled more than one prescription in the 12 months following surgery. Univariate/multivariate analysis was performed to assess for associations with recurrent opioid use.

Main Outcome Measure(s): Opioid prescription details and recurrent opioid use.

Results: The study included 398 patients (cohort 1 = 233, cohort 2 [recurrent opioid user] = 165). Hydrocodone 5 mg was most frequently used. The average duration opioids were prescribed was 5.8 days with an average quantity of tablets of 36.51. Recurrent opioid use in cohort 2 was associated with total morphine milligram equivalents prescribed/d in the first postoperative week (odds ratio [OR] = 1.02, p < 0.001), post-op chronic pain disorder (OR = 2.00, p = 0.04), post-op substance abuse (OR = 2.12, p = 0.05), and post-op anxiety (OR = 1.96, p = 0.02).

Conclusion: Recurrent opioid use following tympanoplasty/mastoidectomy is associated with the amount prescribed per day but not opioid type or duration of treatment. Postoperative diagnoses such as chronic pain disorder, substance abuse, or anxiety could be predictive of or coexistent with recurrent opioid use. Limiting opioids prescribed per day and use of anti-inflammatory medications could decrease the risk of recurrent opioid use.
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http://dx.doi.org/10.1097/MAO.0000000000002709DOI Listing
September 2020

High-Precision, Gas-Phase Hydrogen/Deuterium-Exchange Kinetics by Mass Spectrometry Enabled by Exchange Standards.

Anal Chem 2020 06 18;92(11):7725-7732. Epub 2020 May 18.

Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States.

Mass spectrometry (MS) has become a primary tool for identifying and quantifying biological molecules. In combination with other orthogonal techniques, such as gas-phase hydrogen/deuterium exchange (gHDX), MS is also capable of probing the structure of ions. However, gHDX kinetics can depend strongly on many factors, including laboratory temperature, instrumental conditions, and instrument platform selection. These effects can lead to high variability with gHDX measurements, which has hindered the broader adoption of gHDX for structural MS. Here we introduce an approach for standardizing gHDX measurements using cosampled standards. Quantifying the exchange kinetics for analytes relative to the exchange kinetics of the standards results in greater accuracy and precision than the underlying absolute measurements. The standardization was found to be effective for several types of analytes including small molecules and intact proteins. A subset of analytes showed deviations in their standardized exchange profiles that are attributed to field heating and the concomitant conformational isomerization. Inclusion of helium during the gHDX process for collisional cooling helps mitigate such variations in exchange kinetics related to ion heating. We anticipate that the outcomes of this research will enable the broader use of gHDX in MS-based workflows for molecular identification and isomer differentiation.
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http://dx.doi.org/10.1021/acs.analchem.0c00749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333526PMC
June 2020

Interaction of the Wbl protein WhiD with the principal sigma factor σ depends on the WhiD [4Fe-4S] cluster.

J Biol Chem 2020 07 16;295(28):9752-9765. Epub 2020 Apr 16.

Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom

The bacterial protein WhiD belongs to the Wbl family of iron-sulfur [Fe-S] proteins present only in the actinomycetes. In , it is required for the late stages of sporulation, but precisely how it functions is unknown. Here, we report results from and experiments with WhiD from (WhiD), which differs from WhiD (WhiD) only at the C terminus. We observed that, like WhiD and other Wbl proteins, WhiD binds a [4Fe-4S] cluster that is moderately sensitive to O and highly sensitive to nitric oxide (NO). However, although all previous studies have reported that Wbl proteins are monomers, we found that WhiD exists in a monomer-dimer equilibrium associated with its unusual C-terminal extension. Several Wbl proteins of are known to interact with its principal sigma factor SigA. Using bacterial two-hybrid, gel filtration, and MS analyses, we demonstrate that WhiD interacts with domain 4 of the principal sigma factor of , σ (σ). Using MS, we determined the dissociation constant ( ) for the WhiD-σ complex as ∼0.7 μm, consistent with a relatively tight binding interaction. We found that complex formation was cluster dependent and that a reaction with NO, which was complete at 8-10 NO molecules per cluster, resulted in dissociation into the separate proteins. The WhiD [4Fe-4S] cluster was significantly less sensitive to reaction with O and NO when WhiD was bound to σ, consistent with protection of the cluster in the complex.
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http://dx.doi.org/10.1074/jbc.RA120.012708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363131PMC
July 2020

Clinical Practice Guideline: Ménière's Disease Executive Summary.

Otolaryngol Head Neck Surg 2020 04;162(4):415-434

American Academy of Otolaryngology-Head and Neck Surgery, Alexandria, Virginia, USA.

Objective: Ménière's disease (MD) is a clinical condition defined by spontaneous vertigo attacks (each lasting 20 minutes to 12 hours) with documented low- to midfrequency sensorineural hearing loss in the affected ear before, during, or after one of the episodes of vertigo. It also presents with fluctuating aural symptoms (hearing loss, tinnitus, or ear fullness) in the affected ear. The underlying etiology of MD is not completely clear, yet it has been associated with inner ear fluid volume increases, culminating in episodic ear symptoms (vertigo, fluctuating hearing loss, tinnitus, and aural fullness). Physical examination findings are often unremarkable, and audiometric testing may or may not show low- to midfrequency sensorineural hearing loss. Imaging, if performed, is also typically normal. The goals of MD treatment are to prevent or reduce vertigo severity and frequency; relieve or prevent hearing loss, tinnitus, and aural fullness; and improve quality of life. Treatment approaches to MD are many, and approaches typically include modifications of lifestyle factors (eg, diet) and medical, surgical, or a combination of therapies.

Purpose: The primary purpose of this clinical practice guideline is to improve the quality of the diagnostic workup and treatment outcomes of MD. To achieve this purpose, the goals of this guideline are to use the best available published scientific and/or clinical evidence to enhance diagnostic accuracy and appropriate therapeutic interventions (medical and surgical) while reducing unindicated diagnostic testing and/or imaging.
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http://dx.doi.org/10.1177/0194599820909439DOI Listing
April 2020

Clinical Practice Guideline: Ménière's Disease.

Otolaryngol Head Neck Surg 2020 04;162(2_suppl):S1-S55

American Academy of Otolaryngology-Head and Neck Surgery, Alexandria, Virginia, USA.

Objective: Ménière's disease (MD) is a clinical condition defined by spontaneous vertigo attacks (each lasting 20 minutes to 12 hours) with documented low- to midfrequency sensorineural hearing loss in the affected ear before, during, or after one of the episodes of vertigo. It also presents with fluctuating aural symptoms (hearing loss, tinnitus, or ear fullness) in the affected ear. The underlying etiology of MD is not completely clear, yet it has been associated with inner ear fluid (endolymph) volume increases, culminating in episodic ear symptoms (vertigo, fluctuating hearing loss, tinnitus, and aural fullness). Physical examination findings are often unremarkable, and audiometric testing may or may not show low- to midfrequency sensorineural hearing loss. Conventional imaging, if performed, is also typically normal. The goals of MD treatment are to prevent or reduce vertigo severity and frequency; relieve or prevent hearing loss, tinnitus, and aural fullness; and improve quality of life. Treatment approaches to MD are many and typically include modifications of lifestyle factors (eg, diet) and medical, surgical, or a combination of therapies.

Purpose: The primary purpose of this clinical practice guideline is to improve the quality of the diagnostic workup and treatment outcomes of MD. To achieve this purpose, the goals of this guideline are to use the best available published scientific and/or clinical evidence to enhance diagnostic accuracy and appropriate therapeutic interventions (medical and surgical) while reducing unindicated diagnostic testing and/or imaging.
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http://dx.doi.org/10.1177/0194599820909438DOI Listing
April 2020

Developmentally regulated volatiles geosmin and 2-methylisoborneol attract a soil arthropod to Streptomyces bacteria promoting spore dispersal.

Nat Microbiol 2020 06 6;5(6):821-829. Epub 2020 Apr 6.

Department of Biology, Lund University, Lund, Sweden.

Volatile compounds emitted by bacteria are often sensed by other organisms as odours, but their ecological roles are poorly understood. Well-known examples are the soil-smelling terpenoids geosmin and 2-methylisoborneol (2-MIB), which humans and various animals sense at extremely low concentrations. The conservation of geosmin biosynthesis genes among virtually all species of Streptomyces bacteria (and genes for the biosynthesis of 2-MIB in about 50%), suggests that the volatiles provide a selective advantage for these soil microbes. We show, in the present study, that these volatiles mediate interactions of apparent mutual benefit between streptomycetes and springtails (Collembola). In field experiments, springtails were attracted to odours emitted by Streptomyces colonies. Geosmin and 2-MIB in these odours induce electrophysiological responses in the antennae of the model springtail Folsomia candida, which is also attracted to both compounds. Moreover, the genes for geosmin and 2-MIB synthases are under the direct control of sporulation-specific transcription factors, constraining emission of the odorants to sporulating colonies. F. candida feeds on the Streptomyces colonies and disseminates spores both via faecal pellets and through adherence to its hydrophobic cuticle. The results indicate that geosmin and 2-MIB production is an integral part of the sporulation process, completing the Streptomyces life cycle by facilitating dispersal of spores by soil arthropods.
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http://dx.doi.org/10.1038/s41564-020-0697-xDOI Listing
June 2020

FBXL5 Regulates IRP2 Stability in Iron Homeostasis via an Oxygen-Responsive [2Fe2S] Cluster.

Mol Cell 2020 04 2;78(1):31-41.e5. Epub 2020 Mar 2.

Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. Electronic address:

Cellular iron homeostasis is dominated by FBXL5-mediated degradation of iron regulatory protein 2 (IRP2), which is dependent on both iron and oxygen. However, how the physical interaction between FBXL5 and IRP2 is regulated remains elusive. Here, we show that the C-terminal substrate-binding domain of FBXL5 harbors a [2Fe2S] cluster in the oxidized state. A cryoelectron microscopy (cryo-EM) structure of the IRP2-FBXL5-SKP1 complex reveals that the cluster organizes the FBXL5 C-terminal loop responsible for recruiting IRP2. Interestingly, IRP2 binding to FBXL5 hinges on the oxidized state of the [2Fe2S] cluster maintained by ambient oxygen, which could explain hypoxia-induced IRP2 stabilization. Steric incompatibility also allows FBXL5 to physically dislodge IRP2 from iron-responsive element RNA to facilitate its turnover. Taken together, our studies have identified an iron-sulfur cluster within FBXL5, which promotes IRP2 polyubiquitination and degradation in response to both iron and oxygen concentrations.
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http://dx.doi.org/10.1016/j.molcel.2020.02.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159994PMC
April 2020

When is a transcription factor a NAP?

Curr Opin Microbiol 2020 06 28;55:26-33. Epub 2020 Feb 28.

Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. Electronic address:

Proteins that regulate transcription often also play an architectural role in the genome. Thus, it has been difficult to define with precision the distinctions between transcription factors and nucleoid-associated proteins (NAPs). Anachronistic descriptions of NAPs as 'histone-like' implied an organizational function in a bacterial chromatin-like complex. Definitions based on protein abundance, regulatory mechanisms, target gene number, or the features of their DNA-binding sites are insufficient as marks of distinction, and trying to distinguish transcription factors and NAPs based on their ranking within regulatory hierarchies or positions in gene-control networks is also unsatisfactory. The terms 'transcription factor' and 'NAP' are ad hoc operational definitions with each protein lying along a spectrum of structural and functional features extending from highly specific actors with few gene targets to those with a pervasive influence on the transcriptome. The Streptomyces BldC protein is used to illustrate these issues.
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http://dx.doi.org/10.1016/j.mib.2020.01.019DOI Listing
June 2020

c-di-GMP Arms an Anti-σ to Control Progression of Multicellular Differentiation in Streptomyces.

Mol Cell 2020 02 3;77(3):586-599.e6. Epub 2019 Dec 3.

Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. Electronic address:

Streptomyces are our primary source of antibiotics, produced concomitantly with the transition from vegetative growth to sporulation in a complex developmental life cycle. We previously showed that the signaling molecule c-di-GMP binds BldD, a master repressor, to control initiation of development. Here we demonstrate that c-di-GMP also intervenes later in development to control differentiation of the reproductive hyphae into spores by arming a novel anti-σ (RsiG) to bind and sequester a sporulation-specific σ factor (σ). We present the structure of the RsiG-(c-di-GMP)-σ complex, revealing an unusual, partially intercalated c-di-GMP dimer bound at the RsiG-σ interface. RsiG binds c-di-GMP in the absence of σ, employing a novel E(X)S(X)R(X)Q(X)D motif repeated on each helix of a coiled coil. Further studies demonstrate that c-di-GMP is essential for RsiG to inhibit σ. These findings reveal a newly described control mechanism for σ-anti-σ complex formation and establish c-di-GMP as the central integrator of Streptomyces development.
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http://dx.doi.org/10.1016/j.molcel.2019.11.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7005675PMC
February 2020

Degronomics: Mapping the Interacting Peptidome of a Ubiquitin Ligase Using an Integrative Mass Spectrometry Strategy.

Anal Chem 2019 10 26;91(20):12775-12783. Epub 2019 Sep 26.

Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States.

Human cells make use of hundreds of unique ubiquitin E3 ligases to ensure proteome fidelity and control cellular functions by promoting protein degradation. These processes require exquisite selectivity, but the individual roles of most E3s remain poorly characterized in part due to the challenges associated with identifying, quantifying, and validating substrates for each E3. We report an integrative mass spectrometry (MS) strategy for characterizing protein fragments that interact with KLHDC2, a human E3 that recognizes the extreme C-terminus of substrates. Using a combination of native MS, native top-down MS, MS of destabilized samples, and liquid chromatography MS, we identified and quantified a near complete fraction of the KLHDC2-binding peptidome in cells. This degronome includes peptides that originate from a variety of proteins. Although all identified protein fragments are terminated by diglycine or glycylalanine, the preceding amino acids are diverse. These results significantly expand our understanding of the sequences that can be recognized by KLHDC2, which provides insight into the potential substrates of this E3 in humans. We anticipate that this integrative MS strategy could be leveraged more broadly to characterize the degronomes of other E3 ligase substrate receptors, including those that adhere to the more common N-end rule for substrate recognition. Therefore, this work advances "degronomics," i.e., identifying, quantifying, and validating functional E3:peptide interactions in order to determine the individual roles of each E3.
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http://dx.doi.org/10.1021/acs.analchem.9b02331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6959985PMC
October 2019

Collision-Induced Unfolding Is Sensitive to the Polarity of Proteins and Protein Complexes.

J Am Soc Mass Spectrom 2019 Nov 9;30(11):2430-2437. Epub 2019 Sep 9.

Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA.

Collision-induced unfolding (CIU) uses ion mobility to probe the structures of ions of proteins and noncovalent complexes as a function of the extent of gas-phase activation prior to analysis. CIU can be sensitive to domain structures, isoform identities, and binding partners, which makes it appealing for many applications. Almost all previous applications of CIU have probed cations. Here, we evaluate the application of CIU to anions and compare the results for anions with those for cations. Towards that end, we developed a "similarity score" that we used to quantify the differences between the results of different CIU experiments and evaluate the significance of those differences relative to the variance of the underlying measurements. Many of the differences between anions and cations that were identified can be attributed to the lower absolute charge states of anions. For example, the extents of the increase in collision cross section over the full range of energies depended strongly on absolute charge state. However, over intermediate energies, there are significant difference between anions and cations with the same absolute charge state. Therefore, CIU is sensitive to the polarity of protein ions. Based on these results, we propose that the utility of CIU to differentiate similar proteins or noncovalent complexes may also depend on polarity. More generally, these results indicate that the relationship between the structures and dynamics of native-like cations and anions deserve further attention and that future studies may benefit from integrating results from ions of both polarities.
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http://dx.doi.org/10.1007/s13361-019-02326-zDOI Listing
November 2019

Neuropathological Findings of Dementia Associated With Subjective Hearing Loss.

Otol Neurotol 2019 10;40(9):e883-e893

Department of Otolaryngology-Head and Neck Surgery, University of Kentucky College of Medicine.

Objective: The relationship between hearing loss and cognitive decline is of great importance with growing evidence of hearing loss as an independent modifiable risk factor for dementia. Our goal was to evaluate for differences in dementia neuropathology between subjective normal hearing and hearing loss subjects, as well as subjects who wore hearing aids.

Study Design: Retrospective database.

Setting: Tertiary academic center.

Patients: Brain tissue analyzed from our Center on Aging. Demographics, subjective hearing status, hearing aid use, cognitive status, and dementia neuropathology documented.

Interventions: Dementia neuropathology analyzed in brains of normal hearing and hearing loss subjects.

Main Outcome Measures: Differences in dementia neuropathology between hearing groups. Groups were compared using logistic regression and analysis of covariance (ANCOVA).

Results: Two-hundred and seventy-three subjects were included, 189 normal hearing and 84 subjective hearing loss subjects. No significant difference demonstrated in Alzheimer's disease neuropathology (p > 0.05) or pathologic stage (p = 0.2471). No significant difference observed in neuropathology of other major dementia types, specifically, presence of Lewy bodies (p > 0.05), Lewy body disease pathologic stage (p = 0.9778), or presence of micro-infarcts, macro-infarcts, or arteriosclerosis (p > 0.05). Hearing aid-wearing subjects had a lower prevalence of clinical dementia (39.1% versus 57.9%; p = 0.0208) with no significant difference in dementia neuropathology (p > 0.05).

Conclusion: Subjective hearing loss was not found to be associated with significantly different dementia neuropathology, which counters hypotheses on hearing loss causing permanent neurodegeneration and cognitive decline. Hearing aid users were found to have a lower prevalence of dementia for similar levels of neurodegeneration, suggesting a potential neuroprotective effect of hearing aids.
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http://dx.doi.org/10.1097/MAO.0000000000002381DOI Listing
October 2019

Outpatient healthcare access and utilization for neonatal abstinence syndrome children: A systematic review.

J Clin Transl Sci 2019 Aug 29;4(5):389-397. Epub 2019 Aug 29.

Department of Otolaryngology - Head and Neck Surgery, University of Kentucky Medical Center, Lexington, KY, USA.

Objective: The objective of this study was to systematically assess the literature regarding postnatal healthcare utilization and barriers/facilitators of healthcare in neonatal abstinence syndrome (NAS) children.

Methods: A systematic search was performed in PubMed, Cochrane Database of Systematic Reviews, PsychINFO, Cumulative Index to Nursing and Allied Health Literature (CINAHL), and Web of Science to identify peer-reviewed research. Eligible studies were peer-reviewed articles reporting on broad aspects of primary and specialty healthcare utilization and access in NAS children. Three investigators independently reviewed all articles and extracted data. Study bias was assessed using the Newcastle-Ottawa Assessment Scale and the National Institute of Health Study Quality Assessment Tool.

Results: This review identified 14 articles that met criteria. NAS children have poorer outpatient appointment adherence and have a higher rate of being lost to follow-up. These children have overall poorer health indicated by a significantly higher risk of ER visits, hospital readmission, and early childhood mortality compared with non-NAS infants. Intensive multidisciplinary support provided through outpatient weaning programs facilitates healthcare utilization and could serve as a model that could be applied to other healthcare fields to improve the health among this population.

Conclusions: This review investigated the difficulties in accessing outpatient care as well as the utilization of such care for NAS infants. NAS infants tend to have decreased access to and utilization of outpatient healthcare following hospital birth discharge. Outpatient weaning programs have proven to be effective; however, these programs require intensive resources and care coordination that has yet to be implemented into other healthcare areas for NAS children.
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http://dx.doi.org/10.1017/cts.2019.407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7681131PMC
August 2019

Principles of Ion Selection, Alignment, and Focusing in Tandem Ion Mobility Implemented Using Structures for Lossless Ion Manipulations (SLIM).

J Am Soc Mass Spectrom 2019 Jun 8;30(6):1115-1125. Epub 2019 Apr 8.

Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA.

Tandem ion mobility (IM) enables the characterization of subpopulations of ions from larger ensembles, including differences that cannot be resolved in a single dimension of IM. Tandem IM consists of at least two IM regions that are each separated by an ion selection region. In many implementations of tandem IM, ions eluting from a dimension of separation are filtered and immediately transferred to the subsequent dimension of separation (selection-only experiments). We recently reported a mode of operation in which ions eluting from a dimension are trapped prior to the subsequent dimension (selection-trapping experiments), which was implemented on an instrument constructed using the structures for lossless ion manipulations (SLIM) architecture. Here, we use a combination of experiments and trajectory simulations to characterize aspects of the selection, trapping, and separation processes underlying these modes of operation. For example, the actual temporal profile of filtered ions can be very similar to the width of the waveforms used for selection, but depending on experimental parameters, can differ by up to ± 500 μs. Experiments and simulations indicate that ions in selection-trapping experiments can be spatially focused between dimensions, which removes the broadening that occurred during the preceding dimension. During focusing, individual ions are thermalized, which aligns and establishes common initial conditions for the subsequent dimension. Therefore, selection-trapping experiments appear to offer significant advantages relative to selection-only experiments, which we anticipate will become more pronounced in future experiments that make use of longer IM separations, additional dimensions of analysis, and the outcomes of this study. Graphical Abstract.
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http://dx.doi.org/10.1007/s13361-019-02170-1DOI Listing
June 2019

Rural Adult Perspectives on Impact of Hearing Loss and Barriers to Care.

J Community Health 2019 08;44(4):668-674

School of Public Health, University of California Berkeley, Berkeley, CA, USA.

Adult hearing loss has a significant impact on communication and quality of life. In spite of effective methods of diagnosis and treatment, many rural adults face significant barriers and delays in accessing care. The purpose of this study is to characterize the impact of hearing loss and the barriers for hearing healthcare in rural adults. Using stratified purposeful sampling, the study design involved semi-structured phone interviews with adults in the Appalachian region of Kentucky between 2016 and 2017 to describe perceived susceptibility to hearing loss; knowledge of hearing loss; cues leading to help-seeking; barriers limited access to care; benefits of seeking help; and self-rated confidence in seeking treatment. Thematic qualitative analysis was performed to identify recurring content themes. Forty adults participated in the study. Participants reported susceptibility to noise induced hearing loss with infrequent hearing protection use. Participants described concern with hearing loss-related communication barriers that could affect compliance with medical care, employment performance, personal safety, and relationship communication. Rural adult expressed willingness to seek hearing healthcare but reported a lack of providers in rural areas. The cost and the lack of insurance coverage for hearing aids were the most clearly articulated obstacles influencing access to care. Hearing loss has a significant impact on adults in rural areas. A lack of providers and the overwhelming cost of treatment are barriers to care. Further research is needed to identify novel methods to support rural adults seeking affordable hearing healthcare.
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http://dx.doi.org/10.1007/s10900-019-00656-3DOI Listing
August 2019

Defining the regulon of genes controlled by σ , a key regulator of the cell envelope stress response in Streptomyces coelicolor.

Mol Microbiol 2019 08 29;112(2):461-481. Epub 2019 Apr 29.

Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.

The extracytoplasmic function (ECF) σ factor, σ , is a key regulator of the cell envelope stress response in Streptomyces coelicolor. Although its role in maintaining cell wall integrity has been known for over a decade, a comprehensive analysis of the genes under its control has not been undertaken. Here, using a combination of chromatin immunoprecipitation-sequencing (ChIP-seq), microarray transcriptional profiling and bioinformatic analysis, we attempt to define the σ regulon. Approximately half of the genes identified encode proteins implicated in cell envelope function. Seventeen novel targets were validated by S1 nuclease mapping or in vitro transcription, establishing a σ -binding consensus. Subsequently, we used bioinformatic analysis to look for conservation of the σ target promoters identified in S. coelicolor across 19 Streptomyces species. Key proteins under σ control across the genus include the actin homolog MreB, three penicillin-binding proteins, two L,D-transpeptidases, a LytR-CpsA-Psr-family protein predicted to be involved in cell wall teichoic acid deposition and a predicted MprF protein, which adds lysyl groups to phosphatidylglycerol to neutralize membrane surface charge. Taken together, these analyses provide biological insight into the σ -mediated cell envelope stress response in the genus Streptomyces.
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http://dx.doi.org/10.1111/mmi.14250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6767563PMC
August 2019

Audiology Telemedicine Evaluations: Potential Expanded Applications.

Otolaryngol Head Neck Surg 2019 07 5;161(1):63-66. Epub 2019 Mar 5.

1 Department of Otolaryngology-Head and Neck Surgery, University of Kentucky Medical Center, Lexington, Kentucky, USA.

There is underutilization of cochlear implants with delays in implantation linked to distance from implant centers. Telemedicine could connect cochlear implant specialists with patients in rural locations. We piloted telemedicine cochlear implant testing in a small study, largely composed of normal-hearing volunteers to trial this new application of teleaudiology technology. Thirteen subjects (8 with normal hearing and 5 with hearing loss ranging from mild to profound) underwent a traditional cochlear implant evaluation in person and then via telemedicine technology. Routine audiometry, word recognition testing, and Arizona Biological Test (AzBio) and consonant-nucleus-consonant (CNC) testing were performed. Mean (SD) percent difference in AzBio between in-person and remote testing was 1.7% (2.06%). Pure tone average (PTA), speech reception threshold (SRT), and word recognition were similar between methods. CNC testing showed a mean (SD) difference of 6.8% (10.2%) between methods. Testing conditions were acceptable to audiologists and subjects. Further study to validate this method in cochlear implant candidates and a larger population is warranted.
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http://dx.doi.org/10.1177/0194599819835541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602851PMC
July 2019

BldC Delays Entry into Development To Produce a Sustained Period of Vegetative Growth in Streptomyces venezuelae.

mBio 2019 02 5;10(1). Epub 2019 Feb 5.

Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom

Streptomycetes are filamentous bacteria that differentiate by producing spore-bearing reproductive structures called aerial hyphae. The transition from vegetative to reproductive growth is controlled by the (bald) loci, and mutations in genes prevent the formation of aerial hyphae, either by blocking entry into development (typically mutations in activators) or by inducing precocious sporulation in the vegetative mycelium (typically mutations in repressors). One of the genes, , encodes a 68-residue DNA-binding protein related to the DNA-binding domain of MerR-family transcription factors. Recent work has shown that BldC binds DNA by a novel mechanism, but there is less insight into its impact on development. Here we used ChIP-seq coupled with RNA-seq to define the BldC regulon in the model species , showing that BldC can function both as a repressor and as an activator of transcription. Using electron microscopy and time-lapse imaging, we show that mutants are bald because they initiate development prematurely, bypassing the formation of aerial hyphae. This is consistent with the premature expression of BldC target genes encoding proteins with key roles in development (e.g., , , ), chromosome condensation and segregation (e.g., , ), and sporulation-specific cell division (e.g., ), suggesting that BldC-mediated repression is critical to maintain a sustained period of vegetative growth prior to sporulation. We discuss the possible significance of BldC as an evolutionary link between MerR family transcription factors and DNA architectural proteins. Understanding the mechanisms that drive bacterial morphogenesis depends on the dissection of the regulatory networks that underpin the cell biological processes involved. Recently, has emerged as an attractive model system for the study of morphological differentiation in This has led to significant progress in identifying the genes controlled by the transcription factors that regulate aerial mycelium formation (Bld regulators) and sporulation (Whi regulators). Taking advantage of , we used ChIP-seq coupled with RNA-seq to identify the genes directly under the control of BldC. Because sporulates in liquid culture, the complete spore-to-spore life cycle can be examined using time-lapse microscopy, and we applied this technique to the mutant. These combined approaches reveal BldC to be a member of an emerging class of Bld regulators that function principally to repress key sporulation genes, thereby extending vegetative growth and blocking the onset of morphological differentiation.
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http://dx.doi.org/10.1128/mBio.02812-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6428758PMC
February 2019

Recommendations for reporting ion mobility Mass Spectrometry measurements.

Mass Spectrom Rev 2019 05 1;38(3):291-320. Epub 2019 Feb 1.

University of California, Santa Barbara, California.

Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K ) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/mas.21585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6618043PMC
May 2019

Management of Hearing Loss Through Telemedicine.

JAMA Otolaryngol Head Neck Surg 2019 03;145(3):204-205

Kentucky TeleCare, University of Kentucky Medical Center, Lexington.

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http://dx.doi.org/10.1001/jamaoto.2018.3885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6620156PMC
March 2019