Publications by authors named "Christopher Davies"

179 Publications

Molecular Features of Cephalosporins Important for Activity against Antimicrobial-Resistant .

ACS Infect Dis 2021 02 3;7(2):293-308. Epub 2021 Feb 3.

Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States.

The increasing prevalence of strains exhibiting decreased susceptibility to extended-spectrum cephalosporins (ESCs) presents a challenge for the successful treatment of gonorrhea infections. To address this challenge, we evaluated a panel of 23 cephalosporins against penicillin-binding protein 2 (PBP2) from the ESC-resistant (ESC) strain H041 to determine which molecular features are important for antimicrobial activity. Structure-activity relationships (SARs) developed from acylation rate constants against PBP2 and antimicrobial susceptibilities against the H041 strain of , and interpreted against docking models, reveal that cephalosporins possessing large, lipophilic R side chains and electronegative R side chains with planar groups are associated with higher acylation rates against PBP2, but also that these same amphipathic features can lower antimicrobial activity. Based on these studies, we tested cefoperazone, one of the most effective ESCs for targeting PBP2, in the female mouse model infected with H041 and showed that it was equally or more effective than ceftriaxone or gentamicin for clearing infections. Taken together, our results reveal that two U.S. Food and Drug Administration (FDA)-approved agents (cefoperazone, ceftaroline) and one FDA-qualified infectious disease product (ceftobiprole) have potential as first-line treatments for gonorrhea and provide a framework for the future design of cephalosporins with improved activity against ESC-resistant .
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http://dx.doi.org/10.1021/acsinfecdis.0c00400DOI Listing
February 2021

Quantitative estimates of average geomagnetic axial dipole dominance in deep geological time.

Nat Commun 2020 11 30;11(1):6100. Epub 2020 Nov 30.

Centre for Earth Evolution and Dynamics, University of Oslo, Sem Saelands vei 2A, 0315, Oslo, Norway.

A defining characteristic of the recent geomagnetic field is its dominant axial dipole which provides its navigational utility and dictates the shape of the magnetosphere. Going back through time, much less is known about the degree of axial dipole dominance. Here we use a substantial and diverse set of 3D numerical dynamo simulations and recent observation-based field models to derive a power law relationship between the angular dispersion of virtual geomagnetic poles at the equator and the median axial dipole dominance measured at Earth's surface. Applying this relation to published estimates of equatorial angular dispersion implies that geomagnetic axial dipole dominance averaged over 10-10 years has remained moderately high and stable through large parts of geological time. This provides an observational constraint to future studies of the geodynamo and palaeomagnetosphere. It also provides some reassurance as to the reliability of palaeogeographical reconstructions provided by palaeomagnetism.
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http://dx.doi.org/10.1038/s41467-020-19794-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7704635PMC
November 2020

Variability and trends over time and across centres in haemodialysis weekly duration in Australia and New Zealand.

Nephrology (Carlton) 2021 Feb 22;26(2):153-163. Epub 2020 Oct 22.

Department of Nephrology, Princess Alexandra Hospital, Brisbane, Australia.

Aim: Haemodialysis treatment prescription varies widely internationally. This study explored patient- and centre-level characteristics associated with weekly haemodialysis hours.

Methods: Australia and New Zealand Dialysis and Transplant (ANZDATA) Registry data were analysed. Characteristics associated with weekly duration were evaluated using mixed-effects linear regression models with patient- and centre-level covariates as fixed effects, and dialysis centre and state as random effects using the 2017 prevalent in-centre haemodialysis (ICHD) and home haemodialysis (HHD) cohorts. Evaluation of patterns of weekly duration over time analysed the 2000 to 2017 incident ICHD and HHD cohorts.

Results: Overall, 12 494 ICHD and 1493 HHD prevalent patients in 2017 were included. Median weekly treatment duration was 13.5 (interquartile range [IQR] 12-15) hours for ICHD and 16 (IQR 15-20) hours for HHD. Male sex, younger age, higher body mass index, arteriovenous fistula/graft use, Aboriginal and Torres Strait Islander ethnicity and longer dialysis vintage were associated with longer weekly duration for both ICHD and HHD. No centre characteristics were associated with duration. Variability in duration across centres was very limited in ICHD compared with HHD, with variation in HHD being associated with state. Duration did not vary significantly over time for ICHD, whereas longer weekly HHD treatments were reported between 2006 and 2012 compared with before and after this period.

Conclusion: This study in the Australian and New Zealand haemodialysis population showed that weekly duration was primarily associated with patient characteristics. No centre effect was demonstrated. Practice patterns seemed to differ across states/countries, with more variability in HHD than ICHD.
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http://dx.doi.org/10.1111/nep.13782DOI Listing
February 2021

Intrinsic quantum confinement in formamidinium lead triiodide perovskite.

Nat Mater 2020 Nov 24;19(11):1201-1206. Epub 2020 Aug 24.

Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.

Understanding the electronic energy landscape in metal halide perovskites is essential for further improvements in their promising performance in thin-film photovoltaics. Here, we uncover the presence of above-bandgap oscillatory features in the absorption spectra of formamidinium lead triiodide thin films. We attribute these discrete features to intrinsically occurring quantum confinement effects, for which the related energies change with temperature according to the inverse square of the intrinsic lattice parameter, and with peak index in a quadratic manner. By determining the threshold film thickness at which the amplitude of the peaks is appreciably decreased, and through ab initio simulations of the absorption features, we estimate the length scale of confinement to be 10-20 nm. Such absorption peaks present a new and intriguing quantum electronic phenomenon in a nominally bulk semiconductor, offering intrinsic nanoscale optoelectronic properties without necessitating cumbersome additional processing steps.
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http://dx.doi.org/10.1038/s41563-020-0774-9DOI Listing
November 2020

H3K27me3 expression and methylation status in histological variants of malignant peripheral nerve sheath tumours.

J Pathol 2020 10 1;252(2):151-164. Epub 2020 Sep 1.

Research Department of Pathology, University College London, London, UK.

Diagnosing MPNST can be challenging, but genetic alterations recently identified in polycomb repressive complex 2 (PRC2) core component genes, EED and SUZ12, resulting in global loss of the histone 3 lysine 27 trimethylation (H3K27me3) epigenetic mark, represent drivers of malignancy and a valuable diagnostic tool. However, the reported loss of H3K27me3 expression ranges from 35% to 84%. We show that advances in molecular pathology now allow many MPNST mimics to be classified confidently. We confirm that MPNSTs harbouring mutations in PRC2 core components are associated with loss of H3K27me3 expression; whole-genome doubling was detected in 68%, and SSTR2 was amplified in 32% of MPNSTs. We demonstrate that loss of H3K27me3 expression occurs overall in 38% of MPNSTs, but is lost in 76% of histologically classical cases, whereas loss was detected in only 23% cases with heterologous elements and 14% where the diagnosis could not be provided on morphology alone. H3K27me3 loss is rarely seen in other high-grade sarcomas and was not found to be associated with an inferior outcome in MPNST. We show that DNA methylation profiling distinguishes MPNST from its histological mimics, was unrelated to anatomical site, and formed two main clusters, MeGroups 4 and 5. MeGroup 4 represents classical MPNSTs lacking H3K27me3 expression in the majority of cases, whereas MeGroup 5 comprises MPNSTs exhibiting non-classical histology and expressing H3K27me3 and cluster with undifferentiated sarcomas. The two MeGroups are distinguished by differentially methylated PRC2-associated genes, the majority of which are hypermethylated in the promoter regions in MeGroup 4, indicating that the PRC2 target genes are not expressed in these tumours. The methylation profiles of MPNSTs with retention of H3K27me3 in MeGroups 4 and 5 are independent of mutations in PRC2 core components and the driver(s) in these groups remain to be identified. Our results open new avenues of investigation. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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http://dx.doi.org/10.1002/path.5507DOI Listing
October 2020

Rapid geomagnetic changes inferred from Earth observations and numerical simulations.

Nat Commun 2020 07 6;11(1):3371. Epub 2020 Jul 6.

Institute of Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, 92093-0225, USA.

Extreme variations in the direction of Earth's magnetic field contain important information regarding the operation of the geodynamo. Paleomagnetic studies have reported rapid directional changes reaching 1° yr, although the observations are controversial and their relation to physical processes in Earth's core unknown. Here we show excellent agreement between amplitudes and latitude ranges of extreme directional changes in a suite of geodynamo simulations and a recent observational field model spanning the past 100 kyrs. Remarkably, maximum rates of directional change reach  ~10° yr, typically during times of decreasing field strength, almost 100 times faster than current changes. Detailed analysis of the simulations and a simple analogue model indicate that extreme directional changes are associated with movement of reversed flux across the core surface. Our results demonstrate that such rapid variations are compatible with the physics of the dynamo process and suggest that future searches for rapid directional changes should focus on low latitudes.
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http://dx.doi.org/10.1038/s41467-020-16888-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338531PMC
July 2020

Fatherhood and Kidney Replacement Therapy: Analysis of the Australian and New Zealand Dialysis and Transplant (ANZDATA) Registry.

Am J Kidney Dis 2020 09 28;76(3):444-446. Epub 2020 May 28.

Central and Northern Adelaide Renal and Transplantation Services (CNARTS), Royal Adelaide Hospital, Adelaide, South Australia; Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia; Australian and New Zealand Dialysis and Transplant (ANZDATA) Registry and Australia and New Zealand Organ Donation (ANZOD) Registry, South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia.

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http://dx.doi.org/10.1053/j.ajkd.2020.03.020DOI Listing
September 2020

Parenthood and pregnancy in Australians receiving treatment for end-stage kidney disease: protocol of a national study of perinatal and parental outcomes through population record linkage.

BMJ Open 2020 05 25;10(5):e036329. Epub 2020 May 25.

Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia.

Introduction: Achieving parenthood is challenging in individuals receiving renal replacement therapy (RRT; dialysis or kidney transplantation) for end-stage kidney disease. Decision-making regarding parenthood in RRT recipients should be underpinned by robust data, yet there is limited data on parental factors that drive adverse health outcomes. Therefore, we aim to investigate the perinatal risks and outcomes in parents receiving RRT.

Methods And Analysis: This is a multijurisdictional probabilistic data linkage study of perinatal, hospital, birth, death and renal registers from 1991 to 2013 from New South Wales, Western Australia, South Australia and the Australian Capital Territory. This study includes all babies born ≥20 weeks' gestation or 400 g birth weight captured through mandated data collection in the perinatal data sets. Through linkage with the Australian and New Zealand Dialysis and Transplant (ANZDATA) registry, babies exposed to RRT (and their parents) will be compared with babies who have not been exposed to RRT (and their parents) to determine obstetric and fetal outcomes, birth rates and fertility rates. One of the novel aspects of this study is the method that will be used to link fathers receiving RRT to the mothers and their babies within the perinatal data sets, using the birth register, enabling the identification of family units. The linked data set will be used to validate the parenthood events directly reported to ANZDATA.

Ethics And Dissemination: Ethics approval was obtained from Human Research Ethics Committees (HREC) and Aboriginal HREC in each jurisdiction. Findings of this study will be disseminated at scientific conferences and in peer-reviewed journals in tabular and aggregated forms. De-identified data will be presented and individual patients will not be identified. We will aim to present findings to relevant stakeholders (eg, patients, clinicians and policymakers) to maximise translational impact of research findings.
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http://dx.doi.org/10.1136/bmjopen-2019-036329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7252957PMC
May 2020

Mutations in penicillin-binding protein 2 from cephalosporin-resistant hinder ceftriaxone acylation by restricting protein dynamics.

J Biol Chem 2020 05 6;295(21):7529-7543. Epub 2020 Apr 6.

Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425

The global incidence of the sexually transmitted disease gonorrhea is expected to rise due to the spread of strains with decreased susceptibility to extended-spectrum cephalosporins (ESCs). ESC resistance is conferred by mosaic variants of penicillin-binding protein 2 (PBP2) that have diminished capacity to form acylated adducts with cephalosporins. To elucidate the molecular mechanisms of ESC resistance, we conducted a biochemical and high-resolution structural analysis of PBP2 variants derived from the decreased-susceptibility strain 35/02 and ESC-resistant strain H041. Our data reveal that mutations both lower affinity of PBP2 for ceftriaxone and restrict conformational changes that normally accompany acylation. Specifically, we observe that a G545S substitution hinders rotation of the β3 strand necessary to form the oxyanion hole for acylation and also traps ceftriaxone in a noncanonical configuration. In addition, F504L and N512Y substitutions appear to prevent bending of the β3-β4 loop that is required to contact the R1 group of ceftriaxone in the active site. Other mutations also appear to act by reducing flexibility in the protein. Overall, our findings reveal that restriction of protein dynamics in PBP2 underpins the ESC resistance of .
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http://dx.doi.org/10.1074/jbc.RA120.012617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7247294PMC
May 2020

Variability associated with interpreting drugs within forensic hair analysis: A three-stage interpretation.

J Appl Toxicol 2020 07 3;40(7):868-888. Epub 2020 Mar 3.

Forensic and Investigative Studies, School of Life Science, Faculty of Science and Engineering, Anglia Ruskin University, Cambridge, UK.

Hair analysis is capable of determining both an individual's long-term drug history and a single exposure to a drug, which can be particularly important for corroborating incidents of drug-facilitated crimes. As a source of forensic evidence that may be used in a court of law, it must be credible, impartial and reliable, yet the pathways of drug and metabolite entry into hair are still uncertain. Many variables may influence drug analysis results, most of which are outside of the control of an analyst. An individual's pharmacokinetic and metabolic responses, hair growth rates, drug incorporation routes, axial migration, ethnicity, age and gender, for example, all display interpersonal variability. At present there is little standardization of the analytical processes involved with hair analysis. Both false positives and negative results for drugs are frequently encountered, regardless of whether a person has consumed a drug or not. In this regard, we have categorized these variables and proposed a three-stage analytical approach to facilitate forensic toxicologists, hair analysis experts, judiciaries and service users in the analytical and interpretation process.
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http://dx.doi.org/10.1002/jat.3959DOI Listing
July 2020

Auxin treatment of grapevine (Vitis vinifera L.) berries delays ripening onset by inhibiting cell expansion.

Plant Mol Biol 2020 May 10;103(1-2):91-111. Epub 2020 Feb 10.

CSIRO Agriculture and Food, Locked Bag 2, Glen Osmond, SA, 5064, Australia.

Key Message: Auxin treatment of grape (Vitis vinifera L.) berries delays ripening by inducing changes in gene expression and cell wall metabolism and could combat some deleterious climate change effects. Auxins are inhibitors of grape berry ripening and their application may be useful to delay harvest to counter effects of climate change. However, little is known about how this delay occurs. The expression of 1892 genes was significantly changed compared to the control during a 48 h time-course where the auxin 1-naphthaleneacetic acid (NAA) was applied to pre-veraison grape berries. Principal component analysis showed that the control and auxin-treated samples were most different at 3 h post-treatment when approximately three times more genes were induced than repressed by NAA. There was considerable cross-talk between hormone pathways, particularly between those of auxin and ethylene. Decreased expression of genes encoding putative cell wall catabolic enzymes (including those involved with pectin) and increased expression of putative cellulose synthases indicated that auxins may preserve cell wall structure. This was confirmed by immunochemical labelling of berry sections using antibodies that detect homogalacturonan (LM19) and methyl-esterified homogalacturonan (LM20) and by labelling with the CMB3a cellulose-binding module. Comparison of the auxin-induced changes in gene expression with the pattern of these genes during berry ripening showed that the effect on transcription is a mix of changes that may specifically alter the progress of berry development in a targeted manner and others that could be considered as non-specific changes. Several lines of evidence suggest that cell wall changes and associated berry softening are the first steps in ripening and that delaying cell expansion can delay ripening providing a possible mechanism for the observed auxin effects.
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http://dx.doi.org/10.1007/s11103-020-00977-1DOI Listing
May 2020

Effect of Modulating FcRn Binding on Direct and Pretargeted Tumor Uptake of Full-length Antibodies.

Mol Cancer Ther 2020 04 5;19(4):1052-1058. Epub 2020 Feb 5.

Preclinical and Translational Pharmacokinetics, Genentech Research and Early Development, South San Francisco, California.

Full-length antibodies lack ideal pharmacokinetic properties for rapid targeted imaging, prompting the pursuit of smaller peptides and fragments. Nevertheless, studying the disposition properties of antibody-based imaging agents can provide critical insight into the pharmacology of their therapeutic counterparts, particularly for those coupled with potent payloads. Here, we evaluate modulation of binding to the neonatal Fc receptor (FcRn) as a protein engineering-based pharmacologic strategy to minimize the overall blood pool background with directly labeled antibodies and undesirable systemic click reaction of radiolabeled tetrazine with circulating pretargeted -cyclooctene (TCO)-modified antibodies. Noninvasive SPECT imaging of mice bearing HER2-expressing xenografts was performed both directly (In-labeled antibody) and indirectly (pretargeted TCO-modified antibody followed by In-labeled tetrazine). Pharmacokinetic modulation of antibodies was achieved by two distinct methods: Fc engineering to reduce binding affinity to FcRn, and delayed administration of an antibody that competes with binding to FcRn. Tumor imaging with directly labeled antibodies was feasible in the absence of FcRn binding, rapidly attaining high tumor-to-blood ratios, but accompanied by moderate liver and spleen uptake. Pretargeted imaging of tumors with non-FcRn-binding antibody was also feasible, but systemic click reaction still occurred, albeit at lower levels than with parental antibody. Our findings demonstrate that FcRn binding impairment of full-length IgG antibodies moderately lowers tumor accumulation of radioactivity, and shifts background activity from blood pool to liver and spleen. Furthermore, reduction of FcRn binding did not eliminate systemic click reaction, but yielded greater improvements in tumor-to-blood ratio when imaging with directly labeled antibodies than with pretargeting.
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http://dx.doi.org/10.1158/1535-7163.MCT-19-1015DOI Listing
April 2020

Development and optimization of OspC chimeritope vaccinogens for Lyme disease.

Vaccine 2020 02 17;38(8):1915-1924. Epub 2020 Jan 17.

Dept. Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA 23298-0678, United States. Electronic address:

Experimental Outer surface protein (Osp) C based subunit chimeritope vaccinogens for Lyme disease (LD) were assessed for immunogenicity, structure, ability to elicit antibody (Ab) responses to divergent OspC proteins, and bactericidal activity. Chimeritopes are chimeric epitope based proteins that consist of linear epitopes derived from multiple proteins or multiple variants of a protein. An inherent advantage to chimeritope vaccinogens is that they can be constructed to trigger broadly protective Ab responses. Three OspC chimeritope proteins were comparatively assessed: Chv1, Chv2 and Chv3. The Chv proteins possess the same set of 18 linear epitopes derived from 9 OspC type proteins but differ in the physical ordering of epitopes or by the presence or absence of linkers. All Chv proteins were immunogenic in mice and rats eliciting high titer Ab. Immunoblot and enzyme linked immunosorbent assays demonstrated that the Chv proteins elicit IgG that recognizes a diverse array of OspC type proteins. The panel included OspC proteins produced by N. American and European strains of the LD spirochetes. Rat anti-Chv antisera uniformly labeled intact, non-permeabilized Borreliella burgdorferi demonstrating that vaccinal Ab can bind to targets that are naturally presented on the spirochete cell surface. Vaccinal Ab also displayed potent complement dependent-Ab mediated killing activity. This study highlights the ability of OspC chimeritopes to serve as vaccinogens that trigger potentially broadly protective Ab responses. In addition to the current use of an OspC chimeritope in a canine LD vaccine, chimeritopes can serve as key components of human LD subunit vaccines.
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http://dx.doi.org/10.1016/j.vaccine.2020.01.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7085410PMC
February 2020

Editorial: Bacterial Mechanisms of Antibiotic Resistance: A Structural Perspective.

Front Mol Biosci 2019 14;6:71. Epub 2019 Aug 14.

Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States.

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http://dx.doi.org/10.3389/fmolb.2019.00071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6702466PMC
August 2019

Recognition of the β-lactam carboxylate triggers acylation of penicillin-binding protein 2.

J Biol Chem 2019 09 30;294(38):14020-14032. Epub 2019 Jul 30.

Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425

Resistance of to extended-spectrum cephalosporins (ESCs) has become a major threat to human health. The primary mechanism by which becomes resistant to ESCs is by acquiring a mosaic allele, encoding penicillin-binding protein 2 (PBP2) variants containing up to 62 mutations compared with WT, of which a subset contribute to resistance. To interpret molecular mechanisms underpinning cephalosporin resistance, it is necessary to know how PBP2 is acylated by ESCs. Here, we report the crystal structures of the transpeptidase domain of WT PBP2 in complex with cefixime and ceftriaxone, along with structures of PBP2 in the form and with a phosphate ion bound in the active site at resolutions of 1-7-1.9 Å. These structures reveal that acylation of PBP2 by ESCs is accompanied by rotation of the Thr-498 side chain in the KTG motif to contact the cephalosporin carboxylate, twisting of the β3 strand to form the oxyanion hole, and rolling of the β3-β4 loop toward the active site. Recognition of the cephalosporin carboxylate appears to be the key trigger for formation of an acylation-competent state of PBP2. The structures also begin to explain the impact of mutations implicated in ESC resistance. In particular, a G545S mutation may hinder twisting of β3 because its side chain hydroxyl forms a hydrogen bond with Thr-498. Overall, our data suggest that acylation is initiated by conformational changes elicited or trapped by binding of ESCs and that these movements are restricted by mutations associated with resistance against ESCs.
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http://dx.doi.org/10.1074/jbc.RA119.009942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755799PMC
September 2019

New views on an old enzyme: allosteric regulation and evolution of archaeal pyruvate kinases.

FEBS J 2019 07 26;286(13):2471-2489. Epub 2019 Apr 26.

Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Germany.

Pyruvate kinases (PKs) synthesize ATP as the final step of glycolysis in the three domains of life. PKs from most bacteria and eukarya are allosteric enzymes that are activated by sugar phosphates; for example, the feed-forward regulator fructose-1,6-bisphosphate, or AMP as a sensor of energy charge. Archaea utilize unusual glycolytic pathways, but the allosteric properties of PKs from these species are largely unknown. Here, we present an analysis of 24 PKs from most archaeal clades with respect to allosteric properties, together with phylogenetic analyses constructed using a novel mode of rooting protein trees. We find that PKs from many Thermoproteales, an order of crenarchaeota, are allosterically activated by 3-phosphoglycerate (3PG). We also identify five conserved amino acids that form the binding pocket for 3PG. 3PG is generated via an irreversible reaction in the modified glycolytic pathway of these archaea and therefore functions as a feed-forward regulator. We also show that PKs from hyperthermophilic Methanococcales, an order of euryarchaeota, are activated by AMP. Phylogenetic analyses indicate that 3PG-activated PKs form an evolutionary lineage that is distinct from that of sugar-phosphate activated PKs, and that sugar phosphate-activated PKs originated as AMP-regulated PKs in hyperthermophilic Methanococcales. Since the phospho group of sugar phosphates and 3PG overlap in the allosteric site, our data indicate that the allostery in PKs first started from a progenitor phosphate-binding site that evolved in two spatially distinct directions: one direction generated the canonical site that responds to sugar phosphates and the other gave rise to the 3PG site present in Thermoproteales. Overall, our data suggest an intimate connection between the allosteric properties and evolution of PKs.
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http://dx.doi.org/10.1111/febs.14837DOI Listing
July 2019

Molecular mechanism of a covalent allosteric inhibitor of SUMO E1 activating enzyme.

Nat Commun 2018 12 4;9(1):5145. Epub 2018 Dec 4.

Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, 29425, SC, USA.

E1 enzymes activate ubiquitin (Ub) and ubiquitin-like modifiers (Ubls) in the first step of Ub/Ubl conjugation cascades and represent potential targets for therapeutic intervention in cancer and other life-threatening diseases. Here, we report the crystal structure of the E1 enzyme for the Ubl SUMO in complex with a recently discovered and highly specific covalent allosteric inhibitor (COH000). The structure reveals that COH000 targets a cryptic pocket distinct from the active site that is completely buried in all previous SUMO E1 structures and that COH000 binding to SUMO E1 is accompanied by a network of structural changes that altogether lock the enzyme in a previously unobserved inactive conformation. These structural changes include disassembly of the active site and a 180° rotation of the catalytic cysteine-containing SCCH domain, relative to conformational snapshots of SUMO E1 poised to catalyze adenylation. Altogether, our study provides a molecular basis for the inhibitory mechanism of COH000 and its SUMO E1 specificity, and also establishes a framework for potential development of molecules targeting E1 enzymes for other Ubls at a cryptic allosteric site.
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http://dx.doi.org/10.1038/s41467-018-07015-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6279746PMC
December 2018

Acyl Carrier Protein 3 Is Involved in Oxidative Stress Response in .

Front Microbiol 2018 20;9:2244. Epub 2018 Sep 20.

Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States.

The human opportunistic pathogen expresses three acyl carrier proteins (ACPs): AcpP, Acp1, and Acp3. The function of AcpP in membrane fatty acid synthesis (FAS) was confirmed recently, but the physiological roles of Acp1 and Acp3 remain unclear. To address this, we investigated the physiological role of Acp3 in . We found that expression of Acp3 dramatically increases in the log phase of cell growth and that its transcription is under the control of the QS regulators LasR and RhlR. Deletion of from PAO1 results in thicker biofilm formation, increased resistance of the strain to hydrogen peroxide, and higher persistence in a mouse infection model. Tandem affinity purification (TAP) experiments revealed several novel protein-binding partners of Acp3, including KatA, the major catalase in . Acp3 was found to repress the catalase activity of KatA and, consistent with inhibition by Acp3, less reactive oxygen species are present in the deletion strain. Overall, our study reveals that Acp3 has a distinct function from that of the canonical AcpP and may be involved in the oxidative stress response.
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http://dx.doi.org/10.3389/fmicb.2018.02244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158461PMC
September 2018

H, C, and N resonance assignments of N-acetylmuramyl-L-alanine amidase (AmiC) N-terminal domain (NTD) from Neisseria gonorrhoeae.

Biomol NMR Assign 2019 04 1;13(1):63-66. Epub 2018 Oct 1.

Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA.

Gonorrhea infections are becoming more difficult to treat due to the prevalence of strains exhibiting resistance to antibiotics and new therapeutic approaches are needed. N-acetylmuramyl-L-alanine amidase (AmiC) from Neisseria gonorrhoeae is a hydrolase that functions during cell division by cleaving the bond between the N-acetylmuramyl and L-alanine moieties of peptidoglycan. Inhibiting this enzyme offers the prospect of restoring the efficacy of existing antibiotics as treatments against N. gonorrhoeae. Of its two domains, the C-terminal domain catalyses the hydrolysis reaction and the N-terminal domain (NTD) is believed to target AmiC to its peptidoglycan substrate. Here, we report the H, C, and N resonance assignments of a 131 amino acid NTD construct of AmiC by heteronuclear NMR spectroscopy. The assignments represent the first for N. gonorrhoeae AmiC-NTD, laying the groundwork for detailed examination of its structure and dynamics, and providing a platform for new drug discovery efforts to address antimicrobial-resistant N. gonorrhoeae.
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http://dx.doi.org/10.1007/s12104-018-9852-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6440844PMC
April 2019

The Effects of Doping Density and Temperature on the Optoelectronic Properties of Formamidinium Tin Triiodide Thin Films.

Adv Mater 2018 Nov 17;30(44):e1804506. Epub 2018 Sep 17.

Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK.

Optoelectronic properties are unraveled for formamidinium tin triiodide (FASnI ) thin films, whose background hole doping density is varied through SnF addition during film fabrication. Monomolecular charge-carrier recombination exhibits both a dopant-mediated part that grows linearly with hole doping density and remnant contributions that remain under tin-enriched processing conditions. At hole densities near 10 cm , a strong Burstein-Moss effect increases absorption onset energies by ≈300 meV beyond the bandgap energy of undoped FASnI (shown to be 1.2 eV at 5 K and 1.35 eV at room temperature). At very high doping densities (10 cm ), temperature-dependent measurements indicate that the effective charge-carrier mobility is suppressed through scattering with ionized dopants. Once the background hole concentration is nearer 10 cm and below, the charge-carrier mobility increases with decreasing temperature according to ≈T , suggesting that it is limited mostly by intrinsic interactions with lattice vibrations. For the lowest doping concentration of 7.2 × 10 cm , charge-carrier mobilities reach a value of 67 cm V s at room temperature and 470 cm V s at 50 K. Intraexcitonic transitions observed in the THz-frequency photoconductivity spectra at 5 K reveal an exciton binding energy of only 3.1 meV for FASnI , in agreement with the low bandgap energy exhibited by this perovskite.
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http://dx.doi.org/10.1002/adma.201804506DOI Listing
November 2018

Functional Genomics and Immunologic Tools: The Impact of Viral and Host Genetic Variations on the Outcome of Zika Virus Infection.

Viruses 2018 08 11;10(8). Epub 2018 Aug 11.

Department of Animal Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA.

Zika virus (ZIKV) causes no-to-mild symptoms or severe neurological disorders. To investigate the importance of viral and host genetic variations in determining ZIKV infection outcomes, we created three full-length infectious cDNA clones as bacterial artificial chromosomes for each of three spatiotemporally distinct and genetically divergent ZIKVs: MR-766 (Uganda, 1947), P6-740 (Malaysia, 1966), and PRVABC-59 (Puerto Rico, 2015). Using the three molecularly cloned ZIKVs, together with 13 ZIKV region-specific polyclonal antibodies covering nearly the entire viral protein-coding region, we made three conceptual advances: (i) We created a comprehensive genome-wide portrait of ZIKV gene products and their related species, with several previously undescribed gene products identified in the case of all three molecularly cloned ZIKVs. (ii) We found that ZIKV has a broad cell tropism in vitro, being capable of establishing productive infection in 16 of 17 animal cell lines from 12 different species, although its growth kinetics varied depending on both the specific virus strain and host cell line. More importantly, we identified one ZIKV-non-susceptible bovine cell line that has a block in viral entry but fully supports the subsequent post-entry steps. (iii) We showed that in mice, the three molecularly cloned ZIKVs differ in their neuropathogenicity, depending on the particular combination of viral and host genetic backgrounds, as well as in the presence or absence of type I/II interferon signaling. Overall, our findings demonstrate the impact of viral and host genetic variations on the replication kinetics and neuropathogenicity of ZIKV and provide multiple avenues for developing and testing medical countermeasures against ZIKV.
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http://dx.doi.org/10.3390/v10080422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116225PMC
August 2018

Impact of the Organic Cation on the Optoelectronic Properties of Formamidinium Lead Triiodide.

J Phys Chem Lett 2018 Aug 27;9(16):4502-4511. Epub 2018 Jul 27.

Department of Physics , University of Oxford , Clarendon Laboratory, Parks Road , Oxford OX1 3PU , United Kingdom.

Metal halide perovskites have proven to be excellent light-harvesting materials in photovoltaic devices whose efficiencies are rapidly improving. Here, we examine the temperature-dependent photon absorption, exciton binding energy, and band gap of FAPbI (thin film) and find remarkably different behavior across the β-γ phase transition compared with MAPbI. While MAPbI has shown abrupt changes in the band gap and exciton binding energy, values for FAPbI vary smoothly over a range of 100-160 K in accordance with a more gradual transition. In addition, we find that the charge-carrier mobility in FAPbI exhibits a clear T trend with temperature, in excellent agreement with theoretical predictions that assume electron-phonon interactions to be governed by the Fröhlich mechanism but in contrast to the T dependence previously observed for MAPbI. Finally, we directly observe intraexcitonic transitions in FAPbI at low temperature, from which we determine a low exciton binding energy of only 5.3 meV at 10 K.
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http://dx.doi.org/10.1021/acs.jpclett.8b01628DOI Listing
August 2018

Evaluation of an innovative spinal cord stimulator platform for the treatment of chronic pain.

Pain Manag 2018 May 18;8(3):167-174. Epub 2018 Apr 18.

Department of Anesthesiology, Duke University, Durham, NC 27710, USA.

Spinal cord stimulation (SCS) is an ever-evolving therapy for the treatment of chronic pain. Currently, there are four main companies offering a variety of options for SCS. The Intellis™ system is the latest offering from Medtronic (MN, USA). Intellis offers the smallest implantable SCS pulse generator available and is capable of multiple different modes of stimulation, some of which can be run simultaneously. With an intrinsic accelerometer, the device is capable of sensing various patient positions and can automatically adjust stimulation intensity. Intellis also offers the most comprehensive MRI conditionality to date. Additionally, the new Samsung/Android (Seoul, South Korea) clinician programmer allows for easier programming than previous Medtronic programing systems. The programer can also generate patient activity and usage reports from implantable pulse generator data.
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http://dx.doi.org/10.2217/pmt-2017-0073DOI Listing
May 2018

The dynamic Atg13-free conformation of the Atg1 EAT domain is required for phagophore expansion.

Mol Biol Cell 2018 05 22;29(10):1228-1237. Epub 2018 Mar 22.

Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720.

Yeast macroautophagy begins with the de novo formation of a double-membrane phagophore at the preautophagosomal structure/phagophore assembly site (PAS), followed by its expansion into the autophagosome responsible for cargo engulfment. The kinase Atg1 is recruited to the PAS by Atg13 through interactions between the EAT domain of the former and the tMIM motif of the latter. Mass-spectrometry data have shown that, in the absence of Atg13, the EAT domain structure is strikingly dynamic, but the function of this Atg13-free dynamic state has been unclear. We used structure-based mutational analysis and quantitative and superresolution microscopy to show that Atg1 is present on autophagic puncta at, on average, twice the stoichiometry of Atg13. Moreover, Atg1 colocalizes with the expanding autophagosome in a manner dependent on Atg8 but not Atg13. We used isothermal titration calorimetry and crystal structure information to design an EAT domain mutant allele ATG1 that selectively perturbs the function of the Atg13-free state. Atg1 shows reduced PAS formation and does not support phagophore expansion, showing that the EAT domain has an essential function that is separate from its Atg13-dependent role in autophagy initiation.
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http://dx.doi.org/10.1091/mbc.E17-04-0258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5935072PMC
May 2018

Predicting Technical Success after Fistuloplasty: An Analysis of 176 Procedures.

Ann Vasc Surg 2018 Aug 6;51:141-146.e2. Epub 2018 Mar 6.

Department of Vascular Surgery, Morriston Hospital, Swansea, UK.

Background: Significant stenoses in arteriovenous fistulae (AVFs) or arteriovenous grafts (AVGs) with limitation of flow and dialysis inadequacy should prompt consideration for fistuloplasty. We sought to identify fistulae, lesions, and patient-specific variables, which predict for outcomes after fistuloplasty.

Methods: Data were extracted retrospectively from a renal access database from 2011 to 2016 of patients undergoing fistuloplasty. Demographics, comorbidities, outcomes of intervention, and flow rates documented on preintervention and postintervention duplex were collected. Secondary analysis of factors associated with postfistuloplasty flow rates of >600 mL/min, previously shown to be predictive of not requiring future intervention, was performed.

Results: Of 204 attempted fistuloplasties, 176 were completed. One hundred forty (79.5%) were native AVFs and 34 (19.3%), AVGs (no data for 2). Median stenosis treated was 75%, with a majority (43.8%) in the proximal outflow vein. Flow rate on duplex after fistuloplasty was significantly better in AVFs (mean improvement 189.2 mL/min) than that in AVGs (mean improvement 51.8 mL/min; P = 0.034). Greatest flow improvement occurred for needling site stenotic lesions compared with other locations (from anastomosis to central vein) but was not significant. Brachio-brachial or brachio-axillary AVGs did significantly (P < 0.05) worse than all other fistulae types. The presence of hypertension was predicted for postfistuloplasty flow rate of >600 mL/min.

Conclusions: Flow rates after fistuloplasty vary depending on the type of fistula treated and the presence of hypertension. Knowledge of this can lead to better patient selection and counseling for fistuloplasty.
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http://dx.doi.org/10.1016/j.avsg.2018.01.101DOI Listing
August 2018

The Structure of the Biofilm-controlling Response Regulator BfmR from Acinetobacter baumannii Reveals Details of Its DNA-binding Mechanism.

J Mol Biol 2018 03 10;430(6):806-821. Epub 2018 Feb 10.

Department of Discovery Sciences, RTI International, 3040 E. Cornwallis Road, Research Triangle Park, NC 27709, USA. Electronic address:

The rise of drug-resistant bacterial infections coupled with decreasing antibiotic efficacy poses a significant challenge to global health care. Acinetobacter baumannii is an insidious, emerging bacterial pathogen responsible for severe nosocomial infections aided by its ability to form biofilms. The response regulator BfmR, from the BfmR/S two-component system, is the master regulator of biofilm initiation in A. baumannii and is a tractable therapeutic target. Here we present the structure of A. baumannii BfmR using a hybrid approach combining X-ray crystallography, nuclear magnetic resonance spectroscopy, chemical crosslinking mass spectrometry, and molecular modeling. We also show that BfmR binds the previously proposed bfmRS promoter sequence with moderate affinity. While BfmR shares many traits with other OmpR/PhoB family response regulators, some unusual properties were observed. Most importantly, we observe that when phosphorylated, BfmR binds this promoter sequence with a lower affinity than when not phosphorylated. All other OmpR/PhoB family members studied to date show an increase in DNA-binding affinity upon phosphorylation. Understanding the structural and biochemical mechanisms of BfmR will aid in the development of new antimicrobial therapies.
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http://dx.doi.org/10.1016/j.jmb.2018.02.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861000PMC
March 2018

Bimolecular recombination in methylammonium lead triiodide perovskite is an inverse absorption process.

Nat Commun 2018 01 18;9(1):293. Epub 2018 Jan 18.

Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK.

Photovoltaic devices based on metal halide perovskites are rapidly improving in efficiency. Once the Shockley-Queisser limit is reached, charge-carrier extraction will be limited only by radiative bimolecular recombination of electrons with holes. Yet, this fundamental process, and its link with material stoichiometry, is still poorly understood. Here we show that bimolecular charge-carrier recombination in methylammonium lead triiodide perovskite can be fully explained as the inverse process of absorption. By correctly accounting for contributions to the absorption from excitons and electron-hole continuum states, we are able to utilise the van Roosbroeck-Shockley relation to determine bimolecular recombination rate constants from absorption spectra. We show that the sharpening of photon, electron and hole distribution functions significantly enhances bimolecular charge recombination as the temperature is lowered, mirroring trends in transient spectroscopy. Our findings provide vital understanding of band-to-band recombination processes in this hybrid perovskite, which comprise direct, fully radiative transitions between thermalized electrons and holes.
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http://dx.doi.org/10.1038/s41467-017-02670-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5773627PMC
January 2018

Gene expression and lymphocyte population at the fetal-maternal interface in sheep pregnancies established by somatic cell nuclear transfer.

Reprod Fertil Dev 2018 Jun;30(7):1011-1020

Department of Animal, Dairy and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT 84322, USA.

The hypothesis of this study was that the leukocyte populations and expression levels of genes related to immune response, growth factors and apoptosis would be altered at the fetal-maternal interface in somatic cell nuclear transfer (SCNT)-generated sheep pregnancies. Placental and endometrial samples from sheep pregnancies established by SCNT and natural breeding (control) were collected at 45 days and at term. Expression of genes related to growth factors, apoptosis and immune response was examined using quantitative reverse transcription polymerase chain reaction. Endometrial leukocyte populations and major histocompatibility class I (MHC-I) protein expression were examined by immunohistochemistry. At term we observed altered expression of genes related to apoptosis, growth factors and immune response in placental and endometrial tissue of SCNT pregnancies. In Day-45 pregnancies there was less-pronounced abnormal expression and only genes related to apoptosis and growth factors were abnormal in the placenta. Endometrial gene expression profiles were similar to age-matched controls. Placental MHC-I protein expression was similar in SCNT and controls at 45 days but increased in the SCNT at term. The altered gene expression at the fetal-maternal interface likely contributes to the placental dysfunction and overgrowth observed in sheep SCNT pregnancies.
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http://dx.doi.org/10.1071/RD17224DOI Listing
June 2018

Photocurrent Spectroscopy of Perovskite Solar Cells Over a Wide Temperature Range from 15 to 350 K.

J Phys Chem Lett 2018 Jan 29;9(1):263-268. Epub 2017 Dec 29.

Department of Physics, University of Oxford , Clarendon Laboratory, Parks Road, Oxford OX1 3PU, U.K.

Solar cells based on metal halide perovskite thin films show great promise for energy generation in a range of environments from terrestrial installations to space applications. Here we assess the device characteristics of the prototypical perovskite solar cells based on methylammonium lead triiodide (CHNHPbI) over a broad temperature range from 15 to 350 K (-258 to 77 °C). For these devices, we observe a peak in the short-circuit current density and open-circuit voltage at 200 K (-73 °C) with decent operation maintained up to 350 K. We identify the clear signature of crystalline PbI contributing directly to the low-temperature photocurrent spectra, showing that PbI plays an active role (beyond passivation) in CHNHPbI solar cells. Finally we observe a blue-shift in the photocurrent spectrum with respect to the absorption spectrum at low temperature (15 K), allowing us to extract a lower limit on the exciton binding energy of 9.1 meV for CHNHPbI.
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http://dx.doi.org/10.1021/acs.jpclett.7b02935DOI Listing
January 2018