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Bowman P, Patel KA, McDonald TJ, Holst JJ, Hartmann B, Leveridge M, Shields BM, Hammersley S, Spaull SR, Knight BA, Flanagan SE, Shepherd MH, Andrews RC, Hattersley AT. Incretin hormone responses to carbohydrate and protein/fat are preserved in adults with sulfonylurea-treated KCNJ11 neonatal diabetes. J Diabetes Investig 2023; 14:1378-1382. [PMID: 37602910 PMCID: PMC10688132 DOI: 10.1111/jdi.14071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023] Open
Abstract
The incretin hormones glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP), are thought to be the main drivers of insulin secretion in individuals with sulfonylurea (SU)-treated KCNJ11 permanent neonatal diabetes. The aim of this study was to assess for the first time the incretin hormone response to carbohydrate and protein/fat in adults with sulfonylurea-treated KCNJ11 permanent neonatal diabetes compared with that of controls without diabetes. Participants were given a breakfast high in carbohydrate and an isocaloric breakfast high in protein/fat on two different mornings. Incremental area under the curve and total area under the curve (0-240 minutes) for total GLP-1 and GIP were compared between groups, using non-parametric statistical methods. Post-meal GLP-1 and GIP secretion were similar in cases and controls, suggesting this process is adenosine triphosphate-sensitive potassium channel-independent. Future research will investigate whether treatments targeting the incretin pathway are effective in individuals with KCNJ11 permanent neonatal diabetes who do not have good glycemic control on sulfonylurea alone.
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Rule ME, Chaudhuri‐Vayalambrone P, Krstulovic M, Bauza M, Krupic J, O'Leary T. Variational log-Gaussian point-process methods for grid cells. Hippocampus 2023; 33:1235-1251. [PMID: 37749821 PMCID: PMC10962565 DOI: 10.1002/hipo.23577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/17/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023]
Abstract
We present practical solutions to applying Gaussian-process (GP) methods to calculate spatial statistics for grid cells in large environments. GPs are a data efficient approach to inferring neural tuning as a function of time, space, and other variables. We discuss how to design appropriate kernels for grid cells, and show that a variational Bayesian approach to log-Gaussian Poisson models can be calculated quickly. This class of models has closed-form expressions for the evidence lower-bound, and can be estimated rapidly for certain parameterizations of the posterior covariance. We provide an implementation that operates in a low-rank spatial frequency subspace for further acceleration, and demonstrate these methods on experimental data.
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Patel A, Gill D, Newcombe P, Burgess S. Conditional inference in cis-Mendelian randomization using weak genetic factors. Biometrics 2023; 79:3458-3471. [PMID: 37337418 PMCID: PMC7615409 DOI: 10.1111/biom.13888] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/25/2023] [Indexed: 06/21/2023]
Abstract
Mendelian randomization (MR) is a widely used method to estimate the causal effect of an exposure on an outcome by using genetic variants as instrumental variables. MR analyses that use variants from only a single genetic region (cis-MR) encoding the protein target of a drug are able to provide supporting evidence for drug target validation. This paper proposes methods for cis-MR inference that use many correlated variants to make robust inferences even in situations, where those variants have only weak effects on the exposure. In particular, we exploit the highly structured nature of genetic correlations in single gene regions to reduce the dimension of genetic variants using factor analysis. These genetic factors are then used as instrumental variables to construct tests for the causal effect of interest. Since these factors may often be weakly associated with the exposure, size distortions of standard t-tests can be severe. Therefore, we consider two approaches based on conditional testing. First, we extend results of commonly-used identification-robust tests for the setting where estimated factors are used as instruments. Second, we propose a test which appropriately adjusts for first-stage screening of genetic factors based on their relevance. Our empirical results provide genetic evidence to validate cholesterol-lowering drug targets aimed at preventing coronary heart disease.
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Janes RW, Wallace BA. DichroPipeline: A suite of online and downloadable tools and resources for protein circular dichroism spectroscopic data analyses, interpretations, and their interoperability with other bioinformatics tools and resources. Protein Sci 2023; 32:e4817. [PMID: 37881887 PMCID: PMC10680340 DOI: 10.1002/pro.4817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 09/30/2023] [Indexed: 10/27/2023]
Abstract
Circular Dichroism (CD) spectroscopy is a widely-used method for characterizing individual protein structures in solutions, membranes, films and macromolecular complexes, as well as for probing macromolecular interactions, conformational changes associated with binding substrates, and in different functionally-related environments. This paper describes a series of related computational and display tools that have been developed over many years to aid in those characterizations and functional interpretations. The new DichroPipeline described herein links a series of format-compatible data processing, analysis, and display tools to enable users to facilely produce the spectra, which can then be made available in the Protein Circular Dichroism Data Bank (https://pcddb.cryst.bbk.ac.uk/) resource, in which the CD spectral and associated metadata for each entry are linked to other structural and functional data bases including the Protein Data Bank (PDB), and the UniProt sequence data base, amongst others. These tools and resources thus provide the basis for a wide range of traceable structural characterizations of soluble, membrane and intrinsically-disordered proteins.
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Ahmadzadeh YI, Eilertsen EM, Cheesman R, Rayner C, Ystrom E, Hannigan LJ, McAdams TA. Mothers' symptoms of anxiety and depression and the development of child temperament: A genetically informative, longitudinal investigation. JCPP ADVANCES 2023; 3:e12171. [PMID: 38054053 PMCID: PMC10694534 DOI: 10.1002/jcv2.12171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/03/2023] [Indexed: 12/07/2023] Open
Abstract
Background Child temperament traits and mothers' emotional symptoms relating to anxiety and depression may drive changes in one another, leading to their 'co-development' across time. Alternatively, links between mother and child traits may be attributable to shared genetic propensities. We explored longitudinal associations between mothers' emotional symptoms and child temperament traits and adjusted for genetic effects shared across generations. Methods This study is based on the Norwegian Mother, Father and Child Cohort Study (MoBa). Mothers (n = 34,060) reported on their symptoms of anxiety and depression, and temperament among offspring (n = 42,526), at child ages 1.5, 3 and 5 years. Structural equation models parameterised developmental change in traits, and an extended family design adjusted for genetic effects. Results We found individual differences in stable trait scores and rate of change for all study variables. Longitudinal stability in mothers' emotional symptoms was associated with longitudinal stability in offspring emotionality (r = 0.143), shyness (r = 0.031), and sociability (r = -0.015). Longitudinal change in mothers' symptoms showed very small or negligible correlations with longitudinal change in child temperament. Both genetic and environmental influences explained the stable longitudinal association between mothers' symptoms and child emotionality. Conclusions The studied associations between mother and child traits across time appeared to be due to stable, trait-like factors, involving genetic and environmental influence, rather than their co-development. Findings contribute knowledge on how emotional symptoms develop in families across time, and the methods with which we can explore such development.
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Nanayakkara MPA, He Q, Ruseckas A, Karalasingam A, Matjacic L, Masteghin MG, Basiricò L, Fratelli I, Ciavatti A, Kilbride RC, Jenatsch S, Parnell AJ, Fraboni B, Nisbet A, Heeney M, Jayawardena KDGI, Silva SRP. Tissue Equivalent Curved Organic X-ray Detectors Utilizing High Atomic Number Polythiophene Analogues. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304261. [PMID: 37916896 PMCID: PMC10724441 DOI: 10.1002/advs.202304261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/29/2023] [Indexed: 11/03/2023]
Abstract
Organic semiconductors are a promising material candidate for X-ray detection. However, the low atomic number (Z) of organic semiconductors leads to poor X-ray absorption thus restricting their performance. Herein, the authors propose a new strategy for achieving high-sensitivity performance for X-ray detectors based on organic semiconductors modified with high -Z heteroatoms. X-ray detectors are fabricated with p-type organic semiconductors containing selenium heteroatoms (poly(3-hexyl)selenophene (P3HSe)) in blends with an n-type fullerene derivative ([6,6]-Phenyl C71 butyric acid methyl ester (PC70 BM). When characterized under 70, 100, 150, and 220 kVp X-ray radiation, these heteroatom-containing detectors displayed a superior performance in terms of sensitivity up to 600 ± 11 nC Gy-1 cm-2 with respect to the bismuth oxide (Bi2 O3 ) nanoparticle (NP) sensitized organic detectors. Despite the lower Z of selenium compared to the NPs typically used, the authors identify a more efficient generation of electron-hole pairs, better charge transfer, and charge transport characteristics in heteroatom-incorporated detectors that result in this breakthrough detector performance. The authors also demonstrate flexible X-ray detectors that can be curved to a radius as low as 2 mm with low deviation in X-ray response under 100 repeated bending cycles while maintaining an industry-standard ultra-low dark current of 0.03 ± 0.01 pA mm-2 .
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32
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Luo T, Wang Z, Chen Y, Li H, Peng M, Tuna F, McInnes EJL, Day SJ, An J, Schröder M, Yang S. Photocatalytic Dehalogenative Deuteration of Halides over a Robust Metal-Organic Framework. Angew Chem Int Ed Engl 2023; 62:e202306267. [PMID: 37783657 PMCID: PMC10952292 DOI: 10.1002/anie.202306267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/01/2023] [Accepted: 10/02/2023] [Indexed: 10/04/2023]
Abstract
Deuterium labelling of organic compounds is an important process in chemistry. We report the first example of photocatalytic dehalogenative deuteration of both arylhalides and alkylhalides (40 substrates) over a metal-organic framework, MFM-300(Cr), using CD3 CN as the deuterium source at room temperature. MFM-300(Cr) catalyses high deuterium incorporation and shows excellent tolerance to various functional groups. Synchrotron X-ray powder diffraction reveals the activation of halogenated substrates via confined binding within MFM-300(Cr). In situ electron paramagnetic resonance spectroscopy confirms the formation of carbon-based radicals as intermediates and reveals the reaction pathway. This protocol removes the use of precious-metal catalysts from state-of-the-art processes based upon direct hydrogen isotope exchange and shows high photocatalytic stability, thus enabling multiple catalytic cycles.
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Peiffer C, Brombal L, Maughan Jones CJ, Arfelli F, Astolfo A, Dreossi D, Endrizzi M, Hagen CK, Mazzolani A, Menk R, Rigon L, Olivo A, Munro PRT. On the equivalence of the X-ray scattering retrieval with beam tracking and analyser-based imaging using a synchrotron source. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2023; 56:45LT02. [PMID: 37601626 PMCID: PMC10437003 DOI: 10.1088/1361-6463/acee8c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/25/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023]
Abstract
X-ray phase contrast imaging (XPCI) methods give access to contrast mechanisms that are based on the refractive properties of matter on top of the absorption coefficient in conventional x-ray imaging. Ultra small angle x-ray scattering (USAXS) is a phase contrast mechanism that arises due to multiple refraction events caused by physical features of a scale below the physical resolution of the used imaging system. USAXS contrast can therefore give insight into subresolution structural information, which is an ongoing research topic in the vast field of different XPCI techniques. In this study, we quantitatively compare the USAXS signal retrieved by the beam tracking XPCI technique with the gold standard of the analyzer based imaging XPCI technique using a synchrotron x-ray source. We find that, provided certain conditions are met, the two methods measure the same quantity.
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Shutt RRC, Ramireddy T, Stylianidis E, Di Mino C, Ingle RA, Ing G, Wibowo AA, Nguyen HT, Howard CA, Glushenkov AM, Stewart A, Clancy AJ. Synthesis of Black Phosphorene Quantum Dots from Red Phosphorus. Chemistry 2023; 29:e202301232. [PMID: 37435907 PMCID: PMC10947263 DOI: 10.1002/chem.202301232] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/06/2023] [Accepted: 07/11/2023] [Indexed: 07/13/2023]
Abstract
Black phosphorene quantum dots (BPQDs) are most commonly derived from high-cost black phosphorus, while previous syntheses from the low-cost red phosphorus (Pred ) allotrope are highly oxidised. Herein, we present an intrinsically scalable method to produce high quality BPQDs, by first ball-milling Pred to create nanocrystalline Pblack and subsequent reductive etching using lithium electride solvated in liquid ammonia. The resultant ~25 nm BPQDs are crystalline with low oxygen content, and spontaneously soluble as individualized monolayers in tertiary amide solvents, as directly imaged by liquid-phase transmission electron microscopy. This new method presents a scalable route to producing quantities of high quality BPQDs for academic and industrial applications.
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Weaving H, Lord JS, Haines L, English S. No evidence for direct thermal carryover effects on starvation tolerance in the obligate blood-feeder, Glossina morsitans morsitans. Ecol Evol 2023; 13:e10652. [PMID: 37869424 PMCID: PMC10585125 DOI: 10.1002/ece3.10652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/10/2023] [Accepted: 09/28/2023] [Indexed: 10/24/2023] Open
Abstract
Thermal stress during development can prime animals to cope better with similar conditions in later life. Alternatively, negative effects of thermal stress can persist across life stages and result in poorer quality adults (negative carryover effects). As mean temperatures increase due to climate change, evidence for such effects across diverse taxa is required. Using Glossina morsitans morsitans, a species of tsetse fly and vector of trypanosomiasis, we asked whether (i) adaptive developmental plasticity allows flies to survive for longer under food deprivation when pupal and adult temperatures are matched; or (ii) temperature stress during development persists into adulthood, resulting in a greater risk of death. We did not find any advantage of matched pupal and adult temperature in terms of improved starvation tolerance, and no direct negative carryover effects were observed. There was some evidence for indirect carryover effects-high pupal temperature produced flies of lower body mass, which, in turn, resulted in greater starvation risk. However, adult temperature had the largest impact on starvation tolerance by far: flies died 60% faster at 31°C than those experiencing 25°C, consequently reducing survival time from a median of 8 (interquartile range (IQR) 7-9) to 5 (IQR 5-5.25) days. This highlights differences in temperature sensitivity between life stages, as there was no direct effect of pupal temperature on starvation tolerance. Therefore, for some regions of sub-Saharan Africa, climate change may result in a higher mortality rate in emerging tsetse while they search for their first blood meal. This study reinforces existing evidence that responses to temperature are life stage specific and that plasticity may have limited capacity to buffer the effects of climate change.
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Kim J, Ren X, Zhang Y, Fazzi D, Manikandan S, Andreasen JW, Sun X, Ursel S, Un H, Peralta S, Xiao M, Town J, Marathianos A, Roesner S, Bui T, Ludwigs S, Sirringhaus H, Wang S. Efficient N-Type Organic Electrochemical Transistors and Field-Effect Transistors Based on PNDI-Copolymers Bearing Fluorinated Selenophene-Vinylene-Selenophenes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303837. [PMID: 37551064 PMCID: PMC10582458 DOI: 10.1002/advs.202303837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/24/2023] [Indexed: 08/09/2023]
Abstract
n-Type organic electrochemical transistors (OECTs) and organic field-effect transistors (OFETs) are less developed than their p-type counterparts. Herein, polynaphthalenediimide (PNDI)-based copolymers bearing novel fluorinated selenophene-vinylene-selenophene (FSVS) units as efficient materials for both n-type OECTs and n-type OFETs are reported. The PNDI polymers with oligo(ethylene glycol) (EG7) side chains P(NDIEG7-FSVS), affords a high µC* of > 0.2 F cm-1 V-1 s-1 , outperforming the benchmark n-type Pg4NDI-T2 and Pg4NDI-gT2 by two orders of magnitude. The deep-lying LUMO of -4.63 eV endows P(NDIEG7-FSVS) with an ultra-low threshold voltage of 0.16 V. Moreover, the conjugated polymer with octyldodecyl (OD) side chains P(NDIOD-FSVS) exhibits a surprisingly low energetic disorder with an Urbach energy of 36 meV and an ultra-low activation energy of 39 meV, resulting in high electron mobility of up to 0.32 cm2 V-1 s-1 in n-type OFETs. These results demonstrate the great potential for simultaneously achieving a lower LUMO and a tighter intermolecular packing for the next-generation efficient n-type organic electronics.
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Lindeboom W, Deacy AC, Phanopoulos A, Buchard A, Williams CK. Correlating Metal Redox Potentials to Co(III)K(I) Catalyst Performances in Carbon Dioxide and Propene Oxide Ring Opening Copolymerization. Angew Chem Int Ed Engl 2023; 62:e202308378. [PMID: 37409487 PMCID: PMC10952574 DOI: 10.1002/anie.202308378] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/07/2023]
Abstract
Carbon dioxide copolymerization is a front-runner CO2 utilization strategy but its viability depends on improving the catalysis. So far, catalyst structure-performance correlations have not been straightforward, limiting the ability to predict how to improve both catalytic activity and selectivity. Here, a simple measure of a catalyst ground-state parameter, metal reduction potential, directly correlates with both polymerization activity and selectivity. It is applied to compare performances of 6 new heterodinuclear Co(III)K(I) catalysts for propene oxide (PO)/CO2 ring opening copolymerization (ROCOP) producing poly(propene carbonate) (PPC). The best catalyst shows an excellent turnover frequency of 389 h-1 and high PPC selectivity of >99 % (50 °C, 20 bar, 0.025 mol% catalyst). As demonstration of its utility, neither DFT calculations nor ligand Hammett parameter analyses are viable predictors. It is proposed that the cobalt redox potential informs upon the active site electron density with a more electron rich cobalt centre showing better performances. The method may be widely applicable and is recommended to guide future catalyst discovery for other (co)polymerizations and carbon dioxide utilizations.
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Furmidge R, Jackson CE, Velázquez de la Paz MF, Workman VL, Green NH, Reilly GC, Hearnden V, Claeyssens F. Surfactant-free gelatin-stabilised biodegradable polymerised high internal phase emulsions with macroporous structures. Front Chem 2023; 11:1236944. [PMID: 37681209 PMCID: PMC10481965 DOI: 10.3389/fchem.2023.1236944] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/10/2023] [Indexed: 09/09/2023] Open
Abstract
High internal phase emulsion (HIPE) templating is a well-established method for the generation of polymeric materials with high porosity (>74%) and degree of interconnectivity. The porosity and pore size can be altered by adjusting parameters during emulsification, which affects the properties of the resulting porous structure. However, there remain challenges for the fabrication of polyHIPEs, including typically small pore sizes (∼20-50 μm) and the use of surfactants, which can limit their use in biological applications. Here, we present the use of gelatin, a natural polymer, during the formation of polyHIPE structures, through the use of two biodegradable polymers, polycaprolactone-methacrylate (PCL-M) and polyglycerol sebacate-methacrylate (PGS-M). When gelatin is used as the internal phase, it is capable of stabilising emulsions without the need for an additional surfactant. Furthermore, by changing the concentration of gelatin within the internal phase, the pore size of the resulting polyHIPE can be tuned. 5% gelatin solution resulted in the largest mean pore size, increasing from 53 μm to 80 μm and 28 μm to 94 µm for PCL-M and PGS-M respectively. In addition, the inclusion of gelatin further increased the mechanical properties of the polyHIPEs and increased the period an emulsion could be stored before polymerisation. Our results demonstrate the potential to use gelatin for the fabrication of surfactant-free polyHIPEs with macroporous structures, with potential applications in tissue engineering, environmental and agricultural industries.
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Dhak MS, Arunprasath D, Argent SP, Cuthbertson JD. A Domino Radical Amidation/Semipinacol Approach to All-Carbon Quaternary Centers Bearing an Aminomethyl Group. Chemistry 2023; 29:e202300922. [PMID: 37278542 PMCID: PMC10947466 DOI: 10.1002/chem.202300922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/07/2023]
Abstract
A photoredox-mediated radical amidation ring-expansion sequence that enables the generation of all-carbon quaternary centers bearing a protected aminomethyl substituent is described. The methodology can be applied to both styrene and unactivated alkene substrates generating structurally diverse sp3 -rich amine derivatives in a concise manner.
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Haysom SF, Machin J, Whitehouse JM, Horne JE, Fenn K, Ma Y, El Mkami H, Böhringer N, Schäberle TF, Ranson NA, Radford SE, Pliotas C. Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202218783. [PMID: 38515502 PMCID: PMC10952338 DOI: 10.1002/ange.202218783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Indexed: 03/23/2024]
Abstract
The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E. coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.
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Shields CE, Wang X, Fellowes T, Clowes R, Chen L, Day GM, Slater AG, Ward JW, Little MA, Cooper AI. Experimental Confirmation of a Predicted Porous Hydrogen-Bonded Organic Framework. Angew Chem Int Ed Engl 2023; 62:e202303167. [PMID: 37021635 PMCID: PMC10952618 DOI: 10.1002/anie.202303167] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/07/2023]
Abstract
Hydrogen-bonded organic frameworks (HOFs) with low densities and high porosities are rare and challenging to design because most molecules have a strong energetic preference for close packing. Crystal structure prediction (CSP) can rank the crystal packings available to an organic molecule based on their relative lattice energies. This has become a powerful tool for the a priori design of porous molecular crystals. Previously, we combined CSP with structure-property predictions to generate energy-structure-function (ESF) maps for a series of triptycene-based molecules with quinoxaline groups. From these ESF maps, triptycene trisquinoxalinedione (TH5) was predicted to form a previously unknown low-energy HOF (TH5-A) with a remarkably low density of 0.374 g cm-3 and three-dimensional (3D) pores. Here, we demonstrate the reliability of those ESF maps by discovering this TH5-A polymorph experimentally. This material has a high accessible surface area of 3,284 m2 g-1 , as measured by nitrogen adsorption, making it one of the most porous HOFs reported to date.
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Haysom SF, Machin J, Whitehouse JM, Horne JE, Fenn K, Ma Y, El Mkami H, Böhringer N, Schäberle TF, Ranson NA, Radford SE, Pliotas C. Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells. Angew Chem Int Ed Engl 2023; 62:e202218783. [PMID: 37162386 PMCID: PMC10952311 DOI: 10.1002/anie.202218783] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/26/2023] [Accepted: 05/09/2023] [Indexed: 05/11/2023]
Abstract
The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E. coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.
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Herbert Mainero A, Spence PJ, Reece SE, Kamiya T. The impact of innate immunity on malaria parasite infection dynamics in rodent models. Front Immunol 2023; 14:1171176. [PMID: 37646037 PMCID: PMC10461630 DOI: 10.3389/fimmu.2023.1171176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/07/2023] [Indexed: 09/01/2023] Open
Abstract
Decades of research have probed the molecular and cellular mechanisms that control the immune response to malaria. Yet many studies offer conflicting results on the functional impact of innate immunity for controlling parasite replication early in infection. We conduct a meta-analysis to seek consensus on the effect of innate immunity on parasite replication, examining three different species of rodent malaria parasite. Screening published studies that span four decades of research we collate, curate, and statistically analyze infection dynamics in immune-deficient or -augmented mice to identify and quantify general trends and reveal sources of disagreement among studies. Additionally, we estimate whether host factors or experimental methodology shape the impact of immune perturbations on parasite burden. First, we detected meta-analytic mean effect sizes (absolute Cohen's h) for the difference in parasite burden between treatment and control groups ranging from 0.1475 to 0.2321 across parasite species. This range is considered a small effect size and translates to a modest change in parasitaemia of roughly 7-12% on average at the peak of infection. Second, we reveal that variation across studies using P. chabaudi or P. yoelii is best explained by stochasticity (due to small sample sizes) rather than by host factors or experimental design. Third, we find that for P. berghei the impact of immune perturbation is increased when young or female mice are used and is greatest when effector molecules (as opposed to upstream signalling molecules) are disrupted (up to an 18% difference in peak parasitaemia). Finally, we find little evidence of publication bias suggesting that our results are robust. The small effect sizes we observe, across three parasite species, following experimental perturbations of the innate immune system may be explained by redundancy in a complex biological system or by incomplete (or inappropriate) data reporting for meta-analysis. Alternatively, our findings might indicate a need to re-evaluate the efficiency with which innate immunity controls parasite replication early in infection. Testing these hypotheses is necessary to translate understanding from model systems to human malaria.
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Hanna JC, Corpas-Lopez V, Seizova S, Colon BL, Bacchetti R, Hall GMJ, Sands EM, Robinson L, Baragaña B, Wyllie S, Pawlowic MC. Mode of action studies confirm on-target engagement of lysyl-tRNA synthetase inhibitor and lead to new selection marker for Cryptosporidium. Front Cell Infect Microbiol 2023; 13:1236814. [PMID: 37600947 PMCID: PMC10436570 DOI: 10.3389/fcimb.2023.1236814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Cryptosporidiosis is a leading cause of diarrheal-associated morbidity and mortality, predominantly affecting children under 5 years old in low-and-middle-income countries. There is no effective treatment and no vaccine. New therapeutics are emerging from drug discovery efforts. It is critical that mode of action studies are performed alongside drug discovery to ensure the best clinical outcomes. Unfortunately, technology to identify and validate drug targets for Cryptosporidium is severely lacking. Methods We used C. parvum lysyl-tRNA synthetase (CpKRS) and DDD01510706 as a target-compound pair to develop both chemical and genetic tools for mode of action studies for Cryptosporidium. We adapted thermal proteome profiling (TPP) for Cryptosporidium, an unbiased approach for target identification. Results Using TPP we identified the molecular target of DDD01510706 and confirm that it is CpKRS. Genetic tools confirm that CpKRS is expressed throughout the life cycle and that this target is essential for parasite survival. Parasites genetically modified to over-express CpKRS or parasites with a mutation at the compound-binding site are resistant to treatment with DDD01510706. We leveraged these mutations to generate a second drug selection marker for genetic modification of Cryptosporidium, KRSR. This second selection marker is interchangeable with the original selection marker, NeoR, and expands the range of reverse genetic approaches available to study parasite biology. Due to the sexual nature of the Cryptosporidium life cycle, parental strains containing different drug selection markers can be crossed in vivo. Discussion Selection with both drug markers produces highly efficient genetic crosses (>99% hybrid progeny), paving the way for forward genetics approaches in Cryptosporidium.
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Piplani B, Kumar CMS, Lund PA, Chaudhuri TK. Mycobacterial chaperonins in cellular proteostasis: Evidence for chaperone function of Cpn60.1 and Cpn60.2-mediated protein folding. Mol Microbiol 2023; 120:210-223. [PMID: 37350285 PMCID: PMC10952152 DOI: 10.1111/mmi.15109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023]
Abstract
Mycobacterium tuberculosis encodes two chaperonin proteins, MtbCpn60.1 and MtbCpn60.2, that share substantial sequence similarity with the Escherichia coli chaperonin, GroEL. However, unlike GroEL, MtbCpn60.1 and MtbCpn60.2 purify as lower-order oligomers. Previous studies have shown that MtbCpn60.2 can functionally replace GroEL in E. coli, while the function of MtbCpn60.1 remained an enigma. Here, we demonstrate the molecular chaperone function of MtbCpn60.1 and MtbCpn60.2, by probing their ability to assist the folding of obligate chaperonin clients, DapA, FtsE and MetK, in an E. coli strain depleted of endogenous GroEL. We show that both MtbCpn60.1 and MtbCpn60.2 support cell survival and cell division by assisting the folding of DapA and FtsE, but only MtbCpn60.2 completely rescues GroEL-depleted E. coli cells. We also show that, unlike MtbCpn60.2, MtbCpn60.1 has limited ability to support cell growth and proliferation and assist the folding of MetK. Our findings suggest that the client pools of GroEL and MtbCpn60.2 overlap substantially, while MtbCpn60.1 folds only a small subset of GroEL clients. We conclude that the differences between MtbCpn60.1 and MtbCpn60.2 may be a consequence of their intrinsic sequence features, which affect their thermostability, efficiency, clientomes and modes of action.
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Vuorinen L, LaMoury AT, Hietala H, Koller F. Magnetosheath Jets Over Solar Cycle 24: An Empirical Model. JOURNAL OF GEOPHYSICAL RESEARCH. SPACE PHYSICS 2023; 128:e2023JA031493. [PMID: 38440390 PMCID: PMC10909464 DOI: 10.1029/2023ja031493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/15/2023] [Accepted: 07/10/2023] [Indexed: 03/06/2024]
Abstract
Time History of Events and Macroscale Interactions during Substorms (THEMIS) spacecraft have been sampling the subsolar magnetosheath since the first dayside science phase in 2008, and we finally have observations over a solar cycle. However, we show that the solar wind coverage during these magnetosheath intervals is not always consistent with the solar wind conditions throughout the same year. This has implications for studying phenomena whose occurrence depends strongly on solar wind parameters. We demonstrate this with magnetosheath jets-flows of enhanced earthward dynamic pressure in the magnetosheath. Jets emerge from the bow shock, and some of them can go on and collide into the magnetopause. Their occurrence is highly linked to solar wind conditions, particularly the orientation of the interplanetary magnetic field, as jets are mostly observed downstream of the quasi-parallel shock. We study the yearly occurrence rates of jets recorded by THEMIS over solar cycle 24 (2008-2019) and find that they are biased due to differences in spacecraft orbits and uneven sampling of solar wind conditions during the different years. Thus, we instead use the THEMIS observations and their corresponding solar wind conditions to develop a model of how jet occurrence varies as a function of solar wind conditions. We then use OMNI data of the whole solar cycle to estimate the unbiased yearly jet occurrence rates. For comparison, we also estimate jet occurrence rates during solar cycle 23 (1996-2008). Our results suggest that there is no strong solar cycle dependency in jet formation.
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French DP, Ahern AL, Greaves CJ, Hawkes RE, Higgs S, Pechey R, Sniehotta FF. Preventing type 2 diabetes: A research agenda for behavioural science. Diabet Med 2023; 40:e15147. [PMID: 37171753 PMCID: PMC10947238 DOI: 10.1111/dme.15147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/26/2023] [Accepted: 05/11/2023] [Indexed: 05/13/2023]
Abstract
AIMS The aim of this narrative review was to identify important knowledge gaps in behavioural science relating to type 2 diabetes prevention, to inform future research in the field. METHODS Seven researchers who have published behaviour science research applied to type 2 diabetes prevention independently identified several important gaps in knowledge. They met to discuss these and to generate recommendations to advance research in behavioural science of type 2 diabetes prevention. RESULTS A total of 21 overlapping recommendations for a research agenda were identified. These covered issues within the following broad categories: (a) evidencing the impact of whole population approaches to type 2 diabetes prevention, (b) understanding the utility of disease-specific approaches to type 2 diabetes prevention such as Diabetes Prevention Programmes (DPPs) compared to generic weight loss programmes, (c) identifying how best to increase reach and engagement of DPPs, whilst avoiding exacerbating inequalities, (d) the need to understand mechanism of DPPs, (e) the need to understand how to increase maintenance of changes as part of or following DPPs, (f) the need to assess the feasibility and effectiveness of alternative approaches to the typical self-regulation approaches that are most commonly used, and (g) the need to address emotional aspects of DPPs, to promote effectiveness and avoid harms. CONCLUSIONS There is a clear role for behavioural science in informing interventions to prevent people from developing type 2 diabetes, based on strong evidence of reach, effectiveness and cost-effectiveness. This review identifies key priorities for research needed to improve existing interventions.
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Porta EOJ, Kalesh K, Steel PG. Navigating drug repurposing for Chagas disease: advances, challenges, and opportunities. Front Pharmacol 2023; 14:1233253. [PMID: 37576826 PMCID: PMC10416112 DOI: 10.3389/fphar.2023.1233253] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/18/2023] [Indexed: 08/15/2023] Open
Abstract
Chagas disease is a vector-borne illness caused by the protozoan parasite Trypanosoma cruzi (T. cruzi). It poses a significant public health burden, particularly in the poorest regions of Latin America. Currently, there is no available vaccine, and chemotherapy has been the traditional treatment for Chagas disease. However, the treatment options are limited to just two outdated medicines, nifurtimox and benznidazole, which have serious side effects and low efficacy, especially during the chronic phase of the disease. Collectively, this has led the World Health Organization to classify it as a neglected disease. To address this problem, new drug regimens are urgently needed. Drug repurposing, which involves the use of existing drugs already approved for the treatment of other diseases, represents an increasingly important option. This approach offers potential cost reduction in new drug discovery processes and can address pharmaceutical bottlenecks in the development of drugs for Chagas disease. In this review, we discuss the state-of-the-art of drug repurposing approaches, including combination therapy with existing drugs, to overcome the formidable challenges associated with treating Chagas disease. Organized by original therapeutic area, we describe significant recent advances, as well as the challenges in this field. In particular, we identify candidates that exhibit potential for heightened efficacy and reduced toxicity profiles with the ultimate objective of accelerating the development of new, safe, and effective treatments for Chagas disease.
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Bara‐Estaún A, Harder MC, Lyall CL, Lowe JP, Suturina E, Hintermair U. Paramagnetic Relaxation Agents for Enhancing Temporal Resolution and Sensitivity in Multinuclear FlowNMR Spectroscopy. Chemistry 2023; 29:e202300215. [PMID: 36946535 PMCID: PMC10962566 DOI: 10.1002/chem.202300215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/23/2023]
Abstract
Sensitivity in FlowNMR spectroscopy for reaction monitoring often suffers from low levels of pre-magnetisation due to limited residence times of the sample in the magnetic field. While this in-flow effect is tolerable for high sensitivity nuclei such as 1 H and 19 F, it significantly reduces the signal-to-noise ratio in 31 P and 13 C spectra, making FlowNMR impractical for low sensititvity nuclei at low concentrations. Paramagnetic relaxation agents (PRAs), which enhance polarisation and spin-lattice relaxation, could eliminate the adverse in-flow effect and improve the signal-to-noise ratio. Herein, [Co(acac)3 ], [Mn(acac)3 ], [Fe(acac)3 ], [Cr(acac)3 ], [Ni(acac)2 ]3, [Gd(tmhd)3 ] and [Cr(tmhd)3 ] are investigated for their effectiveness in improving signal intensity per unit time in FlowNMR applications under the additional constraint of chemical inertness towards catalytically active transition metal complexes. High-spin Cr(III) acetylacetonates emerged as the most effective compounds, successfully reducing 31 P T1 values four- to five-fold at PRA concentrations as low as 10 mM without causing adverse line broadening. Whereas [Cr(acac)3 ] showed signs of chemical reactivity with a mixture of triphenylphosphine, triphenylphosphine oxide and triphenylphosphate over the course of several hours at 80° C, the bulkier [Cr(tmhd)3 ] was stable and equally effective as a PRA under these conditions. Compatibility with a range of representative transition metal complexes often used in homogeneous catalysis has been investigated, and application of [Cr(tmhd)3 ] in significantly improving 1 H and 31 P{1 H} FlowNMR data quality in a Rh-catalysed hydroformylation reaction has been demonstrated. With the PRA added, 13 C relaxation times were reduced more than six-fold, allowing quantitative reaction monitoring of substrate consumption and product formation by 13 C{1 H} FlowNMR spectroscopy at natural abundance.
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Morland F, Ewen JG, Simons MJP, Brekke P, Hemmings N. Early-life telomere length predicts life-history strategy and reproductive senescence in a threatened wild songbird. Mol Ecol 2023; 32:4031-4043. [PMID: 37173827 PMCID: PMC10947174 DOI: 10.1111/mec.16981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Telomeres are well known for their associations with lifespan and ageing across diverse taxa. Early-life telomere length can be influenced by developmental conditions and has been shown positively affect lifetime reproductive success in a limited number of studies. Whether these effects are caused by a change in lifespan, reproductive rate or perhaps most importantly reproductive senescence is unclear. Using long-term data on female breeding success from a threatened songbird (the hihi, Notiomystis cincta), we show that the early-life telomere length of individuals predicts the presence and rate of future senescence of key reproductive traits: clutch size and hatching success. In contrast, senescence of fledging success is not associated with early-life telomere length, which may be due to the added influence of biparental care at this stage. Early-life telomere length does not predict lifespan or lifetime reproductive success in this species. Females may therefore change their reproductive allocation strategy depending on their early developmental conditions, which we hypothesise are reflected in their early-life telomere length. Our results offer new insights on the role that telomeres play in reproductive senescence and individual fitness and suggest telomere length can be used as a predictor for future life history in threatened species.
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