Browsing by Author "Edwards PJB"

Now showing 1 - 7 of 7
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    Cell wall permeability in relation to in vitro starch digestion of pea cotyledon cells
    (Elsevier B.V., 2024-08-07) Ajala A; Kaur L; Lee SJ; Edwards PJB; Singh J
    The role of cell wall permeability and rate of starch digestibility in intact cotyledon cells from four different varieties of pea seeds was studied. Pulsed-field gradient nuclear magnetic resonance (PFG NMR) coupled with light and confocal microscopy were employed to evaluate the cotyledon cells' diffusion coefficients and cell wall permeability. The cotyledon cells' diffusion coefficients and cell wall permeability followed a decreasing trend: White/yellow pea > Marrowfat pea > Maple pea > Blue pea. The varying size of internal cavities in the microstructure in the cotyledon cells, as observed by the light and confocal micrographs, may be responsible for this trend. The extent of starch hydrolysis recorded from the cotyledon cells followed the same trend of the cell wall permeability except for Blue pea cotyledon cells. Thus, indicating that the more permeable the cotyledon cell to the starch-degrading enzymes, the higher the extent of intracellular starch hydrolysis. The microstructure changes in the cotyledon cells during digestion also confirmed this observation.
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    Changes in Serum Metabolome Following Low-Energy Diet-Induced Weight Loss in Women with Overweight and Prediabetes: A PREVIEW-New Zealand Sub-Study
    (MDPI (Basel, Switzerland), 2024-08-01) Relva B; Samuelsson LM; Duarte IF; Fasol U; Edwards PJB; Fogelholm M; Raben A; Poppitt SD; Silvestre MP; Rogero MM
    As obesity develops, metabolic changes increase the risk of non-communicable diseases such as type 2 diabetes (T2D). Weight loss is crucial for improving health in T2D and cardiometabolic conditions. However, weight loss rates vary between individuals, even with identical diets or energy restrictions, highlighting the need to identify markers or predictors of weight loss success to enhance intervention outcomes. Using nuclear magnetic resonance (NMR) spectroscopy-based metabolomics, we investigated the change in serum polar metabolites in 28 women with overweight or obesity and prediabetes who completed an 8-week low-energy diet (LED) as part of the PREVIEW (PREVention of diabetes through lifestyle intervention and population studies in Europe and around the World) clinical trial. We aimed to characterize the metabolic shift in substrate oxidation under fixed energy intake (~4 MJ/day) and its relation to weight loss success. Nine of the thirty-four serum metabolites identified significantly changed during the LED phase: 3-hydroxybutyrate, O-acetylcarnitine, 2-hydroxybutyrate, mannose, dimethyl sulfone and isobutyrate increased, whilst choline, creatine and tyrosine decreased. These results confirmed a shift towards lipid oxidation, but no metabolites predicted the response to the LED-induced weight loss. Further studies in larger populations are required to validate these metabolites as biomarkers of diet exposure.
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    Controlling Topology of a Telomeric G-quadruplex DNA With a Chemical Cross-link
    (Wiley-VCH GmbH, Germany, 2025-06-18) Chilton B; Edwards PJB; Jameson GB; Hale TK; Filichev VV
    DNA G-quadruplexes (G4s) are noncanonical structures formed in guanine-rich sequences. Within the human genome, they are nonrandomly distributed and influence DNA replication, gene expression, and genome maintenance. Numerous proteins involved in these processes have been identified as G4-binding proteins. However, the interaction of proteins with G4s in the context of double-stranded DNA in vitro has been difficult to study due to the transient nature of G4s in the presence of complementary DNA. To overcome this challenge, introducing internal covalent cross-links between distant nucleotides within the DNA sequence may promote pre-folding of G4 structures, thereby shifting the thermodynamic equilibrium toward G4-formation. We used a Cu(I)-catalyzed azide–alkyne cycloaddition to create a cross-link between 2′-O-propargylguanosine and N6-azidoethyl-2′-deoxyadenosine in the DNA telomeric sequence (TAG3T)2. A cross-link between G3 and A8 reinforced the parallel G4 topology that was stable in the presence of complementary DNA. Moreover, even in the presence of its complementary strand, this cross-linked G4 recruited the parent native DNA (TAG3T)2 to form a hybrid G4. These results suggest that cross-linking provides a useful tool for stabilizing noncanonical DNA structures in the presence of complementary strands, enabling their study within the context of genomic DNA.
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    Does harvesting age matter? Changes in structure and rheology of a shear-thickening polysaccharide from Cyathea medullaris as a function of age
    (Elsevier Ltd, 2024-04-01) Bisht A; Goh KKT; Sims IM; Edwards PJB; Matia-Merino L
    A shear-thickening polysaccharide from the New Zealand Black tree fern (Cyathea medullaris, commonly known as mamaku) extracted from different age fronds (stage 1: young, stage 2: fully grown and stage 3: old) was characterised in terms of structure and rheological properties. Constituent sugar analysis and 1H and 13C NMR revealed a repeating backbone of −4)-β-D-GlcpA-(1 → 2)-α-D-Manp-(1→, for all mamaku polysaccharide (MP) samples from different age fronds without any alterations in molecular structure. However, the molecular weight (Mw) was reduced with increasing age, from ~4.1 × 106 to ~2.1 × 106 Da from stage 1 to stage 3, respectively. This decrease in Mw (and size) consequently reduced the shear viscosity (ηs-Stage 1 > ηs-Stage 2 > ηs-Stage 3). However, the extent of shear-thickening and uniaxial extensional viscosity of MP stage 2 was greater than MP stage 1, which was attributed to a greater intermolecular interaction occurring in the former. Shear-thickening behaviour was not observed in MP stage 3.
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    Inverted strand polarity yields thermodynamically stable G-quadruplexes and prevents duplex formation within extended DNA.
    (The Royal Society of Chemistry, 2024-08-27) Chilton B; Roach RJ; Edwards PJB; Jameson GB; Hale TK; Filichev VV
    DNA G-quadruplexes (G4) formed in guanine-rich sequences play a key role in genome function and maintenance, interacting with multiple proteins. However, structural and functional studies of G4s within duplex DNA have been challenging because of the transient nature of G4s and thermodynamic preference of G-rich DNA to form duplexes with their complementary strand rather than G4s. To overcome these challenges, we have incorporated native nucleotides in G-rich sequences using commercially available inverted 3'-O-DMT-5'-O-phosphoramidites of native nucleosides, to give 3'-3' and 5'-5' linkages in the centre of the G-tract. Using circular dichroism and 1H nuclear magnetic resonance spectroscopies and native gel electrophoresis, we demonstrate that these polarity-inverted DNA sequences containing four telomeric repeats form G4s of parallel topology with one lateral or diagonal loop across the face of the quadruplex and two propeller loops across the edges of the quadruplex. These G4s were stable even in the presence of complementary C-rich DNA. As an example, G4 assemblies of inverted polarity were shown to bind to the hinge region of Heterochromatin Protein 1α (HP1α), a known G4-interacting domain. As such, internal polarity inversions in DNA provide a useful tool to control G4 topology while also disrupting the formation of other secondary structures, particularly the canonical duplex.
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    Structural characterisation of nucleotide sugar short-chain dehydrogenases/reductases from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus ΔH
    (John Wiley and Sons Ltd on behalf of Federation of European Biochemical Societies, 2025-09-03) Carbone V; Schofield LR; Edwards PJB; Sutherland-Smith AJ; Ronimus RS
    Epimerases and dehydratases are widely studied members of the extendedshort-chain dehydrogenase/reductase (SDR) enzyme superfamily and areimportant in nucleotide sugar conversion and diversification, for example,the interconversion of uridine diphosphate (UDP)-linked glucose andgalactose. Methanothermobacter thermautotrophicus contains a cluster ofgenes, the annotations of which indicate involvement in glycan biosynthesissuch as that of cell walls or capsular polysaccharides. In particular, genesencoding UDP-glucose 4-epimerase related protein (Mth375), UDP-glucose4-epimerase homologue (Mth380) and dTDP-glucose 4,6-dehydrataserelated protein (Mth373) may be involved in the biosynthesis of an unusualaminosugar in pseudomurein. In this paper, we present the structures ofMth375, an archaeal sugar epimerase/dehydratase protein (WbmF) deter-mined to a resolution of 2.0 A. The structure contains an N-terminalRossmann-fold domain with bound nicotinamide adenine dinucleotidehydride (NADH) and a C-terminal catalytic domain with bound UDP. Wealso present the structure for Mth373 co-crystallised with uridine-50-diphosphate-xylopyranose to a resolution of 1.96 A as a NAD+-dependentoxidative decarboxylase (UDP-xylose synthase; EC4.1.1.35). Molecularmodelling has also allowed for the identification of Mth380 as aUDP-N-acetylglucosamine 4-epimerase (WbpP; EC5.1.3.7), Mth631 as aUDP-glucose 4-epimerase (GalE; EC5.1.3.2) and Mth1789 as a classicaldTDP-D-glucose 4,6-dehydratase (EC4.2.1.46). The UDP–sugar specificityof each archaeal nucleotide sugar short-chain dehydrogenase/reductase.
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    Understanding intercalative modulation of G-rich sequence folding: solution structure of a TINA-conjugated antiparallel DNA triplex.
    (Oxford University Press, 2024-01-28) Garavís M; Edwards PJB; Serrano-Chacón I; Doluca O; Filichev VV; González C
    We present here the high-resolution structure of an antiparallel DNA triplex in which a monomer of para-twisted intercalating nucleic acid (para-TINA: (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol) is covalently inserted as a bulge in the third strand of the triplex. TINA is a potent modulator of the hybridization properties of DNA sequences with extremely useful properties when conjugated in G-rich oligonucleotides. The insertion of para-TINA between two guanines of the triplex imparts a high thermal stabilization (ΔTM = 9ºC) to the structure and enhances the quality of NMR spectra by increasing the chemical shift dispersion of proton signals near the TINA location. The structural determination reveals that TINA intercalates between two consecutive triads, causing only local distortions in the structure. The two aromatic moieties of TINA are nearly coplanar, with the phenyl ring intercalating between the flanking guanine bases in the sequence, and the pyrene moiety situated between the Watson-Crick base pair of the two first strands. The precise position of TINA within the triplex structure reveals key TINA-DNA interactions, which explains the high stabilization observed and will aid in the design of new and more efficient binders to DNA.