Browsing by Author "Lake, V"
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- ItemApparent polyploidization after gamma irradiation: pitfalls in the use of quantitative polymerase chain reaction (qPCR) for the estimation of mitochondrial and nuclear DNA gene copy numbers(MDPI AG, 2013-06-01) Kam, WWY; Lake, V; Banos, C; Davies, JB; Banati, RBQuantitative polymerase chain reaction (qPCR) has been widely used to quantify changes in gene copy numbers after radiation exposure. Here, we show that gamma irradiation ranging from 10 to 100 Gy of cells and cell-free DNA samples significantly affects the measured qPCR yield, due to radiation-induced fragmentation of the DNA template and, therefore, introduces errors into the estimation of gene copy numbers. The radiation-induced DNA fragmentation and, thus, measured qPCR yield varies with temperature not only in living cells, but also in isolated DNA irradiated under cell-free conditions. In summary, the variability in measured qPCR yield from irradiated samples introduces a significant error into the estimation of both mitochondrial and nuclear gene copy numbers and may give spurious evidence for polyploidization.© 2013, MDPI Publishing
- ItemGreen fluorescent protein alters the transcriptional regulation of human mitochondrial genes after gamma irradiation(Springer/Plenum Publishers, 2013-07-01) Kam, WWY; Middleton, RJ; Lake, V; Banati, RBGreen fluorescent proteins (GFP), extensively used as reporters in biological and imaging studies, are assumed to be mostly biologically inert. Here, we test the assumption in regard to the transcriptional regulation of 18 mitochondrially encoded genes in GFP expressing human T-cell line (JURKAT cells) exposed to gamma radiation. Using quantitative polymerase chain reaction, we demonstrate that wild type and GFP expressing JURKAT cells have different baseline mitochondrial transcript expression (10 out of the 18 tested genes) and after a single dose of radiation (100 Gy) show a significantly different transcriptional regulation of their mitochondrial genes. While in wild type cells, ten of the tested genes are up-regulated in response to radiation exposure, GFP expressing cells show less transcriptional regulation with a small down-regulation in five genes. Our results indicate that the presence of GFP in the cytoplasm can alter the cellular response to ionizing radiation.© 2013, Springer.
- ItemHigh yield expression and efficient purification of deuterated human protein galectin-2(Elsevier, 2012-07-01) Chen, XJ; Wilde, KL; Wang, H; Lake, V; Holden, PJ; Middelberg, APJ; He, LH; Duff, APStructural studies of biological macromolecules often require deuterated proteins, necessitating an effective bioprocessing strategy for high yield deuteration and purification. The fermentation and bioseparation studies reported here concern deuterated human protein galectin-2 mutant C57M (hGal-2), a protein showing potential for therapeutic applications. Using the vector pET-28a and a defined D2O based minimal medium with glycerol as the sole carbon source and kanamycin for selection, we have demonstrated that a high density of Escherichia coli expressing deuterated protein at a bench bioreactor scale (7L) can be achieved, with due attention to prevention of oxygen limitation. Yields achieved were 58 g\L biomass (wet weight) containing 0.7 g/L hGal-2. Affinity chromatography and ion-exchange chromatography were combined to achieve high purity as well as removal of hGal-2 aggregates, giving an overall yield of 1200 mg deuterated hGal-2. The deuterated hGal-2 was characterized and compared with the non-deuterated protein by size exclusion chromatography (SEC), HPLC, N-terminal sequencing, mass spectrometry (MS) and a dot blot immunoassay, showing that deuteration and subsequent purification did not impact the lactose binding and antibody recognition abilities of hGal-2. MS for both intact and trypsin-digested hGal-2 demonstrated that the extent of labeling of non-exchangeable hydrogen atoms by deuterium was (66 +/- 1)%, which provides sufficient contrast variation for structural studies using small angle neutron scattering. The fermentation and bioseparation method established in this work can be applied to process other deuterated proteins with high yield and purity, opening the way to advanced structural studies. © Institution of Chemical Engineers 2014.
- ItemInvestigating the interactions of the 18 kDa translocator protein and its ligand PK11195 in planar lipid bilayers(Elsevier, 2014-03) Hatty, CR; Le Brun, AP; Lake, V; Clifton, LA; Liu, GJ; James, M; Banati, RBThe functional effects of a drug ligand may be due not only to an interaction with its membrane protein target, but also with the surrounding lipid membrane. We have investigated the interaction of a drug ligand, PK11195, with its primary protein target, the integral membrane 18 kDa translocator protein (TSPO), and model membranes using Langmuir monolayers, quartz crystal microbalance with dissipation monitoring (QCM-D) and neutron reflectometry (NR). We found that PK11195 is incorporated into lipid monolayers and lipid bilayers, causing a decrease in lipid area/molecule and an increase in lipid bilayer rigidity. NR revealed that PK11195 is incorporated into the lipid chain region at a volume fraction of ~ 10%. We reconstituted isolated mouse TSPO into a lipid bilayer and studied its interaction with PK11195 using QCM-D, which revealed a larger than expected frequency response and indicated a possible conformational change of the protein. NR measurements revealed a TSPO surface coverage of 23% when immobilised to a modified surface via its polyhistidine tag, and a thickness of 51 Å for the TSPO layer. These techniques allowed us to probe both the interaction of TSPO with PK11195, and PK11195 with model membranes. It is possible that previously reported TSPO-independent effects of PK11195 are due to incorporation into the lipid bilayer and alteration of its physical properties. There are also implications for the variable binding profiles observed for TSPO ligands, as drug–membrane interactions may contribute to the apparent affinity of TSPO ligands. © 2013, Elsevier B.V.
- ItemPredicted ionisation in mitochondria and observed acute changes in the mitochondrial transcriptome after gamma irradiation: a Monte Carlo simulation and quantitative PCR study(Elsevier B.V., 2013-11-01) Kam, WWY; McNamara, AL; Lake, V; Banos, C; Davies, JB; Kuncic, Z; Banati, RBIt is a widely accepted that the cell nucleus is the primary site of radiation damage while extra-nuclear radiation effects are not yet systematically included into models of radiation damage. We performed Monte Carlo simulations assuming a spherical cell (diameter 11.5 μm) modelled after JURKAT cells with the inclusion of realistic elemental composition data based on published literature. The cell model consists of cytoplasm (density 1 g/cm3), nucleus (diameter 8.5 μm; 40% of cell volume) as well as cylindrical mitochondria (diameter 1 μm; volume 0.5 μm3) of three different densities (1, 2 and 10 g/cm3) and total mitochondrial volume relative to the cell volume (10, 20, 30%). Our simulation predicts that if mitochondria take up more than 20% of a cell's volume, ionisation events will be the preferentially located in mitochondria rather than in the cell nucleus. Using quantitative polymerase chain reaction, we substantiate in JURKAT cells that human mitochondria respond to gamma radiation with early (within 30 min) differential changes in the expression levels of 18 mitochondrially encoded genes, whereby the number of regulated genes varies in a dose-dependent but non-linear pattern (10 Gy: 1 gene; 50 Gy: 5 genes; 100 Gy: 12 genes). The simulation data as well as the experimental observations suggest that current models of acute radiation effects, which largely focus on nuclear effects, might benefit from more systematic considerations of the early mitochondrial responses and how these may subsequently determine cell response to ionising radiation. © 2013 Elsevier B.V.
- ItemA robust and reliable method for high yield deuterated recombinant protein production using Escherichia coli BL21.(International Conference on Neutron Scattering, 2017-07-12) Duff, AP; Wilde, KL; Rekas, A; Lake, V; Holden, PJWe have developed a method that has proven highly reliable for the deuteration of a broad range of proteins by recombinant expression in Escherichia coli BL21. Typical biomass yields are 40-80 g/L wet weight, yielding 50-400mg/L purified protein. This method uses a simple, relatively inexpensive defined medium, and routinely results in a high yield expression without need for optimisation. The key elements are: very tight control of expression, careful starter culture adaption steps, and strict maintenance of aerobic conditions ensuring exponential growth. Temperature is reduced as required to prevent biological oxygen demand exceeding maximum aeration capacity. Glycerol is the sole carbon source. We have not encountered an upper limit for the size of proteins that can be expressed, achieving excellent expression for proteins from 7-112 kDa and the quantity produced at 1L scale ensures that no SANS, NMR or neutron crystallography experiment is limited by the amount of deuterated material. Where difficulties remain, these tend to be cases of protein solubility exacerbated by high protein concentration and slightly increased stickiness of proteins in D O. There are some very few cases in which we have been unable to express a protein by our method despite unlabelled expression being reliable in rich media using induction at low OD. Few proteins tested have not expressed in deuterated medium despite unlabelled expression being reliable.
- ItemTargeted detection of phosphatidylserine in biomimetic membranes and in vitro cell systems using annexin V-containing cubosomes(Elsevier, 2013-11-01) Shen, HH; Lake, V; Le Brun, AP; James, M; Duff, AP; Peng, Y; McLean, KM; Hartley, PGIn this work we have formulated Annexin V (ANX) decorated phosphatidylserine containing phytantriol (PSPhy) cubosomes to act as probes for the enhanced detection of apoptotic membranes in both model and in vitro cell systems. Small angle X-ray scattering (SAXS) and cryogenic-transmission electron microscopy (Cryo-TEM) indicated that ANX-containing PSPhy (ANX-PSPhy) cubosomes retain the Pn3m cubic symmetry and cubic phase nanoparticle characteristics of PSPhy cubosomes. The interaction of ANX-PSPhy cubosomes with apoptotic model and cellular membranes was also investigated using both quartz crystal microbalance with dissipation and confocal microscopy which confirmed that ANX-PSPhy cubosomes can selectively bind to apoptotic cells and model membranes. Neutron reflectometry has also been used to show strong binding of ANX-PSPhy cubosomes to a model apoptotic membrane, and in addition reveals changes in both the bilayer structure and in the internal structure of the cubosome in a region adjacent to the membrane as a result of material exchange. This material exchange between cubosome and apoptotic model bilayer was further demonstrated using Cryo-TEM. We have demonstrated that lipid bound protein, in this case Annexin V, can be used to target cubosome systems to biological surfaces in vitro. © 2013, Elsevier Ltd.