PubMed Health⌕ Search

Biomedical subjects

Alison Rodger

Publications and source records attributed to Alison Rodger.

At least 19 recordsLinked to original sources
PubMed2025

Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics.

BACKGROUND: Early-life gut microbiota affects immune system development, including the lung immune response (gut-lung axis). We aimed to investigate whether gut microbiota composition in neonates in the first week of life is associated with hospital admissions for viral lower respiratory tract infections (vLRTIs). METHODS: The Baby Biome Study (BBS) is a prospective birth cohort, which enrolled mother-baby pairs between Jan 1, 2016, and Dec 31, 2017, at three UK hospitals. In the present study, we only included BBS babies with a sequenced first-week stool sample and successful data linkage. Stool was collected in the first week of life for shotgun-metagenomic sequencing. We examined the following microbiota features: alpha diversity (Chao1, Shannon, and Simpson indices) and community structures (cluster-partitioning against medoids method). The participants were followed up through linkage to the Hospital Episode Statistics-Admitted Patient Care (HES-APC) database to determine vLRTI hospital admission incidence in the first 2 years of life. We used Poisson mixed-effects models for univariable and multivariable analyses to evaluate the association between microbiota features and vLRTI hospital admission incidence, adjusting for confounders identified through direct acyclic graphs. FINDINGS: 3305 (95%) of the 3476 BBS-enrolled babies for whom consent to data linkage was obtained were included in the present study. 1111 (34%) babies had a first-week sequenced stool sample, of whom 1082 (97%; 564 born vaginally and 518 born by caesarean section) were successfully linked to HES-APC, and had median follow-up of 2·0 years (IQR 1·4-2·9). Most babies were born at term (996 [92%] ≥37 weeks gestational age and 1070 [99%] >35 weeks gestational age) and healthy (1050 [97%] had no comorbidities), and 520 (48%) were female and 562 (52%) were male. Higher first-week gut microbiota alpha diversity was associated with reduced rates of vLRTI hospital admission (Chao1 Index adjusted hazard ratio [HR] 0·92 [95% CI 0·85-0·99]; Shannon Index adjusted HR 0·57 [0·33-0·98]; and Simpson Index adjusted HR 0·36 [0·11-1·20]). Three microbiota clusters were identified. Cluster 1 had a mixed composition and cluster 2 was dominated by Bifidobacterium breve, with both clusters observed in babies born vaginally and by caesarean section. Cluster 3 was found only in vaginally born babies and was dominated by Bifidobacterium longum. Having cluster 1 (mixed) or cluster 2 (B breve dominated) was independently associated with increased rates of vLRTI hospital admission compared with cluster 3 (B longum dominated; cluster 1 [mixed] 3·05 [1·25-7·41] and cluster 2 [B breve dominated] 2·80 [1·06-7·44]). INTERPRETATION: We report observational evidence that first-week gut microbiota differences are associated with clinically severe vLRTI in young children. This study identified bacterial species that could be of interest for vLRTI prevention. This finding has important implications for the design of future research and intervention strategies. FUNDING: The Wellcome Trust and Wellcome Sanger Institute core funding.

Humans↗
PubMed2006

An estrogen-platinum terpyridine conjugate: DNA and protein binding and cellular delivery.

A platinum metal complex in which terpyridine joins estradiol (via an ethynyl link) to a platinum with a labile ligand (chloride) has been designed, synthesised and its X-ray crystal structure determined. The aim of this work was to link a targeting motif (in this case estrogen) to a metal-based biomolecule recognition unit (the platinum moiety). The target molecule: 17alpha-[4'-ethynyl-2,2':6',2'-terpyridine]-17beta-estradiol platinum(II) chloride (PtEEtpy) has been shown to bind to both human and bovine serum albumin (SA) and to DNA. FTICR mass spectrometry shows that the bimolecular units are in each case linked through coordination to the platinum with displacement of the chloride ligand. Circular dichroism indicates that a termolecular entity involving PtEEtpy, SA and DNA is formed. A range of electrospray mass spectrometry experiments showed that the PtEEtpy complex breaks and forms coordination bonds relatively easily. A whole cell estrogen receptor assay in an estrogen receptor positive cell (MCF-7) confirms binding of both EEtpy and PtEEtpy to the estrogen receptor in cells. The work demonstrates the concept of linking a targeting moiety (in this case estrogen) to a DNA binding agent.

Animals↗
PubMed2006

Contributions of hydroxyethyl groups to the DNA binding affinities of anthracene probes.

Contributions of hydroxyethyl functions to the DNA binding affinities of substituted anthracenes are evaluated by calorimetry and spectroscopy. Isothermal titration calorimetry indicated that binding of the ligands to calf thymus DNA (5 mM Tris buffer, 50 mM NaCl, pH 7.2, 25 degrees C) is exothermic. The binding constants increased from 1.5 x 10(4) to 1.7 x 10(6) M(-1) as a function of increase in the number of hydroxyethyl functions (0-4). DNA binding was accompanied by red-shifted absorption (approximately 630 cm(-1)), strong hypochromism (>65%), positive induced-circular dichroism bands, and negative linear dichroism signals. DNA binding, in general, increased the helix stabilities to a significant extent (DeltaT(m) approximately 7 degrees C, DeltaDeltaH approximately 3 kcal/mol, DeltaDeltaS approximately 6-20 cal/K.mol). The binding constants showed a strong correlation with the number of hydroxyethyl groups present on the anthracene ring system. Analysis of the binding data using the hydrophobicity parameter (Log P) showed a poor correlation between the binding affinity and hydrophobicity. This observation was also supported by a comparison of the affinities of probes carrying N-ethyl (Kb = 0.8 x 10(5) M(-1)) versus N-hydroxyethyl side chains (Kb = 5.5 x 10(5) M(-1)). These are the very first examples of a strong quantitative correlation between the DNA binding affinity of a probe and the number of hydroxyethyl groups present on the probe. These quantitative findings are useful in the rational design of new ligands for high-affinity binding to DNA.

Anthracenes↗
PubMed2006

Improved curve fitting procedures to determine equilibrium binding constants.

For ligand-biomacromolecule titration experiments it has been traditional practice to extract parameters such as the equilibrium binding constant K and the number of bases per ligand binding site n with relatively labour intensive methods, usually based on single wavelength data, such as the difference method by Rodger and Nordén coupled together with a Scatchard plot. Presented in this paper are both the theory and a least squares fitting method to derive parameters such as K and n more directly from all spectral non-linear experimental data. Both the case of non competitive binding of a metal complex ligand to DNA and the case of displacement by a metal complex ligand of an ethidium marker attached to the DNA are considered. This work may be applied directly to reduce experimental data produced by a spectropolarimeter (for circular or linear dichroism) or a spectrophotometer (for fluorescence or UV-Vis spectroscopy).

Binding Sites↗
PubMed2006

Restriction enzyme kinetics monitored by UV linear dichroism.

The use of linear dichroism (LD) spectroscopy for biological applications has been brought to the forefront recently by our development of thermostated microvolume Couette cells. We present a method for following the digestion of DNA by restriction endonucleases in real time without the use of any extrinsic dyes or labels. This is accomplished using linear dichroism spectroscopy (the differential absorbance of light polarized parallel and perpendicular to the sample orientation axis). The differential absorbance signal depends on the degree of alignment of the molecules. In this case the DNA is aligned by Couette flow (flowing the solution in the annular gap between two concentric cylinders), and we monitor the increase in alignment upon linearization of a circular DNA molecule. In addition, we observe a decrease in alignment upon further digestion and subsequent shortening of the DNA. Ten enzymes were investigated: seven enzymes with a single cut site (EcoRI, KpnI, NdeI, NotI, NruI, SmaI, XbaI), two enzymes with two cut sites (BstZ17I, EagI), and one enzyme with no cut site (ClaI). LD, as implemented in this new assay, is broadly applicable across a wide range of DNA-modifying enzymes and compounds and, as such, is a useful addition to the toolbox of biological characterization.

Deoxyribonuclease EcoRI↗
PubMed2006

Shape effects on the activity of synthetic major-groove binding ligands.

In this work we present the results of a molecular simulation study of two different tetracationic bis iron(II) supramolecular cylinders interacting with DNA. One cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA; the second is a derivative of the first, with additional methyl groups attached so as to give a larger cylinder-radius. The simulations show that both cylinders bind strongly to the major groove of the DNA, and induce complex structural changes in A-T rich regions. Whereas the parent cylinder tends to bind along the major groove, the derivatised cylinder tends to twist so that only one end remains within the major groove. Both G-C rich and A-T rich binding sites for the derivatised cylinder are discussed.

Binding Sites↗
PubMed2006

A DNA-binding copper(I) metallosupramolecular cylinder that acts as an artificial nuclease.

The DNA binding of a dicationic pyridylimine-based dicopper(I) metallosupramolecular cylinder is reported together with its ability to act as an artificial nuclease. The cylinder binds strongly to DNA; more strongly than the spherical dication [Ru(phen)(3)](2+) (phen=1,10-phenanthroline), but more weakly than the corresponding tetracationic cylinders. DNA coiling effects are not observed with this dication, in contrast to the situation with the previously reported tetracationic cylinder involving a similar ligand. Linear dichroism (LD) data suggests that the dicopper cylinder binds in a different orientation from that of the tetracationic iron cylinder. Furthermore, the dicopper cylinder shows DNA-cleavage activity in the presence of peroxide. Of particular note is that the cylinder displays a marked and unusual ability to cleave both DNA strands at the same site, probably reflecting its dinuclear nature and possibly its mode of binding to the DNA.

Copper↗
PubMed2006

Looking at long molecules in solution: what happens when they are subjected to Couette flow?

Knowing the structure of a molecule is one of the keys to deducing its function in a biological system. However, many biomacromolecules are not amenable to structural characterisation by the powerful techniques often used namely NMR and X-ray diffraction because they are too large, or too flexible or simply refuse to crystallize. Long molecules such as DNA and fibrous proteins are two such classes of molecule. In this article the extent to which flow linear dichroism (LD) can be used to characterise the structure and function of such molecules is reviewed. Consideration is given to the issues of fluid dynamics and light scattering by such large molecules. A range of applications of LD are reviewed including (i) fibrous proteins with particular attention being given to actin; (ii) a far from comprehensive discussion of the use of LD for DNA and DNA-ligand systems; (iii) LD for the kinetics of restriction digestion of circular supercoiled DNA; and (iv) carbon nanotubes to illustrate that LD can be used on any long molecules with accessible absorption transitions.

Absorption↗
PubMed2006

Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove.

In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron(II) supramolecular cylinder, [Fe2(C25H20N4)3]4+, and DNA. This supramolecular cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA. The simulations have been designed to elucidate the interactions that lead the cylinder to target the major groove and that drive the subsequent DNA conformational changes. Three sets of multi-nanosecond simulations have been performed: one of the uncomplexed d(CCCCCTTTTTCC) d(GGAAAAAGGGGG) dodecamer; one of this DNA complexed with the cylinder molecule; and one of this DNA complexed with a neutralised version of the cylinder. Coiling of the DNA was observed in the DNA-cylinder simulations, giving insight into the molecular level nature of the supramolecular coiling observed experimentally. The cylinder charge was found not to be essential for the DNA coiling, which implies that the DNA response is moderated by the short range interactions that define the molecular shape. Cylinder charge did, however, affect the integrity of the DNA duplex, to the extent that, under some circumstances, the tetracationic cylinder induced defects in the DNA base pairing at locations adjacent to the cylinder binding site.

Binding Sites↗
PubMed2006

A new method for fibrous protein analysis illustrated by application to tubulin microtubule polymerisation and depolymerisation.

A thermostatted micro volume Couette cell has been designed to enable linear dichroism (LD) data to be collected at a range of temperatures. The cell is a development of the traditional Couette flow LD cell and includes the recent development of micro-volume LD (20-40 microL) coupled with the addition of a heating element, temperature probe and controller. This new micro volume Couette LD cell opens the way not only to the LD analysis of systems where sample volume is critical, but also for the LD analysis of temperature sensitive samples. The polymerization of the microtubule protein tubulin has been followed in a range of different conditions using the thermostatted micro volume Couette LD cell. The focusing lenses on the cell, which are required for the microvolume cell, have the side benefit of significantly reducing the light-scattering artifacts caused by the large size of tubulin microtubules. It is now possible to monitor real-time polymerization and depolymerization kinetics, and any structural rearrangements of chromophores within the polymer. In the case of tubulin, the LD spectra revealed a greater change in the orientation of tryptophan residues at approximately 290 nm during polymerization compared to other contributing chromophores-guanine, phenylalanine, and tyrosine. The improvements in instrumental design have also allowed LD spectra of tubulin to be collected down to approximately 230 nm (previous data have only been available from the near UV region), which means that some indication of protein backbone-orientation changes are now available. It was observed during this work that apparent LD intensity maxima are in fact artifacts when the high-tension voltage is high. The onset of such artifacts has been observed at much lower voltages with light-scattering fibrous proteins (including tubulin) than with nonscattering samples. Therefore, caution must be used when interpreting LD data collected with medium to high photomultiplier tube voltages.

Animals↗
PubMed2005

Validation of new microvolume Couette flow linear dichroism cells.

Long molecules such as fibrous proteins are particularly difficult to characterise structurally. We have recently designed a microvolume Couette flow linear dichroism (LD) cell whose sample volume is only 20-40 microL in contrast to previous cells where the volume of sample required has typically been of the order of 1000-2000 microL. This brings the sample requirements of LD to a level where it can be used for biological samples. Since LD is the difference in absorption of light polarised parallel to an orientation direction and perpendicular to that direction, it is the ideal technique for determining relative orientations of subunits of e.g. fibrous proteins, DNA-drug systems, etc. For solution phase samples, Couette flow orientation, whereby the sample is sandwiched between two cylinders, one of which rotates, has proved to be the optimal technique for LD experiments in many laboratories. Our capillary microvolume LD cell has been designed using extruded quartz rods and capillaries and focusing and collecting lenses. We have developed applications with PCR products, fibrous proteins, liposome-bound membrane proteins, as well as DNA-dye systems. Despite this range of applications, to date there is nothing reported in the literature to enable one to validate the performance of Couette flow LD cells. In this paper we establish validation criteria and show that the data from the microvolume cells are reproducible, vary by less than 1% with sample reloading, follow the Beer-Lambert law, and have signals linear in voltage over a wide voltage range. The microvolume cell data are consistent with those from the large-volume cells for DNA samples. Surprisingly, upon extending the wavelength range by adding the intercalator ethidium bromide, the spectra in the microvolume and large-volume cells differ by a wavelength dependent orientation parameter. This wavelength variation was concluded to be the result of Taylor-vortices in the large-volume cells which have inner rotating cylinders in our laboratory. Thus the microvolume LD cells can be concluded to provide better data than our large-volume LD cells, though the latter are still to be preferred for titration series as it is extremely difficult to add sample to the capillary cells without introducing artefacts.

DNA↗
PubMed2005

Chemical composition and antibacterial activity of the essential oil and the gum of Pistacia lentiscus Var. chia.

The essential oil and gum of Pistacia lentiscus var. chia, commonly known as the mastic tree, are natural antimicrobial agents that have found extensive uses in medicine in recent years. In this work, the chemical composition of mastic oil and gum was studied by GC-MS, and the majority of their components was identified. alpha-Pinene, beta-myrcene, beta-pinene, limonene, and beta-caryophyllene were found to be the major components. The antibacterial activity of 12 components of mastic oil and the oil itself was evaluated using the disk diffusion method. Furthermore, attempts were made to separate the essential oil into different fractions in order to have a better picture of the components responsible for its antibacterial activity. Several trace components that appear to contribute significantly to the antibacterial activity of mastic oil have been identified: verbenone, alpha-terpineol, and linalool. The sensitivity to these compounds was different for different bacteria tested (Escherichia coli, Staphylococcus aureus, and Bacillus subtilis), which suggests that the antibacterial efficacy of mastic oil is due to a number of its components working synergistically. The establishment of a correlation between the antibacterial activity of mastic oil and its components was the main purpose of this research. Mastic gum was also examined, but it proved to be more difficult to handle compared to the essential oil.

Acyclic Monoterpenes↗
PubMed2005

The binding of single-stranded DNA and PNA to single-walled carbon nanotubes probed by flow linear dichroism.

The binding of single-stranded DNAs and a neutral DNA analogue (peptide nucleic acid, PNA) to single-walled carbon nanotubes in solution phase has been probed by absorbance spectroscopy and linear dichroism. The nanotubes are solubilised by aqueous sodium dodecyl sulfate, in which the nucleic acids also dissolve. The linear dichroism (LD) of the nanotubes, when subtracted from that due to the nanotubes/nucleic acid samples, gives the LD of the bound nucleic acid. The binding of the single-stranded DNA to the single-walled nanotubes is quite different from that previously observed for double-stranded DNA. It is likely that the nucleic acid bases lie flat on the nanotube surface with the backbone wrapping round the nanotube at an oblique angle in the region of 45 degrees . The net effect is like beads on a string. The base orientation with the single-stranded PNA is inverted with respect to that of the single-stranded DNA, as shown by their oppositely signed LD signals.

DNA, Single-Stranded↗
PubMed2005

Design and DNA binding of an extended triple-stranded metallo-supramolecular cylinder.

A new tetracationic triple-stranded supramolecular cylinder is prepared from a bis(pyridylimine) ligand containing a diphenylmethane and two ketimine groups in the spacer. The cylinder is longer and slightly wider than the corresponding cylinder containing just diphenylmethane spacers. Inter-strand CH...pi interactions are not observed and this affects the relay of the chiral information within the cylinder; a mixture of rac and meso isomers results, with the meso isomer being the dominant solution species and characterised in the solid state by crystallography. This new cylinder does bind to DNA as confirmed by induced circular dichroism signals in both the metal-to-ligand charge transfer (MLCT) and in-ligand bands of the cylinder. Flow linear dichroism demonstrates that the cylinder binds to DNA in a specific orientation(s) and is consistent with (major) groove-binding as seen for the shorter cylinder. Some DNA bending/coiling is observed but the effect is much less dramatic than observed for the cylinder with diphenylmethane spacers confirming that coiling is not solely a consequence of the tetracationic charge, but rather is related to the precise size and shape of the cylinder.

Benzhydryl Compounds↗
PubMed2005

Expression, purification and crystallization of the cell-division protein YgfE from Escherichia coli.

An open reading frame designated b2910 (ygfE) in the Escherichia coli K12-MG1655 genome sequence, identified as a possible homologue to the cell-division protein ZapA, was cloned into the high-expression plasmid pETDuet-1 and overexpressed in E. coli BL21 (DE3)-AI. The protein was purified in three steps to 99% purity. Crystals were obtained by the hanging-drop vapour-diffusion method at 291 K from a wide range of screened conditions, but principally from solutions containing 0.1 M HEPES pH 7.0, 18% PEG 6000, 5 mM CaCl2. Diffraction data to 1.8 A were collected at the European Synchrotron Radiation Facility (ESRF). The crystals belong to space group P6(1)22 or P6(5)22, with unit-cell parameters a = 53.8, b = 53.8, c = 329.7 A, alpha = beta = 90, gamma = 120 degrees.

Carrier Proteins↗
PubMed2005

Circular dichroism spectroscopy for the study of protein-ligand interactions.

Circular dichroism (CD) is the difference in absorption of left and right circularly polarized light, usually by a solution containing the molecules of interest. A signal is only measured for chiral molecules such as proteins. A CD spectrum provides information about the bonds and structures responsible for this chirality. When a small molecule (or ligand) binds to a protein, it acquires an induced CD (ICD) spectrum through chiral perturbation to its structure or electron rearrangements. The wavelengths of this ICD are determined by the ligand's own absorption spectrum, and the intensity of the ICD spectrum is determined by the strength and geometry of its interaction with the protein. Thus, ICD can be used to probe the binding of ligands to proteins. This chapter outlines protein CD and ICD, together with some of the issues relating to experimental design and implementation.

Actins↗
PubMed2004

Flow linear dichroism to probe binding of aromatic molecules and DNA to single-walled carbon nanotubes.

Structures of carbon nanotube/ligand complexes were studied by flow linear dichroism (the differential absorption of light polarized parallel and perpendicular to the flow orientation direction) with the aim of establishing linear dichroism as a technique to study such systems. Anthracene, naphthalene, and DNA were chosen as ligands, and the potential for flow linear dichroism to probe ligands noncovalently (as well as covalently) bound to single-walled nanotubes is reported. Linear dichroism enables the determination of approximate orientations of the ligands on the carbon nanotubes.

Anthracenes↗