Ashok K. Adya

Host carbon sources modulate cell wall architecture, drug resistance and virulence in a fungal pathogen

The survival of all microbes depends upon their ability to respond to environmental challenges. To establish infection, pathogens such as Candida albicans must mount effective stress responses to counter host defences while adapting to dynamic changes in nutrient status within host niches. Studies of C. albicans stress adaptation have generally been performed on glucose‐grown cells, leaving the effects of alternative carbon sources upon stress resistance largely unexplored. We have shown that growth on alternative carbon sources, such as lactate, strongly influence the resistance of C. albicans to antifungal drugs, osmotic and cell wall stresses. Similar trends were observed in clinical isolates and other pathogenic Candida species. The increased stress resistance of C. albicans was not dependent on key stress (Hog1) and cell integrity (Mkc1) signalling pathways. Instead, increased stress resistance was promoted by major changes in the architecture and biophysical properties of the cell wall. Glucose‐ and lactate‐grown cells displayed significant differences in cell wall mass, ultrastructure, elasticity and adhesion. Changes in carbon source also altered the virulence of C. albicans in models of systemic candidiasis and vaginitis, confirming the importance of alternative carbon sources within host niches during C. albicans infections.

The structure of liquid methanol by H/D substitution technique of neutron diffraction

Neutron diffraction (ND) measurements on liquid methanol (CD3OD,CD3O(H/D),CD3OH) under ambient conditions have been performed to obtain the total (intra-+intermolecular), Gdist(r) and intermolecular, Ginter(r) radial distribution functions (rdfs) for the three samples. The extent to which intermolecular structure is affected by using two different intramolecular models is discussed. The H/D substitution on hydroxyl–hydrogen (Ho) has been used to extract the partial distribution functions, GXHodist/inter(r) (X=C, O, and H—a methyl hydrogen) and GXXdist/inter(r) from the difference techniques of ND at both the distinct and intermolecular levels. The O–Ho bond length, which has been the subject of controversy in the past, is found purely from the partial distribution function, GXHodist(r) to be 0.98±0.01 A. The C–H distance obtained from the GXXdist(r) partial is 1.08±0.01 A. These distances determined by fitting an intramolecular model to the total distinct structure functions are 0.961±0.001 A and 1.096±0.001 A, respectively. The GXXinter(r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho⋯Ho partial pair distribution function (pdf), gHoHo(r), also determined from the second-order difference, shows that only one other Ho atom can be found within a mean Ho⋯Ho separation of 2.36 A. The average position of the O⋯Ho hydrogen bond determined purely from experimental GXHointer(r) partial distribution function, at 1.75±0.03 A is found to lie in the range (1.75–1.95 A) of values reported from computer simulation results.Neutron diffraction (ND) measurements on liquid methanol (CD3OD,CD3O(H/D),CD3OH) under ambient conditions have been performed to obtain the total (intra-+intermolecular), Gdist(r) and intermolecular, Ginter(r) radial distribution functions (rdfs) for the three samples. The extent to which intermolecular structure is affected by using two different intramolecular models is discussed. The H/D substitution on hydroxyl–hydrogen (Ho) has been used to extract the partial distribution functions, GXHodist/inter(r) (X=C, O, and H—a methyl hydrogen) and GXXdist/inter(r) from the difference techniques of ND at both the distinct and intermolecular levels. The O–Ho bond length, which has been the subject of controversy in the past, is found purely from the partial distribution function, GXHodist(r) to be 0.98±0.01 A. The C–H distance obtained from the GXXdist(r) partial is 1.08±0.01 A. These distances determined by fitting an intramolecular model to the total distinct structure functions are 0.961±0.001 A and 1.096±0....

The structure of molten and simulated with polarizable- and rigid-ion models

Molecular dynamics (MD) simulations of molten were carried out using the polarizable-ion model (PIM) and the rigid-ion model (RIM). In these simulations the Born-Mayer-Huggins potential was employed with the same potential parameters for both models. In the PIM the polarization of the chloride ions was supplemented. Although the partial radial distribution functions (rdfs) between Dy and Cl, and between Cl and Cl are very similar for the two models, the rdf between Dy and Dy is quite different. The rdf between Dy and Dy experimentally determined by the isotope substitution method was well reproduced by the PIM. The strong Coulomb interaction between and is screened by the polarization of ions and the interaction distance between and becomes smaller than that given by the RIM. MD simulations for were made similarly. The PIM also reproduced the experimental total structure factor very well.

Discrimination of bladder cancer cells from normal urothelial cells with high specificity and sensitivity: Combined application of atomic force microscopy and modulated Raman spectroscopy

Atomic force microscopy (AFM) and modulated Raman spectroscopy (MRS) were used to discriminate between living normal human urothelial cells (SV-HUC-1) and bladder tumour cells (MGH-U1) with high specificity and sensitivity. MGH-U1 cells were 1.5-fold smaller, 1.7-fold thicker and 1.4-fold rougher than normal SV-HUC-1 cells. The adhesion energy was 2.6-fold higher in the MGH-U1 cells compared to normal SV-HUC-1 cells, which possibly indicates that bladder tumour cells are more deformable than normal cells. The elastic modulus of MGH-U1 cells was 12-fold lower than SV-HUC-1 cells, suggesting a higher elasticity of the bladder cancer cell membranes. The biochemical fingerprints of cancer cells displayed a higher DNA and lipid content, probably due to an increase in the nuclear to cytoplasm ratio. Normal cells were characterized by higher protein contents. AFM studies revealed a decrease in the lateral dimensions and an increase in thickness of cancer cells compared to normal cells; these studies authenticate the observations from MRS. Nanostructural, nanomechanical and biochemical profiles of bladder cells provide qualitative and quantitative markers to differentiate between normal and cancerous cells at the single cellular level. AFM and MRS allow discrimination between adhesion energy, elasticity and Raman spectra of SV-HUC-1 and MGH-U1 cells with high specificity (83, 98 and 95%) and sensitivity (97, 93 and 98%). Such single-cell-level studies could have a pivotal impact on the development of AFM-Raman combined methodologies for cancer profiling and screening with translational significance.

Morphological changes in textile fibres exposed to environmental stresses: Atomic force microscopic examination

The ability of the atomic force microscope (AFM) to investigate the nanoscopic morphological changes in the surfaces of fabrics was examined for the first time. This study focussed on two natural (cotton and wool), and a regenerated cellulose (viscose) textile fibres exposed to various environmental stresses for different lengths of times. Analyses of the AFM images allowed us to measure quantitatively the surface texture parameters of the environmentally stressed fabrics as a function of the exposure time. It was also possible to visualise at the nanoscale the finest details of the surfaces of three weathered fabrics and clearly distinguish between the detrimental effects of the imposed environmental conditions. This study confirmed that the AFM could become a very powerful tool in forensic examination of textile fibres to provide significant fibre evidence due to its capability of distinguishing between different environmental exposures or forced damages to fibres.

The Structure of Liquid Methanol: A Molecular Dynamics Study Using Three-Site Models

Abstract The structure of liquid methanol at 298.15 K is investigated by performing molecular dynamics (MD) simulations in NVE ensemble using two 3-site force field models. The simulated structural results are compared with the recent neutron diffraction (ND) results obtained at the partial pair distribution function (pdf) level by employing H/D substitution on the hydroxyl hydrogen, Ho. Overall agreement is found between the simulated and experimental total intermolecular radial distribution functions (rdfs). The ability of the 3-site model simulations to satisfactorily reproduce experimental X—X (X = C, O or H- a methyl hydrogen) intermolecular partial distribution function, dominated by contributions from the methyl group. demonstrates that the methyl group does not participate in any bonding in the liquid. However, a comparison between the simulated and experimental Ho—Ho and X—Ho functions reveals that discrepancies still exist at a quantitative level.

Microscopic structure of liquid dimethyl sulphoxide and its electrolyte solutions: molecular dynamics simulations

Molecular dynamics (MD) simulations of pure dimethyl sulphoxide (DMSO) and solutions of Na+, Ca2+, Cl−, NaCl and CaCl2 in DMSO have been performed at 298.15 K and 398.15 K in NVT ensembles by using a four-interaction-site model of DMSO and reaction field method for Coulombic interactions. The structure of solvent, ion-solvation shells and ion-pairs have been analysed by employing a concept of coordination centres and characteristic vectors of the solvent molecule. Results are given for atom-atom (corresponding to DMSO), ion-atom and ion-ion radial distribution functions (RDFs), orientation of the DMSO molecules and their geometrical arrangements in the first solvation shells of the ions (Na+, Ca2+, Cl−). A preferential formation of cyclic dimers with antiparallel alignment between dipole moments of nearest-neighbour molecules in the pure solvent is found. Geometrical models of the first coordination shells of the ions in ‘infinitely dilute solutions’ are proposed. Ion-ion RDFs in NaCl-DMSO and CaCl2-DMSO solutions reveal the presence of both solvent separated (SSIP) and contact (CIP) ion pairs. The structures of the solvation shells of such ion pairs are also discussed.

Atomic force microscopic investigation of commercial pressure sensitive adhesives for forensic analysis.

Pressure sensitive adhesive (PSA), such as those used in packaging and adhesive tapes, are very often encountered in forensic investigations. In criminal activities, packaging tapes may be used for sealing packets containing drugs, explosive devices, or questioned documents, while adhesive and electrical tapes are used occasionally in kidnapping cases. In this work, the potential of using atomic force microscopy (AFM) in both imaging and force mapping (FM) modes to derive additional analytical information from PSAs is demonstrated. AFM has been used to illustrate differences in the ultrastructural and nanomechanical properties of three visually distinguishable commercial PSAs to first test the feasibility of using this technique. Subsequently, AFM was used to detect nanoscopic differences between three visually indistinguishable PSAs.

Phase transitions in rare earth chlorides observed by XAFS.

XAFS spectroscopy has increasingly been utilised to elucidate the nearest-neighbour structure in the condensed phases. In this paper, the XAFS spectra of NdCl3 and DyCl3 in both the solid and the liquid phases measured at the Nd and Dy L(III) absorption edges on beam line BM29 of the European Synchrotron Radiation Facility (ESRF) are presented. The Fourier transformed radial structure functions, phi(r) show that the prominent peaks corresponding to M-Cl (M: Nd or Dy) first shell contribution are shifted to shorter distances in the liquid melts as compared to those found in the corresponding solids. Similar behaviour has also been observed from other diffraction techniques in typical ionic melts such as NaCl. From the temperature dependence of the radial structure functions it is clear that the change in the M-Cl distance on melting is much larger in NdCl3 than that in DyCl3.

The structure of liquid methanol: a molecular dynamics study using a six-site model

Molecular dynamics (MD) simulations of pure methanol (216 molecules) have been carried out at 298.15 K in the NVE ensemble using a six-site potential model originally derived by Anwander et al (1992 Chem. Phys. 166 341) from ab initio quantum chemical calculations (QCC) and tested for the first time in this study. MD results of a three-site model where all the methyl hydrogens were considered as a dead load have also been reported recently by us. In this paper, the relative merits of the two models are discussed by comparing the simulated radial distribution functions (rdfs) with the recent experimental neutron diffraction (ND) results obtained at the partial pair distribution function (pdf) level. Although the MD simulations with both the models reproduce the total rdfs rather well, discrepancies begin to appear at the partial pdf level. Both the simulations are found to reproduce equally well the X-X (X = C, O or H, a methyl hydrogen) pdf since it comprises six correlations, and is dominated mainly by contributions from the methyl group. However, the main peaks of the simulated HO-HO partial, where HO is the hydroxyl hydrogen, are found to be slightly higher and shifted to larger distances as compared to the ND results. A comparison of the simulated X-HO intermolecular rdf, in which H-HO correlations dominate, with the ND results shows that, although the three-site model reproduces at least qualitatively the experimental features, the six-site model derived from ab initio QCC fails badly.