Pyrene emission from monolayers 'clicked' onto quartz

A series of quartz surfaces were modifed with a series of crosslinkers and functional groups in order to obtain an azide-terminated monolayer, which was then used to immobilize pyrene onto the surface via alkyne-azide \click" chemistry. During the course of the immobilization, different ratios of tert-butyl diphenyl chlorosilane were used to control the distribution and hence the photophysical properties of the pyrene on the surface. The preparative surface reactions and photophysical properties were investigated with contact angle, X-ray photoelectron spectroscopy, UV-visible absorption and emission spectroscopy. High surface coverage was achieved of just under 1molecule per nm2. At this coverage all emission from the pyrene was in the form of excimer emission. Excimer emission dominated at all surface coverages greater than 0.45 molecules per nm2. Below this coverage the monomer emission could also be observed. The conclusions that can be drawn are important for understanding the interactions of neighboring molecules in molecular monolayers. Our results suggest that at high surface coverage a substantial number of the pyrene molecules are already close enough to their neighbors that pairs of them can be directly excited to form excimer with no requirement for diffusion. This can be stated because the long wavelength end of the pyrene absorption and excitation spectra show a broad tail that is assigned to a charge transfer band resulting from an electron being directly transferred from a ground state pyrene to a neighboring pyrene molecule. Furthermore, absorption spectra shifts also indicate that the pyrene molecules undergo some interactions on the surface when they are closely packed

Characterization of the equine 2\u27-5\u27 oligoadenylate synthetase 1 (OAS1) and ribonuclease L (RNASEL) innate immunity genes

BACKGROUND: The mammalian OAS/RNASEL pathway plays an important role in antiviral host defense. A premature stop-codon within the murine Oas1b gene results in the increased susceptibility of mice to a number of flaviviruses, including West Nile virus (WNV). Mutations in either the OAS1 or RNASEL genes may also modulate the outcome of WNV-induced disease or other viral infections in horses. Polymorphisms in the human OAS gene cluster have been previously utilized for case-control analysis of virus-induced disease in humans. No polymorphisms have yet been identified in either the equine OAS1 or RNASEL genes for use in similar case-control studies. RESULTS: Genomic sequence for equine OAS1 was obtained from a contig assembly generated from a shotgun subclone library of CHORI-241 BAC 100I10. Specific amplification of regions of the OAS1 gene from 13 horses of various breeds identified 33 single nucleotide polymorphisms (SNP) and two microsatellites. RNASEL cDNA sequences were determined for 8 mammals and utilized in a phylogenetic analysis. The chromosomal location of the RNASEL gene was assigned by FISH to ECA5p17-p16 using two selected CHORI-241 BAC clones. The horse genomic RNASEL sequence was assembled. Specific amplification of regions of the RNASEL gene from 13 horses identified 31 SNPs. CONCLUSION: In this report, two dinucleotide microsatellites and 64 single nucleotide polymorphisms within the equine OAS1 and RNASEL genes were identified. These polymorphisms are the first to be reported for these genes and will facilitate future case-control studies of horse susceptibility to infectious diseases

Characterization of the equine 2'-5' oligoadenylate synthetase 1 (OAS1) and ribonuclease L (RNASEL) innate immunity genes

Background The mammalian OAS/RNASEL pathway plays an important role in antiviral host defense. A premature stop-codon within the murine Oas1b gene results in the increased susceptibility of mice to a number of flaviviruses, including West Nile virus (WNV). Mutations in either the OAS1 or RNASEL genes may also modulate the outcome of WNV-induced disease or other viral infections in horses. Polymorphisms in the human OAS gene cluster have been previously utilized for case-control analysis of virus-induced disease in humans. No polymorphisms have yet been identified in either the equine OAS1 or RNASEL genes for use in similar case-control studies. Results Genomic sequence for equine OAS1 was obtained from a contig assembly generated from a shotgun subclone library of CHORI-241 BAC 100I10. Specific amplification of regions of the OAS1 gene from 13 horses of various breeds identified 33 single nucleotide polymorphisms (SNP) and two microsatellites. RNASEL cDNA sequences were determined for 8 mammals and utilized in a phylogenetic analysis. The chromosomal location of the RNASEL gene was assigned by FISH to ECA5p17-p16 using two selected CHORI-241 BAC clones. The horse genomic RNASEL sequence was assembled. Specific amplification of regions of the RNASEL gene from 13 horses identified 31 SNPs. Conclusion In this report, two dinucleotide microsatellites and 64 single nucleotide polymorphisms within the equine OAS1 and RNASEL genes were identified. These polymorphisms are the first to be reported for these genes and will facilitate future case-control studies of horse susceptibility to infectious diseases

Wittgenstein's Thought Experiments and Relativity Theory

In this paper, I discuss the similarity between Wittgenstein’s use of thought experiments and Relativity Theory. I begin with introducing Wittgenstein’s idea of “thought experiments” and a tentative classification of different kinds of thought experiments in Wittgenstein’s work. Then, after presenting a short recap of some remarks on the analogy between Wittgenstein’s point of view and Einstein’s, I suggest three analogies between the status of Wittgenstein’s mental experiments and Relativity theory: the topics of time dilation, the search for invariants, and the role of measuring tools in Special Relativity. This last point will help to better define Wittgenstein’s idea of description as the core of his philosophical enterprise

Transient Brewster angle reflectometry of spiropyran monolayers

Brewster angle reflectometry has been developed as a tool for determining the absorbance and refractive index changes in molecular monolayers containing spiropyran. The method is sensitive to changes in both the real and imaginary parts of the refractive index in the monolayers. It was used to monitor the conversion of spiropyran to merocyanine and the reversal of this reaction when the molecules were immobilised on quartz using silane coupling. An analytical solution of Fresnel formula allowed the transient reflectometry data to be converted into transient absorption information. Absorbances of transients as low as ~10-6 were possible using the current apparatus with a single laser pulse transient measurement. It was found that spiropyran photoconverted to merocyanine with an efficiency of ~0.1. The photochemical reversion of converted merocyanine to spiropyran occurred with efficiencies of 0.03–0.2 and this was probably site dependent. It was found that the thermal conversion from merocyanine to spiropyran was slow and even after 10 min there was no significant thermal reversion. This measurement was possible because the real part of the refractive index of the monolayer could be monitored with time using an off-resonance probe at a wavelength where the merocyanine did not absorb light meaning that the probe did not photobleach the sample. Thus our method also provides a non-intrusive method for probing changes in molecules in thin films

Raman mapping glucose metabolites during human mesenchymal stem cell adipogenesis

Raman mapping was used to determine the lipid distribution inside human mesenchymal stem cells during induced adipogenesis by monitoring C-H stretching bands of the fats inside the lipid droplets. By incorporating deuterated glucose into the cell culture medium during induction it was possible to distinguish whether or not downstream metabolites, either in lipid droplets or in the cytoplasm, had been formed before or after the adipogenic cascade, because C-D stretching bands are 1/√2 shifted compared to the C-H bands. Thus, metabolites formed after the initiation of the process displayed both C-H and C-D stretching bands and so were forming during induced adipogenesis rather than prior to it. With the ability to distinguish small putative lipid drops formed by the induction of adipogenesis from those pre-formed in the cell, it was possible to analyze spectral changes occurring in the droplets at the earliest stages of adipogenesis. There were two key findings. Firstly, Raman spectra of lipid droplets evolved over time, suggesting that their composition at the early stages was not the same as at the later stages. Secondly, it was apparent that the proportion of unsaturated fats in droplets was higher at early stages than it was at later stages, suggesting that unsaturated fats arrive in the droplets faster than saturated ones

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil® and PowerMax® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications

Are Ethnic and Gender Specific Equations Needed to Derive Fat Free Mass from Bioelectrical Impedance in Children of South Asian, Black African-Caribbean and White European Origin? Results of the Assessment of Body Composition in Children Study

Background Bioelectrical impedance analysis (BIA) is a potentially valuable method for assessing lean mass and body fat levels in children from different ethnic groups. We examined the need for ethnic- and gender-specific equations for estimating fat free mass (FFM) from BIA in children from different ethnic groups and examined their effects on the assessment of ethnic differences in body fat. Methods Cross-sectional study of children aged 8–10 years in London Primary schools including 325 South Asians, 250 black African-Caribbeans and 289 white Europeans with measurements of height, weight and arm-leg impedance (Z; Bodystat 1500). Total body water was estimated from deuterium dilution and converted to FFM. Multilevel models were used to derive three types of equation {A: FFM = linear combination(height+weight+Z); B: FFM = linear combination(height2/Z); C: FFM = linear combination(height2/Z+weight)}. Results Ethnicity and gender were important predictors of FFM and improved model fit in all equations. The models of best fit were ethnicity and gender specific versions of equation A, followed by equation C; these provided accurate assessments of ethnic differences in FFM and FM. In contrast, the use of generic equations led to underestimation of both the negative South Asian-white European FFM difference and the positive black African-Caribbean-white European FFM difference (by 0.53 kg and by 0.73 kg respectively for equation A). The use of generic equations underestimated the positive South Asian-white European difference in fat mass (FM) and overestimated the positive black African-Caribbean-white European difference in FM (by 4.7% and 10.1% respectively for equation A). Consistent results were observed when the equations were applied to a large external data set. Conclusions Ethnic- and gender-specific equations for predicting FFM from BIA provide better estimates of ethnic differences in FFM and FM in children, while generic equations can misrepresent these ethnic differences