Peak picking as a pre-processing technique for imaging time of flight secondary ion mass spectrometry

High surface sensitivity and lateral resolution imaging make time-of-flight secondary ion mass spectrometry (ToF-SIMS) a unique and powerful tool for biological analysis. However, with the leaps forward made in the capabilities of the ToF-SIMS instrumentation, the data being recorded from these instruments has dramatically increased. Unfortunately, with these large, often complex, datasets, a bottleneck appears in their processing and interpretation. Here, an application of peak picking is described and applied to ToF-SIMS images allowing for large compression of data, noise removal and improved contrast, while retaining a high percentage of the original signal. Peak picking is performed to locate peaks within ToF-SIMS data. By using this information, signal arising from the same distribution can be summed and overlapping signals separated. As a result, the data size and complexity can be dramatically reduced. This method also acts as an effective noise filter, discarding unwanted noise from the data set. Peak picking and separation are evaluated against the conventional methods of mass binning and manually selecting regions of a peak to image on a model data set

Glacial cycles drive rapid divergence of cryptic field vole species

Understanding the factors that contribute to the generation of reproductively isolated forms is a fundamental goal of evolutionary biology. Cryptic species are an especially interesting challenge to study in this context since they lack obvious morphological differentiation that provides clues to adaptive divergence that may drive reproductive isolation. Geographical isolation in refugial areas during glacial cycling is known to be important for generating genetically divergent populations, but its role in the origination of new species is still not fully understood and likely to be situation dependent. We combine analysis of 35,434 single‐nucleotide polymorphisms (SNPs) with environmental niche modeling (ENM) to investigate genomic and ecological divergence in three cryptic species formerly classified as the field vole (Microtus agrestis). The SNPs demonstrate high genomic divergence (pairwise FST values of 0.45–0.72) and little evidence of gene flow among the three field vole cryptic species, and we argue that genetic drift may have been a particularly important mechanism for divergence in the group. The ENM reveals three areas as potential glacial refugia for the cryptic species and differing climatic niches, although with spatial overlap between species pairs. This evidence underscores the role that glacial cycling has in promoting genetic differentiation and reproductive isolation by subdivision into disjunct distributions at glacial maxima in areas relatively close to ice sheets. Future investigation of the intrinsic barriers to gene flow between the field vole cryptic species is required to fully assess the mechanisms that contribute to reproductive isolation. In addition, the Portuguese field vole (M. rozianus) shows a high inbreeding coefficient and a restricted climatic niche, and warrants investigation into its conservation status

Spatiotemporal lipid profiling during early embryo development of Xenopus laevis using dynamic Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) Imaging

Time-of-Flight secondary ion mass spectrometry (ToF-SIMS) imaging has been used for the direct analysis of single intact Xenopus laevis (X. laevis) embryo surfaces, locating multiple lipids during fertilisation and the early embryo development stages with sub-cellular lateral resolution (~4 Microns). The method avoids the complicated sample preparation for lipid analysis of the embryos, which requires selective chemical extraction of a pool of samples and chromatographic separation, while preserving the spatial distribution of biological species. The results show ToF-SIMS is capable of profiling multiple components (e.g., glycerophosphocholine, sphingomyelin, cholesterol, vitamin E, diacylglycerol, triacylglycerol) in a single X. laevis embryo. We observe lipid remodelling during fertilisation and early embryo development via time course sampling. The study also reveals the lipid distribution on the gametes fusion site. The methodology used in the study opens the possibility of studying developmental biology using high resolution imaging MS and of understanding the functional role of the biological molecules

Substituted dipyridophenazine complexes of Cr(III): synthesis, enantiomeric resolution and binding interactions with calf thymus DNA

[Cr(phen)2(X2dppz)]3+ {X = H, Me, or F} have been synthesised, characterised, and chromatographically resolved into their constituent Δ and Λ enantiomers. The DNA-binding interactions of each of the racemic complexes were investigated, with the results of linear dichroism, thermal denaturation, and emission quenching studies indicative of intercalative binding to CT-DNA with a significant electrostatic contribution. UV/Vis absorption titrations suggest strong DNA binding by each of the racemic complexes, with the methylated analogue [Cr(phen)2(Me 2dppz)]3+ exhibiting the largest equilibrium binding constant. Emission quenching and UV-Vis titrations of the enantiomers of [Cr(phen)2(dppz)]3+ imply similar binding affinities for the Δ and Λ isomers, although significant differences between the circular dichroism spectra of the enantiomers in the presence of DNA connote differences in binding orientation and/or conformation between the two

Phonon-drag effects on thermoelectric power

We carry out a calculation of the phonon-drag contribution $S_g$ to the thermoelectric power of bulk semiconductors and quantum well structures for the first time using the balance equation transport theory extended to the weakly nonuniform systems. Introducing wavevector and phonon-mode dependent relaxation times due to phonon-phonon interactions, the formula obtained can be used not only at low temperatures where the phonon mean free path is determined by boundary scattering, but also at high temperatures. In the linear transport limit, $S_g$ is equivalent to the result obtained from the Boltzmann equation with a relaxation time approximation. The theory is applied to experiments and agreement is found between the theoretical predictions and experimental results. The role of hot-electron effects in $S_g$ is discussed. The importance of the contribution of $S_g$ to thermoelectric power in the hot-electron transport condition is emphasized.Comment: 8 pages, REVTEX 3.0, 7 figures avilable upon reques

A physiological signature of sound meaning in dementia.

The meaning of sensory objects is often behaviourally and biologically salient and decoding of semantic salience is potentially vulnerable in dementia. However, it remains unclear how sensory semantic processing is linked to physiological mechanisms for coding object salience and how that linkage is affected by neurodegenerative diseases. Here we addressed this issue using the paradigm of complex sounds. We used pupillometry to compare physiological responses to real versus synthetic nonverbal sounds in patients with canonical dementia syndromes (behavioural variant frontotemporal dementia - bvFTD, semantic dementia - SD; progressive nonfluent aphasia - PNFA; typical Alzheimer's disease - AD) relative to healthy older individuals. Nonverbal auditory semantic competence was assessed using a novel within-modality sound classification task and neuroanatomical associations of pupillary responses were assessed using voxel-based morphometry (VBM) of patients' brain MR images. After taking affective stimulus factors into account, patients with SD and AD showed significantly increased pupil responses to real versus synthetic sounds relative to healthy controls. The bvFTD, SD and AD groups had a nonverbal auditory semantic deficit relative to healthy controls and nonverbal auditory semantic performance was inversely correlated with the magnitude of the enhanced pupil response to real versus synthetic sounds across the patient cohort. A region of interest analysis demonstrated neuroanatomical associations of overall pupil reactivity and differential pupil reactivity to sound semantic content in superior colliculus and left anterior temporal cortex respectively. Our findings suggest that autonomic coding of auditory semantic ambiguity in the setting of a damaged semantic system may constitute a novel physiological signature of neurodegenerative diseases

Confinement of Therapeutic Enzymes in Selectively Permeable Polymer Vesicles by Polymerization-Induced Self-Assembly (PISA) Reduces Antibody Binding and Proteolytic Susceptibility

Covalent PEGylation of biologics has been widely employed to reduce immunogenicity, while improving stability and half-life in vivo. This approach requires covalent protein modification, creating a new entity. An alternative approach is stabilization by encapsulation into polymersomes; however this typically requires multiple steps, and the segregation requires the vesicles to be permeable to retain function. Herein, we demonstrate the one-pot synthesis of therapeutic enzyme-loaded vesicles with size-selective permeability using polymerization-induced self-assembly (PISA) enabling the encapsulated enzyme to function from within a confined domain. This strategy increased the proteolytic stability and reduced antibody recognition compared to the free protein or a PEGylated conjugate, thereby reducing potential dose frequency and the risk of immune response. Finally, the efficacy of encapsulated l-asparaginase (clinically used for leukemia treatment) against a cancer line was demonstrated, and its biodistribution and circulation behavior in vivo was compared to the free enzyme, highlighting this methodology as an attractive alternative to the covalent PEGylation of enzymes

Phonon drag thermopower and weak localization

Previous experimental work on a two-dimensional (2D) electron gas in a Si-on-sapphire device led to the conclusion that both conductivity and phonon drag thermopower $S^g$ are affected to the same relative extent by weak localization. The present paper presents further experimental and theoretical results on these transport coefficients for two very low mobility 2D electron gases in $\delta-$doped GaAs/Ga$_x$Al$_{1-x}$As quantum wells. The experiments were carried out in the temperature range 3-7K where phonon drag dominates the thermopower and, contrary to the previous work, the changes observed in the thermopower due to weak localization were found to be an order of magnitude less than those in the conductivity. A theoretical framework for phonon drag thermopower in 2D and 3D semiconductors is presented which accounts for this insensitivity of $S^g$ to weak localization. It also provides transparent physical explanations of many previous experimental and theoretical results.Comment: 19 page Revtex file, 3 Postscript figur

Synthesis, characterization and biological activities of semicarbazones and their copper complexes

Substituted semicarbazones/thiosemicarbazones and their copper complexes have been prepared and several single crystal structures examined. The copper complexes of these semicarbazone/thiosemicarbazones were prepared and several crystal structures examined. The single crystal X-ray structure of the pyridyl-substituted semicarbazone showed two types of copper complexes, a monomer and a dimer. We also found that the p-nitrophenyl semicarbazone formed a conventional 'magic lantern' acetate-bridged dimer. Electron Paramagnetic Resonance (EPR) of several of the copper complexes was consistent with the results of single crystal X-ray crystallography. The EPR spectra of the p-nitrophenyl semicarbazone copper complex in dimethylsulfoxide (DMSO) showed the presence of two species, confirming the structural information. Since thiosemicarbazones and semicarbazones have been reported to exhibit anticancer activity, we examined the anticancer activity of several of the derivatives reported in the present study and interestingly only the thiosemicarbazone showed activity while the semicarbazones were not active indicating that introduction of sulphur atom alters the biological profile of these thiosemicarbazones. (C) 2016 Elsevier Inc All rights reserved