Genetic and Epigenetic Profiling of Human Prostate Cancer Cell-Subsets

Perturbation of androgen signalling drives progression of human prostate cancer (CaP) to castration-resistant prostate cancer (CRPC). Additionally, CaP is initiated and maintained by cancer stem cells (CSC)s which are analogous to normal prostate stem cells (SC)s. This study presents a qPCR assay to detect androgen receptor gene amplification (GAAR), which is the most common mechanism of castration resistance (>30%). Also, the epigenetic regulation and function of two SC-silenced genes with tumour-suppressive activity (Latexin (LXN) and Retinoic Acid Receptor Responder 1 (RARRES1)) were interrogated using micro-ChIP, transcriptional profiling and mass spectrometry. Traditionally, GAAR is detected using FISH which is labour-intensive and semi-quantitative, limiting clinical applicability. The mechanism of action of LXN or RARRES1 in CaP is unknown, and epigenetic regulation by DNA methylation has been ruled-out in primary CaP. The qPCR assay can detect GAAR in minor cell populations (~1%) within a heterogeneous sample and also quantifies X chromosome aneuploidy (XCA) - a predictor of poor-prognosis in CaP. GAAR and XCA were detected in near-patient xenografts derived from CRPC-tissue indicating that these abnormalities are present in cells capable of in vivo tumour-reconstitution. Micro-ChIP analysis of fractionated primary CaP cultures identified bivalent chromatin at LXN and RARRES1 promoters. Transcriptomic profiling failed to reveal significant changes in gene expression after transduction with LXN or RARRES1. However, an interactome for LXN and RARRES1 was successfully generated in PC3 cells. Additionally, confocal microscopy of mVenus-tagged LXN revealed a pan-cellular distribution which is reflected in the interactome. Screening for GAAR and XCA, using a high-throughput qPCR assay, could facilitate a targeted-medicine strategy in the treatment of CaP and CRPC. Further investigation of the LXN and RARRES1 interactomes may identify their mechanism(s) of action and the micro-ChIP assay could be used to identify epigenetic-inducers of LXN and RARRES1 which could provide a CSC-targeted strategy for CaP treatment

Mutual Avoidance in the Spectacled Salamander and Centipede: A Discrepancy between Exploratory Field and Laboratory Data

Interactions between amphibians and arthropods encompass a wide range of ecological relationships, predominantly characterized by predator–prey dynamics, with adult amphibians as the predators. In some instances, the roles are reversed. This study focuses on the potential predator-prey relationship between the spectacled salamander (Salamandrina perspicillata) and the centipede Scolopendra cingulata in Central Italy. Building upon previous research on chemical cue perception in amphibians, we investigated potential olfactory cue-mediated avoidance behaviours exhibited by S. perspicillata towards the potential predator S. cingulata through field observations and manipulative experiments. In a natural site, we estimated the degree of negative co-occurrence between the study species under shelters and found an avoidance pattern between S. perspicillata and S. cingulata in refuges. However, when the study species were forced to choose between sharing or not sharing a given shelter, through a manipulative experiment, the avoidance pattern was not confirmed. Potential determinants contributing to the avoidance pattern observed in nature are discussed. Our exploratory results represent a good example of how what often appears to be a strong observation-based pattern in natural settings needs to be carefully scrutinized. Hypotheses testing through experiments in controlled environments remains a valuable approach to exclude potentially misleading processes

Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP.

We used palaeoproteomics and peptide mass fingerprinting to obtain secure species identifications of key specimens of early domesticated fauna from South Africa, dating to ca. 2000 BP. It can be difficult to distinguish fragmentary remains of early domesticates (sheep) from similar-sized local wild bovids (grey duiker, grey rhebok, springbok-southern Africa lacks wild sheep) based on morphology alone. Our analysis revealed a Zooarchaeology by Mass Spectrometry (ZooMS) marker (m/z 1532) present in wild bovids and we demonstrate through LC-MS/MS that it is capable of discriminating between wild bovids and caprine domesticates. We confirm that the Spoegrivier specimen dated to 2105 ± 65 BP is indeed a sheep. This is the earliest directly dated evidence of domesticated animals in southern Africa. As well as the traditional method of analysing bone fragments, we show the utility of minimally destructive sampling methods such as PVC eraser and polishing films for successful ZooMS identification. We also show that collagen extracted more than 25 years ago for the purpose of radiocarbon dating can yield successful ZooMS identification. Our study demonstrates the importance of developing appropriate regional frameworks of comparison for future research using ZooMS as a method of biomolecular species identification

Polyaniline coated micro-capillaries for continuous flow analysis of aqueous solutions

The inner walls of fused silica micro-capillaries were successfully coated with polyaniline nanofibres using the “grafting” approach. The optical response of polyaniline coatings was evaluated during the subsequent redoping–dedoping processes with hydrochloric acid and ammonia solutions, respectively, that were passed inside the micro-capillary in continuous flow. The optical absorbance of the polyaniline coatings was measured and analysed in the wavelength interval of [300–850 nm] to determine its optical sensitivity to different concentrations of ammonia. It was found that the optical properties of polyaniline coatings change in response toammonia solutions in a wide concentration range from 0.2 ppm to 2000 ppm. The polyaniline coatings employed as a sensing material for the optical detection of aqueous ammonia have a fast response time and a fast regeneration time of less than 5 seconds at room temperature. The coating was fully characterised by Scanning Electron Microscopy, Raman Spectroscopy, absorbance measurements and kinetic studies. The response of the coatings showed very good reproducibility, demonstrating that this platform can be used for the development of micro-capillary integrated sensors based on the inherited sensing properties of polyaniline

The biomolecular characterization of a finger ring contextually dated to the emergence of the Early Neolithic from Syltholm, Denmark.

We present the analysis of an osseous finger ring from a predominantly early Neolithic context in Denmark. To characterize the artefact and identify the raw material used for its manufacture, we performed micro-computed tomography scanning, zooarchaeology by mass spectrometry (ZooMS) peptide mass fingerprinting, as well as protein sequencing by liquid chromatography tandem mass spectrometry (LC-MS/MS). We conclude that the ring was made from long bone or antler due to the presence of osteons (Haversian canals). Subsequent ZooMS analysis of collagen I and II indicated that it was made from Alces alces or Cervus elaphus material. We then used LC-MS/MS analysis to refine our species identification, confirming that the ring was made from Cervus elaphus, and to examine the rest of the proteome. This study demonstrates the potential of ancient proteomics for species identification of prehistoric artefacts made from osseous material

Simple top-down preparation of magnetic Bi0.9_{0.9}Gd0.1_{0.1}Fe1−x_{1-x}Tix_xO3_3 nanoparticles by ultrasonication of multiferroic bulk material

We present a simple technique to synthesize ultrafine nanoparticles directly from bulk multiferroic perovskite powder. The starting materials, which were ceramic pellets of the nominal compositions of Bi$_{0.9}$Gd$_{0.1}$Fe$_{1-x}$Ti$_x$O$_3$ (x = 0.00-0.20), were prepared initially by a solid state reaction technique, then ground into micrometer-sized powders and mixed with isopropanol or water in an ultrasonic bath. The particle size was studied as a function of sonication time with transmission electron microscopic imaging and electron diffraction that confirmed the formation of a large fraction of single-crystalline nanoparticles with a mean size of 11-13 nm. A significant improvement in the magnetic behavior of Bi$_{0.9}$Gd$_{0.1}$Fe$_{1-x}$Ti$_x$O$_3$ nanoparticles compared to their bulk counterparts was observed at room temperature. This sonication technique may be considered as a simple and promising route to prepare ultrafine nanoparticles for functional applications.Comment: 7 pages, 5 figure

Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP

Abstract: We used palaeoproteomics and peptide mass fingerprinting to obtain secure species identifications of key specimens of early domesticated fauna from South Africa, dating to ca. 2000 BP. It can be difficult to distinguish fragmentary remains of early domesticates (sheep) from similar-sized local wild bovids (grey duiker, grey rhebok, springbok—southern Africa lacks wild sheep) based on morphology alone. Our analysis revealed a Zooarchaeology by Mass Spectrometry (ZooMS) marker (m/z 1532) present in wild bovids and we demonstrate through LC–MS/MS that it is capable of discriminating between wild bovids and caprine domesticates. We confirm that the Spoegrivier specimen dated to 2105 ± 65 BP is indeed a sheep. This is the earliest directly dated evidence of domesticated animals in southern Africa. As well as the traditional method of analysing bone fragments, we show the utility of minimally destructive sampling methods such as PVC eraser and polishing films for successful ZooMS identification. We also show that collagen extracted more than 25 years ago for the purpose of radiocarbon dating can yield successful ZooMS identification. Our study demonstrates the importance of developing appropriate regional frameworks of comparison for future research using ZooMS as a method of biomolecular species identification