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

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

SPIN enables high throughput species identification of archaeological bone by proteomics

Species determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises with regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce “Species by Proteome INvestigation” (SPIN), a shotgun proteomics workflow for analyzing archaeological bone capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirm the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produces reproducible results between replicates, which are consistent with morphological analysis. Finally, we demonstrate the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.info:eu-repo/semantics/publishedVersio

An integrated analysis of Maglemose bone points reframes the Early Mesolithic of Southern Scandinavia

The extensive peat bogs of Southern Scandinavia have yielded rich Mesolithic archaeological assemblages, with one of the most iconic artefacts being the bone point. Although great in number they remain understudied. Here we present a combined investigation of the typology, protein-based species composition, and absolute chronology of Maglemosian bone points. The majority of the bone points are made from cervids and bovines. However, changes both in species composition and barb morphology can be directly linked to a paucity of finds lasting nearly 600 years in Southern Scandinavia around 10,300 cal BP. We hypothesize that this hiatus was climate-driven and forced hunter-gatherers to abandon the lakes. Furthermore, the marked change in bone points coincides with a change in lithic technology. We, therefore, propose that the Maglemose culture in Southern Scandinavia is fundamentally divided into an Early Complex and a Late Complex