Unsupervised self-organising map classification of Raman spectra from prostate cell lines uncovers substratified prostate cancer disease states.

Prostate cancer is a disease which poses an interesting clinical question: Should it be treated? Only a small subset of prostate cancers are aggressive and require removal and treatment to prevent metastatic spread. However, conventional diagnostics remain challenged to risk-stratify such patients; hence, new methods of approach to biomolecularly sub-classify the disease are needed. Here we use an unsupervised self-organising map approach to analyse live-cell Raman spectroscopy data obtained from prostate cell-lines; our aim is to exemplify this method to sub-stratify, at the single-cell-level, the cancer disease state using high-dimensional datasets with minimal preprocessing.

Raman spectroscopy reveals oxidative stress-induced metabolic vulnerabilities in early-stage AR-negative prostate-cancer versus normal-prostate cell lines.

Quantitative Raman spectroscopy provides information-rich imaging of complex tissues. To illustrate its ability to characterise early-stage disease, we compared live P4E6, a low-grade Gleason-3 prostate-cancer cell line, to PNT2-C2, a normal prostate cell-line equivalent, thereby elucidating key molecular and mechanistic differences. Spectral changes from statistically relevant population sampling show P4E6 is defined by reduced DNA/RNA signatures (primarily base-pair modifications), increased protein-related signatures (synthesis), decreased whole-cell measured saturated and unsaturated fatty acids, and increased cholesterol and cholesterol ester (lipid storage).

Peer-Led Focus Groups Identify Barriers to Healthy Lifestyle in African American Adolescents from Baltimore City.

Objectives: Black youth are disproportionately affected by the US obesity epidemic. Early-age obesity often continues into adulthood and is associated with a higher risk of diabetes, cardiovascular disease, and premature death. Few studies have incorporated community-based participatory research (CBPR) facilitated by youth to provide frank discussions among teens living in inner cities about challenges and facilitators in maintaining a healthy weight and to design teen-identified interventions.

Tight-binding studies of uniaxial strain in T-graphene nanoribbons.

The role of uniaxial strain in armchair, T-graphene nanoribbons (ATGNRs) with symmetric and asymmetric structures is investigated using a nearest-neighbour, tight-binding (TB) model. ATGNRs with structural symmetry and two a sub-lattice structure exhibit Dirac points at zero strain. Application of uniaxial strain to these systems induces multiple Dirac points under compression (up to -20% strain), with the number of these points commensurate with the number of tetra-carbon base-units along the width of the unit cell, accounting also for the mirror symmetry of the structure.

Biomolecular phenotyping and heterogeneity assessment of mesenchymal stromal cells using label-free Raman spectroscopy.

Easy, quantitative measures of biomolecular heterogeneity and high-stratified phenotyping are needed to identify and characterise complex disease processes at the single-cell level, as well as to predict cell fate. Here, we demonstrate how Raman spectroscopy can be used in the difficult-to-assess case of clonal, bone-derived mesenchymal stromal cells (MSCs) to identify MSC lines and group these according to biological function (e.g.

Formation of a Copper(II)-Tyrosyl Complex at the Active Site of Lytic Polysaccharide Monooxygenases Following Oxidation by HO.

Hydrogen peroxide is a cosubstrate for the oxidative cleavage of saccharidic substrates by copper-containing lytic polysaccharide monooxygenases (LPMOs). The rate of reaction of LPMOs with hydrogen peroxide is high, but it is accompanied by rapid inactivation of the enzymes, presumably through protein oxidation. Herein, we use UV-vis, CD, XAS, EPR, VT/VH-MCD, and resonance Raman spectroscopies, augmented with mass spectrometry and DFT calculations, to show that the product of reaction of an AA9 LPMO with HO at higher pHs is a singlet Cu(II)-tyrosyl radical species, which is inactive for the oxidation of saccharidic substrates.

Streptomyces coelicolor strains lacking polyprenol phosphate mannose synthase and protein O-mannosyl transferase are hyper-susceptible to multiple antibiotics.

Polyprenol phosphate mannose (PPM) is a lipid-linked sugar donor used by extra-cytoplasmic glycosyl tranferases in bacteria. PPM is synthesized by polyprenol phosphate mannose synthase, Ppm1, and in most Actinobacteria is used as the sugar donor for protein O-mannosyl transferase, Pmt, in protein glycosylation. Ppm1 and Pmt have homologues in yeasts and humans, where they are required for protein O-mannosylation.

A proposed simulation method for directed self-assembly of nanographene.

A methodology for predictive kinetic self-assembly modeling of bottom-up chemical synthesis of nanographene is proposed. The method maintains physical transparency in using a novel array format to efficiently store molecule information and by using array operations to determine reaction possibilities. Within a minimal model approach, the parameter space for the bond activation energies (i.

Multiparameter Analysis of Human Bone Marrow Stromal Cells Identifies Distinct Immunomodulatory and Differentiation-Competent Subtypes.

Bone marrow stromal cells (BMSCs, also called bone-marrow-derived mesenchymal stromal cells) provide hematopoietic support and immunoregulation and contain a stem cell fraction capable of skeletogenic differentiation. We used immortalized human BMSC clonal lines for multi-level analysis of functional markers for BMSC subsets. All clones expressed typical BMSC cell-surface antigens; however, clones with trilineage differentiation capacity exhibited enhanced vascular interaction gene sets, whereas non-differentiating clones were uniquely CD317 positive with significantly enriched immunomodulatory transcriptional networks and high IL-7 production.

An integrated approach to the taxonomic identification of prehistoric shell ornaments.

Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration.

Long-term resilience of late holocene coastal subsistence system in Southeastern South america.

Isotopic and molecular analysis on human, fauna and pottery remains can provide valuable new insights into the diets and subsistence practices of prehistoric populations. These are crucial to elucidate the resilience of social-ecological systems to cultural and environmental change. Bulk collagen carbon and nitrogen isotopic analysis of 82 human individuals from mid to late Holocene Brazilian archaeological sites (∼6,700 to ∼1,000 cal BP) reveal an adequate protein incorporation and, on the coast, the continuation in subsistence strategies based on the exploitation of aquatic resources despite the introduction of pottery and domesticated plant foods.

Pathogens and host immunity in the ancient human oral cavity.

Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources.

Feasibility of a virtual learning collaborative to implement an obesity QI project in 29 pediatric practices.

Background: Quality improvement (QI) activities are required to maintain board certification in pediatrics. However, because of lack of training and resources, pediatricians may feel overwhelmed by the need to implement QI activities. Pediatricians also face challenges when caring for overweight and obese children.

Tunability of the optical absorption in small silver cluster-polymer hybrid systems.

We have calculated the absorption characteristics of different hybrid systems consisting of Ag, Ag(2), or Ag(3) atomic clusters and poly(methacrylic acid) using the time-dependent density-functional theory. The polymer is found to have an extensive structural-dependency on the spectral patterns of the hybrid systems relative to the bare clusters. The absorption spectrum can be "tuned" to the visible range for hybrid systems with an odd number of electrons per silver cluster, whereas for hybrid systems comprising an even number of electrons per silver cluster, the leading absorption edge can be shifted up to approximately 4.