Macroscopic and spectroscopic analysis of lanthanide adsorption to bacterial cells

This study was designed to combine surface complexation modelling of macroscopic adsorption data with X-ray Absorption Spectroscopic (XAS) measurements to identify lanthanide sorption sites on the bacterial surface. The adsorption of selected representatives for light (La and Nd), middle (Sm and Gd) and heavy (Er and Yb) lanthanides was measured as a function of pH, and biomass samples exposed to 4 mg/L lanthanide at pH 3.5 and 6 were analysed using XAS. Surface complexation modelling was consistent with the light lanthanides adsorbing to phosphate sites, whereas the adsorption of middle and heavy lanthanides could be modelled equally well by carboxyl and phosphate sites. The existence of such mixed mode coordination was confirmed by Extended X-ray Absorption Fine Structure (EXAFS) analysis, which was also consistent with adsorption to phosphate sites at low pH, with secondary involvement of carboxyl sites at high adsorption density (high pH). Thus, the two approaches yield broadly consistent information with regard to surface site identity and lanthanide coordination environment. Furthermore, spectroscopic analysis suggests that coordination to phosphate sites is monodentate at the metal/biomass ratios used. Based on the best-fitting pKa site, we infer that the phosphate sites are located on N-acetylglucosamine phosphate, the most likely polymer on gram-negative cells with potential phosphate sites that deprotonate around neutral pH

Conformational and migrational dynamics of slipped-strand DNA three-way junctions containing trinucleotide repeats

Expansions of CAG/CTG trinucleotide repeats in DNA are the cause of at least 17 degenerative human disorders, including Huntington’s Disease. Repeat instability is thought to occur via the formation of intrastrand hairpins during replication, repair, recombination, and transcription though relatively little is known about their structure and dynamics. We use single-molecule Förster resonance energy transfer to study DNA three-way junctions (3WJs) containing slip-outs composed of CAG or CTG repeats. 3WJs that only have repeats in the slip-out show two-state behavior, which we attribute to conformational flexibility at the 3WJ branchpoint. When the triplet repeats extend into the adjacent duplex, additional dynamics are observed, which we assign to interconversion of positional isomers. We propose a branchpoint migration model that involves conformational rearrangement, strand exchange, and bulge-loop movement. This migration has implications for how repeat slip-outs are processed by the cellular machinery, disease progression, and their development as drug targets

Evaluating implicit feedback models using searcher simulations

In this article we describe an evaluation of relevance feedback (RF) algorithms using searcher simulations. Since these algorithms select additional terms for query modification based on inferences made from searcher interaction, not on relevance information searchers explicitly provide (as in traditional RF), we refer to them as implicit feedback models. We introduce six different models that base their decisions on the interactions of searchers and use different approaches to rank query modification terms. The aim of this article is to determine which of these models should be used to assist searchers in the systems we develop. To evaluate these models we used searcher simulations that afforded us more control over the experimental conditions than experiments with human subjects and allowed complex interaction to be modeled without the need for costly human experimentation. The simulation-based evaluation methodology measures how well the models learn the distribution of terms across relevant documents (i.e., learn what information is relevant) and how well they improve search effectiveness (i.e., create effective search queries). Our findings show that an implicit feedback model based on Jeffrey's rule of conditioning outperformed other models under investigation

A new twist on PIFE: photoisomerisation-related fluorescence enhancement

PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate of cis/trans photoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule and, in this review, we propose that PIFE is thereby renamed according to its fundamental working principle as photoisomerisation-related fluorescence enhancement, keeping the PIFE acronym intact. We discuss the photochemistry of cyanine fluorophores, the mechanism of PIFE, its advantages and limitations, and recent approaches to turn PIFE into a quantitative assay. We provide an overview of its current applications to different biomolecules and discuss potential future uses, including the study of protein-protein interactions, protein-ligand interactions and conformational changes in biomolecules.Comment: No Comment

Two‐photon detection of organotin Schiff base complexes in cancer cells

The early detection of cancer cells and their visualization before and after surgery are essential for successful pre‐ and post‐operative disease management. Although fluorescence imaging is a sensitive and versatile tool that is finding increasing use in clinical applications, there is a lack of tumour‐targeting fluorophores. We report here a family of fluorescent Schiff base organotin dyes (1: Et2N−L‐SnPh2, 2: Et2N−L‐SnBu2, 3: MeO−L‐SnPh2, 4: MeO−L‐SnBu2, 5: HO−L‐SnPh2, and 6: HO−L‐SnBu2, where L=2‐hydroxybenzylidene‐4‐hydroxybenzhydrazine). In addition to one‐photon‐excited fluorescence, efficient two‐photon excitation was demonstrated in compounds 1–4. Two of the compounds (5 and 6), both with hydroxyl substituents, were capable of selective accumulation in HeLa cells, allowing differentiation from normal cells (periodontal ligament cells). Compounds 1 and 3 showed excellent cancer cell staining (HeLa) using two‐photon bioimaging, which is promising for biomedicine applications

Bacteria-instructed synthesis of polymers for self-selective microbial binding and labelling

The detection and inactivation of pathogenic strains of bacteria continues to be an important therapeutic goal. Hence, there is a need for materials that can bind selectively to specific microorganisms, for diagnostic or anti-infective applications, but which can be formed from simple and inexpensive building blocks. Here, we exploit bacterial redox systems to induce a copper-mediated radical polymerisation of synthetic monomers at cell surfaces, generating polymers in situ that bind strongly to the microorganisms which produced them. This ‘bacteria-instructed synthesis’ can be carried out with a variety of microbial strains, and we show that the polymers produced are self-selective binding agents for the ‘instructing’ cell types. We further expand on the bacterial redox chemistries to ‘click’ fluorescent reporters onto polymers directly at the surfaces of a range of clinical isolate strains, allowing rapid, facile and simultaneous binding and visualisation of pathogens

Mann and gender in Old English prose : a pilot study

It has long been known that OE mann was used in gender-neutral as well as gender-specific contexts. Because of the enormous volume of its attestations in Old English prose, the more precise usage patterns of mann remain, however, largely uncharted, and existing lexicographical tools provide only a basic picture. This article aims to present a preliminary study of the various uses of mann as attested in Old English prose, particularly in its surprisingly consistent use by an individual author, namely that of the ninth-century Old English Martyrology. Patterns emerging from this text are then tested against other prose material. Particular attention is paid to gender-specific usage, examples of which are shown to be exceptional for a word which largely occurs in gender-neutral contexts.Publisher PDFPeer reviewe

The impact of surface chemistry modification on macrophage polarisation

Macrophages are innate immune cells that have a central role in combating infection and maintaining tissue homeostasis. They exhibit remarkable plasticity in response to environmental cues. At either end of a broad activation spectrum are pro-inflammatory (M1) and anti-inflammatory (M2) macrophages with distinct functional and phenotypical characteristics. Macrophages also play a crucial role in orchestrating immune responses to biomaterials used in the fabrication of implantable devices and drug delivery systems. To assess the impact of different surface chemistries on macrophage polarisation, human monocytes were cultured for 6 days on untreated hydrophobic polystyrene (PS) and hydrophilic O2 plasma-etched polystyrene (O2-PS40) surface. Our data clearly show that monocytes cultured on the hydrophilic O2-PS40 surface are polarised towards an M1-like phenotype, as evidenced by significantly higher expression of the pro-inflammatory transcription factors STAT1 and IRF5. By comparison, monocytes cultured on the hydrophobic PS surface exhibited an M2-like phenotype with high expression of mannose receptor (MR) and production of the anti-inflammatory cytokines IL-10 and CCL18. While the molecular basis of such different patterns of cell differentiation is yet to be fully elucidated, we hypothesise that it is due to the adsorption of different biomolecules on these surface chemistries. Indeed our surface characterisation data show quantitative and qualitative differences between the protein layers on that the O2-PS40 surface compared to PS surface which could be responsible for the observed differential macrophage polarisation on each surface