A 'DNA replication' signature of progression and negative outcome in colorectal cancer

Colorectal cancer is one of the most frequent cancers worldwide. As the tumor-node-metastasis (TNM) staging classification does not allow to predict the survival of patients in many cases, additional prognostic factors are needed to better forecast their outcome. Genes involved in DNA replication may represent an underexplored source of such prognostic markers. Indeed, accidents during DNA replication can trigger 'replicative stress', one of the main features of cancer from earlier stages onward. In this study, we assessed the expression of 47 'DNA replication' genes in primary tumors and adjacent normal tissues from a homogeneous series of 74 patients. We found that genes coding for translesional (TLS) DNA polymerases, initiation of DNA replication, S-phase signaling and protection of replication forks were significantly deregulated in tumors. We also observed that the overexpression of either the MCM7 helicase or the TLS DNA polymerase POLQ (if also associated with a concomitant overexpression of firing genes) was significantly related to poor patient survival. Our data suggest the existence of a 'DNA replication signature' that might represent a source of new prognostic markers. Such a signature could help in understanding the molecular mechanisms underlying tumor progression in colorectal cancer patients.

The suite of small-angle neutron scattering instruments at Oak Ridge National Laboratory

Oak Ridge National Laboratory is home to the High Flux Isotope Reactor (HFIR), a high-flux research reactor, and the Spallation Neutron Source (SNS), the world's most intense source of pulsed neutron beams. The unique co-localization of these two sources provided an opportunity to develop a suite of complementary small-angle neutron scattering instruments for studies of large-scale structures: the GP-SANS and Bio-SANS instruments at the HFIR and the EQ-SANS and TOF-USANS instruments at the SNS. This article provides an overview of the capabilities of the suite of instruments, with specific emphasis on how they complement each other. A description of the plans for future developments including greater integration of the suite into a single point of entry for neutron scattering studies of large-scale structures is also provided.

Distinct subdomains of the EphA3 receptor mediate ligand binding and receptor dimerization

Eph receptor tyrosine kinases and their ligands (ephrins) are highly conserved protein families implicated in patterning events during development, particularly in the nervous system. In a number of functional studies, strict conservation of structure and function across distantly related vertebrate species has been confirmed. In this study we make use of the observation that soluble human EphA3 (HEK) exerts a dominant negative effect on somite formation and axial organization during zebrafish embryogenesis to probe receptor function. Based on exon structure we have dissected the extracellular region of EphA3 receptor into evolutionarily conserved subdomains and used kinetic BIAcore analysis, mRNA injection into zebrafish embryos, and receptor transphosphorylation analysis to study their function. We show that ligand binding is restricted to the N-terminal region encoded by exon III, and we identify an independent, C-terminal receptor-dimerization domain. Recombinant proteins encoding either region in isolation can function as receptor antagonists in zebrafish. We propose a two-step mechanism of Eph receptor activation with distinct ligand binding and ligand-independent receptor-receptor oligomerization events.

Hysteresis-Free Nanoparticle-Reinforced Hydrogels

The elastic storage and release of mechanical energy has been key to many developments throughout the history of mankind. Resilience, absent hysteresis, has been an elusive goal to achieve, particularly at large deformations. Using a low-crosslink-density polyacrylamide hydrogel at 96% water content having hyperbranched silica nanoparticles (HBSPs) as the major junction points, a hysteresis-free material is realized. The fatigue-free characteristic of these composite hydrogels is evidenced by the invariance of the stress-strain curves at strain ratios of 4, even after 5000 cycles. At a strain ratio of 7, only a 1.3% hysteresis is observed. A markedly increased strain-ratio-at-break of 11.5 is observed. The unique attributes of these resilient hydrogels are manifested in the high-fidelity detection of dynamic deformations under cyclic loading over a broad range of frequencies, difficult to achieve with other materials.

Guidelines of the French society of endocrinology for the management of thyroid nodules

The present document is a follow-up of the clinical practice guidelines of the French Society of Endocrinology, which were established for the use of its members and made available to scientific communities and physicians. Based on a critical analysis of data from the literature, consensuses and guidelines that have already been published internationally, it constitutes an update of the report on the diagnostic management of thyroid nodules that was proposed in France, in 1995, under the auspices of the French National Agency for Medical Evaluation (l'Agence nationale d'évaluation médicale). The current guidelines were deliberated beforehand by a number of physicians that are recognised for their expertise on the subject, coming from the specialities of endocrinology (the French Thyroid Research Group) and surgery (the French Association for Endocrine Surgery), as well as representatives from the fields of biology, ultrasonography, cytology and nuclear medicine. The guidelines were presented and submitted for the opinion of the members of the Society at its annual conference, which was held in Nice from 7-10 October 2009. The amended document was posted on the website of the Society and benefited from additional remarks of its members. The final version that is presented here was not subjected to methodological validation. It does not claim to be universal in its scope and will need to be revised in concert with progress made in technical and developmental concepts. It constitutes a document that the Society deems useful for distribution concerning the management of thyroid nodules, which is current, efficient and cost effective.

An early developmental role for eph-ephrin interaction during vertebrate gastrulation

Eph receptor tyrosine kinases (RTK) and their ephrin ligands are involved in the transmission of signals which regulate cytoskeletal organisation and cell migration, and are expressed in spatially restricted patterns at discrete phases during embryogenesis. Loss of function mutants of Eph RTK or ephrin genes result in defects in neuronal pathfinding or cell migration. In this report we show that soluble forms of human EphA3 and ephrin-A5, acting as dominant negative inhibitors, interfere with early events in zebrafish embryogenesis. Exogenous expression of both proteins results in dose-dependent defects in somite development and organisation of the midbrain-hindbrain boundary and hindbrain. The nature of the defects as well as the distribution and timing of expression of endogenous ligands/receptors for both proteins suggest that Eph-ephrin interaction is required for the organisation of embryonic structures by coordinating the cellular movements of convergence during gastrulation.

Transcriptional activation of Alzheimer's beta-amyloid precursor protein gene by stress

A neuropathological hallmark of Alzheimer's disease (AD) is the neuritic plaque, composed of an extracellular cluster of degenerating nerve terminals with a central core that is in part composed of deposits of a 4 kDa beta-amyloid peptide. Over-expression of the amyloid precursor protein (beta-APP) gene could be a contributing factor in the aberrant processing of the precursor protein, possibly leading to the formation of beta-amyloid. In AD the brain exhibits several features which indicate that neurons affected by AD exist under conditions of stress. Although the heat shock consensus sequence (CTCGACTTTTCTAG) located at position -317 bp is among the regulatory elements of the beta-APP gene, suggesting that this may act in the regulation of the beta-APP gene in response to stress, an induction of beta-APP as a result of interaction of this element with a heat shock factor has so far not been demonstrated. Moreover, there are conflicting reports in the literature regarding the up-regulation of beta-APP with stress. In this study we have used a fragment of the beta-APP promoter which includes the heat shock element, cloned into a luciferase expression vector pxP2 to transiently transfect cultured human NT2 and HeLa cells. Our findings directly demonstrate that transcription of the beta-APP gene is stimulated by various stresses--increase in temperature, treatment with ethanol and sodium arsenite. Gel mobility shift assays confirm the interaction of the heat shock element with a heat shock factor, induced as a result of stress.

Poly(3-hexylthiophene) Molecular Bottlebrushes via Ring-Opening Metathesis Polymerization: Macromolecular Architecture Enhanced Aggregation

We report a facile synthetic strategy based on a grafting through approach to prepare well-defined molecular bottlebrushes composed of regioregular poly(3-hexylthiophene) (rr-P3HT) as the conjugated polymeric side chain. To this end, the exo-norbornenyl-functionalized P3HT macromonomer was synthesized by Kumada catalyst transfer polycondensation (KCTP) followed by postpolymerization modifications, and the resulting conjugated macromonomer was successfully polymerized by ring-opening metathesis polymerization (ROMP) in a controlled manner. The P3HT molecular bottlebrushes display an unprecedented strong physical aggregation upon drying during recovery, as verified by several analyses of the solution and solid states. This remarkably strong aggregation behavior is attributed to a significant enhancement in the number of π-π interactions between grafted P3HT side chains, brought about due to the bottlebrush architecture. This behavior is qualitatively supported by coarse-grained molecular dynamics simulations.

Li+ transport in poly(ethylene oxide) based electrolytes: neutron scattering, dielectric spectroscopy, and molecular dynamics simulations

The dynamics of Li(+) transport in polyethylene oxide (PEO) and lithium bis(trifluoromethanesulfonyl)imde mixtures are investigated by combining neutron spin-echo (NSE) and dielectric spectroscopy with molecular dynamics (MD) simulations. The results are summarized in a relaxation time map covering wide ranges of temperature and time. The temperature dependence of the dc conductivity and the dielectric α relaxation time is found to be identical, indicating a strong coupling between both. The relaxation times obtained from the NSE measurements at 0.05 Å(-1)<q<0.2 Å(-1) are of similar magnitude as the relaxation time of Li(+) predicted by MD simulation. Our results suggest that the characteristic live times of the ions within the oxygen cages are mainly determined by the α relaxation that corresponds to local segmental motions of polymers, to a much lesser extent by the main chain relaxation, and not at all by the β relaxation or other faster processes. It is the first time decisive experimental evidence for a microscopic picture of the Li ion transportation process is shown in which the PEO chain forms EO cages over several monomer units and the Li ion "jump" from cage to cage. The role of the backbone of the polymer is discussed and contributes signifcantly to the Li ion transportation process. Moreover, detailed characteristic length and time scales of the Li(+) transport process in this polymer electrolyte are identified and interpreted.

Iridescence in nematics: Photonic liquid crystals of nanoplates in absence of long-range periodicity

Photonic materials with positionally ordered structure can interact strongly with light to produce brilliant structural colors. Here, we found that the nonperiodic nematic liquid crystals of nanoplates can also display structural color with only significant orientational order. Owing to the loose stacking of the nematic nanodiscs, such colloidal dispersion is able to reflect a broad-spectrum wavelength, of which the reflection color can be further enhanced by adding carbon nanoparticles to reduce background scattering. Upon the addition of electrolytes, such vivid colors of nematic dispersion can be fine-tuned via electrostatic forces. Furthermore, we took advantage of the fluidity of the nematic structure to create a variety of colorful arts. It was expected that the concept of implanting nematic features in photonic structure of lyotropic nanoparticles may open opportunities for developing advanced photonic materials for display, sensing, and art applications.

Heat shock factor-1 mediates the transcriptional activation of Alzheimer's beta-amyloid precursor protein gene in response to stress

Stress may be involved in the pathogenesis of Alzheimer's disease. There is a heat shock element located at position -317 bp on the beta-amyloid precursor protein (beta-APP) gene promoter. Recently we demonstrated [4] that stress, in the form of heat shock, ethanol and sodium arsenite treatment, transcriptionally activates the beta-APP gene. In this report we demonstrate that the nuclear factor that mediates this activation is heat shock factor-1.

Noncanonical Head-to-Head Hairpin DNA Dimerization Is Essential for the Synthesis of Orange Emissive Silver Nanoclusters

DNA secondary structures, such as dimers and hairpins, are important for the synthesis of DNA template-embedded silver nanoclusters (DNA/AgNCs). However, the arrangement of AgNCs within a given DNA template and how the AgNC influences the secondary structure of the DNA template are still unclear. Here, we introduce a noncanonical head-to-head hairpin DNA nanostructure that is driven by orange-emissive AgNCs. Through detailed in-gel analysis, sugar backbone switching, inductively coupled plasma mass spectrometry, small-angle X-ray scattering, and small angle neutron scattering, we show that the orange-emissive AgNCs mediate cytosine-Ag-cytosine bridging between two six-cytosine loop (6C-loop) hairpin DNA templates. Unlike green, red, or far-red emissive AgNCs, which are embedded inside a hairpin and duplex DNA template, the orange-emissive AgNCs are localized on the interface between the two 6C-loop hairpin DNA templates, thereby linking them. Moreover, we found that deoxyribose in the backbone of the 6C-loop at the third and fourth cytosines is crucial for the formation of the orange-emissive AgNCs and the head-to-head hairpin DNA structure. Taken together, we suggest that the specific wavelength of AgNCs fluorescence is determined by the mutual interaction between the secondary or tertiary structures of DNA- and AgNC-mediated intermolecular DNA cross-linking.

[Incidence and characteristics of bronchial colonisation in patient with lung cancer: a retrospective study of 388 cases]

INTRODUCTION

Bronchial colonisation is frequently reported in patients with lung cancer. These colonisations could influence patient therapeutic management and prognosis. The aim of our study is refine incidence and nature of bronchial colonisations in patients presenting with lung cancer.

METHODS

Three hundred and eighty-eight patients with lung cancer underwent a flexible bronchoscopy at the time of diagnosis. Among them, 216 patients had a bacteriological, mycobacteriological and fungal investigation. Type and frequency of these colonisations were analyzed.

RESULTS

Potential pathogens were found in 39.8% of samples, including mainly 39.8% of Gram-negative bacilli (Haemophilus influenzae, Enterobacter sp., Escherichia coli). In addition, we found 0.9% of mycobacteria and 13.9% of Candida albicans. Among these 216 patients where microbiological analysis was performed, patient features and tumor stage were not significantly correlated to microbial colonisation.

CONCLUSIONS

Colonisation of airways is frequently reported when a lung cancer is diagnosed. Our data suggest that bronchial colonisation should be prospectively collected due to its potential interest in the management of lung cancer patients.

Deciphering Melatonin-Stabilized Phase Separation in Phospholipid Bilayers

Lipid bilayers are fundamental building blocks of cell membranes, which contain the machinery needed to perform a range of biological functions, including cell-cell recognition, signal transduction, receptor trafficking, viral budding, and cell fusion. Importantly, many of these functions are thought to take place in the laterally phase-separated regions of the membrane, commonly known as lipid rafts. Here, we provide experimental evidence for the "stabilizing" effect of melatonin, a naturally occurring hormone produced by the brain's pineal gland, on phase-separated model membranes mimicking the outer leaflet of plasma membranes. Specifically, we show that melatonin stabilizes the liquid-ordered/liquid-disordered phase coexistence over an extended range of temperatures. The melatonin-mediated stabilization effect is observed in both nanometer- and micrometer-sized liposomes using small angle neutron scattering (SANS), confocal fluorescence microscopy, and differential scanning calorimetry. To experimentally detect nanoscopic domains in 50 nm diameter phospholipid vesicles, we developed a model using the Landau-Brazovskii approach that may serve as a platform for detecting the existence of nanoscopic lateral heterogeneities in soft matter and biological materials with spherical and planar geometries.

Phosphatidylinositol 4,5-bisphosphate clusters the cell adhesion molecule CD44 and assembles a specific CD44-Ezrin heterocomplex, as revealed by small angle neutron scattering

The cell adhesion molecule CD44 regulates diverse cellular functions, including cell-cell and cell-matrix interaction, cell motility, migration, differentiation, and growth. In cells, CD44 co-localizes with the membrane-cytoskeleton adapter protein Ezrin that links the CD44 assembled receptor signaling complexes to the cytoskeletal actin network, which organizes the spatial and temporal localization of signaling events. Here we report that the cytoplasmic tail of CD44 (CD44ct) is largely disordered. Upon binding to the signaling lipid phosphatidylinositol 4,5-bisphosphate (PIP2), CD44ct clusters into aggregates. Further, contrary to the generally accepted model, CD44ct does not bind directly to the FERM domain of Ezrin or to the full-length Ezrin but only forms a complex with FERM or with the full-length Ezrin in the presence of PIP2. Using contrast variation small angle neutron scattering, we show that PIP2 mediates the assembly of a specific heterotetramer complex of CD44ct with Ezrin. This study reveals the role of PIP2 in clustering CD44 and in assembling multimeric CD44-Ezrin complexes. We hypothesize that polyvalent electrostatic interactions are responsible for the assembly of CD44 clusters and the multimeric PIP2-CD44-Ezrin complexes.

Structural Evolution of Polylactide Molecular Bottlebrushes: Kinetics Study by Size Exclusion Chromatography, Small Angle Neutron Scattering, and Simulations

Structural evolution from poly(lactide) (PLA) macromonomer to resultant PLA molecular bottlebrush during ring opening metathesis polymerization (ROMP) was investigated for the first time by combining size exclusion chromatography (SEC), small-angle neutron scattering (SANS), and coarse-grained molecular dynamics (CG-MD) simulations. Multiple aliquots were collected at various reaction times during ROMP and subsequently analyzed by SEC and SANS. These complementary techniques enable the understanding of systematic changes in conversion, molecular weight and dispersity as well as structural details of PLA molecular bottlebrushes. CG-MD simulation not only predicts the experimental observations, but it also provides further insight into the analysis and interpretation of data obtained in SEC and SANS experiments. We find that PLA molecular bottlebrushes undergo three conformational transitions with increasing conversion (i.e., increasing the backbone length): (1) from an elongated to a globular shape due to longer side chain at low conversion, (2) from a globular to an elongated shape at intermediate conversion caused by excluded volume of PLA side chain, and (3) the saturation of contour length at high conversion due to chain transfer reactions.