Multiscale correlative tomography: an investigation of creep cavitation in 316 stainless steel

Creep cavitation in an ex-service nuclear steam header Type 316 stainless steel sample is investigated through a multiscale tomography workflow spanning eight orders of magnitude, combining X-ray computed tomography (CT), plasma focused ion beam (FIB) scanning electron microscope (SEM) imaging and scanning transmission electron microscope (STEM) tomography. Guided by microscale X-ray CT, nanoscale X-ray CT is used to investigate the size and morphology of cavities at a triple point of grain boundaries. In order to understand the factors affecting the extent of cavitation, the orientation and crystallographic misorientation of each boundary is characterised using electron backscatter diffraction (EBSD). Additionally, in order to better understand boundary phase growth, the chemistry of a single boundary and its associated secondary phase precipitates is probed through STEM energy dispersive X-ray (EDX) tomography. The difference in cavitation of the three grain boundaries investigated suggests that the orientation of grain boundaries with respect to the direction of principal stress is important in the promotion of cavity formation

Quantum control of proximal spins using nanoscale magnetic resonance imaging

Quantum control of individual spins in condensed matter systems is an emerging field with wide-ranging applications in spintronics, quantum computation, and sensitive magnetometry. Recent experiments have demonstrated the ability to address and manipulate single electron spins through either optical or electrical techniques. However, it is a challenge to extend individual spin control to nanoscale multi-electron systems, as individual spins are often irresolvable with existing methods. Here we demonstrate that coherent individual spin control can be achieved with few-nm resolution for proximal electron spins by performing single-spin magnetic resonance imaging (MRI), which is realized via a scanning magnetic field gradient that is both strong enough to achieve nanometric spatial resolution and sufficiently stable for coherent spin manipulations. We apply this scanning field-gradient MRI technique to electronic spins in nitrogen-vacancy (NV) centers in diamond and achieve nanometric resolution in imaging, characterization, and manipulation of individual spins. For NV centers, our results in individual spin control demonstrate an improvement of nearly two orders of magnitude in spatial resolution compared to conventional optical diffraction-limited techniques. This scanning-field-gradient microscope enables a wide range of applications including materials characterization, spin entanglement, and nanoscale magnetometry.Comment: 7 pages, 4 figure

Sphingosine 1-phosphate modulates antigen capture by murine langerhans cells via the S1P2 receptor subtype

Dendritic cells (DCs) play a pivotal role in the development of cutaneous contact hypersensitivity (CHS) and atopic dermatitis as they capture and process antigen and present it to T lymphocytes in the lymphoid organs. Recently, it has been indicated that a topical application of the sphingolipid sphingosine 1-phosphate (S1P) prevents the inflammatory response in CHS, but the molecular mechanism is not fully elucidated. Here we indicate that treatment of mice with S1P is connected with an impaired antigen uptake by Langerhans cells (LCs), the initial step of CHS. Most of the known actions of S1P are mediated by a family of five specific G protein-coupled receptors. Our results indicate that S1P inhibits macropinocytosis of the murine LC line XS52 via S1P2 receptor stimulation followed by a reduced phosphatidylinositol 3-kinase (PI3K) activity. As down-regulation of S1P2 not only diminished S1P-mediated action but also enhanced the basal activity of LCs on antigen capture, an autocrine action of S1P has been assumed. Actually, S1P is continuously produced by LCs and secreted via the ATP binding cassette transporter ABCC1 to the extracellular environment. Consequently, inhibition of ABCC1, which decreased extracellular S1P levels, markedly increased the antigen uptake by LCs. Moreover, stimulation of sphingosine kinase activity, the crucial enzyme for S1P formation, is connected not only with enhanced S1P levels but also with diminished antigen capture. These results indicate that S1P is essential in LC homeostasis and influences skin immunity. This is of importance as previous reports suggested an alteration of S1P levels in atopic skin lesions

A robust, scanning quantum system for nanoscale sensing and imaging

Controllable atomic-scale quantum systems hold great potential as sensitive tools for nanoscale imaging and metrology. Possible applications range from nanoscale electric and magnetic field sensing to single photon microscopy, quantum information processing, and bioimaging. At the heart of such schemes is the ability to scan and accurately position a robust sensor within a few nanometers of a sample of interest, while preserving the sensor's quantum coherence and readout fidelity. These combined requirements remain a challenge for all existing approaches that rely on direct grafting of individual solid state quantum systems or single molecules onto scanning-probe tips. Here, we demonstrate the fabrication and room temperature operation of a robust and isolated atomic-scale quantum sensor for scanning probe microscopy. Specifically, we employ a high-purity, single-crystalline diamond nanopillar probe containing a single Nitrogen-Vacancy (NV) color center. We illustrate the versatility and performance of our scanning NV sensor by conducting quantitative nanoscale magnetic field imaging and near-field single-photon fluorescence quenching microscopy. In both cases, we obtain imaging resolution in the range of 20 nm and sensitivity unprecedented in scanning quantum probe microscopy

Protein crystals in adenovirus type 5-infected cells: requirements for intranuclear crystallogenesis, structural and functional analysis

Intranuclear crystalline inclusions have been observed in the nucleus of epithelial cells infected with Adenovirus serotype 5 (Ad5) at late steps of the virus life cycle. Using immuno-electron microscopy and confocal microscopy of cells infected with various Ad5 recombinants modified in their penton base or fiber domains, we found that these inclusions represented crystals of penton capsomers, the heteromeric capsid protein formed of penton base and fiber subunits. The occurrence of protein crystals within the nucleus of infected cells required the integrity of the fiber knob and part of the shaft domain. In the knob domain, the region overlapping residues 489–492 in the FG loop was found to be essential for crystal formation. In the shaft, a large deletion of repeats 4 to 16 had no detrimental effect on crystal inclusions, whereas deletion of repeats 8 to 21 abolished crystal formation without altering the level of fiber protein expression. This suggested a crucial role of the five penultimate repeats in the crystallisation process. Chimeric pentons made of Ad5 penton base and fiber domains from different serotypes were analyzed with respect to crystal formation. No crystal was found when fiber consisted of shaft (S) from Ad5 and knob (K) from Ad3 (heterotypic S5-K3 fiber), but occurred with homotypic S3K3 fiber. However, less regular crystals were observed with homotypic S35-K35 fiber. TB5, a monoclonal antibody directed against the Ad5 fiber knob was found by immunofluorescence microscopy to react with high efficiency with the intranuclear protein crystals in situ. Data obtained with Ad fiber mutants indicated that the absence of crystalline inclusions correlated with a lower infectivity and/or lower yields of virus progeny, suggesting that the protein crystals might be involved in virion assembly. Thus, we propose that TB5 staining of Ad-infected 293 cells can be used as a prognostic assay for the viability and productivity of fiber-modified Ad5 vectors

Mycolactone Diffuses into the Peripheral Blood of Buruli Ulcer Patients - Implications for Diagnosis and Disease Monitoring.

BACKGROUND: Mycobacterium ulcerans, the causative agent of Buruli ulcer (BU), is unique among human pathogens in its capacity to produce a polyketide-derived macrolide called mycolactone, making this molecule an attractive candidate target for diagnosis and disease monitoring. Whether mycolactone diffuses from ulcerated lesions in clinically accessible samples and is modulated by antibiotic therapy remained to be established. METHODOLOGY/PRINCIPAL FINDING: Peripheral blood and ulcer exudates were sampled from patients at various stages of antibiotic therapy in Ghana and Ivory Coast. Total lipids were extracted from serum, white cell pellets and ulcer exudates with organic solvents. The presence of mycolactone in these extracts was then analyzed by a recently published, field-friendly method using thin layer chromatography and fluorescence detection. This approach did not allow us to detect mycolactone accurately, because of a high background due to co-extracted human lipids. We thus used a previously established approach based on high performance liquid chromatography coupled to mass spectrometry. By this means, we could identify structurally intact mycolactone in ulcer exudates and serum of patients, and evaluate the impact of antibiotic treatment on the concentration of mycolactone. CONCLUSIONS/SIGNIFICANCE: Our study provides the proof of concept that assays based on mycolactone detection in serum and ulcer exudates can form the basis of BU diagnostic tests. However, the identification of mycolactone required a technology that is not compatible with field conditions and point-of-care assays for mycolactone detection remain to be worked out. Notably, we found mycolactone in ulcer exudates harvested at the end of antibiotic therapy, suggesting that the toxin is eliminated by BU patients at a slow rate. Our results also indicated that mycolactone titres in the serum may reflect a positive response to antibiotics, a possibility that it will be interesting to examine further through longitudinal studies

Stress induced polarization of immune-neuroendocrine phenotypes in Gallus gallus

Immune-neuroendocrine phenotypes (INPs) stand for population subgroups differing in immune-neuroendocrine interactions. While mammalian INPs have been characterized thoroughly in rats and humans, avian INPs were only recently described in Coturnix coturnix (quail). To assess the scope of this biological phenomenon, herein we characterized INPs in Gallus gallus (a domestic hen strain submitted to a very long history of strong selective breeding pressure) and evaluated whether a social chronic stress challenge modulates the individuals’ interplay affecting the INP subsets and distribution. Evaluating plasmatic basal corticosterone, interferon-γ and interleukin-4 concentrations, innate/acquired leukocyte ratio, PHA-P skin-swelling and induced antibody responses, two opposite INP profiles were found: LEWIS-like (15% of the population) and FISCHER-like (16%) hens. After chronic stress, an increment of about 12% in each polarized INP frequency was found at expenses of a reduction in the number of birds with intermediate responses. Results show that polarized INPs are also a phenomenon occurring in hens. The observed inter-individual variation suggest that, even after a considerable selection process, the population is still well prepared to deal with a variety of immune-neuroendocrine challenges. Stress promoted disruptive effects, leading to a more balanced INPs distribution, which represents a new substrate for challenging situations.Fil: Nazar, Franco Nicolas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto de Investigaciones Biológicas y Tecnológicas; ArgentinaFil: Estevez, Inma. Centro de Investigación. Neiker - Tecnalia; EspañaFil: Correa, Silvia Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Marin, Raul Hector. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto de Investigaciones Biológicas y Tecnológicas; Argentin

The emergence of the 2013 H7N9 and related viruses in China

Promising Investigator ScholarshipPoster Session: News and Views from the H7N9 OutbreakBackground: The novel H7N9 influenza A virus first detected in March 2013 has caused more than 130 cases of human infection in China, resulting in 39 deaths. This virus is a reassortant of H7, N9 and H9N2 avian influenza viruses and carries some amino acids linked to mammalian receptor binding, raising concerns of a new pandemic. However, neither the source populations of the H7N9 outbreak lineage nor the conditions for its genesis are fully understood. Materials and Methods: Following the initial reports of H7N9 influenza infection in humans, field surveillance was conducted during 4th-18th April in Zhejiang, Shandong and Guangdong provinces. Pairs of oropharyngeal and cloacal samples from chickens and other poultry, together with faecal and water samples from live poultry markets (LPMs), farms and wetlands were collected for virus isolation and whole genomic sequencing. H7, N9, N7 and H9N2 archived isolates, obtained during previous influenza surveillance between 2000-2013 in southern China, were also sequenced and phylogenetically analyzed to pinpoint the genesis of the H7N9 and a related H7N7 virus. The infectivity and pathology of H7N9 and H7N7 viruses were tested in a ferret model. Results: Through a combination of active surveillance, screening of virus archives, and evolutionary analyses, we found that H7 viruses have independently transferred from domestic ducks to chickens in China on at least two occasions. Subsequently they reassorted with enzootic H9N2 viruses to generate the H7N9 outbreak lineage, and a related but previously unrecognized H7N7 lineage. The H7N9 outbreak lineage has spread over a large geographic region and is prevalent in chickens at LPMs that appear to be the immediate source of human infections. In ferrets this virus caused a productive infection and pneumonia. Virus was shed via the nasal route and transmitted to physical contact and some airborne-exposed animals. Like the H7N9 virus, the H7N7 virus was also mainly isolated from chickens at LPMs and it could efficiently infect ferrets, be shed via the nasal and rectal routes, and cause severe pneumonia. Conclusions: These findings provide a clear picture showing how the current H7N9 human viruses emerged. Domestic ducks act as primary vectors to acquire and maintain diversified viruses from migratory birds, and facilitate different subtype combinations between H7 and N9 or N7 viruses and interspecies transmissions to chickens. After being introduced, the H7N9 or H7N7 viruses reassorted with enzootic H9N2 viruses and formed the current reassortant H7N9 or H7N7 viruses seen in chickens. This likely led to outbreaks in chickens, resulting in the rapid spread of the novel reassortant H7N9 virus through LPMs, which then became the source of human infections. Whether the H7N9 outbreak lineage will, or has, become enzootic in China needs further investigation. Our results also indicate that H7 viruses pose a broader threat than the current H7N9 virus. Continued prevalence of this family of H7 viruses in poultry could lead to further sporadic human infections, with an ongoing risk that the virus might acquire efficient human-to-human transmissibility.published_or_final_versio

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi

Deuteron and antideuteron production in Au+Au collisions at sqrt(s_NN)=200 GeV

The production of deuterons and antideuterons in the transverse momentum range 1.1 < p_T < 4.3 GeV/c at mid-rapidity in Au + Au collisions at sqrt(s_NN)=200 GeV has been studied by the PHENIX experiment at RHIC. A coalescence analysis comparing the deuteron and antideuteron spectra with those of protons and antiprotons, has been performed. The coalescence probability is equal for both deuterons and antideuterons and increases as a function of p_T, which is consistent with an expanding collision zone. Comparing (anti)proton yields p_bar/p = 0.73 +/- 0.01, with (anti)deuteron yields: d_bar/d = 0.47 +/- 0.03, we estimate that n_bar/n = 0.64 +/- 0.04.Comment: 326 authors, 6 pages text, 5 figures, 1 Table. Submitted to PRL. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm