Effects of Storage Conditions on Endophyte and Seed Viability in Pasture Grasses

Several important temperate pasture grasses have co-evolved with mutualistic Epichloë fungal endophytes. These endophytes impart beneficial attributes to their host as they enhance the fitness of the grass when under biotic and abiotic stresses. The asexual species of these fungi (formerly classed as Neotyphodium) are obligate symbionts, and efficiently colonise newly formed tillers and infect seed by direct colonisation of the embryo. These endophytes are strictly seed transmitted. Survival of the fungus in this seed is therefore critical for the dissemination of endophyte-infected seed to grassland farmers. Longevity of endophyte in stored seed is primarily determined by the length of storage, temperature, and relative humidity as this is in equilibrium with seed moisture. Elevated temperature and relative humidity both reduce endophyte viability. The relative importance of each of these environmental parameters is unclear. Longevity may be further modified by grass species, cultivar, seed lot, and endophyte strain. Valuable seed requiring long term storage can utilise controlled storage facilities where temperature is preferably ≤ 5oC and relative humidity ≤ 30% (seed moisture \u3c 8%). For large quantities of commercial seed, moisture barrier packaging can be used

Context Mediation in the Semantic Web: Handling OWL Ontology and Data Disparity through Context Interchange

The COntext INterchange (COIN) strategy is an approach to solving the problem of interoperability of semantically heterogeneous data sources through context mediation. COIN has used its own notation and syntax for representing ontologies. More recently, the OWL Web Ontology Language is becoming established as the W3C recommended ontology language. We propose the use of the COIN strategy to solve context disparity and ontology interoperability problems in the emerging Semantic Web – both at the ontology level and at the data level. In conjunction with this, we propose a version of the COIN ontology model that uses OWL and the emerging rules interchange language, RuleML.Singapore-MIT Alliance (SMA

Correcting the z~8 Galaxy Luminosity Function for Gravitational Lensing Magnification Bias

We present a Bayesian framework to account for the magnification bias from both strong and weak gravitational lensing in estimates of high-redshift galaxy luminosity functions. We illustrate our method by estimating the $z\sim8$ UV luminosity function using a sample of 97 Y-band dropouts (Lyman break galaxies) found in the Brightest of Reionizing Galaxies (BoRG) survey and from the literature. We find the luminosity function is well described by a Schechter function with characteristic magnitude of $M^\star = -19.85^{+0.30}_{-0.35}$, faint-end slope of $\alpha = -1.72^{+0.30}_{-0.29}$, and number density of $\log_{10} \Psi^\star [\textrm{Mpc}^{-3}] = -3.00^{+0.23}_{-0.31}$. These parameters are consistent within the uncertainties with those inferred from the same sample without accounting for the magnification bias, demonstrating that the effect is small for current surveys at $z\sim8$, and cannot account for the apparent overdensity of bright galaxies compared to a Schechter function found recently by Bowler et al. (2014a,b) and Finkelstein et al. (2014). We estimate that the probability of finding a strongly lensed $z\sim8$ source in our sample is in the range $\sim 3-15 \%$ depending on limiting magnitude. We identify one strongly-lensed candidate and three cases of intermediate lensing in BoRG (estimated magnification $\mu>1.4$) in addition to the previously known candidate group-scale strong lens. Using a range of theoretical luminosity functions we conclude that magnification bias will dominate wide field surveys -- such as those planned for the Euclid and WFIRST missions -- especially at $z>10$. Magnification bias will need to be accounted for in order to derive accurate estimates of high-redshift luminosity functions in these surveys and to distinguish between galaxy formation models.Comment: Accepted for publication in ApJ. 20 pages, 13 figure

Early detection of Pseudomonas aeruginosa – comparison of conventional versus molecular (PCR) detection directly from adult patients with cystic fibrosis (CF)

BACKGROUND: Pseudomonas aeruginosa (PA) is the most important bacterial pathogen in patients with cystic fibrosis (CF) patients. Currently, routine bacteriological culture on selective/non- selective culture media is the cornerstone of microbiological detection. The aim of this study was to compare isolation rates of PA by conventional culture and molecular (PCR) detection directly from sputum. METHODS: Adult patients (n = 57) attending the regional adult CF centre in Northern Ireland, provided fresh sputum following airways clearance exercise. Following processing of the specimen with sputasol (1:1 vol), the specimen was examined for the presence of PA by plating onto a combination of culture media (Pseudomonas isolation agar, Blood agar & McConkey agar). In addition, from the same specimen, genomic bacterial DNA was extracted (1 ml) and was amplified employing two sequence-specific targets, namely (i) the outer membrane protein (oprL) gene locus and (ii) the exotoxin A (ETA) gene locus. RESULTS: By sputum culture, there were 30 patients positive for PA, whereas by molecular techniques, there were 35 positive patients. In 39 patients (22 PA +ve & 17 PA -ve), there was complete agreement between molecular and conventional detection and with both PCR gene loci. The oprL locus was more sensitive than the ETA locus, as the former was positive in 10 more patients and there were no patients where the ETA was positive and the oprL target negative. Where a PCR +ve/culture -ve result was recorded (10 patients), we followed these patients and recorded that 5 of these patients converted to being culture-positive at times ranging from 4–17 months later, with a mean lag time of 4.5 months. CONCLUSIONS: This study indicates that molecular detection of PA in sputum employing the oprL gene target, is a useful technique in the early detection of PA, gaining on average 4.5 months over conventional culture. It now remains to be established whether aggressive antibiotic intervention at this earlier stage, based on PCR detection, has any significant benefits on clinical outcome

In-flight radiometric calibration of the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS)

A reflectance-based method was used to provide an analysis of the in-flight radiometric performance of AVIRIS. Field spectral reflectance measurements of the surface and extinction measurements of the atmosphere using solar radiation were used as input to atmospheric radiative transfer calculations. Five separate codes were used in the analysis. Four include multiple scattering, and the computed radiances from these for flight conditions were in good agreement. Code-generated radiances were compared with AVIRIS-predicted radiances based on two laboratory calibrations (pre- and post-season of flight) for a uniform highly reflecting natural dry lake target. For one spectrometer (C), the pre- and post-season calibration factors were found to give identical results, and to be in agreement with the atmospheric models that include multiple scattering. This positive result validates the field and laboratory calibration technique. Results for the other spectrometers (A, B and D) were widely at variance with the models no matter which calibration factors were used. Potential causes of these discrepancies are discussed

Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites

BackgroundPsoriasis is a cytokine‐mediated skin disease that can be treated effectively with immunosuppressive biologic agents. These medications, however, are not equally effective in all patients and are poorly suited for treating mild psoriasis. To develop more targeted therapies, interfering with transcription factor (TF) activity is a promising strategy.MethodsMeta‐analysis was used to identify differentially expressed genes (DEGs) in the lesional skin from psoriasis patients (n = 237). We compiled a dictionary of 2935 binding sites representing empirically‐determined binding affinities of TFs and unconventional DNA‐binding proteins (uDBPs). This dictionary was screened to identify “psoriasis response elements” (PREs) overrepresented in sequences upstream of psoriasis DEGs.ResultsPREs are recognized by IRF1, ISGF3, NF‐kappaB and multiple TFs with helix‐turn‐helix (homeo) or other all‐alpha‐helical (high‐mobility group) DNA‐binding domains. We identified a limited set of DEGs that encode proteins interacting with PRE motifs, including TFs (GATA3, EHF, FOXM1, SOX5) and uDBPs (AVEN, RBM8A, GPAM, WISP2). PREs were prominent within enhancer regions near cytokine‐encoding DEGs (IL17A, IL19 and IL1B), suggesting that PREs might be incorporated into complex decoy oligonucleotides (cdODNs). To illustrate this idea, we designed a cdODN to concomitantly target psoriasis‐activated TFs (i.e., FOXM1, ISGF3, IRF1 and NF‐kappaB). Finally, we screened psoriasis‐associated SNPs to identify risk alleles that disrupt or engender PRE motifs. This identified possible sites of allele‐specific TF/uDBP binding and showed that PREs are disproportionately disrupted by psoriasis risk alleles.ConclusionsWe identified new TF/uDBP candidates and developed an approach that (i) connects transcriptome informatics to cdODN drug development and (ii) enhances our ability to interpret GWAS findings. Disruption of PRE motifs by psoriasis risk alleles may contribute to disease susceptibility.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155494/1/ctm2s4016901500545-sup-0001.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155494/2/ctm2s4016901500545-sup-0018.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155494/3/ctm2s4016901500545-sup-0002.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155494/4/ctm2s4016901500545.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155494/5/ctm2s4016901500545-sup-0009.pd

A Holistic Approach to Service Survivability

We present SABER (Survivability Architecture: Block, Evade, React), a proposed survivability architecture that blocks, evades and reacts to a variety of attacks by using several security and survivability mechanisms in an automated and coordinated fashion. Contrary to the ad hoc manner in which contemporary survivable systems are built--using isolated, independent security mechanisms such as firewalls, intrusion detection systems and software sandboxes--SABER integrates several different technologies in an attempt to provide a unified framework for responding to the wide range of attacks malicious insiders and outsiders can launch. This coordinated multi-layer approach will be capable of defending against attacks targeted at various levels of the network stack, such as congestion-based DoS attacks, software-based DoS or code-injection attacks, and others. Our fundamental insight is that while multiple lines of defense are useful, most conventional, uncoordinated approaches fail to exploit the full range of available responses to incidents. By coordinating the response, the ability to survive even in the face of successful security breaches increases substantially. We discuss the key components of SABER, how they will be integrated together, and how we can leverage on the promising results of the individual components to improve survivability in a variety of coordinated attack scenarios. SABER is currently in the prototyping stages, with several interesting open research topics

Molecular Dissection of Psoriasis: Integrating Genetics and Biology

Psoriasis is a common and debilitating disease of the skin, nails, and joints, with an acknowledged but complex genetic basis. Early genome-wide linkage studies of psoriasis focused on segregation of microsatellite markers in families; however, the only locus consistently identified resided in the major histocompatibility complex. Subsequently, several groups mapped this locus to the vicinity of HLA-C, and two groups have reported HLA-Cw6 itself to be the major susceptibility allele. More recently, the development of millions of single-nucleotide polymorphisms, coupled with the development of high-throughput genotyping platforms and a comprehensive map of human haplotypes, has made possible a genome-wide association approach using cases and controls rather than families. Taking advantage of these developments, we participated in a collaborative genome-wide association study of psoriasis involving thousands of cases and controls. Initial analysis of these data revealed and/or confirmed association between psoriasis and seven genetic loci—HLA-C, IL12B, IL23R, IL23A, IL4/IL13, TNFAIP3, and TNIP1—and ongoing studies are revealing additional loci. Here, we review the epidemiology, immunopathology, and genetics of psoriasis, and present a disease model integrating its genetics and immunology

Infrared spectra and fragmentation dynamics of isotopologue-selective mixed-ligand complexes †

Isolated mixed-ligand complexes provide tractable model systems in which to study competitive and cooperative binding effects as well as controlled energy flow. Here, we report spectroscopic and isotopologue-selective infrared photofragmentation dynamics of mixed gas-phase Au(12/13CO)n(N2O)m+ complexes. The rich infrared action spectra, which are reproduced well using simulations of calculated lowest energy structures, clarify previous ambiguities in the assignment of vibrational bands, especially accidental coincidence of CO and N2O bands. The fragmentation dynamics exhibit the same unexpected behaviour as reported previously in which, once CO loss channels are energetically accessible, these dominate the fragmentation branching ratios, despite the much lower binding energy of N2O. We have investigated the dynamics computationally by considering anharmonic couplings between a relevant subset of normal modes involving both ligand stretch and intermolecular modes. Discrepancies between correlated and uncorrelated model fit to the ab initio potential energy curves are quantified using a Boltzmann sampled root mean squared deviation providing insight into efficiency of vibrational energy transfer between high frequency ligand stretches and the softer intermolecular modes which break during fragmentation

Clinical aspects of incorporating cord clamping into stabilisation of preterm infants

Fetal to neonatal transition is characterised by major pulmonary and haemodynamic changes occurring in a short period of time. In the international neonatal resuscitation guidelines, comprehensive recommendations are available on supporting pulmonary transition and delaying clamping of the cord in preterm infants. Recent experimental studies demonstrated that the pulmonary and haemodynamic transition are intimately linked, could influence each other and that the timing of umbilical cord clamping should be incorporated into the respiratory stabilisation. We reviewed the current knowledge on how to incorporate cord clamping into stabilisation of preterm infants and the physiological-based cord clamping (PBCC) approach, with the infant's transitional status as key determinant of timing of cord clamping. This approach could result in optimal timing of cord clamping and has the potential to reduce major morbidities and mortality in preterm infants