Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation.

After domestication, during a process of widespread range extension, barley adapted to a broad spectrum of agricultural environments. To explore how the barley genome responded to the environmental challenges it encountered, we sequenced the exomes of a collection of 267 georeferenced landraces and wild accessions. A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in our data set.

Proceedings of the 2016 Childhood Arthritis and Rheumatology Research Alliance (CARRA) Scientific Meeting : Toronto, Canada. 14-17 April 2016.

P1 Serologic evidence of gut-driven systemic inflammation in juvenile idiopathic arthritis Lampros Fotis, Nur Shaikh, Kevin Baszis, Anthony French, Phillip Tarr P2 Oral health and anti-citrullinated peptide antibodies (ACPA) in juvenile idiopathic arthritis Sriharsha Grevich, Peggy Lee, Sarah Ringold, Brian Leroux, Hannah Leahey, Megan Yuasa, Jessica Foster, Jeremy Sokolove, Lauren Lahey, William Robinson, Joshua Newsom, Anne Stevens P3 Novel autoantigens for endothelial cell antibodies in pediatric rheumatic diseases identified by proteomics Rie Karasawa, Mayumi Tamaki, Megumi Tanaka, Toshiko Sato, Kazuo Yudoh, James N. Jarvis P4 Transcriptional profiling reveals monocyte signature associated with JIA patient poor response to methotrexate Halima Moncrieffe, Mark F. Bennett, Monica Tsoras, Lorie Luyrink, Huan Xu, Sampath Prahalad, Paula Morris, Jason Dare, Peter A.

Improved selectivity of mIBG uptake into neuroblastoma cells in vitro and in vivo by inhibition of organic cation transporter 3 uptake using clinically approved corticosteroids.

Introduction: Radiolabeled meta-iodobenzylguanidine (mIBG) is used for imaging and therapy of neuroblastoma as well as pheochromocytoma. However, non-tumorous tissues also incorporate mIBG mainly by organic cation transporters (OCTs). In this study, we tested different clinically approved corticosteroids as potential inhibitors of the OCT3-mediated uptake in vitro and in vivo, to achieve a more selective mIBG tumor uptake.

Giant photon bunching, superradiant pulse emission and excitation trapping in quantum-dot nanolasers.

Light is often characterized only by its classical properties, like intensity or coherence. When looking at its quantum properties, described by photon correlations, new information about the state of the matter generating the radiation can be revealed. In particular the difference between independent and entangled emitters, which is at the heart of quantum mechanics, can be made visible in the photon statistics of the emitted light.

Murine junctional adhesion molecules JAM-B and JAM-C mediate endothelial and stellate cell interactions during hepatic fibrosis.

Classical junctional adhesion molecules JAM-A, JAM-B and JAM-C influence vascular permeability, cell polarity as well as leukocyte recruitment and immigration into inflamed tissue. As the vasculature becomes remodelled in chronically injured, fibrotic livers we aimed to determine distribution and role of junctional adhesion molecules during this pathological process. Therefore, livers of naïve or carbon tetrachloride-treated mice were analyzed by immunohistochemistry to localize all 3 classical junctional adhesion molecules.

Quantum chaos and breaking of all anti-unitary symmetries in Rydberg excitons.

Symmetries are the underlying principles of fundamental interactions in nature. Chaos in a quantum system may emerge from breaking these symmetries. Compared to vacuum, crystals are attractive for studying quantum chaos, as they not only break spatial isotropy, but also lead to novel quasiparticles with modified interactions.

Non-alcoholic fatty liver disease (NAFLD) potentiates autoimmune hepatitis in the CYP2D6 mouse model.

Non-alcoholic fatty liver disease (NAFLD) and its more severe development non-alcoholic steatohepatitis (NASH) are increasing worldwide. In particular NASH, which is characterized by an active hepatic inflammation, has often severe consequences including progressive fibrosis, cirrhosis, and eventually hepatocellular carcinoma (HCC). Here we investigated how metabolic liver injury is influencing the pathogenesis of autoimmune hepatitis (AIH).

Band-Edge Exciton Fine Structure and Recombination Dynamics in InP/ZnS Colloidal Nanocrystals.

We report on a temperature-, time-, and spectrally resolved study of the photoluminescence of type-I InP/ZnS colloidal nanocrystals with varying core size. By studying the exciton recombination dynamics we assess the exciton fine structure in these systems. In addition to the typical bright-dark doublet, the photoluminescence stems from an upper bright state in spite of its large energy splitting (∼100 meV).

Building a global teledermatology collaboration.

Skin disease is common in low-resource countries and is associated with significant morbidity. The disease burden is often heightened by lack of access to adequate diagnosis and treatment. Teledermatology is a growing healthcare delivery modality that allows access to subspecialty care at a distance.

Sustainability in Biobanking: Model of Biobank Graz.

Research infrastructures remain the key for state-of-the-art and successful research. In the last few decades, biobanks have become increasingly important in this field through standardization of biospecimen processing, sample storage, and standardized data management. Research infrastructure in cohort studies and other sample collection activities are currently experiencing a lack of long-term funding.

Coherent Acoustic Phonons in Colloidal Semiconductor Nanocrystal Superlattices.

The phonon properties of films fabricated from colloidal semiconductor nanocrystals play a major role in thermal conductance and electron scattering, which govern the principles for building colloidal-based electronics and optics including thermoelectric devices with a high ZT factor. The key point in understanding the phonon properties is to obtain the strength of the elastic bonds formed by organic ligands connecting the individual nanocrystallites. In the case of very weak bonding, the ligands become the bottleneck for phonon transport between infinitively rigid nanocrystals.

Influence of the Nuclear Electric Quadrupolar Interaction on the Coherence Time of Hole and Electron Spins Confined in Semiconductor Quantum Dots.

The real-time spin dynamics and the spin noise spectra are calculated for p and n-charged quantum dots within an anisotropic central spin model extended by additional nuclear electric quadrupolar interactions and augmented by experimental data. Using realistic estimates for the distribution of coupling constants including an anisotropy parameter, we show that the characteristic long time scale is of the same order for electron and hole spins strongly determined by the quadrupolar interactions even though the analytical form of the spin decay differs significantly consistent with our measurements. The low frequency part of the electron spin noise spectrum is approximately 1/3 smaller than those for hole spins as a consequence of the spectral sum rule and the different spectral shapes.

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome.

Background: Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of large numbers of SNPs at low cost. However, both NGS data and their analysis are error-prone, which can lead to the generation of false positive (FP) SNPs. We explored the relationship between FP SNPs and seven factors involved in mapping-based variant calling - quality of the reference sequence, read length, choice of mapper and variant caller, mapping stringency and filtering of SNPs by read mapping quality and read depth.

Tablet: Visualizing Next-Generation Sequence Assemblies and Mappings.

This chapter is designed to be a practical guide to using Tablet for the visualization of next/second-generation (NGS) sequencing data. NGS data is being produced more frequently and in greater data volumes every year. As such, it is increasingly important to have tools which enable biologists and bioinformaticians to understand and gain key insights into their data.

Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana.

In Arabidopsis, various cell type-specific whole-genome expression analyses have been conducted. However, the vast majority of these were performed with cellular RNA from root tissues or other easily accessible cell types [1]. Nuclear RNA was neglected for a long time as not being representative for transcriptomic studies.

A simple and versatile cell wall staining protocol to study plant reproduction.

The optical brightener SCRI Renaissance 2200 can be used as versatile dye to study various aspects of plant reproduction by confocal laser scanning microscopy. The study of sexual reproduction of plants has traditionally relied on light microscopy in combination with a variety of staining methods. Transgenic lines that label specific cell or tissue types with fluorescent proteins in combination with confocal laser scanning microscopy were an important development to visualize gametophyte development, the fertilization process, and to follow cell differentiation in the early embryo.

Anti-CD3/Anti-CXCL10 Antibody Combination Therapy Induces a Persistent Remission of Type 1 Diabetes in Two Mouse Models.

Anti-CD3 therapy of type 1 diabetes results in a temporary halt of its pathogenesis but does not constitute a permanent cure. One problem is the reinfiltration of islets of Langerhans with regenerated, autoaggressive lymphocytes. We aimed at blocking such a reentry by neutralizing the key chemokine CXCL10.

Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance.

Combinations of histones carrying different covalent modifications are a major component of epigenetic variation. We have mapped nine modified histones in the barley seedling epigenome by chromatin immunoprecipitation next-generation sequencing (ChIP-seq). The chromosomal distributions of the modifications group them into four different classes, and members of a given class also tend to coincide at the local DNA level, suggesting that global distribution patterns reflect local epigenetic environments.

Observation of High Angular Momentum Excitons in Cuprous Oxide.

The recent observation of dipole-allowed P excitons up to principal quantum numbers of n=25 in cuprous oxide has given insight into exciton states with unprecedented spectral resolution. While so far the exciton description as a hydrogenlike complex has been fully adequate for cubic crystals, we demonstrate here distinct deviations: The breaking of rotational symmetry leads to mixing of high angular momentum F and H excitons with the P excitons so that they can be observed in absorption. The F excitons show a threefold splitting that depends systematically on n, in agreement with theoretical considerations.

Photon-Statistics Excitation Spectroscopy of a Quantum-Dot Micropillar Laser.

We introduce photon-statistics excitation spectroscopy and exemplarily apply it to a quantum-dot micropillar laser. Both the intensity and the photon number statistics of the emission from the micropillar show a strong dependence on the photon statistics of the light used for excitation of the sample. The results under coherent and pseudothermal excitation reveal that a description of the laser properties in terms of mean input photon numbers is not sufficient.

Markers of bone metabolism, serum leptin levels and bone mineral density in preterm babies.

The prospective study assessed the influence of serum leptin levels on markers of bone metabolism and bone mineral density in 2-year-old infants born preterm. A total of 57 randomized preterm Caucasian newborns (32nd-37th week of gestation) were included in the study. Bone metabolism markers were measured every 6 months.

Dissociating the Influence of Affective Word Content and Cognitive Processing Demands on the Late Positive Potential.

The late positive potential (LPP) elicited by affective stimuli in the event-related brain potential (ERP) is often assumed to be a member of the P3 family. The present study addresses the relationship of the LPP to the classic P3b in a published data set, using a non-parametric permutation test for topographical comparisons, and residue iteration decomposition to assess the temporal features of the LPP and the P3b by decomposing the ERP into several component clusters according to their latency variability. The experiment orthogonally manipulated arousal and valence of words, which were either read or judged for lexicality.

WHIRLY1 Functions in the Control of Responses to Nitrogen Deficiency But Not Aphid Infestation in Barley.

WHIRLY1 is largely targeted to plastids, where it is a major constituent of the nucleoids. To explore WHIRLY1 functions in barley (Hordeum vulgare), RNA interference-knockdown lines (W1-1, W1-7, and W1-9) that have very low levels of HvWHIRLY1 transcripts were characterized in plants grown under optimal and stress conditions. The WHIRLY1-1 (W1-1), W1-7, and W1-9 plants were phenotypically similar to the wild type but produced fewer tillers and seeds.