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Selection of reference genes for gene expression analysis by real-time qPCR in avian cells infected with infectious bronchitis virus.

Infectious bronchitis virus (IBV) causes infectious bronchitis in poultry, a respiratory disease that is a source of major economic loss to the poultry industry. Detection and the study of the molecular pathogenesis of the virus often involve the use of real-time quantitative PCR assays (qPCR). To account for error within the experiments, the levels of target gene transcription are normalized to that of suitable reference genes. Despite publication of the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines in 2009, single un-tested reference genes are often used for normalization of qPCR assays in avian research studies. Here, we use the geNorm algorithm to identify suitable reference genes in different avian cell types during infection with apathogenic and pathogenic strains of IBV. We discuss the importance of selecting an appropriate experimental sample subset for geNorm analysis, and show the effect that this selection can have on resultant reference gene selection. The effects of inappropriate normalization on the transcription pattern of a cellular signalling gene, AKT1, and the interferon-inducible, MX1, were studied. We identify the possibility of the misinterpretation of qPCR data when an inappropriate normalization strategy is employed. This is most notable when measuring the transcription of AKT1, where changes are minimal during infection

Emergence of chaotic scattering in ultracold Er and Dy

We show that for ultracold magnetic lanthanide atoms chaotic scattering emerges due to a combination of anisotropic interaction potentials and Zeeman coupling under an external magnetic field. This scattering is studied in a collaborative experimental and theoretical effort for both dysprosium and erbium. We present extensive atom-loss measurements of their dense magnetic Feshbach resonance spectra, analyze their statistical properties, and compare to predictions from a random-matrix-theory inspired model. Furthermore, theoretical coupled-channels simulations of the anisotropic molecular Hamiltonian at zero magnetic field show that weakly-bound, near threshold diatomic levels form overlapping, uncoupled chaotic series that when combined are randomly distributed. The Zeeman interaction shifts and couples these levels, leading to a Feshbach spectrum of zero-energy bound states with nearest-neighbor spacings that changes from randomly to chaotically distributed for increasing magnetic field. Finally, we show that the extreme temperature sensitivity of a small, but sizeable fraction of the resonances in the Dy and Er atom-loss spectra is due to resonant non-zero partial-wave collisions. Our threshold analysis for these resonances indicates a large collision-energy dependence of the three-body recombination rate

Phosphorylation of RyR2 Ser‐2814 by CaMKII mediates β1-adrenergic stress induced Ca 2+ -leak from the sarcoplasmic reticulum

Adrenergic stimulation, while being the central mechanism of cardiac positive inotropy, is a universally acknowledged inductor of undesirable sarcoplasmic reticulum (SR) Ca2+ leak. However, the exact mechanisms for this remained unspecified so far. This study shows that Ca2+/calmodulin-dependent protein kinase II (CaMKII)-specific phosphorylation of ryanodine receptor type 2 at Ser-2814 is the pivotal mechanism by which SR Ca2+ leak develops downstream of β1-adrenergic stress by increase of the leak/load relationship. Cardiomyocytes with a Ser-2814 phosphoresistant mutation (S2814A) were protected from isoproterenol-induced SR Ca2+ leak and consequently displayed improved postrest potentiation of systolic Ca2+ release under adrenergic stress compared to littermate wild-type cells

Aridity drives clinal patterns in leaf traits and responsiveness to precipitation in a broadly distributed Australian tree species

Aridity shapes species distributions and plant growth and function worldwide. Yet, plant traits often show complex relationships with aridity, challenging our understanding of aridity as a driver of evolutionary adaptation. We grew nine genotypes of Eucalyptus camaldulensis subsp. camaldulensis sourced from an aridity gradient together in the field for ~650 days under low and high precipitation treatments. Eucalyptus camaldulesis is considered a phreatophyte (deep-rooted species that utilizes groundwater), so we hypothesized that genotypes from more arid environments would show lower aboveground productivity, higher leaf gas-exchange rates, and greater tolerance/avoidance of dry surface soils (indicated by lower responsiveness) than genotypes from less arid environments. Aridity predicted genotype responses to precipitation, with more arid genotypes showing lower responsiveness to reduced precipitation and dry surface conditions than less arid genotypes. Under low precipitation, genotype net photosynthesis and stomatal conductance increased with home-climate aridity. Across treatments, genotype intrinsic water-use efficiency and osmotic potential declined with increasing aridity while photosynthetic capacity (Rubisco carboxylation and RuBP regeneration) increased with aridity. The observed clinal patterns indicate that E. camaldulensis genotypes from extremely arid environments possess a unique strategy defined by lower responsiveness to dry surface soils, low water-use efficiency, and high photosynthetic capacity. This strategy could be underpinned by deep rooting and could be adaptive under arid conditions where heat avoidance is critical and water demand is high

Inactivation of Fgf3 and Fgf4 within the Fgf3/Fgf4/Fgf15 gene cluster reveals their redundant requirement for mouse inner ear induction and embryonic survival

[Background]: Fibroblast growth factors (Fgfs) are required for survival and organ formation during embryogenesis. Fgfs often execute their functions redundantly. Previous analysis of Fgf3 mutants revealed effects on inner ear formation and embryonic survival with incomplete penetrance. [Results]: Here, we show that presence of a neomycin resistance gene (neo) replacing the Fgf3 coding region leads to reduced survival during embryogenesis and an increased penetrance of inner ear defects. Fgf3neo/neo mutants showed reduced expression of Fgf4, which is positioned in close proximity to the Fgf3 locus in the mouse genome. Conditional inactivation of Fgf4 during inner ear development on a Fgf3 null background using Fgf3/4 cis mice revealed a redundant requirement between these Fgfs during otic placode induction. In contrast, inactivation of Fgf3 and Fgf4 in the pharyngeal region where both Fgfs are also co-expressed using a Foxg1-Cre driver did not affect development of the pharyngeal arches. However, these mutants showed reduced perinatal survival. [Conclusions]: These results highlight the importance of Fgf signaling during development. In particular, different members of the Fgf family act redundantly to guarantee inner ear formation and embryonic survival.Consejería de Educación, Junta de Castilla y León, Grant/Award Number: CSI143P20; Programa Estratégico Instituto de Biología y Genética Molecular (IBGM), Escalera de Excelencia, Junta de Castilla y León, Grant/Award Numbers: CCVC8485, CLU-2019-02; MEC, Grant/Award Number: BFU2004-00860/BF

BrainTrap: a database of 3D protein expression patterns in the Drosophila brain

Protein-trap strains of Drosophila melanogaster provide a very useful tool for examining the 3D-expression patterns of proteins and purification of protein complexes. Here we present BrainTrap, available at http://fruitfly.inf.ed.ac.uk/braintrap, an online database of 3D confocal datasets showing reporter gene expression and protein localization in the adult brain of Drosophila. Full size images throughout the volume of the entire brain can be viewed interactively in a web browser. The database includes searchable annotations linked to the FlyBase Drosophila anatomy ontology. Anatomical search criteria can be specified using automatic completion and a hierarchical browser for the ontology. The provenance of all annotation is retained and the location where the annotator made the conclusion can be highlighted

Quantum Statistics of Surface Plasmon Polaritons in Metallic Stripe Waveguides

Single surface plasmon polaritons are excited using photons generated via spontaneous parametric down-conversion. The mean excitation rates, intensity correlations and Fock state populations are studied. The observed dependence of the second order coherence in our experiment is consistent with a linear uncorrelated Markovian environment in the quantum regime. Our results provide important information about the effect of loss for assessing the potential of plasmonic waveguides for future nanophotonic circuitry in the quantum regime.Comment: 21 pages, 6 figures, published in Nano Letters, publication date (web): March 27 (2012