Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana

Scaffold/matrix attachment regions (S/MARs) are essential for structural organization of the chromatin within the nucleus and serve as anchors of chromatin loop domains. A significant fraction of genes in Arabidopsis thaliana contains intragenic S/MAR elements and a significant correlation of S/MAR presence and overall expression strength has been demonstrated. In this study, we undertook a genome scale analysis of expression level and spatiotemporal expression differences in correlation with the presence or absence of genic S/MAR elements. We demonstrate that genes containing intragenic S/MARs are prone to pronounced spatiotemporal expression regulation. This characteristic is found to be even more pronounced for transcription factor genes. Our observations illustrate the importance of S/MARs in transcriptional regulation and the role of chromatin structural characteristics for gene regulation. Our findings open new perspectives for the understanding of tissue- and organ-specific regulation of gene expression

Enhanced ozone strongly reduces carbon sink strength of adult beech (Fagus sylvatica) – Resume from the free-air fumigation study at Kranzberg Forest

Ground-level ozone (O3) has gained awareness as an agent of climate change. In this respect, key results are comprehended from a unique 8-year free-air O3-fumigation experiment, conducted on adult beech (Fagus sylvatica) at Kranzberg Forest (Germany). A novel canopy O3 exposure methodology was employed that allowed whole-tree assessment in situ under twice-ambient O3 levels. Elevated O3 significantly weakened the C sink strength of the tree–soil system as evidenced by lowered photosynthesis and 44% reduction in whole-stem growth, but increased soil respiration. Associated effects in leaves and roots at the gene, cell and organ level varied from year to year, with drought being a crucial determinant of O3 responsiveness. Regarding adult individuals of a late-successional tree species, empirical proof is provided first time in relation to recent modelling predictions that enhanced ground-level O3 can substantially mitigate the C sequestration of forests in view of climate change

Silicon Photomultiplier Research and Development Studies for the Large Size Telescope of the Cherenkov Telescope Array

The Cherenkov Telescope Array (CTA) is the the next generation facility of imaging atmospheric Cherenkov telescopes; two sites will cover both hemispheres. CTA will reach unprecedented sensitivity, energy and angular resolution in very-high-energy gamma-ray astronomy. Each CTA array will include four Large Size Telescopes (LSTs), designed to cover the low-energy range of the CTA sensitivity ($\sim$20 GeV to 200 GeV). In the baseline LST design, the focal-plane camera will be instrumented with 265 photodetector clusters; each will include seven photomultiplier tubes (PMTs), with an entrance window of 1.5 inches in diameter. The PMT design is based on mature and reliable technology. Recently, silicon photomultipliers (SiPMs) are emerging as a competitor. Currently, SiPMs have advantages (e.g. lower operating voltage and tolerance to high illumination levels) and disadvantages (e.g. higher capacitance and cross talk rates), but this technology is still young and rapidly evolving. SiPM technology has a strong potential to become superior to the PMT one in terms of photon detection efficiency and price per square mm of detector area. While the advantage of SiPMs has been proven for high-density, small size cameras, it is yet to be demonstrated for large area cameras such as the one of the LST. We are working to develop a SiPM-based module for the LST camera, in view of a possible camera upgrade. We will describe the solutions we are exploring in order to balance a competitive performance with a minimal impact on the overall LST camera design.Comment: 8 pages, 5 figures. In Proceedings of the 34th International Cosmic Ray Conference (ICRC2015), The Hague, The Netherlands. All CTA contributions at arXiv:1508.0589

Under fire-simultaneous volatilome and transcriptome analysis unravels fine-scale responses of tansy chemotypes to dual herbivore attack

BACKGROUND: Tansy plants (Tanacetum vulgare L.) are known for their high intraspecific chemical variation, especially of volatile organic compounds (VOC) from the terpenoid compound group. These VOCs are closely involved in plant-insect interactions and, when profiled, can be used to classify plants into groups known as chemotypes. Tansy chemotypes have been shown to influence plant-aphid interactions, however, to date no information is available on the response of different tansy chemotypes to simultaneous herbivory by more than one insect species. RESULTS: Using a multi-cuvette system, we investigated the responses of five tansy chemotypes to feeding by sucking and/or chewing herbivores (aphids and caterpillars; Metopeurum fuscoviride Stroyan and Spodoptera littoralis Boisduval). Herbivory by caterpillars following aphid infestation led to a plant chemotype-specific change in the patterns of terpenoids stored in trichome hairs and in VOC emissions. The transcriptomic analysis of a plant chemotype represents the first de novo assembly of a transcriptome in tansy and demonstrates priming effects of aphids on a subsequent herbivory. Overall, we show that the five chemotypes do not react in the same way to the two herbivores. As expected, we found that caterpillar feeding increased VOC emissions, however, a priori aphid infestation only led to a further increase in VOC emissions for some chemotypes. CONCLUSIONS: We were able to show that different chemotypes respond to the double herbivore attack in different ways, and that pre-treatment with aphids had a priming effect on plants when they were subsequently exposed to a chewing herbivore. If neighbouring chemotypes in a field population react differently to herbivory/dual herbivory, this could possibly have effects from the individual level to the group level. Individuals of some chemotypes may respond more efficiently to herbivory stress than others, and in a group environment these "louder" chemotypes may affect the local insect community, including the natural enemies of herbivores, and other neighbouring plants

The Liquid Argon Jet Trigger of the H1 Experiment at HERA

We report on a novel trigger for the liquid argon calorimeter which was installed in the H1 Experiment at HERA.This trigger, called the “Jet Trigger”, was running at level 1 and implemented a real-time cluster algorithm. Within only 800 ns, the Jet Trigger algorithm found local energy maxima in the calorimeter, summed their immediate neighbors, sorted the resulting jets by energy, and applied topological conditions for the final level 1 trigger decision. The Jet Trigger was in operation from the year 2006 until the end of the HERA running in the summer of 2007. With the Jet Trigger it was possible to substantially reduce the thresholds for triggering on electronsand jets, giving access to a largely extended phase space for physical observables which could not have been reached in H1 before. The concepts of the Jet Trigger may be an interesting upgrade option for the LHC experiments

An optically powered single-channel stimulation implant as test-system for chronic biocompatibility and biostability of miniaturized retinal vision prostheses

A microsystem based microimplant with an optically powered single-channel stimulator was designed and developed as test system for an epi-retinal vision implant. Biostability of the hybrid assembly and the encapsulation materials were evaluated in pilot experiments in chronic implantations in a cat animal model. The implant was fabricated on a flexible polyimide substrate with integrated platinum electrode, interconnection lines, and contact pads for hybrid integration of electronic components. The receiver part was realized with four photodiodes connected in series. A parylene C coating was deposited on the electronic components as insulation layer. Silicone rubber was used to encapsulate the electronics in the shape of an artificial intraocular lens to allow proper implantation in the eye. Pilot experiments showed the biostability of the encapsulation approach and full electric functionality of the microimplant to generate stimulation currents over the implantation period of three months in two cats. In one cat, electrical stimulation of the retina evoked neuronal responses in the visual cortex and indicated the feasibility of the system approach for chronic use

DEXP Values for S/MAR− Genes and as a Function of the Position of the S/MAR within S/MAR+ Genes

<p>The 5% confidence intervals are shown.</p

Median Expression Values of S/MAR− and S/MAR+ Genes in Different Organs, Root Tissues, and Flower Tissues

<p>MPSS data recorded in five different organs are shown (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 1) (A); for Affymetrix-based measurements (B–D), median values for five root tissues (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 2) (B), ten organs (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 4) (C), and five flower tissues (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 6) (D) are given. For MPSS-based experiments (A), tpm are indicated; for experiments based on the Affymetrix platform (B–D), Affymetrix expression values are plotted. The 5% confidence intervals calculated using bootstrap set for all values are shown.</p

DEXP Values for S/MAR+ and S/MAR− TF Genes for Different Datasets

<p>The 5% confidence intervals for all values are shown.</p