The response to forced decompression in six species of Pacific rockfish

Pacific rockfish experience high discard mortality when captured owing to a condition called barotrauma,which is caused by the change in pressure during capture. This condition appears to be species specific at the macroscopic level; however, little is known about the microscopic tissue-level effects of barotrauma. Determining whether tissue-level injuries are also species specific or influenced by factors such as life history and phylogenetic relatedness can improve our management of discard mortality. We evaluated the responses of six species of Pacific rockfish (black rockfish Sebastes melanops, blue rockfish S. mystinus, yellowtail rockfish S. flavidus, quillback rockfish S. maliger, canary rockfish S. pinniger, and yelloweye rockfish S. ruberrimus) captured from varying depths to forced decompression at the histological level (heart ventricle, rete mirabile, head kidney, liver, gill, and eye) as well as the macroscopic level. At the macroscopic level we focused on injuries caused by barotrauma, namely, everted esophaguses, exophthalmia, ocular emphysema, and ruptured swim bladders. Yellowtail and quillback rockfish experienced the fewest macroscopic injuries. Depth of capture influenced the presence of exophthalmia in quillback rockfish and ocular emphysema in quillback and yelloweye rockfish. Tissue injuries as a result of forced decompression included emphysema in the heart ventricle, emboli in the vessels of the rete mirabile, and emboli in the vessels of the head kidney. No injuries were observed at the histological level in the liver, gill, or eye owing to barotrauma. We could not detect a difference in the tissue-level response to barotrauma among the six species, suggesting that all species are susceptible to high internal gas pressure during forced decompression

Molecular architecture of Streptococcus pneumoniae surface thioredoxin-fold lipoproteins crucial for extracellular oxidative stress resistance and maintenance of virulence.

19 pags, 8 figs, tabsThe respiratory pathogen Streptococcus pneumoniae has evolved efficient mechanisms to resist oxidative stress conditions and to displace other bacteria in the nasopharynx. Here we character ize at physiological, functional and structural levels two novel surface-exposed thioredoxin-family lipoproteins, Etrx1 and Etrx2. The impact of both Etrx proteins and their r edox partner methionine sulfoxide reductase SpMsrAB2 on pneumococcal pathogenesis was assessed in mouse virulence studies and phagocytosis assays. The results demonstrate that loss of function of either both Etrx proteins or SpMsrAB2 dramatically attenuated pneumococcal virulence in the acute mouse pneumonia model and that Etrx proteins compensate each other. The deficiency of Etrx proteins or SpMsrAB2 further enhanced bacterial uptake by macrophages, and accelerated pneumococcal killing by H2O2 or free methionine sulfoxides (MetSO). Moreover, the absence of both Etrx redox pathways provokes an accumulation of oxidized SpMsrAB2 in vivo. Taken together our results reveal insights into the role of two extracellular electron pathways required for reduction of SpMsrAB2 and surface-exposed MetSO. Identification of this system and its target proteins paves the w ay for the design of novel a ntimicrobialsThe authors thank the PXIII beamline at SLS and the ESRF beamline ID14‐1 for access to synchrotron radiation. We are also grateful to Kristine Sievert‐Giermann, Nadine Gotzmann and Melanie Skibbe (Department of Genetics, University of Greifswald, Germany) for technical assistance. This work was supported by grants from the Deutsche Forschungsgemeinschaft DFG HA3125/4‐2 (to S.H.), DFG AN746/3‐1 (to H.A.), BFU2011‐25326 and S2010/BMD‐2457 (to J.A.H.) and EU FP7 CAREPNEUMO Grant EU‐CP223111 from the European Union (to J.A.H. and S.H.

Identification of biomarkers indicative of barotrauma and recovery in black rockfish Sebastes melanops

A Sebastes-specific complementary DNA (cDNA) microarray was developed to identify potential biomarkers involved in the capture stress and recovery of Sebastes species if they are assisted in returning to their original depth of capture following barotrauma. Black rockfish Sebastes melanops were exposed to simulated decompression from 450 kPa (c. 35 m depth) (which resulted in barotrauma) and subsequent recompression. Sebastes melanops were sampled for liver tissue at days 3, 15 and 31 post-barotrauma. Potential candidate genes were identified from the microarray and then quantitative real-time PCR (qrt-PCR) was used to validate expression levels in biological replicates. Six potential biomarkers associated with the innate immune system were identified that were up-regulated in liver tissue at 3 days post-barotrauma: complement C1q-like protein 2, complement component C3, complement regulatory plasma protein, serum amyloid A-5, c-type lysozyme and hepcidin precursor type I. In addition, complement c1q was correlated to the presence of a ruptured swimbladder, providing further support that this gene may be a good biomarker of injury and recovery. Immune genes were no longer up-regulated at day 31 post-barotrauma, a good indication of recovery in S. melanops.Keywords: microarray, gene expression, non-model organism, fis

Recovery potential of black rockfish, Sebastes melanops Girard, recompressed following barotrauma

Overfished species of rockfish, Sebastes spp., from the Northeast Pacific experience high bycatch mortality because of ‘barotrauma’, a condition induced from the rapid change in pressure during capture. Field experiments show that it may be possible for rockfish to recover from barotrauma if quickly recompressed; however, no work has followed the physiological recovery of rockfish after recompression or determined whether it is possible for rockfish to survive barotrauma in the long term. Barotrauma was induced in adult black rockfish, Sebastes melanops Girard, from a simulated depth of 35 m, followed by recompression. Blood and selected tissues (eye, heart ventricle, head kidney, liver, rete mirabile and gonad) were sampled at days 3, 15 and 31 post-recompression to evaluate the tissue- and physiologic-level response during recovery. No mortality from barotrauma occurred during the experiments, and feeding resumed in 80% of both treatment and control fish. The primary injury in treatment fish was the presence of a ruptured swimbladder and/or a ruptured tunica externa (outer layer of swimbladder), which was slow to heal. Blood plasma was analysed for glucose, sodium, chloride, potassium, calcium, phosphorus, insulin-like growth factor-1 and cortisol. Plasma analyses indicated no strong effects because of barotrauma, suggesting overall handling stress outweighed any effect from barotrauma. Rockfish with ruptured swimbladders may face compromised competency in the wild; however, it appears the majority of black rockfish decompressed from 35 m have a high potential for recovery if recompressed immediately after capture. This research suggests recompression could be a valuable bycatch mortality reduction tool for rockfish in recreational fisheries.Keywords: recompression, barotrauma, histology, rockfish, decompressio

Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions

During development, signaling networks control the formation of multicellular patterns. To what extent quantitative fluctuations in these complex networks may affect multicellular phenotype remains unclear. Here, we describe a computational approach to predict and analyze the phenotypic diversity that is accessible to a developmental signaling network. Applying this framework to vulval development in C. elegans, we demonstrate that quantitative changes in the regulatory network can render ~500 multicellular phenotypes. This phenotypic capacity is an order-of-magnitude below the theoretical upper limit for this system but yet is large enough to demonstrate that the system is not restricted to a select few outcomes. Using metrics to gauge the robustness of these phenotypes to parameter perturbations, we identify a select subset of novel phenotypes that are the most promising for experimental validation. In addition, our model calculations provide a layout of these phenotypes in network parameter space. Analyzing this landscape of multicellular phenotypes yielded two significant insights. First, we show that experimentally well-established mutant phenotypes may be rendered using non-canonical network perturbations. Second, we show that the predicted multicellular patterns include not only those observed in C. elegans, but also those occurring exclusively in other species of the Caenorhabditis genus. This result demonstrates that quantitative diversification of a common regulatory network is indeed demonstrably sufficient to generate the phenotypic differences observed across three major species within the Caenorhabditis genus. Using our computational framework, we systematically identify the quantitative changes that may have occurred in the regulatory network during the evolution of these species. Our model predictions show that significant phenotypic diversity may be sampled through quantitative variations in the regulatory network without overhauling the core network architecture. Furthermore, by comparing the predicted landscape of phenotypes to multicellular patterns that have been experimentally observed across multiple species, we systematically trace the quantitative regulatory changes that may have occurred during the evolution of the Caenorhabditis genus

Ion acoustic wave experiments in a high school plasma physics laboratory

We describe a successful alliance between a university and several high schools. The alliance is centered on a laboratory experiment constructed by students and faculty. The experiment involves sophisticated concepts and equipment not readily available in high schools. Much of the experiment is directly related to the science and mathematics learned in high school, with opportunities to extend their understanding by applying it to a research experience. The experiment is in plasma physics, but a similar alliance can be implemented in any area of science. Although the number of high school students affected by any one alliance is small, the impact is potentially large in the scientific life of a participating student or teacher

A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions.

Data-independent acquisition mass spectrometry promises higher performance in terms of quantification and reproducibility compared to data-dependent acquisition mass spectrometry methods. To enable high-accuracy quantification of Staphylococcus aureus proteins, we have developed a global ion library for data-independent acquisition approaches employing high-resolution time of flight or Orbitrap instruments for this human pathogen. We applied this ion library resource to investigate the time-resolved adaptation of S. aureus to the intracellular niche in human bronchial epithelial cells and in a murine pneumonia model. In epithelial cells, abundance changes for more than 400 S. aureus proteins were quantified, revealing, e.g., the precise temporal regulation of the SigB-dependent stress response and differential regulation of translation, fermentation, and amino acid biosynthesis. Using an in vivo murine pneumonia model, our data-independent acquisition quantification analysis revealed for the first time the in vivo proteome adaptation of S. aureus. From approximately 2.15 × 1

The Proteolipid Protein Promoter Drives Expression outside of the Oligodendrocyte Lineage during Embryonic and Early Postnatal Development

The proteolipid protein (Plp) gene promoter is responsible for driving expression of one of the major components of myelin – PLP and its splice variant DM-20. Both products are classically thought to express predominantly in oligodendrocytes. However, accumulating evidence suggests Plp expression is more widespread than previously thought. In an attempt to create a mouse model for inducing oligodendrocyte-specific gene deletions, we have generated transgenic mice expressing a Cre recombinase cDNA under control of the mouse Plp promoter. We demonstrate Plp promoter driven Cre expression is restricted predominantly to mature oligodendrocytes of the central nervous system (CNS) at postnatal day 28. However, crosses into the Rosa26LacZ and mT/mG reporter mouse lines reveal robust and widespread Cre activity in neuronal tissues at E15.5 and E10.5 that is not strictly oligodendrocyte lineage specific. By P28, all CNS tissues examined displayed high levels of reporter gene expression well outside of defined white matter zones. Importantly, our study reinforces the emerging idea that Plp promoter activity is not restricted to the myelinating cell lineage, but rather, has widespread activity both during embryonic and early postnatal development in the CNS. Specificity of the promoter to the oligodendrocyte cell lineage, as shown through the use of a tamoxifen inducible Plp-CreERt line, occurs only at later postnatal stages. Understanding the temporal shift in Plp driven expression is of consequence when designing experimental models to study oligodendrocyte biology

Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC

The uncertainty on the calorimeter energy response to jets of particles is derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the calorimeter response to single isolated charged hadrons is measured and compared to the Monte Carlo simulation using proton-proton collisions at centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009 and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter response to specific types of particles (positively and negatively charged pions, protons, and anti-protons) is measured and compared to the Monte Carlo predictions. Finally, the jet energy scale uncertainty is determined by propagating the response uncertainty for single charged and neutral particles to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3% for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table, submitted to European Physical Journal

Expected Performance of the ATLAS Experiment - Detector, Trigger and Physics

A detailed study is presented of the expected performance of the ATLAS detector. The reconstruction of tracks, leptons, photons, missing energy and jets is investigated, together with the performance of b-tagging and the trigger. The physics potential for a variety of interesting physics processes, within the Standard Model and beyond, is examined. The study comprises a series of notes based on simulations of the detector and physics processes, with particular emphasis given to the data expected from the first years of operation of the LHC at CERN