Multi-omics responses in tree swallow (\u3ci\u3eTachycineta bicolor\u3c/i\u3e) nestlings from the Maumee Area of Concern, Maumee River, Ohio

A multi-omics approach was utilized to identify altered biological responses and functions, and to prioritize contaminants to assess the risks of chemical mixtures in the Maumee Area of Concern (AOC), Maumee River, OH, USA. The Maumee AOC is designated by the United States Environmental Protection Agency as having significant beneficial use impairments, including degradation of fish and wildlife populations, bird or animal deformities or reproduction problems, and loss of fish and wildlife habitat. Tree swallow (Tachycineta bicolor) nestlings were collected at five sites along the Maumee River, which included wastewater treatment plants (WWTPs) and industrial land-use sites. Polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), polycyclic aromatic hydrocarbons (PAHs), polychlorinated dibenzo p dioxins and furans (PCDD/Fs), and chlorinated pesticide concentrations were elevated in Maumee tree swallows, relative to a remote reference site, Star Lake, WI, USA. Liver tissue was utilized for non-targeted transcriptome and targeted metabolome evaluation. A significantly differentially expressed gene cluster related to a downregulation in cell growth and cell cycle regulation was identified when comparing all Maumee River sites with the reference site. There was an upregulation of lipogenesis genes, such as PPAR signaling (HMGCS2, SLC22A5), biosynthesis of unsaturated fatty acids (FASN, SCD, ELOVL2, and FADS2), and higher lipogenesis related metabolites, such as docosapentaenoic acid (DPA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and arachidonic acid (AA) at two industrial land-use sites, Ironhead and Maumee, relative to WWTP sites (Perrysburg and SideCut), and the reference site. Toledo Water, in the vicinity of the other two industrial sites and also adjacent to a WWTP, showed a mix of signals between industrial land-use and WWTP land-use. PAHs, oxychlordane, and PBDEs were determined to be the most likely causes of the differentiation in biological responses, including de novo lipogenesis and biosynthesis of unsaturated fatty acids

SENSE: A comparison of photon detection efficiency and optical crosstalk of various SiPM devices

This paper describes a comparison of photon detection efficiency and optical crosstalk measurements performed by three partners: Geneva University, Catania Observatory and Nagoya University. The measurements were compared for three different SiPM devices with different active areas: from 9 $mm^2$ up to 93.6 $mm^2$ produced by Hamamatsu. The objective of this work is to establish the measurements and analysis procedures for calculating the main SiPM parameters and their precision. This work was done in the scope of SENSE project which aims to build roadmap for the last developments in field of sensors for low light level detection

Characterization of Polyphosphoesters by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

FT-ICR mass spectrometry, together with collision-induced dissociation and electron capture dissociation, has been used to characterize the polyphosphoester poly[1,4-bis(hydroxyethyl)terephthalate-alt-ethyloxyphosphate] and its degradation products. Three degradation pathways were elucidated: hydrolysis of the phosphate–[1,4-bis(hydroxyethyl)terephthalate]bonds; hydrolysis of the phosphate–ethoxy bonds; and hydrolysis of the ethyl–terephthalate bonds. The dominant degradation reactions were those that involved the phosphate groups. This work constitutes the first application of mass spectrometry to the characterization of polyphosphoesters and demonstrates the suitability of high mass accuracy FT-ICR mass spectrometry, with CID and ECD, for the structural analysis of polyphosphoesters and their degradation products

Whole proteome analyses on Ruminiclostridium cellulolyticum show a modulation of the cellulolysis machinery in response to cellulosic materials with subtle differences in chemical and structural properties

Lignocellulosic materials from municipal solid waste emerge as attractive resources for anaerobic digestion biorefinery. To increase the knowledge required for establishing efficient bioprocesses, dynamics of batch fermentation by the cellulolytic bacterium Ruminiclostridium cellulolyticum were compared using three cellulosic materials, paper handkerchief, cotton discs and Whatman filter paper. Fermentation of paper handkerchief occurred the fastest and resulted in a specific metabolic profile: it resulted in the lowest acetate-to-lactate and acetate-to-ethanol ratios. By shotgun proteomic analyses of paper handkerchief and Whatman paper incubations, 151 proteins with significantly different levels were detected, including 20 of the 65 cellulosomal components, 8 non-cellulosomal CAZymes and 44 distinct extracytoplasmic proteins. Consistent with the specific metabolic profile observed, many enzymes from the central carbon catabolic pathways had higher levels in paper handkerchief incubations. Among the quantified CAZymes and cellulosomal components, 10 endoglucanases mainly from the GH9 families and 7 other cellulosomal subunits had lower levels in paper handkerchief incubations. An in-depth characterization of the materials used showed that the lower levels of endoglucanases in paper handkerchief incubations could hypothetically result from its lower crystallinity index (50%) and degree of polymerization (970). By contrast, the higher hemicellulose rate in paper handkerchief (13.87%) did not result in the enhanced expression of enzyme with xylanase as primary activity, including enzymes from the xyl-doc cluster. It suggests the absence, in this material, of molecular structures that specifically lead to xylanase induction. The integrated approach developed in this work shows that subtle differences among cellulosic materials regarding chemical and structural characteristics have significant effects on expressed bacterial functions, in particular the cellulolysis machinery, resulting in different metabolic patterns and degradation dynamics.This work was supported by a grant [R2DS 2010-08] from Conseil Regional d'Ile-de-France through DIM R2DS programs (http://www.r2ds-ile-de-france.com/). Irstea (www.irstea.fr/) contributed to the funding of a PhD grant for the first author. The funders provided support in the form of salaries for author [NB], funding for consumables and laboratory equipment, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Omics Services provided support in the form of salaries for authors [VS, MD], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors [NB, VS, MD] are articulated in the 'author contributions' section.info:eu-repo/semantics/publishedVersio

Photoperiod Regulates Lean Mass Accretion, but Not Adiposity, in Growing F344 Rats Fed a High Fat Diet

yesIn this study the effects of photoperiod and diet, and their interaction, were examined for their effects on growth and body composition in juvenile F344 rats over a 4-week period. On long (16L:8D), relative to short (8L:16D), photoperiod food intake and growth rate were increased, but percentage adiposity remained constant (ca 3-4%). On a high fat diet (HFD), containing 22.8% fat (45% energy as fat), food intake was reduced, but energy intake increased on both photoperiods. This led to a small increase in adiposity (up to 10%) without overt change in body weight. These changes were also reflected in plasma leptin and lipid levels. Importantly while both lean and adipose tissue were strongly regulated by photoperiod on a chow diet, this regulation was lost for adipose, but not lean tissue, on HFD. This implies that a primary effect of photoperiod is the regulation of growth and lean mass accretion. Consistent with this both hypothalamic GHRH gene expression and serum IGF-1 levels were photoperiod dependent. As for other animals and humans, there was evidence of central hyposomatotropism in response to obesity, as GHRH gene expression was suppressed by the HFD. Gene expression of hypothalamic AgRP and CRH, but not NPY nor POMC, accorded with the energy balance status on long and short photoperiod. However, there was a general dissociation between plasma leptin levels and expression of these hypothalamic energy balance genes. Similarly there was no interaction between the HFD and photoperiod at the level of the genes involved in thyroid hormone metabolism (Dio2, Dio3, TSHβ or NMU), which are important mediators of the photoperiodic response. These data suggest that photoperiod and HFD influence body weight and body composition through independent mechanisms but in each case the role of the hypothalamic energy balance genes is not predictable based on their known function.Scottish Government (Rural and Environment Science and Analytical Services Division, http://www.scotland.gov.uk/), AWR LR LMT PJM and the BBSRC, (http://www.bbsrc.ac.uk/home/home.aspx, grant BB/K001043/1), AWR GH PJ

ATF2 COMMISSIONING

ATF2 is a final-focus test beam line that aims to focus the low-emittance beam from the ATF damping ring to a beam size of about 37 nm, and at the same time to demonstrate nm beam stability, using numerous advanced beam diagnostics and feedback tools. The construction has been finished at the end of 2008 and the beam commissioning of ATF2 has started in December of 2008. ATF2 is constructed and commissioned by ATF international collaborations with strong US, Asian and European participation