The Relativistic Jet Orientation and Host Galaxy of the Peculiar Blazar PKS 1413+135

PKS 1413+135 is one of the most peculiar blazars known. Its strange properties led to the hypothesis almost four decades ago that it is gravitationally lensed by a mass concentration associated with an intervening galaxy. It exhibits symmetric achromatic variability, a rare form of variability that has been attributed to gravitational milli-lensing. It has been classified as a BL Lac object, and is one of the rare objects in this class with a visible counterjet. BL Lac objects have jet axes aligned close to the line of sight. It has also been classified as a compact symmetric object-objects that have jet axes not aligned close to the line of sight. Intensive efforts to understand this blazar have hitherto failed to resolve even the questions of the orientation of the relativistic jet and the host galaxy. Answering these two questions is important because they challenge our understanding of jets in active galactic nuclei and the classification schemes we use to describe them. We show that the jet axis is aligned close to the line of sight and PKS 1413+135 is almost certainly not located in the apparent host galaxy, but is a background object in the redshift range 0.247 z z = 0.247 provides a natural host for the putative lens responsible for symmetric achromatic variability and is shown to be a Seyfert 2 galaxy. We also show that, as for the radio emission, a "multizone" model is needed to account for the high-energy emission

Integrated Analysis of Residue Coevolution and Protein Structure in ABC Transporters

Intraprotein side chain contacts can couple the evolutionary process of amino acid substitution at one position to that at another. This coupling, known as residue coevolution, may vary in strength. Conserved contacts thus not only define 3-dimensional protein structure, but also indicate which residue-residue interactions are crucial to a protein’s function. Therefore, prediction of strongly coevolving residue-pairs helps clarify molecular mechanisms underlying function. Previously, various coevolution detectors have been employed separately to predict these pairs purely from multiple sequence alignments, while disregarding available structural information. This study introduces an integrative framework that improves the accuracy of such predictions, relative to previous approaches, by combining multiple coevolution detectors and incorporating structural contact information. This framework is applied to the ABC-B and ABC-C transporter families, which include the drug exporter P-glycoprotein involved in multidrug resistance of cancer cells, as well as the CFTR chloride channel linked to cystic fibrosis disease. The predicted coevolving pairs are further analyzed based on conformational changes inferred from outward- and inward-facing transporter structures. The analysis suggests that some pairs coevolved to directly regulate conformational changes of the alternating-access transport mechanism, while others to stabilize rigid-body-like components of the protein structure. Moreover, some identified pairs correspond to residues previously implicated in cystic fibrosis

Plasmalogen enrichment in exosomes secreted by a nematode parasite versus those derived from its mouse host: implications for exosome stability and biology

Extracellular vesicles (EVs) mediate communication between cells and organisms across all 3 kingdoms of life. Several reports have demonstrated that EVs can transfer molecules between phylogenetically diverse species and can be used by parasites to alter the properties of the host environment. Whilst the concept of vesicle secretion and uptake is broad reaching, the molecular composition of these complexes is expected to be diverse based on the physiology and environmental niche of different organisms. Exosomes are one class of EVs originally defined based on their endocytic origin, as these derive from multivesicular bodies that then fuse with the plasma membrane releasing them into the extracellular environment. The term exosome has also been used to describe any small EVs recovered by high-speed ultracentrifugation, irrespective of origin since this is not always well characterized. Here, we use comparative global lipidomic analysis to examine the composition of EVs, which we term exosomes, that are secreted by the gastrointestinal nematode, Heligmosomoides polygyrus, in relation to exosomes secreted by cells of its murine host. Ultra-performance liquid chromatography – tandem mass spectrometry (UPLC-MS/MS) analysis reveals a 9- to 62-fold enrichment of plasmalogens, as well as other classes of ether glycerophospholipids, along with a relative lack of cholesterol and sphingomyelin (SM) in the nematode exosomes compared with those secreted by murine cells. Biophysical analyses of the membrane dynamics of these exosomes demonstrate increased rigidity in those from the nematode, and parallel studies with synthetic vesicles support a role of plasmalogens in stabilizing the membrane structure. These results suggest that nematodes can maintain exosome membrane structure and integrity through increased plasmalogens, compensating for diminished levels of other lipids, including cholesterol and SM. This work also illuminates the prevalence of plasmalogens in some EVs, which has not been widely reported and could have implications for the biochemical or immunomodulatory properties of EVs. Further comparative analyses such as those described here will shed light on diversity in the molecular properties of EVs that enable them to function in cross-species communication

Physical conditions and chemical abundances in photoionized nebulae from optical spectra

This chapter presents a review on the latest advances in the computation of physical conditions and chemical abundances of elements present in photoionized gas H II regions and planetary nebulae). The arrival of highly sensitive spectrographs attached to large telescopes and the development of more sophisticated and detailed atomic data calculations and ionization correction factors have helped to raise the number of ionic species studied in photoionized nebulae in the last years, as well as to reduce the uncertainties in the computed abundances. Special attention will be given to the detection of very faint lines such as heavy-element recombination lines of C, N and O in H II regions and planetary nebulae, and collisionally excited lines of neutron-capture elements (Z >30) in planetary nebulae.Comment: Book Chapter. 31 pages. 6 Figures. Accepted for publication in the book "Reviews in Frontiers of Modern Astrophysics: From Space Debris to Cosmology" (eds Kabath, Jones and Skarka; publisher Springer Nature) funded by the European Union Erasmus+ Strategic Partnership grant "Per Aspera Ad Astra Simul" 2017-1-CZ01-KA203-03556

Carbon and nitrogen cycling in intertidal sediments near Doel, Scheldt Estuary

Carbon and nitrogen cycling in intertidal mud flat sediments in the Scheldt Estuary was studied using measurements of carbon dioxide, methane and nitrous oxide emission rates and pore-water profiles of CO2, ammonium and nitrate. A comparison between chamber measured carbon dioxide fluxes and those based on CO2 pore-water gradients using Fick's First law indicates that apparent diffusion coefficients are 2 to 28 times higher than bulk sediment diffusion coefficients based on molecular diffusion. Seasonal changes in gaseous carbon fluxes or CO2 pore water concentrations cannot be used directly, or in a simple way, to determine seasonal rates of mineralization, because of marked seasonal changes in pore-water storage and exchange parameters.The annual amount of carbon delivered to the sediment is 42 mol m–2, of which about 42% becomes buried, the remaining being emitted as methane (7%) or carbon dioxide (50%). Each year about 2.6 mol N m–2 of particulate nitrogen reaches the sediment; 1.1 mol m–2 is buried and 1.6 mol m–2 is mineralized to ammonium. Only 0.42 mol m–2 yr–1 of the ammonium produced escapes from the sediments, the remaining being first nitrified (1.2 mol m–2 yr–1) and then denitrified (1.7 mol m–2 yr–1). Simple calculations indicate that intertidal sediments may account for about 14% and 30% of the total estuarine retention of nitrogen and carbon, respectively