Immunocytochemical localization of the neural-specific regulatory subunit of the type II cyclic AMP-dependent protein kinase to postsynaptic structures in the rat brain.

The cellular and subcellular distribution of a major cyclic AMP binding protein in the central nervous system, the neural-specific regulatory subunit of the type II cyclic AMP-dependent protein kinase (RII-B), was analyzed in rat brains with light and electron microscopic immunocytochemical methods. The distribution of the non-neural isoform of the regulatory subunit of the enzyme (RII-H) was also analyzed. It was found that RII-B immunoreactivity was predominantly localized to neurons whereas glial and endothelial cells were unlabeled. In the neurons the RII-B immunoreactivity occurred in the perikaryal cytoplasm and in the dendrites; there was no significant accumulation of immunoreaction product in nuclei, myelinated axons and axon terminals. Although immunoreactivity was never detected in axon terminals, it was characteristically associated with the postsynaptic densities and the surrounding non-synaptic sites in somata, dendrites and dendritic spines. The localization of RII-B antigenic sites did not show specificity to any type of neuron or synapse, but the amount of immunoreactivity varied. The distribution of RII-H immunoreactivity was similar to that of RII-B except that RII-H immunoreaction product was also observed in glial cells and occurred more frequently in myelinated axons. Our data confirm that RII-B is one of the major cyclic AMP binding proteins in neurons, and provide morphological support for the involvement of the type II cyclic AMP-dependent protein kinase in postsynaptic neural functions

T Cell Recognition of the Dominant I-Ak–Restricted Hen Egg Lysozyme Epitope: Critical Role for Asparagine Deamidation

Type-B T cells raised against the immunodominant peptide in hen egg lysozyme (HEL48–62) do not respond to whole lysozyme, and this has been thought to indicate that peptide can bind to l-Ak in different conformations. Here we demonstrate that such T cells recognize a deamidated form of the HEL peptide and not the native peptide. The sequence of the HEL epitope facilitates rapid and spontaneous deamidation when present as a free peptide or within a flexible domain. However, this deamidated epitope is not created within intact lysozyme, most likely because it resides in a highly structured part of the protein. These findings argue against the existence of multiple conformations of the same peptide–MHC complex and have important implications for the design of peptide-based vaccines. Furthermore, as the type-B T cells are known to selectively evade induction of tolerance when HEL is expressed as a transgene, these results suggest that recognition of posttranslationally modified self-antigen may play a role in autoimmunity

Fishing profiles of Danish seiners and bottom trawlers in relation to current EU management regulations

Danish seines and bottom trawls operate differently and have different catching processes. Both gears belong to the same legislative category in European fisheries, but different management strategies in other countries and criticism by fishers on grouping Danish seines and trawls together indicate disagreement on current gear classification. This study compared both gears in terms of their fishing characteristics and catches of commercial species based on 16 years of observer data. Danish seining is a specialised fishing method that targeted few species but with higher total catch rates than bottom trawlers. Bottom trawling is a more all-purpose fishing method that targets a larger number of species, and bottom trawlers use larger engines than Danish seiners. A generalised additive mixed model indicated that catch rates of flatfish are generally higher for Danish seines, and catch rates of roundfish species are higher fortrawlers. The results do not directly suggest a separation of the gears in terms of legislation as the quantities of fish below current minimum size were similar, but for example future survival studies may reach different conclusions. Additional factors were found to be important in determining catches of both gear

A high accuracy computed water line list

A computed list of H$_{2}$$^{16}$O infra-red transition frequencies and intensities is presented. The list, BT2, was produced using a discrete variable representation two-step approach for solving the rotation-vibration nuclear motions. It is the most complete water line list in existence, comprising over 500 million transitions (65% more than any other list) and it is also the most accurate (over 90% of all known experimental energy levels are within 0.3 cm$^{-1}$ of the BT2 values). Its accuracy has been confirmed by extensive testing against astronomical and laboratory data. The line list has been used to identify individual water lines in a variety of objects including: comets, sunspots, a brown dwarf and the nova-like object V838 Mon. Comparison of the observed intensities with those generated by BT2 enables physical values to be derived for these objects. The line list can also be used to provide an opacity for models of the atmospheres of M-dwarf stars and assign previously unknown water lines in laboratory spectra.Comment: 8 Pages, zero figures. Submitted to MNRAS. On line data at: ftp://cdsarc.u-strasbg.fr/cats/VI/11

Cruel to be kind but not cruel for cash : harm aversion in the dictator game

People regularly take prosocial actions, making individual sacrifices for the greater good. Similarly, people generally avoid causing harm to others. These twin desires to do good and avoid harm often align, but sometimes they can diverge, creating situations of moral conflict. Here, we examined this moral conflict using a modified dictator game. Participants chose how much money to allocate away from a recipient who was designated as an orphan, creating a sense of harm. This money was then reallocated to either the participant or a charity. People were strongly prosocial: they allocated more money away from the orphan for charity than for themselves. Furthermore, people left more money with the orphan when the harm was framed as a means (taking) than as a side effect (splitting). As is predicted by dual-process theories of moral decision making, response times were longer with the take action and were positively correlated with the amount taken from the orphan. We concluded that just as people take positive actions for the greater good, they are similarly more willing to cause harm when it benefits others rather than themselves

Practical guidelines and recent advances in the Itrax XRF core-scanning procedure

XRF core scanning has evolved to become a standard analytical technique for the rapid assessment of elemental, density and textural variations in a wide range of sediments and other materials, with applications ranging from palaeoceanography, paleoclimatology, geology, and environmental forensics to environmental protection. In general, scanning provides rapid, non-destructive acquisition of elemental and textural variations at sub-millimetre resolution for a wide range of materials. Numerous procedural adaptations have been developed for the growing number of applications, such as analyses of unconsolidated, water-rich sediments, powdered soil samples, or resin bags. Here, practical expertise and guidance from the Itrax community, gained over 15 years, is presented that should provide insights for new and experienced users

Structural correlations in bacterial metabolic networks

<p>Abstract</p> <p>Background</p> <p>Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the metabolic networks of 134 bacterial species with known phylogenetic relationships, and by studying a neutral model of metabolic network evolution.</p> <p>Results</p> <p>We consider the 'union-network' of 134 bacterial metabolisms, and also the union of two smaller subsets of closely related species. Each reaction-node is tagged with the number of organisms it belongs to, which we denote organism degree (OD), a key concept in our study. Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are also more likely to be connected to each other compared to a random OD relabelling based on their occurrence in the real data. This trend persists up to a distance of around five reactions. A simple growth model of metabolic networks is used to investigate the biochemical constraints put on metabolic-network evolution. Despite this seemingly drastic simplification, a 'union-network' of a collection of unrelated model networks, free of any selective pressure, still exhibit similar structural features as their bacterial counterpart.</p> <p>Conclusions</p> <p>The OD distribution quantifies topological properties of the evolutionary history of bacterial metabolic networks, and lends additional support to the importance of horizontal gene transfer during bacterial metabolic evolution where new reactions are attached at the periphery of the network. The neutral model of metabolic network growth can reproduce the main features of real networks, but we observe that the real networks contain a smaller common core, while they are more similar at the periphery of the network. This suggests that natural selection and biochemical correlations can act both to diversify and to narrow down metabolic evolution.</p

Inferring fish escape behaviour in trawls based on catch comparison data: Model development and evaluation based on data from Skagerrak, Denmark

During the fishing process, fish react to a trawl with a series of behaviours that often are species and size specific. Thus, a thorough understanding of fish behaviour in relation to fishing gear and a scientific understanding of the ability of different gear designs to utilize or stimulate various behavioural patterns during the catching process are essential for developing more efficient, selective, and environmentally friendly trawls. Although many behavioural studies using optical and acoustic observation systems have been conducted, harsh observation conditions on the fishing grounds often hamper the ability to directly observe fish behaviour in relation to fishing gear. As an alternative to optical and acoustic methods, we developed and applied a new mathematical model to catch data to extract detailed and quantitative information about species- and size-dependent escape behaviour in towed fishing gear such as trawls. We used catch comparison data collected with a twin trawl setup; the only difference between the two trawls was that a 12 m long upper section was replaced with 800 mm diamond meshes in one of them. We investigated the length-based escape behaviour of cod (Gadus morhua), haddock (Melanogrammus aeglefinus), saithe (Pollachius virens), witch flounder (Glyptocephalus cynoglossus), and lemon sole (Microstomus kitt) and quantified the extent to which behavioural responses set limits for the large mesh panel's selective efficiency. Around 85% of saithe, 80% of haddock, 44% of witch flounder, 55% of lemon sole, and 55% of cod (below 68 cm) contacted the large mesh panel and escaped. We also demonstrated the need to account for potential selectivity in the trawl body, as it can bias the assessment of length-based escape behaviour. Our indirect assessment of fish behaviour was in agreement with the direct observations made for the same species in a similar section of the trawl body reported in the literature