PIT-tagging Italian spined loach (Cobitis bilineata): Methodology,survival and behavioural effects

The Italian spined loach (Cobitis bilineata) is an elongated, small-sized (<12 cm) spined loach native to northern Italy, Slovenia and Croatia. As for loaches in general, little is known about the individual movements of this loach in nature. Passive integrated transponders (PIT-tags) are small (typically 7–32 mm), relatively cheap and allow tracking of individual fish movements and behaviour. A fundamental assumption in animal telemetry is that the performance of a tagged animal does not deviate substantially from its natural performance. Although PIT-tagged fish often display high survival and tag retention, the effect varies between species and contexts, and few studies have looked at behavioural effects of PIT-tagging. Here we demonstrate a PIT-tagging methodology for spined loaches, and compare survival, activity and provoked escape response (maximum swimming speed) between tagged and control fish. We also track tag retention in the tagged fish. Italian spined loaches tagged with 12 mm PIT-tags displayed high tag retention and no extra mortality, and no effects of tagging on activity or maximum swimming speed were observed. The tag-to-fish weight and length ratios in our study ranged from 2% to 5% and from 10% to 16%, respectively, and we conclude that PIT-tagging, within these ratios, appears suitable for Italian spined loach.     

Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb

DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be—and often has been—done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.     

Evidence for the conformation about the C(5′)-O(5′) bond of AMP complexed to AMP kinase: Substrate properties of a vinyl phosphonate analog of AMP

A vinyl phosphonate analog of adenosine 5′-phosphate (AMP) was synthesized in which the CH₂OP system of AMP is replaced by CHCHP. The V_max values of this analog relative to AMP were 0.7% with rabbit muscle AMP aminohydrolase, 13.4% with rabbit muscle AMP kinase, and 6.6% with pig muscle AMP kinase. The vinyl analog of ADP produced by the kinases was a substrate of rabbit muscle pyruvate kinase. These results, together with substrate specificity properties at the AMP sites of the enzymes indicate that the C(4′)-C(5′)-O(5′)-P system of AMP is of trans character during conversion of AMP to ADP by pig or rabbit AMP kinase.     

Expression of atrial natriuretic peptide in thymic macrophages after dexamethasone treatment of rats

Summary The rat thymus represents a site of synthesis of atrial natriuretic peptide (ANP); the immunosuppressor dexamethasone strikingly increases ANP-expression in this immune organ. The presented data suggest that this increase can be attributed to macrophages. By means of immunohistochemistry and Northern blot analysis these immune cells were found to express ANP-immunoreactivity as well as mRNA coding for ANP. In contrast, macrophages of control thymi displayed only weak ANP-immunoreactivity. Thus, ANP appears to be a constituent of rat thymic macrophages, and its synthesis in the thymus is strongly elevated by acute exposure of the animals to glucocorticoids.     

Dissecting the binding mechanism of the linker histone in live cells: an integrated FRAP analysis

The linker histone H1 has a fundamental role in DNA compaction. Although models for H1 binding generally involve the H1 C‐terminal tail and sites S1 and S2 within the H1 globular domain, there is debate about the importance of these binding regions and almost nothing is known about how they work together. Using a novel fluorescence recovery after photobleaching (FRAP) procedure, we have measured the affinities of these regions individually, in pairs, and in the full molecule to demonstrate for the first time that binding among several combinations is cooperative in live cells. Our analysis reveals two preferred H1 binding pathways and we find evidence for a novel conformational change required by both. These results paint a complex, highly dynamic picture of H1–chromatin binding, with a significant fraction of H1 molecules only partially bound in metastable states that can be readily competed against. We anticipate the methods we have developed here will be broadly applicable, particularly for deciphering the binding kinetics of other nuclear proteins that, similar to H1, interact with and modify chromatin.     

Mechanisms of suicidal erythrocyte death.

Erythrocyte injury such as osmotic shock, oxidative stress or energy depletion stimulates the formation of prostaglandin E2 through activation of cyclooxygenase which in turn activates a Ca2+ permeable cation channel. Increasing cytosolic Ca2+ concentrations activate Ca2+ sensitive K+ channels leading to hyperpolarization, subsequent loss of KCl and (further) cell shrinkage. Ca2+ further stimulates a scramblase shifting phosphatidylserine from the inner to the outer cell membrane. The scramblase is sensitized for the effects of Ca2+ by ceramide which is formed by a sphingomyelinase following several stressors including osmotic shock. The sphingomyelinase is activated by platelet activating factor PAF which is released by activation of phospholipase A2. Phosphatidylserine at the erythrocyte surface is recognised by macrophages which engulf and degrade the affected cells. Moreover, phosphatidylserine exposing erythrocytes may adhere to the vascular wall and thus interfere with microcirculation. Erythrocyte shrinkage and phosphatidylserine exposure ('eryptosis') mimic features of apoptosis in nucleated cells which however, involves several mechanisms lacking in erythrocytes. In kidney medulla, exposure time is usually too short to induce eryptosis despite high osmolarity. Beyond that high Cl- concentrations inhibit the cation channel and high urea concentrations the sphingomyelinase. Eryptosis is inhibited by erythropoietin which thus extends the life span of circulating erythrocytes. Several conditions trigger premature eryptosis thus favouring the development of anemia. On the other hand, eryptosis may be a mechanism of defective erythrocytes to escape hemolysis. Beyond their significance for erythrocyte survival and death the mechanisms involved in 'eryptosis' may similarly contribute to apoptosis of nucleated cells.     

Predicting in situ soil N2O emission using NOE algorithm and soil database

This paper presents a new algorithm, Nitrous Oxide Emission (NOE) for simulating the emission of the greenhouse gas N₂O from agricultural soils. N₂O fluxes are calculated as the result of production through denitrification and nitrification and reduction through the last step of denitrification. Actual denitrification and nitrification rates are calculated from biological parameters and soil water‐filled pore space, temperature and mineral nitrogen contents. New suggestions in NOE consisted in introducing (1) biological site‐specific parameters of soil N₂O reduction and (2) reduction of the N₂O produced through nitrification to N₂ through denitrification. This paper includes a database of 64 N₂O fluxes measured on the field scale with corresponding environmental parameters collected from five agricultural situations in France. This database was used to test the validity of this algorithm. Site per site comparison of simulated N₂O fluxes against observed data leads to mixed results. For 80% of the tested points, measured and simulated fluxes are in accordance whereas the others resulted in an important discrepancy. The origin of this discrepancy is discussed. On the other hand, mean annual fluxes measured on each site were strongly correlated to mean simulated annual fluxes. The biological site‐specific parameter of soil N₂O reduction introduced into NOE appeared particularly useful to discriminate the general level of N₂O emissions from site to site. Furthermore, the relevance of NOE was confirmed by comparing measured and simulated N₂O fluxes using some data from the US TRAGNET database. We suggest the use of NOE on a regional scale in order to predict mean annual N₂O emissions.     

Molecular phylogeny of Eois (Lepidoptera,Geometridae): evolution of wing patterns and host plant use in a species‐rich group of Neotropical moths

Strutzenberger, P., Brehm, G., Bodner, F. & Fiedler K. (2010). Molecular phylogeny of Eois (Lepidoptera, Geometridae): evolution of wing patterns and host plant use in a species‐rich group of Neotropical moths. —Zoologica Scripta, 39, 603–620. Eois is a pantropical genus of Geometridae moths with currently 250 valid described species, the majority of which occur in the Neotropics. Eois is a prominent component of Andean moth communities locally accounting for up to ～10% of geometrid individuals. We address the evolution of wing patterns and host plant use in Neotropical Eois and provide a preliminary assessment on the monophyly and biogeographic history of the entire genus as well as affinities within the subfamily Larentiinae. We applied Bayesian, maximum likelihood and maximum parsimony methods of phylogenetic reconstruction to a 142 taxon dataset of partial COI (1220 bp) and Ef1α (1066 bp) sequences resulting in the largest taxon set of geometrid moths analyzed in a molecular phylogenetic study so far. Monophyly of Eois was always strongly supported. Ten monophyletic clades were found with good support, seven of which have characteristic wing pattern phenotypes. Only one wing pattern type occurs in two clades. Trophic associations with representatives of the family Piperaceae occur in all 8 (of 9) Neotropical clades for which host information is available. Apart from feeding on Piper, at least two Eois species in Ecuador feed on Peperomia, and one on Manekia (all Piperaceae); two further species live on Hedyosmum (Chloranthaceae). Species feeding on Peperomia, Manekia and Hedyosmum are usually nested in Piper‐associated clades. Single records of associations with Gesneriaceae and Monimiaceae are scattered in otherwise Piperaceae‐associated clades. These patterns suggest multiple parallel host shifts away from Piper as ancestral food plant. Old World Eois were recovered as monophylum and sister to Neotropical Eois. Within the subfamily Larentiinae the genus Eois has previously been placed close to the tribe Eupitheciini, but this was not supported in our phylogenetic analyses.