LTR-Retrotransposons in R. exoculata and Other Crustaceans: The Outstanding Success of GalEa-Like Copia Elements

Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. They can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. LTR-retrotransposons have been reported in many diverse eukaryote species, describing a ubiquitous distribution. Given their abundance, diversity and their extended ranges in C-values, environment and life styles, crustaceans are a great taxon to investigate the genomic component of adaptation and its possible relationships with TEs. However, crustaceans have been greatly underrepresented in transposable element studies. Using both degenerate PCR and in silico approaches, we have identified 35 Copia and 46 Gypsy families in 15 and 18 crustacean species, respectively. In particular, we characterized several full-length elements from the shrimp Rimicaris exoculata that is listed as a model organism from hydrothermal vents. Phylogenic analyses show that Copia and Gypsy retrotransposons likely present two opposite dynamics within crustaceans. The Gypsy elements appear relatively frequent and diverse whereas Copia are much more homogeneous, as 29 of them belong to the single GalEa clade, and species- or lineage-dependent. Our results also support the hypothesis of the Copia retrotransposon scarcity in metazoans compared to Gypsy elements. In such a context, the GalEa-like elements present an outstanding wide distribution among eukaryotes, from fishes to red algae, and can be even highly predominant within a large taxon, such as Malacostraca. Their distribution among crustaceans suggests a dynamics that follows a “domino days spreading” branching process in which successive amplifications may interact positively.     

Making Sense of a New Transport System: An Ethnographic Study of the Cambridgeshire Guided Busway

An increase in public transport use has the potential to contribute to improving population health, and there is growing interest in innovative public transport systems. Yet how new public transport infrastructure is experienced and integrated (or not) into daily practice is little understood. We investigated how the Cambridgeshire Guided Busway, UK, was used and experienced in the weeks following its opening, using the method of participant observation (travelling on the busway and observing and talking to passengers) and drawing on Normalization Process Theory to interpret our data. Using excerpts of field notes to support our interpretations, we describe how the ease with which the new transport system could be integrated into existing daily routines was important in determining whether individuals would continue to use it. It emerged that there were two groups of passengers with different experiences and attitudes. Passengers who had previously travelled frequently on regular bus services did not perceive the new system to be an improvement; consequently, they were frustrated that it was differentiated from and not coherent with the regular system. In contrast, passengers who had previously travelled almost exclusively by car appraised the busway positively and perceived it to be a novel and superior form of travel. Our rich qualitative account highlights the varied and creative ways in which people learn to use new public transport and integrate it into their everyday lives. This has consequences for the introduction and promotion of future transport innovations. It is important to emphasise the novelty of new public transport, but also the ways in which its use can become ordinary and routine. Addressing these issues could help to promote uptake of other public transport interventions, which may contribute to increasing physical activity and improving population health.     

Territoriality of Giant Otter Groups in an Area with Seasonal Flooding

Territoriality carries costs and benefits, which are commonly affected by the spatial and temporal abundance and predictability of food, and by intruder pressure. Giant otters (Pteronura brasiliensis) live in groups that defend territories along river channels during the dry season using chemical signals, loud vocalizations and agonistic encounters. However, little is known about the territoriality of giant otters during the rainy season, when groups leave their dry season territories and follow fish dispersing into flooded areas. The objective of this study was to analyze long-term territoriality of giant otter groups in a seasonal environment. The linear extensions of the territories of 10 giant otter groups were determined based on locations of active dens, latrines and scent marks in each season. Some groups overlapped the limits of neighboring territories. The total territory extent of giant otters was correlated with group size in both seasons. The extent of exclusive territories of giant otter groups was negatively related to the number of adults present in adjacent groups. Territory fidelity ranged from 0 to 100% between seasons. Some groups maintained their territory for long periods, which demanded constant effort in marking and re-establishing their territories during the wet season. These results indicate that the defense capacity of groups had an important role in the maintenance of giant otter territories across seasons, which may also affect the reproductive success of alpha pairs.     

A revision and phylogenetic analysis of Stoiba Spaeth?1909 (Coleoptera,Chrysomelidae)

Stoiba Spaeth, 1909 is revised with a phylogenetic analysis of 38 adult morphological characters for nine Stoiba species and 11 outgroup species (Mesomphaliini, Ischyrosonychini, and Hemisphaerotini). Four Cuban species of Stoiba were not sampled. Parsimony analysis located the four most parsimonious trees. The strict consensus (CI=0.59, RI=0.78, Steps=83) resolved the monophyly of Stoiba. The monophyly of Stoiba is supported by pale yellow antennae, antennomere VII broader than its length, and rounded basal line of pronotum. An illustrated key to ten species of Stoiba is provided along with a distribution map of 11 species. Stoiba rufa Blake is synonymized with Stoiba swartzii (Thunberg) by a morphological comparison which includes female genitalia.     

A critical switch in the enzymatic properties of the Cid1 protein deciphered from its product-bound crystal structure

The addition of uridine nucleotide by the poly(U) polymerase (PUP) enzymes has a demonstrated impact on various classes of RNAs such as microRNAs (miRNAs), histone-encoding RNAs and messenger RNAs. Cid1 protein is a member of the PUP family. We solved the crystal structure of Cid1 in complex with non-hydrolyzable UMPNPP and a short dinucleotide compound ApU. These structures revealed new residues involved in substrate/product stabilization. In particular, one of the three catalytic aspartate residues explains the RNA dependence of its PUP activity. Moreover, other residues such as residue N165 or the β-trapdoor are shown to be critical for Cid1 activity. We finally suggest that the length and sequence of Cid1 substrate RNA influence the balance between Cid1''s processive and distributive activities. We propose that particular processes regulated by PUPs require the enzymes to switch between the two types of activity as shown for the miRNA biogenesis where PUPs can either promote DICER cleavage via short U-tail or trigger miRNA degradation by adding longer poly(U) tail. The enzymatic properties of these enzymes may be critical for determining their particular function in vivo.     

Elucidation of the mechanism involved in the regulation of protease production by immobilizedMyxococcus xanthus cells

Summary The mechanism involved in the positive effect of immobilization on protease production byMyxococcus xanthus was investigated. The results have shown that this phenomenon was not related to the difficulty encountered by the potential repressors to diffuse through the gel beads. The positive effect of immobilization on protease synthesis is the result of a different physiological state of the cells due to the stress caused by immobilization.     

Discovery and structure-guided drug design of inhibitors of 11β-hydroxysteroid-dehydrogenase type I based on a spiro-carboxamide scaffold

Spiro-carboxamides were identified as inhibitors of 11β-hydroxysteroid-dehydrogenase type 1 by high-throughput screening. Structure-based drug design was used to optimise the initial hit yielding a sub-nanomolar IC₅₀ inhibitor (0.5 nM) on human 11β-HSD1 with a high binding efficiency index (BEI of 32.7) which was selective against human 11β-HSD2 (selectivity ratio > 200000).