New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and Metagenomics

Rattus norvegicus (R. norvegicus) are ubiquitous and their presence has several effects on the human populations in our urban areas on a global scale. Both historically and presently, this close interaction has facilitated the dissemination of many pathogens to humans, making screening for potentially zoonotic and emerging viruses in rats highly relevant. We have investigated faecal samples from R. norvegicus collected from urban areas using a protocol based on metagenomic enrichment of circular DNA genomes and subsequent sequencing. We found a new type of papillomavirus, with a L1 region 82% identical to that of the known R. norvegicus Papillomavirus 2. Additionally, we found 20 different circular replication associated protein (Rep)-encoding single stranded DNA (CRESS-DNA) virus-like genomes, one of which has homology to the replication-associated gene of Beak and feather disease virus. Papillomaviruses are a group of viruses known for their carcinogenic potential, and although they are known to infect several different vertebrates, they are mainly studied and characterised in humans. CRESS-DNA viruses are found in many different environments and tissue types. Both papillomaviruses and CRESS-DNA viruses are known to have pathogenic potential and screening for novel and known viruses in R. norvegicus could help identify viruses with pathogenic potential.     

Longitudinal differentiation of the human Yq heterochromatin as revealed by the restriction enzyme TaqI

The restriction endonuclease TaqI cleaves DNA at TCGA sites which are very common in human satellite DNAs. However, this enzyme was not used successfully up to now to digest constitutive heterochromatin of human chromosomes, where those highly repetitive DNAs are preferentially located. In this work, we show that TaqI is able to cut and extract DNA from the major heterochromatic regions on chromosomes 1, 9, 15, and 16 which appear as unstained gaps. Yq heterochromatin displays moderate digestion along its entire length but a middle region can be distinguished which is usually more affected. Complete digestion of Yq heterochromatin can be achieved when this block has been previously undercondensed by treating cell cultures with the cytidine analog, 5-azacytidine. Thus, it may be deduced that some factors related to chromatin organization might be involved in the action of TaqI. These results come to reinforce previous data about heterogeneity of Yq heterochromatin, and allow us to subdivide it into three different regions according to their differential response to TaqI digestion.     

Relationship of different feeding groups of true bugs (Hemiptera: Heteroptera) with habitat and landscape features in Pannonic salt grasslands

Eastern European grasslands are still inhabited by a rich arthropod fauna, but the drivers and mechanisms influencing their communities have to be understood to ensure their future survival. Heteroptera communities were studied in 20 plot-pairs in Pannonic salt steppe–salt marsh mosaics in Hungary. The effects of vegetation characteristics, landscape diversity and the proportion of surrounding grasslands on the composition, species richness and abundance of different feeding groups of true bugs (carnivores, specialist and generalist herbivores) were examined using ordinations and mixed-effect models. We found distinct herbivorous assemblages corresponding to microtopography-driven differences in water regime and vegetation between steppe and marsh plots, but this pattern was less pronounced in carnivorous assemblages. A higher species richness of true bugs was found in the more diverse steppe vegetation than in the salt marsh vegetation, while the abundance pattern of true bugs was opposite. Landscape diversity had a positive effect on the species richness and abundance of generalist herbivores and carnivores. Our results suggested that generalist herbivores and carnivores appear to drive diversity patterns in the local landscape due to their high dispersal abilities and the broader range of resources they can utilize. Specialist herbivores strongly influence the local insect biomass in relation to the distribution and density of their host plants. The present study highlights the importance of both habitat and landscape diversity for local insect diversity in Pannonic salt grasslands and suggests that the main threats for arthropod diversity are those processes and activities that homogenize these areas.     

Assessment of biofilm formation by Scedosporium apiospermum,S. aurantiacum,S. minutisporum and Lomentospora prolificans

Reported herein is the ability of Scedosporium apiospermum, S. aurantiacum, S. minutisporum and Lomentospora prolificans conidia to adhere, differentiate into hyphae and form biofilms on both polystyrene and lung epithelial cells. To different degrees, all of the fungi adhered to polystyrene after 4 h, with a predominance of those with germinated conidia. Prolonged fungi–polystyrene contact resulted in the formation of a monolayer of intertwined mycelia, which was identified as a typical biofilm structure due to the presence of a viable mycelial biomass, extracellular matrix and enhanced antifungal resistance. Ultrastructural details were revealed by SEM and CLSM, showing the dense compaction of the mycelial biomass and the presence of channels within the organized biofilm. A similar biofilm structure was observed following the co-culture of each fungus with A549 cells, revealing a mycelial trap covering all of the lung epithelial monolayer. Collectively, these results highlight the potential for biofilm formation by these clinically relevant fungal pathogens.     

Changes in the acoustic behavior of resident bottlenose dolphins near operating vessels

Maritime traffic is an issue of major ecological concern, and vessel noise may be an important source of disturbance for coastal cetaceans. In the Sado estuary, Portugal, core habitat areas of a small resident population of bottlenose dolphins (Tursiops truncatus) overlap with routes of intense maritime traffic, which presents an opportunity to assess vocal responses of these dolphins to specific vessel noise sources. Field recordings of dolphin vocalizations were made from April to November 2011, using a calibrated system. Dolphin behavior and group size were recorded, as well as the operating boat condition (no boats or specific boat type) in a 1,000 m radius. Spectral analyses of vocalizations allowed the categorization and quantitative analysis of echolocation click trains and social calls, including whistles. Mean overall call rates decreased significantly in the presence of operating vessels. Creaks (fast click trains) were significantly reduced in the presence of ferry boats. Significant differences were also observed in the whistles' minimum, maximum, and start frequencies. These changes in call emission rates and temporary shifts in whistles characteristics may be a vocal response to the proximity of operating vessels, facilitating communication in this busy, noisy estuary.     

Effect of inhibitors on conformational changes in hen lysozyme around thermal transition point in solution and solid state

Carbon-13 NMR spectroscopy has been used to further document the interaction, at low and high temperatures, of N-acetylglucosamine and its short polymers with hen egg-white lysozyme. The results have been compared with the corresponding X-ray crystallographic data. Two domains, the active site and the hydrophobic box, have been found by NMR to undergo conformational rearrangement while X-ray crystallography only detected changes located in the active site. The extent of the modifications induced by inhibitor binding was proportional to the inhibitor size. The two techniques concurred to show that even in the presence of monosaccharide (N-acetylglucosamine), more than one subsite of the enzyme was occupied at high temperature, the binding at the C-site being the best defined. The thermal transition of lysozyme still occurred in solution when inhibitors were bound. However, in the solid state, crystallographic data showed that the transition was hindered.