Draft genome sequence of the Coccolithovirus Emiliania huxleyi virus 203

The Coccolithoviridae are a recently discovered group of viruses that infect the marine coccolithophorid Emiliania huxleyi. Emiliania huxleyi virus 203 (EhV-203) has a 160- to 180-nm-diameter icosahedral structure and a genome of approximately 400 kbp, consisting of 464 coding sequences (CDSs). Here we describe the genomic features of EhV-203 together with a draft genome sequence and its annotation, highlighting the homology and heterogeneity of this genome in comparison with the EhV-86 reference genome.     

Evaluation of the viability and germination of tempisque [<i>Sideroxylon capiri</i> (A.DC.) Pittier Sapotaceae]

The tempisque (Sideroxylon capiri) is a tree native to Mexico used by the rural population for housing construction, poles and hedges, as fuel (wood) and also for fodder and ornamental purposes, among others. It is considered an endangered species. In order to contribute to its preservation and sustainable management, it was considered important to determine the proportion of viable seeds, the loss of viability due to storage period and the germination process by applying pregerminative treatments. We found that freshly collected seeds showed 100% viability, which decreased to 0% after 5 months of storage. According to the cumulative germination significant differences between treatments (p≤0.01) were found. It was observed that seeds can accelerate their time of germination with the previous exposure of 24 h in water at room temperature. The soaking treatment in water for 24 h at room temperature obtained final germination of 55%, while with the control 39% was reached. Soaking in hydrogen peroxide and scarification were the treatments with lower germination percentage (33 and 23%, respectively). To get a higher percentage of germinated seeds in a short time, it is necessary to give a soaking treatment in water for 24 h before sowing.     

Influence of habitat characteristics on small mammals in a Mexican high-altitude grassland

Small mammals in a high-altitude grassland area close to Mexico City were studied. Populations of 10 species were censused using live traps in 48 sample quadrats. Within each quadrat, vegetation characterization, including complete floristic listings, cover values for species and layers and values of habitat modification, were assessed. Habitats were described according to plant communities identified using ordination and classification methods. Nine different plant communities were obtained. Densities and abundance of all small mammal species were calculated for each of the habitats classified. Peromyscus alsloni was the most abundant species in all habitats, reaching maximum densities of 55 ha⁻¹ in pine forest with dense ground and herb layer. Peromyscus melanotis also occurred in all habitats but at lower densities (maximum 29 ha⁻¹). Reithrodontomys megalotis was found in all habitats except in tall dense grassland. Densities for this species were generally low (1-9 ha⁻¹) but reached 19 ha⁻¹ in short dense grassland. All other species were largely absent from 4–8 habitats and showed very low densities (0.75–4 ha⁻¹). The densities of the more abundant species were largely correlated with more open habitats and higher indices of habitat modification. Lower altitude grassland habitats have a greater abundance of small mammals and a higher species richness than the medium and higher altitude, physiognomically more complex habitats. Species richness was highest in tall pine-alder forest with a species-rich, dense herb layer and lowest in pine forest with dense ground and herb layers. Species richness was positively correlated with overall small mammal density.     

Hydrodynamic characterization of the DEAD-box RNA helicase DbpA

The Escherichia coli DEAD-box protein A (DbpA) belongs to the highly conserved superfamily-II of nucleic acid helicases that play key roles in RNA metabolism. A central question regarding helicase activity is whether the process of coupling ATP hydrolysis to nucleic acid unwinding requires an oligomeric form of the enzyme. We have investigated the structural and functional properties of DbpA by multi-angle laser light-scattering, size-exclusion chromatography, analytical ultracentrifugation, chemical cross-linking and hydrodynamic modeling. DbpA is monomeric in solution up to a concentration of 25 microM and over the temperature range of 4 degrees C to 22 degrees C. Binding of neither nucleotide (ATP or ADP) nor peptidyl transferase center (PTC) RNA, the presumed physiological RNA substrate, favor oligomerization. The hydrodynamic parameters were used together with hydrodynamic bead modeling and structural homology in conjunction with ab initio structure prediction methods to define plausible shapes of DbpA. Collectively, the results favor models where DbpA functions as an active monomer that possesses two distinct RNA binding sites, one in the helicase core domain and the other in the carboxyl-terminal domain that recognizes 23S rRNA and interacts specifically with hairpin 92 of the PTC.     

Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe

Genome sequencing of the 5,300-year-old mummy of the Tyrolean Iceman, found in 1991 on a glacier near the border of Italy and Austria, has yielded new insights into his origin and relationship to modern European populations. A key finding of that study was an apparent recent common ancestry with individuals from Sardinia, based largely on the Y chromosome haplogroup and common autosomal SNP variation. Here, we compiled and analyzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closely related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hypothesize that this genetic affinity of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographically widespread across Europe during the Neolithic, likely related to migrations and population expansions associated with the spread of agriculture.     

IgG4 can induce an M2-like phenotype in human monocyte-derived macrophages through FcγRI

Antibodies evoke cellular responses through the binding of their Fc region to Fc receptors, most of which contain immunoreceptor tyrosine-based activation motif domains and are thus considered “activating.” However, there is a growing appreciation of these receptors for their ability to deliver an inhibitory signal as well. We previously described one such phenomenon whereby interferon (IFN)γ signaling is inhibited by immune complex signaling through FcγRI. To understand the implications of this in the context of therapeutic antibodies, we assessed individual IgG subclasses to determine their ability to deliver this anti-inflammatory signal in monocyte-derived macrophages. Like IgG1, we found that IgG4 is fully capable of inhibiting IFNγ-mediated events. In addition, F(ab’)2 fragments that interfere with FcγRI signaling reversed this effect. For mAbs developed with either an IgG1 or an IgG4 constant region for indications where inflammation is undesirable, further examination of a potential Fc-dependent contribution to their mechanism of action is warranted.     

Modelling bird habitat suitability based on landscape parameters at different scales

Habitat suitability as characterized by the presence of a species and by reproductive success was modelled in relation to different parameters of landscape diversity at different scales. Parameters characterizing landscape pattern were determined for the UTM 10 km × 10 km cells covering the whole of Estonia and were correlated to the distribution of over 30 forest bird species. The landscape parameters include areas of lakes, mires and built-up areas, length of borders between different land cover units and length of selected line elements, share of different kinds of forest and peatland. The bird species are grouped by correlation into three major groups: (a) independent, (b) wetland preferring (with subgroups of those avoiding built-up areas and roads and those not) and (c) built-up area dependent (with subgroups depending on the importance of line elements). For selected predator species, nesting success was related to landscape parameters on a finer scale, using cells of 10 km². Land pattern was characterized by total length of line elements (streams, roads, borders, ecotones) and certain areal coverage (forest, mires, fields, built-up areas) within the cell. The impact of variations of food availability was linked to the relation. Possibilities for downscaling and upscaling of relations determined at different scales and areal coverage are discussed.     

Dynamics of biological invasions and pathways over time: a case study of a temperate coastal sea

Coastal and regional sea ecosystems suffer from several human-induced stressors, including human mediated bioinvasions. The Baltic Sea is generally considered to be susceptible to invasions by non-indigenous species (NIS). Out of the total of 132 NIS and cryptogenic species recorded, 59% are currently established in at least one country surrounding the Baltic Sea. On average, each country currently hosts 27 such species with 15% of the established species being found in at least 50% of the countries. Benthic macroinvertebrates dominate, both among those recorded (48%) and established (59%) species. Shipping, deliberate stocking and natural spread of NIS previously introduced to the North Sea are the main introduction pathways, with considerable dynamics over time. Amongst the pathways responsible for the currently established species, shipping and natural spread strongly dominate. Substantial uncertainty in the information on introduction pathways (except for deliberate releases) hampers detailed analyses and poses major challenges for management. Spatio-temporal variability in the invasion dynamics reflects both the spatial differences in the main hydrographic conditions of the Baltic Sea as well as the availability of introduction pathways. We conclude that the Baltic Sea cannot be considered as a uniform waterbody in terms of the established introduced species and at least two major regions with differing hydrographic conditions and introduction pathways can be clearly distinguished. Due to the importance of natural spread of NIS from the North Sea, regional cooperation in bioinvasion management should be enhanced in the future.