Development of a cellular assay system to study the genome replication of high- and low-risk mucosal and cutaneous human papillomaviruses

We found that recircularized high-risk (type 16 and 18) and low-risk mucosal (type 6b and 11) and cutaneous (type 5 and 8) human papillomavirus (HPV) genomes replicate readily when delivered into U2OS cells by electroporation. The replication efficiency is dependent on the amount of input HPV DNA and can be followed for more than 3 weeks in proliferating cell culture without selection. Cotransfection of recircularized HPV genomes with a linear G418 resistance marker plasmid has allowed subcloning of cell lines, which, in a majority of cases, carry multicopy episomal HPV DNA. Analysis of the HPV DNA status in these established cell lines showed that HPV genomes exist in these cells as stable extrachromosomal oligomers. When the cell lines were cultivated as confluent cultures, a 3- to 10-fold amplification of the HPV genomes per cell was induced. Two-dimensional (2D) agarose gel electrophoresis confirmed amplification of mono- and oligomeric HPV genomes in these confluent cell cultures. Amplification occurred as a result of the initiation of semiconservative two-dimensional replication from one active origin in the HPV oligomer. Our data suggest that the system described here might be a valuable, cost-effective, and efficient tool for use in HPV DNA replication studies, as well as for the design of cell-based assays to identify potential inhibitors of all stages of HPV genome replication.     

Variable expression of lineage regulators in differentiated stromal cells indicates distinct mechanisms of differentiation towards common cell fate

Mesenchymal stem cells (MSCs) possess a multi-lineage differentiation capacity that makes them important players in the field of regenerative medicine. MSC populations derived from different tissues or donors have been shown to exhibit variable gene expression patterns. Further, it is widely acknowledged that MSC isolates are heterogeneous mixtures of cells at different developmental stages. However, the heterogeneity of expression of lineage regulators has not been linked to differentiation potential of different MSC populations towards mesenchymal lineages. Here, we analyzed variation of expression of differentiation markers across whole population and between single differentiating cells of multipotent stromal cell populations derived from adipose tissue (AdMSCs) and skin (FBs) of seven donors. The results of the analyses show that all cell populations exhibit similar differentiation potential towards adipocyte, osteoblast and chondrocyte lineages despite tissue type- and donor-specific variations of expression of differentiation-associated genes. Further, we detected variable expression of lineage regulators in individual differentiating cells. Together, our data indicate that single cells of stromal cell populations could use distinct molecular mechanisms to reach a common cell fate.     

A generalized chain binomial model with application to HIV infection

The original Reed-Frost formulation of the chain binomial model is mathematically equivalent to a stochastic model allowing a Poisson number of effective contacts in a time interval. Their formulation cannot accommodate survey data that necessarily correspond to more complex distributions of partners or contacts, or to large populations where complete random mixing is unlikely. This paper generalizes the Reed-Frost model to accommodate these situations in both the one- and two-population settings. The extension to multiple populations is also outlined. Using the model to predict HIV incidence in San Francisco's homosexual population, we show that the total number of contacts over all partners is more important than the distribution of contacts among partners in determining the number of infected.     

Diverse effects of invasive ecosystem engineers on marine biodiversity and ecosystem functions: A global review and meta‐analysis

Invasive ecosystem engineers (IEE) are potentially one of the most influential types of biological invaders. They are expected to have extensive ecological impacts by altering the physical–chemical structure of ecosystems, thereby changing the rules of existence for a broad range of resident biota. To test the generality of this expectation, we used a global systematic review and meta‐analysis to examine IEE effects on the abundance of individual species and communities, biodiversity (using several indices) and ecosystem functions, focusing on marine and estuarine environments. We found that IEE had a significant effect (positive and negative) in most studies testing impacts on individual species, but the overall (cumulative) effect size was small and negative. Many individual studies showed strong IEE effects on community abundance and diversity, but the direction of effects was variable, leading to statistically non‐significant overall effects in most categories. In contrast, there was a strong overall effect on most ecosystem functions we examined. IEE negatively affected metabolic functions and primary production, but positively affected nutrient flux, sedimentation and decomposition. We use the results to develop a conceptual model by highlighting pathways whereby IEE impact communities and ecosystem functions, and identify several sources of research bias in the IEE‐related invasion literature. Only a few of the studies simultaneously quantified IEE effects on community/diversity and ecosystem functions. Therefore, understanding how IEE may alter biodiversity–ecosystem function relationships should be a primary focus of future studies of invasion biology. Moreover, the clear effects of IEE on ecosystem functions detected in our study suggest that scientists and environmental managers ought to examine how the effects of IEE might be manifested in the services that marine ecosystems provide to humans.     

Macroalgal blooms alter community structure and primary productivity in marine ecosystems

Eutrophication, coupled with loss of herbivory due to habitat degradation and overharvesting, has increased the frequency and severity of macroalgal blooms worldwide. Macroalgal blooms interfere with human activities in coastal areas, and sometimes necessitate costly algal removal programmes. They also have many detrimental effects on marine and estuarine ecosystems, including induction of hypoxia, release of toxic hydrogen sulphide into the sediments and atmosphere, and the loss of ecologically and economically important species. However, macroalgal blooms can also increase habitat complexity, provide organisms with food and shelter, and reduce other problems associated with eutrophication. These contrasting effects make their overall ecological impacts unclear. We conducted a systematic review and meta‐analysis to estimate the overall effects of macroalgal blooms on several key measures of ecosystem structure and functioning in marine ecosystems. We also evaluated some of the ecological and methodological factors that might explain the highly variable effects observed in different studies. Averaged across all studies, macroalgal blooms had negative effects on the abundance and species richness of marine organisms, but blooms by different algal taxa had different consequences, ranging from strong negative to strong positive effects. Blooms' effects on species richness also depended on the habitat where they occurred, with the strongest negative effects seen in sandy or muddy subtidal habitats and in the rocky intertidal. Invertebrate communities also appeared to be particularly sensitive to blooms, suffering reductions in their abundance, species richness, and diversity. The total net primary productivity, gross primary productivity, and respiration of benthic ecosystems were higher during macroalgal blooms, but blooms had negative effects on the productivity and respiration of other organisms. These results suggest that, in addition to their direct social and economic costs, macroalgal blooms have ecological effects that may alter their capacity to deliver important ecosystem services.     

Comparative Study of Seed Germination and Genetic Variation of Rare Endemic Rhinanthus osiliensis and Related Widespread Congener R. rumelicus (Orobanchaceae)

Genetic diversity is affected by breeding systems, life history traits and the distribution of species. Generally, inbred species with restricted geographic distribution have lower genetic variation compared to common outbreeding plant species. Rhinanthus osiliensis is a narrow endemic growing in calcareous spring fens on the island Saaremaa, Estonia. Presumably the closest congener of R. osiliensis is R. rumelicus, which is widely distributed in Eastern and Central Europe and the Balkan Peninsula. Isozymes were used to describe the mating system, levels of genetic variation and differentiation between the populations of R. osiliensis and R. rumelicus. Genetic diversity was found to be higher in widespread R. rumelicus compared to the endemic R. osiliensis. A significantly higher inbreeding coefficient with a low germination rate indicated substantial autogamy in R. osiliensis, whereas R. rumelicus displayed a mixed mating mode with a moderate inbreeding coefficient and a high germination rate. The low genetic differentiation between R. osiliensis and R. rumelicus confirmed their close affinity and the short evolutionary period of both taxa after the postglacial colonization. Considering the restricted geographic range and inbreeding in populations of R. osiliensis, this species may face a loss of genetic variation in the future.     

Recombination-Dependent Oligomerization of Human Papillomavirus Genomes upon Transient DNA Replication

We describe the extensive and progressive oligomerization of human papillomavirus (HPV) genomes after transfection into the U2OS cell line. The HPV genomic oligomers are extrachromosomal concatemeric molecules containing the viral genome in a head-to-tail orientation. The process of oligomerization does not depend on the topology of the input DNA, and it does not require any other viral factors besides replication proteins E1 and E2. We provide evidence that oligomerization of the HPV18 and HPV11 genomes involves homologous recombination. We also demonstrate oligomerization of the HPV18 and HPV11 genomes in SiHa, HeLa, and C-33 A cell lines and provide examples of oligomeric HPV genomes in clinical samples obtained from HPV-infected patients.     

Predicting the cover and richness of intertidal macroalgae in remote areas: a case study in the Antarctic Peninsula

Antarctica is an iconic region for scientific explorations as it is remote and a critical component of the global climate system. Recent climate change causes a dramatic retreat of ice in Antarctica with associated impacts to its coastal ecosystem. These anthropogenic impacts have a potential to increase habitat availability for Antarctic intertidal assemblages. Assessing the extent and ecological consequences of these changes requires us to develop accurate biotic baselines and quantitative predictive tools. In this study, we demonstrated that satellite‐based remote sensing, when used jointly with in situ ground‐truthing and machine learning algorithms, provides a powerful tool to predict the cover and richness of intertidal macroalgae. The salient finding was that the Sentinel‐based remote sensing described a significant proportion of variability in the cover and richness of Antarctic macroalgae. The highest performing models were for macroalgal richness and the cover of green algae as opposed to the model of brown and red algal cover. When expanding the geographical range of the ground‐truthing, even involving only a few sample points, it becomes possible to potentially map other Antarctic intertidal macroalgal habitats and monitor their dynamics. This is a significant milestone as logistical constraints are an integral part of the Antarctic expeditions. The method has also a potential in other remote coastal areas where extensive in situ mapping is not feasible.     

‘In vitro’ and ‘in situ’ decomposition of nuisance macroalgae Cladophora glomerata and Pilayella littoralis

The decomposition of two macroalgal species Cladophora glomerata (CHLOROPHYTA) and Pilayella littoralis (PHAEOPHYTA) was studied in the laboratory and field conditions. These species are known to cause the extensive macroalgal blooms in the whole coastal range of the Baltic Sea. The objective of the experiments was to determine decomposition rates of the macroalgae, follow the changes in tissue nutrient content and validate the role of benthic invertebrates in this process. In the laboratory conditions, the differences in the decomposition rates of the algae were mainly due to the oxygen conditions. The weight loss of C. glomerata was slightly higher in anaerobic conditions than in aerobic conditions. If 99% of initial dry weight of P. littoralis was lost in aerobic conditions then only 20% was lost in anaerobic conditions. In general, the loss of phosphorus and nitrogen in algal tissues followed the weight loss. As an exception, the amount of nitrogen changed very little during the decomposition of C. glomerata. In field conditions, the photosynthetic activity exceeded the decomposition rate of C. glomerata at lower temperatures in spring. The decomposition of P. littoralis was estimated at 49% of its initial dry weight. The addition of benthic invertebrates had no effect on the decomposition process. In summer, the decomposition rates were estimated at 65% for C. glomerata and 68% for P. littoralis being in the same order of magnitude as observed in laboratory conditions. If the decomposition of C. glomerata was faster at the end of the experiment, the most significant losses of weight of P. littoralis took place during the first 2 weeks of deployment. Idotea baltica significantly contributed to the loss of C. glomerata. The decomposition rate of P. littoralis was reduced by the presence of Mytilus edulis and increased by Gammarus oceanicus.     

Essential oil in Betula spp. leaves naturally growing in Estonia

The essential oils of the leaves of Betula pendula Roth., Betula pubescens Ehrh., Betula humilis Schrank and Betula nana L. (Betulaceae), and B. pendula buds were obtained using hydrodistillation and their chemical compositions were analyzed using gas chromatography and gas chromatography – mass spectrometry. The yield of essential oil was the highest (0.27%) in leaves of. B. humilis and the lowest in the leaves of B. pendula (0.11%), B. pubescens (0.05%) and B. nana (traces). Overall, 35–60 compounds were identified representing more than 92% of the total volume of the oils investigated. The bicyclical sesquiterpenoids found in the essential oils extracted from the leaves of B. pendula, B. pubescens and B. humilis and from the buds of B. pendula where α-betulenol (20.4–33.1%), α-betulenol acetate (5,6–28.9%), β-betulenal (5.5–6.2%) and β-betulenol (2.0–5.8%). The buds of B. pendula contained more birkenal, (E)-β-caryophyllene, δ-cadinene and caryophyllene oxide, but less α-betulenol acetate, β-betulenal and aliphatic compounds than the oils extracted from the leaves investigated. The oil composition of B. humilis and B. nana leaves was studied for the first time. The content of essential oil of B. nana leaves was much more varied: the oil contained less bicyclical sesquiterpenoids and more aliphatic compounds than the other Betula species investigated. The findings of our study could be used in chemosystematics of birch species, especially for B. nana.