Microbial communities in a boreal forest podzol profile and responses to the presence of Pinus sylvestris seedling roots

The boreal biome consists of coniferous forests that cover much of the northern hemisphere, and constitute an important natural resource for the forest industry, but has also gained attention in the light of global warming in acting as potential sinks of atmospheric carbon dioxide. Both forest production and carbon sequestration are closely connected to the activities of soil microorganisms, which play major roles in nutrient cycling and decomposition of plant biomass. Boreal forest soils are commonly classified as podzols, which are characterized by their clear horizon development with depth. Ecological surveys of soil biota commonly focus on the topsoil. The aim of this experiment was to examine if the organic, eluvial and illuvial horizons of a Swedish boreal forest podzol harboured distinct communities of fungi, bacteria and archaea, and further if roots of Scots pine seedlings, through input of rhizodeposition, would induce shifts in microbial communities in the different soil categories. The study was conducted as a microcosm experiment in combination with denaturing gradient gel electrophoresis (DGGE) fingerprinting of phylogenetic marker sequences, ITS rDNA for fungi and 16S rDNA for archaea and bacteria. Soil sampled at the time of experimental set-up served as control for community shifts caused by incubation time alone. All soil horizons harboured distinct communities of fungi, bacteria and archaea. Fungi and bacteria displayed complex community profiles for all soil samples, but richness for both groups tended to be highest in the organic soil. The archaeal community profiles were relatively simple for all soil samples, though their richness appeared to be highest in the eluvial soil. Fungi was the microbial group that displayed the strongest response to the presence of Scots pine seedling roots, and ectomycorrhizas were observed in all microcosms with seedling, although the organic, eluvial and illuvial horizons harboured distinct morphotypes. In contrast, neither bacteria nor archaea responded much to the presence of Scots pine seedlings, but the bacterial communities underwent a clear shift in composition during the incubation period, especially in the organic soil. These results highlight the importance of including all layers in a soil profile to obtain a holistic view on the ecology of soil microorganisms and their roles in ecosystem functioning

Performance of Ultra-Deep Pyrosequencing in Analysis of HIV-1 pol Gene Variation

INTRODUCTION: Ultra-deep pyrosequencing (UDPS) has been used to detect minority variants within HIV-1 populations. Some aspects of the quality and reproducibility of UDPS have been previously evaluated, but comprehensive studies are still needed. PRINCIPAL FINDING: In this study the UDPS technology (FLX platform) was evaluated by analyzing a 120 base pair fragment of the HIV-1 pol gene from plasma samples from two patients and artificial mixtures of molecular clones. UDPS was performed using an optimized experimental protocol and an in-house data cleaning strategy. Nine samples and mixtures were analyzed and the average number of reads per sample was 19,404 (range 8,858-26,846). The two patient plasma samples were analyzed twice and quantification of viral variants was found to be highly repeatable for variants representing >0.27% of the virus population, whereas some variants representing 0.11-0.27% were detected in only one of the two UDPS runs. Bland-Altman analysis showed that a repeated measurement would have a 95% likelihood to lie approximately within ±0.5 log(10) of the initial estimate. A similar level of agreement was observed for variant frequency estimates in forward vs. reverse sequencing direction, but here the agreement was higher for common variants than for rare variants. UDPS following PCR amplification with alternative primers indicated that some variants may be incorrectly quantified due to primer-related selective amplification. Finally, the in vitro recombination rate during PCR was evaluated using artificial mixtures of clones and was found to be low. The most abundant in vitro recombinant represented 0.25% of all UDPS reads. CONCLUSION: This study demonstrates that this UDPS protocol results in low experimental noise and high repeatability, which is relevant for future research and clinical use of the UDPS technology. The low rate of in vitro recombination suggests that this UDPS system can be used to study genetic variants and mutational linkage

Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing

Background: Ultra-deep pyrosequencing (UDPS) allows identification of rare HIV-1 variants and minority drug resistance mutations, which are not detectable by standard sequencing. Principal Findings: Here, UDPS was used to analyze the dynamics of HIV-1 genetic variation in reverse transcriptase (RT) (amino acids 180–220) in six individuals consecutively sampled before, during and after failing 3TC and AZT containing antiretroviral treatment. Optimized UDPS protocols and bioinformatic software were developed to generate, clean and analyze the data. The data cleaning strategy reduced the error rate of UDPS to an average of 0.05%, which is lower than previously reported. Consequently, the cut-off for detection of resistance mutations was very low. A median of 16,016 (range 2,406–35,401) sequence reads were obtained per sample, which allowed detection and quantification of minorit

Medias framställning av sexuella övergrepp. En kvalitativ dokumentanalys av svenska dags- och kvällstidningar

Syftet med uppsatsen är att beskriva och analysera vad och hur svenska nyhetstidningar framställer gällande sexuella övergrepp från tidsperioden 2015-2017. Vidare är syftet att belysa och analysera hur media gestaltar sexuella övergrepp i den samhälleliga debatten. Detta gjorde vi genom en kvalitativ innehållsanalys. De teorier som användes i analysen av empirin var dagordnings- gestaltnings-, genus- och maktteori. Empirin bestod av 16 artiklar från Dagens Nyheter, Svenska Dagbladet, Aftonbladet och Göteborgs-Posten. Från dessa fyra tidningar valde vi ut nyhetsartiklar, krönikor och debattartiklar. Vår studie visade att media använder många tekniker för att påverka läsaren i sin framställning av sexuella övergrepp. Vi fann att empirin genomsyrades av en feministisk ton, där artikelförfattare visade hur utsatta kvinnor är och alltid har varit, i samband med sexuella övergrepp. Vi lyfter detta genom att diskutera hur maktstrukturer verkar på såväl individ- som samhällsnivå. Vår slutsats är, i linje med stor del av tidigare forskning samt empiri, att arbetet med sexuella övergrepp främst bör bedrivas på en strukturell nivå