Characteristics of Arctic low-tropospheric humidity inversions based on radio soundings

Humidity inversions have a high potential importance in the Arctic climate system, especially for cloud formation and maintenance, in wide spatial and temporal scales. Here we investigate the climatology and characteristics of humidity inversions in the Arctic, including their spatial and temporal variability, sensitivity to the methodology applied and differences from the Antarctic humidity inversions. The study is based on data of the Integrated Global Radiosonde Archive (IGRA) from 36 Arctic stations between the years 2000 and 2009. The results indicate that humidity inversions are present on multiple levels nearly all the time in the Arctic atmosphere. Almost half (48%) of the humidity inversions were found at least partly within the same vertical layer with temperature inversions, whereas the existence of the other half may, at least partly, be linked to uneven vertical distribution of horizontal moisture transport. A high atmospheric surface pressure was found to increase the humidity inversion occurrence, whereas relationships between humidity inversion properties and cloud cover were generally relatively weak, although for some inversion properties they were systematic. For example, humidity inversions occurred slightly more often and were deeper under clear sky than in overcast conditions for almost all stations. The statistics of Arctic humidity inversion properties, especially inversion strength, depth and base height, proved to be very sensitive to the instruments and methodology applied. For example, the median strength of the strongest inversion in a profile was twice as large as the median of all Arctic inversions. The most striking difference between the Arctic and Antarctic humidity inversions was the much larger range of the seasonal cycle of inversion properties in the Arctic. Our results offer a baseline for validation of weather prediction and climate models and also encourage further studies on humidity inversions due to the vital, but so far poorly understood, role of humidity inversions in Arctic cloud processes

Migration and Intra-Urban Residential Mobility in the Helsinki Metropolitan Area

This paper was contributed to IIASA's workshop on "Dynamics of Metropolitan Areas" in Rotterdam, June 1984. It contains an assessment of migration process in the Helsinki region and examines in particular age-dependent mobility of life-cycle type. As such it also provides a background to the study on housing dynamics in the Helsinki region

Sensitivity of Small RNA-Based Detection of Plant Viruses

Plants recognize unrelated viruses by the antiviral defense system called RNA interference (RNAi). RNAi processes double-stranded viral RNA into small RNAs (sRNAs) of 21-24 nucleotides, the reassembly of which into longer strands in silico allows virus identification by comparison with the sequences available in databases. The aim of this study was to compare the virus detection sensitivity of sRNA-based virus diagnosis with the established virus species-specific polymerase chain reaction (PCR) approach. Viruses propagated in tobacco plants included three engineered, infectious clones of Potato virus A (PVA), each carrying a different marker gene, and an infectious clone of Potato virus Y (PVY). Total RNA (containing sRNA) was isolated and subjected to reverse-transcription real-time PCR (RT-RT-PCR) and sRNA deep-sequencing at different concentrations. RNA extracted from various crop plants was included in the reactions to normalize RNA concentrations. Targeted detection of selected viruses showed a similar threshold for the sRNA and reverse-transcription quantitative PCR (RT-qPCR) analyses. The detection limit for PVY and PVA by RT-qPCR in this study was 3 and 1.5 fg of viral RNA, respectively, in 50 ng of total RNA per PCR reaction. When knowledge was available about the viruses likely present in the samples, sRNA-based virus detection was 10 times more sensitive than RT-RT-PCR. The advantage of sRNA analysis is the detection of all tested viruses without the need for virus-specific primers or probes.Peer reviewe

Development of FRET-based high-throughput screening for viral RNase III inhibitors

The class 1 ribonuclease III (RNase III) encoded by Sweet potato chlorotic stunt virus (CSR3) suppresses RNA silencing in plant cells and thereby counters the host antiviral response by cleaving host small interfering RNAs, which are indispensable components of the plant RNA interference (RNAi) pathway. The synergy between sweet potato chlorotic stunt virus and sweet potato feathery mottle virus can reduce crop yields by 90%. Inhibitors of CSR3 might prove efficacious to counter this viral threat, yet no screen has been carried out to identify such inhibitors. Here, we report a novel high-throughput screening (HTS) assay based on fluorescence resonance energy transfer (FRET) for identifying inhibitors of CSR3. For monitoring CSR3 activity via HTS, we used a small interfering RNA substrate that was labelled with a FRET-compatible dye. The optimized HTS assay yielded 109 potential inhibitors of CSR3 out of 6,620 compounds tested from different small-molecule libraries. The three best inhibitor candidates were validated with a dose-response assay. In addition, a parallel screen of the selected candidates was carried out for a similar class 1 RNase III enzyme from Escherichia coli (EcR3), and this screen yielded a different set of inhibitors. Thus, our results show that the CSR3 and EcR3 enzymes were inhibited by distinct types of molecules, indicating that this HTS assay could be widely applied in drug discovery of class 1 RNase III enzymes.Peer reviewe

Sunagoke Moss (Racomitrium japonicum) Used for Greening Roofs Is Severely Damaged by Sclerotium delphinii and Protected by a Putative Bacillus amyloliquefaciens Isolate

Mosses are ecologically important plants also used for greening, gardening, and decorative purposes. Knowledge of the microbial flora associated with mosses is expected to be important for control and preservation of global and local environments. However, the moss-associated microbial flora is often poorly known. Moss-associated fungi and bacteria may promote plant growth and pest control, but they may be alternative hosts for pathogens of vascular plants. In this study, the fungus Sclerotinia delphinii was identified for the first time as a pathogen that causes severe damage to Sunagoke moss (Racomitrium japonicum). This moss is used for greening roofs and walls of buildings in urban environments owing to its notable tolerance of environmental stresses. Inoculation with the S. delphinii strain SR1 of the mono- and dicotyledonous seed plants Hordeum vulgare, Brassica rapa var. pekinensis, Lactuca sativa, and Spinacia oleracea, in addition to the liverwort Marchantia polymorpha and the moss Physcomitrella patens, showed that the fungus has a wide host range. Colonization with SR1 progressed more rapidly in non-vascular than in vascular plant species. Studies with P. patens under controlled conditions showed that SR1 secreted a fluid during colonization. Treatment with the secretion induced production of reactive oxygen species in the moss. Endogenous peroxidase partially inhibited SR1 colonization of P. patens. A bacterial isolate, most likely Bacillus amyloliquefaciens, that coexists with R. japonicum was antagonistic to SR1 growth. Taken together, the present results suggest that fungal colonization of mosses may be prevented by a peroxidase secreted by the moss and an antagonistic bacterium coexisting in the moss habitat. The findings suggest that there is potential to apply biological control measures for protection of mosses against fungal pathogens.Peer reviewe

Nuclear proteome of virus-infected and healthy potato leaves

BackgroundInfection of plants by viruses interferes with expression and subcellular localization of plant proteins. Potyviruses comprise the largest and most economically damaging group of plant-infecting RNA viruses. In virus-infected cells, at least two potyviral proteins localize to nucleus but reasons remain partly unknown.ResultsIn this study, we examined changes in the nuclear proteome of leaf cells from a diploid potato line (Solanum tuberosum L.) after infection with potato virus A (PVA; genus Potyvirus; Potyviridae) and compared the data with that acquired for healthy leaves. Gel-free liquid chromatography-coupled to tandem mass spectrometry was used to identify 807 nuclear proteins in the potato line v2-108; of these proteins, 370 were detected in at least two samples of healthy leaves. A total of 313 proteins were common in at least two samples of healthy and PVA-infected leaves; of these proteins, 8 showed differential accumulation. Sixteen proteins were detected exclusively in the samples from PVA-infected leaves, whereas other 16 proteins were unique to healthy leaves. The protein Dnajc14 was only detected in healthy leaves, whereas different ribosomal proteins, ribosome-biogenesis proteins, and RNA splicing-related proteins were over-represented in the nuclei of PVA-infected leaves. Two virus-encoded proteins were identified in the samples of PVA-infected leaves.ConclusionsOur results show that PVA infection alters especially ribosomes and splicing-related proteins in the nucleus of potato leaves. The data increase our understanding of potyvirus infection and the role of nucleus in infection. To our knowledge, this is the first study of the nuclear proteome of potato leaves and one of the few studies of changes occurring in nuclear proteomes in response to plant virus infection.Peer reviewe

Soil bacterial community in potato tuberosphere following repeated applications of a common scab suppressive antagonist

Disease suppressive soils are important for managing soil-borne diseases that cannot be controlled with chemicals. One such disease is the potato common scab caused by Streptomyces species. Suppressiveness against common scab can develop spontaneously in fields where potato is grown for years without interruption, and this has been attributed to non-pathogenic Streptomyces strains. Streptomyces spp. have been used as inoculants in biological control, but their long-term effects have gained less attention. In our previous studies, a nonpathogenic Streptomyces strain (Str272) isolated from a potato common scab lesion suppressed common scab in field trials lasting over 5 years. In this study, bacterial communities in the tuberosphere i.e. in the soil adjacent to potato tubers, were analysed by next generation sequencing (NGS). The aim was to compare bacterial communities in untreated control plots to those in which seed tubers were treated with Str272 in one or several growing seasons. Str272 applications increased soil bacterial diversity and affected the bacterial composition in the potato tuberosphere. The most pronounced differences were observed between the untreated control and the treatments in which the antagonist had been applied in three or four consecutive years. The differences remained similar until the following growing season. Bacterial composition after repeated antagonist applications was associated with lower common scab severity. The antagonist applications had no or only slight effect on the number or abundance of OTUs belonging to Actinobacteria or Streptomyces, and no differences in quantities of pathogenic Streptomyces populations were detected by qPCR. This indicates that suppression of common scab by Str272 may not be based on direct effect on the common scab pathogens but is more likely to be associated with the alterations of the soil bacterial community. The most abundant bacteria phyla in the potato tuberosphere were Actinobacteria, Proteobacteria and Acidobacteria. However, the OTUs responding greatest to the antagonist treatments belonged to Bacterioidetes and Gemmatimonadetes. Results indicate that repeated applications of Str272 can change the bacterial community in the potato tuberosphere and lead to development of soil that is suppressive against potato common scab for several growing seasons after the last application.Peer reviewe