Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola (Violaceae)

<p>Abstract</p> <p>Background</p> <p>DNA-dependent RNA polymerase IV and V (Pol IV and V) are multi-subunit enzymes occurring in plants. The origin of Pol V, specific to angiosperms, from Pol IV, which is present in all land plants, is linked to the duplication of the gene encoding the largest subunit and the subsequent subneofunctionalization of the two paralogs (<it>NRPD1 </it>and <it>NRPE1</it>). Additional duplication of the second-largest subunit, <it>NRPD2/NRPE2</it>, has happened independently in at least some eudicot lineages, but its paralogs are often subject to concerted evolution and gene death and little is known about their evolution nor their affinity with Pol IV and Pol V.</p> <p>Results</p> <p>We sequenced a ~1500 bp <it>NRPD2/E2</it>-like fragment from 18 <it>Viola </it>species, mostly paleopolyploids, and 6 non-<it>Viola </it>Violaceae species. Incongruence between the <it>NRPD2/E2</it>-like gene phylogeny and species phylogeny indicates a first duplication of <it>NRPD2 </it>relatively basally in Violaceae, with subsequent sorting of paralogs in the descendants, followed by a second duplication in the common ancestor of <it>Viola </it>and <it>Allexis</it>. In <it>Viola</it>, the mutation pattern suggested (sub-) neofunctionalization of the two <it>NRPD2/E2</it>-like paralogs, <it>NRPD2/E2-a </it>and <it>NRPD2/E2-b</it>. The <it>d</it>_<it>N</it>/<it>d</it>_{<it>S </it>}ratios indicated that a 54 bp region exerted strong positive selection for both paralogs immediately following duplication. This 54 bp region encodes a domain that is involved in the binding of the Nrpd2 subunit with other Pol IV/V subunits, and may be important for correct recognition of subunits specific to Pol IV and Pol V. Across all <it>Viola </it>taxa 73 <it>NRPD2/E2</it>-like sequences were obtained, of which 23 (32%) were putative pseudogenes - all occurring in polyploids. The <it>NRPD2 </it>duplication was conserved in all lineages except the diploid MELVIO clade, in which <it>NRPD2/E2-b </it>was lost, and its allopolyploid derivates from hybridization with the CHAM clade, section <it>Viola </it>and section <it>Melanium</it>, in which <it>NRPD2/E2-a </it>occurred in multiple copies while <it>NRPD2/E2-b </it>paralogs were either absent or pseudogenized.</p> <p>Conclusions</p> <p>Following the relatively recent split of Pol IV and Pol V, our data indicate that these two multi-subunit enzymes are still in the process of specialization and each acquiring fully subfunctionalized copies of their subunit genes. Even after specialization, the <it>NRPD2/E2</it>-like paralogs are prone to pseudogenization and gene conversion and <it>NRPD2 </it>and <it>NRPE2 </it>copy number is a highly dynamic process modulated by allopolyploidy and gene death.</p

Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells

Eukaryotic organisms are continuously exposed to bacteriophages, which are efficient gene transfer agents in bacteria. However, bacteriophages are considered not to pass the eukaryotic cell membrane and enter nonphagocytic cells. Here we report the binding and penetration of Escherichia coli PK1A2 bacteriophage into live eukaryotic neuroblastoma cells in vitro. The phage interacts with cell surface polysialic acid, which shares structural similarity with the bacterial phage receptor. Using fluorescence and electron microscopy, we show that phages are internalized via the endolysosomal route and persist inside the human cells up to one day without affecting cell viability. Phage capsid integrity is lost in lysosomes, and the phage DNA is eventually degraded. We did not detect the entry of phage DNA into the nucleus; however, we speculate that this might occur as a rare event, and propose that this potential mechanism could explain prokaryote-eukaryote gene flow.Peer reviewe

Smartphone placement within vehicles

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordSmartphone-based driver monitoring is quickly gaining ground as a feasible alternative to competing in-vehicle and aftermarket solutions. Currently the main challenges for data analysts studying smartphone-based driving data stem from the mobility of the smartphone. In this paper, we use kernel-based k-means clustering to infer the placement of smartphones within vehicles. The trip segments are mapped into fifteen different placement clusters. As a part of the presented framework, we discuss practical considerations concerning e.g., trip segmentation, cluster initialization, and parameter selection. The proposed method is evaluated on more than 10 000 kilometers of driving data collected from approximately 200 drivers. To validate the interpretation of the clusters, we compare the data associated with different clusters and relate the results to real-world knowledge of driving behavior. The clusters associated with the label “Held by hand” are shown to display high gyroscope variances, low maximum speeds, low correlations between the measurements from smartphone-embedded and vehicle-fixed accelerometers, and short segment durations

Geographical distribution of salmonella infected pig, cattle and sheep herds in Sweden 1993-2010

<p>Abstract</p> <p>Background</p> <p>The Swedish salmonella control programme covers the entire production chain, from feed to food. All salmonella serotypes are notifiable. On average, less than 20 cases of salmonella in food-producing animals are reported every year. In some situations, the cases would be expected to cluster geographically. The aim of this study was to illustrate the geographic distribution of the salmonella cases detected in pigs, cattle and sheep.</p> <p>Methods</p> <p>Data on all herds with pigs, cattle and sheep found to be infected with salmonella during the time period from 1993 to 2010 were obtained from the Swedish Board of Agriculture. Using the ArcGIS software, various maps were produced of infected herds, stratified on animal species as well as salmonella serotype. Based on ocular inspection of all maps, some were collapsed and some used separately. Data were also examined for temporal trends.</p> <p>Results</p> <p>No geographical clustering was observed for ovine or porcine cases. Cattle herds infected with Salmonella Dublin were mainly located in the southeast region and cattle herds infected with Salmonella Typhimurium in the most southern part of the country. Some seasonal variation was seen in cattle, but available data was not sufficient for further analyses.</p> <p>Conclusions</p> <p>Analyses of data on salmonella infected herds revealed some spatial and temporal patterns for salmonella in cattle. However, despite using 18 years' of data, the number of infected herds was too low for any useful statistical analyses.</p

Brain Gene Expression Signatures From Cerebrospinal Fluid Exosome RNA Profiling

While the Visual Impairment and Intracranial Pressure (VIIP) syndrome observations have focused on ocular symptoms, spaceflight has been also associated with a number of other performance and neurologic signs, such as headaches, cognitive changes, vertigo, nausea, sleep/circadian disruption and mood alterations, which, albeit likely multifactorial, can also result from elevation of intracranial pressure (ICP). We therefore hypothesize that these various symptoms are caused by disturbances in the neurophysiology of the brain structures and are correlated with molecular markers in the cerebrospinal fluid (CSF) as indicators of neurophysiological changes. Exosomes are 30-200 nm microvesicles shed into all biofluids, including blood, urine, and CSF, carrying a highly rich source of intact protein and RNA cargo. Exosomes have been identified in human CSF, and their proteome and RNA pool is a potential new reservoir for biomarker discovery in neurological disorders. The purpose of this study is to investigate changes in brain gene expression via exosome analysis in patients suffering from ICP elevation of varied severity (idiopathic intracranial hypertension -IIH), a condition which shares some of the neuroophthalmological features of VIIP, as a first step toward obtaining evidence suggesting that cognitive function and ICP levels can be correlated with biomarkers in the CSF. Our preliminary work, reported last year, validated the exosomal technology applicable to CSF analysis and demonstrated that it was possible to obtain gene expression evidence of inflammation processes in traumatic brain injury patients. We are now recruiting patients with suspected IIH requiring lumbar puncture at Baylor College of Medicine. Both CSF (5 ml) and human plasma (10 ml) are being collected in order to compare the pattern of differentially expressed genes observed in CSF and in blood. Since blood is much more accessible than CSF, we would like to determine whether plasma biomarkers for elevated ICP can be identified. This may eventually lead to a blood test to diagnose intracranial hypertension

A comprehensive organic nitrate chemistry: insights into the lifetime of atmospheric organic nitrates

Organic nitrate chemistry is the primary control over the lifetime of nitrogen oxides (NOx) in rural and remote continental locations. As NOx emissions decrease, organic nitrate chemistry becomes increasingly important to urban air quality. However, the lifetime of individual organic nitrates and the reactions that lead to their production and removal remain relatively poorly constrained, causing organic nitrates to be poorly represented by models. Guided by recent laboratory and field studies, we developed a detailed gas-phase chemical mechanism representing most of the important individual organic nitrates. We use this mechanism within the Weather Research and Forecasting (WRF) model coupled with Chemistry (WRF-Chem) to describe the role of organic nitrates in nitrogen oxide chemistry and in comparisons to observations. We find the daytime lifetime of total organic nitrates with respect to all loss mechanisms to be 2.6&thinsp;h in the model. This is consistent with analyses of observations at a rural site in central Alabama during the Southern Oxidant and Aerosol Study (SOAS) in summer 2013. The lifetime of the first-generation organic nitrates is  ∼ 2&thinsp;h versus the 3.2&thinsp;h lifetime of secondary nitrates produced by oxidation of the first-generation nitrates. The different generations are subject to different losses, with dry deposition to the surface being the dominant loss process for the second-generation organic nitrates and chemical loss being dominant for the first-generation organic nitrates. Removal by hydrolysis is found to be responsible for the loss of  ∼ 30&thinsp;&thinsp;% of the total organic nitrate pool.</p

Source apportionment of organic carbon in Centreville, AL using organosulfates in organic tracer-based positive matrix factorization

Organic tracer-based positive matrix factorization (PMF) was used to apportion fine particulate (PM_(2.5)) organic carbon (OC) to its sources in Centreville, AL, USA, a rural forested site influenced by anthropogenic emissions, during the Southern Oxidant and Aerosol Study (SOAS) in the summer of 2013. Model inputs included organosulfates, a group of organic compounds that are tracers of anthropogenically-influenced biogenic secondary organic aerosols (SOA), as well as, OC, elemental carbon, water-soluble organic carbon, and other organic tracers for primary and secondary sources measured during day and night. The organic tracer-based PMF resolved eight factors that were identified as biomass burning (11%, average contribution to PM_(2.5) OC), vehicle emissions (8%), isoprene SOC formed under low-NO_x conditions (13%), isoprene SOC formed under high-NO_x conditions (11%), SOC formed by photochemical reactions (9%), oxidatively aged biogenic SOC (6%), sulfuric acid-influenced SOC (21%, that also includes isoprene and monoterpene SOC), and monoterpene SOC formed under high-NO_x conditions (21%). These results indicate that OC in Centreville during summer is mainly secondary in origin (81%). Fossil fuel combustion is the major source of NO_x, ozone, and sulfuric acid that play a key role in SOA formation in the southeastern US. Fossil fuel was found to influence 61–76% of OC through vehicle emissions and SOA formation. Together with prescribed burns, which were the major type of biomass burning during this study, the OC influenced by anthropogenic activities reached 87%. The organic tracer-based PMF results were further compared with two complementary source apportionment techniques: PMF factors resolved for submicron organic aerosols measured using aerosol mass spectrometry (AMS) by Xu et al. (2015a) in Centreville during SOAS; biomass burning organic aerosols (BBOA, 11% of OC), isoprene-derived organic aerosols (isoprene-OA, 20% of OC), more-oxidized oxygenated organic aerosols (MO-OOA, 34% of OC), and less-oxidized oxygenated organic aerosols (LO-OOA, 35% of OC); and PM_(2.5) OC apportioned by chemical-mass balance model (CMB), considering the same chemical species as this study, save for organosulfates; biomass burning (5%), diesel engines (2%), gasoline smokers (3%), vegetative detritus (1%), isoprene SOC (23%) and monoterpene SOC (34%), and other (likely biogenic secondary) sources (33%). Overall, this study indicates the primary and secondary sources resolved by the organic tracer-based PMF are in good agreement with CMB and AMS-PMF results, while the organic tracer-based PMF provides additional insight to the SOC formation pathways through the inclusion of organosulfates and other organic tracers measured during day and night

Classification images for aerial images capture visual expertise for binocular disparity and a prior for lighting from above

Using a novel approach to classification images (CIs), we investigated the visual expertise of surveyors for luminance and binocular disparity cues simultaneously after screening for stereoacuity. Stereoscopic aerial images of hedges and ditches were classified in 10,000 trials by six trained remote sensing surveyors and six novices. Images were heavily masked with luminance and disparity noise simultaneously. Hedge and ditch images had reversed disparity on around half the trials meaning hedges became ditch-like and vice versa. The hedge and ditch images were also flipped vertically on around half the trials, changing the direction of the light source and completing a 2 × 2 × 2 stimulus design. CIs were generated by accumulating the noise textures associated with "hedge" and "ditch" classifications, respectively, and subtracting one from the other. Typical CIs had a central peak with one or two negative side-lobes. We found clear differences in the amplitudes and shapes of perceptual templates across groups and noise-type, with experts prioritizing binocular disparity and using this more effectively. Contrariwise, novices used luminance cues more than experts meaning that task motivation alone could not explain group differences. Asymmetries in the luminance CIs revealed individual differences for lighting interpretation, with experts less prone to assume lighting from above, consistent with their training on aerial images of UK scenes lit by a southerly sun. Our results show that (i) dual noise in images can be used to produce simultaneous CI pairs, (ii) expertise for disparity cues does not depend on stereoacuity, (iii) CIs reveal the visual strategies developed by experts, (iv) top-down perceptual biases can be overcome with long-term learning effects, and (v) CIs have practical potential for directing visual training