Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

Pseudomonas virus vB_PaeM_PA5oct is proposed as a model jumbo bacteriophage to investigate phage-bacteria interactions and is a candidate for phage therapy applications. Combining hybrid sequencing, RNA-Seq and mass spectrometry allowed us to accurately annotate its 286,783 bp genome with 461 coding regions including four non-coding RNAs (ncRNAs) and 93 virion-associated proteins. PA5oct relies on the host RNA polymerase for the infection cycle and RNA-Seq revealed a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. PA5oct is not organized into strictly contiguous regions of temporal transcription, but some genomic regions transcribed in early, middle and late phases of infection can be discriminated. Interestingly, we observe regions showing limited transcription activity throughout the infection cycle. We show that PA5oct upregulates specific bacterial operons during infection including operons pncA-pncB1-nadE involved in NAD biosynthesis, psl for exopolysaccharide biosynthesis and nap for periplasmic nitrate reductase production. We also observe a downregulation of T4P gene products suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position our isolate amongst other phages using a gene-sharing network. This integrative omics study illustrates the molecular diversity of jumbo viruses and raises new questions towards cellular regulation and phage-encoded hijacking mechanisms

Characterization of the newly isolated lytic bacteriophages KTN6 and KT28 and their efficacy against Pseudomonas aeruginosa biofilm

We here describe two novel lytic phages, KT28 and KTN6, infecting Pseudomonas aeruginosa, isolated from a sewage sample from an irrigated field near Wroclaw, in Poland. Both viruses show characteristic features of Pbunalikevirus genus within the Myoviridae family with respect to shape and size of head/tail, as well as LPS host receptor recognition. Genome analysis confirmed the similarity to other PB1-related phages, ranging between 48 and 96%. Pseudomonas phage KT28 has a genome size of 66,381 bp and KTN6 of 65,994 bp. The latent period, burst size, stability and host range was determined for both viruses under standard laboratory conditions. Biofilm eradication efficacy was tested on peg-lid plate assay and PET membrane surface. Significant reduction of colony forming units was observed (70-90%) in 24 h to 72 h old Pseudomonas aeruginosa PAO1 biofilm cultures for both phages. Furthermore, a pyocyanin and pyoverdin reduction tests reveal that tested phages lowers the amount of both secreted dyes in 48-72 h old biofilms. Diffusion and goniometry experiments revealed the increase of diffusion rate through the biofilm matrix after phage application. These characteristics indicate these phages could be used to prevent Pseudomonas aeruginosa infections and biofilm formation. It was also shown, that PB1-related phage treatment of biofilm caused the emergence of stable phage-resistant mutants growing as small colony variants

The Development of Web3D-based Open-pit Mine Monitoring System

Large-scale open-pit mines are critical infrastructure for acquiring natural resources. However, this type of mine can experience environmental and safety problems during operations and thus requires continuous monitoring. In this study, a web three-dimensional(3D)-based monitoring system is constructed using geospatial information open platform and open-source geospatial information software which targets open-pit mines in Gangwon-do, Korea. The purpose is to develop a monitoring system of open-pit mines that enables any person to monitor the topographic and environmental changes caused by mine operations and to develop and restore the area’s ecology. Open-pit mines were classified into active or inactive mines and monitoring items and methodologies were established for each type of mine. Cesium which is a WebGL-based open-source platform was chosen as it supports dynamic data visualization and hardware-accelerated graphics related to elapsed time which is the essential factor in the monitoring. The open-pit mine monitoring system was developed based on the geospatial database which contains information required for mine monitoring as time elapses, and by developing the open-source-based system software. The geospatial information database for monitoring consists of digital imagery and terrain data and also includes vector data and the restoration plan datas. The basic geospatial information used in the monitoring includes high resolution ortho image(GSD 0.5 m or above) for all areas of the mines. This is acquired by periodically using an airborne laser scanning system and a LiDAR DEM (grid size 1m × 1 m). In addition, geospatial information data were acquired by using an UAV and terrestrial LiDAR for small-scale areas; these tools are frequently used for rapid and irregular data acquisition. The geospatial information acquired for the monitoring of the open-pit mines represents various spatial resolutions and different terrain data. The database was constructed by converging this geospatial information with the Cesium-based geospatial information open platform of the ESRI World Imagery map and with SDK World Terrain meshes. The problems that resulted from the process of fusing aerial imagery and terrain data were solved in the Cesium-based open source environment. The prototype menu for the monitoring system was designed according to the monitoring item which was determined by the type of mine. The scene of the mine and changes in terrain were controlled and analyzed using the raster function of PostGIS according to the elapsed time. Using the GeoServer, the aerial imagery, terrain and restoration information for each period were serviced using the web standard interface, and the monitoring system was completed by visualizing these elements in Cesium in 3D format according to the elapsed time. This study has established a monitoring methodology for open-pit mines according to the type of mine and proposes a method for upgrading the imagery and terrain data required for monitoring. The study also showed the possibility of developing a Web3D-based open-pit mine monitoring system that is applicable to a wide range of mashup service developments

Institutional case volume and mortality after aortic and mitral valve replacement: a nationwide study in two Korean cohorts

Background : There are only a handful of published studies regarding the volume-outcome relationship in heart valve surgery. We evaluated the association between institutional case volume and mortality after aortic valve replacement (AVR) and mitral valve replacement (MVR). Methods : Two separate cohorts of all adults who underwent AVR or MVR, respectively, between 2009 and 2016 were analyzed using a Korean healthcare insurance database. Hospitals performing AVRs were divided into three groups according to the average annual case volume: the low- ( 70 cases/year). Hospitals performing MVRs were also grouped as the low- ( 40 cases/year). In-hospital mortality after AVR or MVR were compared among the groups. Results : In total, 7875 AVR and 5084 MVR cases were analyzed. In-hospital mortality after AVR was 8.3% (192/2318), 4.0% (84/2102), and 2.6% (90/3455) in the low-, medium-, and high-volume centers, respectively. The adjusted risk was higher in the low- (OR 2.31, 95% CI 1.73–3.09) and medium-volume centers (OR 1.53, 95% CI 1.09–2.15) compared to the high-volume centers. In-hospital mortality after MVR was 9.3% (155/1663), 6.3% (94/1501), and 2.9% (56/1920) in the low-, medium-, and high-volume centers, respectively. Compared to the high-volume centers, the medium- (OR 1.97, 95% CI 1.35–2.88) and low-volume centers (OR 2.29, 95% CI 1.60–3.27) showed higher adjusted risk of in-hospital mortality. Conclusions : Lower case volume is associated with increased in-hospital mortality after AVR and MVR. The results warrant a comprehensive discussion regarding regionalization/centralization of cardiac valve replacements to optimize patient outcomes

A Patient With Dysphagia due to an Aortic Aneurysm

Dysphagia aortica is difficulty in swallowing caused by extrinsic compression of the esophagus due to an ectatic, tortuous, or aneurysmatic atherosclerotic thoracic aorta. This condition is very uncommon, and it is usually associated with old age, women with short stature, hypertension, and kyphosis. We report herein a case involving a patient with dysphagia who had an aortic aneurysm

Evaluation of changes in random blood glucose and body mass index during and after completion of chemotherapy in children with acute lymphoblastic leukemia

PurposeImproved survival of patients with childhood acute lymphoblastic leukemia (ALL) has drawn attention to the potential for late consequences of previous treatments among survivors, including metabolic syndrome. In this study, we evaluated changes in 3 parameters, namely, random blood glucose, body mass index (BMI), and Z score for BMI (Z-BMI), in children with ALL during chemotherapy and after completion of treatment.MethodsPatients newly diagnosed with ALL from January, 2005 to December, 2008 at Saint Mary's Hospital, The Catholic University of Korea, who completed treatment with chemotherapy only were included (n=107). Random glucose, BMI, and Z-BMI were recorded at 5 intervals: at diagnosis, before maintenance treatment, at completion of maintenance treatment, and 6 and 12 months after completion of maintenance treatment. Similar analyses were conducted on 2 subcohorts based on ALL risk groups.ResultsFor random glucose, a paired comparison showed significantly lower levels at 12 months post-treatment compared to those at initial diagnosis (P<0.001) and before maintenance (P<0.001). The Z-BMI score was significantly higher before maintenance than at diagnosis (P<0.001), but decreased significantly at the end of treatment (P<0.001) and remained low at 6 months (P<0.001) and 12 months (P<0.001) post-treatment. Similar results were obtained upon analysis of risk group-based subcohorts.ConclusionFor a cohort of ALL patients treated without allogeneic transplantation or cranial irradiation, decrease in random glucose and Z-BMI after completion of chemotherapy does not indicate future glucose intolerance or obesity

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

© 2019, The Author(s), under exclusive licence to Springer Nature America, Inc. Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification

Host-linked soil viral ecology along a permafrost thaw gradient

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1,2,3,4,5,6,7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8,9,10, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling

The assessment of efficacy of porcine reproductive respiratory syndrome virus inactivated vaccine based on the viral quantity and inactivation methods

<p>Abstract</p> <p>Background</p> <p>There have been many efforts to develop efficient vaccines for the control of porcine reproductive and respiratory syndrome virus (PRRSV). Although inactivated PRRSV vaccines are preferred for their safety, they are weak at inducing humoral immune responses and controlling field PRRSV infection, especially when heterologous viruses are involved.</p> <p>Results</p> <p>In all groups, the sample to positive (S/P) ratio of IDEXX ELISA and the virus neutralization (VN) titer remained negative until challenge. While viremia did not reduce in the vaccinated groups, the IDEXX-ELISA-specific immunoglobulin G increased more rapidly and to significantly greater levels 7 days after the challenge in all the vaccinated groups compared to the non-vaccinated groups (<it>p </it>< 0.05). VN titer was significantly different in the 10⁶PFU/mL PRRSV vaccine-inoculated and binary ethylenimine (BEI)-inactivated groups 22 days after challenge (<it>p </it>< 0.05). Consequently, the inactivated vaccines tested in this study provided weak memory responses with sequential challenge without any obvious active immune responses in the vaccinated pigs.</p> <p>Conclusions</p> <p>The inactivated vaccine failed to show the humoral immunity, but it showed different immune response after the challenge compared to mock group. Although the 10⁶PFU/mL-vaccinated and BEI-inactivated groups showed significantly greater VN titers 22 days after challenge, all the groups were already negative for viremia.</p