Core-Genome Multilocus Sequence Typing for Epidemiological and Evolutionary Analyses of Phytopathogenic Xanthomonas citri

Xanthomonas citri subsp. citri is the cause of bacterial citrus canker, responsible for major economic losses to the citrus industry. X. citri subspecies and pathovars are responsible for diseases in soybean, common bean, mango, pomegranate, and cashew. X. citri disease has been tracked using several typing methods, but recent studies using genomic sequencing have been key to understanding the evolutionary relationships within the species, including fundamental differences among X. citri subsp. citri pathotypes. Here, we describe a core-genome multilocus sequence typing (cgMLST) scheme for X. citri based on 250 genomes comprising multiple examples of X. citri subsp. citri pathotypes A, A*, and Aw; X. citri subsp. malvacearum; X. citri pv. aurantifolii, pv. fuscans, pv. glycines, pv. mangiferaeindicae, pv. viticola, and pv. vignicola; and single isolates of X. citri pv. dieffenbachiae and pv. punicae. This data set included genomic sequencing of 100 novel X. citri subsp. citri isolates. cgMLST, based on 1,618 core genes across 250 genomes, is implemented at PubMLST (https://pubmlst.org/organisms/xanthomonas-citri/). GrapeTree minimum-spanning tree and Interactive Tree of Life (iTOL) neighbor-joining phylogenies generated from the cgMLST data resolved almost identical groupings of isolates to a core-genome single nucleotide polymorphism (SNP)-based neighbor-joining phylogeny. These resolved identical groupings of X. citri subsp. citri pathotypes and X. citri subspecies and pathovars. X. citri cgMLST should prove to be an increasingly valuable resource for the study of this key species of plant-pathogenic bacteria. Users can submit genomic data and associated metadata for comparison with previously characterized isolates at PubMLST to allow the rapid characterization of the local, national, and global epidemiology of these pathogens and examine evolutionary relationships

Anaerobic removal of 1-methoxy-2-propanol under ambient temperature in an EGSB reactor

Two laboratory-scale expanded granular sludge bed (EGSB) reactors were operated at 18 and 25 C, respectively, for the treatment of synthetic wastewater composed of ethanol and 1-methoxy-2-propanol (M2P) in a mass ratio of 4:1. Reactors were operated first with continuous wastewater supply and after with discontinuous substrate supply (5 days a week, 16 h a day) to simulate shift working conditions. Under continuous wastewater supply chemical oxygen demand (COD), removal efficiency higher than 95 % was achieved at the end of the trial applying organic loading rates (OLR) of 29 and 43 kg COD m-3 day-1 at 18 and 25 C; thus, corresponding to M2P OLR of 6.4 and 9.3 kg COD m-3 day-1, respectively. During intermittent supply of substrate, good performance was recorded at both temperatures with an OLR of 30 kg COD m-3 day-1 (M2P OLR of 6.6 kg COD m-3 day-1). After 56 h without substrate supply, a decline in methane yield of 15¿30 % was observed due to the deactivation of the biomass. Specific methanogenic activity (SMA) assays were carried out at the end of the experiments. SMA values using 1-methoxy-2-propanol as substrate were 24.3 and 7.8 ml CH4 gVSS-1 day-1 at 25 C and at 18 C, respectively. This is the first attempt to investigate the removal of 1-methoxy-2-propanol by EGSB reactors

Electrostatic charging of jumping droplets

With the broad interest in and development of superhydrophobic surfaces for self-cleaning, condensation heat transfer enhancement and anti-icing applications, more detailed insights on droplet interactions on these surfaces have emerged. Specifically, when two droplets coalesce, they can spontaneously jump away from a superhydrophobic surface due to the release of excess surface energy. Here we show that jumping droplets gain a net positive charge that causes them to repel each other mid-flight. We used electric fields to quantify the charge on the droplets and identified the mechanism for the charge accumulation, which is associated with the formation of the electric double layer at the droplet–surface interface. The observation of droplet charge accumulation provides insight into jumping droplet physics as well as processes involving charged liquid droplets. Furthermore, this work is a starting point for more advanced approaches for enhancing jumping droplet surface performance by using external electric fields to control droplet jumping.United States. Dept. of Energy. Office of Basic Energy Sciences (Solid-State Solar-Thermal Energy Conversion Center Award DE-FG02-09ER46577)United States. Office of Naval ResearchNational Science Foundation (U.S.) (Major Research Instrumentation Grant for Rapid Response Research (MRI- RAPID))National Science Foundation (U.S.) (Award ECS-0335765)National Science Foundation (U.S.). Graduate Research Fellowship Program (Grant 1122374

Predictive significance of the six-minute walk distance for long-term survival in chronic hypercapnic respiratory failure

Background: The 6-min walk distance ( 6-MWD) is a global marker of functional capacity and prognosis in chronic obstructive pulmonary disease ( COPD), but less explored in other chronic respiratory diseases. Objective: To study the role of 6-MWD in chronic hypercapnic respiratory failure ( CHRF). Methods: In 424 stable patients with CHRF and non-invasive ventilation ( NIV) comprising COPD ( n = 197), restrictive diseases ( RD; n = 112) and obesity-hypoventilation- syndrome ( OHS; n = 115), the prognostic value of 6-MWD for long- term survival was assessed in relation to that of body mass index (BMI), lung function, respiratory muscle function and laboratory parameters. Results: 6-MWD was reduced in patients with COPD ( median 280 m; quartiles 204/350 m) and RD ( 290 m; 204/362 m) compared to OHS ( 360 m; 275/440 m; p <0.001 each). Overall mortality during 24.9 (13.1/40.5) months was 22.9%. In the 424 patients with CHRF, 6-MWD independently predicted mortality in addition to BMI, leukocytes and forced expiratory volume in 1 s ( p <0.05 each). In COPD, 6-MWD was strongly associated with mortality using the median {[} p <0.001, hazard ratio ( HR) = 3.75, 95% confidence interval (CI): 2.24-6.38] or quartiles as cutoff levels. In contrast, 6-MWD was only significantly associated with impaired survival in RD patients when it was reduced to 204 m or less (1st quartile; p = 0.003, HR = 3.31, 95% CI: 1.73-14.10), while in OHS 6-MWD had not any prognostic value. Conclusions: In patients with CHRF and NIV, 6-MWD was predictive for long- term survival particularly in COPD. In RD only severely reduced 6-MWD predicted mortality, while in OHS 6-MWD was relatively high and had no prognostic value. These results support a disease-specific use of 6-MWD in the routine assessment of patients with CHRF. Copyright (C) 2007 S. Karger AG, Basel

Abnormalities in autonomic function in obese boys at-risk for insulin resistance and obstructive sleep apnea.

Study objectivesCurrent evidence in adults suggests that, independent of obesity, obstructive sleep apnea (OSA) can lead to autonomic dysfunction and impaired glucose metabolism, but these relationships are less clear in children. The purpose of this study was to investigate the associations among OSA, glucose metabolism, and daytime autonomic function in obese pediatric subjects.MethodsTwenty-three obese boys participated in: overnight polysomnography; a frequently sampled intravenous glucose tolerance test; and recordings of spontaneous cardiorespiratory data in both the supine (baseline) and standing (sympathetic stimulus) postures.ResultsBaseline systolic blood pressure and reactivity of low-frequency heart rate variability to postural stress correlated with insulin resistance, increased fasting glucose, and reduced beta-cell function, but not OSA severity. Baroreflex sensitivity reactivity was reduced with sleep fragmentation, but only for subjects with low insulin sensitivity and/or low first-phase insulin response to glucose.ConclusionsThese findings suggest that vascular sympathetic activity impairment is more strongly affected by metabolic dysfunction than by OSA severity, while blunted vagal autonomic function associated with sleep fragmentation in OSA is enhanced when metabolic dysfunction is also present

Evolutionary potential and adaptation of Banksia attenuata (Proteaceae) to climate and fire regime in southwestern Australia, a global biodiversity hotspot

Substantial climate changes are evident across Australia, with declining rainfall and rising temperature in conjunction with frequent fires. Considerable species loss and range contractions have been predicted; however, our understanding of how genetic variation may promote adaptation in response to climate change remains uncertain. Here we characterized candidate genes associated with rainfall gradients, temperatures, and fire intervals through environmental association analysis. We found that overall population adaptive genetic variation was significantly affected by shortened fire intervals, whereas declining rainfall and rising temperature did not have a detectable influence. Candidate SNPs associated with rainfall and high temperature were diverse, whereas SNPs associated with specific fire intervals were mainly fixed in one allele. Gene annotation further revealed four genes with functions in stress tolerance, the regulation of stomatal opening and closure, energy use, and morphogenesis with adaptation to climate and fire intervals. B. attenuata may tolerate further changes in rainfall and temperature through evolutionary adaptations based on their adaptive genetic variation. However, the capacity to survive future climate change may be compromised by changes in the fire regime

Hospital Networks and the Dispersal of Hospital-Acquired Pathogens by Patient Transfer

Hospital-acquired infections (HAI) are often seen as preventable incidents that result from unsafe practices or poor hospital hygiene. This however ignores the fact that transmissibility is not only a property of the causative organisms but also of the hosts who can translocate bacteria when moving between hospitals. In an epidemiological sense, hospitals become connected through the patients they share. We here postulate that the degree of hospital connectedness crucially influences the rates of infections caused by hospital-acquired bacteria. To test this hypothesis, we mapped the movement of patients based on the UK-NHS Hospital Episode Statistics and observed that the proportion of patients admitted to a hospital after a recent episode in another hospital correlates with the hospital-specific incidence rate of MRSA bacteraemia as recorded by mandatory reporting. We observed a positive correlation between hospital connectedness and MRSA bacteraemia incidence rate that is significant for all financial years since 2001 except for 2008–09. All years combined, this correlation is positive and significantly different from zero (partial correlation coefficient r = 0.33 (0.28 to 0.38)). When comparing the referral pattern for English hospitals with referral patterns observed in the Netherlands, we predict that English hospitals more likely see a swifter and more sustained spread of HAIs. Our results indicate that hospitals cannot be viewed as individual units but rather should be viewed as connected elements of larger modular networks. Our findings stress the importance of cooperative effects that will have a bearing on the planning of health care systems, patient management and hospital infection control

Overlapping Community Discovery Methods: A Survey

The detection of overlapping communities is a challenging problem which is gaining increasing interest in recent years because of the natural attitude of individuals, observed in real-world networks, to participate in multiple groups at the same time. This review gives a description of the main proposals in the field. Besides the methods designed for static networks, some new approaches that deal with the detection of overlapping communities in networks that change over time, are described. Methods are classified with respect to the underlying principles guiding them to obtain a network division in groups sharing part of their nodes. For each of them we also report, when available, computational complexity and web site address from which it is possible to download the software implementing the method.Comment: 20 pages, Book Chapter, appears as Social networks: Analysis and Case Studies, A. Gunduz-Oguducu and A. S. Etaner-Uyar eds, Lecture Notes in Social Networks, pp. 105-125, Springer,201

Protein Function Assignment through Mining Cross-Species Protein-Protein Interactions

Background: As we move into the post genome-sequencing era, an immediate challenge is how to make best use of the large amount of high-throughput experimental data to assign functions to currently uncharacterized proteins. We here describe CSIDOP, a new method for protein function assignment based on shared interacting domain patterns extracted from cross-species protein-protein interaction data. Methodology/Principal Findings: The proposed method is assessed both biologically and statistically over the genome of H. sapiens. The CSIDOP method is capable of making protein function prediction with accuracy of 95.42 % using 2,972 gene ontology (GO) functional categories. In addition, we are able to assign novel functional annotations for 181 previously uncharacterized proteins in H. sapiens. Furthermore, we demonstrate that for proteins that are characterized by GO, the CSIDOP may predict extra functions. This is attractive as a protein normally executes a variety of functions in different processes and its current GO annotation may be incomplete. Conclusions/Significance: It can be shown through experimental results that the CSIDOP method is reliable and practical in use. The method will continue to improve as more high quality interaction data becomes available and is readily scalable t