Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes

© The Authors 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Functional & Integrative Genomics 10 (2010): 97-110, doi:10.1007/s10142-009-0142-y.Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1.This research was supported by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research under the Genomics: GTL Program via the Shewanella Federation consortium

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

<p>Abstract</p> <p>Background</p> <p>A widely-used approach for discovering functional and physical interactions among proteins involves phylogenetic profile comparisons (PPCs). Here, proteins with similar profiles are inferred to be functionally related under the assumption that proteins involved in the same metabolic pathway or cellular system are likely to have been co-inherited during evolution.</p> <p>Results</p> <p>Our experimentation with <it>E. coli </it>and yeast proteins with 16 different carefully composed reference sets of genomes revealed that the phyletic patterns of proteins in prokaryotes alone could be adequate enough to make reasonably accurate functional linkage predictions. A slight improvement in performance is observed on adding few eukaryotes into the reference set, but a noticeable drop-off in performance is observed with increased number of eukaryotes. Inclusion of most parasitic, pathogenic or vertebrate genomes and multiple strains of the same species into the reference set do not necessarily contribute to an improved sensitivity or accuracy. Interestingly, we also found that evolutionary histories of individual pathways have a significant affect on the performance of the PPC approach with respect to a particular reference set. For example, to accurately predict functional links in carbohydrate or lipid metabolism, a reference set solely composed of prokaryotic (or bacterial) genomes performed among the best compared to one composed of genomes from all three super-kingdoms; this is in contrast to predicting functional links in translation for which a reference set composed of prokaryotic (or bacterial) genomes performed the worst. We also demonstrate that the widely used random null model to quantify the statistical significance of profile similarity is incomplete, which could result in an increased number of false-positives.</p> <p>Conclusion</p> <p>Contrary to previous proposals, it is not merely the number of genomes but a careful selection of informative genomes in the reference set that influences the prediction accuracy of the PPC approach. We note that the predictive power of the PPC approach, especially in eukaryotes, is heavily influenced by the primary endosymbiosis and subsequent bacterial contributions. The over-representation of parasitic unicellular eukaryotes and vertebrates additionally make eukaryotes less useful in the reference sets. Reference sets composed of highly non-redundant set of genomes from all three super-kingdoms fare better with pathways showing considerable vertical inheritance and strong conservation (e.g. translation apparatus), while reference sets solely composed of prokaryotic genomes fare better for more variable pathways like carbohydrate metabolism. Differential performance of the PPC approach on various pathways, and a weak positive correlation between functional and profile similarities suggest that caution should be exercised while interpreting functional linkages inferred from genome-wide large-scale profile comparisons using a single reference set.</p

Stakeholder perceptions on Community-Based Ecological Mangrove Restoration (CBEMR):a case study in Thailand

Mangroves are a unique ecosystem that provides various benefits to people. In Thailand, Mangrove Action Project (MAP) has introduced Community-Based Ecological Mangrove Restoration (CBEMR), a novel technique to restore degraded mangroves. Unlike conventional tree planting, CBEMR does not require a planting phase. It emphasizes preproject assessments of mangrove ecology and hydrology to facilitate natural regeneration. Therefore, this study aims to (1) investigate the perception of stakeholders on the value of mangroves; (2) examine the understanding of stakeholders on conventional mangrove planting and CBEMR as mangrove restoration techniques; (3) understand the challenges and motivations of the CBEMR efforts in the Andaman Coast of Southern Thailand. We use Q Methodology, a semi-quantitative method that requires participants to rank a set of statements to analyze their perceptions according to the research questions. As a result, we can identify three clusters of perceptions; D1 demands more CBEMR and less conventional planting. D2 believes mangrove planting is good, given suitable conditions. D3 thinks restoring mangroves brings benefits, but most conventional planting often fails. This study highlighted that all CBEMR stakeholders believe inadequate technical knowledge is the root cause of mismatch restoration practices. Mangrove planting should be done with suitable species, conditions, and areas. Conventional planting of mangroves without considering ecological factors and local engagement should be avoided as it fails to achieve sustainable outcomes. Enhancing knowledge of mangrove ecology and restoration techniques is therefore a sustainable route to the long-term success of mangrove restoration in Thailand.</p

Ambulatory Toxicity Management (AToM) in patients receiving adjuvant or neo-adjuvant chemotherapy for early stage breast cancer - a pragmatic cluster randomized trial protocol

Abstract Background Population-based studies suggest that emergency department visits and hospitalizations are common among patients receiving chemotherapy and that rates in routine practice are higher than expected from clinical trials. Chemotherapy-related toxicities are often predictable and, consequently, acute care visits may be preventable with adequate treatment planning and support between visits to the cancer centre. We will evaluate the impact of proactive telephone-based toxicity management on emergency department visits and hospitalizations in women with early stage breast cancer receiving chemotherapy. Methods In this pragmatic covariate constraint-based cluster randomized trial, 20 centres in Ontario, Canada are randomly allocated to either proactive telephone toxicity management (intervention) or routine care (control). The primary outcome is the cluster-level mean number of ED + H visits per patient evaluated using Ontario administrative healthcare data. Participants are all patients with early stage (I-III) breast cancer commencing adjuvant or neo-adjuvant chemotherapy at participating institutions during the intervention period. At least 25 patients at each centre participate in a patient reported outcomes sub-study involving the collection of standardized questionnaires to measure: severity of treatment toxicities, self-care, self-efficacy, quality of life, and coordination of care. Patients participating in the patient reported outcomes (PRO) sub-study are asked to provide written consent to link their PRO data to administrative data. Unit costs will be applied to each per person resource utilized, and a total cost per population and patient will be generated. An incremental cost-effectiveness analysis will be undertaken to compare the incremental costs and outcomes between the intervention and control groups from the health system perspective. Discussion This study evaluates the effectiveness of a proactive toxicity management intervention in a routine care setting. The use of administrative healthcare data to evaluate the primary outcome enables an evaluation in a real world setting and at a much larger scale than previous studies. Trial registration Clinicaltrials.gov , NCT02485678. Registered 30 June 2015

A new storm-petrel species from Chile

We describe a new species of storm-petrel, Oceanites pincoyae (Pincoya Storm-Petrel), from the Puerto Montt and Chacao channel area, Chile. The description is based on 1 specimen collected at sea in Seno Reloncavi on 19 February 2011 and 11 other individuals that were caught, examined, and released. The new taxon's foraging ecology and behavioral habits are unique among the southern Oceanitinae, including "mouse-runs" and repeated diving beneath the surface to retrieve food items. Its distinctive appearance includes bold white ulnar bars, extensive white panels to the underwing, and white to the lower belly and vent. Among species of Oceanites, it is unique in showing white outer vanes to the outer two pairs of rectrices. It further differs from all other storm-petrels in having a distinctive juvenile plumage. Morphometrically it is distinct from Oceanites gracilis gracilis (Elliot's Storm-Petrel) and smaller than O. oceananicus chilensis (the Fuegian form of Wilson's Storm-Petrel), h

Antibiotic resistance in invasive Streptococcus pneumoniae isolates identified in Scotland between 1999 and 2007

Data from 4727 invasive isolates of Streptococcus pneumoniae submitted to the Scottish Haemophilus, Legionella, Meningococcus and Pneumococcus Reference Laboratory between 1999 and 2007 were analysed to establish susceptibility profiles to penicillin, erythromycin and cefotaxime. Pneumococcal resistance to penicillin over the study period remained low, with only 0.2?% (n=7/4727) of isolates falling into this category (MIC ?2?mg l(-1)). These isolates have been sporadic, and have mainly represented serogroup 14 (ST9) and 9 (ST156). In comparison, the 'intermediate sensitivity' group (MIC 0.12-1?mg l(-1)) ranged between 2 and 6?% per year, the majority from serogroup 9 (ST156). Over the study period, we found that 12?% (n=585/4727) of isolates were erythromycin-resistant (MIC &gt;0.5?mg l(-1)), with the majority (n=467; 80?%) of these isolates identified as serogroup 14 (ST9). Cephalosporin resistance (cefotaxime MIC &gt;1?mg l(-1)) was found in only 0.06?% (n=2/3135) of isolates. Internationally recognized clones (Pneumococcal Molecular Epidemiology Network) accounted for 35?% (n=28/81) of the penicillin non-susceptible isolates and 75?% (n=248/330) of the macrolide-resistant isolates, with ST9 and ST306 predominating. Between 1999 and 2007 we found that 11.6?% (n=18/155) of the penicillin non-susceptible isolates and 4.8?% (n=28/585) of the macrolide-resistant isolates were from serogroups not covered by the 7-valent conjugate pneumococcal vaccine in use in the UK since 2006. Susceptibility to first-line antimicrobial agents for invasive pneumococcal disease in Scotland remained high over the period 1999-200