Genome content and phylogenomics reveal both ancestral and lateral evolutionary pathways in plant-pathogenic Streptomyces species

© 2016, American Society for Microbiology. All Rights Reserved. Streptomyces spp. are highly differentiated actinomycetes with large, linear chromosomes that encode an arsenal of biologically active molecules and catabolic enzymes. Members of this genus are well equipped for life in nutrient-limited environments and are common soil saprophytes. Out of the hundreds of species in the genus Streptomyces, a small group has evolved the ability to infect plants. The recent availability of Streptomyces genome sequences, including four genomes of pathogenic species, provided an opportunity to characterize the gene content specific to these pathogens and to study phylogenetic relationships among them. Genome sequencing, comparative genomics, and phylogenetic analysis enabled us to discriminate pathogenic from saprophytic Streptomyces strains; moreover, we calculated that the pathogen-specific genome contains 4,662 orthologs. Phylogenetic reconstruction suggested that Streptomyces scabies and S. ipomoeae share an ancestor but that their biosynthetic clusters encoding the required virulence factor thaxtomin have diverged. In contrast, S. turgidiscabies and S. acidiscabies, two relatively unrelated pathogens, possess highly similar thaxtomin biosynthesis clusters, which suggests that the acquisition of these genes was through lateral gene transfer

Advancing environmental risk assessment of regulated products under EFSA's remit

The pre‐market environmental risk assessment (ERA ) of regulated products such as genetically modified organisms, plant protection products and feed additives is an important process to safeguard the desired level of protection of the environment and biodiversity. ERA evaluates the potential adverse effects on the environment of certain actions, and is an important analytical scientific tool to support regulatory decision‐making. Significant advances have been made in the field in recent years. Potential avenues to the further advancement of ERA of regulated products under EFSA 's remit were discussed during the breakout session ‘Advancing environmental risk assessment’ held at the EFSA 2nd Scientific Conference ‘Shaping the Future of Food Safety, Together’ (Milan, Italy, 14–16 October 2015). The value of ERA and its relevance to decision‐making can be increased by: (1) using the ecosystem services approach to make protection goals operational; (2) relying on problem formulation to enhance the relevance of ERA studies; (3) complying with quality standards to warrant the reliability of ERA studies; (4) making ERA more contextual by accounting for multiple stressors and environmental benefits; and (5) acknowledging the strengths and limitations of post‐market environmental monitoring as a tool to resolve scientific uncertainties

Misapplication of the Tarasoff duty to driving cases: A call for a reframing of theory

In the years since the original Tarasoff cases created a new duty for psychotherapists toward third parties harmed by patients' violence, a series of cases nationwide-so called "driving casesv-have applied Tarasoff-like reasoning to situations where a patient injured others while driving a car. Our thesis in this paper is that such application is inappropriate since it represents an unjustified and largely unexamined assumption that driving injury is an expression of the mental-illnessderived intended violence that justifies the Tarasoff duty and its inevitable associated breach of confidentiality. We suggest to the contrary that driving cases almost invariably result from a patient's negligent driving rather than intentional violence stemming from mental illness; that clinicians in most instances have almost no capacity, training, or clinical bases on which to predict a patient's future negligence, violence aside; and that the theory of driving cases should be revised

A Comparison of Honey Bee-Collected Pollen From Working Agricultural Lands Using Light Microscopy and ITS Metabarcoding

Taxonomic identification of pollen has historically been accomplished via light microscopy but requires specialized knowledge and reference collections, particularly when identification to lower taxonomic levels is necessary. Recently, next-generation sequencing technology has been used as a cost-effective alternative for identifying beecollected pollen; however, this novel approach has not been tested on a spatially or temporally robust number of pollen samples. Here, we compare pollen identification results derived from light microscopy and DNA sequencing techniques with samples collected from honey bee colonies embedded within a gradient of intensive agricultural landscapes in the Northern Great Plains throughout the 2010–2011 growing seasons. We demonstrate that at all taxonomic levels, DNA sequencing was able to discern a greater number of taxa, and was particularly useful for the identification of infrequently detected species. Importantly, substantial phenological overlap did occur for commonly detected taxa using either technique, suggesting that DNA sequencing is an appropriate, and enhancing, substitutive technique for accurately capturing the breadth of bee-collected species of pollen present across agricultural landscapes. We also show that honey bees located in high and low intensity agricultural settings forage on dissimilar plants, though with overlap of the most abundantly collected pollen taxa.We highlight practical applications of utilizing sequencing technology, including addressing ecological issues surrounding land use, climate change, importance of taxa relative to abundance, and evaluating the impact of conservation program habitat enhancement efforts

Further characterization of Vibrio vulnificus rugose variants and identification of a capsular and rugose exopolysaccharide gene cluster

Capsular polysaccharide (CPS) is a major virulence factor in Vibrio vulnificus, and encapsulated strains have an opaque, smooth (OpS) colony morphology, while nonencapsulated strains have a translucent, smooth (TrS) colony morphology. Previously, we showed that OpS and TrS parental strains can yield a third colony type, rugose (R), and that the resulting strains, with the OpR and TrR phenotypes, respectively, form copious biofilms. Here we show that while OpR and TrR strains both produce three-dimensional biofilm structures that are indicative of rugose extracellular polysaccharide (rEPS) production, OpR strains also retain expression of CPS and are virulent in an iron-supplemented mouse model, while TrR strains lack CPS and are avirulent. Chlorine resistance assays further distinguished OpR and TrR isolates as exposure to 3 μg/ml NaOCl eradicated both OpS and OpR strains, while both TrS and TrR strains survived, but at rates which were significantly different from one another. Taken together, these results further emphasize the importance of CPS for virulence of V. vulnificus and establish a correlation between CPS expression and chlorine sensitivity in this organism. Using reverse transcriptase PCR, we also identified a nine-gene cluster associated with both CPS and rEPS expression in V. vulnificus, designated the wcr (capsular and rugose polysaccharide) locus, with expression occurring primarily in R variants. The latter results set the stage for characterization of functional determinants which individually or collectively contribute to expression of multiple EPS forms in this pathogen. Copyright © 2008, American Society for Microbiology. All Rights Reserved

Political institutions and debt crises

This paper shows that political institutions matter in explaining defaults on external and domestic debt obligations. We explore a large number of political and macroeconomic variables using a non-parametric technique to predict safety from default. The advantage of this technique is that it is able to identify patterns in the data that are not captured in standard probit analysis. We find that political factors matter, and do so in different ways for democratic and non-democratic regimes, and for domestic and external debt. In democracies, a parliamentary system or sufficient checks and balances almost guarantee the absence of default on external debt when economic fundamentals or liquidity are sufficiently strong. In dictatorships, high stability and tenure play a similar role for default on domestic debt

How fast is fast enough? Academic behavioural science impacting public health policy and practice

Background: COVID-19 emphasised the crucial role behaviour change plays in protecting population health. However, the interchange between academic behavioural science and Public Health (PH) policy and practice could be strengthened. We aimed to establish a sustainable method of joint working between two groups in North Scotland to enable rapid impact of behavioural science on population health.Methods: An implementation-sciences based approach tested the initial 4 steps of an 8-step collaboration process model, designed to identify a health problem (step 1), develop and test messaging interventions (step 2-4), implement the intervention (steps 5-6), and evaluate impact (steps 7-8).Results: Since October 2022, fortnightly meetings were established, implementing the process model. This project will focus on the following outcomes: perceived collaboration usefulness, collaboration-process barriers, and facilitators.Conclusions: Unless a sustainable method of joint working can be established in times where there are no urgent PH priorities, it is unlikely that the fruits of behavioural science can be aligned with PH challenges when outbreaks are happening to rapidly impact population health.<br/

Ropeless fishing to prevent large whale entanglements: Ropeless Consortium report

The 2017 North Atlantic right whale (NARW) unusual mortality event and an increase in humpback whale entanglements off the U.S. West Coast have driven significant interest in ropeless trap/pot fishing. Removing the vertical buoy lines used to mark traps on the sea floor and haul them up would dramatically reduce or eliminate entanglements, the leading cause of NARW mortality, while potentially allowing fishermen to harvest in areas that would otherwise need to be closed to protect whales. At the first annual Ropeless Consortium meeting, researchers, fishing industry representatives, manufacturers, conservationists, and regulators discussed existing and developing technological replacements for the marking and retrieval functions of buoy lines. Fishermen and NGO partners shared their experience demonstrating ropeless systems and provided feedback to improve the designs. U.S. and Canadian federal regulators discussed prospects to use ropeless fishing gear in areas closed to fishing with vertical lines, as well as other options to reduce entanglements, and a Massachusetts official shared additional regulatory considerations involved in ropeless fishing in state waters. Sustainable seafood experts discussed consumer market advantages and endangered, threatened, and protected species impacts in sustainability standards and certifications. Moving forward, there is an immediate need to (1) work with industry partners to iteratively test and improve ropeless retrieval and marking systems to adapt them to the specific conditions of the relevant trap/pot fisheries, (2) create data sharing and communications protocols for ropeless gear location marking, and (3) develop regulatory procedures and enforcement capacity to allow legal ropeless gear use.This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.2020-06-2