Minimum Information about a Biosynthetic Gene cluster

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.Netherlands Organization for Scientific Research (NWO)/Rubicon/825.13.001EU/FP7/Joint Call OCEANBiotechnology and Biological Sciences Research Council (BBSRC)Natural Environment Research Council (UK)National Institute for Energy Ethics and Society (NIEeS; UK)Gordon and Betty Moore FoundationNational Science Foundation (NSF; US)US Department of EnergyEngineering and Physical Sciences Research Council (EPSRC

Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips

Background: Illumina's Infinium SNP BeadChips are extensively used in both small and large-scale genetic studies. A fundamental step in any analysis is the processing of raw allele A and allele B intensities from each SNP into genotype calls (AA, AB, BB). Various algorithms which make use of different statistical models are available for this task. We compare four methods (GenCall, Illuminus, GenoSNP and CRLMM) on data where the true genotypes are known in advance and data from a recently published genome-wide association study.Results: In general, differences in accuracy are relatively small between the methods evaluated, although CRLMM and GenoSNP were found to consistently outperform GenCall. The performance of Illuminus is heavily dependent on sample size, with lower no call rates and improved accuracy as the number of samples available increases. For X chromosome SNPs, methods with sex-dependent models (Illuminus, CRLMM) perform better than methods which ignore gender information (GenCall, GenoSNP). We observe that CRLMM and GenoSNP are more accurate at calling SNPs with low minor allele frequency than GenCall or Illuminus. The sample quality metrics from each of the four methods were found to have a high level of agreement at flagging samples with unusual signal characteristics.Conclusions: CRLMM, GenoSNP and GenCall can be applied with confidence in studies of any size, as their performance was shown to be invariant to the number of samples available. Illuminus on the other hand requires a larger number of samples to achieve comparable levels of accuracy and its use in smaller studies (50 or fewer individuals) is not recommended

Spatial variation and antecedent sea surface temperature conditions influence Hawaiian intertidal community structure

Global sea surface temperatures (SSTs) are increasing, and in Hawaiʻi, rates of ocean warming are projected to double by the end of the 21st century. However, current nearshore warming trends and their possible impacts on intertidal communities are not well understood. This study represents the first investigation into the possible effects of rising SST on intertidal algal and invertebrate communities across the Main Hawaiian Islands (MHI). By utilizing citizen-science data coupled with high-resolution, daily SST satellite measurements from 12 intertidal sites across the MHI from 2004–2019, the response of intertidal algal and invertebrate abundance and community diversity to changes in SST was investigated across multiple spatial scales. Results show high rates of SST warming (0.40°C Decade-1) over this study’s timeframe, similar to predicted rates of warming for Hawaiʻi by the end of the 21st century. Changes in abundance and diversity in response to SST were variable among intertidal sites, but differences in antecedent SST among intertidal sites were significantly associated with community dissimilarity. In addition, a statistically significant positive relationship was found between SST and Simpson’s diversity index, and a significant relationship was also found between SST and the abundance of six dominant taxa. For five of these six dominant taxa, antecedent SSTs over the 6–12 months preceding sampling were the most influential for describing changes to abundance. The increase in community diversity in response to higher SSTs was best explained by temperatures in the 10 months preceding sampling, and the resultant decreased abundance of dominant turf algae. These results highlight rapidly warming nearshore SSTs in Hawaiʻi and the longer-term effects of antecedent SSTs as significant drivers of change within Hawaiian intertidal communities. Therefore, we suggest that future research and management should consider the possibility of lagging effects of antecedent SST on intertidal communities in Hawaiʻi and elsewhere

Flinders Island spotted fever rickettsioses caused by "marmionii" strain of rickettsia honei, Eastern Australia

Australia has 4 rickettsial diseases: murine typhus, Queensland tick typhus, Flinders Island spotted fever, and scrub typhus. We describe 7 cases of a rickettsiosis with an acute onset and symptoms of fever (100%), headache (71%), arthralgia (43%), myalgia (43%), cough (43%), maculopapular/petechial rash (43%), nausea (29%), pharyngitis (29%), lymphadenopathy (29%), and eschar (29%). Cases were most prevalent in autumn and from eastern Australia, including Queensland, Tasmania, and South Australia. One patient had a history of tick bite (Haemaphysalis novaeguineae). An isolate shared 99.2%, 99.8%, 99.8%, 99.9%, and 100% homology with the 17 kDa, ompA, gltA, 16S rRNA, and Sca4 genes, respectively, of Rickettsia honei. This Australian rickettsiosis has similar symptoms to Flinders Island spotted fever, and the strain is genetically related to R. honei. It has been designated the "marmionii" strain of R. honei, in honor of Australian physician and scientist Barrie Marmion

A short, robust brain activation control task optimised for pharmacological fMRI studies

This work was supported by Invicro Ltd.Background: Functional magnetic resonance imaging (fMRI) is a popular method for examining pharmacological effects on the brain; however, the BOLD response is dependent on intact neurovascular coupling, and potentially modulated by a number of physiological factors. Pharmacological fMRI is therefore vulnerable to confounding effects of pharmacological probes on general physiology or neurovascular coupling. Controlling for such non-specific effects in pharmacological fMRI studies is therefore an important consideration, and there is an additional need for well-validated fMRI task paradigms that could be used to control for such effects, or for general testing purposes. Methods: We have developed two variants of a standardized control task that are short (5 minutes duration) simple (for both the subject and experimenter), widely applicable, and yield a number of readouts in a spatially diverse set of brain networks. The tasks consist of four functionally discrete three-second trial types (plus additional null trials) and contain visual, auditory, motor and cognitive (eye-movements, and working memory tasks in the two task variants) stimuli. Performance of the tasks was assessed in a group of 15 subjects scanned on two separate occasions, with test-retest reliability explicitly assessed using intra-class correlation coefficients. Results:  Both tasks produced robust patterns of brain activation in the expected brain regions, and region of interest-derived reliability coefficients for the tasks were generally high, with four out of eight task conditions rated as ‘excellent’ or ‘good’, and only one out of eight rated as ‘poor’. Median values in the voxel-wise reliability measures were also >0.7 for all task conditions, and therefore classed as ‘excellent’ or ‘good’. The spatial concordance between the most highly activated voxels and those with the highest reliability coefficients was greater for the sensory (auditory, visual) conditions than the other (motor, cognitive) conditions Discussion: Either of the two task variants would be suitable for use as a control task in future pharmacological fMRI studies or for any other investigation where a short, reliable, basic task paradigm is required. Stimulus code is available online for re-use by the scientific community.Publisher PDFPeer reviewe

Does wage rank affect employees' well-being?

How do workers make wage comparisons? Both an experimental study and an analysis of 16,000 British employees are reported. Satisfaction and well-being levels are shown to depend on more than simple relative pay. They depend upon the ordinal rank of an individual's wage within a comparison group. “Rank” itself thus seems to matter to human beings. Moreover, consistent with psychological theory, quits in a workplace are correlated with pay distribution skewness

Steady-state modulation of voltage-gated K+ channels in rat arterial smooth muscle by cyclic AMP-dependent protein kinase and protein phosphatase 2B

Voltage-gated potassium channels (Kv) are important regulators of membrane potential in vascular smooth muscle cells, which is integral to controlling intracellular Ca2+ concentration and regulating vascular tone. Previous work indicates that Kv channels can be modulated by receptor-driven alterations of cyclic AMP-dependent protein kinase (PKA) activity. Here, we demonstrate that Kv channel activity is maintained by tonic activity of PKA. Whole-cell recording was used to assess the effect of manipulating PKA signalling on Kv and ATP-dependent K+ channels of rat mesenteric artery smooth muscle cells. Application of PKA inhibitors, KT5720 or H89, caused a significant inhibition of Kv currents. Tonic PKA-mediated activation of Kv appears maximal as application of isoprenaline (a β-adrenoceptor agonist) or dibutyryl-cAMP failed to enhance Kv currents. We also show that this modulation of Kv by PKA can be reversed by protein phosphatase 2B/calcineurin (PP2B). PKA-dependent inhibition of Kv by KT5720 can be abrogated by pre-treatment with the PP2B inhibitor cyclosporin A, or inclusion of a PP2B auto-inhibitory peptide in the pipette solution. Finally, we demonstrate that tonic PKA-mediated modulation of Kv requires intact caveolae. Pre-treatment of the cells with methyl-β-cyclodextrin to deplete cellular cholesterol, or adding caveolin-scaffolding domain peptide to the pipette solution to disrupt caveolae-dependent signalling each attenuated PKA-mediated modulation of the Kv current. These findings highlight a novel, caveolae-dependent, tonic modulatory role of PKA on Kv channels providing new insight into mechanisms and the potential for pharmacological manipulation of vascular tone

Critical animal and media studies: Expanding the understanding of oppression in communication research

Critical and communication studies have traditionally neglected the oppression conducted by humans towards other animals. However, our (mis)treatment of other animals is the result of public consent supported by a morally speciesist-anthropocentric system of values. Speciesism or anthroparchy, as much as any other mainstream ideologies, feeds the media and at the same time is perpetuated by them. The goal of this article is to remedy this neglect by introducing the subdiscipline of Critical Animal and Media Studies. Critical Animal and Media Studies takes inspiration both from critical animal studies – which is so far the most consolidated critical field of research in the social sciences addressing our exploitation of other animals – and from the normative-moral stance rooted in the cornerstones of traditional critical media studies. The authors argue that the Critical Animal and Media Studies approach is an unavoidable step forward for critical media and communication studies to engage with the expanded circle of concerns of contemporary ethical thinking

Supercooled liquid fogs over the central Greenland Ice Sheet

Radiation fogs at Summit Station, Greenland (72.58∘&thinsp;N, 38.48∘&thinsp;W; 3210&thinsp;m&thinsp;a.s.l.), are frequently reported by observers. The fogs are often accompanied by fogbows, indicating the particles are composed of liquid; and because of the low temperatures at Summit, this liquid is supercooled. Here we analyze the formation of these fogs as well as their physical and radiative properties. In situ observations of particle size and droplet number concentration were made using scattering spectrometers near 2 and 10&thinsp;m height from 2012 to 2014. These data are complemented by colocated observations of meteorology, turbulent and radiative fluxes, and remote sensing. We find that liquid fogs occur in all seasons with the highest frequency in September and a minimum in April. Due to the characteristics of the boundary-layer meteorology, the fogs are elevated, forming between 2 and 10&thinsp;m, and the particles then fall toward the surface. The diameter of mature particles is typically 20&ndash;25&thinsp;&micro;m in summer. Number concentrations are higher at warmer temperatures and, thus, higher in summer compared to winter. The fogs form at temperatures as warm as &minus;5&thinsp;∘C, while the coldest form at temperatures approaching &minus;40&thinsp;∘C. Facilitated by the elevated condensation, in winter two-thirds of fogs occurred within a relatively warm layer above the surface when the near-surface air was below &minus;40&thinsp;∘C, as cold as &minus;57&thinsp;∘C, which is too cold to support liquid water. This implies that fog particles settling through this layer of cold air freeze in the air column before contacting the surface, thereby accumulating at the surface as ice without riming. Liquid fogs observed under otherwise clear skies annually imparted 1.5&thinsp;W&thinsp;m&minus;2 of cloud radiative forcing (CRF). While this is a small contribution to the surface radiation climatology, individual events are influential. The mean CRF during liquid fog events was 26&thinsp;W&thinsp;m&minus;2, and was sometimes much higher. An extreme case study was observed to radiatively force 5&thinsp;∘C of surface warming during the coldest part of the day, effectively damping the diurnal cycle. At lower elevations of the ice sheet where melting is more common, such damping could signal a role for fogs in preconditioning the surface for melting later in the day. </div