Plasticity of fimbrial genotype and serotype within populations of <em>Bordetella pertussis</em>:analysis by paired flow cytometry and genome sequencing

The fimbriae of Bordetella pertussis are required for colonization of the human respiratory tract. Two serologically distinct fimbrial subunits, Fim2 and Fim3, considered important vaccine components for many years, are included in the Sanofi Pasteur 5-component acellular pertussis vaccine, and the World Health Organization recommends the inclusion of strains expressing both fimbrial serotypes in whole-cell pertussis vaccines. Each of the fimbrial major subunit genes, fim2, fim3, and fimX, has a promoter poly(C) tract upstream of its −10 box. Such monotonic DNA elements are susceptible to changes in length via slipped-strand mispairing in vitro and in vivo, which potentially causes on/off switching of genes at every cell division. Here, we have described intra-culture variability in poly(C) tract lengths and the resulting fimbrial phenotypes in 22 recent UK B. pertussis isolates. Owing to the highly plastic nature of fimbrial promoters, we used the same cultures for both genome sequencing and flow cytometry. Individual cultures of B. pertussis contained multiple fimbrial serotypes and multiple different fimbrial promoter poly(C) tract lengths, which supports earlier serological evidence that B. pertussis expresses both serotypes during infection.</jats:p

Marine and estuarine ecosystem and habitat classification

The Ecological Society of America and NOAA's Offices of Habitat Conservation and Protected Resources sponsored a workshop to develop a national marine and estuarine ecosystem classification system. Among the 22 people involved were scientists who had developed various regional classification systems and managers from NOAA and other federal agencies who might ultimately use this system for conservation and management. The objectives were to: (1) review existing global and regional classification systems; (2) develop the framework of a national classification system; and (3) propose a plan to expand the framework into a comprehensive classification system. Although there has been progress in the development of marine classifications in recent years, these have been either regionally focused (e.g., Pacific islands) or restricted to specific habitats (e.g., wetlands; deep seafloor). Participants in the workshop looked for commonalties across existing classification systems and tried to link these using broad scale factors important to ecosystem structure and function

Implementation of genomic surveillance of SARS-CoV-2 in the Caribbean: Lessons learned for sustainability in resource-limited settings

The COVID-19 pandemic highlighted the importance of global genomic surveillance to monitor the emergence and spread of SARS-CoV-2 variants and inform public health decision-making. Until December 2020 there was minimal capacity for viral genomic surveillance in most Caribbean countries. To overcome this constraint, the COVID-19: Infectious disease Molecular epidemiology for PAthogen Control & Tracking (COVID-19 IMPACT) project was implemented to establish rapid SARS-CoV-2 whole genome nanopore sequencing at The University of the West Indies (UWI) in Trinidad and Tobago (T&T) and provide needed SARS-CoV-2 sequencing services for T&T and other Caribbean Public Health Agency Member States (CMS). Using the Oxford Nanopore Technologies MinION sequencing platform and ARTIC network sequencing protocols and bioinformatics pipeline, a total of 3610 SARS-CoV-2 positive RNA samples, received from 17 CMS, were sequenced in-situ during the period December 5th 2020 to December 31st 2021. Ninety-one Pango lineages, including those of five variants of concern (VOC), were identified. Genetic analysis revealed at least 260 introductions to the CMS from other global regions. For each of the 17 CMS, the percentage of reported COVID-19 cases sequenced by the COVID-19 IMPACT laboratory ranged from 0·02% to 3·80% (median = 1·12%). Sequences submitted to GISAID by our study represented 73·3% of all SARS-CoV-2 sequences from the 17 CMS available on the database up to December 31st 2021. Increased staffing, process and infrastructural improvement over the course of the project helped reduce turnaround times for reporting to originating institutions and sequence uploads to GISAID. Insights from our genomic surveillance network in the Caribbean region directly influenced non-pharmaceutical countermeasures in the CMS countries. However, limited availability of associated surveillance and clinical data made it challenging to contextualise the observed SARS-CoV-2 diversity and evolution, highlighting the need for development of infrastructure for collecting and integrating genomic sequencing data and sample-associated metadata

Marine Biodiversity in the Caribbean: Regional Estimates and Distribution Patterns

This paper provides an analysis of the distribution patterns of marine biodiversity and summarizes the major activities of the Census of Marine Life program in the Caribbean region. The coastal Caribbean region is a large marine ecosystem (LME) characterized by coral reefs, mangroves, and seagrasses, but including other environments, such as sandy beaches and rocky shores. These tropical ecosystems incorporate a high diversity of associated flora and fauna, and the nations that border the Caribbean collectively encompass a major global marine biodiversity hot spot. We analyze the state of knowledge of marine biodiversity based on the geographic distribution of georeferenced species records and regional taxonomic lists. A total of 12,046 marine species are reported in this paper for the Caribbean region. These include representatives from 31 animal phyla, two plant phyla, one group of Chromista, and three groups of Protoctista. Sampling effort has been greatest in shallow, nearshore waters, where there is relatively good coverage of species records; offshore and deep environments have been less studied. Additionally, we found that the currently accepted classification of marine ecoregions of the Caribbean did not apply for the benthic distributions of five relatively well known taxonomic groups. Coastal species richness tends to concentrate along the Antillean arc (Cuba to the southernmost Antilles) and the northern coast of South America (Venezuela – Colombia), while no pattern can be observed in the deep sea with the available data. Several factors make it impossible to determine the extent to which these distribution patterns accurately reflect the true situation for marine biodiversity in general: (1) highly localized concentrations of collecting effort and a lack of collecting in many areas and ecosystems, (2) high variability among collecting methods, (3) limited taxonomic expertise for many groups, and (4) differing levels of activity in the study of different taxa

The SAMI Galaxy Survey: Data Release One with emission-line physics value-added products

We present the first major release of data from the SAMI Galaxy Survey. This data release focuses on the emission-line physics of galaxies. Data Release One includes data for 772 galaxies, about 20 per cent of the full survey. Galaxies included have the redshift range 0.004 &lt; z &lt; 0.092, a large mass range (7.6 &lt; logM*/M⊙ &lt; 11.6), and star formation rates of ~10-4 to ~101M⊙ yr-1. For each galaxy, we include two spectral cubes and a set of spatially resolved 2D maps: single- and multi-component emission-line fits (with dust-extinction corrections for strong lines), local dust extinction, and star formation rate. Calibration of the fibre throughputs, fluxes, and differential atmospheric refraction has been improved over the Early Data Release. The data have average spatial resolution of 2.16 arcsec (full width at half-maximum) over the 15 arcsec diameter field of view and spectral (kinematic) resolution of R = 4263 (σ = 30 km s-1) around Ha. The relative flux calibration is better than 5 per cent, and absolute flux calibration has an rms of 10 per cent. The data are presented online through the Australian Astronomical Observatory's Data Central

The SAMI Galaxy Survey : data release one with emission-line physics value-added products

SAMI DR1 data products available from http://datacentral.aao.gov.au/asvo/surveys/sami/We present the first major release of data from the SAMI Galaxy Survey. This data release focuses on the emission-line physics of galaxies. Data Release One includes data for 772 galaxies, about 20% of the full survey. Galaxies included have the redshift range 0.004 <  z < 0.092, a large massrange (7.6 < log M∗/M⊙ < 11.6), and star-formation rates of ∼10−4 to ∼101 M⊙yr−1. For each galaxy, we include two spectral cubes and a set of spatially resolved 2D maps: single- and multi-component emission-line fits (with dust extinction corrections for strong lines), local dust extinction and star-formation rate. Calibration of the fibre throughputs, fluxes and differential-atmospheric-refraction has been improved over the Early Data Release. The data have average spatial resolution of 2.16 arcsec (FWHM) over the 15 arcsec diameter field of view and spectral (kinematic) resolution R= 4263 (σ= 30 km s−1) around Hα. The relative flux calibration is better than 5% and absolute flux calibration better than ±0.22 mag, with the latter estimate limited by galaxy photometry. The data are presented online through the Australian Astronomical Observatory’s Data Central.Publisher PDFPeer reviewe

The year’s work in stylistics 2009

At a recent conference on the linguistics of English (ISLE, Freiburg, 2008) I was surprised by the number of talks on topics that for me were clearly related to stylistics. My surprise was not that stylistics papers should be so prevalent at a linguistics conference but that the presenters of these papers seemed not to consider their work as primarily stylistic in nature. Most positioned themselves as historical linguists or sociolinguists and presented their work as contributions to historical linguistics and sociolinguistics respectively, despite the fact that all of them were concerned with aspects of style. Along with a number of PALA colleagues, I gave a paper in a dedicated stylistics strand, though in retrospect it now seems that it would perhaps have been more valuable to have integrated our explicitly stylistic papers into the conference generally; after all, the interest in stylistics was clearly there, even if it was not designated as such