A System for Series Magnetic Measurements of the LHC Main Quadrupoles

More than 400 twin aperture lattice quadrupoles are needed for the Large Hadron Collider (LHC) which is under construction at CERN. The main quadrupole is assembled with correction magnets in a common cryostat called the Short Straight Section (SSS). We plan to measure all SSS's in cold conditions with an unprecedented accuracy: integrated gradient of the field within 150 ppm, harmonics in a range of 1 to 5 ppm, magnetic axis of all elements within 0.1 mm and their field direction within 0.2 mrad. In this paper we describe the automatic measurement system that we have designed, built and calibrated. Based on the results obtained on the two first prototypes of the SSS's (SSS3 and SSS4) we show that this system meets all above requirements

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina datasets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as 1 nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures + supplement. Significantly revised for clarity, references added, results not change

Correction to: Detection of the phycotoxin pectenotoxin-2 in waters around King George Island, Antarctica

A correction to this paper has been published: https://doi.org/10.1007/s00300-021-02834-3</jats:p

The time-of-day of myocardial infarction onset affects healing through oscillations in cardiac neutrophil recruitment

Myocardial infarction (MI) is the leading cause of death in Western countries. Epidemiological studies show acute MI to be more prevalent in the morning and to be associated with a poorer outcome in terms of mortality and recovery. The mechanisms behind this association are not fully understood. Here, we report that circadian oscillations of neutrophil recruitment to the heart determine infarct size, healing, and cardiac function after MI Preferential cardiac neutrophil recruitment during the active phase (Zeitgeber time, ZT13) was paralleled by enhanced myeloid progenitor production, increased circulating numbers of CXCR2(hi) neutrophils as well as upregulated cardiac adhesion molecule and chemokine expression. MI at ZT13 resulted in significantly higher cardiac neutrophil infiltration compared to ZT5, which was inhibited by CXCR2 antagonism or neutrophil-specific CXCR2 knockout. Limiting exaggerated neutrophilic inflammation at this time point significantly reduced the infarct size and improved cardiac function

Twin Rotating Coils for Cold Magnetic Measurements of 15 m Long LHC Dipoles

We describe here a new harmonic coil system for the field measurement of the superconducting, twin aperture LHC dipoles and the associated corrector magnets. Besides field measurements the system can be used as an antenna to localize the quench origin. The main component is a 16 m long rotating shaft, made up of 13 ceramic segments, each carrying two tangential coils plus a central radial coil, all working in parallel. The segments are connected with flexible Ti-alloy bellows, allowing the piecewise straight shaft to follow the curvature of the dipole while maintaining high torsional rigidity. At each interconnection the structure is supported by rollers and ball bearings, necessary for the axial movement for installation and for the rotation of the coil during measurement. Two such shafts are simultaneously driven by a twin-rotating unit, thus measuring both apertures of a dipole at the same time. This arrangement allows very short measurement times (typically 10 s) and is essential to perform cold magnetic measurements of all dipoles. The coil surface and direction are calibrated using a reference dipole. In this paper we describe the twin rotating coil system and its calibration facility, and we give the typical resolution and accuracy achieved with the first commissioned unit

Response of a natural Antarctic phytoplankton assemblage to changes in temperature and salinity

The climate around the Western Antarctic Peninsula (WAP) is rapidly changing and dramatically affecting marine coastal waters. Increases in air and seawater temperatures, not matter how small, can alter coastal biological communities due to both temperature increases as well as salinity reduction from glacier melting. The aim of this study was to evaluate the individual and combined effects of elevated sea surface temperature (+4 °C) and decreased salinity (−4) on growth and assemblage composition of natural summer phytoplankton from Potter Cove (King George Island, South Shetlands, northern WAP), using an outdoor microcosm experiment. Pigment composition was analyzed by high performance liquid chromatography (HPLC/Chemtax) and species composition by light and electron microscopy. Increases in phytoplankton biomass during the first 3 days at elevated-temperatures coincided with an increase in the abundance and the specific growth rate of small centric diatoms (Chaetoceros socialis and Shionodiscus gaarderae, mostly observed in temperate waters) and unidentified small phytoflagellates &lt;5 μm. In contrast, pennate diatoms significantly decreased. At the end of the experiment on day 7, under nitrate and phosphate limitation, chlorophytes abundances increased under low salinity whereas prasinophytes decreased in all treatments. This study suggests that climate change could notably affect Antarctic phytoplankton composition by favouring temperate-water species previously undetected in Antarctic waters, such us S. gaarderae. Moreover, the observed changes in phytoplankton structure, associated with an increase of nano- over micro-size taxa, could have important implications for future Antarctic food webs

Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions

Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational complexity and lack of documentation hinder researchers from analyzing their high-throughput data to its true potential. In this chapter we detail our data-driven, transkingdom network (TransNet) analysis protocol to integrate and interrogate multi-omics data. This systems biology approach has allowed us to successfully identify important causal relationships between different taxonomic kingdoms (e.g. mammals and microbes) using diverse types of data

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse donor strains. This fraction, comprising 80% of the identified transconjugants, thus has the potential to dominate IncP- and IncPromA-type plasmid transfer in soil. Our results demonstrate that these broad host range plasmids have a hitherto unrecognized potential to transfer readily to very diverse bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids.Fil: Klumper, Uli. Technical University of Denmark; DinamarcaFil: Riber, Leise. Universidad de Copenhagen; DinamarcaFil: Dechesne, Arnaud. Technical University of Denmark; DinamarcaFil: Sannazzaro, Analía Inés. Universidad de Copenhagen; DinamarcaFil: Hansen, Lars H.. Universidad de Copenhagen; Dinamarca. Aarhus University. Roskilde; DinamarcaFil: Sørensen, Søren. Universidad de Copenhagen; DinamarcaFil: Smets, Barth F. Technical University of Denmark; Dinamarc

The Diversity of Coral Reefs: What Are We Missing?

Tropical reefs shelter one quarter to one third of all marine species but one third of the coral species that construct reefs are now at risk of extinction. Because traditional methods for assessing reef diversity are extremely time consuming, taxonomic expertise for many groups is lacking, and marine organisms are thought to be less vulnerable to extinction, most discussions of reef conservation focus on maintenance of ecosystem services rather than biodiversity loss. In this study involving the three major oceans with reef growth, we provide new biodiversity estimates based on quantitative sampling and DNA barcoding. We focus on crustaceans, which are the second most diverse group of marine metazoans. We show exceptionally high numbers of crustacean species associated with coral reefs relative to sampling effort (525 species from a combined, globally distributed sample area of 6.3 m2). The high prevalence of rare species (38% encountered only once), the low level of spatial overlap (81% found in only one locality) and the biogeographic patterns of diversity detected (Indo-West Pacific>Central Pacific>Caribbean) are consistent with results from traditional survey methods, making this approach a reliable and efficient method for assessing and monitoring biodiversity. The finding of such large numbers of species in a small total area suggests that coral reef diversity is seriously under-detected using traditional survey methods, and by implication, underestimated

Bacterial community development in experimental gingivitis.

Current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. This study used 454-pyrosequencing of the V1-V3 region of 16S rRNA genes (approximately 500 bp), and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. A total of 20 healthy volunteers abstained from oral hygiene for two weeks, allowing plaque to accumulate and gingivitis to develop. Plaque samples were analyzed at baseline, and after one and two weeks. In addition, plaque samples from 20 chronic periodontitis patients were analyzed for cross-sectional comparison to the experimental gingivitis cohort. All of the healthy volunteers developed gingivitis after two weeks. Pyrosequencing yielded a final total of 344,267 sequences after filtering, with a mean length of 354 bases, that were clustered into an average of 299 species-level Operational Taxonomic Units (OTUs) per sample. Principal coordinates analysis (PCoA) plots revealed significant shifts in the bacterial community structure of plaque as gingivitis was induced, and community diversity increased significantly after two weeks. Changes in the relative abundance of OTUs during the transition from health to gingivitis were correlated to bleeding on probing (BoP) scores and resulted in the identification of new health- and gingivitis-associated taxa. Comparison of the healthy volunteers to the periodontitis patients also confirmed the association of a number of putative periodontal pathogens with chronic periodontitis. Taxa associated with gingivitis included Fusobacterium nucleatum subsp. polymorphum, Lachnospiraceae [G-2] sp. HOT100, Lautropia sp. HOTA94, and Prevotella oulorum, whilst Rothia dentocariosa was associated with periodontal health. Further study of these taxa is warranted and may lead to new therapeutic approaches to prevent periodontal disease.BBSRC Industrial Case Studentship ref no. BB/G01714X/1 in collaboration with GlaxoSmithKline