85 research outputs found
A global perspective on marine photosynthetic picoeukaryote community structure
A central goal in ecology is to understand the factors affecting the temporal dynamics and spatial distribution of microorganisms and the underlying processes causing differences in community structure and composition. However, little is known in this respect for photosynthetic picoeukaryotes (PPEs), algae that are now recognised as major players in marine CO2 fixation. Here, we analysed dot blot hybridisation and cloning–sequencing data, using the plastid-encoded 16S rRNA gene, from seven research cruises that encompassed all four ocean biomes. We provide insights into global abundance, α- and β-diversity distribution and the environmental factors shaping PPE community structure and composition. At the class level, the most commonly encountered PPEs were Prymnesiophyceae and Chrysophyceae. These taxa displayed complementary distribution patterns, with peak abundances of Prymnesiophyceae and Chrysophyceae in waters of high (25:1) or low (12:1) nitrogen:phosphorus (N:P) ratio, respectively. Significant differences in phylogenetic composition of PPEs were demonstrated for higher taxonomic levels between ocean basins, using Unifrac analyses of clone library sequence data. Differences in composition were generally greater between basins (interbasins) than within a basin (intrabasin). These differences were primarily linked to taxonomic variation in the composition of Prymnesiophyceae and Prasinophyceae whereas Chrysophyceae were phylogenetically similar in all libraries. These data provide better knowledge of PPE community structure across the world ocean and are crucial in assessing their evolution and contribution to CO2 fixation, especially in the context of global climate change
Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean
Background: Photosynthetic picoeukaryotes (PPE) with a cell size less than 3 µm play a critical role in oceanic primary production. In recent years, the composition of marine picoeukaryote communities has been intensively investigated by molecular approaches, but their photosynthetic fraction remains poorly characterized. This is largely because the classical approach that relies on constructing 18S rRNA gene clone libraries from filtered seawater samples using universal eukaryotic primers is heavily biased toward heterotrophs, especially alveolates and stramenopiles, despite the fact that autotrophic cells in general outnumber heterotrophic ones in the euphotic zone.
Methodology/Principal Findings: In order to better assess the composition of the eukaryotic picophytoplankton in the South East Pacific Ocean, encompassing the most oligotrophic oceanic regions on earth, we used a novel approach based on flow cytometry sorting followed by construction of 18S rRNA gene clone libraries. This strategy dramatically increased the recovery of sequences from putative autotrophic groups. The composition of the PPE community appeared highly variable both vertically down the water column and horizontally across the South East Pacific Ocean. In the central gyre, uncultivated lineages dominated: a recently discovered clade of Prasinophyceae (IX), clades of marine Chrysophyceae and Haptophyta, the latter division containing a potentially new class besides Prymnesiophyceae and Pavlophyceae. In contrast, on the edge of the gyre and in the coastal Chilean upwelling, groups with cultivated representatives (Prasinophyceae clade VII and Mamiellales) dominated.
Conclusions/Significance: Our data demonstrate that a very large fraction of the eukaryotic picophytoplankton still escapes cultivation. The use of flow cytometry sorting should prove very useful to better characterize specific plankton populations by molecular approaches such as gene cloning or metagenomics, and also to obtain into culture strains representative of these novel groups
Virtual Compton Scattering and the Generalized Polarizabilities of the Proton at Q^2=0.92 and 1.76 GeV^2
Virtual Compton Scattering (VCS) on the proton has been studied at Jefferson
Lab using the exclusive photon electroproduction reaction (e p --> e p gamma).
This paper gives a detailed account of the analysis which has led to the
determination of the structure functions P_LL-P_TT/epsilon and P_LT, and the
electric and magnetic generalized polarizabilities (GPs) alpha_E(Q^2) and
beta_M(Q^2) at values of the four-momentum transfer squared Q^2= 0.92 and 1.76
GeV^2. These data, together with the results of VCS experiments at lower
momenta, help building a coherent picture of the electric and magnetic GPs of
the proton over the full measured Q^2-range, and point to their non-trivial
behavior.Comment: version 2: modified according to PRC Editor's and Referee's
recommendations. Archival paper for the E93-050 experiment at JLab Hall A. 28
pages, 23 figures, 5 cross-section tables. To be submitted to Phys.Rev.
Backward electroproduction of pi0 mesons on protons in the region of nucleon resonances at four momentum transfer squared Q**2 = 1.0 GeV**2
Exclusive electroproduction of pi0 mesons on protons in the backward
hemisphere has been studied at Q**2 = 1.0 GeV**2 by detecting protons in the
forward direction in coincidence with scattered electrons from the 4 GeV
electron beam in Jefferson Lab's Hall A. The data span the range of the total
(gamma* p) center-of-mass energy W from the pion production threshold to W =
2.0 GeV. The differential cross sections sigma_T+epsilon*sigma_L, sigma_TL, and
sigma_TT were separated from the azimuthal distribution and are presented
together with the MAID and SAID parametrizations.Comment: 17 pages, 11 figures, information can be found at
http://hallaweb.jlab.org/experiment/E93-050/vcs.html updated content about
SAID analysis updated MAID results following new reference nucl-th/0310041
updated figure
Large Momentum Transfer Measurements of the Deuteron Elastic Structure Function A(Q^2) at Jefferson Laboratory
The deuteron elastic structure function A(Q^2) has been extracted in the Q^2
range 0.7 to 6.0 (GeV/c)^2 from cross section measurements of elastic
electron-deuteron scattering in coincidence using the Hall A Facility of
Jefferson Laboratory. The data are compared to theoretical models based on the
impulse approximation with inclusion of meson-exchange currents, and to
predictions of quark dimensional scaling and perturbative quantum
chromodynamicsComment: Submitted to Physical Review Letter
New Measurement of Parity Violation in Elastic Electron-Proton Scattering and Implications for Strange Form Factors
We have measured the parity-violating electroweak asymmetry in the elastic
scattering of polarized electrons from the proton. The result is A = -15.05 +-
0.98(stat) +- 0.56(syst) ppm at the kinematic point theta_lab = 12.3 degrees
and Q^2 = 0.477 (GeV/c)^2. The measurement implies that the value for the
strange form factor (G_E^s + 0.392 G_M^s) = 0.025 +- 0.020 +- 0.014, where the
first error is experimental and the second arises from the uncertainties in
electromagnetic form factors. This measurement is the first fixed-target parity
violation experiment that used either a `strained' GaAs photocathode to produce
highly polarized electrons or a Compton polarimeter to continuously monitor the
electron beam polarization.Comment: 8 pages, 4 figures, Tex, elsart.cls; revised version as accepted for
Phys. Lett.
Virtual Compton Scattering and Neutral Pion Electroproduction in the Resonance Region up to the Deep Inelastic Region at Backward Angles
We have made the first measurements of the virtual Compton scattering (VCS)
process via the H exclusive reaction in the nucleon resonance
region, at backward angles. Results are presented for the -dependence at
fixed GeV, and for the -dependence at fixed near 1.5 GeV.
The VCS data show resonant structures in the first and second resonance
regions. The observed -dependence is smooth. The measured ratio of
H to H cross sections emphasizes the different
sensitivity of these two reactions to the various nucleon resonances. Finally,
when compared to Real Compton Scattering (RCS) at high energy and large angles,
our VCS data at the highest (1.8-1.9 GeV) show a striking -
independence, which may suggest a transition to a perturbative scattering
mechanism at the quark level.Comment: 20 pages, 8 figures. To appear in Phys.Rev.
Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling
Among small photosynthetic eukaryotes that play a key role in oceanic food webs, picoplanktonic Mamiellophyceae such as Bathycoccus, Micromonas, and Ostreococcus are particularly important in coastal regions. By using a combination of cell sorting by flow cytometry, whole genome amplification (WGA), and 454 pyrosequencing, we obtained metagenomic data for two natural picophytoplankton populations from the coastal upwelling waters off central Chile. About 60% of the reads of each sample could be mapped to the genome of Bathycoccus strain from the Mediterranean Sea (RCC1105), representing a total of 9 Mbp (sample T142) and 13 Mbp (sample T149) of non-redundant Bathycoccus genome sequences. WGA did not amplify all regions uniformly, resulting in unequal coverage along a given chromosome and between chromosomes. The identity at the DNA level between the metagenomes and the cultured genome was very high (96.3% identical bases for the three larger chromosomes over a 360 kbp alignment). At least two to three different genotypes seemed to be present in each natural sample based on read mapping to Bathycoccus RCC1105 genome
Rotavirus group : a genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018
Background
Kenya introduced the monovalent G1P [8] Rotarix® vaccine into the infant immunization schedule in July 2014. We examined trends in rotavirus group A (RVA) genotype distribution pre- (January 2010–June 2014) and post- (July 2014–December 2018) RVA vaccine introduction.
Methods
Stool samples were collected from children aged < 13 years from four surveillance sites across Kenya: Kilifi County Hospital, Tabitha Clinic Nairobi, Lwak Mission Hospital, and Siaya County Referral Hospital (children aged < 5 years only). Samples were screened for RVA using enzyme linked immunosorbent assay (ELISA) and VP7 and VP4 genes sequenced to infer genotypes.
Results
We genotyped 614 samples in pre-vaccine and 261 in post-vaccine introduction periods. During the pre-vaccine introduction period, the most frequent RVA genotypes were G1P [8] (45.8%), G8P [4] (15.8%), G9P [8] (13.2%), G2P [4] (7.0%) and G3P [6] (3.1%). In the post-vaccine introduction period, the most frequent genotypes were G1P [8] (52.1%), G2P [4] (20.7%) and G3P [8] (16.1%). Predominant genotypes varied by year and site in both pre and post-vaccine periods. Temporal genotype patterns showed an increase in prevalence of vaccine heterotypic genotypes, such as the commonly DS-1-like G2P [4] (7.0 to 20.7%, P < .001) and G3P [8] (1.3 to 16.1%, P < .001) genotypes in the post-vaccine introduction period. Additionally, we observed a decline in prevalence of genotypes G8P [4] (15.8 to 0.4%, P < .001) and G9P [8] (13.2 to 5.4%, P < .001) in the post-vaccine introduction period. Phylogenetic analysis of genotype G1P [8], revealed circulation of strains of lineages G1-I, G1-II and P [8]-1, P [8]-III and P [8]-IV. Considerable genetic diversity was observed between the pre and post-vaccine strains, evidenced by distinct clusters.
Conclusion
Genotype prevalence varied from before to after vaccine introduction. Such observations emphasize the need for long-term surveillance to monitor vaccine impact. These changes may represent natural secular variation or possible immuno-epidemiological changes arising from the introduction of the vaccine. Full genome sequencing could provide insights into post-vaccine evolutionary pressures and antigenic diversity
Measurement of the Generalized Polarizabilities of the Proton in Virtual Scattering at Q2=0.92 and 1.76 GeV2: I. Low Energy Expansion Analysis
Virtual Compton Scattering is studied at the Thomas Jefferson National
Accelerator Facility at low Center-of-Mass energies, below pion threshold.
Following the Low Energy Theorem for the process, we obtain
values for the two structure functions Pll-Ptt/epsilon and Plt at four-momentum
transfer squared Q2=0.92 and 1.76 GeV2.Comment: 4 pages, 2 figures, to be submitted to PRL. Figs 1 and 2, lettering
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