6,206 research outputs found
Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge
Microbial communities and their associated metabolic activity in
marine sediments have a profound impact on global biogeochemical
cycles. Their composition and structure are attributed to geochemical
and physical factors, but finding direct correlations has remained a
challenge. Here we show a significant statistical relationship between
variation in geochemical composition and prokaryotic community
structure within deep-sea sediments. We obtained comprehensive
geochemical data from two gravity cores near the hydrothermal
vent field Loki’s Castle at the Arctic Mid-Ocean Ridge, in the Norwegian-
Greenland Sea. Geochemical properties in the rift valley
sediments exhibited strong centimeter-scale stratigraphic variability.
Microbial populations were profiled by pyrosequencing from
15 sediment horizons (59,364 16S rRNA gene tags), quantitatively
assessed by qPCR, and phylogenetically analyzed. Although the
same taxa were generally present in all samples, their relative
abundances varied substantially among horizons and fluctuated
between Bacteria- and Archaea-dominated communities. By independently
summarizing covariance structures of the relative
abundance data and geochemical data, using principal components
analysis, we found a significant correlation between changes in
geochemical composition and changes in community structure.
Differences in organic carbon and mineralogy shaped the relative
abundance of microbial taxa. We used correlations to build hypotheses
about energy metabolisms, particularly of the Deep Sea Archaeal
Group, specific Deltaproteobacteria, and sediment lineages
of potentially anaerobic Marine Group I Archaea. We demonstrate
that total prokaryotic community structure can be directly correlated
to geochemistry within these sediments, thus enhancing our
understanding of biogeochemical cycling and our ability to predict
metabolisms of uncultured microbes in deep-sea sediments
Comparative CRISPR type III-based knockdown of essential genes in hyperthermophilic Sulfolobales and the evasion of lethal gene silencing
CRISPR type III systems, which are abundantly found in archaea, recognize and degrade RNA in their specific response to invading nucleic acids. Therefore, these systems can be harnessed for gene knockdown technologies even in hyperthermophilic archaea to study essential genes. We show here the broader usability of this posttranscriptional silencing technology by expanding the application to further essential genes and systematically analysing and comparing silencing thresholds and escape mutants. Synthetic guide RNAs expressed from miniCRISPR cassettes were used to silence genes involved in cell division (cdvA), transcription (rpo8), and RNA metabolism (smAP2) of the two crenarchaeal model organisms Saccharolobus solfataricus and Sulfolobus acidocaldarius. Results were systematically analysed together with those obtained from earlier experiments of cell wall biogenesis (slaB) and translation (aif5A). Comparison of over 100 individual transformants revealed gene-specific silencing maxima ranging between 40 and 75%, which induced specific knockdown phenotypes leading to growth retardation. Exceedance of this threshold by strong miniCRISPR constructs was not tolerated and led to specific mutation of the silencing miniCRISPR array and phenotypical reversion of cultures. In two thirds of sequenced reverted cultures, the targeting spacers were found to be precisely excised from the miniCRISPR array, indicating a still hypothetical, but highly active recombination system acting on the dynamics of CRISPR spacer arrays. Our results indicate that CRISPR type III - based silencing is a broadly applicable tool to study in vivo functions of essential genes in Sulfolobales which underlies a specific mechanism to avoid malignant silencing overdose
Signal-to-Noise Measurements on Irradiated CMS Tracker Detector Modules in an Electron Testbeam
The CMS experiment at the Large Hadron Collider at CERN is in the last phase of its construction. The harsh radiation environment at LHC will put strong demands in radiation hardness to the innermost parts of the detector. To assess the performance of irradiated microstrip detector modules, a testbeam was conducted at the Testbeam 22 facility of the DESY research center. The primary objective was the signal-to-noise measurement of irradiated CMS Tracker modules to ensure their functionality up to 10 years of LHC operation. The paper briefly summarises the basic setup at the facility and the hardware and software used to collect and analyse the data. Some interesting subsidiary results are shown, which confirm the expected behaviour of the detector with respect to the signal-to-noise performance over the active detector area and for different electron energies. The main focus of the paper are the results of the signal-to-noise measurements for CMS Tracker Modules which were exposed to different radiation doses
Fluxes of atmospheric muons underwater depending on the small-x gluon density
The prompt muon contribution to the deep-sea atmospheric muon flux can serve
as a tool for probing into the small-x feature of the gluon density inside of a
nucleon, if the muon energy threshold could be lifted to 100 TeV. The prompt
muon flux underwater is calculated taking into consideration predictions of
recent charm production models in which the small-x behaviour of the gluon
distribution is probed. We discuss the possibility of distinguishing the PQCD
models of the charm production differing in the small-x exponent of the gluon
distribution, in measurements of the muon flux at energies 10-100 TeV with
neutrino telescopes.Comment: 9 pages, 4 eps figures, uses iopart.st
A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution
Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (for example, methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.Research in the A.S.-P. group was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 851647) and the Spanish Ministry of Science and Innovation (PGC2018-098210-A-I00). We also acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the CERCA Programme (Generalitat de Catalunya). C.N. is supported by an FPI PhD fellowship from the Spanish Ministry of Economy, Industry and Competitiveness (MEIC). X.G.-B. is supported by a Juan de la Cierva fellowship (FJC2018-036282-I) from MEIC. I.R.-T. was supported by a European Research Council (grant no. 616960). B.F.L. was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC; RGPIN-2017-05411) and by the ‘Fonds de Recherche Nature et Technologie’, Quebec. P.L.-G. and D.M. were supported by a Moore and Simons foundations grant (GBMF9739) and by European Research Council advanced grants (322669, 787904). Research in the C.S. group was supported by the ERC through project TACKLE (advanced grant no. 695192)
Searches at HERA for Squarks in R-Parity Violating Supersymmetry
A search for squarks in R-parity violating supersymmetry is performed in e^+p
collisions at HERA at a centre of mass energy of 300 GeV, using H1 data
corresponding to an integrated luminosity of 37 pb^(-1). The direct production
of single squarks of any generation in positron-quark fusion via a Yukawa
coupling lambda' is considered, taking into account R-parity violating and
conserving decays of the squarks. No significant deviation from the Standard
Model expectation is found. The results are interpreted in terms of constraints
within the Minimal Supersymmetric Standard Model (MSSM), the constrained MSSM
and the minimal Supergravity model, and their sensitivity to the model
parameters is studied in detail. For a Yukawa coupling of electromagnetic
strength, squark masses below 260 GeV are excluded at 95% confidence level in a
large part of the parameter space. For a 100 times smaller coupling strength
masses up to 182 GeV are excluded.Comment: 32 pages, 14 figures, 3 table
Forward pi^0 Production and Associated Transverse Energy Flow in Deep-Inelastic Scattering at HERA
Deep-inelastic positron-proton interactions at low values of Bjorken-x down
to x \approx 4.10^-5 which give rise to high transverse momentum pi^0 mesons
are studied with the H1 experiment at HERA. The inclusive cross section for
pi^0 mesons produced at small angles with respect to the proton remnant (the
forward region) is presented as a function of the transverse momentum and
energy of the pi^0 and of the four-momentum transfer Q^2 and Bjorken-x.
Measurements are also presented of the transverse energy flow in events
containing a forward pi^0 meson. Hadronic final state calculations based on QCD
models implementing different parton evolution schemes are confronted with the
data.Comment: 27 pages, 8 figures and 3 table
Multi-Jet Event Rates in Deep Inelastic Scattering and Determination of the Strong Coupling Constant
Jet event rates in deep inelastic ep scattering at HERA are investigated
applying the modified JADE jet algorithm. The analysis uses data taken with the
H1 detector in 1994 and 1995. The data are corrected for detector and
hadronization effects and then compared with perturbative QCD predictions using
next-to-leading order calculations. The strong coupling constant alpha_S(M_Z^2)
is determined evaluating the jet event rates. Values of alpha_S(Q^2) are
extracted in four different bins of the negative squared momentum
transfer~\qq in the range from 40 GeV2 to 4000 GeV2. A combined fit of the
renormalization group equation to these several alpha_S(Q^2) values results in
alpha_S(M_Z^2) = 0.117+-0.003(stat)+0.009-0.013(syst)+0.006(jet algorithm).Comment: 17 pages, 4 figures, 3 tables, this version to appear in Eur. Phys.
J.; it replaces first posted hep-ex/9807019 which had incorrect figure 4
Multiplicity Structure of the Hadronic Final State in Diffractive Deep-Inelastic Scattering at HERA
The multiplicity structure of the hadronic system X produced in
deep-inelastic processes at HERA of the type ep -> eXY, where Y is a hadronic
system with mass M_Y< 1.6 GeV and where the squared momentum transfer at the pY
vertex, t, is limited to |t|<1 GeV^2, is studied as a function of the invariant
mass M_X of the system X. Results are presented on multiplicity distributions
and multiplicity moments, rapidity spectra and forward-backward correlations in
the centre-of-mass system of X. The data are compared to results in e+e-
annihilation, fixed-target lepton-nucleon collisions, hadro-produced
diffractive final states and to non-diffractive hadron-hadron collisions. The
comparison suggests a production mechanism of virtual photon dissociation which
involves a mixture of partonic states and a significant gluon content. The data
are well described by a model, based on a QCD-Regge analysis of the diffractive
structure function, which assumes a large hard gluonic component of the
colourless exchange at low Q^2. A model with soft colour interactions is also
successful.Comment: 22 pages, 4 figures, submitted to Eur. Phys. J., error in first
submission - omitted bibliograph
Differential (2+1) Jet Event Rates and Determination of alpha_s in Deep Inelastic Scattering at HERA
Events with a (2+1) jet topology in deep-inelastic scattering at HERA are
studied in the kinematic range 200 < Q^2< 10,000 GeV^2. The rate of (2+1) jet
events has been determined with the modified JADE jet algorithm as a function
of the jet resolution parameter and is compared with the predictions of Monte
Carlo models. In addition, the event rate is corrected for both hadronization
and detector effects and is compared with next-to-leading order QCD
calculations. A value of the strong coupling constant of alpha_s(M_Z^2)=
0.118+- 0.002 (stat.)^(+0.007)_(-0.008) (syst.)^(+0.007)_(-0.006) (theory) is
extracted. The systematic error includes uncertainties in the calorimeter
energy calibration, in the description of the data by current Monte Carlo
models, and in the knowledge of the parton densities. The theoretical error is
dominated by the renormalization scale ambiguity.Comment: 25 pages, 6 figures, 3 tables, submitted to Eur. Phys.
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