In the sub-TeV regime, the most widely used hadronic interaction models disagree significantly in their predictions for post-first interaction and ground-level particle spectra from cosmic ray ...induced air showers. These differences generate an important source of systematic uncertainty in their experimental use. We investigate the nature and impact of model uncertainties through a simultaneous analysis of ground level particles and first interaction scenarios. We focus on air shower primaries with energies close to the transition between high and low energy hadronic interaction models, where the dissimilarities have been shown to be the largest and well within the range of accelerator measurements. Interaction models are shown to diverge as several shower scenarios are compared, reflecting intrinsic differences in the model theoretical frameworks. Finally, we discuss the importance of interactions in the energy regime where the switching between models occurs (
<
1
TeV) and the effect of the choice of model on the number of hadronic interactions within cosmic ray induced air showers of higher energies.
.
Open and hidden heavy-flavor physics in high-energy nuclear collisions are entering a new and exciting stage towards reaching a clearer understanding of the new experimental results with the ...possibility to link them directly to the advancement in lattice Quantum Chromo-Dynamics (QCD). Recent results from experiments and theoretical developments regarding open and hidden heavy-flavor dynamics have been debated at the Lorentz Workshop
Tomography of the Quark-Gluon Plasma with Heavy Quarks
, which was held in October 2016 in Leiden, The Netherlands. In this contribution, we summarize identified common understandings and developed strategies for the upcoming five years, which aim at achieving a profound knowledge of the dynamical properties of the quark-gluon plasma.
Circadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model ...cyanobacterium Synechococcus elongatus PCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating. However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear.
Using a universal BLAST analyses, we identified putative KaiC-based timing systems in organisms outside as well as variations within Cyanobacteria. A systematic analyses of publicly available microarray data elucidated interesting variations in circadian gene expression between different cyanobacterial strains, which might be correlated to the diversity of genome encoded clock components. Based on statistical analyses of co-occurrences of the clock components homologous to Synechococcus elongatus PCC 7942, we propose putative networks of reduced and fully functional clock systems. Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs. Biochemical characterization of exemplary cyanobacterial KaiC proteins as well as homologs from two thermophilic Archaea demonstrated that kinase activity is always present. However, a KaiA-mediated phosphorylation is only detectable in KaiC1 orthologs.
Our analysis of 11,264 genomes clearly demonstrates that components of the Synechococcus elongatus PCC 7942 circadian clock are present in Bacteria and Archaea. However, all components are less abundant in other organisms than Cyanobacteria and KaiA, Pex, LdpA, and CdpA are only present in the latter. Thus, only reduced KaiBC-based or even simpler, solely KaiC-based timing systems might exist outside of the cyanobacterial phylum, which might be capable of driving diurnal oscillations.
CyanoCyc cyanobacterial web portal Moore, Lisa R; Caspi, Ron; Campbell, Douglas A ...
Frontiers in microbiology,
2024, Letnik:
15
Journal Article
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CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to ...address the needs of the cyanobacterial research and biotechnology communities. The 277 annotated cyanobacterial genomes currently in CyanoCyc are supplemented with computational inferences including predicted metabolic pathways, operons, protein complexes, and orthologs; and with data imported from external databases, such as protein features and Gene Ontology (GO) terms imported from UniProt. Five of the genome databases have undergone manual curation with input from more than a dozen cyanobacteria experts to correct errors and integrate information from more than 1,765 published articles. CyanoCyc has bioinformatics tools that encompass genome, metabolic pathway and regulatory informatics; omics data analysis; and comparative analyses, including visualizations of multiple genomes aligned at orthologous genes, and comparisons of metabolic networks for multiple organisms. CyanoCyc is a high-quality, reliable knowledgebase that accelerates scientists' work by enabling users to quickly find accurate information using its powerful set of search tools, to understand gene function through expert mini-reviews with citations, to acquire information quickly using its interactive visualization tools, and to inform better decision-making for fundamental and applied research.
Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st ...Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories-e.g. bottom-up and top-down, RNA world vs. metabolism-first-have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research.
•The ALEPH detector at LEP is used to measure cosmic ray muons.•Momentum spectrum and charge ratio of vertical muons at surface level are determined.•Results are compared to and interpreted by Monte ...Carlo models.•Information about energy spectrum and chemical composition of cosmic ray primaries is inferred.
The ALEPH detector at LEP has been used to measure the momentum spectrum and charge ratio of vertical cosmic ray muons underground. The sea-level cosmic ray muon spectrum for momenta up to 2.5TeV/c has been obtained by correcting for the overburden of 320m water equivalent (mwe). The results are compared with Monte Carlo models for air shower development in the atmosphere. From the analysis of the spectrum the total flux and the spectral index of the cosmic ray primaries is inferred. The charge ratio suggests a dominantly light composition of cosmic ray primaries with energies in the energy range between 103 and 105GeV.
Precisely timing the regulation of gene expression by anticipating recurring environmental changes is a fundamental part of global gene regulation. Circadian clocks are one form of this regulation, ...which is found in both eukaryotes and prokaryotes, providing a fitness advantage for these organisms. Whereas many different eukaryotic groups harbour circadian clocks, cyanobacteria are the only known oxygenic phototrophic prokaryotes to regulate large parts of their genes in a circadian fashion. A decade of intensive research on the mechanisms and functionality using computational and mathematical approaches in addition to the detailed biochemical and biophysical understanding make this the best understood circadian clock. Here, we summarize the findings and insights into various parts of the cyanobacterial circadian clock made by mathematical modelling. These findings have implications for eukaryotic circadian research as well as synthetic biology harnessing the power and efficiency of global gene regulation.
A test of lepton universality, performed by measuring the ratio of the branching fractions of the $B^0 → K^{*0}μ^+μ^-$ and $B^0$ → $K^{*0}e^+e^-$ decays, $R_{K^{*0}}$, is presented. The $K^{*0}$ ...meson is reconstructed in the final state $K^+π^-$, which is required to have an invariant mass within 100 MeV/c2 of the known $K^*$ (892)0 mass. The analysis is performed using proton-proton collision data, corresponding to an integrated luminosity of about 3 fb-1, collected by the LHCb experiment at centre-of-mass energies of 7 and 8 TeV. The ratio is measured in two regions of the dilepton invariant mass squared, q2, to be R K ∗ 0 = { 0.66 − + 0.07 0.11 ( s t a t ) ± 0.03 ( s y s t ) f o r 0.045 < q 2 < 1.1 G e V 2 / c 4 , 0.69 − + 0.07 0.11 ( s t a t ) ± 0.05 ( s y s t ) f o r 1.1 < q 2 < 6.0 G e V 2 / c 4 . The corresponding 95.4% confidence level intervals are 0.52, 0.89 and 0.53, 0.94. The results, which represent the most precise measurements of $R_{K^{*0}}$ to date, are compatible with the Standard Model expectations at the level of 2.1–2.3 and 2.4–2.5 standard deviations in the two q2 regions, respectively.
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First evidence of a structure in the J/ψΛ invariant mass distribution is obtained from an amplitude analysis of Ξb-→J/ψΛK- decays. The observed structure is consistent with being due ...to a charmonium pentaquark with strangeness with a significance of 3.1σ including systematic uncertainties and look-elsewhere effect. Its mass and width are determined to be 4458.8±2.9-1.1+4.7MeV and 17.3±6.5-5.7+8.0MeV, respectively, where the quoted uncertainties are statistical and systematic. The structure is also consistent with being due to two resonances. In addition, the narrow excited Ξ- states, Ξ1690- and Ξ1820-, are seen for the first time in a Ξb- decay, and their masses and widths are measured with improved precision. The analysis is performed using pp collision data corresponding to a total integrated luminosity of 9 fb-1, collected with the LHCb experiment at centre-of-mass energies of 7, 8 and 13 TeV.
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