Search results for "clock"
showing 10 items of 230 documents
A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes
2013
Summary Background Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought. Results Here, we use mitochondrial genome sequences from ten securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from e…
Flexible modeling for anatomically-based cardiac conduction system construction.
2010
We present a method to automatically deploy the peripheral section of the cardiac conduction system in ventricles. The method encodes anatomical information thorough rules that ensure that Purkinje network structures generated are realistic and comparable to those observed in ex-vivo studies. The core methodology is based in non-deterministic production rules that are parameterized by means of statistical functions. Input parameters allow the construction of a great diversity of Purkinje structures that could be incorporated in fine element ventricular models to perform electrophysiology simulations. Resulting Purkinje trees show good geometrical approximations of Purkinje core network and …
Molecular phylogeny of the harvestmen genus Sabacon (Arachnida: Opiliones: Dyspnoi) reveals multiple Eocene–Oligocene intercontinental dispersal even…
2012
Abstract We investigated the phylogeny and biogeographic history of the Holarctic harvestmen genus Sabacon , which shows an intercontinental disjunct distribution and is presumed to be a relatively old taxon. Molecular phylogenetic relationships of Sabacon were estimated using multiple gene regions and Bayesian inference for a comprehensive Sabacon sample. Molecular clock analyses, using relaxed clock models implemented in BEAST, are applied to date divergence events. Biogeographic scenarios utilizing S-DIVA and Lagrange C++ are reconstructed over sets of Bayesian trees, allowing for the incorporation of phylogenetic uncertainty and quantification of alternative reconstructions over time. F…
Nocturnin in the demosponge Suberites domuncula: a potential circadian clock protein controlling glycogenin synthesis in sponges
2012
Sponges are filter feeders that consume a large amount of energy to allow a controlled filtration of water through their aquiferous canal systems. It has been shown that primmorphs, three-dimensional cell aggregates prepared from the demosponge Suberites domuncula and cultured in vitro , change their morphology depending on the light supply. Upon exposure to light, primmorphs show a faster and stronger increase in DNA, protein and glycogen content compared with primmorphs that remain in the dark. The sponge genome contains nocturnin, a light/dark-controlled clock gene, the protein of which shares a high sequence similarity with the related molecule of higher metazoans. The sponge nocturnin …
Interaction of Circadian Clock Proteins CRY1 and PER2 Is Modulated by Zinc Binding and Disulfide Bond Formation
2014
SummaryPeriod (PER) proteins are essential components of the mammalian circadian clock. They form complexes with cryptochromes (CRY), which negatively regulate CLOCK/BMAL1-dependent transactivation of clock and clock-controlled genes. To define the roles of mammalian CRY/PER complexes in the circadian clock, we have determined the crystal structure of a complex comprising the photolyase homology region of mouse CRY1 (mCRY1) and a C-terminal mouse PER2 (mPER2) fragment. mPER2 winds around the helical mCRY1 domain covering the binding sites of FBXL3 and CLOCK/BMAL1, but not the FAD binding pocket. Our structure revealed an unexpected zinc ion in one interface, which stabilizes mCRY1-mPER2 int…
Palaeoclimatic changes explain Anatolian mountain frog evolution: a test for alternating vicariance and dispersal events
2002
Holarctic biodiversity has been influenced by climatic fluctuations since the Pliocene. Asia Minor was one of the major corridors for postglacial invasions in the Palearctic. Today this area is characterized by an extraordinarily rich fauna with close affiliation to European, Asian and Indo-African biota. However, exact scenarios of range expansion and contraction are lacking. Using a phylogeographical approach we (i) identify monophyletic lineages among Anatolian mountain frogs and (ii) derive a spatio-temporal hypothesis for the invasion process in Anatolia. We sequenced 540 bp of the mitochondrial 16S rRNA gene from 40 populations of mountain frogs from Anatolia, the Elburz Mountains and…
Phylogeny and evolution of the Arctium-Cousinia complex (Compositae, Cardueae-Carduinae)
2009
The phylogeny and evolution of the Arctium-Cousinia complex, including Arctium, Cousinia as one of the largest genera of Asteraceae, Hypacanthium and Schmalhausenia, is investigated. This group of genera has its highest diversity in the Irano-Turanian region and the mountains of Central Asia. We generated ITS and rpS4-trnT-trnL sequences for altogether 138 species, including 129 (of ca. 600) species of Cousinia. As found in previous analyses, Cousinia is not monophyletic. Instead, Cousinia subgg. Cynaroides and Hypacanthodes with together ca. 30 species are more closely related to Arctium, Hypacanthium and Schmalhausenia (Arctioid clade) than to subg. Cousinia (Cousinioid clade). The Arctio…
Rhythmicity of Intestinal IgA Responses Confers Oscillatory Commensal Microbiota Mutualism
2021
ABSTRACTMutualistic interactions with the commensal microbiota are enforced through a range of immune responses that confer metabolic benefits for the host and ensure tissue health and homeostasis. Immunoglobulin (Ig)A responses directly determine the composition of commensal species that colonize the intestinal tract but require significant metabolic resources to fuel antibody production by tissue-resident plasma cells. Here we demonstrate IgA responses are subject to diurnal regulation by dietary-derived metabolic cues and a cell-intrinsic circadian clock. Rhythmicity in IgA secretion conferred oscillatory patterns on the commensal microbial community and its associated metabolic activity…
The Mu3e Data Acquisition
2020
The Mu3e experiment aims to find or exclude the lepton flavour violating decay $\mu^+\to e^+e^-e^+$ with a sensitivity of one in 10$^{16}$ muon decays. The first phase of the experiment is currently under construction at the Paul Scherrer Institute (PSI, Switzerland), where beams with up to 10$^8$ muons per second are available. The detector will consist of an ultra-thin pixel tracker made from High-Voltage Monolithic Active Pixel Sensors (HV-MAPS), complemented by scintillating tiles and fibres for precise timing measurements. The experiment produces about 100 Gbit/s of zero-suppressed data which are transported to a filter farm using a network of FPGAs and fast optical links. On the filte…
Melastomeae come full circle: biogeographic reconstruction and molecular clock dating.
2001
Rhexia, with 11 species in the Coastal Plain province of North America, is the only temperate zone endemic of the tropical eudicot family Melastomataceae. It is a member of the only pantropical tribe of that family, Melastomeae. Based on the chloroplast gene ndhF, we use a fossil-calibrated molecular clock to address the question of the geographic origin and age of Rhexia. Sequences from 37 species in 21 genera representing the tribe's geographical range were analyzed together with five outgroups. To obtain better clade support, another chloroplast region, the rpl16 intron, was added for 24 of the species. Parsimony analysis of the combined data and maximum-likelihood analysis of ndhF alone…