115 research outputs found
Activity of comets: Gas Transport in the Near-Surface Porous Layers of a Cometary Nucleus
The gas transport through non-volatile random porous media is investigated
numerically. We extend our previous research of the transport of molecules
inside the uppermost layer of a cometary surface (Skorov and Rickmann, 1995;
Skorov et al. 2001). We assess the validity of the simplified capillary model
and its assumptions to simulate the gas flux trough the porous dust mantle as
it has been applied in cometary physics. A new microphysical computational
model for molecular transport in random porous media formed by packed spheres
is presented. The main transport characteristics such as the mean free path
distribution and the permeability are calculated for a wide range of model
parameters and compared with those obtained by more idealized models. The focus
in this comparison is on limitations inherent in the capillary model. Finally a
practical way is suggested to adjust the algebraic Clausing formula taking into
consideration the nonlinear dependence of permeability on layer porosity. The
retrieved dependence allows us to accurately calculate the permeability of
layers whose thickness and porosity vary in the range of values expected for
the near-surface regions of a cometary nucleus.Comment: 25 pages, 9 figure
A bacteriophage transcription regulator inhibits bacterial transcription initiation by Sigma-factor displacement
Bacteriophages (phages) appropriate essential processes of bacterial hosts to benefit their own development. The multisubunit bacterial RNA polymerase (RNAp) enzyme, which catalyses DNA transcription, is targeted by phage-encoded transcription regulators that selectively modulate its activity. Here, we describe the structural and mechanistic basis for the inhibition of bacterial RNAp by the transcription regulator P7 encoded by Xanthomonas oryzae phage Xp10. We reveal that P7 uses a two-step mechanism to simultaneously interact with the catalytic β and β’ subunits of the bacterial RNAp and inhibits transcription initiation by inducing the displacement of the σ70-factor on initial engagement of RNAp with promoter DNA. The new mode of interaction with and inhibition mechanism of bacterial RNAp by P7 underscore the remarkable variety of mechanisms evolved by phages to interfere with host transcription
The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling
Cellular RNA polymerases RNAPs can become trapped on DNA or RNA, threatening genome stability and limiting free enzyme pools, but how RNAP recycling into active states is achieved remains elusive. In Bacillus subtilis, the RNAP amp; 948; subunit and NTPase HelD have been implicated in RNAP recycling. We structurally analyzed Bacillus subtilis RNAP amp; 948; HelD complexes. HelD has two long arms a Gre cleavage factor like coiled coil inserts deep into the RNAP secondary channel, dismantling the active site and displacing RNA, while a unique helical protrusion inserts into the main channel, prying the amp; 946; and amp; 946; amp; 8242; subunits apart and, aided by amp; 948;, dislodging DNA. RNAP is recycled when, after releasing trapped nucleic acids, HelD dissociates from the enzyme in an ATP dependent manner. HelD abundance during slow growth and a dimeric RNAP amp; 948; HelD 2 structure that resembles hibernating eukaryotic RNAP I suggest that HelD might also modulate active enzyme pools in response to cellular cue
Evolution of scaling emergence in large-scale spatial epidemic spreading
Background: Zipf's law and Heaps' law are two representatives of the scaling
concepts, which play a significant role in the study of complexity science. The
coexistence of the Zipf's law and the Heaps' law motivates different
understandings on the dependence between these two scalings, which is still
hardly been clarified.
Methodology/Principal Findings: In this article, we observe an evolution
process of the scalings: the Zipf's law and the Heaps' law are naturally shaped
to coexist at the initial time, while the crossover comes with the emergence of
their inconsistency at the larger time before reaching a stable state, where
the Heaps' law still exists with the disappearance of strict Zipf's law. Such
findings are illustrated with a scenario of large-scale spatial epidemic
spreading, and the empirical results of pandemic disease support a universal
analysis of the relation between the two laws regardless of the biological
details of disease. Employing the United States(U.S.) domestic air
transportation and demographic data to construct a metapopulation model for
simulating the pandemic spread at the U.S. country level, we uncover that the
broad heterogeneity of the infrastructure plays a key role in the evolution of
scaling emergence.
Conclusions/Significance: The analyses of large-scale spatial epidemic
spreading help understand the temporal evolution of scalings, indicating the
coexistence of the Zipf's law and the Heaps' law depends on the collective
dynamics of epidemic processes, and the heterogeneity of epidemic spread
indicates the significance of performing targeted containment strategies at the
early time of a pandemic disease.Comment: 24pages, 7figures, accepted by PLoS ON
Model theory of finite and pseudofinite groups
This is a survey, intended both for group theorists and model theorists, concerning the structure of pseudofinite groups, that is, infinite models of the first-order theory of finite groups. The focus is on concepts from stability theory and generalisations in the context of pseudofinite groups, and on the information this might provide for finite group theory
Precision and accuracy of single-molecule FRET measurements - a multi-laboratory benchmark study
Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods
Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP
Little is known about how archaeal viruses perturb the transcription machinery of their hosts. Here we provide the first example of an archaeo-viral transcription factor that directly targets the host RNA polymerase (RNAP) and efficiently represses its activity. ORF145 from the temperate Acidianus two-tailed virus (ATV) forms a high-affinity complex with RNAP by binding inside the DNA-binding channel where it locks the flexible RNAP clamp in one position. This counteracts the formation of transcription pre-initiation complexes in vitro and represses abortive and productive transcription initiation, as well as elongation. Both host and viral promoters are subjected to ORF145 repression. Thus, ORF145 has the properties of a global transcription repressor and its overexpression is toxic for Sulfolobus. On the basis of its properties, we have re-named ORF145 RNAP Inhibitory Protein (RIP)
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