123,581 research outputs found
Extrusion without a motor:a new take on the loop extrusion model of genome organization
No full textChromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and extrusion is the only model to date which can explain this. However, the model requires a motor to generate the loops, and although cohesin is a strong candidate for the extruding factor, a suitable motor protein (or a motor activity in cohesin itself) has yet to be found. Here we explore a new hypothesis: that there is no motor, and thermal motion within the nucleus drives extrusion. Using theoretical modelling and computer simulations we ask whether such diffusive extrusion could feasibly generate loops. Our simulations uncover an interesting ratchet effect (where an osmotic pressure promotes loop growth), and suggest, by comparison to recent in vitro and in vivo measurements, that diffusive extrusion can in principle generate loops of the size observed in the data. Extra View on : C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, and D. Marenduzzo "Non-equilibrium chromosome looping via molecular slip-links", Physical Review Letters 119 138101 (2017).</p
Updated Version of Table 1 from Morozov (2024)
No full textThis is an updated version of Table 1 from: Morozov, S. S. (2024). Non-dinosaurian predation and scavenging on dinosaurs: a list of direct evidence. paleoRxiv. https://doi.org/10.31233/osf.io/bew86. The link: https://docs.google.com/spreadsheets/d/1uNDmaVBBLOAeuaoKPko0Uu90UmQdbN5APROo7307AKc
Reply to “Comment on ‘Attenuation, source parameters and site effects in the Irpinia–Basilicata region (southern Apennines, Italy)’ by I.B. Morozov”
No full textWe thank Igor B. Morozov for his interest in our article and for his comment (Morozov 2011)
regarding the non-parametric attenuation curves for the Irpinia–Basilicata region obtained
by generalized spectral inversion (Cantore et al. 2011). Morozov's comment has its root in a
new model proposed by Morozov (2008, 2010) for the interpretation of seismic attenuation
data, where the author comes to the conclusion that the typically used geometrical
spreading terms are oversimplified and argues in favor of a new geometrical spreading ...Published91-934T. Fisica dei terremoti e scenari cosismiciJCR Journalrestricte
Topological Spectra and Entropy of Chromatin Loop Networks
No full textThe 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fiber is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors and RNA polymerases. This physical model leads to the natural emergence of clusters of proteins and binding sites, accompanied by the folding of chromatin into a set of topologies, each associated with a different network of loops. Here, we combine numerics and analytics to first classify these networks and then find their relative importance or statistical weight, when the properties of the underlying polymer are those relevant to chromatin. Unlike polymer networks previously studied, our chromatin networks have finite average distances between successive binding sites, and this leads to giant differences between the weights of topologies with the same number of edges and nodes but different wiring. These weights strongly favor rosettelike structures with a local cloud of loops with respect to more complicated nonlocal topologies. Our results suggest that genes should overwhelmingly fold into a small fraction of all possible 3D topologies, which can be robustly characterized by the framework we propose here
Combinatorics and topological weights of chromatin loop networks
No full textPolymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop networks, both in the case where TUs are labeled and where they are unlabeled. We then combine these mathematical results with those of computer simulations aimed at finding the inter-TU energy required to form a target loop network. We show that different topologies are vastly different in terms of both their combinatorial weight and energy of formation. We explain the latter result qualitatively by computing the topological weight of a given network - i.e., its partition function in statistical mechanics language - in the approximation where excluded volume interactions are neglected. Our results show that networks featuring local loops are statistically more likely with respect to networks including more nonlocal contacts. We suggest our classification of loop networks, together with our estimate of the combinatorial and topological weight of each network, will be relevant to catalog three-dimensional structures of chromatin fibers around eukaryotic genes, and to estimate their relative frequency in both simulations and experiments
RussianCognates
No full textThis dataset contains a few number of cognate and non-cognate pairs of Russian words. 5 types of pairs are presented: 1) not cognate (totally different roots), 2) not cognate (homonymic roots), 3) not cognate (synonyms), 4) cognate (literal matching roots), 5) cognate (roots with alternations). Current dataset contains 140 pairs of each type and will be increased
A novel intermediate in transcription initiation by human mitochondrial RNA polymerase
No full textThe mitochondrial genome is transcribed by a single-subunit T7 phage-like RNA polymerase (mtRNAP), structurally unrelated to cellular RNAPs. In higher eukaryotes, mtRNAP requires two transcription factors for efficient initiation—TFAM, a major nucleoid protein, and TFB2M, a transient component of mtRNAP catalytic site. The mechanisms behind assembly of the mitochondrial transcription machinery and its regulation are poorly understood. We isolated and identified a previously unknown human mitochondrial transcription intermediate— a pre-initiation complex that includes mtRNAP, TFAM and promoter DNA. Using protein– protein cross-linking, we demonstrate that human TFAM binds to the N-terminal domain of mtRNAP, which results in bending of the promoter DNA around mtRNAP. The subsequent recruitment of TFB2M induces promoter melting and formation of an open initiation complex. Our data indicate that the pre-initiation complex is likely to be an important target for transcription regulation and provide basis for further structural, biochemical and biophysical studies of mitochondrial transcription
Numerical analysis of a 3-D printed porous trailing edge for broadband noise reduction
No full textLattice Boltzmann simulations were carried out to investigate the noise mitigation mechanisms of a 3-D printed porous trailing-edge insert, elucidating the link between noise reduction and material permeability. The porous insert is based on a unit cell resembling a lattice of diamond atoms. It replaces the last 20 % chord of a NACA 0018 at zero angle-of-attack. A partially blocked insert is considered by adding a solid partition between 84 % and 96 % of the aerofoil chord. The regular porous insert achieves a substantial noise reduction at low frequencies, although a slight noise increase is found at high frequencies. The partially blocked porous insert exhibits a lower noise reduction level, but the noise emission at mid-to-high frequency is slightly affected. The segment of the porous insert near the tip plays a dominant role in promoting noise mitigation, whereas the solid-porous junction contributes, in addition to the rough surface, towards the high-frequency excess noise. The current study demonstrates the existence of an entrance length associated with the porous material geometry, which is linked to the pressure release process that is responsible for promoting noise mitigation. This process is characterised by the aerodynamic interaction between pressure fluctuations across the porous medium, which is found at locations where the porous insert thickness is less than twice the entrance length. Present results also suggest that the noise attenuation level is related to both the chordwise extent of the porous insert and the streamwise turbulent length scale. The porous inserts also cause a slight drag increase compared to their solid counterpart. Wind Energ
Suberites cebriones Morozov & Sabirov & Zimina 2019, sp. nov.
No full textSuberites cebriones sp. nov. (Figure 9 (a – f)) Material examined The holotype was collected in the central part of the Laptev Sea (75.19°N, 128.46°E); it is deposited in the Edward Eversman Zoology Museum (identification number 2.2.8.441). Paratypes localities: one specimen from same locality as holotype (75.19°N, 128.46°E); two specimens from north of the New Siberian Islands (76.25°N, 139.05° E; 77.23°N, 137.06°E); one specimen from the central part of the Laptev Sea (76.05° N, 122.75°E). Description (Figure 9 (d – e)). Sponge cup shaped or club shaped (only small juvenile forms), up to 3.5 cm in height and 4 cm in width. The inner surface of cup-shaped sponge is covered with evenly scattered small pores (about 0.1 mm in diameter), forming a sieve. In the case of juvenile forms (which may easily be confused with corresponding forms of s. montalbidus) the single osculum is located on the top. Surface is smooth. The body is tolerably firm, only slightly compressible in consistency. Sometimes provided with weakly pronounced peduncle. Colour (in alcohol) is beige. Spicules Styles (tylo- and subtylostyles) straight, rather short-pointed (spicules with blunt apical end occasionally found), dimensions: 124.8 – 395.4 – 677 × 5.5 – 11.4 (n = 200) µm; microxea and microstrongyles centrotylote, spined, dimensions 21.3 – 41 – 67.4 (n = 60) µm and 9.87 – 19.37 – 28.22 (n = 60) µm, respectively. Etymology In Greek mythology, Cebriones was the illegitimate son of King Priam of Troy and participated in the Trojan War as charioteer for his half-brother Hector. Remarks In the examined materials, we observed that several specimens differed substantially in their outer morphology from the above-mentioned representatives of suberites montalbidus. However, the spicular analysis did not reveal any differences between them. The reason to allocate suberites cebriones sp. nov. as a new species is the uniqueness of its skeletal architecture; in the case of s. montalbidus, the microscleres are confined to the thin cortical layer, while in s. cebriones sp. nov., they are also distributed in large numbers throughout the interior (Figure 9 (a – b)).Published as part of Morozov, Grigori, Sabirov, Rushan & Zimina, Olga, 2019, Sponge fauna of the New Siberian Shoal: biodiversity and some features of formation, pp. 2961-2992 in Journal of Natural History 52 (47) on pages 2961-2992, DOI: 10.1080/00222933.2018.1554166, http://zenodo.org/record/365416
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