Chromosome compaction and chromatin stiffness enhance diffusive loop extrusion by slip-link proteins

We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to explain the extrusion of chromatin loops of hundreds of kilo-base-pairs (kbp), which may then be stabilised by interactions between cohesin and CTCF proteins. Here we show that the flexibility of the chromatin fibre strongly affects this dynamical process, and find that diffusive loop extrusion is more efficient on stiffer chromatin regions. We also show that the dynamics of loop formation are faster in confined and collapsed chromatin conformations but that this enhancement is counteracted by the increased crowding. We provide a simple theoretical argument explaining why stiffness and collapsed conformations favour diffusive extrusion. In light of the heterogeneous physical and conformational properties of eukaryotic chromatin, we suggest that our results are relevant to understand the looping and organisation of interphase chromosomes in vivo

Variabilidade genética de Magnaporthe oryzae do trigo e os tipos compatíveis de populações simpátricas do patógeno.

Coorientador: João Leodato Nunes Maciel

Fast Two-Robot Disk Evacuation with Wireless Communication

In the fast evacuation problem, we study the path planning problem for two robots who want to minimize the worst-case evacuation time on the unit disk. The robots are initially placed at the center of the disk. In order to evacuate, they need to reach an unknown point, the exit, on the boundary of the disk. Once one of the robots finds the exit, it will instantaneously notify the other agent, who will make a beeline to it. The problem has been studied for robots with the same speed~\cite{s1}. We study a more general case where one robot has speed $1$ and the other has speed $s \geq 1$. We provide optimal evacuation strategies in the case that $s \geq c_{2.75} \approx 2.75$ by showing matching upper and lower bounds on the worst-case evacuation time. For $1\leq s < c_{2.75}$, we show (non-matching) upper and lower bounds on the evacuation time with a ratio less than $1.22$. Moreover, we demonstrate that a generalization of the two-robot search strategy from~\cite{s1} is outperformed by our proposed strategies for any $s \geq c_{1.71} \approx 1.71$.Comment: 18 pages, 10 figure

Adiabatic quantum algorithm for search engine ranking

We propose an adiabatic quantum algorithm for generating a quantum pure state encoding of the PageRank vector, the most widely used tool in ranking the relative importance of internet pages. We present extensive numerical simulations which provide evidence that this algorithm can prepare the quantum PageRank state in a time which, on average, scales polylogarithmically in the number of webpages. We argue that the main topological feature of the underlying web graph allowing for such a scaling is the out-degree distribution. The top ranked $\log(n)$ entries of the quantum PageRank state can then be estimated with a polynomial quantum speedup. Moreover, the quantum PageRank state can be used in "q-sampling" protocols for testing properties of distributions, which require exponentially fewer measurements than all classical schemes designed for the same task. This can be used to decide whether to run a classical update of the PageRank.Comment: 7 pages, 5 figures; closer to published versio

Otimização do método de extração de DNA de Magnaporthe oryzae de trigo.

bitstream/item/114990/1/2014-Comunicado-tecnico-online-343.pd

Predictions for surveys with the SPICA Mid-infrared Instrument

We present predictions for number counts and redshift distributions of galaxies detectable in continuum and in emission lines with the Mid-infrared (MIR) Instrument (SMI) proposed for the Space Infrared Telescope for Cosmology and Astrophysics. We have considered 24 MIR fine-structure lines, four polycyclic aromatic hydrocarbon bands (at 6.2, 7.7, 8.6 and 11.3 mu m) and two silicate bands (in emission and in absorption) at 9.7 and 18.0 mu m. Six of these lines are primarily associated with active galactic nuclei (AGNs), the others with star formation. A survey with the SMI spectrometers of 1-h integration per field of view (FoV) over an area of 1 deg(2) will yield 5 sigma detections of similar or equal to 140 AGN lines and of similar or equal to 5.2 x 10(4) star-forming galaxies, similar or equal to 1.6 x 10(4) of which will be detected in at least two lines. The combination of a shallow (20.0 deg(2), 1.4 x 10(-1) h integration per FoV) and a deep survey (6.9 x 10(-3) deg(2), 635 h integration time), with the SMI camera, for a total of similar to 1000 h, will accurately determine the MIR number counts of galaxies and of AGNs over five orders of magnitude in flux density, reaching values more than one order of magnitude fainter than the deepest Spitzer 24 mu m surveys. This will allow us to determine the cosmic star formation rate (SFR) function down to SFRs more than 100 times fainter than reached by the Herschel Observatory

Meiotic Arrest Compromises Pollen Fertility in an Interspecific Hybrid Between \u3cem\u3eBrachiaria Ruziziensis\u3c/em\u3e X \u3cem\u3eBrachiaria Decumbens\u3c/em\u3e (Gramineae)

Disruptions in meiosis, development of the free microspores, microspore mitosis, pollen differentiation or anthesis can result in male-sterile plants (Glover et al., 1998). An understanding of the meiotic process is pivotal to work on reproduction, fertility, genetics and breeding in plants, with serious implications in crop production (Armstrong & Jones, 2003). Some African species of Brachiaria are the most important for pastures in the American tropics due to good adaptation and production. Artificial hybridization is underway in Embrapa to improve production, quality and insect resistance (Valle & Miles, 2001). For a cultivar to be successfully adopted good seed production and pollen viability are required. This paper reports on meiotic abnormalities impairing pollen fertility in a hybrid between B. ruziziensis x B. decumbens

Analysis of Genomic Affinity Between \u3cem\u3eBrachiaria Ruziziensis\u3c/em\u3e and \u3cem\u3eB. Brizantha\u3c/em\u3e Through Meiotic Behaviour

Genetic divergence between polyploid hybrids is displayed in chromosome pairing and in the rate of chromosome elimination due to differences in cell cycle between the two combined genomes (Sundberg et al. 1991). In Brachiaria, a genus of African grasses reaching continental proportions as a tropical pasture in Latin America, genome analysis has never been performed. The majority of accessions in this genus is polyploid and apomictic, which restricts breeding. The relative ease of obtaining fertile interspecific hybrids once ploidy barriers are overcome (Pereira et al. 2001) confirms the phylogenetic proximity among B. ruziziensis, B. decumbens and B. brizantha. Hybrids were synthesised using sexual artificial 4x as the female genitor and natural apomictic 4x as the pollen donors. Genome affinity is a pre-requisite for chosen genitors to produce fertile hybrids and plenty of viable seed to assure adoption of the new cultivar. Microsporogenesis of a hybrid between B. ruziziensis and B. brizantha is described in this paper, focusing on the behaviour of both genomes

Thermal Decays in a Hot Fermi Gas

We present a study of the decay of metastable states of a scalar field via thermal activation, in the presence of a finite density of fermions. The process we consider is the nucleation of ``{\it droplets}'' of true vacuum inside the false one. We analyze a one-dimensional system of interacting bosons and fermions, considering the latter at finite temperature and with a given chemical potential. As a consequence of a non-equilibrium formalism previously developed, we obtain time-dependent decay rates.Comment: 18 pages, REVTEX, 9 figures available upon reques

Extração de DNA genômico de Brachiaria e Panicum maximum.

bitstream/CNPGC/10572/1/COT79.pd