Multi layer chromosome organization through DNA bending, bridging and extrusion

All living cells have to master the extraordinarily extended and tangly nature of genomic DNA molecules in particular during cell division when sister chromosomes are resolved from one another and confined to opposite halves of a cell. Bacteria have evolved diverse sets of proteins, which collectively ensure the formation of compact and yet highly dynamic nucleoids. Some of these players act locally by changing the path of DNA through the bending of its double helical backbone. Other proteins have wider or even global impact on chromosome organization, for example by interconnecting two distant segments of chromosomal DNA or by actively relocating DNA within a cell. Here, I highlight different modes of chromosome organization in bacteria and on this basis consider models for the function of SMC protein complexes, whose mechanism of action is only poorly understood so far

Microarray gene expression profiling of neural tissues in bovine spastic paresis

Abstract: Background: Bovine Spastic Paresis (BSP) is a neuromuscular disorder which affects both male and female cattle. BSP is characterized by spastic contraction and overextension of the gastrocnemious muscle of one or both limbs and is associated with a scarce increase in body weight. This disease seems to be caused by an autosomal and recessive gene, with incomplete penetration, although no genes clearly involved with its onset have been so far identified. We employed cDNA microarrays to identify metabolic pathways affected by BSP in Romagnola cattle breed. Investigation of those pathways at the genome level can help to understand this disease. Results: Microarray analysis of control and affected individuals resulted in 268 differentially expressed genes. These genes were subjected to KEGG pathway functional clustering analysis, revealing that they are predominantly involved in Cell Communication, Signalling Molecules and Interaction and Signal Transduction, Diseases and Nervous System classes. Significantly enriched KEGG pathway's classes for the differentially expressed genes were calculated; interestingly, all those significantly under-expressed in the affected samples are included in Neurodegenerative Diseases. To identify genome locations possibly harbouring gene(s) involved in the disease, the chromosome distribution of the differentially expressed genes was also investigated. Conclusions: The cDNA microarray we used in this study contains a brain library and, even if carrying an incomplete transcriptome representation, it has proven to be a valuable tool allowing us to add useful and new information to a poorly studied disease. By using this tool, we examined nearly 15000 transcripts and analysed gene pathways affected by the disease. Particularly, our data suggest also a defective glycinergic synaptic transmission in the development of the disease and an alteration of calcium signalling proteins. We provide data to acquire knowledge of a genetic disease for which literature still presents poor results and that could be further and specifically analysed in the next future. Moreover this study, performed in livestock, may also harbour molecular information useful for understanding human diseases

Sparsity-Sensitive Finite Abstraction

Abstraction of a continuous-space model into a finite state and input dynamical model is a key step in formal controller synthesis tools. To date, these software tools have been limited to systems of modest size (typically $\leq$ 6 dimensions) because the abstraction procedure suffers from an exponential runtime with respect to the sum of state and input dimensions. We present a simple modification to the abstraction algorithm that dramatically reduces the computation time for systems exhibiting a sparse interconnection structure. This modified procedure recovers the same abstraction as the one computed by a brute force algorithm that disregards the sparsity. Examples highlight speed-ups from existing benchmarks in the literature, synthesis of a safety supervisory controller for a 12-dimensional and abstraction of a 51-dimensional vehicular traffic network

Langevin equation for the extended Rayleigh model with an asymmetric bath

In this paper a one-dimensional model of two infinite gases separated by a movable heavy piston is considered. The non-linear Langevin equation for the motion of the piston is derived from first principles for the case when the thermodynamic parameters and/or the molecular masses of gas particles on left and right sides of the piston are different. Microscopic expressions involving time correlation functions of the force between bath particles and the piston are obtained for all parameters appearing in the non-linear Langevin equation. It is demonstrated that the equation has stationary solutions corresponding to directional fluctuation-induced drift in the absence of systematic forces. In the case of ideal gases interacting with the piston via a quadratic repulsive potential, the model is exactly solvable and explicit expressions for the kinetic coefficients in the non-linear Langevin equation are derived. The transient solution of the non-linear Langevin equation is analyzed perturbatively and it is demonstrated that previously obtained results for systems with the hard-wall interaction are recovered.Comment: 10 pages. To appear in Phys. Rev.

Results from a Second RXTE Observation of the Coma Cluster

The RXTE satellite observed the Coma cluster for 177 ksec during November and December 2000, a second observation motivated by the intriguing results from the first 87 ksec observation in 1996. Analysis of the new dataset confirms that thermal emission from isothermal gas does not provide a good fit to the spectral distribution of the emission from the inner 1 degree radial region. While the observed spectrum may be fit by emission from gas with a substantial temperature gradient, it is more likely that the emission includes also a secondary non-thermal component. If so, non-thermal emission comprises ~8% of the total 4--20 keV flux. Interpreting this emission as due to Compton scattering of relativistic electrons (which produce the known extended radio emission) by the cosmic microwave background radiation, we determine that the mean, volume-averaged magnetic field in the central region of Coma is B = 0.1-0.3 microgauss.Comment: 10 pages, 1 figure; APJ, in pres

Field efficacy evaluation and post-treatment contamination risk assessment of an ultraviolet disinfection and safe storage system.

Inconsistent use of household water treatment and safe storage (HWTS) systems reduces their potential health benefits. Ultraviolet (UV) disinfection is more convenient than some existing HWTS systems, but it does not provide post-treatment residual disinfectant, which could leave drinking water vulnerable to recontamination. In this paper, using as-treated analyses, we report on the field efficacy of a UV disinfection system at improving household drinking water quality in rural Mexico. We further assess the risk of post-treatment contamination from the UV system, and develop a process-based model to better understand household risk factors for recontamination. This study was part of a larger cluster-randomized stepped wedge trial, and the results complement previously published population-level results of the intervention on diarrheal prevalence and water quality. Based on the presence of Escherichia coli (proportion of households with ≥ 1 E. coli/100 mL), we estimated a risk difference of -28.0% (95% confidence interval (CI): -33.9%, -22.1%) when comparing intervention to control households; -38.6% (CI: -48.9%, -28.2%) when comparing post- and pre-intervention results; and -37.1% (CI: -45.2%, -28.9%) when comparing UV disinfected water to alternatives within the household. We found substantial increases in post-treatment E. coli contamination when comparing samples from the UV system effluent (5.0%) to samples taken from the storage container (21.1%) and drinking glasses (26.0%). We found that improved household infrastructure, additional extractions from the storage container, additional time from when the storage container was filled, and increased experience of the UV system operator were associated with reductions in post-treatment contamination. Our results suggest that the UV system is efficacious at improving household water quality when used as intended. Promoting safe storage habits is essential for an effective UV system dissemination. The drinking glass appears to represent a small but significant source of recontamination that is likely to impact all HWTS systems

Positive Measure Spectrum for Schroedinger Operators with Periodic Magnetic Fields

We study Schroedinger operators with periodic magnetic field in Euclidean 2-space, in the case of irrational magnetic flux. Positive measure Cantor spectrum is generically expected in the presence of an electric potential. We show that, even without electric potential, the spectrum has positive measure if the magnetic field is a perturbation of a constant one.Comment: 17 page