Critical bending point in the Lyapunov localization spectra of many-particle systems

The localization spectra of Lyapunov vectors in many-particle systems at low density exhibit a characteristic bending behavior. It is shown that this behavior is due to a restriction on the maximum number of the most localized Lyapunov vectors determined by the system configuration and mutual orthogonality. For a quasi-one-dimensional system this leads to a predicted bending point at n_c \approx 0.432 N for an N particle system. Numerical evidence is presented that confirms this predicted bending point as a function of the number of particles N.Comment: 4 pages, 4 figure

A CRISPR/Cas9 Vector System for Tissue-Specific Gene Disruption in Zebrafish

SummaryCRISPR/Cas9 technology of genome editing has greatly facilitated the targeted inactivation of genes in vitro and in vivo in a wide range of organisms. In zebrafish, it allows the rapid generation of knockout lines by simply injecting a guide RNA (gRNA) and Cas9 mRNA into one-cell stage embryos. Here, we report a simple and scalable CRISPR-based vector system for tissue-specific gene inactivation in zebrafish. As proof of principle, we used our vector with the gata1 promoter driving Cas9 expression to silence the urod gene, implicated in heme biosynthesis, specifically in the erythrocytic lineage. Urod targeting yielded red fluorescent erythrocytes in zebrafish embryos, recapitulating the phenotype observed in the yquem mutant. While F0 embryos displayed mosaic gene disruption, the phenotype appeared very penetrant in stable F1 fish. This vector system constitutes a unique tool to spatially control gene knockout and greatly broadens the scope of loss-of-function studies in zebrafish

The ePetri dish, an on-chip cell imaging platform based on subpixel perspective sweeping microscopy (SPSM)

We report a chip-scale lensless wide-field-of-view microscopy imaging technique, subpixel perspective sweeping microscopy, which can render microscopy images of growing or confluent cell cultures autonomously. We demonstrate that this technology can be used to build smart Petri dish platforms, termed ePetri, for cell culture experiments. This technique leverages the recent broad and cheap availability of high performance image sensor chips to provide a low-cost and automated microscopy solution. Unlike the two major classes of lensless microscopy methods, optofluidic microscopy and digital in-line holography microscopy, this new approach is fully capable of working with cell cultures or any samples in which cells may be contiguously connected. With our prototype, we demonstrate the ability to image samples of area 6 mm × 4 mm at 660-nm resolution. As a further demonstration, we showed that the method can be applied to image color stained cell culture sample and to image and track cell culture growth directly within an incubator. Finally, we showed that this method can track embryonic stem cell differentiations over the entire sensor surface. Smart Petri dish based on this technology can significantly streamline and improve cell culture experiments by cutting down on human labor and contamination risks

Equivalence of kinetic-theory and random-matrix approaches to Lyapunov spectra of hard-sphere systems

In the study of chaotic behaviour of systems of many hard spheres, Lyapunov exponents of small absolute value exhibit interesting characteristics leading to speculations about connections to non-equilibrium statistical mechanics. Analytical approaches to these exponents so far can be divided into two groups, macroscopically oriented approaches, using kinetic theory or hydrodynamics, and more microscopically oriented random-matrix approaches in quasi-one-dimensional systems. In this paper, I present an approach using random matrices and weak disorder expansion in an arbitrary number of dimensions. Correlations between subsequent collisions of a particle are taken into account. It is shown that the results are identical to those of a previous approach based on an extended Enskog-equation. I conclude that each approach has its merits, and provides different insights into the approximations made, which include the Sto{\ss}zahlansatz, the continuum limit, and the long-wavelength approximation. The comparison also gives insight into possible connections between Lyapunov exponents and fluctuations

Covariant Lyapunov vectors for rigid disk systems

We carry out extensive computer simulations to study the Lyapunov instability of a two-dimensional hard disk system in a rectangular box with periodic boundary conditions. The system is large enough to allow the formation of Lyapunov modes parallel to the x axis of the box. The Oseledec splitting into covariant subspaces of the tangent space is considered by computing the full set of covariant perturbation vectors co-moving with the flow in tangent-space. These vectors are shown to be transversal, but generally not orthogonal to each other. Only the angle between covariant vectors associated with immediate adjacent Lyapunov exponents in the Lyapunov spectrum may become small, but the probability of this angle to vanish approaches zero. The stable and unstable manifolds are transverse to each other and the system is hyperbolic.Comment: 23 pages, 17 figures; Chemical Physics, in press, June 2010. Chem. Phys. (2010): cited as: H. Bosetti, H.A. Posch, Chem. Phys. (2010), doi:10.1016/j.chemphys.2010.06.01

Definition of the zebrafish genome using flow cytometry and cytogenetic mapping

<p>Abstract</p> <p>Background</p> <p>The zebrafish (<it>Danio rerio</it>) is an important vertebrate model organism system for biomedical research. The syntenic conservation between the zebrafish and human genome allows one to investigate the function of human genes using the zebrafish model. To facilitate analysis of the zebrafish genome, genetic maps have been constructed and sequence annotation of a reference zebrafish genome is ongoing. However, the duplicative nature of teleost genomes, including the zebrafish, complicates accurate assembly and annotation of a representative genome sequence. Cytogenetic approaches provide "anchors" that can be integrated with accumulating genomic data.</p> <p>Results</p> <p>Here, we cytogenetically define the zebrafish genome by first estimating the size of each linkage group (LG) chromosome using flow cytometry, followed by the cytogenetic mapping of 575 bacterial artificial chromosome (BAC) clones onto metaphase chromosomes. Of the 575 BAC clones, 544 clones localized to apparently unique chromosomal locations. 93.8% of these clones were assigned to a specific LG chromosome location using fluorescence <it>in situ </it>hybridization (FISH) and compared to the LG chromosome assignment reported in the zebrafish genome databases. Thirty-one BAC clones localized to multiple chromosomal locations in several different hybridization patterns. From these data, a refined second generation probe panel for each LG chromosome was also constructed.</p> <p>Conclusion</p> <p>The chromosomal mapping of the 575 large-insert DNA clones allows for these clones to be integrated into existing zebrafish mapping data. An accurately annotated zebrafish reference genome serves as a valuable resource for investigating the molecular basis of human diseases using zebrafish mutant models.</p

Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits

Genome-wide association studies identify genomic variants associated with human traits and diseases. Most trait-associated variants are located within cell-type-specific enhancers, but the molecular mechanisms governing phenotypic variation are less well understood. Here, we show that many enhancer variants associated with red blood cell (RBC) traits map to enhancers that are co-bound by lineage-specific master transcription factors (MTFs) and signaling transcription factors (STFs) responsive to extracellular signals. The majority of enhancer variants reside on STF and not MTF motifs, perturbing DNA binding by various STFs (BMP/TGF-β-directed SMADs or WNT-induced TCFs) and affecting target gene expression. Analyses of engineered human blood cells and expression quantitative trait loci verify that disrupted STF binding leads to altered gene expression. Our results propose that the majority of the RBC-trait-associated variants that reside on transcription-factor-binding sequences fall in STF target sequences, suggesting that the phenotypic variation of RBC traits could stem from altered responsiveness to extracellular stimuli