Gene expression analysis of bovine embryonic disc, trophoblast and parietal hypoblast at the start of gastrulation

In cattle early gastrulation-stage embryos (Stage 5), four tissues can be discerned: (i) the top layer of the embryonic disc consisting of embryonic ectoderm (EmE); (ii) the bottom layer of the disc consisting of mesoderm, endoderm and visceral hypoblast (MEH); (iii) the trophoblast (TB); and (iv) the parietal hypoblast. We performed microsurgery followed by RNA-seq to analyse the transcriptome of these four tissues as well as a developmentally earlier pre-gastrulation embryonic disc. The cattle EmE transcriptome was similar at Stages 4 and 5, characterised by the OCT4/SOX2/NANOG pluripotency network. Expression of genes associated with primordial germ cells suggest their presence in the EmE tissue at these stages. Anterior visceral hypoblast genes were transcribed in the Stage 4 disc, but no longer by Stage 5. The Stage 5 MEH layer was equally similar to mouse embryonic and extraembryonic visceral endoderm. Our data suggest that the first mesoderm to invaginate in cattle embryos is fated to become extraembryonic. TGFβ, FGF, VEGF, PDGFA, IGF2, IHH and WNT signals and receptors were expressed, however the representative members of the FGF families differed from that seen in equivalent tissues of mouse embryos. The TB transcriptome was unique and differed significantly from that of mice. FGF signalling in the TB may be autocrine with both FGFR2 and FGF2 expressed. Our data revealed a range of potential inter-tissue interactions, highlighted significant differences in early development between mice and cattle and yielded insight into the developmental events occurring at the start of gastrulation

Locating the Source of Diffusion in Large-Scale Networks

How can we localize the source of diffusion in a complex network? Due to the tremendous size of many real networks--such as the Internet or the human social graph--it is usually infeasible to observe the state of all nodes in a network. We show that it is fundamentally possible to estimate the location of the source from measurements collected by sparsely-placed observers. We present a strategy that is optimal for arbitrary trees, achieving maximum probability of correct localization. We describe efficient implementations with complexity O(N^{\alpha}), where \alpha=1 for arbitrary trees, and \alpha=3 for arbitrary graphs. In the context of several case studies, we determine how localization accuracy is affected by various system parameters, including the structure of the network, the density of observers, and the number of observed cascades.Comment: To appear in Physical Review Letters. Includes pre-print of main paper, and supplementary materia

Kinematics of the swimming of Spiroplasma

\emph{Spiroplasma} swimming is studied with a simple model based on resistive-force theory. Specifically, we consider a bacterium shaped in the form of a helix that propagates traveling-wave distortions which flip the handedness of the helical cell body. We treat cell length, pitch angle, kink velocity, and distance between kinks as parameters and calculate the swimming velocity that arises due to the distortions. We find that, for a fixed pitch angle, scaling collapses the swimming velocity (and the swimming efficiency) to a universal curve that depends only on the ratio of the distance between kinks to the cell length. Simultaneously optimizing the swimming efficiency with respect to inter-kink length and pitch angle, we find that the optimal pitch angle is 35.5$^\circ$ and the optimal inter-kink length ratio is 0.338, values in good agreement with experimental observations.Comment: 4 pages, 5 figure

Efficiency of initiating cell adhesion in hydrodynamic flow

We theoretically investigate the efficiency of initial binding between a receptor-coated sphere and a ligand-coated wall in linear shear flow. The mean first passage time for binding decreases monotonically with increasing shear rate. Above a saturation threshold of the order of a few 100 receptor patches, the binding efficiency is enhanced only weakly by increasing their number and size, but strongly by increasing their height. This explains why white blood cells in the blood flow adhere through receptor patches localized to the tips of microvilli, and why malaria-infected red blood cells form elevated receptor patches (knobs).Comment: 4 pages, Revtex, 4 Postscript figures included, to appear in PR

Tin dioxide sol-gel derived thin films deposited on porous silicon

Undoped and Sb-doped SnO2 sol¿gel derived thin films have been prepared for the first time from tin (IV) ethoxide precursor and SbCl3 in order to be utilised for gas sensing applications where porous silicon is used as a substrate. Transparent, crack-free and adherent layers were obtained on different types of substrates (Si, SiO2/Si). The evolution of the Sn¿O chemical bonds in the SnO2 during film consolidation treatments was monitored by infrared spectroscopy. By energy dispersive X-ray spectroscopy performed on the cross section of the porosified silicon coupled with transmission electron microscopy, the penetration of the SnO2 sol¿gel derived films in the nanometric pores of the porous silicon has been experimentally proved

Large deviations for ideal quantum systems

We consider a general d-dimensional quantum system of non-interacting particles, with suitable statistics, in a very large (formally infinite) container. We prove that, in equilibrium, the fluctuations in the density of particles in a subdomain of the container are described by a large deviation function related to the pressure of the system. That is, untypical densities occur with a probability exponentially small in the volume of the subdomain, with the coefficient in the exponent given by the appropriate thermodynamic potential. Furthermore, small fluctuations satisfy the central limit theorem.Comment: 28 pages, LaTeX 2

Gain control in molecular information processing: Lessons from neuroscience

Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitate adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain control. Here we argue that a certain simple mechanism of gain control, understood well in the context of systems neuroscience, also works for molecular signaling. The mechanism allows to transmit more than one bit (on or off) of information about the signal independently of the signal variance. It does not require additional molecular circuitry beyond that already present in many molecular systems, and, in particular, it does not depend on existence of feedback loops. The mechanism provides a potential explanation for abundance of ultrasensitive response curves in biological regulatory networks.Comment: 10 pages, 5 figure

Information retrieval system

Generalized information storage and retrieval system capable of generating and maintaining a file, gathering statistics, sorting output, and generating final reports for output is reviewed. File generation and file maintenance programs written for the system are general purpose routines

An efficient, multiple range random walk algorithm to calculate the density of states

We present a new Monte Carlo algorithm that produces results of high accuracy with reduced simulational effort. Independent random walks are performed (concurrently or serially) in different, restricted ranges of energy, and the resultant density of states is modified continuously to produce locally flat histograms. This method permits us to directly access the free energy and entropy, is independent of temperature, and is efficient for the study of both 1st order and 2nd order phase transitions. It should also be useful for the study of complex systems with a rough energy landscape.Comment: 4 pages including 4 ps fig

Phases of the infinite U Hubbard model

We apply the density matrix renormalization group (DMRG) to study the phase diagram of the infinite U Hubbard model on 2-, 4-, and 6-leg ladders. Where the results are largely insensitive to the ladder width, we consider the results representative of the 2D square lattice model. We find a fully polarized ferromagnetic Fermi liquid phase when n, the density of electrons per site, is in the range 1>n>n_F ~ 4/5. For n=3/4 we find an unexpected commensurate insulating "checkerboard" phase with coexisting bond density order with 4 sites per unit cell and block spin antiferromagnetic order with 8 sites per unit cell. For 3/4 > n, the wider ladders have unpolarized groundstates, which is suggestive that the same is true in 2D