Identifying short motifs by means of extreme value analysis

The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability can display large fluctuations from one putative binding site to another. Here we use a self-consistent statistical procedure that accounts correctly for the large deviations of the matching probability to predict the location of short binding sites. We apply it in two distinct situations: (a) the detection of the binding sites for three specific transcription factors on a set of 134 estrogen-regulated genes; (b) the identification, in a set of 138 possible transcription factors, of the ones binding a specific set of nine genes. In both instances, experimental findings are reproduced (when available) and the number of false positives is significantly reduced with respect to the other methods commonly employed.Comment: 6 pages, 5 figure

Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank

Hammerhead ribozymes previously were found in satellite RNAs from plant viroids and in repetitive DNA from certain species of newts and schistosomes. To determine if this catalytic RNA motif has a wider distribution, we decided to scrutinize the GenBank database for RNAs that contain hammerhead or hammerhead-like motifs. The search shows a widespread distribution of this kind of RNA motif in different sequences suggesting that they might have a more general role in RNA biology. The frequency of the hammerhead motif is half of that expected from a random distribution, but this fact comes From the low CpG representation in vertebrate sequences and the bias of the GenBank for those sequences. Intriguing motifs include those found in several families of repetitive sequences, in the satellite RNA from the carrot red leaf luteovirus, in plant viruses like the spinach latent virus and the elm mottle virus, in animal viruses like the hepatitis E virus and the caprine encephalitis virus, and in mRNAs such as those coding for cytochrome P450 oxidoreductase in the rat and the hamster

Chromomagnetism in nuclear matter

Quarks are color charged particles. Due to their motion there is a strong possibility of generation of color magnetic field. It is shown that however hadrons are color singlet particles they may have non-zero color magnetic moment. Due to this color magnetic moment hadrons can show color interaction. In this paper we have studied the chromomagnetic properties of nuclear matter.Comment: 6 pages, 1 figure, accepted for publication in Int. J. Theor. Phy

Ultrasound Imaging of Gene Expression in Mammalian Cells

The study of cellular processes occurring inside intact organisms requires methods to visualize cellular functions such as gene expression in deep tissues. Ultrasound is a widely used biomedical technology enabling noninvasive imaging with high spatial and temporal resolution. However, no genetically encoded molecular reporters are available to connect ultrasound contrast to gene expression in mammalian cells. To address this limitation, we introduce mammalian acoustic reporter genes. Starting with a gene cluster derived from bacteria, we engineered a eukaryotic genetic program whose introduction into mammalian cells results in the expression of intracellular air-filled protein nanostructures called gas vesicles, which produce ultrasound contrast. Mammalian acoustic reporter genes allow cells to be visualized at volumetric densities below 0.5% and permit high-resolution imaging of gene expression in living animals

Measurements of Sheath Currents and Equilibrium Potential on the Explorer VIII Satellite (1960 xi)

Experimental data were obtained from the Explorer VIII satellite on five parameters pertinent to the problem of the interaction of space vehicles with an ionized atmosphere. The five parameters are: photoemission current due to electrons emitted from the satellite surfaces as a result of solar radiation; electron and positive ion currents due to the diffusion of charged particles from the medium to the spacecraft; the vehicle potential relative to the medium, and the ambient electron temperature. Included in the experimental data is the aspect dependence of the photoemission and diffusion currents. On the basis of the observations, certain characteristics of the satellite's plasma sheath are postulated

Acoustic reporter genes for noninvasive imaging of microorganisms in mammalian hosts

The mammalian microbiome has many important roles in health and disease1,2, and genetic engineering is enabling the development of microbial therapeutics and diagnostics3,4,5,6,7. A key determinant of the activity of both natural and engineered microorganisms in vivo is their location within the host organism8,9. However, existing methods for imaging cellular location and function, primarily based on optical reporter genes, have limited deep tissue performance owing to light scattering or require radioactive tracers10,11,12. Here we introduce acoustic reporter genes, which are genetic constructs that allow bacterial gene expression to be visualized in vivo using ultrasound, a widely available inexpensive technique with deep tissue penetration and high spatial resolution13,14,15. These constructs are based on gas vesicles, a unique class of gas-filled protein nanostructures that are expressed primarily in water-dwelling photosynthetic organisms as a means to regulate buoyancy16,17. Heterologous expression of engineered gene clusters encoding gas vesicles allows Escherichia coli and Salmonella typhimurium to be imaged noninvasively at volumetric densities below 0.01% with a resolution of less than 100 μm. We demonstrate the imaging of engineered cells in vivo in proof-of-concept models of gastrointestinal and tumour localization, and develop acoustically distinct reporters that enable multiplexed imaging of cellular populations. This technology equips microbial cells with a means to be visualized deep inside mammalian hosts, facilitating the study of the mammalian microbiome and the development of diagnostic and therapeutic cellular agents

Path integrals on a flux cone

This paper considers the Schroedinger propagator on a cone with the conical singularity carrying magnetic flux (``flux cone''). Starting from the operator formalism and then combining techniques of path integration in polar coordinates and in spaces with constraints, the propagator and its path integral representation are derived. "Quantum correction" in the Lagrangian appears naturally and no a priori assumption is made about connectivity of the configuration space.Comment: LaTeX file, 9 page

Aspects of classical and quantum motion on a flux cone

Motion of a non-relativistic particle on a cone with a magnetic flux running through the cone axis (a ``flux cone'') is studied. It is expressed as the motion of a particle moving on the Euclidean plane under the action of a velocity-dependent force. Probability fluid (``quantum flow'') associated with a particular stationary state is studied close to the singularity, demonstrating non trivial Aharonov-Bohm effects. For example, it is shown that near the singularity quantum flow departs from classical flow. In the context of the hydrodynamical approach to quantum mechanics, quantum potential due to the conical singularity is determined and the way it affects quantum flow is analysed. It is shown that the winding number of classical orbits plays a role in the description of the quantum flow. Connectivity of the configuration space is also discussed.Comment: LaTeX file, 21 pages, 8 figure

Phase Space Reduction and Vortex Statistics: An Anyon Quantization Ambiguity

We examine the quantization of the motion of two charged vortices in a Ginzburg--Landau theory for the fractional quantum Hall effect recently proposed by the first two authors. The system has two second-class constraints which can be implemented either in the reduced phase space or Dirac-Gupta-Bleuler formalism. Using the intrinsic formulation of statistics, we show that these two ways of implementing the constraints are inequivalent unless the vortices are quantized with conventional statistics; either fermionic or bosonic.Comment: 14 pages, PHYZZ