Symmetry in nucleic-acid double helices

In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. Focusing on double helices, we describe the crucial role played by symmetry in shaping DNA and RNA structure. The base pairs in nucleic-acid double helices display rotational pseudo-symmetry. In the Watson–Crick base pairs found in naturally occurring DNA and RNA duplexes, the symmetry axis lies in the base-pair plane, giving rise to two different helical grooves. In contrast, anti-Watson-Crick base pairs have a dyad axis perpendicular to the base-pair plane and identical grooves. In combination with the base-pair symmetry, the syn/anti conformation of paired nucleotides determines the parallel or antiparallel strand orientation of double helices. DNA and RNA duplexes in nature are exclusively antiparallel. Watson-Crick base-paired DNA or RNA helices display either right-handed or left-handed helical (pseudo-) symmetry. Genomic DNA is usually in the right-handed B-form, and RNA double helices adopt the right-handed A-conformation. Finally, there is a higher level of helical symmetry in superhelical DNA in which B-form double strands are intertwined in a right- or left-handed sense

A case study in model-driven synthetic biology

We report on a case study in synthetic biology, demonstrating the modeldriven design of a self-powering electrochemical biosensor. An essential result of the design process is a general template of a biosensor, which can be instantiated to be adapted to specific pollutants. This template represents a gene expression network extended by metabolic activity. We illustrate the model-based analysis of this template using qualitative, stochastic and continuous Petri nets and related analysis techniques, contributing to a reliable and robust design

Minimalist AdaBoost for blemish identification in potatoes

We present a multi-class solution based on minimalist Ad- aBoost for identifying blemishes present in visual images of potatoes. Using training examples we use Real AdaBoost to rst reduce the fea- ture set by selecting ve features for each class, then train binary clas- siers for each class, classifying each testing example according to the binary classier with the highest certainty. Against hand-drawn ground truth data we achieve a pixel match of 83% accuracy in white potatoes and 82% in red potatoes. For the task of identifying which blemishes are present in each potato within typical industry dened criteria (10% coverage) we achieve accuracy rates of 93% and 94%, respectively

Turbulent resistivity evaluation in MRI generated turbulence

(abriged) MRI turbulence is a leading mechanism for the generation of an efficient turbulent transport of angular momentum in an accretion disk through a turbulent viscosity effect. It is believed that the same process could also transport large-scale magnetic fields in disks, reshaping the magnetic structures in these objects. This process, known as turbulent resistivity, has been suggested and used in several accretion-ejection models and simulations to produce jets. Still, the efficiency of MRI-driven turbulence to transport large-scale magnetic fields is largely unknown. We investigate this problem both analytically and numerically. We introduce a linear calculation of the MRI in the presence of a spatially inhomogeneous mean magnetic field. We show that, in this configuration, MRI modes lead to an efficient magnetic field transport, on the order of the angular momentum transport. We next use fully non linear simulations of MRI turbulence to compute the turbulent resistivity in several magnetic configurations. We find that the turbulent resistivity is on the order of the turbulent viscosity in all our simulations, although somewhat lower. The turbulent resistivity tensor is found to be highly anisotropic with a diffusion coefficient 3 times greater in the radial direction than in the vertical direction. These results support the possibility of driving jets from turbulent disks; the resulting jets may not be steady.Comment: 11 pages, 8 figures, accepted for publication in Astronomy and Astrophysic

Cold-shock domains - abundance, structure, properties, and nucleic-acid binding

The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains' ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration

Self-Similar Magnetocentrifugal Disk Winds with Cylindrical Asymptotics

We construct a two-parameter family of models for self-collimated, radially self-similar magnetized outflows from accretion disks. A flow at zero initial poloidal speed leaves the surface of a rotating disk and is accelerated and redirected toward the pole by helical magnetic fields threading the disk. At large distances from the disk, the flow streamlines asymptote to wrap around the surfaces of nested cylinders. In constrast to previous disk wind modeling, we have explicitly implemented the cylindrical asymptotic boundary condition to examine the consequences for flow dynamics. The solutions are characterized by the logarithmic gradient of the magnetic field strength and the ratios between the footpoint radius R_0 and asymptotic radius R_1 of streamlines; the Alfven radius must be found as an eigenvalue. Cylindrical solutions require the magnetic field to drop less steeply than 1/R. We find that the asymptotic poloidal speed on any streamline is typically just a few tenths of the Kepler speed at the corresponding disk footpoint. The asymptotic toroidal Alfven speed is, however, a few times the footpoint Kepler speed. We discuss the implications of the models for interpretations of observed optical jets and molecular outflows from young stellar systems. We suggest that the difficulty of achieving strong collimation in vector velocity simultaneously with a final speed comparable to the disk rotation rate argues against isolated jets and in favor of models with broader winds.Comment: 39 pages, Latex (uses AAS Latex macros), 6 eps figures, postscript preprint with embedded figures available from http://www.astro.umd.edu/~ostriker/professional/publications.html , to appear in ApJ 9/1/9

Structural basis of gene regulation by the Grainyhead/CP2 transcription factor family

Grainyhead (Grh)/CP2 transcription factors are highly conserved in multicellular organisms as key regulators of epithelial differentiation, organ development and skin barrier formation. In addition, they have been implicated as being tumor suppressors in a variety of human cancers. Despite their physiological importance, little is known about their structure and DNA binding mode. Here, we report the first structural study of mammalian Grh/CP2 factors. Crystal structures of the DNA-binding domains of grainyhead-like (Grhl) 1 and Grhl2 reveal a closely similar conformation with immunoglobulin-like core. Both share a common fold with the tumor suppressor p53, but differ in important structural features. The Grhl1 DNA-binding domain binds duplex DNA containing the consensus recognition element in a dimeric arrangement, supporting parsimonious target-sequence selection through two conserved arginine residues. We elucidate the molecular basis of a cancer-related mutation in Grhl1 involving one of these arginines, which completely abrogates DNA binding in biochemical assays and transcriptional activation of a reporter gene in a human cell line. Thus, our studies establish the structural basis of DNA target-site recognition by Grh transcription factors and reveal how tumor-associated mutations inactivate Grhl proteins. They may serve as points of departure for the structure-based development of Grh/CP2 inhibitors for therapeutic applications

Searches for Physics Beyond the Standard Model at Colliders

All experimental measurements of particle physics today are beautifully described by the Standard Model. However, there are good reasons to believe that new physics may be just around the corner at the TeV energy scale. This energy range is currently probed by the Tevatron and HERA accelerators and selected results of searches for physics beyond the Standard Model are presented here. No signals for new physics have been found and limits are placed on the allowed parameter space for a variety of different particles.Comment: Proceedings for 2007 Europhysics Conference on High Energy Physics, Manchester, July 200