Thermal and Cold Neutron Computed Tomography at the Los Alamos Neutron Scattering Center Using an Amorphous Silicon Detector Array

The use of the EG&G-Heimann RTM 128 [1] or dpiX FS20 [2] amorphous silicon (a-Si) detector array for thermal neutron radiography/computed tomography has proven to be a quick and efficient means of producing high quality digital radiographic images. The resolution, although not as good as film, is about 750 μm with the RTM and 127 μm with the dpiX array with a dynamic range in excess of 2800. In many respects using an amorphous silicon detector is an improvement over other techniques such as imaging with a CCD camera, using a storage phosphor plate or film radiography. Unlike a CCD camera, which is highly susceptible to radiation damage, a-Si detectors can be placed in the beam directly behind the object under examination and do not require any special optics or turning mirrors. The amorphous silicon detector also allows enough data to be acquired to construct a digital image in just a few seconds (minimum gate time 40 ms) whereas film or storage plate exposures can take many minutes and need to be digitized with a scanner. The flat panel can, therefore, acquire a complete 3D computed tomography data set in just a few tens of minutes. While a-Si detectors have been proposed for use in imaging neutron beams [3], this is the first reported implementation of such a detector for neutron imaging [4]

Time-gated energy-selected cold neutron radiography

A technique is under development at the Los Alamos Neutron Science Center (LANSCE), Manuel Lujan Jr. Neutron Scattering Center (Lujan Center) for producing neutron radiography using only a narrow energy range of cold neutrons. The technique, referred to as Time-Gated Energy-Selected (TGES) neutron radiography, employs the pulsed neutron source at the Lujan Center with time of flight to obtain a neutron pulse having an energy distribution that is a function of the arrival time at the imager. The radiograph is formed on a short persistence scintillator and a gated, intensified, cooled CCD camera is employed to record the images, which are produced at the specific neutron energy range determined by the camera gate. The technique has been used to achieve a degree of material discrimination in radiographic images. For some materials, such as beryllium and carbon, at energies above the Bragg cutoff the neutron scattering cross section is relatively high while at energies below the Bragg cutoff the scattering cross section drops significantly. This difference in scattering characteristics can be recorded in the TGES radiography and, because the Bragg cutoff occurs at different energy levels for various materials, the approach can be used to differentiate among these materials. This paper outlines the TGES radiography technique and shows an example of radiography using the approach

Attraction between DNA molecules mediated by multivalent ions

The effective force between two parallel DNA molecules is calculated as a function of their mutual separation for different valencies of counter- and salt ions and different salt concentrations. Computer simulations of the primitive model are used and the shape of the DNA molecules is accurately modelled using different geometrical shapes. We find that multivalent ions induce a significant attraction between the DNA molecules whose strength can be tuned by the averaged valency of the ions. The physical origin of the attraction is traced back either to electrostatics or to entropic contributions. For multivalent counter- and monovalent salt ions, we find a salt-induced stabilization effect: the force is first attractive but gets repulsive for increasing salt concentration. Furthermore, we show that the multivalent-ion-induced attraction does not necessarily correlate with DNA overcharging.Comment: 51 pages and 13 figure

Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees

Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome

Transboundary water interaction III: contest and compliance

This paper serves international water conflict resolution efforts by examining the ways that states contest hegemonic transboundary water arrangements. The conceptual framework of dynamic transboundary water interaction that it presents integrates theories about change and counter-hegemony to ascertain coercive, leverage, and liberating mechanisms through which contest and transformation of an arrangement occur. While the mechanisms can be active through sociopolitical processes either of compliance or of contest of the arrangement, most transboundary water interaction is found to contain elements of both. The role of power asymmetry is interpreted through classification of intervention strategies that seek to either influence or challenge the arrangements. Coexisting contest and compliance serve to explain in part the stasis on the Jordan and Ganges rivers (where the non-hegemons have in effect consented to the arrangement), as well as the changes on the Tigris and Mekong rivers, and even more rapid changes on the Amu Darya and Nile rivers (where the non-hegemons have confronted power asymmetry through influence and challenge). The framework also stresses how transboundary water events that may appear isolated are more accurately read within the many sociopolitical processes and arrangements they are shaped by. By clarifying the typically murky dynamics of interstate relations over transboundary waters, furthermore, the framework exposes a new suite of entry points for hydro-diplomatic initiatives

Molecular Evolution of Phosphoprotein Phosphatases in Drosophila

Phosphoprotein phosphatases (PPP), these ancient and important regulatory enzymes are present in all eukaryotic organisms. Based on the genome sequences of 12 Drosophila species we traced the evolution of the PPP catalytic subunits and noted a substantial expansion of the gene family. We concluded that the 18–22 PPP genes of Drosophilidae were generated from a core set of 8 indispensable phosphatases that are present in most of the insects. Retropositons followed by tandem gene duplications extended the phosphatase repertoire, and sporadic gene losses contributed to the species specific variations in the PPP complement. During the course of these studies we identified 5, up till now uncharacterized phosphatase retrogenes: PpY+, PpD5+, PpD6+, Pp4+, and Pp6+ which are found only in some ancient Drosophila. We demonstrated that all of these new PPP genes exhibit a distinct male specific expression. In addition to the changes in gene numbers, the intron-exon structure and the chromosomal localization of several PPP genes was also altered during evolution. The G−C content of the coding regions decreased when a gene moved into the heterochromatic region of chromosome Y. Thus the PPP enzymes exemplify the various types of dynamic rearrangements that accompany the molecular evolution of a gene family in Drosophilidae

The primary cilium as a dual sensor of mechanochemical signals in chondrocytes

The primary cilium is an immotile, solitary, and microtubule-based structure that projects from cell surfaces into the extracellular environment. The primary cilium functions as a dual sensor, as mechanosensors and chemosensors. The primary cilia coordinate several essential cell signaling pathways that are mainly involved in cell division and differentiation. A primary cilium malfunction can result in several human diseases. Mechanical loading is sense by mechanosensitive cells in nearly all tissues and organs. With this sensation, the mechanical signal is further transduced into biochemical signals involving pathways such as Akt, PKA, FAK, ERK, and MAPK. In this review, we focus on the fundamental functional and structural features of primary cilia in chondrocytes and chondrogenic cells