The effect of topology on the structure and free energy landscape of DNA kissing complexes

We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain constant. By studying systems with linking numbers -1, 0 or 1 we show that the average number of interstrand base pairs is larger when the topology is more favourable for the right-handed wrapping of strands around each other. The thermodynamic stability of the kissing complex also decreases when the linking number changes from -1 to 0 to 1. The structures of the kissing complexes typically involve two intermolecular helices that coaxially stack with the hairpin stems at a parallel four-way junction

Evaluation of Candidate Millimeter Wave Sensors for Synthetic Vision

The goal of the Synthetic Vision Technology Demonstration Program was to demonstrate and document the capabilities of current technologies to achieve safe aircraft landing, take off, and ground operation in very low visibility conditions. Two of the major thrusts of the program were (1) sensor evaluation in measured weather conditions on a tower overlooking an unused airfield and (2) flight testing of sensor and pilot performance via a prototype system. The presentation first briefly addresses the overall technology thrusts and goals of the program and provides a summary of MMW sensor tower-test and flight-test data collection efforts. Data analysis and calibration procedures for both the tower tests and flight tests are presented. The remainder of the presentation addresses the MMW sensor flight-test evaluation results, including the processing approach for determination of various performance metrics (e.g., contrast, sharpness, and variability). The variation of the very important contrast metric in adverse weather conditions is described. Design trade-off considerations for Synthetic Vision MMW sensors are presented

Sisyphus Cooling of Electrically Trapped Polyatomic Molecules

The rich internal structure and long-range dipole-dipole interactions establish polar molecules as unique instruments for quantum-controlled applications and fundamental investigations. Their potential fully unfolds at ultracold temperatures, where a plethora of effects is predicted in many-body physics, quantum information science, ultracold chemistry, and physics beyond the standard model. These objectives have inspired the development of a wide range of methods to produce cold molecular ensembles. However, cooling polyatomic molecules to ultracold temperatures has until now seemed intractable. Here we report on the experimental realization of opto-electrical cooling, a paradigm-changing cooling and accumulation method for polar molecules. Its key attribute is the removal of a large fraction of a molecule's kinetic energy in each step of the cooling cycle via a Sisyphus effect, allowing cooling with only few dissipative decay processes. We demonstrate its potential by reducing the temperature of about 10^6 trapped CH_3F molecules by a factor of 13.5, with the phase-space density increased by a factor of 29 or a factor of 70 discounting trap losses. In contrast to other cooling mechanisms, our scheme proceeds in a trap, cools in all three dimensions, and works for a large variety of polar molecules. With no fundamental temperature limit anticipated down to the photon-recoil temperature in the nanokelvin range, our method eliminates the primary hurdle in producing ultracold polyatomic molecules. The low temperatures, large molecule numbers and long trapping times up to 27 s will allow an interaction-dominated regime to be attained, enabling collision studies and investigation of evaporative cooling toward a BEC of polyatomic molecules

A high-density Diversity Arrays Technology (DArT) microarray for genome-wide genotyping in Eucalyptus

<p>Abstract</p> <p>Background</p> <p>A number of molecular marker technologies have allowed important advances in the understanding of the genetics and evolution of <it>Eucalyptus</it>, a genus that includes over 700 species, some of which are used worldwide in plantation forestry. Nevertheless, the average marker density achieved with current technologies remains at the level of a few hundred markers per population. Furthermore, the transferability of markers produced with most existing technology across species and pedigrees is usually very limited. High throughput, combined with wide genome coverage and high transferability are necessary to increase the resolution, speed and utility of molecular marker technology in eucalypts. We report the development of a high-density DArT genome profiling resource and demonstrate its potential for genome-wide diversity analysis and linkage mapping in several species of <it>Eucalyptus</it>.</p> <p>Findings</p> <p>After testing several genome complexity reduction methods we identified the <it>Pst</it>I/<it>Taq</it>I method as the most effective for <it>Eucalyptus </it>and developed 18 genomic libraries from <it>Pst</it>I/<it>Taq</it>I representations of 64 different <it>Eucalyptus </it>species. A total of 23,808 cloned DNA fragments were screened and 13,300 (56%) were found to be polymorphic among 284 individuals. After a redundancy analysis, 6,528 markers were selected for the operational array and these were supplemented with 1,152 additional clones taken from a library made from the <it>E. grandis </it>tree whose genome has been sequenced. Performance validation for diversity studies revealed 4,752 polymorphic markers among 174 individuals. Additionally, 5,013 markers showed segregation when screened using six inter-specific mapping pedigrees, with an average of 2,211 polymorphic markers per pedigree and a minimum of 859 polymorphic markers that were shared between any two pedigrees.</p> <p>Conclusions</p> <p>This operational DArT array will deliver 1,000-2,000 polymorphic markers for linkage mapping in most eucalypt pedigrees and thus provide high genome coverage. This array will also provide a high-throughput platform for population genetics and phylogenetics in <it>Eucalyptus</it>. The transferability of DArT across species and pedigrees is particularly valuable for a large genus such as <it>Eucalyptus </it>and will facilitate the transfer of information between different studies. Furthermore, the DArT marker array will provide a high-resolution link between phenotypes in populations and the <it>Eucalyptus </it>reference genome, which will soon be completed.</p

Receptor selectivity between the G proteins Gα12 and Gα13 is defined by a single leucine-to-isoleucine variation

Despite recent advances in structural definition of GPCR–G protein complexes, the basis of receptor selectivity between G proteins remains unclear. The Gα12 and Gα13 subtypes together form the least studied group of heterotrimeric G proteins. G protein–coupled receptor 35 (GPR35) has been suggested to couple efficiently to Gα13 but weakly to Gα12. Using combinations of cells genome-edited to not express G proteins and bioluminescence resonance energy transfer–based sensors, we confirmed marked selectivity of GPR35 for Gα13. Incorporating Gα12/Gα13 chimeras and individual residue swap mutations into these sensors defined that selectivity between Gα13 and Gα12 was imbued largely by a single leucine-to-isoleucine variation at position G.H5.23. Indeed, leucine could not be substituted by other amino acids in Gα13 without almost complete loss of GPR35 coupling. The critical importance of leucine at G.H5.23 for GPR35–G protein interaction was further demonstrated by introduction of this leucine into Gαq, resulting in the gain of coupling to GPR35. These studies demonstrate that Gα13 is markedly the most effective G protein for interaction with GPR35 and that selection between Gα13 and Gα12 is dictated largely by a single conservative amino acid variation.—Mackenzie, A. E., Quon, T., Lin, L.-C., Hauser, A. S., Jenkins, L., Inoue, A., Tobin, A. B., Gloriam, D. E., Hudson, B. D., Milligan, G. Receptor selectivity between the G proteins Gα12 and Gα13 is defined by a single leucine-to-isoleucine variation

A structured collaborative approach to intervention design using a modified intervention mapping approach: a case study using the Management and Interventions for Asthma (MIA) project for South Asian children

Background: To describe how using a combined approach of community-based participatory research and intervention mapping principles could inform the development of a tailored complex intervention to improve management of asthma for South Asian (SA) children; Management and Interventions for Asthma (MIA) study. / Methods: A qualitative study using interviews, focus groups, workshops, and modified intervention mapping procedures to develop an intervention planning framework in an urban community setting in Leicester, UK. The modified form of intervention mapping (IM) included: systematic evidence synthesis; community study; families and healthcare professionals study; and development of potential collaborative intervention strategies. Participants in the community study were 63 SA community members and 12 key informants; in-depth semi-structured interviews involved 30 SA families, 14 White British (WB) families and 37 Healthcare Professionals (HCPs) treating SA children living with asthma; prioritisation workshops involved 145 SA, 6 WB and 37 HCP participants; 30 participants in finalisation workshops. / Results: Two key principles were utilised throughout the development of the intervention; community-based participatory research (CBPR) principles and intervention mapping (IM) procedures. The CBPR approach allowed close engagement with stakeholders and generated valuable knowledge to inform intervention development. It accounted for diverse perceptions and experiences with regard to asthma and recognised the priorities of patients and their families/caregivers for service improvement. The ‘ACT on Asthma’ programme was devised, comprising four arms of an intervention strategy: education and training, clinical support, advice centre and raising awareness, to be co-ordinated by a central team. / Conclusions: The modified IM principles utilised in this study were systematic and informed by theory. The combined IM and participatory approach could be considered when tailoring interventions for other clinical problems within diverse communities. The IM approach to intervention development was however resource intensive. Working in meaningful collaboration with minority communities requires specific resources and a culturally competent methodology