Folding and Base Pairing of a Fibrinogen Specific DNA Aptamer

Abstract Nucleic acid aptamers can be directed to bind to a variety of target molecules that range widely in molecular size. Their high specificity and selectivity for their targets, in addition to the relative ease in generating aptamers, have sparked their development as drugs and use in diagnostic applications. The 90-mer DNA aptamer (Ap90), specific for the glycoprotein fibrinogen was analyzed by a combination of gel electrophoresis, secondary structure prediction software and NMR spectroscopy to determine what structural motifs are formed prior to binding to its target. Native gel electrophoresis and structure prediction indicate that the aptamer is partially folded. This was further supported by the NMR studies focusing on base pairing. The NMR experiments revealed that the aptamer only forms a maximum of 4-5 AT and 6-8 GC base pairs. Using several model substrates, the base paired region was identified as a hairpin structure originating from the primer region. Changing the solvent conditions did not elicit additional base pairs or promote stable tertiary structures. These results demonstrate that the majority of the aptamer has no established structure prior to binding and guides the design of more efficient aptamers

We Have the Spaceship; But Where's the Start Button: Human Engineering Issues in the Age of Long Duration Space Exploration

As long duration space exploration and habitation becomes more commonplace, a number of Human Engineering factors (Gravitational Adaptation, 2-D to 3-D Movement Adaptation, Design Form/Function, and Space Ergonomics to name a few) will become more pronounced. More research and development is needed in these areas or the explorers may find themselves in painful or dangerous situations

KH 15D: A Spectroscopic Binary

We present the results of a high-resolution spectroscopic monitoring program of the eclipsing pre-main-sequence star KH 15D that reveal it to be a single-line spectroscopic binary. We find that the best-fit Keplerian model has a period P = 48.38 days, which is nearly identical to the photometric period. Thus, we find the best explanation for the periodic dimming of KH 15D is that the binary motion carries the currently visible star alternately above and below the edge of an obscuring cloud. The data are consistent with the models involving an inclined circumstellar disk, as recently proposed by Winn et al. (2004) and Chiang & Murray-Clay (2004). We show that the mass ratio expected from models of PMS evolution, together with the mass constraints for the visible star, restrict the orbital eccentricity to 0.68 < e < 0.80 and the mass function to 0.125 < Fm < 0.5 Msun.Comment: 8 pages, 4 figures, 3 tables, accepted for publication in September AJ. Discussion of rotational velocity deferred to Hamilton, et al. (2004, in prep). Previously reported vsini value in error; Replaced Table 3 with new Figure 3; Added new Table 2 showing individual radial velocities w.r.t. each reference star; Fixed typo in Figure

Rootless tephra stratigraphy and emplacement processes

Volcanic rootless cones are the products of thermohydraulic explosions involving rapid heat transfer from active lava (fuel) to external sources of water (coolant). Rootless eruptions are attributed to molten fuel–coolant interactions (MFCIs), but previous studies have not performed systematic investigations of rootless tephrostratigraphy and grain-size distributions to establish a baseline for evaluating relationships between environmental factors, MFCI efficiency, fragmentation, and patterns of tephra dispersal. This study examines a 13.55-m-thick vertical section through an archetypal rootless tephra sequence, which includes a rhythmic succession of 28 bed pairs. Each bed pair is interpreted to be the result of a discrete explosion cycle, with fine-grained basal material emplaced dominantly as tephra fall during an energetic opening phase, followed by the deposition of coarser-grained material mainly as ballistic ejecta during a weaker coda phase. Nine additional layers are interleaved throughout the stratigraphy and are interpreted to be dilute pyroclastic density current (PDC) deposits. Overall, the stratigraphy divides into four units: unit 1 contains the largest number of sediment-rich PDC deposits, units 2 and 3 are dominated by a rhythmic succession of bed pairs, and unit 4 includes welded layers. This pattern is consistent with a general decrease in MFCI efficiency due to the depletion of locally available coolant (i.e., groundwater or wet sediments). Changing conduit/vent geometries, mixing conditions, coolant and melt temperatures, and/or coolant impurities may also have affected MFCI efficiency, but the rhythmic nature of the bed pairs implies a periodic explosion process, which can be explained by temporary increases in the water-to-lava mass ratio during cycles of groundwater recharge.We acknowledge financial support from the National Science Foundation (NSF) grant EAR-119648, National Aeronautics and Space Administration (NASA) Mars Data Analysis Program (MDAP) grant NNG05GQ39G, NASA Mars Fundamental Research Program (MFRP) grant NNG05GM08G, NASA Postdoctoral Program (NPP), Geological Society of America (GSA), and Icelandic Centre for Research (RANNÍS). We are grateful to Stephen Scheidt for his help developing photogrammetric reconstructions of Cone 53 and we thank Richard Brown for his editorial handing of this manuscript as well as Peter Reynolds and Adrian Pittari for their constructive reviews.Peer Reviewe

Sequential measurement of δ15N, δ13C and δ34S values in archaeological bone collagen at the Scottish Universities Environmental Research Centre (SUERC): a new analytical frontier

Rationale: The use of multi‐isotopic analysis (δ15N, δ13C and δ34S values) of archaeological bone collagen to assist in the interpretation of diet, movement and mobility of prehistoric populations is gradually increasing, yet many researchers have traditionally avoided investigating sulphur due to its very low concentrations (&lt;0.3%) in mammalian collagen. For this reason, and as a consequence of analytical detection limits, sulphur is usually measured separately from carbon and nitrogen, which leads to longer analytical times and higher costs. Methods: A Thermo ScientificTM EA IsoLinkTM IRMS system, with the ability to rapidly heat a gas‐chromatography (GC) column and concentrate the sample gas online without cryo‐trapping, was used at the Radiocarbon Laboratory at SUERC. Optimisation of the GC temperature and carrier gas flow rate in the elemental analyser resulted in improved signal‐to‐noise ratio and sensitivity for SO2. This allowed for routine sequential N2, CO2 and SO2 measurements on small samples of bone collagen. Results: Improvements in sample gas transfer to the mass spectrometer allows for sequential δ15N, δ13C and δ34S values to be measured in 1–1.5 mg samples of bone collagen. Moreover, the sensitivity and signal‐to‐noise ratio of the sample gas, especially SO2, is improved, resulting in precisions of ±0.15‰ for δ15N values, ±0.1‰ for δ13C values and ±0.3‰ for δ34S values. Previous instrumentation allowed for the analysis of ~30 unknown samples before undertaking maintenance; however, ~150 unknown samples can now be measured, meaning a 5‐fold increase in sample throughput. Conclusions: The ability to sequentially measure δ15N, δ13C and δ34S values rapidly in archaeological bone collagen is an attractive option to researchers who want to build larger, more succinct datasets for their sites of interest, at a much‐reduced analytical cost and without destroying larger quantities of archaeological material

Topographic and Stochastic Influences on Pahoehoe Lava Lobe Emplacement

A detailed understanding of phoehoe emplacement is necessary for developing accurate models of flow field development, assessing hazards, and interpreting the significance of lava morphology on Earth and other planetary surfaces. Active pahoehoe lobes on Kilauea Volcano, Hawaii, were examined on 21-26 February 2006 using oblique time-series stereo-photogrammetry and differential global positioning system (DGPS) measurements. During this time, the local discharge rate for peripheral lava lobes was generally constant at 0.0061 +/- 0.0019 m3/s, but the areal coverage rate of the lobes exhibited a periodic increase every 4.13 +/- 0.64 minutes. This periodicity is attributed to the time required for the pressure within the liquid lava core to exceed the cooling induced strength of its margins. The pahoehoe flow advanced through a series of down slope and cross-slope breakouts, which began as approximately 0.2 m-thick units (i.e., toes) that coalesced and inflated to become approximately meter-thick lobes. The lobes were thickest above the lowest points of the initial topography and above shallow to reverse facing slopes, defined relative to the local flow direction. The flow path was typically controlled by high-standing topography, with the zone directly adjacent to the final lobe margin having an average relief that was a few centimeters higher than the lava inundated region. This suggests that toe-scale topography can, at least temporarily, exert strong controls on pahoehoe flow paths by impeding the lateral spreading of the lobe. Observed cycles of enhanced areal spreading and inflated lobe morphology are also explored using a model that considers the statistical likelihood of sequential breakouts from active flow margins and the effects of topographic barriers

Reflected Light from Sand Grains in the Terrestrial Zone of a Protoplanetary Disk

We show that grains have grown to ~mm size (sand sized) or larger in the terrestrial zone (within ~3 AU) of the protoplanetary disk surrounding the 3 Myr old binary star KH 15D. We also argue that the reflected light in the system reaches us by back scattering off the far side of the same ring whose near side causes the obscuration.Comment: 22 pages, 5 figures. To be published in Nature, March 13, 2008. Contains a Supplemen

Differentiating Fissure-Fed Lava Flow Types and Facies Using RADAR and LiDAR: An Example from the 2014–2015 Holuhraun Lava Flow-field

Distinguishing between lava types and facies using remote sensing data is important for interpreting the emplacement history of lava flow-fields on Earth and other planetary bodies. Lava facies typically include a mixture of lava types and record the collective emplacement history of material preserved at a particular location. We seek to determine if lava facies in the 2014–2015 Holuhraun lava flow-field are discernible using radar roughness analysis. Furthermore, we also seek to distinguish between lava types using high resolution Light Detection and Ranging (LiDAR) data. We extracted circular polarization ratios (CPR) from the Uninhabited Aerial Vehicle Synthetic Aperture Radar and cross-polarization (VH/VV) data from the Sentinel-1 satellite to analyze the surface roughness of three previously mapped lava facies: rubbly, spiny, and undifferentiated rubbly–spiny. Using the Kruskal-Wallis test, we reveal that all but one pair of the facies are statistically separable. However, the populations overlap by 88%–89% for CPR and 64%–67% for VH/VV. Therefore, owing to large sample populations (n \u3e 2 × 105), slight differences in radar data may be used to probabilistically infer the presence of a particular facies, but not directly map them. We also calculated the root-mean-square slope and Hurst exponents of five different lava types using LiDAR topography (5 cm/pixel). Our results show minute differences between most of the lava types, with the exception of the rubbly pāhoehoe, which is discernible at 1σ. In brief, the presence of “transitional” lava types (e.g., rubbly pāhoehoe) within fissure-fed lava flow-fields complicates remote sensing-based mapping