Contamination study

The time dependence of the angular reflectance from molecularly contaminated optical surfaces in the Vacuum Ultraviolet (VUV) is measured. The light scattering measurements are accomplished in situ on optical surfaces in real time during deposition of molecular contaminants. The measurements are taken using non-coherent VUV sources with the predominant wavelengths being the Krypton resonance lines at 1236 and 1600 A. Detection of the scattered light is accomplished using a set of three solar blind VUV photomultipliers. An in-plane VUV BRDF (Bidirectional Reflectance Distribution Functions) experiment is described and details of the ongoing program to characterize optical materials exposed to the space environment is reported

A novel mechanism of selectivity against AZT by the human mitochondrial DNA polymerase

Native nucleotides show a hyperbolic concentration dependence of the pre-steady-state rate of incorporation while maintaining concentration-independent amplitude due to fast, largely irreversible pyrophosphate release. The kinetics of 3′-azido-2′,3′-dideoxythymidine (AZT) incorporation exhibit an increase in amplitude and a decrease in rate as a function of nucleotide concentration, implying that pyrophosphate release must be slow so that nucleotide binding and incorporation are thermodynamically linked. Here we develop assays to measure pyrophosphate release and show that it is fast following incorporation of thymidine 5′-triphosphate (TTP). However, pyrophosphate release is slow (0.0009 s−1) after incorporation of AZT. Modeling of the complex kinetics resolves nucleotide binding (230 µM) and chemistry forward and reverse reactions, 0.38 and 0.22 s−1, respectively. This unique mechanism increases selectivity against AZT incorporation by allowing reversal of the reaction and release of substrate, thereby reducing kcat/Km (7 × 10−6 μ M−1 s−1). Other azido-nucleotides (AZG, AZC and AZA) and 8-oxo-7,8-dihydroguanosine-5′-triphosphate (8-oxo-dGTP) show this same phenomena

Crystal structure of the DNA polymerase III β subunit (β-clamp) from the extremophile Deinococcus radiodurans

Published version, also available at http://dx.doi.org/10.1186/s12900-015-0032-6Background: Deinococcus radiodurans is an extremely radiation and desiccation resistant bacterium which can tolerate radiation doses up to 5,000 Grays without losing viability. We are studying the role of DNA repair and replication proteins for this unusual phenotype by a structural biology approach. The DNA polymerase III β subunit (β-clamp) acts as a sliding clamp on DNA, promoting the binding and processivity of many DNA-acting proteins, and here we report the crystal structure of D. radiodurans β-clamp (Drβ-clamp) at 2.0 Å resolution. Results: The sequence verification process revealed that at the time of the study the gene encoding Drβ-clamp was wrongly annotated in the genome database, encoding a protein of 393 instead of 362 amino acids. The short protein was successfully expressed, purified and used for crystallisation purposes in complex with Cy5-labeled DNA. The structure, which was obtained from blue crystals, shows a typical ring-shaped bacterial β-clamp formed of two monomers, each with three domains of identical topology, but with no visible DNA in electron density. A visualisation of the electrostatic surface potential reveals a highly negatively charged outer surface while the inner surface and the dimer forming interface have a more even charge distribution. Conclusions: The structure of Drβ-clamp was determined to 2.0 Å resolution and shows an evenly distributed electrostatic surface charge on the DNA interacting side. We hypothesise that this charge distribution may facilitate efficient movement on encircled DNA and help ensure efficient DNA metabolism in D. radiodurans upon exposure to high doses of ionizing irradiation or desiccation

Protein and Lysine Content of Grain, Endosperm, and Bran of Wheats from the USDA World Wheat Collection

The effects of relative amounts and the protein and lysine concentrations of kernel components on whole grain protein and lysine in wheat (Triticum aestivum L.) were studied. Wheats from the USDA World Wheat Collection that differed in whole grain protein and lysine content were compared. The correlation of grain protein with endosperm protein was r = 0.98, showing that whole grain protein percentages accurately reflect endosperm protein content in wheat. The correlation of grain and endosperm lysine percentages was lower. Endosperm percent protein had the largest effect on grain lysine content of any of the factors tested. The combined effect of percent of bran, bran percent protein, and bran lysine (% of protein) on whole grain lysine content was great as the effect of endosperm lysine (% of protein). Wheats with high grain lysine content do not always have high endosperm lyslne content. Differences were detected among the wheats studied for endosperm and bran protein and lysine content

Protein and Lysine Contents of Endosperm and Bran of the Parents and Progenies of Crosses of Common Wheat

Grain samples from parent and progeny rows of the common wheat (Triticum aestivum L.) crosses, \u27Nap Hal\u27/ \u27Atlas 66* and Nap Hal/\u27Super X\u27, were fractionated into their starchy endosperm and bran components to determine the within-kernel site of their variation in protein and lysine concentration. Nap Hal and Atlas 66 are highprotein wheats. Nap Hal also has elevated grain lysine content. Super X has average protein and lysine content. Transgressive segregation existed both for high and low endosperm protein concentration among the F3 progeny rows of Nap Hal/Atlas 66. Low-protein progeny rows had endosperm protein percentages that were 3 to 5 percentage points lower than the parental mean (19.5%). High-protein progeny lines were 2 to 4 percentage points higher than the parental mean. Nap Hal and some of the progeny rows were 5 percentage points higher in bran protein content than Atlas 66. Endosperm and bran protein percentages of Nap Hal/Super X F4 progeny were within the parental range. Some progeny rows had endosperm and bran protein concentrations equal to those of Nap Hal. Variation among the progeny rows for endosperm and bran lysine (% of protein) concentrations was within the range of variability of the replicated parental rows. Variation for grain protein content among the progeny rows of both crosses was due to variation for both endosperm and bran protein content. Variation for grain lysine (% of sample) among the Nap Hal/Atlas 66 progeny rows was due primarily to variation in endosperm and bran protein content with endosperm and bran lysine (% of protein) being of lesser importance

Stratigraphic distributions of genera and species of Neogene to Recent Caribbean reef corals

To document evolutionary patterns in late Cenozoic Caribbean reef corals, we compiled composite stratigraphic ranges of 49 genera and 175 species using Neogene occurrences in the Cibao Valley sequence of the northern Dominican Republic and faunal lists for 24 Miocene to Recent sites across the Caribbean region. This new compilation benefits in particular from increased sampling at late Miocene to early Pleistocene sites and from increased resolution and greater taxonomic consistency provided by the use of morphometric procedures in species recognition. Preliminary examination and quantitative analysis of origination and extinction patterns suggest that a major episode of turnover took place between 4 and 1 Ma during Plio-Pleistocene time. During the episode, extinctions were approximately simultaneous in species of all reef-building families, except the Mussidae. Most strongly affected were the Pocilloporidae (Stylophora and Pocillopora), Agariciidae (Pavona and Gardineroseris), and free-living members of the Faviidae and Meandrinidae. At the genus level, mono- and paucispecific as well as more speciose genera became regionally extinct. Many of the extinct genera live today in the Indo-Pacific region, and some are important components of modern eastern Pacific reefs. Global extinctions were concentrated in free-living genera. During the turnover episode, no new genera or higher taxa arose. Instead, new species originated within the surviving Caribbean genera at approximately the same time as the extinctions, including many dominant modern Caribbean reef-building corals (e.g., Acropora palmata and the Montastraea annularis complex). Excluding this episode, the taxonomic composition of the Caribbean reef-coral fauna remained relatively unchanged during the Neogene. Minor exceptions include: 1) high originations in the Agariciidae and free-living corals during late Miocene time; and 2) regional or global extinctions of several important Oligocene Caribbean reef builders during early to middle Miocene tim

Biomass Production of Monocultures and Mixtures of Cup Plant and Native Grasses on Prime and Marginal Cropland

To date, most candidate systems for producing herbaceous cellulosic biomass have been composed of monocultures of perennial or annual grasses. Ecosystem goods and services provided from these biomass feedstock production systems could be increased dramatically with mixing of one or more forb species that would increase biodiversity and provide habitat for pollinators. Cup plant (Silphium perfoliatum L.) is featured with many desirable characteristics, such as high biomass potential, adaptation to marginal soils, and attractiveness to pollinators, desirable in a dicot species to grow in mixtures with perennial warm-season grasses. The objective of this study was to compare cup plant, switchgrass (Panicum virgatum L.), and prairie cordgrass (Spartina pectinata Link) monocultures to their mixtures for biomass production on prime and poorly drained marginal crop land for two years in both South Dakota and Wisconsin. In Wisconsin, monocultures of prairie cordgrass and cup plant and their mixture produced more biomass (8.1 Mg·ha-1) than the switchgrass monoculture and switchgrass/cup plant mixture (5.3 Mg·ha-1) on both prime and marginal land. While in South Dakota, drought and meristem destruction by the cup plant moth (Eucosma giganteana Riley) caused large reductions in biomass production (1.7 Mg·ha-1) in both years, with the switchgrass/cup plant mixture on marginal land having the highest yield (2.1 Mg·ha-1). Our study showed binary mixtures of cup plant and native warm-season grasses have great potential for increasing biodiversity and other ecosystem goods and services, relative to monocultures, for sustainable biomass feedstock production on poorly drained marginal land in the northcentral USA

Urban Evolution: The Role of Water

The structure, function, and services of urban ecosystems evolve over time scales from seconds to centuries as Earth’s population grows, infrastructure ages, and sociopolitical values alter them. In order to systematically study changes over time, the concept of “urban evolution” was proposed. It allows urban planning, management, and restoration to move beyond reactive management to predictive management based on past observations of consistent patterns. Here, we define and review a glossary of core concepts for studying urban evolution, which includes the mechanisms of urban selective pressure and urban adaptation. Urban selective pressure is an environmental or societal driver contributing to urban adaptation. Urban adaptation is thesequential process by which an urban structure, function, or services becomes more fitted to its changing environment or human choices. The role of water is vital to driving urban evolution as demonstrated by historical changes in drainage, sewage flows, hydrologic pulses, and long-term chemistry. In the current paper, we show how hydrologic traits evolve across successive generations of urban ecosystems via shifts in selective pressures and adaptations over time. We explore multiple empirical examples including evolving: (1) urban drainage from stream burial to stormwater management; (2) sewage flows and water quality in response to wastewater treatment; (3) amplification of hydrologic pulses due to the interaction between urbanization and climate variability; and (4) salinization and alkalinization of fresh water due to human inputs and accelerated weathering. Finally, we propose a new conceptual model for the evolution of urban waters from the Industrial Revolution to the present day based on empirical trends and historical information. Ultimately, we propose that water itself is a critical driver of urban evolution that forces urban adaptation, which transforms the structure, function, and services of urban landscapes, waterways, and civilizations over time