Analysis of Regolith Simulant Ejecta Distributions from Normal Incident Hypervelocity Impact

The National Aeronautics and Space Administration (NASA) has established the Constellation Program. The Constellation Program has defined one of its many goals as long-term lunar habitation. Critical to the design of a lunar habitat is an understanding of the lunar surface environment; of specific importance is the primary meteoroid and subsequent ejecta environment. The document, NASA SP-8013 'Meteoroid Environment Model Near Earth to Lunar Surface', was developed for the Apollo program in 1969 and contains the latest definition of the lunar ejecta environment. There is concern that NASA SP-8013 may over-estimate the lunar ejecta environment. NASA's Meteoroid Environment Office (MEO) has initiated several tasks to improve the accuracy of our understanding of the lunar surface ejecta environment. This paper reports the results of experiments on projectile impact into powdered pumice and unconsolidated JSC-1A Lunar Mare Regolith simulant targets. Projectiles were accelerated to velocities between 2.45 and 5.18 km/s at normal incidence using the Ames Vertical Gun Range (AVGR). The ejected particles were detected by thin aluminum foil targets strategically placed around the impact site and angular ejecta distributions were determined. Assumptions were made to support the analysis which include; assuming ejecta spherical symmetry resulting from normal impact and all ejecta particles were of mean target particle size. This analysis produces a hemispherical flux density distribution of ejecta with sufficient velocity to penetrate the aluminum foil detectors

Comparison of Ejecta Distributions from Normal Incident Hypervelocity Impact on Lunar Regolith Simulant

The National Aeronautics and Space Administration (NASA) is progressing toward long-term lunar habitation. Critical to the design of a lunar habitat is an understanding of the lunar surface environment; of specific importance is the primary meteoroid and subsequent ejecta environment. The document, NASA SP-8013, was developed for the Apollo program and is the latest definition of the ejecta environment. There is concern that NASA SP-8013 may over-estimate the lunar ejecta environment. NASA's Meteoroid Environment Office (MEO) has initiated several tasks to improve the accuracy of our understanding of the lunar surface ejecta environment. This paper reports the results of experiments on projectile impact into powered pumice and unconsolidated JSC-1A Lunar Mare Regolith stimulant (JSC-1A) targets. The Ames Vertical Gun Range (AVGR) was used to accelerate projectiles to velocities in excess of 5 km/s and impact the targets at normal incidence. The ejected particles were detected by thin aluminum foil targets placed around the impact site and angular distributions were determined for ejecta. Comparison of ejecta angular distribution with previous works will be presented. A simplistic technique to characterize the ejected particles was formulated and improvements to this technique will be discussed for implementation in future tests

Success and Growth of Corals Transplanted to Cement Armor Mat Tiles in Southeast Florida: Implications for Reef Restoration

In 1997, 271 scleractinian corals growing on a sewer outfall pipe were used in a transplantation study offshore from North Dade County, Florida, USA. Corals were removed from the outfall pipe and transplanted onto concrete armor mat tiles used to cover the pipe. Success (number of corals still attached and alive), mortality (number of dead corals), and growth rates of the transplants were assessed between December 1997 and December 1999. Colony surface area and radius length were measured on scanned photographs to estimate horizontal growth rate. After two years post-transplantation, success rate and overall mortality were 87% and 7.8% respectively. In comparison, seven sites of nearby natural substrate corals had mean success rates of 83% and mortality rates ranging from 11-17%. The two most numerous transplant species, Solenastrea bournoniand Siderastrea siderea, had comparable success and mortality rates; however, S. bournoni had a significantly faster growth rate (increase in horizontal radius and surface area). The colony size at time of transplantation was not related to the rate of growth; however, mortality and partial mortality rates increased with smaller size colonies. The methodology used in this investigation is useful for assessing transplanted corals because it is non-invasive, allows continual monitoring, and is applicable to corals growing on natural and artificial substrates

Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs

<div><p>In many parts of the world the damaging potato late blight pathogen, <i>Phytophthora infestans</i>, is spread as a succession of clonal lineages. The discrimination of genetic diversity within such evolving populations provides insights into the processes generating novel lineages and the pathways and drivers of pathogen evolution and dissemination at local and global scales. This knowledge, in turn, helps optimise management practices. Here we combine two key methods for dissecting mitochondrial and nuclear diversity and resolve intra and inter-lineage diversity of over 100 <i>P</i>. <i>infestans</i> isolates representative of key clonal lineages found globally. A novel set of PCR primers that amplify five target regions are provided for mitochondrial DNA sequence analysis. These five loci increased the number of mtDNA haplotypes resolved from four with the PCR RFLP method to 37 (17, 6, 8 and 4 for Ia, Ib, IIa, and IIb haplotypes, respectively, plus 2 Herb-1 haplotypes). As with the PCR RFLP method, two main lineages, I and II were defined. Group I contained 25 mtDNA haplotypes that grouped broadly according to the Ia and Ib types and resolved several sub-clades amongst the global sample. Group II comprised two distinct clusters with four haplotypes corresponding to the RFLP type IIb and eight haplotypes resolved within type IIa. The 12-plex SSR assay revealed 90 multilocus genotypes providing accurate discrimination of dominant clonal lineages and other genetically diverse isolates. Some association of genetic diversity and geographic region of contemporary isolates was observed; US and Mexican isolates formed a loose grouping, distinct from isolates from Europe, South America and other regions. Diversity within clonal lineages was observed that varied according to the age of the clone. In combination, these fine-scale nuclear and maternally inherited mitochondrial markers enabled a greater level of discrimination among isolates than previously available and provided complementary perspectives on evolutionary questions relating to the diversity, phylogeography and the origins and spread of clonal lineages of <i>P</i>. <i>infestans</i>.</p></div

DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems

Isolation techniques supplemented by sequencing of DNA from axenic cultures have provided a robust methodology for the study of Phytophthora communities in agricultural and natural ecosystems. Recently, metabarcoding approaches have emerged as new paradigms for the detection of Phytophthora species in environmental samples. In this study, Illumina DNA metabarcoding and a conventional leaf baiting isolation technique were compared to unravel the variability of Phytophthora communities in different environments. Overall, 39 rhizosphere soil samples from a natural, a semi-natural and a horticultural small-scale ecosystem, respectively, were processed by both baiting and metabarcoding. Using both detection techniques, 28 out of 39 samples tested positive for Phytophthora. Overall, 1,406,613 Phytophthora internal transcribed spacer 1 (ITS1) sequences and 155 Phytophthora isolates were obtained, which grouped into 21 taxa, five retrieved exclusively by baiting (P. bilorbang; P. cryptogea; P. gonapodyides; P. parvispora and P. pseudocryptogea), 12 exclusively by metabarcoding (P. asparagi; P. occultans; P. psycrophila; P. syringae; P. aleatoria/P. cactorum; P. castanetorum/P. quercina; P. iranica-like; P. unknown sp. 1; P. unknown sp. 2; P. unknown sp. 3; P. unknown sp. 4; P. unknown sp. 5) and four with both techniques (P. citrophthora, P. multivora, P. nicotianae and P. plurivora). Both techniques complemented each other in describing the variability of Phytophthora communities from natural and managed ecosystems and revealing the presence of rare or undescribed Phytophthora taxa

Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm

We live in an era of abundant data. This has necessitated the development of new and innovative statistical algorithms to get the most from experimental data. For example, faster algorithms make practical the analysis of larger genomic data sets, allowing us to extend the utility of cutting-edge statistical methods. We present a randomised algorithm that accelerates the clustering of time series data using the Bayesian Hierarchical Clustering (BHC) statistical method. BHC is a general method for clustering any discretely sampled time series data. In this paper we focus on a particular application to microarray gene expression data. We define and analyse the randomised algorithm, before presenting results on both synthetic and real biological data sets. We show that the randomised algorithm leads to substantial gains in speed with minimal loss in clustering quality. The randomised time series BHC algorithm is available as part of the R package BHC, which is available for download from Bioconductor (version 2.10 and above) via http://bioconductor.org/packages/2.10/bioc/html/BHC.html. We have also made available a set of R scripts which can be used to reproduce the analyses carried out in this paper. These are available from the following URL. https://sites.google.com/site/randomisedbhc/

THAPBI PICT - a fast, cautious, and accurate metabarcoding analysis pipeline

THAPBI PICT is an open source software pipeline for metabarcoding analysis with multiplexed Illumina paired-end reads, including where diûerent amplicons are sequenced together. We demonstrate using worked examples with our own and public data sets how, with appropriate primer settings and a custom database, THAPBI PICT can be applied to other amplicons and organisms, and used for reanalysis of existing datasets. The core dataûow of the implementation is (i) data reduction to unique marker sequences, often called amplicon sequence variants (ASVs), (ii) dynamic thresholds for discarding low abundance sequences to remove noise and artifacts (rather than error correction by default), before (iii) classiûcation using a curated reference database. The default classiûer assigns a label to each query sequence based on a database match that is either perfect, or a single base pair edit away (substitution, deletion or insertion). Abundance thresholds for inclusion can be set by the user or automatically using per-batch negative or synthetic control samples. Output is designed for practical interpretation by non- specialists and includes a read report (ASVs with classiûcation and counts per sample), sample report (samples with counts per species classiûcation), and a topological graph of ASVs as nodes with short edit distances as edges. Source code available from https://github.com/peterjc/thapbi-pict/ with documentation including installation instructions

The Metagalactic Ionizing Radiation Field at Low Redshift

We compute the ionizing radiation field at low redshift, arising from Seyferts, QSOs, and starburst galaxies. This calculation combines recent Seyfert luminosity functions, extrapolated ultraviolet fluxes from our IUE-AGN database, and a new intergalactic opacity model based on Hubble Space Telescope and Keck Ly-alpha absorber surveys. At z = 0 for AGN only, our best estimate for the specific intensity at 1 Ryd is I_0 = 1.3 (+0.8/-0.5) x 10^-23 ergs/cm^2/s/Hz/sr, independent of H_0, Omega_0, and Lambda. The one-sided ionizing photon flux is Phi_ion = 3400 (+2100/-1300) photons/cm^2/s, and the H I photoionization rate is Gamma_HI = 3.2 (+2.0/-1.2) x 10^-14 s^-1 for alpha_s = 1.8. We also derive Gamma_ HI for z = 0 - 4. These error ranges reflect uncertainties in the spectral indexes for the ionizing EUV (alpha_s = 1.8 +/- 0.3) and the optical/UV (alpha_UV = 0.86 +/- 0.05), the IGM opacity model, the range of Seyfert luminosities (0.001 - 100 L*) and the completeness of the luminosity functions. Our estimate is a factor of three lower than the most stringent upper limits on the ionizing background (Phi_ion < 10^4 photons/cm^2/s) obtained from H-alpha observations in external clouds, and it lies within the range implied by other indirect measures. Starburst galaxies with a sufficiently large Lyman continuum escape fraction, f_ esc > 0.05, may provide a comparable background to AGN, I_0 (z=0) = 1.1 (+1.5/-0.7) x 10^{-23). An additional component of the ionizing background of this magnitude would violate neither upper limits from H-alpha observations nor the acceptable range from other measurements.Comment: 30 pages, 9 figures, accepted for Astronomical J. (Oct. 1999

Highly Diverse Phytophthora infestans Populations Infecting Potato Crops in Pskov Region, North-West Russia

There is limited understanding of the genetic variability in Phytophthora infestans in the major potato cultivation region of north-western Russia, where potato is grown primarily by small households with limited chemical treatment of late blight. In this study, the mating type, sensitivity to metalaxyl, and genotype and population genetic diversity (based on 12 simple sequence repeat (SSR) markers) of 238 isolates of P. infestans from the Pskov region during the years 2010–2013 were characterized. The aim was to examine the population structure, phenotypic and genotypic diversity, and the prevalent reproductive mode of P. infestans, as well as the influence of the location, time, and agricultural management practices on the pathogen population. The frequency of the A2 mating was stable over the four seasons and ranged from 33 to 48% of the sampled population. Both mating types occurred simultaneously in 90% of studied fields, suggesting the presence of sexual reproduction and oospore production in P. infestans in the Pskov region. Metalaxyl-sensitive isolates prevailed in all four years (72%), however, significantly fewer sensitive isolates were found in samples from large-scale conventional fields. A total of 50 alleles were detected in the 141 P. infestans isolates analyzed for genetic diversity. Amongst the 83 SSR multilocus genotypes (MLGs) detected, 65% were unique and the number of MLGs varied between locations from 3 to 20. These results, together with the high genotypic diversity observed in all the locations and the lack of significance of linkage disequilibrium, suggest that sexual recombination is likely responsible for the unique MLGs and the high genetic diversity found in the Pskov region population, resembling those of north-eastern European populations