Comparative Phylogenomics of Pathogenic and Nonpathogenic Species.

The Ascomycete Onygenales order embraces a diverse group of mammalian pathogens, including the yeast-forming dimorphic fungal pathogens Histoplasma capsulatum, Paracoccidioides spp. and Blastomyces dermatitidis, the dermatophytes Microsporum spp. and Trichopyton spp., the spherule-forming dimorphic fungal pathogens in the genus Coccidioides, and many nonpathogens. Although genomes for all of the aforementioned pathogenic species are available, only one nonpathogen had been sequenced. Here, we enhance comparative phylogenomics in Onygenales by adding genomes for Amauroascus mutatus, Amauroascus niger, Byssoonygena ceratinophila, and Chrysosporium queenslandicum--four nonpathogenic Onygenales species, all of which are more closely related to Coccidioides spp. than any other known Onygenales species. Phylogenomic detection of gene family expansion and contraction can provide clues to fungal function but is sensitive to taxon sampling. By adding additional nonpathogens, we show that LysM domain-containing proteins, previously thought to be expanding in some Onygenales, are contracting in the Coccidioides-Uncinocarpus clade, as are the self-nonself recognition Het loci. The denser genome sampling presented here highlights nearly 800 genes unique to Coccidiodes, which have significantly fewer known protein domains and show increased expression in the endosporulating spherule, the parasitic phase unique to Coccidioides spp. These genomes provide insight to gene family expansion/contraction and patterns of individual gene gain/loss in this diverse order--both major drivers of evolutionary change. Our results suggest that gene family expansion/contraction can lead to adaptive radiations that create taxonomic orders, while individual gene gain/loss likely plays a more significant role in branch-specific phenotypic changes that lead to adaptation for species or genera

A Study of the Physical Factors Affecting the Properties of Coke for the Blast Furnace

(i) The significance of the "plastic" state, in relation to the properties of blast furnace coke, is discussed and the importance of swelling pressure is emphasised. (ii) The aims of the investigation are drawn up. They include the development of a method, using di-electric heating, for the measurement of the swelling pressure of "plastic" coals and the study of the variation of this property with coal rank, etc. (iii) Previous methods of measuring swelling pressure are reviewed and their sources of error indicated. (iv) The theory of di-electric heating is described and the possibility of this technique giving uniform volume heating, in a coal sample is put forward. (v) The experimental apparatus is described. (vi) A detailed account of the development work entailed in the application of this novel technique is given. The most striking point arising from the development work is the critical effect of small amounts of oxygen in reducing the swelling properties of a coal. (vii) The finally adopted experimental method is described The results are presented in the following four sections, viz:- (a) Swelling Pressure - Swelling Volume relationship for a Durham (Sacriston) coal by a "constant volume" method. Swelling Pressure - Swelling Volume relationship for a Scottish (Kingshill) coal by a "constant pressure" method. (c) Swelling Pressure - Swelling Volume relationship for the Durham coal by a "constant pressure" method (d) An investigation of swelling mechanism. (viii) Recent work on the physico-chemical nature of coal and carbonised coal is reviewed in so far as it is relevant to the investigation. (ix) The results of (d) paragraph (vii), are discussed and compared with previous similar investigations. (x) The swelling pressure-swelling volume relationships obtained by the "constant pressure" method, are analysed. Specific permeability figures are deduced therefrom and the variation of these with pressure, temperature and volume, for the two coals tested, is discussed. An analysis of the swelling pressure-swelling volume relationship, obtained by the "constant volume" method, indicated that little useful information could be deduced from this complex relationship

Configurations and relative efficiencies of shrimp trawls employed in southeastern United States waters

Common shrimp trawl designs employed in the southeastern United States shrimp fishery are the flat, balloon, semiballoon, jib, and super X-3. Recent innovations in trawl design and rigging, including the twin trawl rigging and tongue trawl design, have improved the efficiency of shrimp trawling gear. A description of the construction techniques for the different designs indicate differences which affect gear performance. Measurements of horizontal spread and vertical opening for 76 trawl configurations indicate the relative efficiencies of the different designs. Maximum horizontal spreading efficiency was achieved by the "twin" and "tongue" trawl designs followed by the super X-3, jib, balloon, and semiballoon designs. Designs having the greatest vertical openings were the tongue and flat trawl designs followed by the semiballoon. Maximum total gape dimension was demonstrated by the "Mongoose" tongue trawl. Comparison of trawl spreading efficiency and door area to headrope length ratio indicates that a range of 70-80 in square (per door) of door area is required for each foot of trawl headrope length for maximum efficiency with conventional trawl designs and 66-75 in square per foot of headrope for tongue trawl designs. (PDF file contains 18 pages.

Environmental effects on lunar astronomical observatories

The Moon offers a stable platform with excellent seeing conditions for astronomical observations. Some troublesome aspects of the lunar environment will need to be overcome to realize the full potential of the Moon as an observatory site. Mitigation of negative effects of vacuum, thermal radiation, dust, and micrometeorite impact is feasible with careful engineering and operational planning. Shields against impact, dust, and solar radiation need to be developed. Means of restoring degraded surfaces are probably essential for optical and thermal control surfaces deployed in long-lifetime lunar facilities. Precursor missions should be planned to validate and enhance the understanding of the lunar environment (e.g., dust behavior without and with human presence) and to determine environmental effects on surfaces and components. Precursor missions should generate data useful in establishing keepout zones around observatory facilities where rocket launches and landings, mining, and vehicular traffic could be detrimental to observatory operation

Environmental effects on an optical-UV-IR synthesis array

The Moon offers a stable platform with excellent seeing conditions for the Lunar Optical-UV-IR Synthesis Array (LOUISA). Some troublesome aspects of the lunar environment will need to be overcome to realize the full potential of the Moon as an observatory site. Mitigation of negative effects of vacuum, thermal radiation, dust, and micrometeorite impact is feasible with careful engineering and operational planning. Shields against impact, dust, and solar radiation need to be developed. Means of restoring degraded surfaces are probably essential for optical and thermal control surfaces deployed in long-lifetime lunar facilities. Precursor missions should be planned to validate and enhance the understanding of the lunar environment (e.g., dust behavior without and with human presence and to determine environmental effects on surfaces and components. Precursor missions should generate data useful in establishing keepout zones around observatory facilities while rocket launches and landings, mining, and vehicular traffic could be detrimental to observatory operation

Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances.

The indoor microbiome is a complex system that is thought to depend on dispersal from the outdoor biome and the occupants' microbiome combined with selective pressures imposed by the occupants' behaviors and the building itself. We set out to determine the pattern of fungal diversity and composition in indoor air on a local scale and to identify processes behind that pattern. We surveyed airborne fungal assemblages within 1-month time periods at two seasons, with high replication, indoors and outdoors, within and across standardized residences at a university housing facility. Fungal assemblages indoors were diverse and strongly determined by dispersal from outdoors, and no fungal taxa were found as indicators of indoor air. There was a seasonal effect on the fungi found in both indoor and outdoor air, and quantitatively more fungal biomass was detected outdoors than indoors. A strong signal of isolation by distance existed in both outdoor and indoor airborne fungal assemblages, despite the small geographic scale in which this study was undertaken (<500 m). Moreover, room and occupant behavior had no detectable effect on the fungi found in indoor air. These results show that at the local level, outdoor air fungi dominate the patterning of indoor air. More broadly, they provide additional support for the growing evidence that dispersal limitation, even on small geographic scales, is a key process in structuring the often-observed distance-decay biogeographic pattern in microbial communities

The application of time-series MODIS NDVI profiles for the acquisition of crop information across Afghanistan

We investigated and developed a prototype crop information system integrating 250 m Moderate Resolution Imaging Spectroradiometer (MODIS) normalized difference vegetation index (NDVI) data with other available remotely sensed imagery, field data, and knowledge as part of a wider project monitoring opium and cereal crops. NDVI profiles exhibited large geographical variations in timing, height, shape, and number of peaks, with characteristics determined by underlying crop mixes, growth cycles, and agricultural practices. MODIS pixels were typically bigger than the field sizes, but profiles were indicators of crop phenology as the growth stages of the main first-cycle crops (opium poppy and cereals) were in phase. Profiles were used to investigate crop rotations, areas of newly exploited agriculture, localized variation in land management, and environmental factors such as water availability and disease. Near-real-time tracking of the current years’ profile provided forecasts of crop growth stages, early warning of drought, and mapping of affected areas. Derived data products and bulletins provided timely crop information to the UK Government and other international stakeholders to assist the development of counter-narcotic policy, plan activity, and measure progress. Results show the potential for transferring these techniques to other agricultural systems

Cloning, purification and characterization of the 6-phospho-3-hexulose isomerase YckF from Bacillus subtilis

The enzyme 6-phospho-3-hexulose isomerase (YckF) from Bacillus subtilis has been prepared and crystallized in a form suitable for X-ray crystallographic analysis. Crystals were grown by the hanging-drop method at 291 K using polyethylene glycol 2000 monomethylether as precipitant. They diffract beyond 1.7 A using an in-house Cu Kalpha source and belong to either space group P6(5)22 or P6(1)22, with unit-cell parameters a = b = 72.4, c = 241.2 A, and have two molecules of YckF in the asymmetric unit