ThermoPhyl : a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples

The ability to specifically and sensitively target genotypes of interest is critical for the success of many PCR-based analyses of environmental or clinical samples that contain multiple templates.Next-generation sequence data clearly show that such samples can harbour hundreds to thousands of operational taxonomic units; a richness which precludes the manual evaluation of candidate assay specificity and sensitivity using multiple sequence alignments. To solve this problem we have developed and validated a free software tool which automates the identification of PCR assays targeting specific genotypes in complex samples. ThermoPhyl uses user-defined target and non-target sequence databases to assess the phylogenetic sensitivity and specificity of thermodynamically optimised candidate assays derived from primer design software packages. ThermoPhyl takes its name from its central premise of testing Thermodynamically optimal assays for Phylogenetic specificity and sensitivity and can be used for two primer (traditional PCR) or two primers with an internal probe (e.g. TaqMan® qPCR) applications and potentially for oligonucleotide probes.Here we describe the use of ThermoPhyl for traditional PCR and qPCR assays. PCR assays selected using ThermoPhyl were validated using 454 pyrosequencing of a traditional specific PCR assay and with a set of four genotype-specific qPCR assays applied to estuarine sediment samples

Chemistry and Apparent Quality of Surface Water and Ground Water Associated with Coal Basins

Personnel of the Arkansas Mining and Mineral Resources Research Institute conducted preliminary investigations on the chemistry and quality of surface and ground water associated with 12 coal-bearing sub-basins in the Arkansas Valley coal field. The coal field is approximately 60 miles long and 33 miles wide but only in 12 areas coal is thick enough and has proper quality to be termed commercial. Both surface and underground sample sites were established in each of the sub-basins with some minor variations in four areas where not all types of sites could be located. Water was collected from 19 surface points and 19 underground points in the established areas. Both field and laboratory analyses were made and elemental contents are reported herein. In the main, the chemistry and water quality suggests that all water is suitable for agricultural and industrial uses. To obtain potable water, treatment must be made to reduce calcium, magnesium, sodium sulfate and iron. The mineral content of the water is due to its contact with coal-bearing zones and, as such, reflects the mineral content of the coal. However, it is recommended that additional studies on the petrography and geochemistry of the coal, overburden and underburden is in order. Also, it is recommended that at least one detailed study be made of one of the coal sub-basins where geologic parameters can be completely established with regard to hydrogeology. This report is an important first step in determining the character and quality of Arkansas coal which must be fully understood to fully utilize this important mineral resource

Mothers Against Democracy: Hebe de Bonafini\u27s Rhetorical Strategies of Resistance, 1988-2003

The Madres de Plaza de Mayo was once a small group of grieving mothers in Buenos Aires who sought solace during a dictatorship that began in 1976. As their resistance developed, they grew into a social and political organization whose purpose is to keep the memory of their children alive and to generate justice in Argentina and worldwide. Their leader, Hebe de Bonafini, is atypical because there was no oratorical tradition for her to follow: she created one. Throughout the thirty-four years of the mothers\u27 movement\u27s existence, Bonafini\u27s rhetoric has changed and has taken a new shape. The permanent disappearance of the Madres\u27 loved ones led to the strategies that allowed the Madres a voice during a dictatorship that silenced an entire country. A year into Argentina\u27s military dictatorship, Bonafini framed her arguments around the injustices of the dictatorship, yet as the Madres\u27 organization transformed to political activism and their movement split, her rhetoric became more aggressive and revolutionary. Even though democracy was established in 1983, Bonafini\u27s resistance discourse continued for twenty-three more years, until 2006, as the Madres sustained their resistance to the Argentine government. This study is about social movements, women, mothers, and power. The focus is five of Bonafini\u27s major speeches, chronologically dated from 1988 to 2003, analyzed to identify her rhetorical instruments of power. A close reading provides a better understanding of the speech texts which identify three consistent themes: motherhood metaphors, denial of agency and the use of prosopopoeia, and scapegoating. Strategies that generate revolution are important to study. Bonafini began to speak during a brutal dictatorship and continued to use her oratorical skills to resist the elected government after the dictatorship ended. Her rise to fame was dependent upon her rhetorical strategies; hence, a study of how Bonafini motivates and influences others by the use of verbal and nonverbal symbols is central to understanding more about this rare social movement phenomenon. A critique of Bonafini\u27s speeches given during the late stage of this accidental yet calculated mothers\u27 movement will provide us with much insight into their particularly persistent resistance

Health and cancer prevention: knowledge and beliefs of children and young people

Objective: To collect information from children and young people about their knowledge of and attitudes towards cancer and their understanding of health and health related behaviours to inform future health promotion work. Design: Questionnaire survey of 15-16 year olds, and interviews with play materials with 9-10 year old children. Setting: Six inner city, suburban, and rural schools. Subjects: 226 children aged 15-16 years and 100 aged 9-10 years. Main outcome measures: Knowledge about different types of cancer; beliefs about health; sources of information; quality of research data obtainable from young children about cancer and health. Results: Both samples knew most about lung cancer, but there was also some knowledge of breast and skin cancer and leukaemia. Smoking, together with pollution and other environmental factors, were seen as the dominant causes of cancer. Environmental factors were mentioned more often by the inner city samples. Television and the media were the most important sources of information. Young people were more worried about unemployment than about ill health. More than half the young people did not describe their health as good, and most said they did not have a healthy lifestyle. Children were able to provide detailed information about their knowledge and understanding by using drawings as well as interviews. Conclusions: Children and young people possess considerable knowledge about cancer, especially about lung cancer and smoking, and show considerable awareness of predominant health education messages. Despite this knowledge, many lead less than healthy lifestyles. Health is not seen as the most important goal in life by many young people; the circumstances in which many children and young people live are not experienced as health promoting

Large volume fibered knots in 3-manifolds

We prove that for hyperbolic fibered knots in any closed, connected, oriented 3-manifold the volume and genus are unrelated. As an application we answer a question of Hirose, Kalfagianni, and Kin about volumes of mapping tori that are double branched covers.Comment: 9 pages, 5 figure

GENETIC REGULATION OF HEMATOPOIETIC STEM CELL AGING

It is well documented that both quantitative and qualitative changes in the murine hematopoietic stem cell (HSC) population occur with age. In mice, the effect of aging on stem cells is highly strain-specific, thus suggesting genetic regulation plays a role in HSC aging. In C57BL/6 (B6) mice, the HSC population steadily increases with age, whereas in DBA/2 (D2) mice, this population declines. Our lab has previously mapped a quantitative trait locus (QTL) to murine chromosome 2 that is associated with the variation in frequency of HSCs between aged B6 and D2 mice. In these dissertation studies, I first aim to characterize the congenic mouse model which was generated by introgressing D2 alleles in the QTL onto a B6 background. Using a surrogate assay to mimic aging, I analyzed the cell cycle, apoptotic and self-renewal capabilities of congenic and B6 HSCs and show that D2 alleles in the QTL affect the apoptotic and selfrenewal capabilities of HSCs. In the second aim of these studies, I used oligonucleotide arrays to compare the differential expression of B6 and congenic cells using a population enriched for primitive stem and progenitor cells. Extensive analysis of the expression arrays pointed to two strong candidates, the genes encoding Retinoblastoma like protein 1 (p107) and Sorting nexin 5 (Snx5). B6 alleles were associated with increased p107 and Snx5 expression in old HSCs therefore both genes were hypothesized to be positive regulators of stem cell number in aged mice. Finally, in the third aim of these studies, I show that the individual overexpression of p107 and Snx5 in congeic HSCs increases day35 cobblestone area forming cell (CAFC) numbers, therefore confirming their roles as positive regulators of HSC number in vitro. These studies uncover novel roles for p107 and Snx5 in the regulation of HSC numbers and provide additional clues in the complex regulation of HSC aging

Tracking performance with two breathing oxygen concentrations after high altitude rapid decompression

Current military aircraft Liquid Oxygen (LOX) systems supply 99.5 pct. gaseous Aviator's Breathing Oxygen (ABO) to aircrew. Newer Molecular Sieve Oxygen Generation Systems (MSOGS) supply breathing gas concentration of 93 to 95 pct. O2. The margin is compared of hypoxia protection afforded by ABO and MSOGS breathing gas after a 5 psi differential rapid decompression (RD) in a hypobaric research chamber. The barometric pressures equivalent to the altitudes of 46000, 52000, 56000, and 60000 ft were achieved from respective base altitudes in 1 to 1.5 s decompressions. During each exposure, subjects remained at the simulated peak altitude breathing either 100 or 94 pct. O2 with positive pressure for 60 s, followed by a rapid descent to 40000 ft. Subjects used the Tactical Life Support System (TLSS) for high altitude protection. Subcritical tracking task performance on the Performance Evaluation Device (PED) provided psychomotor test measures. Overall tracking task performance results showed no differences between the MSOGS breathing O2 concentration of 94 pct. and ABO. Significance RMS error differences were found between the ground level and base altitude trials compared to peak altitude trials. The high positive breathing pressures occurring at the peak altitudes explained the differences

English Channel towed sledge seabed images. Phase 2: Analysis of selected tow images

During the 1970s and 1980s, the late Dr Norman Holme undertook extensive towed sledge surveys in the English Channel and some in the Irish Sea. Only a minority of the resulting images were analysed and reported before his death in 1989 but logbooks, video and film material has been archived in the National Marine Biological Library (NMBL) in Plymouth. A study was therefore commissioned by the Joint Nature Conservation Committee and as a part of the Mapping European Seabed Habitats (MESH) project to identify the value of the material archived and the procedure and cost to undertake further work (Phase 1 of the study reported here: Oakley & Hiscock, 2005). Some image analysis was undertaken as a part of Phase 1. Phase 2 (this report) was to further analyse selected images. Having determined in Phase 1 that only the 35 mm photographic transparencies provided sufficient clarity to identify species and biotopes, the tows selected for analysis were ones where 35mm images had been taken. The tows selected for analysis of images were mainly in the vicinity of Plymouth and especially along the area between Rame Head and the region of the Eddystone. The 35 mm films were viewed under a binocular microscope and the taxa that could be recognised recorded in note form. Twenty-five images were selected for inclusion in the report. Almost all of the images were of level sediment seabed. Where rocks were included, it was usually unplanned and the sled was hauled before being caught or damaged. The main biotopes or biotope complexes identified were: SS.SMU.CSaMu. Circalittoral sandy mud. Extensively present between the shore and the Eddystone Reef complex and at depths of about 48 to 52 m. At one site offshore of Plymouth Sound, the turret shell Turritella communis was abundant. In some areas, this biotope had dense anemones, Mesacmaea mitchelli and (more rarely) Cerianthus lloydii. Queen scallops, Aequipecten opercularis and king scallops, Pecten maximus, were sometimes present in small numbers. Hard substratum species such as hydroids, dead mens fingers Alcyonium digitatum and the cup coral Caryophyllia smithii occurred in a few places, probably attached to shells or stones beneath the surface. South of the spoil ground off Hilsea Point at 57m depth, the sediment was muddier but is still assigned to this biotope complex. It is notable that three small sea pens, most likely Virgularia mirabilis, were seen here. SS.SMx.CMx. Circalittoral mixed sediment. Further offshore but at about the same depth as SS.SMU.CSaMu occurred, coarse gravel with some silt was present. The sediment was characterised must conspicuously by small queen scallops, Aequipecten opercularis. Peculiarly, there were ‘bundles’ of the branching bryozoan Cellaria sp. – a species normally found attached to rock. It could not be seen whether these bundles of Cellaria had been brought-together by terebellid worms but it is notable that Cellaria is recorded in historical surveys. As with many other sediments, there were occasional brittle stars, Ophiocomina nigra and Ophiura ophiura. Where sediments were muddy, the burrowing anemone Mesacmaea mitchelli was common. Where pebbles or cobbles occurred, there were attached species such as Alcyonium digitatum, Caryophyllia smithii and the fleshy bryozoan Alcyonidium diaphanum. Undescribed biotope. Although most likely a part of SS.SMx.CMx, the biotope visually dominated by a terebellid worm believed to be Thelepus cincinnatua, is worth special attention as it may be an undescribed biotope. The biotope occurred about 22 nautical miles south of the latitude of the Eddystone and in depths in excess of 70 m. SS.SCS.CCS.Blan. Branchiostoma lanceolatum in circalittoral coarse sand with shell gravel at about 48m depth and less. This habitat was the ‘classic’ ‘Eddystone Shell Gravel’ which is sampled for Branchiostoma lanceolatum. However, no Branchiostoma lanceolatum could be seen. The gravel was almost entirely bare of epibiota. There were occasional rock outcrops or cobbles which had epibiota including encrusting calcareous algae, the sea fan Eunicella verrucosa, cup corals, Caryophyllia smithii, hydroids and a sea urchin Echinus esculentus. The variety of species visible on the surface is small and therefore identification to biotope not usually possible. Historical records from sampling surveys that used grabs and dredges at the end of the 19th century and early 20th century suggest similar species present then. Illustrations of some of the infaunal communities from work in the 1920’s is included in this report to provide a context to the epifaunal photographs

Shock accelerated vortex ring

The interaction of a shock wave with a spherical density inhomogeneity leads to the development of a vortex ring through the impulsive deposition of baroclinic vorticity. The present fluid dynamics videos display this phenomenon and were experimentally investigated at the Wisconsin Shock Tube Laboratory's (WiSTL) 9.2 m, downward firing shock tube. The tube has a square internal cross-section (0.25 m x 0.25 m) with multiple fused silica windows for optical access. The spherical soap bubble is generated by means of a pneumatically retracted injector and released into free-fall 200 ms prior to initial shock acceleration. The downward moving, M = 2.07 shock wave impulsively accelerates the bubble and reflects off the tube end wall. The reflected shock wave re-accelerates the bubble (reshock), which has now developed into a vortex ring, depositing additional vorticity. In the absence of any flow disturbances, the flow behind the reflected shock wave is stationary. As a result, any observed motion of the vortex ring is due to circulation. The shocked vortex ring is imaged at 12,500 fps with planar Mie scattering.Comment: For Gallery of Fluid Motion 200

Holistic hamstring health: not just the Nordic hamstring exercise

This was an editorial piece discussing the importance of a more holistic approach to hamstring conditioning