HLA-A, -B, -C, -DRB1, DRB3, DRB4, DRB5 and DQB1 polymorphism detected by PCR-SSP in a semi-urban HIV-positive Ugandan population.

PCR-SSP was used to HLA-type a cohort of Ugandan HIV-positive individuals. The results represent a more comprehensive description of HLA in an African population than previously described and are in concordance with data from a general Black population. Substantial differences exist between this population and Caucasoid populations in which immunological responses to HIV have been investigated; this emphasises that the main HLA-restrictive elements for HIV-specific cytotoxic T lymphocytes will most likely be different for each population

Axial cyclic loading of piles in low to medium density chalk

Comprehensive field investigations into the axial cyclic loading behaviour of open-steel pipe piles driven and aged in low-to-medium density chalk identify the conditions under which behaviour is stable, unstable or metastable. Post-cycling monotonic tests confirmed that stable cycling enhanced pile capacity marginally, while unstable cases suffered potentially large losses of shaft capacity. Metastable conditions led to intermediate outcomes. The patterns by which axial deflections grew under cyclic loading varied systematically with the normalised loading parameters and could be captured by simple fitting expressions. Cyclic stiffnesses also varied with loading conditions, with the highest operational shear stiffnesses falling far below the in-situ seismic test values. The monotonic and cyclic axial responses of the test piles were controlled by the behaviour of, and conditions within, the reconsolidated, de-structured, chalk putty annuli formed around pile shafts during driving. Fibre-optic strain gauges identified progressive failure from the pile tip upwards. Large factors of safety were required for piles to survive repetitive loading under high-level, two-way, conditions involving low mean loads, while low amplitude one-way cycling had little impact. A simple ‘global’ prediction procedure employing interface shear and cyclic triaxial tests is shown to provide broadly representative predictions for field behaviour

Evolved Gas Analysis and X-Ray Diffraction of Carbonate Samples from the 2009 Arctic Mars Analog Svalbard Expedition: Implications for Mineralogical Inferences from the Mars Science Laboratory

The 2009 Arctic Mars Analog Svalbard Expedition (AMASE) investigated several geologic settings using methodologies and techniques being developed or considered for future Mars missions, such as the Mars Science Laboratory (MSL), ExoMars, and Mars Sample Return (MSR). AMASE-related research comprises both analyses conducted during the expedition and further analyses of collected samples using laboratory facilities at a variety of institutions. The Sample Analysis at Mars (SAM) instrument suite, which will be part of the Analytical Laboratory on MSL, consists of a quadrupole mass spectrometer (QMS), a gas chromatograph (GC), and a tunable laser spectrometer (TLS). An Evolved Gas Analysis Mass Spectrometer (EGA-MS) was used during AMASE to represent part of the capabilities of SAM. The other instrument included in the MSL Analytical Laboratory is CheMin, which uses X-Ray Diffraction (XRD) and X-Ray Fluorescence (XRF) to perform quantitative mineralogical characterization of samples. Field-portable versions of CheMin were used during the AMASE 2009. Here, we discuss the preliminary interpretation of EGA and XRD analyses of selected AMASE carbonate samples and implications for mineralogical interpretations from MSL. Though CheMin will be the primary mineralogical tool on MSL, SAM EGA could be used to support XRD identifications or indicate the presence of volatile-bearing minerals which may be near or below XRD detection limits. Data collected with instruments in the field and in comparable laboratory setups (e.g., the SAM breadboard) will be discussed

Mineralogy of Vera Rubin Ridge in Gale Crater from the Mars Science Laboratory CheMin instrument

Gale crater was selected as the landing site for the Mars Science Laboratory Curiosity rover because of orbital evidence for a variety of secondary minerals in the lower slopes of Aeolis Mons (aka Mount Sharp) that indicate changes in aqueous conditions over time. Distinct units demonstrate orbital spectral signatures of hematite, phyllosilicate (smectite), and sulfate minerals, which suggest that ancient aqueous environments in Gale crater varied in oxidation potential, pH, and water activity. Vera Rubin ridge (VRR) is the first of these units identified from orbit to have been studied by Curiosity. Orbital near-infrared data from VRR show a strong band at 860 nm indicative of hematite. Before Curiosity arrived at VRR, the hypotheses to explain the formation of hematite included (1) precipitation at a redox interface where aqueous Fe2+ was oxidized to Fe3+, and (2) acidic alteration of olivine in oxic fluids. Studying the composition and sedimentology of the rocks on VRR allow us to test and refine these hypotheses and flesh out the depositional and diagenetic history of the ridge. Here, we focus on the mineralogical results of four rock powders drilled from and immediately below VRR as determined by CheMin

Detection of Siderite (FeCO3) in Glen Torridon Samples by the Mars Science Laboratory Rover

Siderite (FeCO3) has been detected in Gale Crater for the first time by the Mars Science Laboratory (MSL) Curiosity and is seen in multiple samples in the Glen Torridon (GT) region. The identification of siderite is based on evolved gas analysis (EGA) data from the Sample Analysis at Mars (SAM) instrument and X-ray diffraction (XRD) data from the Chemistry and Mineralogy (CheMin) instrument. Curiosity descended off of the Vera Rubin ridge (VRR) into the Glen Torridon region on Sol 2300. Glen Torridon is of particular interest because a strong clay mineral signature had been detected by orbital instruments [1]. To date, four drilled samples have been collected at two different drill locations: Kilmarie and Aberlady from adjacent blocks at the base of the south side of VRR in the Jura member and Glen Etive 1 and 2 on the same block in the Knockfarril member

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant staphylococcus aureus pandemic

The widespread use of antibiotics in association with high-density clinical care has driven the emergence of drug-resistant bacteria that are adapted to thrive in hospitalized patients. Of particular concern are globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clones that cause outbreaks and epidemics associated with health care. The most rapidly spreading and tenacious health-care-associated clone in Europe currently is EMRSA-15, which was first detected in the UK in the early 1990s and subsequently spread throughout Europe and beyond. Using phylogenomic methods to analyze the genome sequences for 193 S. aureus isolates, we were able to show that the current pandemic population of EMRSA-15 descends from a health-care-associated MRSA epidemic that spread throughout England in the 1980s, which had itself previously emerged from a primarily community-associated methicillin-sensitive population. The emergence of fluoroquinolone resistance in this EMRSA-15 subclone in the English Midlands during the mid-1980s appears to have played a key role in triggering pandemic spread, and occurred shortly after the first clinical trials of this drug. Genome-based coalescence analysis estimated that the population of this subclone over the last 20 yr has grown four times faster than its progenitor. Using comparative genomic analysis we identified the molecular genetic basis of 99.8% of the antimicrobial resistance phenotypes of the isolates, highlighting the potential of pathogen genome sequencing as a diagnostic tool. We document the genetic changes associated with adaptation to the hospital environment and with increasing drug resistance over time, and how MRSA evolution likely has been influenced by country-specific drug use regimens

Glen Torridon Mineralogy and the Sedimentary History of the Clay Mineral Bearing Unit

Clay minerals are common in ancient terrains on Mars and their presence at the surface alludes to aqueous processes in the Noachian to Early Hesperian (>3.5 Ga). Gale crater was selected as Curiositys landing site largely because of the identification of clay mineral rich strata from orbit. On Earth, the types of clay minerals (i.e., smectites) identified in Gale crater are typically juvenile weathering products that ultimately record the interaction between primary igneous minerals with the hydrosphere, atmosphere, and biosphere. Trioctahedral and dioctahedral smectite were identified by Curiosity in units stratigraphically below the Clay Mineral-Bearing Unit (CBU) identified from orbit. Compositional and sedimentological data suggest the smectite formed via authigenesis in a lake environment and may have been altered during early diagenesis. The CBU is stratigraphically equivalent to a hematite-rich unit to the north and stratigraphically underlies sulfate-rich units to the south, suggesting a dynamic environment and evolving history of water in the ancient Gale crater lake. Targeting these clay mineral rich areas on Mars with rover missions provides an opportunity to explore the aqueous and sedimentary history of the planet

A two-step strategy for the complementation of M. tuberculosis mutants

The sequence of Mycobacterium tuberculosis, completed in 1998, facilitated both the development of genomic tools, and the creation of a number of mycobacterial mutants. These mutants have a wide range of phenotypes, from attenuated to hypervirulent strains. These phenotypes must be confirmed, to rule out possible secondary mutations that may arise during the generation of mutant strains. This may occur during the amplification of target genes or during the generation of the mutation, thus constructing a complementation strain, which expresses the wild-type copy of the gene in the mutant strain, becomes necessary. In this study we have introduced a two-step strategy to construct complementation strains using the Ag85 promoter. We have constitutively expressed dosR and have shown dosR expression is restored to wild-type level