Geomicrobiology and Microbial Geochemistry

Geomicrobiology and microbial geochemistry (GMG) investigates the interaction between Earth, environmental systems, and microbial life. Microbes shape their geochemical surroundings through their metabolic and growth needs and thereby exert significant geochemical and mineralogical control on their local environments. In turn, local geochemical conditions dictate what metabolic processes are possible. These mutual influences mean that microbial evolution has occurred in concert with changing geosphere conditions and that microbes have driven major shifts in ocean, continent and atmospheric chemistry. If one wishes to understand element cycling in any system containing water, one must realize that microbes are critical to the story

Response induction coil magnetometers to perturbations in orientation

We explore the data collected by a 3-component induction coil magnetometer system with respect to motion of the instruments in earths static magnetic field. The sensitivtiy of the inductiuon coil magnetometer leads to unprecediented accuracy on tilt measurements. We model the signals observed during seismic events as being perturbations in coil orientation. In theory, these perturbations can include ground roll, ocean motion, nearby cultural seismicity, or any other field with a tilting effect. Using data from a magnetic observatory near Parkfield CA we invert several time series of coil data during different levels of seismic activity in an attempt to determine the magnitudes of rotation at which our model accurately describes the coil data. Finally, we explore the transfer function between the coils and nearby seismic instruments (accelerometers, tiltmeters, and velocity seismometers)

Consequences of self and foreign superantigen interaction with specific VB elements of the murine TCR aB

Journal ArticleThe aB T-cell receptor (TCRaB) recognizes a ligand composed of an antigen fragment complexed with a product of the major histocompatibility complex (MHC). The repertoire of receptors is limited both by the germ line of receptor variable elements and by selective events that take place during T-cell development. The current view is that the germ-line repertoire is expressed in the thymus randomly but that only those T cells bearing receptors that successfully interact with MHC molecules expressed on thymic cortical epithelial cells are allowed to mature (Bevan and Fink 1978; Zinkernagel et al. 1978; Kisielow et al. 1988; Sha et al. 1988). Furthermore, during the process of establishing tolerance to self-antigens, this positively selected population is further reduced by the deletion or inactivation of clones whose receptors continue to interact with self-antigen/MHC ligands (Kappler et al. 1987a, 1988; MacDonald et al. 1988; Pullen et al. 1988). Thus, positive and negative selections reduce expressed receptor repertoire in the periphery to a fraction of the germ-line repertoire

A preliminary checklist of fungi at the Boston Harbor Islands

Between December 2012 and May 2017, we conducted a fungal inventory at the Boston Harbor Islands National Recreation Area (BHI) in Massachusetts. We extensively sampled 4 sites (Grape Island, Peddocks Island, Thompson Island, and World's End peninsula) and occasionally visited 4 others for sampling (Calf Island, Great Brewster Island, Slate Island, and Webb Memorial State Park). We made over 900 collections, of which 313 have been identified. The survey yielded 172 species in 123 genera, 62 families, 24 orders, 11 classes, and 2 phyla. We report 4 species as new, but not formally described, in the genera Orbilia, Resupinatus, and Xylaria. Another collection in the genus Lactarius may be new to science, but further morphological and molecular work is needed to confirm this conclusion. Additionally, Orbilia aprilis is a new report for North America, Proliferodiscus earoleucus represents only the second report for the US, and Chrysosporium sulfureum, a common fungus of some cheeses, was discovered on woodlice (Crustacea: Malacostraca: Isopoda: Oniscidea). We discuss our findings in the light of DNA-based identifications using the ITS ribosomal DNA region, including the advantages and disadvantages of this approach, and stress the need for biodiversity studies in urbanized areas during all seasons

Phototrophic Fe(II) oxidation in an atmosphere of H_2: implications for Archean banded iron formations

The effect of hydrogen on the rate of phototrophic Fe(II) oxidation by two species of purple bacteria was measured at two different bicarbonate concentrations. Hydrogen slowed Fe(II) oxidation to varying degrees depending on the bicarbonate concentration, but even the slowest rate of Fe(II) oxidation remained on the same order of magnitude as that estimated to have been necessary to deposit the Hamersley banded iron formations. Given the hydrogen and bicarbonate concentrations inferred for the Archean, our data suggest that Fe(II) phototrophy could have been a viable process at this time

Physics Analysis Expert PAX: First Applications

PAX (Physics Analysis Expert) is a novel, C++ based toolkit designed to assist teams in particle physics data analysis issues. The core of PAX are event interpretation containers, holding relevant information about and possible interpretations of a physics event. Providing this new level of abstraction beyond the results of the detector reconstruction programs, PAX facilitates the buildup and use of modern analysis factories. Class structure and user command syntax of PAX are set up to support expert teams as well as newcomers in preparing for the challenges expected to arise in the data analysis at future hadron colliders.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 7 pages, LaTeX, 10 eps figures. PSN THLT00

Evidence for equilibrium iron isotope fractionation by nitrate-reducing iron(II)-oxidizing bacteria

Iron isotope fractionations produced during chemical and biological Fe(II) oxidation are sensitive to the proportions and nature of dissolved and solid-phase Fe species present, as well as the extent of isotopic exchange between precipitates and aqueous Fe. Iron isotopes therefore potentially constrain the mechanisms and pathways of Fe redox transformations in modern and ancient environments. In the present study, we followed in batch experiments Fe isotope fractionations between Fe(II)_(aq) and Fe(III) oxide/hydroxide precipitates produced by the Fe(III) mineral encrusting, nitrate-reducing, Fe(II)-oxidizing Acidovorax sp. strain BoFeN1. Isotopic fractionation in ^(56)Fe/^(54)Fe approached that expected for equilibrium conditions, assuming an equilibrium Δ^(56)Fe_(Fe(OH)3–Fe(II)aq) fractionation factor of +3.0‰. Previous studies have shown that Fe(II) oxidation by this Acidovorax strain occurs in the periplasm, and we propose that Fe isotope equilibrium is maintained through redox cycling via coupled electron and atom exchange between Fe(II)_(aq) and Fe(III) precipitates in the contained environment of the periplasm. In addition to the apparent equilibrium isotopic fractionation, these experiments also record the kinetic effects of initial rapid oxidation, and possible phase transformations of the Fe(III) precipitates. Attainment of Fe isotope equilibrium between Fe(III) oxide/hydroxide precipitates and Fe(II)_(aq) by neutrophilic, Fe(II)-oxidizing bacteria or through abiologic Fe(II)_(aq) oxidation is generally not expected or observed, because the poor solubility of their metabolic product, i.e. Fe(III), usually leads to rapid precipitation of Fe(III) minerals, and hence expression of a kinetic fractionation upon precipitation; in the absence of redox cycling between Fe(II)_(aq) and precipitate, kinetic isotope fractionations are likely to be retained. These results highlight the distinct Fe isotope fractionations that are produced by different pathways of biological and abiological Fe(II) oxidation