Geomicrobiology of the ocean crust : the phylogenetic diversity, abundance, and distribution of microbial communities inhabiting basalt and implications for rock alteration processes

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2007Basaltic ocean crust has the potential to host one of the largest endolithic communities on Earth. This portion of the biosphere, however, remains largely unexplored. In this study, we utilize molecular biological, microscopic, and geochemical tools to gain a better understanding of the geomicrobiology of the ocean crust. Specifically, we examine the phylogenetic diversity of microorganisms inhabiting basaltic lavas, the activities and abundances of these microorganisms, the spatial extent of the biosphere, and the potential effect that microbial activity has on the geochemistry of the ocean crust and overlying water column. Our study demonstrates that young, fresh volcanic lavas near mid-ocean ridges host an incredibly diverse and dense population of microorganisms dominated by Bacteria, quite distinct from the microbial communities found in surrounding deep seawater and hydrothermal vents. Furthermore, these communities may contribute to the elemental cycling of Fe, S, Mn, N, and C in this environment. The inability to definitively identify microorganisms in drill-cores of old (> 15 Ma) ocean crust, however, implies that these once prolific communities may become scarce as the crust ages and moves further away from the ridge axis. Finally, we provide evidence suggesting that these communities are fueled by oxidative alteration reactions occurring in the basaltic crust.Funding for this project came from: RIDGE 2000 Grant #OCE-0241791 awarded to Katrina J. Edwards and Wolfgang Bach, the NASA Astrobiology Institute - Cycle 3 CAN-02-OSS-02 awarded to Katrina J. Edwards, USSSP ODP Post-cruise funding Grant #TX A&M F001724 awarded to Cara M. Santelli and Katrina J. Edwards, and a Schlanger Ocean Drilling Fellowship awarded to Cara M. Santelli

Assessing the effects of local contexts on the mobility choices of university students in Campania region in Italy

The mobility of university students in Italy has been framed as a phenomenon linked to so-called intellectual migrations and as a subset of the historical and consolidated internal migration path explained in terms of South–North trajectory. This study describes the most important mobility trajectories of students across macro-areas and disciplinary fields, and then evaluates, using a multilevel logistic regression model, the factors that encouraged student cohort, who were enrolled in a degree program in the academic years 2014–2015, to move elsewhere from the Campania region. Beyond fixed and interaction effects related to the students’ personal characteristics, the model included possible random effects linked to the high schools attended by the students to capture the possible influence of the local context on migration choices

Profiling microbial communities in manganese remediation systems treating coal mine drainage

Author Posting. © American Society for Microbiology, 2015. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 81 (2015): 2189-2198, doi:10.1128/AEM.03643-14.Water discharging from abandoned coal mines can contain extremely high manganese levels. Removing this metal is an ongoing challenge. Passive Mn(II) removal beds (MRBs) contain microorganisms that oxidize soluble Mn(II) to insoluble Mn(III/IV) minerals, but system performance is unpredictable. Using amplicon pyrosequencing, we profiled the bacterial, fungal, algal and archaeal communities in four variably-performing MRBs in Pennsylvania to determine whether they differed among MRBs and from surrounding soil, and to establish the relative abundance of known Mn(II)-oxidizers. Archaea were not detected; PCRs with archaeal primers returned only non-target bacterial sequences. Fungal taxonomic profiles differed starkly between sites that remove the majority of influent Mn and those that do not, with the former dominated by Ascomycota (mostly Dothideomycetes) and the latter by Basidiomycota (almost entirely Agaricomycetes). Taxonomic profiles for the other groups did not differ significantly between MRBs, but OTU-based analyses showed significant clustering by MRB with all four groups (p<0.05). Soil samples clustered separately from MRBs in all groups except fungi, whose soil samples clustered loosely with their respective MRB. Known Mn(II) oxidizers accounted for a minor proportion of bacterial sequences (up to 0.20%) but a greater proportion of fungal sequences (up to 14.78%). MRB communities are more diverse than previously thought, and more organisms may be capable of Mn(II) oxidation than are currently known.This project was funded by Smithsonian Scholarly Studies and Next-Generation Sequencing grants to C.M.S., by a Smithsonian Postdoctoral Fellowship to D.L.C., and by the National Science Foundation, grant numbers EAR-1249489 (awarded to C.M.H.) and CBET-1336496 (awarded to C.M.H. and C.M.S.)

Evaluation of the London Measure of Unplanned Pregnancy in a United States population of women

Copyright @ 2012 Morof et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Objective: To evaluate the reliability and validity of the London Measure of Unplanned Pregnancy (a U.K.-developed measure of pregnancy intention), in English and Spanish translation, in a U.S. population of women. Methods: A psychometric evaluation study of the London Measure of Unplanned Pregnancy (LMUP), a six-item, self-completion paper measure was conducted with 346 women aged 15–45 who presented to San Francisco General Hospital for termination of pregnancy or antenatal care. Analyses of the two language versions were carried out separately. Reliability (internal consistency) was assessed using Cronbach’s alpha and item-total correlations. Test-retest reliability (stability) was assessed using weighted Kappa. Construct validity was assessed using principal components analysis and hypothesis testing. Results: Psychometric testing demonstrated that the LMUP was reliable and valid in both U.S. English (alpha = 0.78, all item-total correlations .0.20, weighted Kappa = 0.72, unidimensionality confirmed, hypotheses met) and Spanish translation (alpha = 0.84, all item-total correlations .0.20, weighted Kappa = 0.77, unidimensionality confirmed, hypotheses met). Conclusion: The LMUP was reliable and valid in U.S. English and Spanish translation and therefore may now be used with U.S. women.The study was funded by an anonymous donation

Characterization of natural convection between spherical shells

In this manuscript, it is analysed the onset and evolution of natural convection of an incompressible fluid between spherical shells. The shells are kept at a fixed temperature difference and aspect ratio, and the Rayleigh-Benard convection is driven by different radial gravity profiles. The analysis has been carried out by using a finite difference scheme to solve the three-dimensional Navier-Stokes equations in spherical coordinates. Numerical results are compared with theoretical predictions from linear and non-linear stability analysis, and differ from the expected critical Rayleigh number Ra_c = 1708 by less than 1 percent. In the range of Prandlt numbers Pr studied, and for all the different gravity profiles analysed, the system presents a dependence on its starting condition and flow history. Even in the region just above the onset of convection, two stable states are observed, with qualitative and quantitative differences, and exploring higher values of Ra introduces new modes and time dependency phenomena in the flow. These results are corroborated by spectral analysis

Comparação de técnicas analíticas para a determinação de sódio, potássio e fósforo em mostras de solos tropicais.

O fósforo, sódio e potássio são elementos importantes para a avaliação da fertilidade de solos (1, 2). A grande maioria dos laboratórios de análise de fertilidade de solo no Brasil utiliza a fotometria de chama para a determinação de sódio e potássio e a espectrofotometria molecular no UV-VIS para a determinação de fósforo(1). Entretanto, estes elementos também podem ser determinados por espectrometria de emissão óptica com plasma indutivamente acoplado (ICP OES)(3, 4, 5). Apesar dessa técnica apresentar inúmeras vantagens, há uma carência de estudos que a validem para a determinação de K, P, Na em amostras de solos tropicais(1, 2, 4). O objetivo deste trabalho foi comparar os resultados de fósforo disponível assim como potássio e sódio trocáveis após serem extraídos com solução Mehlich 1 e determinados por espectrofotometria UV-VIS (P) e fotometria de chama (Na e K) com aqueles obtidos pelo ICP OES, utilizando um teste de identidade entre métodos analíticos(6). Foram analisadas quinze amostras de solo, amostradas em diferentes regiões do Brasil, oriundas do programa de análise da qualidade de laboratórios de fertilidade (PAQLF) realizado pela EMBRAPA. Foi utilizado um ICP OES Perkin Elmer modelo OPTIMA 3000, vista radial

Promotion of Mn(II) Oxidation and Remediation of Coal Mine Drainage in Passive Treatment Systems by Diverse Fungal and Bacterial Communities

Biologically active, passive treatment systems are commonly employed for removing high concentrations of dissolved Mn(II) from coal mine drainage (CMD). Studies of microbial communities contributing to Mn attenuation through the oxidation of Mn(II) to sparingly soluble Mn(III/IV) oxide minerals, however, have been sparse to date. This study reveals a diverse community of Mn(II)-oxidizing fungi and bacteria existing in several CMD treatment systems.Organismic and Evolutionary Biolog

Uso de ICP OES e titrimetria para a determinação de cálcio, magnésio e alumínio em amostras de solos.

O crescente interesse dos laboratórios brasileiros de análise de fertilidade de solos pela espectrometria de emissão óptica com plasma indutivamente acoplado (ICP OES) em detrimento da técnica de titrimetria deve-se à possibilidade da determinação simultânea de diferentes metais em uma ampla faixa de concentrações em extratos de interesse agronômico. Este estudo compara a precisão, reprodutibilidade e exatidão das duas técnicas de determinação de Ca, Mg e Al trocáveis extraídos com KCl 1 mol L-1 em amostras de solos. Foram analisadas 15 amostras de solos de referência, sendo três deles selecionados para avaliar a precisão e a reprodutibilidade das técnicas de determinação. A titrimetria e o ICP OES forneceram resultados mais reprodutíveis e precisos para a determinação de Ca, Mg e Al quando o extrato foi analisado sem diluição. As técnicas de determinação diferiram estatisticamente (p < 0,05) pelo teste de identidade aplicado para comparação dos resultados de Ca, Mg e Al. Nas condições testadas, não se recomenda o uso de ICP OES para as determinações de Ca, Mg e Al trocáveis em amostras de solos

PTP4A1 promotes TGFβ signaling and fibrosis in systemic sclerosis.

Systemic sclerosis (SSc) is an autoimmune disease characterized by fibrosis of skin and internal organs. Protein tyrosine phosphatases have received little attention in the study of SSc or fibrosis. Here, we show that the tyrosine phosphatase PTP4A1 is highly expressed in fibroblasts from patients with SSc. PTP4A1 and its close homolog PTP4A2 are critical promoters of TGFβ signaling in primary dermal fibroblasts and of bleomycin-induced fibrosis in vivo. PTP4A1 promotes TGFβ signaling in human fibroblasts through enhancement of ERK activity, which stimulates SMAD3 expression and nuclear translocation. Upstream from ERK, we show that PTP4A1 directly interacts with SRC and inhibits SRC basal activation independently of its phosphatase activity. Unexpectedly, PTP4A2 minimally interacts with SRC and does not promote the SRC-ERK-SMAD3 pathway. Thus, in addition to defining PTP4A1 as a molecule of interest for TGFβ-dependent fibrosis, our study provides information regarding the functional specificity of different members of the PTP4A subclass of phosphatases