Organic synthesis associated with serpentinization and carbonation on early Mars.

Water-rock interactions are relevant to planetary habitability, influencing mineralogical diversity and the production of organic molecules. We examine carbonates and silicates in the martian meteorite Allan Hills 84001 (ALH 84001), using colocated nanoscale analyses, to characterize the nature of water-rock reactions on early Mars. We find complex refractory organic material associated with mineral assemblages that formed by mineral carbonation and serpentinization reactions. The organic molecules are colocated with nanophase magnetite; both formed in situ during water-rock interactions on Mars. Two potentially distinct mechanisms of abiotic organic synthesis operated on early Mars during the late Noachian period (3.9 to 4.1 billion years ago).

The shifting picture of HIV treatment, comorbidity and substance use among US MSM living with HIV.

OBJECTIVES: People living with HIV (PLWH) have increased risk of chronic disease and poor mental health. We aimed to explore HIV disease indicators, comorbidity, and risk behavior of recent antiretroviral therapy (ART) initiators to inform current needs of PLWH. METHODS: Men who have sex with men (MSM) in the Multicenter AIDS Cohort Study (MACS) who initiated ART between 2010 and 2018 (recent initiators) were compared with age-, race- and geographic location-matched men who initiated ART during 2000-2009 (early initiators). Measures of HIV disease, behavior, comorbidity and mental health were collected prospectively every 6 months using standardized forms. RESULTS: Recent initiators had higher current CD4 (median CD4 451 vs. 307 cells/µL, P < 0.0001) and nadir CD4 (451 vs. 300 cells/µL, P < 0.0001) than earlier initiators. The proportion achieving viral suppression within a year of starting ART was significantly higher in recent compared with earlier initiators (92% vs. 74%, P < 0.0001). Median [interquartile range (IQR)] time from HIV diagnosis to ART initiation was 5.4 (1.7-23.1) months in recent initiators. Comorbidity prevalence was high in recent initiators, including obesity (24%), hypertension (25%) and kidney disease (15%). Substance use continues to be common, including cigarette use (40%), daily alcohol use (88%) and marijuana use (46%). CONCLUSIONS: Improvements in getting individuals onto ART at an early stage have led to substantially higher CD4 cell counts at initiation. However, the high burden of comorbidity, substance use and poor mental health affecting MSM living with HIV in the US underscore ongoing challenges and our need to adapt and coordinate care.

Vertical redox zones of Fe-S-As coupled mineralogy in the sediments of Hetao Basin - Constraints for groundwater As contamination.

The formation of iron-sulfur-arsenic (Fe-S-As) minerals during biogeochemical processes in As contaminated aquifers remains poorly understood despite their importance to understanding As release and transport in such systems. In this study, X-ray absorption and Mössbauer spectroscopies complemented by electron microscopy, and chemical extractions were used to examine vertical changes of As, Fe and S speciation for the example of sediments in the Hetao Basin. Reduction of Fe(III), As(V) and SO42- species were shown to co-occur in the aquifers. Iron oxides were observed to be predominantly goethite and hematite (36 - 12%) and appeared to decrease in abundance with depth. Furthermore, reduced As (including arsenite and As sulfides) and sulfur species (including S(-II), S(-I) and S0) increased from 16% to 76% and from 13% to 44%, respectively. Iron oxides were the major As carrier in the sediments, and the lower groundwater As concentration consists with less desorbable and reducible As in the sediments. The formation of As-Fe sulfides (e.g., As containing pyrite and greigite) induced by redox heterogeneities likely contribute to localized lower groundwater As concentrations. These results help to further elucidate the complex relationship between biogeochemical processes and minerals formation in As contaminated aquifers.

Molecular identification of fungi microfossils in a Neoproterozoic shale rock.

Precambrian fossils of fungi are sparse, and the knowledge of their early evolution and the role they played in the colonization of land surface are limited. Here, we report the discovery of fungi fossils in a 810 to 715 million year old dolomitic shale from the Mbuji-Mayi Supergroup, Democratic Republic of Congo. Syngenetically preserved in a transitional, subaerially exposed paleoenvironment, these carbonaceous filaments of ~5 µm in width exhibit low-frequency septation (pseudosepta) and high-angle branching that can form dense interconnected mycelium-like structures. Using an array of microscopic (SEM, TEM, and confocal laser scanning fluorescence microscopy) and spectroscopic techniques (Raman, FTIR, and XANES), we demonstrated the presence of vestigial chitin in these fossil filaments and document the eukaryotic nature of their precursor. Based on those combined evidences, these fossil filaments and mycelium-like structures are identified as remnants of fungal networks and represent the oldest, molecularly identified remains of Fungi.

Beam-induced oxidation of mixed-valent Fe (oxyhydr)oxides (green rust) monitored by STEM-EELS.

Analytical transmission electron microscopy (TEM) is often used to investigate morphologies, crystal structures, chemical compositions and oxidation states of highly reactive mixed-valent mineral phases. Of prime interest, due to its potential role in toxic metal remediation, is green rust sulphate (GRSO4) an FeII-FeIII layered double hydroxide. In this study, we quantified the effects that TEM analysis has on GRSO4 in order to ensure the measured material properties are a result of synthesis and reaction kinetics, and not due to sample preparation and analysis technique. To do this, we compared two sample preparation techniques (anoxic drop-cast with drying, and frozen-hydrated cryogenic) and exposed samples to the electron beam for several minutes, acquiring fluence series between ca. 40 e- Å-2 and 10,000 e- Å-2. TEM imaging and electron diffraction showed that the hexagonal plate-like morphology and crystal structure of GRSO4 were largely unaffected by sample preparation and analysis technique. However, quantitative analysis of a series of monochromated Fe L3,2-edge electron energy loss spectra (EELS) showed that electron irradiation induces oxidation. We measured an Fe(II)/Fe(III) ratio of 1.94 (as expected for GRSO4) at 50 e- Å-2. However, above this fluence, the ratio logarithmically decreased and dropped to ca. 0.5 after 1000 e- Å-2. This trend was approximately the same for both sample preparation techniques implying that it is the beam alone which causes valence state changes, and not exposure to oxygen during transfer into the TEM or the vacuum of the TEM column. Ultimately this work demonstrates that GR valence can be quantified by EELS provided that the sample is not over exposed to electrons. This also opens the possibility of quantifying the effect of redox-sensitive toxic metals (e.g., As, Cr, Se) on Fe oxidation state in GR phases (relevant to the treatment of contaminated soils and water) with a higher spatial resolution than other techniques (e.g., Mössbauer spectroscopy).

Droplet digital PCR of serum miR-499, miR-21 and miR-208a for the detection of functionally relevant coronary artery disease.

BACKGROUND: microRNAs (miRNAs) have shown promise as potential new biomarkers for myocardial injury and myocardial ischemia. New digital polymerase chain reaction (PCR) techniques allow for highly precise and reliable absolute direct quantification. METHODS: In this pilot study we used droplet digital PCR (ddPCR) to assess if miRNAs might be released into circulation in patients with functionally relevant coronary artery disease (CAD). Blood samples for measurement of high-sensitivity cardiac troponin I (hs-cTnI) and miRNAs were obtained before, immediately after peak stress, and 2 h after stress testing in a blinded manner in consecutive patients referred for rest/stress myocardial perfusion single-photon emission tomography/computer tomography (MPI-SPECT/CT). ddPCR was used to directly quantify the serum concentrations of miR-21, miR-208a, and miR-499 as potential markers of myocardial injury/ischemia. Functionally relevant CAD was determined by expert interpretation of MPI-SPECT/CT, coronary angiography and fractional flow reserve, if performed. RESULTS: Overall, 200 patients were included and functionally relevant CAD was detected in 85 of them (42%). Neither miR-21, miR-208a, nor miR-499 concentrations differed at rest, stress, or 2-h after stress when comparing patients with versus without functionally relevant CAD, while hs-cTnI concentrations were significantly higher in patients with functionally relevant CAD (P < 0.001). Exercise-induced changes in miRNA or hs-cTnI concentrations did not have diagnostic utility and were similar in patients with versus without functionally relevant CAD. CONCLUSION: miR-208a, miR-21 and miR-499 concentrations at rest, after exercise and exercise-induced changes do not provide additional clinical value regarding the detection of functionally relevant CAD.

Organic synthesis on Mars by electrochemical reduction of CO2.

The sources and nature of organic carbon on Mars have been a subject of intense research. Steele et al. (2012) showed that 10 martian meteorites contain macromolecular carbon phases contained within pyroxene- and olivine-hosted melt inclusions. Here, we show that martian meteorites Tissint, Nakhla, and NWA 1950 have an inventory of organic carbon species associated with fluid-mineral reactions that are remarkably consistent with those detected by the Mars Science Laboratory (MSL) mission. We advance the hypothesis that interactions among spinel-group minerals, sulfides, and a brine enable the electrochemical reduction of aqueous CO2 to organic molecules. Although documented here in martian samples, a similar process likely occurs wherever igneous rocks containing spinel-group minerals and/or sulfides encounter brines.

Not just fractal surfaces, but surface fractal aggregates: Derivation of the expression for the structure factor and its applications.

Densely packed surface fractal aggregates form in systems with high local volume fractions of particles with very short diffusion lengths, which effectively means that particles have little space to move. However, there are no prior mathematical models, which would describe scattering from such surface fractal aggregates and which would allow the subdivision between inter- and intraparticle interferences of such aggregates. Here, we show that by including a form factor function of the primary particles building the aggregate, a finite size of the surface fractal interfacial sub-surfaces can be derived from a structure factor term. This formalism allows us to define both a finite specific surface area for fractal aggregates and the fraction of particle interfacial sub-surfaces at the perimeter of an aggregate. The derived surface fractal model is validated by comparing it with an ab initio approach that involves the generation of a "brick-in-a-wall" von Koch type contour fractals. Moreover, we show that this approach explains observed scattering intensities from in situ experiments that followed gypsum (CaSO4 ⋅ 2H2O) precipitation from highly supersaturated solutions. Our model of densely packed "brick-in-a-wall" surface fractal aggregates may well be the key precursor step in the formation of several types of mosaic- and meso-crystals.

Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals.

Trees and their associated rhizosphere organisms play a major role in mineral weathering driving calcium fluxes from the continents to the oceans that ultimately control long-term atmospheric CO2 and climate through the geochemical carbon cycle. Photosynthate allocation to tree roots and their mycorrhizal fungi is hypothesized to fuel the active secretion of protons and organic chelators that enhance calcium dissolution at fungal-mineral interfaces. This was tested using (14)CO2 supplied to shoots of Pinus sylvestris ectomycorrhizal with the widespread fungus Paxillus involutus in monoxenic microcosms, revealing preferential allocation by the fungus of plant photoassimilate to weather grains of limestone and silicates each with a combined calcium and magnesium content of over 10 wt.%. Hyphae had acidic surfaces and linear accumulation of weathered calcium with secreted oxalate, increasing significantly in sequence: quartz, granite < basalt, olivine, limestone < gabbro. These findings confirmed the role of mineral-specific oxalate exudation in ectomycorrhizal weathering to dissolve calcium bearing minerals, thus contributing to the geochemical carbon cycle.

Bacterially mediated removal of phosphorus and cycling of nitrate and sulfate in the waste stream of a "zero-discharge" recirculating mariculture system.

Simultaneous removal of nitrogen and phosphorus by microbial biofilters has been used in a variety of water treatment systems including treatment systems in aquaculture. In this study, phosphorus, nitrate and sulfate cycling in the anaerobic loop of a zero-discharge, recirculating mariculture system was investigated using detailed geochemical measurements in the sludge layer of the digestion basin. High concentrations of nitrate and sulfate, circulating in the overlying water (∼15 mM), were removed by microbial respiration in the sludge resulting in a sulfide accumulation of up to 3 mM. Modelling of the observed S and O isotopic ratios in the surface sludge suggested that, with time, major respiration processes shifted from heterotrophic nitrate and sulfate reduction to autotrophic nitrate reduction. The much higher inorganic P content of the sludge relative to the fish feces is attributed to conversion of organic P to authigenic apatite. This conclusion is supported by: (a) X-ray diffraction analyses, which pointed to an accumulation of a calcium phosphate mineral phase that was different from P phases found in the feces, (b) the calculation that the pore waters of the sludge were highly oversaturated with respect to hydroxyapatite (saturation index = 4.87) and (c) there was a decrease in phosphate (and in the Ca/Na molar ratio) in the pore waters simultaneous with an increase in ammonia showing there had to be an additional P removal process at the same time as the heterotrophic breakdown of organic matter.

Plant-driven weathering of apatite--the role of an ectomycorrhizal fungus.

Ectomycorrhizal (EcM) fungi are increasingly recognized as important agents of mineral weathering and soil development, with far-reaching impacts on biogeochemical cycles. Because EcM fungi live in a symbiotic relationship with trees and in close contact with bacteria and archaea, it is difficult to distinguish between the weathering effects of the fungus, host tree and other micro-organisms. Here, we quantified mineral weathering by the fungus Paxillus involutus, growing in symbiosis with Pinus sylvestris under sterile conditions. The mycorrhizal trees were grown in specially designed sterile microcosms in which the supply of soluble phosphorus (P) in the bulk media was varied and grains of the calcium phosphate mineral apatite mixed with quartz, or quartz alone, were provided in plastic wells that were only accessed by their fungal partner. Under P limitation, pulse labelling of plants with (14)CO(2) revealed plant-to-fungus allocation of photosynthates, with 17 times more (14)C transferred into the apatite wells compared with wells with only quartz. Fungal colonization increased the release of P from apatite by almost a factor of three, from 7.5 (±1.1) × 10(-10) mol m(-2) s(-1) to 2.2 (±0.52) × 10(-9) mol m(-2) s(-1). On increasing the P supply in the microcosms from no added P, through apatite alone, to both apatite and orthophosphate, the proportion of biomass in roots progressively increased at the expense of the fungus. These three observations, (i) proportionately more plant energy investment in the fungal partner under P limitation, (ii) preferential fungal transport of photosynthate-derived carbon towards patches of apatite grains and (iii) fungal enhancement of weathering rate, reveal the tightly coupled plant-fungal interactions underpinning enhanced EcM weathering of apatite and its utilization as P source.

The role and implications of bassanite as a stable precursor phase to gypsum precipitation.

Calcium sulfate minerals such as gypsum play important roles in natural and industrial processes, but their precipitation mechanisms remain largely unexplored. We used time-resolved sample quenching and high-resolution microscopy to demonstrate that gypsum forms via a three-stage process: (i) homogeneous precipitation of nanocrystalline hemihydrate bassanite below its predicted solubility, (ii) self-assembly of bassanite into elongated aggregates co-oriented along their c axis, and (iii) transformation into dihydrate gypsum. These findings indicate that a stable nanocrystalline precursor phase can form below its bulk solubility and that in the CaSO(4) system, the self-assembly of nanoparticles plays a crucial role. Understanding why bassanite forms prior to gypsum can lead to more efficient anti-scaling strategies for water desalination and may help to explain the persistence of CaSO(4) phases in regions of low water activity on Mars.

Effect of primer selection on estimates of GB virus C (GBV-C) prevalence and response to antiretroviral therapy for optimal testing for GBV-C viremia.

GB virus C (GBV-C; also called hepatitis G virus) is a common cause of infection associated with prolonged survival among HIV-infected individuals. The prevalences of GBV-C viremia vary widely in different studies, and there has been poor agreement among different laboratories performing GBV-C RNA detection in quality control studies. To determine the optimal method of measuring GBV-C RNA in clinical samples, samples obtained from 939 HIV-infected subjects were studied using reverse transcription (RT)-PCR methods amplifying four separate regions of the GBV-C genome. Primers amplifying the E2 coding region were 100% specific; however, their sensitivity was only 76.6%. In contrast, primers amplifying three additional conserved regions of the GBV-C genome (the 5' nontranslated region and the nonstructural protein-coding regions 3 and 5A) were more sensitive but produced higher rates of false-positive results. Using low-specificity primer sets influenced the significance of association between GBV-C viremia and response to antiretroviral therapy. Using a quantitative GBV-C RNA method, the GBV-C RNA concentration did not correlate with baseline or set point HIV RNA levels; however, a correlation between negative, low, and high GBV-C RNA levels and increasing reduction in HIV RNA following antiretroviral therapy was observed. Subjects with both GBV-C E2 antibody and viremia had significantly lower GBV-C RNA levels than did viremic subjects without E2 antibody. These studies demonstrate that accurate detection of GBV-C RNA by nested RT-PCR requires the use of primers representing multiple genome regions. Analyses based on testing with single primers do not lead to reliable conclusions about the association between GBV-C infection and clinical outcomes.

Longitudinal variability of human immunodeficiency virus type 1 RNA viral load measurements by nucleic acid sequence-based amplification and NucliSens assays in a large multicenter study.

Human immunodeficiency virus type 1 (HIV-1) RNA measurements were evaluated within an externally controlled multilaboratory program. Three external standards (1.5 x 10(3) to 1.5 x 10(6) copies/ml) were included in 814 assay runs by four laboratories. Results indicate that HIV-1 RNA levels can be measured with a precision equal to that of the pre-highly active antiretroviral therapy era (standard deviations, +/-0.16 to 0.25 log10 units).

Evolution of cervical abnormalities among women with HIV-1: evidence from surveillance cytology in the women's interagency HIV study.

OBJECTIVE: To determine incidence, progression, and regression rates for abnormal cervical cytology and their correlates among women with HIV. METHODS: In a multicenter prospective cohort study conducted October 1, 1994, through September 30, 1999 at university, public, and private medical centers and clinics, 1639 HIV-seropositive and 452 seronegative women were evaluated every 6 months for up to 5 years using history, cervical cytology, T-cell subsets, and quantitative plasma HIV RNA. Human papillomavirus (HPV) typing at baseline was determined by polymerase chain reaction. Cytology was read using the Bethesda system, with any smear showing at least atypia considered abnormal. Poisson regression identified factors associated with incident cytologic abnormalities whereas logistic regression identified those associated with progression and regression after an abnormality. RESULTS: At least one abnormal smear was found during all of follow-up among 73.0% of HIV-seropositive patients and 42.3% of seronegatives (p <.001). Only 5.9% of seropositives ever developed high-grade lesions, and the proportion with high-grade findings did not rise over time. Incidence of atypical squamous cells of uncertain significance (ASCUS) or more severe lesions among HIV-seropositive patients and seronegative patients was 26.4 and 11.0/100 woman-years (rate ratio [RR], 2.4; 95% confidence interval [CI], 1.9-3.0), whereas that of at least low-grade squamous intraepithelial lesions (SIL) was 8.9 and 2.2/100 (RR, 4.0; CI, 2.6-6.1). HIV status, detection of the presence of human papillomavirus (HPV), CD4 lymphocyte count, and HIV RNA level predicted incidence of abnormal cytology (p <.05); HPV detection and HIV RNA level predicted progression (p <.01); and HPV detection, CD4 lymphocyte count, and HIV RNA level predicted regression (p <.001). Rates of incidence, progression, and regression of abnormal cytology did not differ between HIV seronegative women and seropositive women with CD4 lymphocyte counts >200/mm(3) and HIV RNA levels <4000/ml of similar HPV status. CONCLUSIONS: Although HIV infected women were at high risk for abnormal cytology, high-grade changes were uncommon. HIV status, HPV detection, CD4 lymphocyte count, and HIV RNA level predicted the incidence of cervical cytologic abnormalities. Progression was significantly increased only among the most immunosuppressed women, while regression was significantly reduced in all HIV seropositive women except those with the best controlled HIV disease.