Monitoring underwater volcano degassing using fiber-optic sensing.

Continuous monitoring of volcanic gas emissions is crucial for understanding volcanic activity and potential eruptions. However, emissions of volcanic gases underwater are infrequently studied or quantified. This study explores the potential of Distributed Acoustic Sensing (DAS) technology to monitor underwater volcanic degassing. DAS converts fiber-optic cables into high-resolution vibration recording arrays, providing measurements at unprecedented spatio-temporal resolution. We conducted an experiment at Laacher See volcano in Germany, immersing a fiber-optic cable in the lake and interrogating it with a DAS system. We detected and analyzed numerous acoustic signals that we associated with bubble emissions in different lake areas. Three types of text-book bubbles exhibiting characteristic waveforms are all found from our detections, indicating different nucleation processes and bubble sizes. Using clustering algorithms, we classified bubble events into four distinct clusters based on their temporal and spectral characteristics. The temporal distribution of the events provided insights into the evolution of gas seepage patterns. This technology has the potential to revolutionize underwater degassing monitoring and provide valuable information for studying volcanic processes and estimating gas emissions. Furthermore, DAS can be applied to other applications, such as monitoring underwater carbon capture and storage operations or methane leaks associated with climate change.

Community Health Impacts From Natural Gas Pipeline Compressor Stations.

Compressor stations maintain pressure along natural gas pipelines to sustain gas flow. Unfortunately, they present human health concerns as they release chemical pollutants into the air, sometimes at levels higher than national air quality standards. Further, compressor stations are often placed in rural areas with higher levels of poverty and/or minority populations, contributing to environmental justice concerns. In this paper we investigate what chemical pollutants are emitted by compressor stations, the impacts of emitted pollutants on human health, and local community impacts. Based on the information gained from these examinations, we provide the following policy recommendations with the goal of minimizing harm to those affected by natural gas compressor stations: the Environmental Protection Agency (EPA) and relevant state agencies must increase air quality monitoring and data transparency; the EPA should direct more resources to monitoring programs specifically at compressor stations; the EPA should provide free indoor air quality monitoring to homes near compressor stations; the EPA needs to adjust its National Ambient Air Quality Standards to better protect communities and assess cumulative impacts; and decision-makers at all levels must pursue meaningful involvement from potentially affected communities. We find there is substantial evidence of negative impacts to strongly support these recommendations.

Real-time three-dimensional echocardiography for left atrial volume assessment in Thoroughbred racehorses: Observer variability and comparison with two-dimensional echocardiography.

BACKGROUND: Left atrial size predicts cardiac morbidity and mortality in humans and dogs. Real-time three-dimensional echocardiography (3DE) may be reliable for assessing left atrial volume (LAV) in horses. OBJECTIVES: To determine intra- and interobserver variability estimates of 3DE-LAV and compare it to that of 2DE-LAV estimates. STUDY DESIGN: Method comparison. METHODS: 3DE datasets were obtained from 40 horses, then graded for quality, creating a final study population of 22 horses. The 3DE and 2DE maximum LAV (LAVmax ) and minimum LAV (LAVmin ) were measured, and left atrial emptying volume (LA EV) and left atrial ejection fraction (LA EF) were calculated, from the same 3D dataset on four occasions using (a) a semi-automatic surface recognition algorithm and (b) a modified Simpson's method of discs. 3DE LAV measurements were repeated by a second observer. RESULTS: For 3DE, median LAVmax was 596cm3 for observer one, and 852 cm3 for observer two, LAVmin was 373 cm3 for observer one and 533 cm3 for observer two. Low intraobserver measurement variation was observed for LAVmax and LAVmin , with horse-level intraclass correlation coefficients (ICChorse ) for both observers between 76% and 85% (horse added as random effect). The interobserver ICC was 58% for LAVmax and 50% for LAVmin on averaged measurements (with observer added as random effect), indicating consistent differences between observers. While intraobserver variation was similar for 2DE LAVmax measurements, it was greater for LAVmin (ICChorse  = 67%). The intermethod ICC for 3DE vs 2DE was low at 14% for LAVmax and ~0% for LAVmin , indicating less-consistent differences with method. MAIN LIMITATIONS: Small study population, low observer number, use of different imaging modalities (fundamental frequency and octave harmonics). CONCLUSIONS: 3DE assessment of LAV was reliable, suggesting suitability for longitudinal evaluation of clinical cases. Clinicians should be aware of differences in LAV measurements between observers. More defined measurement guidelines may improve repeatability.

Ready display of antigenic peptides in a protein 'mimogen'.

Given the dependence of much modern biology upon the use of antibodies as tools and reagents, their variability and the often associated lack-of-detail about function and identity creates experimental errors. Here we describe the proof-of-principle for a potentially general, versatile method for the display of antigens in a soluble yet standard format on a lateral protein scaffold that mimics normal epitopes in a protein antigen (a 'mimogen') and confirm their utility in phosphorylation-dependent recognition by specific antibodies.

Insights into electron flux through manipulation of fermentation conditions and assessment of protein expression profiles in Clostridium thermocellum.

While annotation of the genome sequence of Clostridium thermocellum has allowed predictions of pathways catabolizing cellobiose to end products, ambiguities have persisted with respect to the role of various proteins involved in electron transfer reactions. A combination of growth studies modulating carbon and electron flow and multiple reaction monitoring (MRM) mass spectrometry measurements of proteins involved in central metabolism and electron transfer was used to determine the key enzymes involved in channeling electrons toward fermentation end products. Specifically, peptides belonging to subunits of ferredoxin-dependent hydrogenase and NADH:ferredoxin oxidoreductase (NFOR) were low or below MRM detection limits when compared to most central metabolic proteins measured. The significant increase in H2 versus ethanol synthesis in response to either co-metabolism of pyruvate and cellobiose or hypophosphite mediated pyruvate:formate lyase inhibition, in conjunction with low levels of ferredoxin-dependent hydrogenase and NFOR, suggest that highly expressed putative bifurcating hydrogenases play a substantial role in reoxidizing both reduced ferredoxin and NADH simultaneously. However, product balances also suggest that some of the additional reduced ferredoxin generated through increased flux through pyruvate:ferredoxin oxidoreductase must be ultimately converted into NAD(P)H either directly via NADH-dependent reduced ferredoxin:NADP(+) oxidoreductase (NfnAB) or indirectly via NADPH-dependent hydrogenase. While inhibition of hydrogenases with carbon monoxide decreased H2 production 6-fold and redirected flux from pyruvate:ferredoxin oxidoreductase to pyruvate:formate lyase, the decrease in CO2 was only 20 % of that of the decrease in H2, further suggesting that an alternative redox system coupling ferredoxin and NAD(P)H is active in C. thermocellum in lieu of poorly expressed ferredoxin-dependent hydrogenase and NFOR.

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park.

Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population inhabiting acidic iron-oxide mats in YNP. Detailed analysis of conserved ribosomal and informational processing genes indicates that the replicate assemblies represent a new candidate phylum within the domain Archaea referred to here as 'Geoarchaeota' or 'novel archaeal group 1 (NAG1)'. The NAG1 organisms contain pathways necessary for the catabolism of peptides and complex carbohydrates as well as a bacterial-like Form I carbon monoxide dehydrogenase complex likely used for energy conservation. Moreover, this novel population contains genes involved in the metabolism of oxygen including a Type A heme copper oxidase, a bd-type terminal oxidase and a putative oxygen-sensing protoglobin. NAG1 has a variety of unique bacterial-like cofactor biosynthesis and transport genes and a Type3-like CRISPR system. Discovery of NAG1 is critical to our understanding of microbial community structure and function in extant thermophilic iron-oxide mats of YNP, and will provide insight regarding the evolution of Archaea in early Earth environments that may have important analogs active in YNP today.

Infection-dependent phenotypes in MHC-congenic mice are not due to MHC: can we trust congenic animals?

BACKGROUND: Congenic strains of mice are assumed to differ only at a single gene or region of the genome. These mice have great importance in evaluating the function of genes. However, their utility depends on the maintenance of this true congenic nature. Although, accumulating evidence suggests that congenic strains suffer genetic divergence that could compromise interpretation of experimental results, this problem is usually ignored. During coinfection studies with Salmonella typhimurium and Theiler's murine encephalomyelitis virus (TMEV) in major histocompatibility complex (MHC)-congenic mice, we conducted the proper F2 controls and discovered significant differences between these F2 animals and MHC-genotype-matched P0 and F1 animals in weight gain and pathogen load. To systematically evaluate the apparent non-MHC differences in these mice, we infected all three generations (P0, F1 and F2) for 5 MHC genotypes (b/b, b/q and q/q as well as d/d, d/q, and q/q) with Salmonella and TMEV. RESULTS: Infected P0 MHC q/q congenic homozygotes lost significantly more weight (p = 0.02) and had significantly higher Salmonella (p < 0.01) and TMEV (p = 0.02) titers than the infected F2 q/q homozygotes. Neither weight nor pathogen load differences were present in sham-infected controls. CONCLUSIONS: These data suggest that these strains differ for genes other than those in the MHC congenic region. The most likely explanation is that deleterious recessive mutations affecting response to infection have accumulated in the more than 40 years that this B10.Q-H-2q MHC-congenic strain has been separated from its B10-H-2b parental strain. During typical experiments with congenic strains, the phenotypes of these accumulated mutations will be falsely ascribed to the congenic gene(s). This problem likely affects any strains separated for appreciable time and while usually ignored, can be avoided with the use of F2 segregants.

Negative regulation of neural stem/progenitor cell proliferation by the Pten tumor suppressor gene in vivo.

The mechanisms controlling neural stem cell proliferation are poorly understood. Here we demonstrate that the PTEN tumor suppressor plays an important role in regulating neural stem/progenitor cells in vivo and in vitro. Mice lacking PTEN exhibited enlarged, histoarchitecturally abnormal brains, which resulted from increased cell proliferation, decreased cell death, and enlarged cell size. Neurosphere cultures revealed a greater proliferation capacity for tripotent Pten-/- central nervous system stem/progenitor cells, which can be attributed, at least in part, to a shortened cell cycle. However, cell fate commitments of the progenitors were largely undisturbed. Our results suggest that PTEN negatively regulates neural stem cell proliferation.

Macrophage tropism of human immunodeficiency virus type 1 isolates from brain and lymphoid tissues predicts neurotropism independent of coreceptor specificity.

The viral determinants that underlie human immunodeficiency virus type 1 (HIV-1) neurotropism are unknown, due in part to limited studies on viruses isolated from brain. Previous studies suggest that brain-derived viruses are macrophage tropic (M-tropic) and principally use CCR5 for virus entry. To better understand HIV-1 neurotropism, we isolated primary viruses from autopsy brain, cerebral spinal fluid, blood, spleen, and lymph node samples from AIDS patients with dementia and HIV-1 encephalitis. Isolates were characterized to determine coreceptor usage and replication capacity in peripheral blood mononuclear cells (PBMC), monocyte-derived macrophages (MDM), and microglia. Env V1/V2 and V3 heteroduplex tracking assay and sequence analyses were performed to characterize distinct variants in viral quasispecies. Viruses isolated from brain, which consisted of variants that were distinct from those in lymphoid tissues, used CCR5 (R5), CXCR4 (X4), or both coreceptors (R5X4). Minor usage of CCR2b, CCR3, CCR8, and Apj was also observed. Primary brain and lymphoid isolates that replicated to high levels in MDM showed a similar capacity to replicate in microglia. Six of 11 R5 isolates that replicated efficiently in PBMC could not replicate in MDM or microglia due to a block in virus entry. CD4 overexpression in microglia transduced with retroviral vectors had no effect on the restricted replication of these virus strains. Furthermore, infection of transfected cells expressing different amounts of CD4 or CCR5 with M-tropic and non-M-tropic R5 isolates revealed a similar dependence on CD4 and CCR5 levels for entry, suggesting that the entry block was not due to low levels of either receptor. Studies using TAK-779 and AMD3100 showed that two highly M-tropic isolates entered microglia primarily via CXCR4. These results suggest that HIV-1 tropism for macrophages and microglia is restricted at the entry level by a mechanism independent of coreceptor specificity. These findings provide evidence that M-tropism rather than CCR5 usage predicts HIV-1 neurotropism.

Impaired response to HAART in HIV-infected individuals with high autonomic nervous system activity.

Neurotransmitters can accelerate HIV-1 replication in vitro, leading us to examine whether differences in autonomic nervous system (ANS) activity might promote residual HIV-1 replication in patients treated with highly active antiretroviral therapy. Patients who showed constitutively high levels of ANS activity before highly active antiretroviral therapy experienced poorer suppression of plasma viral load and poorer CD4(+) T cell recovery over 3-11 months of therapy. ANS activity was not related to demographic or behavioral characteristics that might influence pathogenesis. However, the ANS neurotransmitter norepinephrine enhanced replication of both CCR5- and CXCR4-tropic strains of HIV-1 in vitro via chemokine receptor up-regulation and enhanced viral gene expression, suggesting that neural activity may directly promote residual viral replication.

HIV-1 actively replicates in naive CD4(+) T cells residing within human lymphoid tissues.

Although HIV-1 gene expression is detected in naive, resting T cells in vivo, such cells are resistant to productive infection in vitro. However, we found that the endogenous microenvironment of human lymphoid tissues supports de novo infection and depletion of this population. Cell cycle analysis and DNA labeling experiments established that these cells were definitively quiescent and thus infected de novo. Quantitation of the "burst size" within naive cells further demonstrated that these cells were productively infected and contributed to the local viral burden. These findings demonstrate that lymphoid tissues support active HIV-1 replication in resting, naive T cells. Moreover, these cells are not solely reservoirs of latent virus but are permissive hosts for viral replication that likely targets them for elimination.

Nosocomial primary bloodstream infections in intensive care unit patients in a nonteaching community medical center: a 21-month prospective study.

All patients admitted to the medical and surgical intensive care units of a 500-bed nonteaching suburban hospital were followed prospectively for the occurrence of nosocomial primary bloodstream infections for 21 months. The incidence of primary bloodstream infection was 38 (1%) of 3163 patients; among patients with central venous catheters, it was 34 (4%) of 920 patients, or 4.0 infections per 1000 catheter-days. Ventilator-associated pneumonia, congestive heart failure, and each intravascular catheter inserted were independently associated with the development of a nosocomial primary bloodstream infection. Among infected patients, the crude mortality rate was 53%, and these patients had longer stays in intensive care units and the hospital than did uninfected patients. Bloodstream infection, however, was not an independent risk factor for death. The incidence, risk factors, and serious outcomes of bloodstream infections in a nonteaching community hospital were similar to those seen in tertiary-care teaching hospitals.

Upregulation of CD4 on CD8+ T cells: CD4dimCD8bright T cells constitute an activated phenotype of CD8+ T cells.

Aside from an intermediate stage in thymic T-cell development, the expression of CD4 and CD8 is generally thought to be mutually exclusive, associated with helper or cytotoxic T-cell functions, respectively. Stimulation of CD8+ T cells, however, induces the de novo expression of CD4. We demonstrate that while superantigen (staphylococcal enterotoxin B, SEB) and anti-CD3/CD28 costimulation of purified CD8+ T cells induced the expression of CD4 on CD8+ T cells by 30 and 17%, respectively, phytohaemagglutinin (PHA) stimulation did not induce CD4 expression on purified CD8+ T cells but significantly induced the expression of both CD4 on CD8 (CD4dimCD8bright) and CD8 on CD4 (CD4brightCD8dim) T cells in unfractionated peripheral blood mononuclear cells (PBMC). The level of the PHA-mediated induction of CD4dimCD8bright and CD4brightCD8dim was at 27 and 17%, respectively. Depletion of CD4+ T cells from PBMC abrogated this PHA-mediated effect. Autologous CD4+ and CD8+ T-cell co-cultures in the presence of PHA induced this CD4dimCD8bright T-cell expression by 33%, demonstrating a role for CD4 cells in the PHA-mediated induction of the double positive cells. The induction of CD4dimCD8bright was independent of a soluble factor(s). Phenotypic analysis of CD4dimCD8bright T cells indicated significantly higher levels of CD95, CD25, CD38, CD69, CD28, and CD45RO expression than their CD8+CD4- counterparts. CD4dimCD8bright T cells were also negative for CD1a expression and were predominantly T-cell receptor (TCR) alphabeta cells. Our data demonstrate that CD4dimCD8bright T cells are an activated phenotype of CD8+ T cells and suggest that CD4 upregulation on CD8+ T cells may function as an additional marker to identify activated CD8+ T cells.

Generation of HIV latency during thymopoiesis.

The use of combination antiretroviral therapy results in a substantial reduction in viremia, a rebound of CD4+ T cells and increased survival for HIV-infected individuals. However, this treatment does not result in the total eradication of HIV. Rather, the virus is thought to remain latent in a subset of cells, where it avoids elimination by the immune system. In this state the virus is capable of reactivation of productive infection following cessation of therapy. These latently infected cells are very few in number and it has thus been difficult to determine their origin and to study the molecular nature of the latent viral genome. HIV replication is linked to cellular gene transcription and requires target cell activation. Therefore, should an activated, infected cell become transcriptionally inactive prior to cytopathic effects, the viral genome might be maintained in a latent state. We used the SCID-hu (Thy/Liv) mouse model to establish that activation-inducible HIV can be generated at high frequency during thymopoiesis, a process where previously activated cells mature towards quiescence. Moreover, we showed that these cells can be exported into the periphery where the virus remains latent until T-cell receptor stimulation, indicating that the thymus might be a source of latent HIV in humans.