Methane cycling dynamics in sediments of Alaskan Arctic Foothill lakes

We measured aspects of sediment methane (CH4) cycling dynamics in 3 shallow (mean depth, z = 2.1 m) and 3 deep (z = 6.5 m) Alaskan Arctic Foothill lakes to establish reference data to evaluate future climate-mediated changes in these systems and to identify lake-size-dependent differences in rates and controls on CH4 production and consumption or sensitivity to changing climate. The mean sedimentation rate and sediment oxygen (O2) penetration depth were significantly higher and lower, respectively, in shallow versus deep lakes. The molar carbon to nitrogen (C:N) ratio of 12 for sedimenting material across lakes indicated a dominance by phytodetritus. Pore water dissolved organic C and CH4 concentrations were higher in shallow than in deep lakes at comparable depths below the sediment surface. The average area-based rate of methanogenesis was significantly higher in shallow lakes, exceeding the mean of deep lakes by a factor of 4; however, the mean potential area-based rate of CH4 oxidation was comparable between lake classes due to the reduced sediment O2 penetration depth in shallow lakes. All lake sediments responded similarly to chemical amendments. Hydrogen addition significantly stimulated rates of methanogenesis relative to unamended controls, while rates were unchanged by alternate electron acceptors (SO42−, Fe3+, NO3−, Mn4+), suggesting that other microbial groups did not compete with methanogens for common substrates or produce toxic intermediates. Across all lakes, 30% of assimilated CH4 was converted to methanotophic biomass, and methanotrophic C production could be as much as 23% of epipelic primary production, pointing to the potential importance of CH4-derived C in Arctic lacustrine food webs

Relationships between lake transparency, thermocline depth, and sediment oxygen demand in Arctic lakes

The burial of organic matter within lake sediments can be a significant component of landscape carbon cycling. Whether organic matter deposited in lake sediments is sequestered or mineralized depends on factors limiting the decomposition rate of organic matter, such as temperature and the availability of oxygen. In stratified lakes, the distribution of temperature and oxygen is determined by the depth of the thermocline, and therefore sediment organic matter burial should be sensitive to changes in thermocline depth. Using a survey of more than 30 lakes over 3 years in the Alaskan Arctic, we found that thermocline depth during the summer was positively correlated with water transparency. Furthermore, using sediment incubations from 3 lakes, we found that variation in sediment oxygen demand is primarily affected by variation in temperature and the availability of oxygen with limited effect of the source of the sediments. Because variation in temperature and oxygen concentration in stratified lakes is mainly determined by the depth of thermocline, these results indicate that changes in transparency can have indirect effects on the rate of organic matter mineralization in lakes. A reduction in thermocline depth that results from decreased lake transparency may decrease the breakdown of sediment organic matter and increase the storage of organic carbon in lake sediments

Systematic review of TST responses in people living with HIV in under-resourced settings: implications for isoniazid preventive therapy.

BACKGROUND: People living with HIV (PLWH) who have positive tuberculin skin tests (TST) benefit from isoniazid preventive therapy (IPT) whereas those testing TST-negative do not. Revised World Health Organization guidelines explicitly state that assessment of TST is not a requirement for initiation of IPT. However, it is not known what proportions of patients will benefit from IPT if implemented without targeting according to TST status. We therefore determined the proportions of PLWH who test TST-positive. METHODOLOGY/PRINCIPAL FINDINGS: We systematically reviewed the literature published between January 1990 and February 2012 to determine the proportions of patients without active tuberculosis attending HIV care services in low and middle-income countries who tested TST-positive (≥5 mm induration). Proportions were also determined for different CD4 count strata. Data from 19 studies with 9,478 PLWH from sub-Saharan Africa, Asia and Central and South America were summarized. The vast majority were not receiving antiretroviral therapy (ART). A sub-analysis was conducted of 5 studies (5,567 subjects) from high TB prevalence countries of PLWH with negative TB screens attending HIV care and treatment settings for whom CD4 stratified data were available. The median proportion of PLWH testing TST-positive overall was 22.8% (range, 19.5-32.6%). The median (range) proportions with CD4 cell counts of <200, 200-499 or ≥500 cells/µL who tested positive were 12.4% (8.2-15.3%), 28.4% (20.1-36.9%) and 37.4% (31.3-56.3%), respectively. Heterogeneity in the data precluded calculation of pooled summary estimates. CONCLUSIONS/SIGNIFICANCE: In most settings, if IPT is administered to PLWH pre-ART without assessment of TST status, only a minority of those treated are likely to benefit, especially among those with the lowest CD4 cell counts. This may be inefficient use of resources and cost-effectiveness analyses should take this into account. Local knowledge of TST response rates may help inform policies. New simple means of identifying those who will benefit from IPT are needed to permit appropriate targeting of this intervention

The Alliance for Cellular Signaling Plasmid Collection: A Flexible Resource for Protein Localization Studies and Signaling Pathway Analysis

Cellular responses to inputs that vary both temporally and spatially are determined by complex relationships between the components of cell signaling networks. Analysis of these relationships requires access to a wide range of experimental reagents and techniques, including the ability to express the protein components of the model cells in a variety of contexts. As part of the Alliance for Cellular Signaling, we developed a robust method for cloning large numbers of signaling ORFs into Gateway® entry vectors, and we created a wide range of compatible expression platforms for proteomics applications. To date, we have generated over 3000 plasmids that are available to the scientific community via the American Type Culture Collection. We have established a website at www.signaling-gateway.org/data/plasmid/ that allows users to browse, search, and blast Alliance for Cellular Signaling plasmids. The collection primarily contains murine signaling ORFs with an emphasis on kinases and G protein signaling genes. Here we describe the cloning, databasing, and application of this proteomics resource for large scale subcellular localization screens in mammalian cell lines

Climate Process Team on internal wave–driven ocean mixing

Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 98 (2017): 2429-2454, doi:10.1175/BAMS-D-16-0030.1.Diapycnal mixing plays a primary role in the thermodynamic balance of the ocean and, consequently, in oceanic heat and carbon uptake and storage. Though observed mixing rates are on average consistent with values required by inverse models, recent attention has focused on the dramatic spatial variability, spanning several orders of magnitude, of mixing rates in both the upper and deep ocean. Away from ocean boundaries, the spatiotemporal patterns of mixing are largely driven by the geography of generation, propagation, and dissipation of internal waves, which supply much of the power for turbulent mixing. Over the last 5 years and under the auspices of U.S. Climate Variability and Predictability Program (CLIVAR), a National Science Foundation (NSF)- and National Oceanic and Atmospheric Administration (NOAA)-supported Climate Process Team has been engaged in developing, implementing, and testing dynamics-based parameterizations for internal wave–driven turbulent mixing in global ocean models. The work has primarily focused on turbulence 1) near sites of internal tide generation, 2) in the upper ocean related to wind-generated near inertial motions, 3) due to internal lee waves generated by low-frequency mesoscale flows over topography, and 4) at ocean margins. Here, we review recent progress, describe the tools developed, and discuss future directions.We are grateful to U.S. CLIVAR for their leadership in instigating and facilitating the Climate Process Team program. We are indebted to NSF and NOAA for sponsoring the CPT series.2018-06-0

Climate Process Team On Internal Wave-Driven Ocean Mixing

The study summarizes recent advances in our understanding of internal wave–driven turbulent mixing in the ocean interior and introduces new parameterizations for global climate ocean models and their climate impacts

Climate Process Team on Internal-Wave Driven Ocean Mixing

Diapycnal mixing plays a primary role in the thermodynamic balance of the ocean, and consequently, in oceanic heat and carbon uptake and storage. Though observed mixing rates are on average consistent with values required by inverse models, recent attention has focused on the dramatic spatial variability, spanning several orders of magnitude, of mixing rates in both the upper and deep ocean. Climate models have been shown to be very sensitive not only to the overall level but to the detailed distribution of mixing; sub-grid-scale parameterizations based on accurate physical processes will allow model forecasts to evolve with a changing climate. Spatio-temporal patterns of mixing are largely driven by the geography of generation, propagation and destruction of internal waves, which are thought to supply much of the power for turbulent mixing. Over the last five years and under the auspices of US CLIVAR, a NSF and NOAA supported Climate Process Team has been engaged in developing, implementing and testing dynamics-base parameterizations for internal-wave driven turbulent mixing in global ocean models. The work has primarily focused on turbulence 1) near sites of internal tide generation, 2) in the upper ocean related to wind-generated near inertial motions, 3) due to internal lee waves generated by low-frequency mesoscale flows over topography, and 4) at ocean margins. Here we review recent progress, describe the tools developed, and discuss future directions

High acceptance of home-based HIV counseling and testing in an urban community setting in Uganda

<p>Abstract</p> <p>Background</p> <p>HIV testing is a key component of prevention and an entry point into HIV/AIDS treatment and care however, coverage and access to testing remains low in Uganda. Home-Based HIV Counseling and Testing (HBHCT) has potential to increase access and early identification of unknown HIV/AIDS disease. This study investigated the level of acceptance of Home-Based HIV Counseling and Testing (HBHCT), the HIV sero-prevalence and the factors associated with acceptance of HBHCT in an urban setting.</p> <p>Methods</p> <p>A cross-sectional house-to-house survey was conducted in Rubaga division of Kampala from January-June 2009. Residents aged ≥ 15 years were interviewed and tested for HIV by trained nurse-counselors using the national standard guidelines. Acceptance of HBHCT was defined as consenting, taking the HIV test and receipt of results offered during the home visit. Multivariable logistic regression analysis was performed to determine significant factors associated with acceptance of HBHCT.</p> <p>Results</p> <p>We enrolled 588 participants, 408 (69%, 95% CI: 66%-73%) accepted testing. After adjusting for confounding, being male (adj. OR 1.65; 95%CI 1.03, 2.73), age 25-34 (adj. OR 0.63; 95% CI 0.40, 0.94) and ≥35 years (adj. OR 0.30; 95%CI 0.17, 0.56), being previously married (adj. OR 3.22; 95%CI 1.49, 6.98) and previous HIV testing (adj. OR 0.50; 95%CI 0.30, 0.74) were significantly associated with HBHCT acceptance. Of 408 who took the test, 30 (7.4%, 95% CI: 4.8%- 9.9%) previously unknown HIV positive individuals were identified and linked to HIV care.</p> <p>Conclusions</p> <p>Acceptance of home-based counseling and testing was relatively high in this urban setting. This strategy provided access to HIV testing for previously untested and unknown HIV-infected individuals in the community. Age, sex, marital status and previous HIV test history are important factors that may be considered when designing programs for home-based HIV testing in urban settings in Uganda.</p

Aβ42 Mutants with Different Aggregation Profiles Induce Distinct Pathologies in Drosophila

Aggregation of the amyloid-β-42 (Aβ42) peptide in the brain parenchyma is a pathological hallmark of Alzheimer's disease (AD), and the prevention of Aβ aggregation has been proposed as a therapeutic intervention in AD. However, recent reports indicate that Aβ can form several different prefibrillar and fibrillar aggregates and that each aggregate may confer different pathogenic effects, suggesting that manipulation of Aβ42 aggregation may not only quantitatively but also qualitatively modify brain pathology. Here, we compare the pathogenicity of human Aβ42 mutants with differing tendencies to aggregate. We examined the aggregation-prone, EOFAD-related Arctic mutation (Aβ42Arc) and an artificial mutation (Aβ42art) that is known to suppress aggregation and toxicity of Aβ42 in vitro. In the Drosophila brain, Aβ42Arc formed more oligomers and deposits than did wild type Aβ42, while Aβ42art formed fewer oligomers and deposits. The severity of locomotor dysfunction and premature death positively correlated with the aggregation tendencies of Aβ peptides. Surprisingly, however, Aβ42art caused earlier onset of memory defects than Aβ42. More remarkably, each Aβ induced qualitatively different pathologies. Aβ42Arc caused greater neuron loss than did Aβ42, while Aβ42art flies showed the strongest neurite degeneration. This pattern of degeneration coincides with the distribution of Thioflavin S-stained Aβ aggregates: Aβ42Arc formed large deposits in the cell body, Aβ42art accumulated preferentially in the neurites, while Aβ42 accumulated in both locations. Our results demonstrate that manipulation of the aggregation propensity of Aβ42 does not simply change the level of toxicity, but can also result in qualitative shifts in the pathology induced in vivo

Vaccinia Virus Proteins A52 and B14 Share a Bcl-2–Like Fold but Have Evolved to Inhibit NF-κB rather than Apoptosis

Vaccinia virus (VACV), the prototype poxvirus, encodes numerous proteins that modulate the host response to infection. Two such proteins, B14 and A52, act inside infected cells to inhibit activation of NF-κB, thereby blocking the production of pro-inflammatory cytokines. We have solved the crystal structures of A52 and B14 at 1.9 Å and 2.7 Å resolution, respectively. Strikingly, both these proteins adopt a Bcl-2–like fold despite sharing no significant sequence similarity with other viral or cellular Bcl-2–like proteins. Unlike cellular and viral Bcl-2–like proteins described previously, A52 and B14 lack a surface groove for binding BH3 peptides from pro-apoptotic Bcl-2–like proteins and they do not modulate apoptosis. Structure-based phylogenetic analysis of 32 cellular and viral Bcl-2–like protein structures reveals that A52 and B14 are more closely related to each other and to VACV N1 and myxoma virus M11 than they are to other viral or cellular Bcl-2–like proteins. This suggests that a progenitor poxvirus acquired a gene encoding a Bcl-2–like protein and, over the course of evolution, gene duplication events have allowed the virus to exploit this Bcl-2 scaffold for interfering with distinct host signalling pathways