Extracellular superoxide production by key microbes in the global ocean

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sutherland, K. M., Coe, A., Gast, R. J., Plummer, S., Suffridge, C. P., Diaz, J. M., Bowman, J. S., Wankel, S. D., & Hansel, C. M. Extracellular superoxide production by key microbes in the global ocean. Limnology and Oceanography, (2019), doi:10.1002/lno.11247.Bacteria and eukaryotes produce the reactive oxygen species superoxide both within and outside the cell. Although superoxide is typically associated with the detrimental and sometimes fatal effects of oxidative stress, it has also been shown to be involved in a range of essential biochemical processes, including cell signaling, growth, differentiation, and defense. Light‐independent extracellular superoxide production has been shown to be widespread among many marine heterotrophs and phytoplankton, but the extent to which this trait is relevant to marine microbial physiology and ecology throughout the global ocean is unknown. Here, we investigate the dark extracellular superoxide production of five groups of organisms that are geographically widespread and represent some of the most abundant organisms in the global ocean. These include Prochlorococcus, Synechococcus, Pelagibacter, Phaeocystis, and Geminigera. Cell‐normalized net extracellular superoxide production rates ranged seven orders of magnitude, from undetectable to 14,830 amol cell−1 h−1, with the cyanobacterium Prochlorococcus being the lowest producer and the cryptophyte Geminigera being the most prolific producer. Extracellular superoxide production exhibited a strong inverse relationship with cell number, pointing to a potential role in cell signaling. We demonstrate that rapid, cell‐number–dependent changes in the net superoxide production rate by Synechococcus and Pelagibacter arose primarily from changes in gross production of extracellular superoxide, not decay. These results expand the relevance of dark extracellular superoxide production to key marine microbes of the global ocean, suggesting that superoxide production in marine waters is regulated by a diverse suite of marine organisms in both dark and sunlit waters.The authors would like to acknowledge their funding sources including NASA NESSF NNX15AR62H (K.M.S.), NASA Exobiology grant NNX15AM04G to S.D.W. and C.M.H., NSF‐OCE grant 1355720 to C.M.H., NSF‐OPP 1641019 (J.S.B), and Simons Foundation SCOPE Award ID 329108 (Sallie W. Chisholm). The authors would also like to thank the Harvey lab (Skidaway Institute of Oceanography) for use of their flow cytometer in this study. We thank Stephen Giovannoni and Sallie Chisholm for providing bacteria strains and laboratory facilities. Additional thanks to Marianne Acker, Rogier Braakman, and Aldo Arellano for assistance in lab and helpful conversations

Mechanical response of cardiac microtissues to acute localized injury

After a myocardial infarction (MI), the heart undergoes changes including local remodeling that can lead to regional abnormalities in mechanical and electrical properties, ultimately increasing the risk of arrhythmias and heart failure. Although these responses have been successfully recapitulated in animal models of MI, local changes in tissue and cell-level mechanics caused by MI remain difficult to study in vivo. Here, we developed an in vitro cardiac microtissue (CMT) injury system that through acute focal injury recapitulates aspects of the regional responses seen following an MI. With a pulsed laser, cell death was induced in the center of the microtissue causing a loss of calcium signaling and a complete loss of contractile function in the injured region and resulting in a 39% reduction in the CMT's overall force production. After 7 days, the injured area remained void of cardiomyocytes (CMs) and showed increased expression of vimentin and fibronectin, two markers for fibrotic remodeling. Interestingly, although the injured region showed minimal recovery, calcium amplitudes in uninjured regions returned to levels comparable with control. Furthermore, overall force production returned to preinjury levels despite the lack of contractile function in the injured region. Instead, uninjured regions exhibited elevated contractile function, compensating for the loss of function in the injured region, drawing parallels to changes in tissue-level mechanics seen in vivo. Overall, this work presents a new in vitro model to study cardiac tissue remodeling and electromechanical changes after injury.NEW & NOTEWORTHY We report an in vitro cardiac injury model that uses a high-powered laser to induce regional cell death and a focal fibrotic response within a human-engineered cardiac microtissue. The model captures the effects of acute injury on tissue response, remodeling, and electromechanical recovery in both the damaged region and surrounding healthy tissue, modeling similar changes to contractile function observed in vivo following myocardial infarction.R21 EB028491 - NIBIB NIH HHSPublished versio

Projection, Spatial Correlations, and Anisotropies in a Large and Complete Sample of Abell Clusters

An analysis of R >= 1 Abell clusters is presented for samples containing recent redshifts from the MX Northern Abell Cluster Survey. The newly obtained redshifts from the MX Survey as well as those from the ESO Nearby Abell Cluster Survey (ENACS) provide the necessary data for the largest magnitude-limited correlation analysis of rich clusters in the entire sky (excluding the galactic plane) to date. We find 19.4 <= r_0 <= 23.3 h^-1Mpc, -1.92 <= gamma <= -1.83 for four different subsets of Abell/ACO clusters, including a large sample (N=104) of cD clusters. We have used this dataset to look for line-of-sight anisotropies within the Abell/ACO catalogs. We show that the strong anisotropies present in previously studied Abell cluster datasets are not present in our R >= 1 samples. There are, however, indications of residual anisotropies which we show are the result of two elongated superclusters, Ursa Majoris and Corona Borealis, whose axes lie near the line-of-sight. After rotating these superclusters so that their semi-major axes are prependicular to the line-of-sight, we find no anisotropies as indicated by the correlation function. The amplitude and slope of the two-point correlation function remain the same before and after these rotations. We also remove a subset of R = 1 Abell/ACO clusters that show sizable foreground/background galaxy contamination and again find no change in the amplitude or slope of the correlation function. We conclude that the correlation length of R >= 1 Abell clusters is not artificially enhanced by line-of-sight anisotropies.Comment: 37 pages, 8 figures, AASTeX Accepted for publication in Ap

Mortality on Mount Everest, 1921-2006: descriptive study

Objective To examine patterns of mortality among climbers on Mount Everest over an 86 year period

The C4 Clustering Algorithm: Clusters of Galaxies in the Sloan Digital Sky Survey

We present the "C4 Cluster Catalog", a new sample of 748 clusters of galaxies identified in the spectroscopic sample of the Second Data Release (DR2) of the Sloan Digital Sky Survey (SDSS). The C4 cluster--finding algorithm identifies clusters as overdensities in a seven-dimensional position and color space, thus minimizing projection effects which plagued previous optical clusters selection. The present C4 catalog covers ~2600 square degrees of sky with groups containing 10 members to massive clusters having over 200 cluster members with redshifts. We provide cluster properties like sky location, mean redshift, galaxy membership, summed r--band optical luminosity (L_r), velocity dispersion, and measures of substructure. We use new mock galaxy catalogs to investigate the sensitivity to the various algorithm parameters, as well as to quantify purity and completeness. These mock catalogs indicate that the C4 catalog is ~90% complete and 95% pure above M_200 = 1x10^14 solar masses and within 0.03 <=z <= 0.12. The C4 algorithm finds 98% of X-ray identified clusters and 90% of Abell clusters within 0.03 <= z <= 0.12. We show that the L_r of a cluster is a more robust estimator of the halo mass (M_200) than the line-of-sight velocity dispersion or the richness of the cluster. L_r. The final SDSS data will provide ~2500 C4 clusters and will represent one of the largest and most homogeneous samples of local clusters.Comment: 32 pages of figures and text accepted in AJ. Electronic version with additional tables, links, and figures is available at http://www.ctio.noao.edu/~chrism/c

Relaxation time for a dimer covering with height representation

This paper considers the Monte Carlo dynamics of random dimer coverings of the square lattice, which can be mapped to a rough interface model. Two kinds of slow modes are identified, associated respectively with long-wavelength fluctuations of the interface height, and with slow drift (in time) of the system-wide mean height. Within a continuum theory, the longest relaxation time for either kind of mode scales as the system size N. For the real, discrete model, an exact lower bound of O(N) is placed on the relaxation time, using variational eigenfunctions corresponding to the two kinds of continuum modes.Comment: 12 pages, LaTeX; 1 figure in PostScript file; to appear, J. Stat. Phys. Sections and subsections were reshuffled to improve presentation, some text added on quantum-dimer model, fully-frustrated Ising model, and application to general class of "height" model

Obesity-induced insulin resistance in human skeletal muscle is characterised by defective activation of p42/p44 MAP kinase

Insulin resistance (IR), an impaired cellular, tissue and whole body response to insulin, is a major pathophysiological defect of type 2 diabetes mellitus. Although IR is closely associated with obesity, the identity of the molecular defect(s) underlying obesity-induced IR in skeletal muscle remains controversial; reduced post-receptor signalling of the insulin receptor substrate 1 (IRS1) adaptor protein and downstream effectors such as protein kinase B (PKB) have previously been implicated. We examined expression and/or activation of a number of components of the insulin-signalling cascade in skeletal muscle of 22 healthy young men (with body mass index (BMI) range, 20–37 kg/m2). Whole body insulin sensitivity (M value) and body composition was determined by the hyperinsulinaemic (40 mU. min−1.m−2.), euglycaemic clamp and by dual energy X-ray absorptiometry (DEXA) respectively. Skeletal muscle (vastus lateralis) biopsies were taken before and after one hour of hyperinsulinaemia and the muscle insulin signalling proteins examined by western blot and immunoprecipitation assay. There was a strong inverse relationship between M-value and BMI. The most striking abnormality was significantly reduced insulin-induced activation of p42/44 MAP kinase, measured by specific assay, in the volunteers with poor insulin sensitivity. However, there was no relationship between individuals' BMI or M-value and protein expression/phosphorylation of IRS1, PKB, or p42/44 MAP kinase protein, under basal or hyperinsulinaemic conditions. In the few individuals with poor insulin sensitivity but preserved p42/44 MAP kinase activation, other signalling defects were evident. These findings implicate defective p42/44 MAP kinase signalling as a potential contributor to obesity-related IR in a non-diabetic population, although clearly multiple signalling defects underlie obesity associated IR

Understanding Urban Demand for Wild Meat in Vietnam: Implications for Conservation Actions

Vietnam is a significant consumer of wildlife, particularly wild meat, in urban restaurant settings. To meet this demand, poaching of wildlife is widespread, threatening regional and international biodiversity. Previous interventions to tackle illegal and potentially unsustainable consumption of wild meat in Vietnam have generally focused on limiting supply. While critical, they have been impeded by a lack of resources, the presence of increasingly organised criminal networks and corruption. Attention is, therefore, turning to the consumer, but a paucity of research investigating consumer demand for wild meat will impede the creation of effective consumer-centred interventions. Here we used a mixed-methods research approach comprising a hypothetical choice modelling survey and qualitative interviews to explore the drivers of wild meat consumption and consumer preferences among residents of Ho Chi Minh City, Vietnam. Our findings indicate that demand for wild meat is heterogeneous and highly context specific. Wild-sourced, rare, and expensive wild meat-types are eaten by those situated towards the top of the societal hierarchy to convey wealth and status and are commonly consumed in lucrative business contexts. Cheaper, legal and farmed substitutes for wild-sourced meats are also consumed, but typically in more casual consumption or social drinking settings. We explore the implications of our results for current conservation interventions in Vietnam that attempt to tackle illegal and potentially unsustainable trade in and consumption of wild meat and detail how our research informs future consumer-centric conservation actions

AEGIS: Demographics of X-ray and Optically Selected AGNs

We develop a new diagnostic method to classify galaxies into AGN hosts, star-forming galaxies, and absorption-dominated galaxies by combining the [O III]/Hbeta ratio with rest-frame U-B color. This can be used to robustly select AGNs in galaxy samples at intermediate redshifts (z<1). We compare the result of this optical AGN selection with X-ray selection using a sample of 3150 galaxies with 0.3<z<0.8 and I_AB<22, selected from the DEEP2 Galaxy Redshift Survey and the All-wavelength Extended Groth Strip International Survey (AEGIS). Among the 146 X-ray sources in this sample, 58% are classified optically as emission-line AGNs, the rest as star-forming galaxies or absorption-dominated galaxies. The latter are also known as "X-ray bright, optically normal galaxies" (XBONGs). Analysis of the relationship between optical emission lines and X-ray properties shows that the completeness of optical AGN selection suffers from dependence on the star formation rate and the quality of observed spectra. It also shows that XBONGs do not appear to be a physically distinct population from other X-ray detected, emission-line AGNs. On the other hand, X-ray AGN selection also has strong bias. About 2/3 of all emission-line AGNs at L_bol>10^44 erg/s in our sample are not detected in our 200 ks Chandra images, most likely due to moderate or heavy absorption by gas near the AGN. The 2--7 keV detection rate of Seyfert 2s at z~0.6 suggests that their column density distribution and Compton-thick fraction are similar to that of local Seyferts. Multiple sample selection techniques are needed to obtain as complete a sample as possible.Comment: 24 pages, 14 figures, submitted to ApJ. Version 2 matches the ApJ accepted version. Sec 3 was reorganized and partly rewritten with one additional figure (Fig.3

A four-helix bundle stores copper for methane oxidation

Methane-oxidising bacteria (methanotrophs) require large quantities of copper for the membrane-bound (particulate) methane monooxygenase (pMMO). Certain methanotrophs are also able to switch to using the iron-containing soluble MMO (sMMO) to catalyse methane oxidation, with this switchover regulated by copper. MMOs are Nature’s primary biological mechanism for suppressing atmospheric levels of methane, a potent greenhouse gas. Furthermore, methanotrophs and MMOs have enormous potential in bioremediation and for biotransformations producing bulk and fine chemicals, and in bioenergy, particularly considering increased methane availability from renewable sources and hydraulic fracturing of shale rock. We have discovered and characterised a novel copper storage protein (Csp1) from the methanotroph Methylosinus trichosporium OB3b that is exported from the cytosol, and stores copper for pMMO. Csp1 is a tetramer of 4-helix bundles with each monomer binding up to 13 Cu(I) ions in a previously unseen manner via mainly Cys residues that point into the core of the bundle. Csp1 is the first example of a protein that stores a metal within an established protein-folding motif. This work provides a detailed insight into how methanotrophs accumulate copper for the oxidation of methane. Understanding this process is essential if the wide-ranging biotechnological applications of methanotrophs are to be realised. Cytosolic homologues of Csp1 are present in diverse bacteria thus challenging the dogma that such organisms do not use copper in this location