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  • Frontiers Media
  • Periodicals Archive Online (PAO)
  • 2020-2023  (145)
  • 2010-2014  (8,053)
  • 1995-1999  (3,483)
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  • 1
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    Constraints on superoxide mediated formation of manganese oxides (2014)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 262, doi:10.3389/fmicb.2013.00262.
    Description: Manganese (Mn) oxides are among the most reactive sorbents and oxidants within the environment, where they play a central role in the cycling of nutrients, metals, and carbon. Recent discoveries have identified superoxide (O−2) both of biogenic and abiogenic origin as an effective oxidant of Mn(II) leading to the formation of Mn oxides. Here we examined the conditions under which abiotically produced superoxide led to oxidative precipitation of Mn and the solid-phases produced. Oxidized Mn, as both aqueous Mn(III) and Mn(III/IV) oxides, was only observed in the presence of active catalase, indicating that hydrogen peroxide (H2O2), a product of the reaction of O−2 with Mn(II), inhibits the oxidation process presumably through the reduction of Mn(III). Citrate and pyrophosphate increased the yield of oxidized Mn but decreased the amount of Mn oxide produced via formation of Mn(III)-ligand complexes. While complexing ligands played a role in stabilizing Mn(III), they did not eliminate the inhibition of net Mn(III) formation by H2O2. The Mn oxides precipitated were highly disordered colloidal hexagonal birnessite, similar to those produced by biotically generated superoxide. Yet, in contrast to the large particulate Mn oxides formed by biogenic superoxide, abiotic Mn oxides did not ripen to larger, more crystalline phases. This suggests that the deposition of crystalline Mn oxides within the environment requires a biological, or at least organic, influence. This work provides the first direct evidence that, under conditions relevant to natural waters, oxidation of Mn(II) by superoxide can occur and lead to formation of Mn oxides. For organisms that oxidize Mn(II) by producing superoxide, these findings may also point to other microbially mediated processes, in particular enzymatic hydrogen peroxide degradation and/or production of organic ligand metabolites, that allow for Mn oxide formation.
    Description: This project was supported by the National Science Foundation, grants EAR-1245919/1025077 (awarded to Colleen M. Hansel and Bettina M. Voelker), and by the Radcliffe Institute for Advanced Study at Harvard University (through a fellowship to Bettina M. Voelker).
    Keywords: Manganese oxidation ; Manganese oxides ; Superoxide ; Reactive oxygen species ; Mn(III) complexes ; Organic ligands
    Repository Name: Woods Hole Open Access Server
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  • 2
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    The marine phosphorus cycle (2014)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 105, doi:10.3389/fmicb.2013.00105.
    Description: Phosphorus, the 13th element to be discovered on our planet, has a rich and varied history spanning match-making, bombs, fertilizer, and pesticides. Entire islands economies (Nauru) have collapsed in the mad hunt for phosphorus rock (Gowdy and McDaniel, 1999). Mineral reserves of this critical and valuable element are now being so rapidly mined from our Earth's crust that we are approaching a point where demand exceeds supply (Cordell et al., 2009). Why such a storied element? The answer rests in the fact that phosphorus is an essential ingredient in every known recipe for life: it is integral for energy storage, cell structure, and the very genetic material that encodes all life on the planet. Phosphorus is in fact, the staff of life (Karl, 2000), the scaffolding on which all biomass is built. Just as phosphorus fertilizer supports the growth of agricultural crops, phosphorus supply supports the growth of photosynthetic organisms, or phytoplankton, at the base of the marine food web.
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  • 3
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    Next-generation transgenic mice for optogenetic analysis of neural circuits (2014)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Neural Circuits 7 (2013): 160, doi:10.3389/fncir.2013.00160.
    Description: Here we characterize several new lines of transgenic mice useful for optogenetic analysis of brain circuit function. These mice express optogenetic probes, such as enhanced halorhodopsin or several different versions of channelrhodopsins, behind various neuron-specific promoters. These mice permit photoinhibition or photostimulation both in vitro and in vivo. Our results also reveal the important influence of fluorescent tags on optogenetic probe expression and function in transgenic mice.
    Description: This work was supported by a CRP grant from the National Research Foundation of Singapore and by the World Class Institute (WCI )Program of the National Research Foundation of Korea (NRF )funded by the Ministry of Education, Science and Technology of Korea (MEST) (NRF Grant Number: WCI2009-003).
    Keywords: Optogenetics ; Channelrhodopsin ; Photostimulation ; Photoinhibition ; Cerebellum ; Cortex ; Hippocampus ; Pons
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Estimated tissue and blood N2 levels and risk of decompression sickness in deep-, intermediate-, and shallow-diving toothed whales during exposure to naval sonar (2014)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Physiology 3 (2012): 125, doi:10.3389/fphys.2012.00125.
    Description: Naval sonar has been accused of causing whale stranding by a mechanism which increases formation of tissue N2 gas bubbles. Increased tissue and blood N2 levels, and thereby increased risk of decompression sickness (DCS), is thought to result from changes in behavior or physiological responses during diving. Previous theoretical studies have used hypothetical sonar-induced changes in both behavior and physiology to model blood and tissue N2 tension (PN2), but this is the first attempt to estimate the changes during actual behavioral responses to sonar. We used an existing mathematical model to estimate blood and tissue N2 tension (PN2) from dive data recorded from sperm, killer, long-finned pilot, Blainville’s beaked, and Cuvier’s beaked whales before and during exposure to Low- (1–2 kHz) and Mid- (2–7 kHz) frequency active sonar. Our objectives were: (1) to determine if differences in dive behavior affects risk of bubble formation, and if (2) behavioral- or (3) physiological responses to sonar are plausible risk factors. Our results suggest that all species have natural high N2 levels, with deep diving generally resulting in higher end-dive PN2 as compared with shallow diving. Sonar exposure caused some changes in dive behavior in both killer whales, pilot whales and beaked whales, but this did not lead to any increased risk of DCS. However, in three of eight exposure session with sperm whales, the animal changed to shallower diving, and in all these cases this seem to result in an increased risk of DCS, although risk was still within the normal risk range of this species. When a hypothetical removal of the normal dive response (bradycardia and peripheral vasoconstriction), was added to the behavioral response during model simulations, this led to an increased variance in the estimated end-dive N2 levels, but no consistent change of risk. In conclusion, we cannot rule out the possibility that a combination of behavioral and physiological responses to sonar have the potential to alter the blood and tissue end-dive N2 tension to levels which could cause DCS and formation of in vivo bubbles, but the actually observed behavioral responses of cetaceans to sonar in our study, do not imply any significantly increased risk of DCS.
    Description: This study was funded by the Norwegian Ministry of Defence, US-Office of Naval Research, the Netherlands Ministry of Defence, the Norwegian Research Council and WWF-Norway.
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Differential responses of ammonia-oxidizing archaea and bacteria to long-term fertilization in a New England salt marsh (2013)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Aquatic Microbiology 3 (2013): 445, doi:10.3389/fmicb.2012.00445.
    Description: Since the discovery of ammonia-oxidizing archaea (AOA), new questions have arisen about population and community dynamics and potential interactions between AOA and ammonia-oxidizing bacteria (AOB). We investigated the effects of long-term fertilization on AOA and AOB in the Great Sippewissett Marsh, Falmouth, MA, USA to address some of these questions. Sediment samples were collected from low and high marsh habitats in July 2009 from replicate plots that received low (LF), high (HF), and extra high (XF) levels of a mixed NPK fertilizer biweekly during the growing season since 1974. Additional untreated plots were included as controls (C). Terminal restriction fragment length polymorphism analysis of the amoA genes revealed distinct shifts in AOB communities related to fertilization treatment, but the response patterns of AOA were less consistent. Four AOB operational taxonomic units (OTUs) predictably and significantly responded to fertilization, but only one AOA OTU showed a significant pattern. Betaproteobacterial amoA gene sequences within the Nitrosospira-like cluster dominated at C and LF sites, while sequences related to Nitrosomonas spp. dominated at HF and XF sites. We identified some clusters of AOA sequences recovered primarily from high fertilization regimes, but other clusters consisted of sequences recovered from all fertilization treatments, suggesting greater physiological diversity. Surprisingly, fertilization appeared to have little impact on abundance of AOA or AOB. In summary, our data reveal striking patterns for AOA and AOB in response to long-term fertilization, and also suggest a missing link between community composition and abundance and nitrogen processing in the marsh.
    Description: This work was supported in part by the National Science Foundation award DEB-0814586 (to Anne E. Bernhard). Additional support was provided by the George and Carol Milne Endowment at Connecticut College.
    Keywords: AmoA ; TRFLP ; Great Sippewissett Marsh ; Fertilization ; Salt marsh
    Repository Name: Woods Hole Open Access Server
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  • 6
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    Proteomic responses of oceanic Synechococcus WH8102 to phosphate and zinc scarcity and cadmium additions (2014)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 387, doi:10.3389/fmicb.2013.00387.
    Description: Synechococcus sp. WH 8102 is a motile marine cyanobacterium isolated originally from the Sargasso Sea. To test the response of this organism to cadmium (Cd), generally considered a toxin, cultures were grown in a matrix of high and low zinc (Zn) and phosphate (PO43−) and were then exposed to an addition of 4.4 pM free Cd2+ at mid-log phase and harvested after 24 h. Whereas Zn and PO43− had little effect on overall growth rates, in the final 24 h of the experiment three growth effects were noticed: (i) low PO43− treatments showed increased growth rates relative to high PO43− treatments, (ii) the Zn/high PO43− treatment appeared to enter stationary phase, and (iii) Cd increased growth rates further in both the low PO43− and Zn treatments. Global proteomic analysis revealed that: (i) Zn appeared to be critical to the PO43− response in this organism, (ii) bacterial metallothionein (SmtA) appears correlated with PO43− stress-associated proteins, (iii) Cd has the greatest influence on the proteome at low PO43− and Zn, (iv) Zn buffered the effects of Cd, and (v) in the presence of both replete PO43− and added Cd the proteome showed little response to the presence of Zn. Similar trends in alkaline phosphate (ALP) and SmtA suggest the possibility of a Zn supply system to provide Zn to ALP that involves SmtA. In addition, proteome results were consistent with a previous transcriptome study of PO43− stress (with replete Zn) in this organism, including the greater relative abundance of ALP (PhoA), ABC phosphate binding protein (PstS) and other proteins. Yet with no Zn in this proteome experiment the PO43− response was quite different including the greater relative abundance of five hypothetical proteins with no increase in PhoA or PstS, suggesting that Zn nutritional levels are connected to the PO43− response in this cyanobacterium. Alternate ALP PhoX (Ca) was found to be a low abundance protein, suggesting that PhoA (Zn, Mg) may be more environmentally relevant than PhoX.
    Description: We would like to thank the Gordon and Betty Moore Foundation (#2724), C-MORE, the Office of Naval Research, and NSF Chemical Oceanography (OCE-1031271, OCE-1233261, OCE-1220484) for support.
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  • 7
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    Deep subsurface microbiology : a guide to the research topic papers (2014)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 122, doi:10.3389/fmicb.2013.00122.
    Description: Deep subsurface microbiology is a rising field in geomicrobiology, environmental microbiology and microbial ecology that focuses on the molecular detection and quantification, cultivation, biogeographic examination, and distribution of bacteria, archaea, and eukarya that permeate the subsurface biosphere. The deep biosphere includes a variety of subsurface habitats, such as terrestrial deep aquifer systems or mines, deeply buried hydrocarbon reservoirs, marine sediments and the basaltic ocean crust. The deep subsurface biosphere abounds with uncultured, only recently discovered and—at best—incompletely understood microbial populations. So far, microbial cells and DNA remain detectable at sediment depths of more than 1 km and life appears limited mostly by heat in the deep subsurface. Severe energy limitation, either as electron acceptor or donor shortage, and scarcity of microbially degradable organic carbon sources are among the evolutionary pressures that may shape the genomic and physiological repertoire of the deep subsurface biosphere. Its biogeochemical importance in long-term carbon sequestration, subsurface elemental cycling and crustal aging, is a major focus of current research at the interface of microbiology, geochemistry, and biosphere/geosphere evolution.
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  • 8
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    Microbes in nature are limited by carbon and energy : the starving-survival lifestyle in soil and consequences for estimating microbial rates (2014)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 324, doi:10.3389/fmicb.2013.00324.
    Description: Understanding microbial transformations in soils is important for predicting future carbon sequestration and nutrient cycling. This review questions some methods of assessing one key microbial process, the uptake of labile organic compounds. First, soil microbes have a starving-survival life style of dormancy, arrested activity, and low activity. Yet they are very abundant and remain poised to completely take up all substrates that become available. As a result, dilution assays with the addition of labeled substrates cannot be used. When labeled substrates are transformed into 14CO2, the first part of the biphasic release follows metabolic rules and is not affected by the environment. As a consequence, when identical amounts of isotopically substrates are added to soils from different climate zones, the same percentage of the substrate is respired and the same half-life of the respired 14CO2 from the labeled substrate is estimated. Second, when soils are sampled by a variety of methods from taking 10 cm diameter cores to millimeter-scale dialysis chambers, amino acids (and other organic compounds) appear to be released by the severing of fine roots and mycorrhizal networks as well as from pressing or centrifuging treatments. As a result of disturbance as well as of natural root release, concentrations of individual amino acids of ~10 μM are measured. This contrasts with concentrations of a few nanomolar found in aquatic systems and raises questions about possible differences in the bacterial strategy between aquatic and soil ecosystems. The small size of the hyphae (2–10 μm diameter) and of the fine roots (0.2–2 mm diameter), make it very difficult to sample any volume of soil without introducing artifacts. Third, when micromolar amounts of labeled amino acids are added to soil, some of the isotope enters plant roots. This may be an artifact of the high micromolar concentrations applied.
    Description: This work was supported by the National Science Foundation’s Office of Polar Programs (1108074), Division of Environmental Biology (1026843 and 0423385), and Division of Ocean Sciences (OCE-1238212).
    Keywords: Microbes ; Soil ; Water ; Activity ; Labeled substrate ; Amino acids ; Sugars
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  • 9
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    Editorial: role of protein palmitoylation in synaptic plasticity and neuronal differentiation (2020)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Yoshii, A., & Green, W. N. Editorial: role of protein palmitoylation in synaptic plasticity and neuronal differentiation. Frontiers in Synaptic Neuroscience, 12(27), (2020), doi:10.3389/fnsyn.2020.00027.
    Description: Protein palmitoylation, the reversible addition of palmitate to proteins, is a dynamic post-translational modification. Both membrane (e.g., channels, transporters, and receptors) and cytoplasmic proteins (e.g., cell adhesion, scaffolding, cytoskeletal, and signaling molecules) are substrates. In mammals, palmitoylation is mediated by 23-24 palmitoyl acyltransferases (PATs), also called ZDHHCs for their catalytic aspartate-histidine-histidine-cysteine (DHCC) domain. PATs are integral membrane proteins found in cellular membranes. In the palmitoylation cycle, palmitate is removed by the depalmitoylation enzymes, acyl palmitoyl transferases (APT1 and 2), and α/β Hydrolase domain-containing protein 17 (ABHD17A-C). These are cytoplasmic proteins that are targeted to membranes where they are substrates for PATs. The second class of depalmitoylating enzymes are palmitoyl thioesterases, PPT1 and 2, discovered through their association with infantile neuronal ceroid lipofuscinosis. These are secreted proteins found in the lumen of intracellular organelles, primarily lysosomes, where their function as depalmitoylating enzymes is unclear.
    Description: This work was supported by University of Illinois start-up fund (to AY) and NIH/NIDA (grant DA044760 to WG).
    Keywords: palmitoylation and depalmitoylation ; synaptic plasticity ; axonal growth ; lysosome ; neurodegenerative disease ; neuronal ceroid lipofuscinoses (NCL) ; Huntington disease
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  • 10
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    The use of diagnostic imaging for identifying abnormal gas accumulations in cetaceans and pinnipeds (2014)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Physiology 3 (2012): 181, doi:10.3389/fphys.2012.00181.
    Description: Recent dogma suggested that marine mammals are not at risk of decompression sickness due to a number of evolutionary adaptations. Several proposed adaptations exist. Lung compression and alveolar collapse that terminate gas-exchange before a depth is reached where supersaturation is significant and bradycardia with peripheral vasoconstriction affecting the distribution, and dynamics of blood and tissue nitrogen levels. Published accounts of gas and fat emboli and dysbaric osteonecrosis in marine mammals and theoretical modeling have challenged this view-point, suggesting that decompression-like symptoms may occur under certain circumstances, contrary to common belief. Diagnostic imaging modalities are invaluable tools for the non-invasive examination of animals for evidence of gas and have been used to demonstrate the presence of incidental decompression-related renal gas accumulations in some stranded cetaceans. Diagnostic imaging has also contributed to the recognition of clinically significant gas accumulations in live and dead cetaceans and pinnipeds. Understanding the appropriate application and limitations of the available imaging modalities is important for accurate interpretation of results. The presence of gas may be asymptomatic and must be interpreted cautiously alongside all other available data including clinical examination, clinical laboratory testing, gas analysis, necropsy examination, and histology results.
    Keywords: Computed tomography ; Ultrasound ; Magnetic resonance imaging ; Cetacean ; Decompression sickness ; Bends ; Pinniped ; Gas bubbles
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