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Sample records for microbial cell cycle

  1. The microbial cell cycle

    SciTech Connect

    Nurse, P.; Streiblova, E.

    1984-01-01

    This book concentrates on the major problems of cell cycle control in microorganisms. A wide variety of microorganisms, ranging from bacteria and yeasts to hyphal fungi, algae, and ciliates are analyzed, with emphasis on the basic similarities among the organisms. Different ways of looking at cell cycle control which emphasize aspects of the problem such as circadian rhythms, limit cycle oscillators, and cell size models, are considered. New approaches such as the study of cell cycle mutants, and cloning of cell cycle control genes are also presented.

  2. Single cell visualization of sulfur cycling in intertidal microbial mats

    NASA Astrophysics Data System (ADS)

    Dawson, K.; Green, A.; Orphan, V. J.

    2014-12-01

    Chemoautrophic microbial mats form in shallow intertidal pools adjacent to sulfidic hydrothermal vents in San Pedro, CA. Sulfide is primarily geologically derived. However, microscopy revealed deltaproteobacteria closely associated with Beggiatoa -like filaments, indicating an additional biogenic sulfide source, derived from sulfate reduction or sulfur disproportionation. At small scales the intercellular interaction of sulfide producing and sulfide consuming bacteria may play a important role in biogeochemical sulfur cycling. We explored the intracellular transfer of biologically derived sulfide in this system with triple and quadruple stable isotope labeling experiments: 13C, 15N, 33S, and 34S. Silicon wafers colonized by microbial mats in situ, were then incubated with 34SO42- or 34SO42- and 33S0 as well as 13C-acetate and 15NH4+and analyzed by fluorescent in situ hybridization (FISH) coupled to nanometer-scale secondary ion mass spectrometry (NanoSIMS). We observed enrichment of 34S and 33S in both deltaproteobacteria and sulfide oxidizing gammaproteobacteria. Greater enrichment relative to killed controls occurred in deltaproteobacteria than the sulfide oxidizers during both sulfate reducing (Δ34Sdelta-killed = 240‰, Δ34Sgamma-killed = 40‰) and sulfur disproportionating incubations (Δ33Sdelta-killed = 1730‰, Δ33Sgamma-killed = 1050‰). These results provide a direct visualization of interspecies sulfur transfer and indicate that biogenic sulfide derived from either sulfate or intermediate oxidation state sulfur species plays a role in sulfur cycling in this system.

  3. Duty Cycling Influences Current Generation in Multi-Anode Environmental Microbial Fuel Cells

    SciTech Connect

    Gardel, EJ; Nielsen, ME; Grisdela, PT; Girguis, PR

    2012-05-01

    Improving microbial fuel cell (MFC) performance continues to be the subject of research, yet the role of operating conditions, specifically duty cycling, on MFC performance has been modestly addressed. We present a series of studies in which we use a 15-anode environmental MFC to explore how duty cycling (variations in the time an anode is connected) influences cumulative charge, current, and microbial composition. The data reveal particular switching intervals that result in the greatest time-normalized current. When disconnection times are sufficiently short, there is a striking decrease in current due to an increase in the overall electrode reaction resistance. This was observed over a number of whole cell potentials. Based on these results, we posit that replenishment of depleted electron donors within the biofilm and surrounding diffusion layer is necessary for maximum charge transfer, and that proton flux may be not limiting in the highly buffered aqueous phases that are common among environmental MFCs. Surprisingly, microbial diversity analyses found no discernible difference in gross community composition among duty cycling treatments, suggesting that duty cycling itself has little or no effect. Such duty cycling experiments are valuable in determining which factors govern performance of bioelectrochemical systems and might also be used to optimize field-deployed systems.

  4. The microbial nitrogen cycle.

    PubMed

    Jetten, Mike S M

    2008-11-01

    This special issue highlights several recent discoveries in the microbial nitrogen cycle including the diversity of nitrogen-fixing bacteria in special habitats, distribution and contribution of aerobic ammonium oxidation by bacteria and crenarchaea in various aquatic and terrestrial ecosystems, regulation of metabolism in nitrifying bacteria, the molecular diversity of denitrifying microorganisms and their enzymes, the functional diversity of freshwater and marine anammox bacteria, the physiology of nitrite-dependent anaerobic methane oxidation and the degradation of recalcitrant organic nitrogen compounds. Simultaneously the articles in this issue show that many questions still need to be addressed, and that the microbes involved in catalyzing the nitrogen conversions still harbour many secrets that need to be disclosed to fully understand the biogeochemical nitrogen cycle, and make future predictions and global modelling possible.

  5. [Microbial geochemical calcium cycle].

    PubMed

    Zavarzin, G A

    2002-01-01

    The participation of microorganisms in the geochemical calcium cycle is the most important factor maintaining neutral conditions on the Earth. This cycle has profound influence on the fate of inorganic carbon, and, thereby, on the removal of CO2 from the atmosphere. The major part of calcium deposits was formed in the Precambrian, when prokaryotic biosphere predominated. After that, calcium recycling based on biogenic deposition by skeletal organisms became the main process. Among prokaryotes, only a few representatives, e.g., cyanobacteria, exhibit a special calcium function. The geochemical calcium cycle is made possible by the universal features of bacteria involved in biologically mediated reactions and is determined by the activities of microbial communities. In the prokaryotic system, the calcium cycle begins with the leaching of igneous rock predominantly through the action of the community of organotrophic organisms. The release of carbon dioxide to the soil air by organotrophic aerobes leads to leaching with carbonic acid and soda salinization. Under anoxic conditions, of major importance is the organic acid production by primary anaerobes (fermentative microorganisms). Calcium carbonate is precipitated by secondary anaerobes (sulfate reducers) and to a smaller degree by methanogens. The role of the cyanobacterial community in carbonate deposition is exposed by stromatolites, which are the most common organo-sedimentary Precambrian structures. Deposition of carbonates in cyanobacterial mats as a consequence of photoassimilation of CO2 does not appear to be a significant process. It is argued that carbonates were deposited at the boundary between the "soda continent", which emerged as a result of subaerial leaching with carbonic acid, and the ocean containing Ca2+. Such ecotones provided favorable conditions for the development of the benthic cyanobacterial community, which was a precursor of stromatolites.

  6. A microbial avenue to cell cycle control in the plant superkingdom.

    PubMed

    Tulin, Frej; Cross, Frederick R

    2014-10-01

    Research in yeast and animals has resulted in a well-supported consensus model for eukaryotic cell cycle control. The fit of this model to early diverging eukaryotes, such as the plant kingdom, remains unclear. Using the green alga Chlamydomonas reinhardtii, we developed an efficient pipeline, incorporating robotics, semiautomated image analysis, and deep sequencing, to molecularly identify >50 genes, mostly conserved in higher plants, specifically required for cell division but not cell growth. Mutated genes include the cyclin-dependent kinases CDKA (resembling yeast and animal Cdk1) and the plant-specific CDKB. The Chlamydomonas cell cycle consists of a long G1 during which cells can grow >10-fold, followed by multiple rapid cycles of DNA replication and segregation. CDKA and CDKB execute nonoverlapping functions: CDKA promotes transition between G1 and entry into the division cycle, while CDKB is essential specifically for spindle formation and nuclear division, but not for DNA replication, once CDKA-dependent initiation has occurred. The anaphase-promoting complex is required for similar steps in the Chlamydomonas cell cycle as in Opisthokonts; however, the spindle assembly checkpoint, which targets the APC in Opisthokonts, appears severely attenuated in Chlamydomonas, based on analysis of mutants affecting microtubule function. This approach allows unbiased integration of the consensus cell cycle control model with innovations specific to the plant lineage.

  7. A Microbial Avenue to Cell Cycle Control in the Plant Superkingdom[C][W][OPEN

    PubMed Central

    Tulin, Frej; Cross, Frederick R.

    2014-01-01

    Research in yeast and animals has resulted in a well-supported consensus model for eukaryotic cell cycle control. The fit of this model to early diverging eukaryotes, such as the plant kingdom, remains unclear. Using the green alga Chlamydomonas reinhardtii, we developed an efficient pipeline, incorporating robotics, semiautomated image analysis, and deep sequencing, to molecularly identify >50 genes, mostly conserved in higher plants, specifically required for cell division but not cell growth. Mutated genes include the cyclin-dependent kinases CDKA (resembling yeast and animal Cdk1) and the plant-specific CDKB. The Chlamydomonas cell cycle consists of a long G1 during which cells can grow >10-fold, followed by multiple rapid cycles of DNA replication and segregation. CDKA and CDKB execute nonoverlapping functions: CDKA promotes transition between G1 and entry into the division cycle, while CDKB is essential specifically for spindle formation and nuclear division, but not for DNA replication, once CDKA-dependent initiation has occurred. The anaphase-promoting complex is required for similar steps in the Chlamydomonas cell cycle as in Opisthokonts; however, the spindle assembly checkpoint, which targets the APC in Opisthokonts, appears severely attenuated in Chlamydomonas, based on analysis of mutants affecting microtubule function. This approach allows unbiased integration of the consensus cell cycle control model with innovations specific to the plant lineage. PMID:25336509

  8. Microbial Fuel Cell as Life Detector: Arsenic Cycling in Hypersaline Environments

    NASA Astrophysics Data System (ADS)

    Miller, L. G.; Blum, J. S.; Oremland, R. S.

    2006-12-01

    Detection of extant life on Mars or Europa is a future goal of exobiology. For the present, biosignatures arising from life in extreme environments on Earth suggest how to search for life elsewhere. One such biosignature is the electrical current derived from the metabolic activity of microorganisms, which may be measured using microbial fuel cells (MFCs). MFCs generate electricity by coupling bacterially mediated redox transformations to electrochemical reactions through a circuit. Our laboratory fuel cell employs solid graphite electrodes and uses a proton exchange membrane to separate anode (anaerobic) and cathode (aerobic) chambers. Mineral salts media are circulated by peristaltic pump through the chambers and through temperature-controlled reservoirs that are sparged with nitrogen (anode) or oxygen (cathode). In experiments with pure cultures, bacteria reduced arsenate to arsenite in the anode chamber, and produced electrical power in the process. Power production was sustained in the MFC only while bacteria were active. An arsenate respiring bacterium, Bacillus selenitireducens, isolated from moderately-hypersaline Mono Lake, CA grew on lactate using arsenate as the electron acceptor and also grew without arsenate, using the anode as the electron acceptor. Power densities (per unit area of anode surface) of 60 μW m-2 were achieved during growth without arsenate. Less power (3 μW m-2) was produced when arsenate was available because arsenate acted as an alternate electron acceptor to the anode. Another arsenate respiring bacterium, strain SLAS-1, isolated from extremely-hypersaline Searles Lake, CA respired lactate and reduced arsenate in the MFC, albeit more slowly. An arsenite oxidizing bacterium, Alkalilimnicola ehrlichii, isolated from Mono Lake will also be tested for its ability to generate electricity before proceeding to an examination of biocurrent production using natural sediments and waters from Mono Lake and Searles Lake.

  9. Microbial Regulation of Glucose Metabolism and Cell-Cycle Progression in Mammalian Colonocytes

    PubMed Central

    Donohoe, Dallas R.; Wali, Aminah; Brylawski, Bruna P.; Bultman, Scott J.

    2012-01-01

    A prodigious number of microbes inhabit the human body, especially in the lumen of the gastrointestinal (GI) tract, yet our knowledge of how they regulate metabolic pathways within our cells is rather limited. To investigate the role of microbiota in host energy metabolism, we analyzed ATP levels and AMPK phosphorylation in tissues isolated from germfree and conventionally-raised C57BL/6 mice. These experiments demonstrated that microbiota are required for energy homeostasis in the proximal colon to a greater extent than other segments of the GI tract that also harbor high densities of bacteria. This tissue-specific effect is consistent with colonocytes utilizing bacterially-produced butyrate as their primary energy source, whereas most other cell types utilize glucose. However, it was surprising that glucose did not compensate for butyrate deficiency. We measured a 3.5-fold increase in glucose uptake in germfree colonocytes. However, 13C-glucose metabolic-flux experiments and biochemical assays demonstrated that they shifted their glucose metabolism away from mitochondrial oxidation/CO2 production and toward increased glycolysis/lactate production, which does not yield enough ATPs to compensate. The mechanism responsible for this metabolic shift is diminished pyruvate dehydrogenase (PDH) levels and activity. Consistent with perturbed PDH function, the addition of butyrate, but not glucose, to germfree colonocytes ex vivo stimulated oxidative metabolism. As a result of this energetic defect, germfree colonocytes exhibited a partial block in the G1-to-S-phase transition that was rescued by a butyrate-fortified diet. These data reveal a mechanism by which microbiota regulate glucose utilization to influence energy homeostasis and cell-cycle progression of mammalian host cells. PMID:23029553

  10. Interconnection between tricarboxylic acid cycle and energy generation in microbial fuel cell performed by desulfuromonas acetoxidans IMV B-7384

    NASA Astrophysics Data System (ADS)

    Vasyliv, Oresta M.; Maslovska, Olga D.; Ferensovych, Yaroslav P.; Bilyy, Oleksandr I.; Hnatush, Svitlana O.

    2015-05-01

    Desulfuromonas acetoxidans IMV B-7384 is exoelectrogenic obligate anaerobic sulfur-reducing bacterium. Its one of the first described electrogenic bacterium that performs complete oxidation of an organic substrate with electron transfer directly to the electrode in microbial fuel cell (MFC). This bacterium is very promising for MFC development because of inexpensive cultivation medium, high survival rate and selective resistance to various heavy metal ions. The size of D. acetoxidans IMV B-7384 cells is comparatively small (0.4-0.8×1-2 μm) that is highly beneficial while application of porous anode material because of complete bacterial cover of an electrode area with further significant improvement of the effectiveness of its usage. The interconnection between functioning of reductive stage of tricarboxylic acid (TCA) cycle under anaerobic conditions, and MFC performance was established. Malic, pyruvic, fumaric and succinic acids in concentration 42 mM were separately added into the anode chamber of MFC as the redox agents. Application of malic acid caused the most stabile and the highest power generation in comparison with other investigated organic acids. Its maximum equaled 10.07±0.17mW/m2 on 136 hour of bacterial cultivation. Under addition of pyruvic, succinic and fumaric acids into the anode chamber of MFC the maximal power values equaled 5.80±0.25 mW/m2; 3.2±0.11 mW/m2, and 2.14±0.19 mW/m2 respectively on 40, 56 and 32 hour of bacterial cultivation. Hence the malic acid conversion via reductive stage of TCA cycle is shown to be the most efficient process in terms of electricity generation by D. acetoxidans IMV B-7384 in MFC under anaerobic conditions.

  11. Microbial extracellular enzymes and the marine carbon cycle.

    PubMed

    Arnosti, Carol

    2011-01-01

    Extracellular enzymes initiate microbial remineralization of organic matter by hydrolyzing substrates to sizes sufficiently small to be transported across cell membranes. As much of marine primary productivity is processed by heterotrophic microbes, the substrate specificities of extracellular enzymes, the rates at which they function in seawater and sediments, and factors controlling their production, distribution, and active lifetimes, are central to carbon cycling in marine systems. In this review, these topics are considered from biochemical, microbial/molecular biological, and geochemical perspectives. Our understanding of the capabilities and limitations of heterotrophic microbial communities has been greatly advanced in recent years, in part through genetic and genomic approaches. New methods to measure enzyme activities in the field are needed to keep pace with these advances and to pursue intriguing evidence that patterns of enzyme activities in different environments are linked to differences in microbial community composition that may profoundly affect the marine carbon cycle.

  12. Nitrogen cycle in microbial mats: completely unknown?

    NASA Astrophysics Data System (ADS)

    Coban, O.; Bebout, B.

    2015-12-01

    Microbial mats are thought to have originated around 3.7 billion years ago, most likely in the areas around submarine hydrothermal vents, which supplied a source of energy in the form of reduced chemical species from the Earth's interior. Active hydrothermal vents are also believed to exist on Jupiter's moon Europa, Saturn's moon Enceladus, and on Mars, earlier in that planet's history. Microbial mats have been an important force in the maintenance of Earth's ecosystems and the first photosynthesis was also originated there. Microbial mats are believed to exhibit most, if not all, biogeochemical processes that exist in aquatic ecosystems, due to the presence of different physiological groups of microorganisms therein. While most microbially mediated biogeochemical transformations have been shown to occur within microbial mats, the nitrogen cycle in the microbial mats has received very little study in spite of the fact that nitrogen usually limits growth in marine environments. We will present the first results in the determination of a complete nitrogen budget for a photosynthetic microbial mat. Both in situ sources and sinks of nitrogen in photosynthetic microbial mats are being measured using stable isotope techniques. Our work has a particular focus on recently described, but poorly understood, processes, e.g., anammox and dissimilatory nitrate reduction, and an emphasis on understanding the role that nitrogen cycling may play in generating biogenic nitrogen isotopic signatures and biomarker molecules. Measurements of environmental controls on nitrogen cycling should offer insight into the nature of co-evolution of these microbial communities and their planets of origin. Identifying the spatial (microscale) as well as temporal (diel and seasonal) distribution of nitrogen transformations, e.g., rates of nitrification and denitrification, within mats, particularly with respect to the distribution of photosynthetically-produced oxygen, is anticipated. The results

  13. Simulated Carbon Cycling in a Model Microbial Mat.

    NASA Astrophysics Data System (ADS)

    Decker, K. L.; Potter, C. S.

    2006-12-01

    We present here the novel addition of detailed organic carbon cycling to our model of a hypersaline microbial mat ecosystem. This ecosystem model, MBGC (Microbial BioGeoChemistry), simulates carbon fixation through oxygenic and anoxygenic photosynthesis, and the release of C and electrons for microbial heterotrophs via cyanobacterial exudates and also via a pool of dead cells. Previously in MBGC, the organic portion of the carbon cycle was simplified into a black-box rate of accumulation of simple and complex organic compounds based on photosynthesis and mortality rates. We will discuss the novel inclusion of fermentation as a source of carbon and electrons for use in methanogenesis and sulfate reduction, and the influence of photorespiration on labile carbon exudation rates in cyanobacteria. We will also discuss the modeling of decomposition of dead cells and the ultimate release of inorganic carbon. The detailed modeling of organic carbon cycling is important to the accurate representation of inorganic carbon flux through the mat, as well as to accurate representation of growth models of the heterotrophs under different environmental conditions. Because the model ecosystem is an analog of ancient microbial mats that had huge impacts on the atmosphere of early earth, this MBGC can be useful as a biological component to either early earth models or models of other planets that potentially harbor life.

  14. Optimization of bioelectricity generation in fed-batch microbial fuel cell: effect of electrode material, initial substrate concentration, and cycle time.

    PubMed

    Cirik, Kevser

    2014-05-01

    Effective wastewater treatment and electricity generation using dual-chamber microbial fuel cell (MFC) will require a better understanding of how operational parameters affect system performance. Therefore, the main aim of this study is to investigate the bioelectricity production in a dual-chambered MFC-operated batch mode under different operational conditions. Initially, platinum (Pt) and mixed metal oxide titanium (Ti-TiO2) electrodes were used to investigate the influence of the electrode materials on the power generation at initial dissolved organic carbon (DOC) concentration of 400 mg/L and cycle time of 15 days. MFC equipped with Ti-TiO2 electrode performed better and was used to examine the effect of influent DOC concentration and cycle time on MFC performance. Increasing influent DOC concentration resulted in improving electricity generation, corresponding to a 1.65-fold increase in power density. However, decrease in cycle time from 15 to 5 days adversely affected reactor performance. Maximum DOC removal was 90 ± 3 %, which was produced at 15-day cycle time with an initial DOC of 3,600 mg/L, corresponding to maximum power generation of about 7,205 mW/m(2).

  15. Applications of Microbial Cell Sensors

    NASA Astrophysics Data System (ADS)

    Shimomura-Shimizu, Mifumi; Karube, Isao

    Since the first microbial cell sensor was studied by Karube et al. in 1977, many types of microbial cell sensors have been developed as analytical tools. The microbial cell sensor utilizes microbes as a sensing element and a transducer. The characteristics of microbial cell sensors as sensing devices are a complete contrast to those of enzyme sensors or immunosensors, which are highly specific for the substrates of interest, although the specificity of the microbial cell sensor has been improved by genetic modification of the microbe used as the sensing element. Microbial cell sensors have the advantages of tolerance to measuring conditions, a long lifetime, and good cost performance, and have the disadvantage of a long response time. In this review, applications of microbial cell sensors are summarized.

  16. Microbial community profiles and microbial carbon cycling in Orca Basin

    NASA Astrophysics Data System (ADS)

    Hyde, A.; Teske, A.; Joye, S. B.; Montoya, J. P.; Nigro, L.

    2016-12-01

    Orca Basin is the largest seafloor brine pools in the world, covering over 400 km2 and reaching brine layer depths of 200 m. The brine pool contains water 8 times denser than the overlying seawater and is separated from the overlying water column by a sharp pycnocline that prevents vertical mixing. The transition from ambient seawater to brine occurs over 100 m [2150 to 2250 m] and is characterized by distinct changes in temperature, salinity, chemical conditions, oxygen, and organic matter concentration. The sharp brine-seawater interface results in a sharp pycnocline, which serves as a particle trap for sinking marine organic matter. Previous studies have used lipids to show that this organic-rich interface is host to an active microbial community which is potentially involved in deep-sea carbon remineralization and metal-cycling. Additionally, previous work on methane, ethane, and propane concentrations and 13C-isotopic signatures has also implicated the brine pool, as well as the interface, as sources for biogenic low-molecular weight hydrocarbons, resulting from the high concentration of suspended organic matter above and within the brine pool. Here we investigate the profiles of microbial community composition and metabolic potential in Orca Basin, ranging from seawater through the Orca Basin chemocline and into the deep Orca Basin brine. To characterize the microbial community and stratification, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing of filtered water above, within, and below the Orca Basin chemocline. Our sequence data shows that three distinct and unique communities exist in the Orca Basin water column. We also use thermodynamic modeling of hydrocarbon degradation to investigate the favorability of C1-C3 hydrocarbon oxidation at the brine-seawater interface and the potential for Orca Basin to serve as a deep-sea hydrocarbon sink.

  17. Microbial Cell Imaging

    SciTech Connect

    Doktycz, Mitchel John; Sullivan, Claretta; Mortensen, Ninell P; Allison, David P

    2011-01-01

    the maximum scan size (roughly 100 x 100 {mu}m) and the restricted movement of the cantilever in the Z (or height) direction. In most commercial AFMs, the Z range is restricted to roughly 10 {mu}m such that the height of cells to be imaged must be seriously considered. Nevertheless, AFM can provide structural-functional information at nanometer resolution and do so in physiologically relevant environments. Further, instrumentation for scanning probe microscopy continues to advance. Systems for high-speed imaging are becoming available, and techniques for looking inside the cells are being demonstrated. The ability to combine AFM with other imaging modalities is likely to have an even greater impact on microbiological studies. AFM studies of intact microbial cells started to appear in the literature in the 1990s. For example, AFM studies of Saccharomyces cerevisiae examined buddings cars after cell division and detailed changes related to cell growth processes. Also, the first AFM studies of bacterial biofilms appeared. In the late 1990s, AFM studies of intact fungal spores described clear changes in spore surfaces upon germination, and studies of individual bacterial cells were also described. These early bacterial imaging studies examined changes in bacterial morphology due to antimicrobial peptides exposure and bacterial adhesion properties. The majority of these early studies were carried out on dried samples and took advantage of the resolving power of AFM. The lack of cell mounting procedures presented an impediment for cell imaging studies. Subsequently, several approaches to mounting microbial cells have been developed, and these techniques are described later. Also highlighted are general considerations for microbial imaging and a description of some of the various applications of AFM to microbiology.

  18. Microbial fuel cells

    SciTech Connect

    Nealson, Kenneth H; Pirbazari, Massoud; Hsu, Lewis

    2013-04-09

    A microbial fuel cell includes an anode compartment with an anode and an anode biocatalyst and a cathode compartment with a cathode and a cathode biocatalyst, with a membrane positioned between the anode compartment and the cathode compartment, and an electrical pathway between the anode and the cathode. The anode biocatalyst is capable of catalyzing oxidation of an organic substance, and the cathode biocatalyst is capable of catalyzing reduction of an inorganic substance. The reduced organic substance can form a precipitate, thereby removing the inorganic substance from solution. In some cases, the anode biocatalyst is capable of catalyzing oxidation of an inorganic substance, and the cathode biocatalyst is capable of catalyzing reduction of an organic or inorganic substance.

  19. Microbial Fuel Cells and Microbial Electrolyzers

    SciTech Connect

    Borole, Abhijeet P

    2015-01-01

    Microbial Fuel Cells and microbial electrolyzers represent an upcoming technology for production of electricity and hydrogen using a hybrid electrocatalytic-biocatalytic approach. The combined catalytic efficiency of these processes has potential to make this technology highly efficient among the various renewable energy production alternatives. This field has attracted electrochemists, biologists and many other disciplines due to its potential to contribute to the energy, water and environment sectors. A brief introduction to the technology is provided followed by current research needs from a bioelectrochemical perspective. Insights into the operation and limitations of these systems achieved via cyclic voltammetry and impedance spectroscopy are discussed along with the power management needs to develop the application aspects. Besides energy production, other potential applications in bioenergy, bioelectronics, chemical production and remediation are also highlighted.

  20. Sulphur cycling in a Neoarchaean microbial mat.

    PubMed

    Meyer, N R; Zerkle, A L; Fike, D A

    2017-01-27

    Multiple sulphur (S) isotope ratios are powerful proxies to understand the complexity of S biogeochemical cycling through Deep Time. The disappearance of a sulphur mass-independent fractionation (S-MIF) signal in rocks <~2.4 Ga has been used to date a dramatic rise in atmospheric oxygen levels. However, intricacies of the S-cycle before the Great Oxidation Event remain poorly understood. For example, the isotope composition of coeval atmospherically derived sulphur species is still debated. Furthermore, variation in Archaean pyrite δ(34) S values has been widely attributed to microbial sulphate reduction (MSR). While petrographic evidence for Archaean early-diagenetic pyrite formation is common, textural evidence for the presence and distribution of MSR remains enigmatic. We combined detailed petrographic and in situ, high-resolution multiple S-isotope studies (δ(34) S and Δ(33) S) using secondary ion mass spectrometry (SIMS) to document the S-isotope signatures of exceptionally well-preserved, pyritised microbialites in shales from the ~2.65-Ga Lokammona Formation, Ghaap Group, South Africa. The presence of MSR in this Neoarchaean microbial mat is supported by typical biogenic textures including wavy crinkled laminae, and early-diagenetic pyrite containing <26‰ μm-scale variations in δ(34) S and Δ(33) S = -0.21 ± 0.65‰ (±1σ). These large variations in δ(34) S values suggest Rayleigh distillation of a limited sulphate pool during high rates of MSR. Furthermore, we identified a second, morphologically distinct pyrite phase that precipitated after lithification, with δ(34) S = 8.36 ± 1.16‰ and Δ(33) S = 5.54 ± 1.53‰ (±1σ). We propose that the S-MIF signature of this secondary pyrite does not reflect contemporaneous atmospheric processes at the time of deposition; instead, it formed by the influx of later-stage sulphur-bearing fluids containing an inherited atmospheric S-MIF signal and/or from magnetic isotope effects during

  1. The Chlamydomonas cell cycle.

    PubMed

    Cross, Frederick R; Umen, James G

    2015-05-01

    The position of Chlamydomonas within the eukaryotic phylogeny makes it a unique model in at least two important ways: as a representative of the critically important, early-diverging lineage leading to plants; and as a microbe retaining important features of the last eukaryotic common ancestor (LECA) that has been lost in the highly studied yeast lineages. Its cell biology has been studied for many decades and it has well-developed experimental genetic tools, both classical (Mendelian) and molecular. Unlike land plants, it is a haploid with very few gene duplicates, making it ideal for loss-of-function genetic studies. The Chlamydomonas cell cycle has a striking temporal and functional separation between cell growth and rapid cell division, probably connected to the interplay between diurnal cycles that drive photosynthetic cell growth and the cell division cycle; it also exhibits a highly choreographed interaction between the cell cycle and its centriole-basal body-flagellar cycle. Here, we review the current status of studies of the Chlamydomonas cell cycle. We begin with an overview of cell-cycle control in the well-studied yeast and animal systems, which has yielded a canonical, well-supported model. We discuss briefly what is known about similarities and differences in plant cell-cycle control, compared with this model. We next review the cytology and cell biology of the multiple-fission cell cycle of Chlamydomonas. Lastly, we review recent genetic approaches and insights into Chlamydomonas cell-cycle regulation that have been enabled by a new generation of genomics-based tools. © 2015 The Authors The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

  2. Microbial iron-redox cycling in subsurface environments.

    PubMed

    Roden, Eric E

    2012-12-01

    In addition to its central role in mediating electron-transfer reactions within all living cells, iron undergoes extracellular redox transformations linked to microbial energy generation through utilization of Fe(II) as a source of chemical energy or Fe(III) as an electron acceptor for anaerobic respiration. These processes permit microbial populations and communities to engage in cyclic coupled iron oxidation and reduction within redox transition zones in subsurface environments. In the present paper, I review and synthesize a few case studies of iron-redox cycling in subsurface environments, highlighting key biochemical aspects of the extracellular iron-redox metabolisms involved. Of specific interest are the coupling of iron oxidation and reduction in field and experimental systems that model redox gradients and fluctuations in the subsurface, and novel pathways and organisms involved in the redox cycling of insoluble iron-bearing minerals. These findings set the stage for rapid expansion in our knowledge of the range of extracellular electron-transfer mechanisms utilized by subsurface micro-organisms. The observation that closely coupled oxidation and reduction of iron can take place under conditions common to the subsurface motivates this expansion in pursuit of molecular tools for studying iron-redox cycling communities in situ.

  3. Why should cell biologists study microbial pathogens?

    PubMed

    Welch, Matthew D

    2015-12-01

    One quarter of all deaths worldwide each year result from infectious diseases caused by microbial pathogens. Pathogens infect and cause disease by producing virulence factors that target host cell molecules. Studying how virulence factors target host cells has revealed fundamental principles of cell biology. These include important advances in our understanding of the cytoskeleton, organelles and membrane-trafficking intermediates, signal transduction pathways, cell cycle regulators, the organelle/protein recycling machinery, and cell-death pathways. Such studies have also revealed cellular pathways crucial for the immune response. Discoveries from basic research on the cell biology of pathogenesis are actively being translated into the development of host-targeted therapies to treat infectious diseases. Thus there are many reasons for cell biologists to incorporate the study of microbial pathogens into their research programs.

  4. Specific cell cycle synchronization with butyrate and cell cycle analysis

    USDA-ARS?s Scientific Manuscript database

    Synchronized cells have been invaluable for many kinds of cell cycle and cell proliferation studies. Butyrate induces cell cycle arrest and apoptosis in MDBK cells. To explore the possibility of using butyrate-blocked cells to obtain synchronized cells, we investigated the property of the cell cyc...

  5. Elevated CO2 influences microbial carbon and nitrogen cycling

    PubMed Central

    2013-01-01

    Background Elevated atmospheric CO2 (eCO2) has been shown to have significant effects on terrestrial ecosystems. However, little is known about its influence on the structure, composition, and functional potential of soil microbial communities, especially carbon (C) and nitrogen (N) cycling. A high-throughput functional gene array (GeoChip 3.0) was used to examine the composition, structure, and metabolic potential of soil microbial communities from a grassland field experiment after ten-year field exposure to ambient and elevated CO2 concentrations. Results Distinct microbial communities were established under eCO2. The abundance of three key C fixation genes encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), carbon monoxide dehydrogenase (CODH) and propionyl-CoA/acetyl-CoA carboxylase (PCC/ACC), significantly increased under eCO2, and so did some C degrading genes involved in starch, cellulose, and hemicellulose. Also, nifH and nirS involved in N cycling were significantly stimulated. In addition, based on variation partitioning analysis (VPA), the soil microbial community structure was largely shaped by direct and indirect eCO2-driven factors. Conclusions These findings suggest that the soil microbial community structure and their ecosystem functioning for C and N cycling were altered dramatically at eCO2. This study provides new insights into our understanding of the feedback response of soil microbial communities to elevated CO2 and global change. PMID:23718284

  6. Cell Cycle Regulators and Cell Death in Immunity

    PubMed Central

    Zebell, Sophia G.; Dong, Xinnian

    2015-01-01

    Summary Various cell death mechanisms are integral to host defense in both plants and mammals. Plant defense against biotrophic pathogens is associated with programmed cell death (PCD) of the infected cell. This effector-triggered PCD is partly analogous to pyroptosis, an inflammatory host cell death process that plays a crucial role in defense against microbial infections in mammals. Plant effector-triggered PCD also shares with mammalian apoptosis the involvement of cell cycle regulators as signaling components. Here we explore the similarities between these different cell death programs as they relate to host defense and their relationship to the cell-cycle. PMID:26468745

  7. Cell-Cycle Regulators and Cell Death in Immunity.

    PubMed

    Zebell, Sophia G; Dong, Xinnian

    2015-10-14

    Various cell death mechanisms are integral to host defense in both plants and mammals. Plant defense against biotrophic pathogens is associated with programmed cell death (PCD) of the infected cell. This effector-triggered PCD is partly analogous to pyroptosis, an inflammatory host cell death process that plays a crucial role in defense against microbial infections in mammals. Plant effector-triggered PCD also shares with mammalian apoptosis the involvement of cell-cycle regulators as signaling components. Here we explore the similarities between these different cell death programs as they relate to host defense and their relationship to the cell cycle. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Microbial Fuel Cells and Sensors

    DTIC Science & Technology

    2007-11-02

    funding foreign research over Quality U.S. research needs to be investigated by government officials. PATENT INFORMATION: Improved fuel cell designs and...Zeikus. Analysis of microbial electrochemical activity in marine sediment. (In preparation) REPOT D CUM NTA ON AGEForm Approved REPOT D CUM NTATON

  9. Energy from algae using microbial fuel cells.

    PubMed

    Velasquez-Orta, Sharon B; Curtis, Tom P; Logan, Bruce E

    2009-08-15

    Bioelectricity production from a phytoplankton, Chlorella vulgaris, and a macrophyte, Ulva lactuca was examined in single chamber microbial fuel cells (MFCs). MFCs were fed with the two algae (as powders), obtaining differences in energy recovery, degradation efficiency, and power densities. C. vulgaris produced more energy generation per substrate mass (2.5 kWh/kg), but U. lactuca was degraded more completely over a batch cycle (73 +/- 1% COD). Maximum power densities obtained using either single cycle or multiple cycle methods were 0.98 W/m(2) (277 W/m(3)) using C. vulgaris, and 0.76 W/m(2) (215 W/m(3)) using U. lactuca. Polarization curves obtained using a common method of linear sweep voltammetry (LSV) overestimated maximum power densities at a scan rate of 1 mV/s. At 0.1 mV/s, however, the LSV polarization data was in better agreement with single- and multiple-cycle polarization curves. The fingerprints of microbial communities developed in reactors had only 11% similarity to inocula and clustered according to the type of bioprocess used. These results demonstrate that algae can in principle, be used as a renewable source of electricity production in MFCs.

  10. Microbial activities and phosphorus cycling: An application of oxygen isotope ratios in phosphate

    NASA Astrophysics Data System (ADS)

    Stout, Lisa M.; Joshi, Sunendra R.; Kana, Todd M.; Jaisi, Deb P.

    2014-08-01

    Microorganisms carry out biochemical transformations of nutrients that make up their cells. Therefore, understanding how these nutrients are transformed or cycled in natural environments requires knowledge of microbial activity. Commonly used indicators for microbial activity typically include determining microbial respiration by O2/CO2 measurements, cell counts, and measurement of enzyme activities. However, coupled studies on nutrient cycling and microbial activity are not given enough emphasis. Here we apply phosphate oxygen isotope ratios (δ18OP) as a tool for measurement of microbial activity and compare the rate of isotope exchange with methods of measuring microbial activities that are more commonly applied in environmental studies including respiration, dehydrogenase activity, alkaline phosphatase activity, and cell counts. Our results show that different bacteria may have different strategies for P uptake, storage and release, their respiration and consequently expression of DHA and APase activities, but in general the trend of their enzyme activities are comparable. Phosphate δ18OP values correlated well with these other parameters used to measure microbial activity with the strongest linear relationships between δ18OP and CO2 evolution (r = -0.99). Even though the rate of isotope exchange for each microorganism used in this study is different, the rate per unit CO2 respiration showed one general trend, where δ18OP values move towards equilibrium while CO2 is generated. While this suggests that P cycling among microorganisms used in this study can be generalized, further research is needed to determine whether the microorganism-specific isotope exchange trend may occur in natural environments. In summary, phosphate oxygen isotope measurements may offer an alternative for use as a tracer to measure microbial activity in soils, sediments, and many other natural environments.

  11. Global biogeography of microbial nitrogen-cycling traits in soil

    NASA Astrophysics Data System (ADS)

    Nelson, M.; Martiny, A.; Martiny, J. B. H.

    2016-12-01

    Microorganisms drive much of the Earth's nitrogen (N) cycle. However, despite their importance, many ecosystem models do not explicitly consider microbial communities and their functions. One obstacle in doing this is that we lack a complete understanding of the role that microbes play in biogeochemical processes. To address this challenge we used metagenomics to assess various N cycling traits of soil microorganisms in samples from around the globe. As measurable characteristics of an organism, traits can be used to quantify the role of microbes in ecosystem processes. Using 365 publically available soil metagenomes, we characterized the biogeography of microbial N cycling traits, defined as the abundance and composition of eight N pathways. We found strong biogeographic patterns in the frequency of N pathway traits; however, our models explained much less variation in taxonomic composition across sites. Focusing on individual N pathways, we identified the prominent taxa harboring these pathways. In addition, we found an unexpectedly high frequency of Bacteria encoding the dissimilatory nitrate reduction to ammonium (DNRA) pathway, a little studied N cycle process in soils. Finally, across all N pathways, phylogenetic analysis revealed that some phyla seem to be N cycle generalists (i.e delta-Proteobacteria), with the potential to carry out many N transformations, whereas others seem to be specialists (i.e. Cyanobacteria). As the most comprehensive map to date of the global distribution of microbial N traits, this study provides a springboard for further investigation of the prominent players in N cycling in soils. Overall, biogeographic patterns of traits can provide a foundation for understanding how microbial diversity impacts ecosystem processes and ultimately predicting how this diversity may shift in the face of global change.

  12. Microbial biomass dynamics dominate N cycle responses to warming in a sub-arctic peatland

    NASA Astrophysics Data System (ADS)

    Weedon, J. T.; Aerts, R.; Kowalchuk, G. K.; van Bodegom, P. M.

    2012-04-01

    The balance of primary production and decomposition in sub-arctic peatlands may shift with climate change. Nitrogen availability will modulate this shift, but little is known about the drivers of soil nitrogen dynamics in these environments, and how they are influenced by rising soil temperatures. We used a long-term open top chamber warming experiment in Abisko, Sweden, to test for the interactive effects of spring warming, summer warming and winter snow addition on soil organic and inorganic nitrogen fluxes, potential activities of carbon and nitrogen cycle enzymes, and the structure of the soil-borne microbial communities. Summer warming increased the flux of soil organic nitrogen over the growing season, while simultaneously causing a seasonal decrease in microbial biomass, suggesting that N flux is driven by large late-season dieback of microbes. This change in N cycle dynamics was not reflected in any of the measured potential enzyme activities. Moreover, the soil microbial community structure was stable across treatments, suggesting non-specific microbial dieback. To further test whether the observed patterns were driven by direct temperature effects or indirect effects (via microbial biomass dynamics), we conducted follow-up controlled experiments in soil mesocosms. Experimental additions of dead microbial cells had stronger effects on N pool sizes and enzyme activities than either plant litter addition or a 5 °C alteration in incubation temperatures. Peat respiration was positively affected by both substrate addition and higher incubation temperatures, but the temperature-only effect was not sufficient to account for the increases in respiration observed in previous field experiments. We conclude that warming effects on peatland N cycling (and to some extent C cycling) are dominated by indirect effects, acting through alterations to the seasonal flux of microbe-derived organic matter. We propose that climate change models of soil carbon and nitrogen

  13. Towards a Microbial Thermoelectric Cell

    PubMed Central

    Rodríguez-Barreiro, Raúl; Abendroth, Christian; Vilanova, Cristina; Moya, Andrés; Porcar, Manuel

    2013-01-01

    Microbial growth is an exothermic process. Biotechnological industries produce large amounts of heat, usually considered an undesirable by-product. In this work, we report the construction and characterization of the first microbial thermoelectric cell (MTC), in which the metabolic heat produced by a thermally insulated microbial culture is partially converted into electricity through a thermoelectric device optimized for low ΔT values. A temperature of 41°C and net electric voltage of around 250–600 mV was achieved with 1.7 L baker’s yeast culture. This is the first time microbial metabolic energy has been converted into electricity with an ad hoc thermoelectric device. These results might contribute towards developing a novel strategy to harvest excess heat in the biotechnology industry, in processes such as ethanol fermentation, auto thermal aerobic digestion (ATAD) or bioremediation, which could be coupled with MTCs in a single unit to produce electricity as a valuable by-product of the primary biotechnological product. Additionally, we propose that small portable MTCs could be conceived and inoculated with suitable thermophilic of hyperthermophilic starter cultures and used for powering small electric devices. PMID:23468862

  14. Cell cycle effects of drugs

    SciTech Connect

    Dethlefsen, L.A.

    1986-01-01

    This book contains 11 chapters. Some of the chapter titles are: Cell Growth and Division Cycle; Cell Cycle Effects of Alkylating Agents; Biological Effects of Folic Acid Antagonists with Antineoplastic Activity; and Bleomycin-Mode of Action with Particular Reference to the Cell Cycle.

  15. Regenerable Microbial Check Valve - Life cycle tests results

    NASA Technical Reports Server (NTRS)

    Atwater, James E.; Wheeler, Richard R., Jr.; Olivadoti, J. T.; Sauer, Richard L.; Flanagan, David T.

    1992-01-01

    Life cycle regeneration testing of the Microbial Check Valve (MCV) that is used on the Shuttle Orbiter to provide microbial control of potable water is currently in progress. Four beds are being challenged with simulated reclaimed waters and repeatedly regenerated. Preliminary results indicate that contaminant systems exhibit unique regeneration periodicities. Cyclic throughput diminishes with increasing cumulative flow. It is considered to be feasible to design a regenerable MCV system which will function without human intervention and with minimal resupply penalty for the 30 year life of the Space Station.

  16. Photosynthetic Microbial Fuel Cells.

    PubMed

    Laureanti, Joseph A; Jones, Anne K

    2017-01-10

    This chapter presents the current state of research on bioelectrochemical systems that include phototrophic organisms. First, we describe what is known of how phototrophs transfer electrons from internal metabolism to external substrates. This includes efforts to understand both the source of electrons and transfer pathways within cells. Second, we consider technological progress toward producing bio-photovoltaic devices with phototrophs. Efforts to improve these devices by changing the species included, the electrode surfaces, and chemical mediators are described. Finally, we consider future directions for this research field.

  17. Global biogeography of microbial nitrogen-cycling traits in soil

    PubMed Central

    Nelson, Michaeline B.; Martiny, Jennifer B. H.

    2016-01-01

    Microorganisms drive much of the Earth’s nitrogen (N) cycle, but we still lack a global overview of the abundance and composition of the microorganisms carrying out soil N processes. To address this gap, we characterized the biogeography of microbial N traits, defined as eight N-cycling pathways, using publically available soil metagenomes. The relative frequency of N pathways varied consistently across soils, such that the frequencies of the individual N pathways were positively correlated across the soil samples. Habitat type, soil carbon, and soil N largely explained the total N pathway frequency in a sample. In contrast, we could not identify major drivers of the taxonomic composition of the N functional groups. Further, the dominant genera encoding a pathway were generally similar among habitat types. The soil samples also revealed an unexpectedly high frequency of bacteria carrying the pathways required for dissimilatory nitrate reduction to ammonium, a little-studied N process in soil. Finally, phylogenetic analysis showed that some microbial groups seem to be N-cycling specialists or generalists. For instance, taxa within the Deltaproteobacteria encoded all eight N pathways, whereas those within the Cyanobacteria primarily encoded three pathways. Overall, this trait-based approach provides a baseline for investigating the relationship between microbial diversity and N cycling across global soils. PMID:27432978

  18. Repeated Anaerobic Microbial Redox Cycling of Iron▿†

    PubMed Central

    Coby, Aaron J.; Picardal, Flynn; Shelobolina, Evgenya; Xu, Huifang; Roden, Eric E.

    2011-01-01

    Some nitrate- and Fe(III)-reducing microorganisms are capable of oxidizing Fe(II) with nitrate as the electron acceptor. This enzymatic pathway may facilitate the development of anaerobic microbial communities that take advantage of the energy available during Fe-N redox oscillations. We examined this phenomenon in synthetic Fe(III) oxide (nanocrystalline goethite) suspensions inoculated with microflora from freshwater river floodplain sediments. Nitrate and acetate were added at alternate intervals in order to induce repeated cycles of microbial Fe(III) reduction and nitrate-dependent Fe(II) oxidation. Addition of nitrate to reduced, acetate-depleted suspensions resulted in rapid Fe(II) oxidation and accumulation of ammonium. High-resolution transmission electron microscopic analysis of material from Fe redox cycling reactors showed amorphous coatings on the goethite nanocrystals that were not observed in reactors operated under strictly nitrate- or Fe(III)-reducing conditions. Microbial communities associated with N and Fe redox metabolism were assessed using a combination of most-probable-number enumerations and 16S rRNA gene analysis. The nitrate-reducing and Fe(III)-reducing cultures were dominated by denitrifying Betaproteobacteria (e.g., Dechloromonas) and Fe(III)-reducing Deltaproteobacteria (Geobacter), respectively; these same taxa were dominant in the Fe cycling cultures. The combined chemical and microbiological data suggest that both Geobacter and various Betaproteobacteria participated in nitrate-dependent Fe(II) oxidation in the cycling cultures. Microbially driven Fe-N redox cycling may have important consequences for both the fate of N and the abundance and reactivity of Fe(III) oxides in sediments. PMID:21742920

  19. Cell cycle in mouse development.

    PubMed

    Ciemerych, Maria A; Sicinski, Peter

    2005-04-18

    Mice likely represent the most-studied mammalian organism, except for humans. Genetic engineering in embryonic stem cells has allowed derivation of mouse strains lacking particular cell cycle proteins. Analyses of these mutant mice, and cells derived from them, facilitated the studies of the functions of cell cycle apparatus at the organismal and cellular levels. In this review, we give some background about the cell cycle progression during mouse development. We next discuss some insights about in vivo functions of the cell cycle proteins, gleaned from mouse knockout experiments. Our text is meant to provide examples of the recent experiments, rather than to supply an extensive and complete list.

  20. How do prokaryotic cells cycle?

    PubMed

    Margolin, William; Bernander, Rolf

    2004-09-21

    This issue of Current Biology features five reviews covering various key aspects of the eukaryotic cell cycle. The topics include initiation of chromosome replication, assembly of the mitotic spindle, cytokinesis, the regulation of cell-cycle progression, and cell-cycle modeling, focusing mainly on budding yeast, fission yeast and animal cell model systems. The reviews underscore common themes as well as key differences in the way these processes are carried out and regulated among the different model organisms. Consequently, an important question is how cell-cycle mechanisms and controls have evolved, particularly in the broader perspective of the three domains of life.

  1. NETs and cell cycle regulation.

    PubMed

    Robson, Michael I; Le Thanh, Phu; Schirmer, Eric C

    2014-01-01

    There are many ways that the nuclear envelope can influence the cell cycle. In addition to roles of lamins in regulating the master cell cycle regulator pRb and nuclear envelope breakdown in mitosis, many other nuclear envelope proteins influence the cell cycle through regulatory or structural functions. Of particular note among these are the nuclear envelope transmembrane proteins (NETs) that appear to influence cell cycle regulation through multiple separate mechanisms. Some NETs and other nuclear envelope proteins accumulate on the mitotic spindle, suggesting functional or structural roles in the cell cycle. In interphase exogenous overexpression of some NETs promotes an increase in G1 populations, while others promote an increase in G2/M populations, sometimes associated with the induction of senescence. Intriguingly, most of the NETs linked to the cell cycle are highly restricted in their tissue expression; thus, their misregulation in cancer could contribute to the many tissue-specific types of cancer.

  2. Elevated temperature alters carbon cycling in a model microbial community

    NASA Astrophysics Data System (ADS)

    Mosier, A.; Li, Z.; Thomas, B. C.; Hettich, R. L.; Pan, C.; Banfield, J. F.

    2013-12-01

    Earth's climate is regulated by biogeochemical carbon exchanges between the land, oceans and atmosphere that are chiefly driven by microorganisms. Microbial communities are therefore indispensible to the study of carbon cycling and its impacts on the global climate system. In spite of the critical role of microbial communities in carbon cycling processes, microbial activity is currently minimally represented or altogether absent from most Earth System Models. Method development and hypothesis-driven experimentation on tractable model ecosystems of reduced complexity, as presented here, are essential for building molecularly resolved, benchmarked carbon-climate models. Here, we use chemoautotropic acid mine drainage biofilms as a model community to determine how elevated temperature, a key parameter of global climate change, regulates the flow of carbon through microbial-based ecosystems. This study represents the first community proteomics analysis using tandem mass tags (TMT), which enable accurate, precise, and reproducible quantification of proteins. We compare protein expression levels of biofilms growing over a narrow temperature range expected to occur with predicted climate changes. We show that elevated temperature leads to up-regulation of proteins involved in amino acid metabolism and protein modification, and down-regulation of proteins involved in growth and reproduction. Closely related bacterial genotypes differ in their response to temperature: Elevated temperature represses carbon fixation by two Leptospirillum genotypes, whereas carbon fixation is significantly up-regulated at higher temperature by a third closely related genotypic group. Leptospirillum group III bacteria are more susceptible to viral stress at elevated temperature, which may lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, this proteogenomics approach revealed the effects of climate change on carbon cycling pathways and other

  3. Microbial diversity and carbon cycling in San Francisco Bay wetlands

    SciTech Connect

    Theroux, Susanna; Hartman, Wyatt; He, Shaomei; Tringe, Susannah

    2014-03-21

    Wetland restoration efforts in San Francisco Bay aim to rebuild habitat for endangered species and provide an effective carbon storage solution, reversing land subsidence caused by a century of industrial and agricultural development. However, the benefits of carbon sequestration may be negated by increased methane production in newly constructed wetlands, making these wetlands net greenhouse gas (GHG) sources to the atmosphere. We investigated the effects of wetland restoration on below-ground microbial communities responsible for GHG cycling in a suite of historic and restored wetlands in SF Bay. Using DNA and RNA sequencing, coupled with real-time GHG monitoring, we profiled the diversity and metabolic potential of wetland soil microbial communities. The wetland soils harbor diverse communities of bacteria and archaea whose membership varies with sampling location, proximity to plant roots and sampling depth. Our results also highlight the dramatic differences in GHG production between historic and restored wetlands and allow us to link microbial community composition and GHG cycling with key environmental variables including salinity, soil carbon and plant species.

  4. Microbial electrolysis cell with a microbial biocathode.

    PubMed

    Jeremiasse, Adriaan W; Hamelers, Hubertus V M; Buisman, Cees J N

    2010-04-01

    This study demonstrates, for the first time, the proof-of-principle of an MEC in which both the anodic and cathodic reaction are catalyzed by microorganisms. No expensive chemical catalysts, such as platinum, are needed. Two of these MECs were simultaneously operated and reached a maximum of 1.4 A/m(2) at an applied cell voltage of 0.5 V. At a cathode potential of -0.7 V, the biocathode in the MECs had a higher current density (MEC 1: 1.9 A/m(2), MEC 2: 3.3 A/m(2)) than a control cathode (0.3 A/m(2), graphite felt without biofilm) in an electrochemical half cell. This indicates that hydrogen production is catalyzed at the biocathode, likely by electrochemically active microorganisms. The cathodic hydrogen recovery was 17% for MEC 1 and 21% for MEC 2. Hydrogen losses were ascribed to diffusion through membrane and tubing, and methane formation. After 1600 h of operation, the current density of the MECs had decreased to 0.6 A/m(2), probably caused by precipitation of calcium phosphate on the biocathode. The slow deteriorating effect of calcium phosphate, and the production of methane show the importance of studying the combination of bioanode and biocathode in one electrochemical cell, and of studying long term performance of such an MEC.

  5. Microbial fuel cells: novel microbial physiologies and engineering approaches.

    PubMed

    Lovley, Derek R

    2006-06-01

    The possibility of generating electricity with microbial fuel cells has been recognized for some time, but practical applications have been slow to develop. The recent development of a microbial fuel cell that can harvest electricity from the organic matter stored in marine sediments has demonstrated the feasibility of producing useful amounts of electricity in remote environments. Further study of these systems has led to the discovery of microorganisms that conserve energy to support their growth by completely oxidizing organic compounds to carbon dioxide with direct electron transfer to electrodes. This suggests that self-sustaining microbial fuel cells that can effectively convert a diverse range of waste organic matter or renewable biomass to electricity are feasible. Significant progress has recently been made to increase the power output of systems designed to convert organic wastes to electricity, but substantial additional optimization will be required for large-scale electricity production.

  6. Isotopic insights into microbial sulfur cycling in oil reservoirs

    PubMed Central

    Hubbard, Christopher G.; Cheng, Yiwei; Engelbrekston, Anna; Druhan, Jennifer L.; Li, Li; Ajo-Franklin, Jonathan B.; Coates, John D.; Conrad, Mark E.

    2014-01-01

    Microbial sulfate reduction in oil reservoirs (biosouring) is often associated with secondary oil production where seawater containing high sulfate concentrations (~28 mM) is injected into a reservoir to maintain pressure and displace oil. The sulfide generated from biosouring can cause corrosion of infrastructure, health exposure risks, and higher production costs. Isotope monitoring is a promising approach for understanding microbial sulfur cycling in reservoirs, enabling early detection of biosouring, and understanding the impact of souring. Microbial sulfate reduction is known to result in large shifts in the sulfur and oxygen isotope compositions of the residual sulfate, which can be distinguished from other processes that may be occurring in oil reservoirs, such as precipitation of sulfate and sulfide minerals. Key to the success of this method is using the appropriate isotopic fractionation factors for the conditions and processes being monitored. For a set of batch incubation experiments using a mixed microbial culture with crude oil as the electron donor, we measured a sulfur fractionation factor for sulfate reduction of −30‰. We have incorporated this result into a simplified 1D reservoir reactive transport model to highlight how isotopes can help discriminate between biotic and abiotic processes affecting sulfate and sulfide concentrations. Modeling results suggest that monitoring sulfate isotopes can provide an early indication of souring for reservoirs with reactive iron minerals that can remove the produced sulfide, especially when sulfate reduction occurs in the mixing zone between formation waters (FW) containing elevated concentrations of volatile fatty acids (VFAs) and injection water (IW) containing elevated sulfate. In addition, we examine the role of reservoir thermal, geochemical, hydrological, operational and microbiological conditions in determining microbial souring dynamics and hence the anticipated isotopic signatures. PMID:25285094

  7. Isotopic insights into microbial sulfur cycling in oil reservoirs.

    PubMed

    Hubbard, Christopher G; Cheng, Yiwei; Engelbrekston, Anna; Druhan, Jennifer L; Li, Li; Ajo-Franklin, Jonathan B; Coates, John D; Conrad, Mark E

    2014-01-01

    Microbial sulfate reduction in oil reservoirs (biosouring) is often associated with secondary oil production where seawater containing high sulfate concentrations (~28 mM) is injected into a reservoir to maintain pressure and displace oil. The sulfide generated from biosouring can cause corrosion of infrastructure, health exposure risks, and higher production costs. Isotope monitoring is a promising approach for understanding microbial sulfur cycling in reservoirs, enabling early detection of biosouring, and understanding the impact of souring. Microbial sulfate reduction is known to result in large shifts in the sulfur and oxygen isotope compositions of the residual sulfate, which can be distinguished from other processes that may be occurring in oil reservoirs, such as precipitation of sulfate and sulfide minerals. Key to the success of this method is using the appropriate isotopic fractionation factors for the conditions and processes being monitored. For a set of batch incubation experiments using a mixed microbial culture with crude oil as the electron donor, we measured a sulfur fractionation factor for sulfate reduction of -30‰. We have incorporated this result into a simplified 1D reservoir reactive transport model to highlight how isotopes can help discriminate between biotic and abiotic processes affecting sulfate and sulfide concentrations. Modeling results suggest that monitoring sulfate isotopes can provide an early indication of souring for reservoirs with reactive iron minerals that can remove the produced sulfide, especially when sulfate reduction occurs in the mixing zone between formation waters (FW) containing elevated concentrations of volatile fatty acids (VFAs) and injection water (IW) containing elevated sulfate. In addition, we examine the role of reservoir thermal, geochemical, hydrological, operational and microbiological conditions in determining microbial souring dynamics and hence the anticipated isotopic signatures.

  8. The Abbreviated Pluripotent Cell Cycle

    PubMed Central

    Kapinas, Kristina; Grandy, Rodrigo; Ghule, Prachi; Medina, Ricardo; Becker, Klaus; Pardee, Arthur; Zaidi, Sayyed K.; Lian, Jane; Stein, Janet; van Wijnen, Andre; Stein, Gary

    2013-01-01

    Human embryonic stem cells and induced pluripotent stem cells proliferate rapidly and divide symmetrically producing equivalent progeny cells. In contrast, lineage committed cells acquire an extended symmetrical cell cycle. Self-renewal of tissue-specific stem cells is sustained by asymmetric cell division where one progeny cell remains a progenitor while the partner progeny cell exits the cell cycle and differentiates. There are three principal contexts for considering the operation and regulation of the pluripotent cell cycle: temporal, regulatory andstructural. The primary temporal context that the pluripotent self-renewal cell cycle of human embryonic stem cells (hESCs) is a short G1 period without reducing periods of time allocated to S phase, G2, and mitosis. The rules that govern proliferation in hESCs remain to be comprehensively established. However, several lines of evidence suggest a key role for the naïve transcriptome of hESCs, which is competent to stringently regulate the ESC cell cycle. This supports the requirements of pluripotent cells to self propagate while suppressing expression of genes that confer lineage commitment and/or tissue specificity. However, for the first time, we consider unique dimensions to the architectural organization and assembly of regulatory machinery for gene expression in nuclear microenviornments that define parameters of pluripotency. From both fundamental biological and clinical perspectives, understanding control of the abbreviated embryonic stem cell cycle can provide options to coordinate control of proliferation versus differentiation. Wound healing, tissue engineering, and cell-based therapy to mitigate developmental aberrations illustrate applications that benefit from knowledge of the biology of the pluripotent cell cycle. PMID:22552993

  9. The abbreviated pluripotent cell cycle.

    PubMed

    Kapinas, Kristina; Grandy, Rodrigo; Ghule, Prachi; Medina, Ricardo; Becker, Klaus; Pardee, Arthur; Zaidi, Sayyed K; Lian, Jane; Stein, Janet; van Wijnen, Andre; Stein, Gary

    2013-01-01

    Human embryonic stem cells (hESCs) and induced pluripotent stem cells proliferate rapidly and divide symmetrically producing equivalent progeny cells. In contrast, lineage committed cells acquire an extended symmetrical cell cycle. Self-renewal of tissue-specific stem cells is sustained by asymmetric cell division where one progeny cell remains a progenitor while the partner progeny cell exits the cell cycle and differentiates. There are three principal contexts for considering the operation and regulation of the pluripotent cell cycle: temporal, regulatory, and structural. The primary temporal context that the pluripotent self-renewal cell cycle of hESCs is a short G1 period without reducing periods of time allocated to S phase, G2, and mitosis. The rules that govern proliferation in hESCs remain to be comprehensively established. However, several lines of evidence suggest a key role for the naïve transcriptome of hESCs, which is competent to stringently regulate the embryonic stem cell (ESC) cell cycle. This supports the requirements of pluripotent cells to self-propagate while suppressing expression of genes that confer lineage commitment and/or tissue specificity. However, for the first time, we consider unique dimensions to the architectural organization and assembly of regulatory machinery for gene expression in nuclear microenviornments that define parameters of pluripotency. From both fundamental biological and clinical perspectives, understanding control of the abbreviated ESC cycle can provide options to coordinate control of proliferation versus differentiation. Wound healing, tissue engineering, and cell-based therapy to mitigate developmental aberrations illustrate applications that benefit from knowledge of the biology of the pluripotent cell cycle.

  10. Cell cycle regulation in hematopoietic stem cells.

    PubMed

    Pietras, Eric M; Warr, Matthew R; Passegué, Emmanuelle

    2011-11-28

    Hematopoietic stem cells (HSCs) give rise to all lineages of blood cells. Because HSCs must persist for a lifetime, the balance between their proliferation and quiescence is carefully regulated to ensure blood homeostasis while limiting cellular damage. Cell cycle regulation therefore plays a critical role in controlling HSC function during both fetal life and in the adult. The cell cycle activity of HSCs is carefully modulated by a complex interplay between cell-intrinsic mechanisms and cell-extrinsic factors produced by the microenvironment. This fine-tuned regulatory network may become altered with age, leading to aberrant HSC cell cycle regulation, degraded HSC function, and hematological malignancy.

  11. Enzymatic assays of sediments from North Pond (IODP Expedition 336) to elucidate microbial phosphorus cycling strategies

    NASA Astrophysics Data System (ADS)

    Defforey, D.; Paytan, A.

    2015-12-01

    Phosphorus (P) is a key macronutrient for living cells and its availability is limited in the deep subseafloor environment, a habitat estimated to contain up to 1% of Earth's total biomass. The existence and activity of deep subseafloor microbial populations have profound implications on global biogeochemical cycles and our understanding of the limits of life. However, little is known about the impact of the deep biosphere on sedimentary P cycling and P diagenetic processes. Our previous work has shown that sedimentary P at North Pond is mainly present in mineral phases, and that refractory organic P is detectable throughout the sediment column. The latter could constitute a P source to the deep biosphere. Alternatively, microorganisms could have mechanisms to harvest P from recalcitrant mineral phases. The aim of this study is to determine the presence and maximum potential activity of enzymes involved in microbial P uptake in deep-sea sediments. These include phosphomonoesterases, such as alkaline phosphatase, phosphodiesterases, pyrophosphatase and phosphonatases. The sediment samples used for this study were collected at North Pond, a sediment pond located on the western flank of the Mid-Atlantic Ridge, during IODP Expedition 336. This work will provide key insights into the microbial P uptake mechanisms at play in open ocean sediments, and their effects on sedimentary P cycling. These results, in conjunction with our previous work investigating P geochemistry at North Pond, will yield valuable information regarding the impact of the deep biosphere on P cycling in open ocean sediments.

  12. Microbial Carbon Cycling in Permafrost-Affected Soils

    SciTech Connect

    Vishnivetskaya, T.; Liebner, Susanne; Wilhelm, Ronald; Wagner, Dirk

    2011-01-01

    The Arctic plays a key role in Earth s climate system as global warming is predicted to be most pronounced at high latitudes and because one third of the global carbon pool is stored in ecosystems of the northern latitudes. In order to improve our understanding of the present and future carbon dynamics in climate sensitive permafrost ecosystems, present studies concentrate on investigations of microbial controls of greenhouse gas fluxes, on the activity and structure of the involved microbial communities, and on their response to changing environmental conditions. Permafrost-affected soils can function as both a source and a sink for carbon dioxide and methane. Under anaerobic conditions, caused by flooding of the active layer and the effect of backwater above the permafrost table, the mineralization of organic matter can only be realized stepwise by specialized microorganisms. Important intermediates of the organic matter decomposition are hydrogen, carbon dioxide and acetate, which can be further reduced to methane by methanogenic archaea. Evolution of methane fluxes across the subsurface/atmosphere boundary will thereby strongly depend on the activity of anaerobic methanogenic archaea and obligately aerobic methane oxidizing proteobacteria, which are known to be abundant and to significantly reduce methane emissions in permafrost-affected soils. Therefore current studies on methane-cycling microorganisms are the object of particular attention in permafrost studies, because of their key role in the Arctic methane cycle and consequently of their significance for the global methane budget.

  13. The cell cycle and pluripotency.

    PubMed

    Hindley, Christopher; Philpott, Anna

    2013-04-15

    PSCs (pluripotent stem cells) possess two key properties that have made them the focus of global research efforts in regenerative medicine: they have unlimited expansion potential under conditions which favour their preservation as PSCs and they have the ability to generate all somatic cell types upon differentiation (pluripotency). Conditions have been defined in vitro in which pluripotency is maintained, or else differentiation is favoured and is directed towards specific somatic cell types. However, an unanswered question is whether or not the core cell cycle machinery directly regulates the pluripotency and differentiation properties of PSCs. If so, then manipulation of the cell cycle may represent an additional tool by which in vitro maintenance or differentiation of PSCs may be controlled in regenerative medicine. The present review aims to summarize our current understanding of links between the core cell cycle machinery and the maintenance of pluripotency in ESCs (embryonic stem cells) and iPSCs (induced PSCs).

  14. Cell Cycle Regulation by Checkpoints

    PubMed Central

    Barnum, Kevin J.; O’Connell, Matthew J.

    2016-01-01

    Cell cycle checkpoints are surveillance mechanisms that monitor the order, integrity, and fidelity of the major events of the cell cycle. These include growth to the appropriate cell size, the replication and integrity of the chromosomes, and their accurate segregation at mitosis. Many of these mechanisms are ancient in origin and highly conserved, and hence have been heavily informed by studies in simple organisms such as the yeasts. Others have evolved in higher organisms, and control alternative cell fates with significant impact on tumor suppression. Here, we consider these different checkpoint pathways and the consequences of their dysfunction on cell fate. PMID:24906307

  15. Cell cycle regulation by checkpoints.

    PubMed

    Barnum, Kevin J; O'Connell, Matthew J

    2014-01-01

    Cell cycle checkpoints are surveillance mechanisms that monitor the order, integrity, and fidelity of the major events of the cell cycle. These include growth to the appropriate cell size, the replication and integrity of the chromosomes, and their accurate segregation at mitosis. Many of these mechanisms are ancient in origin and highly conserved, and hence have been heavily informed by studies in simple organisms such as the yeasts. Others have evolved in higher organisms, and control alternative cell fates with significant impact on tumor suppression. Here, we consider these different checkpoint pathways and the consequences of their dysfunction on cell fate.

  16. Iron cycling microbial communities in sediments of the Baltic Sea

    NASA Astrophysics Data System (ADS)

    Reyes, Carolina; Delwig, Olaf; Noriega-Ortega, Beatriz; Dähnke, Kirstin; Böttcher, Michael E.; Friedrich, Michael W.

    2014-05-01

    The biogeochemical cycling of iron is a key early diagenetic process. However, limited information exists about the diversity and metabolic pathways of microorganisms linked to iron cycling in marine sediments. The goal of this study was to determine the bacterial community diversity in sediments showing ongoing dissimilatory iron reduction using 454-pyrosequencing as a first step in characterizing microorganisms potentially involved in iron reduction. For this purpose, two 35 cm cores were sampled from ferruginous sediments in the Skagerrak (SK) and the Bothnian Bay (BB) from the North-Sea Baltic Sea and the northern Baltic Sea respectively. Pore water profiles showed Fe2+ and Mn2+ levels of ~140-150 µM throughout the core below a 6 cm thick oxidized surface layer in SK sediments and ~300 µM below a 2 cm thick surface layer in BB sediments. Dissolved sulphide levels were below detection in both sediments. No significant depletion of SO42- occurred at both sites, further supported by stable S and O isotope analyses of dissolved sulfate at SK site. Only very minor net sulfate reduction is suggested here from the trend in sulphur isotope signatures, in agreement with previously reported gross microbial sulphate rate measurements (Canfield et al., 1993;GCA). Based on these biogeochemical constraints, Fe reduction in the studied sediments is therefore dominated by microbial dissimilatory iron reduction, while cryptic Fe-S-cycling can be largely excluded. 16S rRNA gene sequences indicate Proteobacteria as the dominating microbial group in these sediments. Potential iron and manganese reducing bacteria included Geobacteraceae, Pelobacteraceae, Shewanellaceae, and Oceanospirillales. Additionally, Actinobacteria and Bacteroidetes were present. Also, Fe-oxidizers were present and their occurrence correlated in depth with a Fe-oxide-rich layer, most likely a former buried Fe-oxidation front. Gene sequences point to the presence of Mariprofundus in SK sediments and

  17. Microbial Influences on Trace Metal Cycling in a Meromictic Lake, Fayetteville Green Lake, NY

    NASA Astrophysics Data System (ADS)

    Zerkle, A. L.; House, C.; Kump, L.

    2002-12-01

    Microorganisms can exist in aquatic environments at very high cell densities of up to 1011 cells/L, and can accumulate significant quantities of trace metals. Bacteria actively take up bioactive trace metals, including Fe, Zn, Mn, Co, Ni, Cu, and Mo, which function as catalytic centers in metalloproteins and metal-activated enzymes involved in virtually all cellular functions. In addition, bacteria may catalyze the release of trace metals from inorganic substrates by processes such as the reduction of iron and manganese oxides, suggesting that trace metal distributions within a natural environment dominated by microbial processes may be controlled primarily by microbial ecology. Fayetteville Green Lake (FGL), NY, is a permanently stratified meromictic lake that has a well-oxygenated surface water mass (mixolimnion) overlying a relatively stagnant, anoxic deep water mass (monimolimnion). A chemocline separates the water masses at around 20m depth, where oxygen concentrations decrease and sulfate and methane concentrations increase. In addition, previous studies have indicated that trace metals such as V, Cr, Co, Mn, and Fe reach elevated concentrations at the chemocline. Using fluorescent in situ hybridization (FISH) of FGL samples from depths of up to 40m with bacterial and archaeal probes, we have shown that fluctuating redox conditions within the FGL water column correlate with significant variations in the composition and distribution of microbial populations with depth. The mixolimnion is dominated by Eubacteria, with increasing concentrations of Archaea in the lower anoxic zone. Increases in microbial cell densities coincide with increases in trace metals at the chemocline, suggesting microbial activity may be responsible for trace metal release at this boundary. 16S rRNA PCR cloning techniques are currently being used to identify dominant microbial populations at various levels within the FGL water column. Future studies will focus on the potential for these

  18. Myc and cell cycle control.

    PubMed

    Bretones, Gabriel; Delgado, M Dolores; León, Javier

    2015-05-01

    Soon after the discovery of the Myc gene (c-Myc), it became clear that Myc expression levels tightly correlate to cell proliferation. The entry in cell cycle of quiescent cells upon Myc enforced expression has been described in many models. Also, the downregulation or inactivation of Myc results in the impairment of cell cycle progression. Given the frequent deregulation of Myc oncogene in human cancer it is important to dissect out the mechanisms underlying the role of Myc on cell cycle control. Several parallel mechanisms account for Myc-mediated stimulation of the cell cycle. First, most of the critical positive cell cycle regulators are encoded by genes induced by Myc. These Myc target genes include Cdks, cyclins and E2F transcription factors. Apart from its direct effects on the transcription, Myc is able to hyperactivate cyclin/Cdk complexes through the induction of Cdk activating kinase (CAK) and Cdc25 phosphatases. Moreover, Myc antagonizes the activity of cell cycle inhibitors as p21 and p27 through different mechanisms. Thus, Myc is able to block p21 transcription or to induce Skp2, a protein involved in p27 degradation. Finally, Myc induces DNA replication by binding to replication origins and by upregulating genes encoding proteins required for replication initiation. Myc also regulates genes involved in the mitotic control. A promising approach to treat tumors with deregulated Myc is the synthetic lethality based on the inhibition of Cdks. Thus, the knowledge of the Myc-dependent cell cycle regulatory mechanisms will help to discover new therapeutic approaches directed against malignancies with deregulated Myc. This article is part of a Special Issue entitled: Myc proteins in cell biology and pathology. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Effect of temperature and cycle length on microbial competition in PHB-producing sequencing batch reactor

    PubMed Central

    Jiang, Yang; Marang, Leonie; Kleerebezem, Robbert; Muyzer, Gerard; van Loosdrecht, Mark C M

    2011-01-01

    The impact of temperature and cycle length on microbial competition between polyhydroxybutyrate (PHB)-producing populations enriched in feast-famine sequencing batch reactors (SBRs) was investigated at temperatures of 20 °C and 30 °C, and in a cycle length range of 1–18 h. In this study, the microbial community structure of the PHB-producing enrichments was found to be strongly dependent on temperature, but not on cycle length. Zoogloea and Plasticicumulans acidivorans dominated the SBRs operated at 20 °C and 30 °C, respectively. Both enrichments accumulated PHB more than 75% of cell dry weight. Short-term temperature change experiments revealed that P. acidivorans was more temperature sensitive as compared with Zoogloea. This is particularly true for the PHB degradation, resulting in incomplete PHB degradation in P. acidivorans at 20 °C. Incomplete PHB degradation limited biomass growth and allowed Zoogloea to outcompete P. acidivorans. The PHB content at the end of the feast phase correlated well with the cycle length at a constant solid retention time (SRT). These results suggest that to establish enrichment with the capacity to store a high fraction of PHB, the number of cycles per SRT should be minimized independent of the temperature. PMID:21107441

  20. Effect of temperature and cycle length on microbial competition in PHB-producing sequencing batch reactor.

    PubMed

    Jiang, Yang; Marang, Leonie; Kleerebezem, Robbert; Muyzer, Gerard; van Loosdrecht, Mark C M

    2011-05-01

    The impact of temperature and cycle length on microbial competition between polyhydroxybutyrate (PHB)-producing populations enriched in feast-famine sequencing batch reactors (SBRs) was investigated at temperatures of 20 °C and 30 °C, and in a cycle length range of 1-18 h. In this study, the microbial community structure of the PHB-producing enrichments was found to be strongly dependent on temperature, but not on cycle length. Zoogloea and Plasticicumulans acidivorans dominated the SBRs operated at 20 °C and 30 °C, respectively. Both enrichments accumulated PHB more than 75% of cell dry weight. Short-term temperature change experiments revealed that P. acidivorans was more temperature sensitive as compared with Zoogloea. This is particularly true for the PHB degradation, resulting in incomplete PHB degradation in P. acidivorans at 20 °C. Incomplete PHB degradation limited biomass growth and allowed Zoogloea to outcompete P. acidivorans. The PHB content at the end of the feast phase correlated well with the cycle length at a constant solid retention time (SRT). These results suggest that to establish enrichment with the capacity to store a high fraction of PHB, the number of cycles per SRT should be minimized independent of the temperature.

  1. Microbial cycling of volatile organic sulfur compounds in anoxic environments.

    PubMed

    Lomans, B P; Pol, A; Op den Camp, H J M

    2002-01-01

    Microbial cycling of volatile organic sulfur compounds (VOSC) is investigated due to the impact these compounds are thought to have on environmental processes like global temperature control, acid precipitation and the global sulfur cycle. Moreover, in several kinds of industries like composting plants and the paper industry VOSC are released causing odor problems. Waste streams containing these compounds must be treated in order to avoid the release of these compounds to the atmosphere. This paper describes the general mechanisms for the production and degradation of methanethiol (MT) and dimethyl sulfide (DMS), two ubiquitous VOSC in anaerobic environments. Slurry incubations indicated that methylation of sulfide and MT resulting in MT and DMS, respectively, is one of the major mechanisms for VOSC in sulfide-rich anaerobic environments. An anaerobic bacterium that is responsible for the formation of MT and DMS through the anaerobic methylation of H2S and MT was isolated from a freshwater pond after enrichment with syringate as a methyl group donating compound and sole carbon source. In spite of the continuous formation of MT and DMS, steady state concentrations are generally very low. This is due to the microbial degradation of these compounds. Experiments with sulfate-rich and sulfate-amended sediment slurries demonstrated that besides methanogens, sulfate-reducing bacteria can also degrade MT and DMS, provided that sulfate is available. A methanogen was isolated that is able to grow on DMS as the sole carbon source. A large survey of sediments slurries of various origin demonstrated that both isolates are commonly occurring inhabitants of anaerobic environments.

  2. Microbial Fuel Cells for Powering Navy Devices

    DTIC Science & Technology

    2014-01-20

    the anode is generated by fermentation of glucose by other microorganisms in the sediment represented by clostridium in Fig. 4. The products of the...MICROBIAL FUEL CELLS (ADAPTED FROM REF. A1) INTRODUCTION Dissimilatory metal-reducing bacteria (DMRB) are a class of microorganisms that...anode catalysts in microbial fuel cells. In the case of Geobacter spp., which are Deltaproteobacteria, a group of bacteria that share many similar

  3. What cycles the cell? -Robust autonomous cell cycle models.

    PubMed

    Lavi, Orit; Louzoun, Yoram

    2009-12-01

    The cell cycle is one of the best studied cellular mechanisms at the experimental and theoretical levels. Although most of the important biochemical components and reactions of the cell cycle are probably known, the precise way the cell cycle dynamics are driven is still under debate. This phenomenon is not atypical to many other biological systems where the knowledge of the molecular building blocks and the interactions between them does not lead to a coherent picture of the appropriate dynamics. We here propose a methodology to develop plausible models for the driving mechanisms of embryonic and cancerous cell cycles. We first define a key property of the system (a cyclic behaviour in the case of the embryonic cell cycle) and set mathematical constraints on the types of two variable simplified systems robustly reproducing such a cyclic behaviour. We then expand these robust systems to three variables and reiterate the procedure. At each step, we further limit the type of expanded systems to fit the known microbiology until a detailed description of the system is obtained. This methodology produces mathematical descriptions of the required biological systems that are more robust to changes in the precise function and rate constants. This methodology can be extended to practically any type of subcellular mechanism.

  4. Microbial nitrogen cycling response to forest-based bioenergy production.

    PubMed

    Minick, Kevan J; Strahm, Brian D; Fox, Thomas R; Sucre, Eric B; Leggett, Zakiya H

    2015-12-01

    Concern over rising atmospheric CO2 and other greenhouse gases due to fossil fuel combustion has intensified research into carbon-neutral energy production. Approximately 15.8 million ha of pine plantations exist across the southeastern United States, representing a vast land area advantageous for bioenergy production without significant landuse change or diversion of agricultural resources from food production. Furthermore, intercropping of pine with bioenergy grasses could provide annually harvestable, lignocellulosic biomass feedstocks along with production of traditional wood products. Viability of such a system hinges in part on soil nitrogen (N) availability and effects of N competition between pines and grasses on ecosystem productivity. We investigated effects of intercropping loblolly pine (Pinus taeda) with switchgrass (Panicum virgatum) on microbial N cycling processes in the Lower Coastal Plain of North Carolina, USA. Soil samples were collected from bedded rows of pine and interbed space of two treatments, composed of either volunteer native woody and herbaceous vegetation (pine-native) or pure switchgrass (pine-switchgrass) in interbeds. An in vitro 15N pool-dilution technique was employed to quantify gross N transformations at two soil depths (0-5 and 5-15 cm) on four dates in 2012-2013. At the 0-5 cm depth in beds of the pine-switchgrass treatment, gross N mineralization was two to three times higher in November and February compared to the pine-native treatment, resulting in increased NH4(+) availability. Gross and net nitrification were also significantly higher in February in the same pine beds. In interbeds of the pine-switchgrass treatment, gross N mineralization was lower from April to November, but higher in February, potentially reflecting positive effects of switchgrass root-derived C inputs during dormancy on microbial activity. These findings indicate soil N cycling and availability has increased in pine beds of the pine

  5. Microbial Character Related Sulfur Cycle under Dynamic Environmental Factors Based on the Microbial Population Analysis in Sewerage System

    PubMed Central

    Dong, Qian; Shi, Hanchang; Liu, Yanchen

    2017-01-01

    The undesired sulfur cycle derived by microbial population can ultimately causes the serious problems of sewerage systems. However, the microbial community characters under dynamic environment factors in actual sewerage system is still not enough. This current study aimed to character the distributions and compositions of microbial communities that participate in the sulfur cycle under the dynamic environmental conditions in a local sewerage system. To accomplish this, microbial community compositions were assessed using 454 high-throughput sequencing (16S rDNA) combined with dsrB gene-based denaturing gradient gel electrophoresis. The results indicated that a higher diversity of microbial species was present at locations in sewers with high concentrations of H2S. Actinobacteria and Proteobacteria were dominant in the sewerage system, while Actinobacteria alone were dominant in regions with high concentrations of H2S. Specifically, the unique operational taxonomic units could aid to characterize the distinct microbial communities within a sewerage manhole. The proportion of sulfate-reducing bacteria, each sulfur-oxidizing bacteria (SOB) were strongly correlated with the liquid parameters (DO, ORP, COD, Sulfide, NH3-N), while the Mycobacterium and Acidophilic SOB (M&A) was strongly correlated with gaseous factors within the sewer, such as H2S, CH4, and CO. Identifying the distributions and proportions of critical microbial communities within sewerage systems could provide insights into how the microbial sulfur cycle is affected by the dynamic environmental conditions that exist in sewers and might be useful for explaining the potential sewerage problems. PMID:28261160

  6. Microbial Character Related Sulfur Cycle under Dynamic Environmental Factors Based on the Microbial Population Analysis in Sewerage System.

    PubMed

    Dong, Qian; Shi, Hanchang; Liu, Yanchen

    2017-01-01

    The undesired sulfur cycle derived by microbial population can ultimately causes the serious problems of sewerage systems. However, the microbial community characters under dynamic environment factors in actual sewerage system is still not enough. This current study aimed to character the distributions and compositions of microbial communities that participate in the sulfur cycle under the dynamic environmental conditions in a local sewerage system. To accomplish this, microbial community compositions were assessed using 454 high-throughput sequencing (16S rDNA) combined with dsrB gene-based denaturing gradient gel electrophoresis. The results indicated that a higher diversity of microbial species was present at locations in sewers with high concentrations of H2S. Actinobacteria and Proteobacteria were dominant in the sewerage system, while Actinobacteria alone were dominant in regions with high concentrations of H2S. Specifically, the unique operational taxonomic units could aid to characterize the distinct microbial communities within a sewerage manhole. The proportion of sulfate-reducing bacteria, each sulfur-oxidizing bacteria (SOB) were strongly correlated with the liquid parameters (DO, ORP, COD, Sulfide, NH3-N), while the Mycobacterium and Acidophilic SOB (M&A) was strongly correlated with gaseous factors within the sewer, such as H2S, CH4, and CO. Identifying the distributions and proportions of critical microbial communities within sewerage systems could provide insights into how the microbial sulfur cycle is affected by the dynamic environmental conditions that exist in sewers and might be useful for explaining the potential sewerage problems.

  7. Autoradiography and the Cell Cycle.

    ERIC Educational Resources Information Center

    Jones, C. Weldon

    1992-01-01

    Outlines the stages of a cell biology "pulse-chase" experiment in which the students apply autoradiography techniques to learn about the concept of the cell cycle. Includes (1) seed germination and plant growth; (2) radioactive labeling and fixation of root tips; (3) feulgen staining of root tips; (4) preparation of autoradiograms; and…

  8. Autoradiography and the Cell Cycle.

    ERIC Educational Resources Information Center

    Jones, C. Weldon

    1992-01-01

    Outlines the stages of a cell biology "pulse-chase" experiment in which the students apply autoradiography techniques to learn about the concept of the cell cycle. Includes (1) seed germination and plant growth; (2) radioactive labeling and fixation of root tips; (3) feulgen staining of root tips; (4) preparation of autoradiograms; and…

  9. Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

    PubMed

    Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2016-06-15

    The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling.

  10. Microbial Cell Factories for Diol Production.

    PubMed

    Sabra, W; Groeger, C; Zeng, An-Ping

    2016-01-01

    Diols are compounds with two hydroxyl groups and have a wide range of appealing applications as chemicals and fuels. In particular, five low molecular diol compounds, namely 1,3-propanediol (1,3-PDO), 1,2-propanediol (1,2-PDO), 2,3-butanediol (2,3-BDO), 1,3-butanediol (1,3-BDO), and 1,4-butanediol (1,4-BDO), can be biotechnologically produced by direct microbial bioconversion of renewable materials. In this review, we summarize recent developments in the microbial production of diols, especially regarding the engineering of typical microbial strains as cell factory and the development of corresponding bioconversion processes.

  11. Cell Cycle Regulation and Melanoma.

    PubMed

    Xu, Wen; McArthur, Grant

    2016-06-01

    Dysregulation of cell cycle control is a hallmark of melanomagenesis. Agents targeting the G1-S and G2-M checkpoints, as well as direct anti-mitotic agents, have all shown promising preclinical activity in melanoma. However, in vivo, standalone single agents targeting cell cycle regulation have only demonstrated modest efficacy in unselected patients. The advent of specific CDK 4/6 inhibitors targeting the G1-S transition, with an improved therapeutic index, is a significant step forward. Potential synergy exists with the combination of CDK4/6 inhibitors with existing therapies targeting the MAPK pathway, particularly in subsets of metastatic melanomas such as NRAS and BRAF mutants. This reviews summaries of the latest developments in both preclinical and clinical data with cell cycle-targeted therapies in melanoma.

  12. Functionally stable and phylogenetically diverse microbial enrichments from microbial fuel cells during wastewater treatment.

    PubMed

    Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M; Nealson, Kenneth H; Sekiguchi, Yuji; Gorby, Yuri A; Bretschger, Orianna

    2012-01-01

    Microbial fuel cells (MFCs) are devices that exploit microorganisms as biocatalysts to recover energy from organic matter in the form of electricity. One of the goals of MFC research is to develop the technology for cost-effective wastewater treatment. However, before practical MFC applications are implemented it is important to gain fundamental knowledge about long-term system performance, reproducibility, and the formation and maintenance of functionally-stable microbial communities. Here we report findings from a MFC operated for over 300 days using only primary clarifier effluent collected from a municipal wastewater treatment plant as the microbial resource and substrate. The system was operated in a repeat-batch mode, where the reactor solution was replaced once every two weeks with new primary effluent that consisted of different microbial and chemical compositions with every batch exchange. The turbidity of the primary clarifier effluent solution notably decreased, and 97% of biological oxygen demand (BOD) was removed after an 8-13 day residence time for each batch cycle. On average, the limiting current density was 1000 mA/m(2), the maximum power density was 13 mW/m(2), and coulombic efficiency was 25%. Interestingly, the electrochemical performance and BOD removal rates were very reproducible throughout MFC operation regardless of the sample variability associated with each wastewater exchange. While MFC performance was very reproducible, the phylogenetic analyses of anode-associated electricity-generating biofilms showed that the microbial populations temporally fluctuated and maintained a high biodiversity throughout the year-long experiment. These results suggest that MFC communities are both self-selecting and self-optimizing, thereby able to develop and maintain functional stability regardless of fluctuations in carbon source(s) and regular introduction of microbial competitors. These results contribute significantly toward the practical application

  13. Functionally Stable and Phylogenetically Diverse Microbial Enrichments from Microbial Fuel Cells during Wastewater Treatment

    PubMed Central

    Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M.; Nealson, Kenneth H.; Sekiguchi, Yuji; Gorby, Yuri A.; Bretschger, Orianna

    2012-01-01

    Microbial fuel cells (MFCs) are devices that exploit microorganisms as biocatalysts to recover energy from organic matter in the form of electricity. One of the goals of MFC research is to develop the technology for cost-effective wastewater treatment. However, before practical MFC applications are implemented it is important to gain fundamental knowledge about long-term system performance, reproducibility, and the formation and maintenance of functionally-stable microbial communities. Here we report findings from a MFC operated for over 300 days using only primary clarifier effluent collected from a municipal wastewater treatment plant as the microbial resource and substrate. The system was operated in a repeat-batch mode, where the reactor solution was replaced once every two weeks with new primary effluent that consisted of different microbial and chemical compositions with every batch exchange. The turbidity of the primary clarifier effluent solution notably decreased, and 97% of biological oxygen demand (BOD) was removed after an 8–13 day residence time for each batch cycle. On average, the limiting current density was 1000 mA/m2, the maximum power density was 13 mW/m2, and coulombic efficiency was 25%. Interestingly, the electrochemical performance and BOD removal rates were very reproducible throughout MFC operation regardless of the sample variability associated with each wastewater exchange. While MFC performance was very reproducible, the phylogenetic analyses of anode-associated electricity-generating biofilms showed that the microbial populations temporally fluctuated and maintained a high biodiversity throughout the year-long experiment. These results suggest that MFC communities are both self-selecting and self-optimizing, thereby able to develop and maintain functional stability regardless of fluctuations in carbon source(s) and regular introduction of microbial competitors. These results contribute significantly toward the practical application of

  14. Stable isotope approaches for tracking C cycling and function in microbial communities

    NASA Astrophysics Data System (ADS)

    Pett-Ridge, J.

    2008-12-01

    Identifying the microorganisms responsible for specific processes in C cycling remains a major challenge in environmental microbiology, one that requires integration of multiple techniques. Stable isotope probing, or SIP, has come to represent a variety of powerful approaches that allow simultaneous identification of identity and function in microbial communities. Bulk methods such as DNA/RNA-SIP and PLFA-SIP are well developed and allow tracking of a multitude of C substrates (acetate, cellulose, CH4, CO2, and plant litter) into specific microbial consumers. However, to understand the spatio-temporal context of may key C transformations and microbial interactions, new imaging technologies are needed to analyze processes and properties of macromolecule complexes, microbes, plant root cells, soil (micro)aggregates, phytoplankton and marine snow as they undergoes formation and decomposition. New and sensitive in situ approaches include NanoSIMS single cell analysis, isotope arrays, and combinations of immuno- or FISH labeling with high resolution isotope imaging. Recent work illustrates how these powerful new techniques use targeted stable isotope probing to measure biological, physical and chemical processes and can be used in soil systems to study microbial mats or rhizosphere interactions. In both terrestrial and aquatic systems, they allow us to directly link C and other nutrient metabolism at the organismal level. Lastly, these new aproaches may be of great use in the study of trophic cascades and metabolic networks. While cross-feeding is often thought of as a confounding effect in SIP-type studies, with fine scale temporal sampling and FISH-SIMS analysis, we have the opportunity trace C flows through microbial foodwebs and to their eventual fate in stabilized organic-mineral complexes.

  15. Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem

    PubMed Central

    Andrade, Karen; Logemann, Jörn; Heidelberg, Karla B; Emerson, Joanne B; Comolli, Luis R; Hug, Laura A; Probst, Alexander J; Keillar, Angus; Thomas, Brian C; Miller, Christopher S; Allen, Eric E; Moreau, John W; Brocks, Jochen J; Banfield, Jillian F

    2015-01-01

    Marine microbial communities experience daily fluctuations in light and temperature that can have important ramifications for carbon and nutrient cycling. Elucidation of such short time scale community-wide dynamics is hindered by system complexity. Hypersaline aquatic environments have lower species richness than marine environments and can be well-defined spatially, hence they provide a model system for diel cycle analysis. We conducted a 3-day time series experiment in a well-defined pool in hypersaline Lake Tyrrell, Australia. Microbial communities were tracked by combining cultivation-independent lipidomic, metagenomic and microscopy methods. The ratio of total bacterial to archaeal core lipids in the planktonic community increased by up to 58% during daylight hours and decreased by up to 32% overnight. However, total organism abundances remained relatively consistent over 3 days. Metagenomic analysis of the planktonic community composition, resolved at the genome level, showed dominance by Haloquadratum species and six uncultured members of the Halobacteriaceae. The post 0.8 μm filtrate contained six different nanohaloarchaeal types, three of which have not been identified previously, and cryo-transmission electron microscopy imaging confirmed the presence of small cells. Notably, these nano-sized archaea showed a strong diel cycle, with a pronounced increase in relative abundance over the night periods. We detected no eukaryotic algae or other photosynthetic primary producers, suggesting that carbon resources may derive from patchily distributed microbial mats at the sediment-water interface or from surrounding land. Results show the operation of a strong community-level diel cycle, probably driven by interconnected temperature, light abundance, dissolved oxygen concentration and nutrient flux effects. PMID:25918833

  16. Microbial fuel cells: Running on gas

    NASA Astrophysics Data System (ADS)

    Ren, Zhiyong Jason

    2017-06-01

    Methane is an abundant energy source that is used for power generation in thermal power plants via combustion, but direct conversion to electricity in fuel cells remains challenging. Now, a microbial fuel cell is demonstrated to efficiently convert methane directly to current by careful selection of a consortium of microorganisms.

  17. Variations in microbial carbon sources and cycling in the deep continental subsurface

    NASA Astrophysics Data System (ADS)

    Simkus, Danielle N.; Slater, Greg F.; Lollar, Barbara Sherwood; Wilkie, Kenna; Kieft, Thomas L.; Magnabosco, Cara; Lau, Maggie C. Y.; Pullin, Michael J.; Hendrickson, Sarah B.; Wommack, K. Eric; Sakowski, Eric G.; van Heerden, Esta; Kuloyo, Olukayode; Linage, Borja; Borgonie, Gaetan; Onstott, Tullis C.

    2016-01-01

    Deep continental subsurface fracture water systems, ranging from 1.1 to 3.3 km below land surface (kmbls), were investigated to characterize the indigenous microorganisms and elucidate microbial carbon sources and their cycling. Analysis of phospholipid fatty acid (PLFA) abundances and direct cell counts detected varying biomass that was not correlated with depth. Compound-specific carbon isotope analyses (δ13C and Δ14C) of the phospholipid fatty acids (PLFAs) and carbon substrates combined with genomic analyses did identify, however, distinct carbon sources and cycles between the two depth ranges studied. In the shallower boreholes at circa 1 kmbls, isotopic evidence indicated microbial incorporation of biogenic CH4 by the in situ microbial community. At the shallowest site, 1.05 kmbls in Driefontein mine, this process clearly dominated the isotopic signal. At slightly deeper depths, 1.34 kmbls in Beatrix mine, the isotopic data indicated the incorporation of both biogenic CH4 and dissolved inorganic carbon (DIC) derived from CH4 oxidation. In both of these cases, molecular genetic analysis indicated that methanogenic and methanotrophic organisms together comprised a small component (<5%) of the microbial community. Thus, it appears that a relatively minor component of the prokaryotic community is supporting a much larger overall bacterial community in these samples. In the samples collected from >3 kmbls in Tau Tona mine (TT107, TT109 Bh2), the CH4 had an isotopic signature suggesting a predominantly abiogenic origin with minor inputs from microbial methanogenesis. In these samples, the isotopic enrichments (δ13C and Δ14C) of the PLFAs relative to CH4 were consistent with little incorporation of CH4 into the biomass. The most 13C-enriched PLFAs were observed in TT107 where the dominant CO2-fixation pathway was the acetyl-CoA pathway by non-acetogenic bacteria. The differences in the δ13C of the PLFAs and the DIC and DOC for TT109 Bh2 were ∼-24‰ and 0

  18. Mitochondrial dynamics during cell cycling.

    PubMed

    Horbay, Rostyslav; Bilyy, Rostyslav

    2016-12-01

    Mitochondria are the cell's power plant that must be in a proper functional state in order to produce the energy necessary for basic cellular functions, such as proliferation. Mitochondria are 'dynamic' in that they are constantly undergoing fission and fusion to remain in a functional state throughout the cell cycle, as well as during other vital processes such as energy supply, cellular respiration and programmed cell death. The mitochondrial fission/fusion machinery is involved in generating young mitochondria, while eliminating old, damaged and non-repairable ones. As a result, the organelles change in shape, size and number throughout the cell cycle. Such precise and accurate balance is maintained by the cytoskeletal transporting system via microtubules, which deliver the mitochondrion from one location to another. During the gap phases G1 and G2, mitochondria form an interconnected network, whereas in mitosis and S-phase fragmentation of the mitochondrial network will take place. However, such balance is lost during neoplastic transformation and autoimmune disorders. Several proteins, such as Drp1, Fis1, Kif-family proteins, Opa1, Bax and mitofusins change in activity and might link the mitochondrial fission/fusion events with processes such as alteration of mitochondrial membrane potential, apoptosis, necrosis, cell cycle arrest, and malignant growth. All this indicates how vital proper functioning of mitochondria is in maintaining cell integrity and preventing carcinogenesis.

  19. Cell cycle regulation and regeneration.

    PubMed

    Heber-Katz, Ellen; Zhang, Yong; Bedelbaeva, Khamila; Song, Fengyu; Chen, Xiaoping; Stocum, David L

    2013-01-01

    Regeneration of ear punch holes in the MRL mouse and amputated limbs of the axolotl show a number of similarities. A large proportion of the fibroblasts of the uninjured MRL mouse ear are arrested in G2 of the cell cycle, and enter nerve-dependent mitosis after injury to form a ring-shaped blastema that regenerates the ear tissue. Multiple cell types contribute to the establishment of the regeneration blastema of the urodele limb by dedifferentiation, and there is substantial reason to believe that the cells of this early blastema are also arrested in G2, and enter mitosis under the influence of nerve-dependent factors supplied by the apical epidermal cap. Molecular analysis reveals other parallels, such as; (1) the upregulation of Evi5, a centrosomal protein that prevents mitosis by stabilizing Emi1, a protein that inhibits the degradation of cyclins by the anaphase promoting complex and (2) the expression of sodium channels by the epidermis. A central feature in the entry into the cell cycle by MRL ear fibroblasts is a natural downregulation of p21, and knockout of p21 in wild-type mice confers regenerative capacity on non-regenerating ear tissue. Whether the same is true for entry into the cell cycle in regenerating urodele limbs is presently unknown.

  20. [Cell cycle regulation in cancer stem cells].

    PubMed

    Takeishi, Shoichiro

    2015-05-01

    In addition to the properties of self-renewal and multipotency, cancer stem cells share the characteristics of their distinct cell cycle status with somatic stem cells. Cancer stem cells (CSCs) are maintained in a quiescent state with this characteristic conferring resistance to anticancer therapies that target dividing cells. Elucidation of the mechanisms of CSC quiescence might therefore be expected to provide further insight into CSC behaviors and lead to the elimination of cancer. This review summarizes several key regulators of the cell cycle in CSCs as well as attempts to define future challenges in this field, especially from the point of view of the application of our current understandings to the clinical medicine.

  1. Microbial interactions in the arsenic cycle: adoptive strategies and applications in environmental management.

    PubMed

    Dhuldhaj, Umesh Praveen; Yadav, Ishwar Chandra; Singh, Surendra; Sharma, Naveen Kumar

    2013-01-01

    Arsenic (As) is a nonessential element that is often present in plants and in other organisms. However, it is one of the most hazardous of toxic elements globally. In many parts of the world, arsenic contamination in groundwater is a serious and continuing threat to human health. Microbes play an important role in regulating the environmental fate of arsenic. Different microbial processes influence the biogeochemical cycling of arsenic in ways that affect the accumulation of different arsenic species in various ecosystem compartments. For example, in soil, there are bacteria that methylate arsenite to trimethylarsine gas, thereby releasing arsenic to the atmosphere.In marine ecosystems, microbes exist that can convert inorganic arsenicals to organic arsenicals (e.g., di- and tri-methylated arsenic derivatives, arsenocholine,arsenobetaine, arsenosugars, arsenolipids). The organo arsenicals are further metabolized to complete the arsenic cycle.Microbes have developed various strategies that enable them to tolerate arsenic and to survive in arsenic-rich environments. Such strategies include As exclusion from cells by establishing permeability barrier, intra- and extracellular sequestration,active efflux pumps, enzymatic reduction, and reduction in the sensitivity of cellular targets. These strategies are used either singly or in combination. In bacteria,the genes for arsenic resistance/detoxification are encoded by the arsenic resistance operons (ars operon).In this review, we have addressed and emphasized the impact of different microbial processes (e.g., arsenite oxidation, cytoplasmic arsenate reduction, respiratory arsenate reduction, arsenite methylation) on the arsenic cycle. Microbes are the only life forms reported to exist in heavy arsenic-contaminated environments. Therefore,an understanding of the strategies adopted by microbes to cope with arsenic stress is important in managing such arsenic-contaminated sites. Further future insights into the different

  2. Virus manipulation of cell cycle.

    PubMed

    Nascimento, R; Costa, H; Parkhouse, R M E

    2012-07-01

    Viruses depend on host cell resources for replication and access to those resources may be limited to a particular phase of the cell cycle. Thus manipulation of cell cycle is a commonly employed strategy of viruses for achieving a favorable cellular environment. For example, viruses capable of infecting nondividing cells induce S phase in order to activate the host DNA replication machinery and provide the nucleotide triphosphates necessary for viral DNA replication (Flemington in J Virol 75:4475-4481, 2001; Sullivan and Pipas in Microbiol Mol Biol Rev 66:179-202, 2002). Viruses have developed several strategies to subvert the cell cycle by association with cyclin and cyclin-dependent kinase complexes and molecules that regulate their activity. Viruses tend to act on cellular proteins involved in a network of interactions in a way that minimal protein-protein interactions lead to a major effect. The complex and interactive nature of intracellular signaling pathways controlling cell division affords many opportunities for virus manipulation strategies. Taking the maxim "Set a thief to catch a thief" as a counter strategy, however, provides us with the very same virus evasion strategies as "ready-made tools" for the development of novel antivirus therapeutics. The most obvious are attenuated virus vaccines with critical evasion genes deleted. Similarly, vaccines against viruses causing cancer are now being successfully developed. Finally, as viruses have been playing chess with our cell biology and immune responses for millions of years, the study of their evasion strategies will also undoubtedly reveal new control mechanisms and their corresponding cellular intracellular signaling pathways.

  3. Coastal microbial fuel cell: scaling laws and systems

    NASA Astrophysics Data System (ADS)

    Bandyopadhyay, Promode R.; McNeilly, Frank J.; Thivierge, Daniel P.; Fredette, Albert R.

    2006-05-01

    Microbes, like Geobacters, have inhabited the seafloors around the world since the early days of earth. Such regions are anaerobic and they gain energy by using the widely prevalent iron oxides and organic matters. Because they appear to colonize conducting surfaces that act as sinks of electrons, microbial fuel cells have been shown to convert organic matter to electricity. A microbial fuel cell system has been deployed in Narragansett Bay in Newport, Rhode Island for a year. Currently, the cathode and anode areas are of the order of that of a small wind mill. Measurements have been carried out to determine the marine scaling laws of power harvesting in passive benthic microbial fuel cells. The focus has been on the ocean engineering aspects such as marine scaling laws and the integration of the biochemical and the electronic systems. The characteristics examined are: the relationship of electrode surface area and power produced, the stabilization rates of ionic paths, that is, the effects of location depth of cathodes on stabilization after deployment, the effects of solar and lunar cycles in the Narragansett Bay on the dynamic components of power produced, and the hysteresis effects between periods of active power harvesting and dormancy; the effects of 'on sediment surface' versus 'in sediment' anode deployment have been examined for smaller electrode areas so far. A capacitance model of power consumption and harvesting has been proposed for the marine environment. It is assumed that the primordial benthic microbe laden layer of the earth acts like a giant capacitor. In the microbial fuel cell, this charged benthic layer acts in series with a smaller constant voltage DC power source. This giant benthic capacitance is a result of untapped accumulated charge from the microbes while the DC source originates from the real-time production due to the microbes. Finally, the microbial fuel cell is integrated with a power conversion system to intermittently energize a

  4. [Advances in microbial solar cells--A review].

    PubMed

    Guo, Xiaoyun; Yu, Changping; Zheng, Tianling

    2015-08-04

    The energy crisis has become one of the major problems hindering the development of the world. The emergence of microbial fuel cells provides a new solution to the energy crisis. Microbial solar cells, integrating photosynthetic organisms such as plants and microalgae into microbial fuel cells, can convert solar energy into electrical energy. Microbial solar cell has steady electric energy, and broad application prospects in wastewater treatment, biodiesel processing and intermediate metabolites production. Here we reviewed recent progress of microbial solar cells from the perspective of the role of photosynthetic organisms in microbial fuel cells, based on a vast amount of literature, and discussed their advantages and deficiency. At last, brief analysis of the facing problems and research needs of microbial fuel cells are undertaken. This work was expected to be beneficial for the application of the microbial solar cells technology.

  5. Nitrogen cycling and water pulses in semiarid grasslands: Are microbial and plant processes temporarily asynchronous?

    USDA-ARS?s Scientific Manuscript database

    Precipitation pulses in arid ecosystems can lead to temporal asynchrony in microbial and plant processing of nitrogen (N) during drying/wetting cycles causing increased N loss. In contrast, more consistent availability of soil moisture in mesic ecosystems can synchronize microbial and plant processe...

  6. Autonomous, Retrievable, Deep Sea Microbial Fuel Cell

    NASA Astrophysics Data System (ADS)

    Richter, K.

    2014-12-01

    Microbial fuel cells (MFCs) work by providing bacteria in anaerobic sediments with an electron acceptor (anode) that stimulates metabolism of organic matter. The buried anode is connected via control circuitry to a cathode exposed to oxygen in the overlying water. During metabolism, bacteria release hydrogen ions into the sediment and transfer electrons extra-cellularly to the anode, which eventually reduce dissolved oxygen at the cathode, forming water. The open circuit voltage is approximately 0.8 v. The voltage between electrodes is operationally kept at 0.4 v with a potentiastat. The current is chiefly limited by the rate of microbial metabolism at the anode. The Office of Naval Research has encouraged development of microbial fuel cells in the marine environment at a number of academic and naval institutions. Earlier work in shallow sediments of San Diego Bay showed that the most important environmental parameters that control fuel cell power output in San Diego Bay were total organic carbon in the sediment and seasonal water temperature. Current MFC work at SPAWAR includes extension of microbial fuel cell tests to the deep sea environment (>1000 m) and, in parallel, testing microbial fuel cells in the laboratory under deep sea conditions. One question we are asking is whether MFC power output from deep water sediments repressurized and chilled in the laboratory comparable to those measured in situ. If yes, mapping the power potential of deep sea sediments may be made much easier, requiring sediment grabs and lab tests rather than deployment and retrieval of fuel cells. Another question we are asking is whether in situ temperature and total organic carbon in the deep sea sediment can predict MFC power. If yes, then we can make use of the large collection of publicly available, deep sea oceanographic measurements to make these predictions, foregoing expensive work at sea. These regressions will be compared to those derived from shallow water measurements.

  7. Interval scanning photomicrography of microbial cell populations.

    NASA Technical Reports Server (NTRS)

    Casida, L. E., Jr.

    1972-01-01

    A single reproducible area of the preparation in a fixed focal plane is photographically scanned at intervals during incubation. The procedure can be used for evaluating the aerobic or anaerobic growth of many microbial cells simultaneously within a population. In addition, the microscope is not restricted to the viewing of any one microculture preparation, since the slide cultures are incubated separately from the microscope.

  8. Electricity production and microbial characterization of thermophilic microbial fuel cells.

    PubMed

    Dai, Kun; Wen, Jun-Li; Zhang, Fang; Ma, Xi-Wen; Cui, Xiang-Yu; Zhang, Qi; Zhao, Ting-Jia; Zeng, Raymond J

    2017-07-01

    Thermophilic microbial fuel cell (TMFC) offers many benefits, but the investigations on the diversity of exoelectrogenic bacteria are scarce. In this study, a two-chamber TMFC was constructed using ethanol as an electron donor, and the microbial dynamics were analyzed by high-throughput sequencing and 16S rRNA clone-library sequencing. The open-circuit potential of TMFC was approximately 650mV, while the maximum voltage was around 550mV. The maximum power density was 437mW/m(2), and the columbic efficiency in this work was 20.5±6.0%. The Firmicutes bacteria, related to the uncultured bacterium clone A55_D21_H_B_C01 with a similarity of 99%, accounted for 90.9% of all bacteria in the TMFC biofilm. This unknown bacterium has the potential to become a new thermophilic exoelectrogenic bacterium that is yet to be cultured. The development of TMFC-involved biotechnologies will be beneficial for the production of valuable chemicals and generation of energy in the future. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Microbial sulfur cycle in two hydrothermal chimneys on the Southwest Indian Ridge.

    PubMed

    Cao, Huiluo; Wang, Yong; Lee, On On; Zeng, Xiang; Shao, Zongze; Qian, Pei-Yuan

    2014-01-28

    Sulfur is an important element in sustaining microbial communities present in hydrothermal vents. Sulfur oxidation has been extensively studied due to its importance in chemosynthetic pathways in hydrothermal fields; however, less is known about sulfate reduction. Here, the metagenomes of hydrothermal chimneys located on the ultraslow-spreading Southwest Indian Ridge (SWIR) were pyrosequenced to elucidate the associated microbial sulfur cycle. A taxonomic summary of known genes revealed a few dominant bacteria that participated in the microbial sulfur cycle, particularly sulfate-reducing Deltaproteobacteria. The metagenomes studied contained highly abundant genes related to sulfur oxidation and reduction. Several carbon metabolic pathways, in particular the Calvin-Benson-Bassham pathway and the reductive tricarboxylic acid cycles for CO2 fixation, were identified in sulfur-oxidizing autotrophic bacteria. In contrast, highly abundant genes related to the oxidation of short-chain alkanes were grouped with sulfate-reducing bacteria, suggesting an important role for short-chain alkanes in the sulfur cycle. Furthermore, sulfur-oxidizing bacteria were associated with enrichment for genes involved in the denitrification pathway, while sulfate-reducing bacteria displayed enrichment for genes responsible for hydrogen utilization. In conclusion, this study provides insights regarding major microbial metabolic activities that are driven by the sulfur cycle in low-temperature hydrothermal chimneys present on an ultraslow midocean ridge. There have been limited studies on chimney sulfides located at ultraslow-spreading ridges. The analysis of metagenomes of hydrothermal chimneys on the ultraslow-spreading Southwest Indian Ridge suggests the presence of a microbial sulfur cycle. The sulfur cycle should be centralized within a microbial community that displays enrichment for sulfur metabolism-related genes. The present study elucidated a significant role of the microbial sulfur

  10. Single-cell transcriptomics for microbial eukaryotes.

    PubMed

    Kolisko, Martin; Boscaro, Vittorio; Burki, Fabien; Lynn, Denis H; Keeling, Patrick J

    2014-11-17

    One of the greatest hindrances to a comprehensive understanding of microbial genomics, cell biology, ecology, and evolution is that most microbial life is not in culture. Solutions to this problem have mainly focused on whole-community surveys like metagenomics, but these analyses inevitably loose information and present particular challenges for eukaryotes, which are relatively rare and possess large, gene-sparse genomes. Single-cell analyses present an alternative solution that allows for specific species to be targeted, while retaining information on cellular identity, morphology, and partitioning of activities within microbial communities. Single-cell transcriptomics, pioneered in medical research, offers particular potential advantages for uncultivated eukaryotes, but the efficiency and biases have not been tested. Here we describe a simple and reproducible method for single-cell transcriptomics using manually isolated cells from five model ciliate species; we examine impacts of amplification bias and contamination, and compare the efficacy of gene discovery to traditional culture-based transcriptomics. Gene discovery using single-cell transcriptomes was found to be comparable to mass-culture methods, suggesting single-cell transcriptomics is an efficient entry point into genomic data from the vast majority of eukaryotic biodiversity.

  11. Reduced Gas Cycling in Microbial Mats: Implications for Early Earth

    NASA Technical Reports Server (NTRS)

    Hoehler, Tori M.; Bebout, Brad M.; DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    For more than half the history of life on Earth, biological productivity was dominated by photosynthetic microbial mats. During this time, mats served as the preeminent biological influence on earth's surface and atmospheric chemistry and also as the primary crucible for microbial evolution. We find that modern analogs of these ancient mat communities generate substantial quantities of hydrogen, carbon monoxide, and methane. Escape of these gases from the biosphere would contribute strongly to atmospheric evolution and potentially to the net oxidation of earth's surface; sequestration within the biosphere carries equally important implications for the structure, function, and evolution of anaerobic microbial communities within the context of mat biology.

  12. Microbial fuel cells for biosensor applications.

    PubMed

    Yang, Huijia; Zhou, Minghua; Liu, Mengmeng; Yang, Weilu; Gu, Tingyue

    2015-12-01

    Microbial fuel cells (MFCs) face major hurdles for real-world applications as power generators with the exception of powering small sensor devices. Despite tremendous improvements made in the last two decades, MFCs are still too expensive to build and operate and their power output is still too small. In view of this, in recently years, intensive researches have been carried out to expand the applications into other areas such as acid and alkali production, bioremediation of aquatic sediments, desalination and biosensors. Unlike power applications, MFC sensors have the immediate prospect to be practical. This review covers the latest developments in various proposed biosensor applications using MFCs including monitoring microbial activity, testing biochemical oxygen demand, detection of toxicants and detection of microbial biofilms that cause biocorrosion.

  13. The microbial arsenic cycle in Mono Lake, California

    USGS Publications Warehouse

    Oremland, Ronald S.; Stolz, John F.; Hollibaugh, James T.

    2004-01-01

    Significant concentrations of dissolved inorganic arsenic can be found in the waters of a number of lakes located in the western USA and in other water bodies around the world. These lakes are often situated in arid, volcanic terrain. The highest concentrations of arsenic occur in hypersaline, closed basin soda lakes and their remnant brines. Although arsenic is a well-known toxicant to eukaryotes and prokaryotes alike, some prokaryotes have evolved biochemical mechanisms to exploit arsenic oxyanions (i.e., arsenate and arsenite); they can use them either as an electron acceptor for anaerobic respiration (arsenate), or as an electron donor (arsenite) to support chemoautotrophic fixation of CO2 into cell carbon. Unlike in freshwater or marine ecosystems, these processes may assume quantitative significance with respect to the carbon cycle in arsenic-rich soda lakes. For the past several years our research has focused on the occurrence and biogeochemical manifestations of these processes in Mono Lake, a particularly arsenic-rich environment. Herein we review some of our findings concerning the biogeochemical arsenic cycle in this lake, with the hope that it may broaden the understanding of the influence of microorganisms upon the speciation of arsenic in more common, less “extreme” environments, such as drinking water aquifers.

  14. The microbial arsenic cycle in Mono Lake, California.

    PubMed

    Oremland, Ronald S; Stolz, John F; Hollibaugh, James T

    2004-04-01

    Significant concentrations of dissolved inorganic arsenic can be found in the waters of a number of lakes located in the western USA and in other water bodies around the world. These lakes are often situated in arid, volcanic terrain. The highest concentrations of arsenic occur in hypersaline, closed basin soda lakes and their remnant brines. Although arsenic is a well-known toxicant to eukaryotes and prokaryotes alike, some prokaryotes have evolved biochemical mechanisms to exploit arsenic oxyanions (i.e., arsenate and arsenite); they can use them either as an electron acceptor for anaerobic respiration (arsenate), or as an electron donor (arsenite) to support chemoautotrophic fixation of CO(2) into cell carbon. Unlike in freshwater or marine ecosystems, these processes may assume quantitative significance with respect to the carbon cycle in arsenic-rich soda lakes. For the past several years our research has focused on the occurrence and biogeochemical manifestations of these processes in Mono Lake, a particularly arsenic-rich environment. Herein we review some of our findings concerning the biogeochemical arsenic cycle in this lake, with the hope that it may broaden the understanding of the influence of microorganisms upon the speciation of arsenic in more common, less "extreme" environments, such as drinking water aquifers.

  15. The Importance of the Microbial N Cycle in Soil for Crop Plant Nutrition.

    PubMed

    Hirsch, Penny R; Mauchline, Tim H

    2015-01-01

    Nitrogen is crucial for living cells, and prior to the introduction of mineral N fertilizer, fixation of atmospheric N2 by diverse prokaryotes was the primary source of N in all ecosystems. Microorganisms drive the N cycle starting with N2 fixation to ammonia, through nitrification in which ammonia is oxidized to nitrate and denitrification where nitrate is reduced to N2 to complete the cycle, or partially reduced to generate the greenhouse gas nitrous oxide. Traditionally, agriculture has relied on rotations that exploited N fixed by symbiotic rhizobia in leguminous plants, and recycled wastes and manures that microbial activity mineralized to release ammonia or nitrate. Mineral N fertilizer provided by the Haber-Bosch process has become essential for modern agriculture to increase crop yields and replace N removed from the system at harvest. However, with the increasing global population and problems caused by unintended N wastage and pollution, more sustainable ways of managing the N cycle in soil and utilizing biological N2 fixation have become imperative. This review describes the biological N cycle and details the steps and organisms involved. The effects of various agricultural practices that exploit fixation, retard nitrification, and reduce denitrification are presented, together with strategies that minimize inorganic fertilizer applications and curtail losses. The development and implementation of new technologies together with rediscovering traditional practices are discussed to speculate how the grand challenge of feeding the world sustainably can be met. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Rapid count of microbial cells in dialysate.

    PubMed

    Shimakita, Tomonori; Yamamoto, Hidenori; Naramura, Tomotaka; Fujimori, Akira; Ide, Takao; Tashiro, Yoshikazu; Saito, Mikako; Matsuoka, Hideaki

    2007-10-01

    An apparatus for the non-culture method (NCM) of microbial cell count was formerly developed and named a bioplorer. The bioplorer NCM is based on the double staining of cells with 4', 6-diamidino-2-phenylindole (DAPI) and propidium iodide (PI) and the automatic analysis of their fluorescent microscopic images. Viable cells can be stained with DAPI, while dead cells can be stained with DAPI and PI. In this study, the bioplorer NCM has been applied to the dialysate. The viable and dead cells in dialysate could be counted within 20 min. The detection limit expressed by log(10)[cells/100 mL] was 2.0. When cell-spiked dialysate samples containing prescribed number of Bacillus subtilis cells were assayed, the numbers of cells determined by the bioplorer NCM (N(VIA)(NCM)) and a conventional culture method (CM) on R2A medium (N(VIA)(R2A-CM)) were similar in the range of 2.6-4.6 within the 95% confidence interval (NCM-CM equivalent range). When test solutions sampled from a practical facility in a hospital were assayed, N(VIA)(NCM) was greater than, but comparable to, N(VIA)(R2A-CM). The endotoxin (ET) in the test samples were assayed as well using a test kit for limulus amoebocyte lysate assay. The results of microbial cells and ET concentration indicated that the dialysate supplying line was clean and well maintained. The bioplorer NCM can determine if the microbial contamination of dialysate supplying facilities is greater than 2.6 (398 cells/100 mL).

  17. Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events

    PubMed Central

    Mooshammer, Maria; Hofhansl, Florian; Frank, Alexander H.; Wanek, Wolfgang; Hämmerle, Ieda; Leitner, Sonja; Schnecker, Jörg; Wild, Birgit; Watzka, Margarete; Keiblinger, Katharina M.; Zechmeister-Boltenstern, Sophie; Richter, Andreas

    2017-01-01

    Predicted changes in the intensity and frequency of climate extremes urge a better mechanistic understanding of the stress response of microbially mediated carbon (C) and nutrient cycling processes. We analyzed the resistance and resilience of microbial C, nitrogen (N), and phosphorus (P) cycling processes and microbial community composition in decomposing plant litter to transient, but severe, temperature disturbances, namely, freeze-thaw and heat. Disturbances led temporarily to a more rapid cycling of C and N but caused a down-regulation of P cycling. In contrast to the fast recovery of the initially stimulated C and N processes, we found a slow recovery of P mineralization rates, which was not accompanied by significant changes in community composition. The functional and structural responses to the two distinct temperature disturbances were markedly similar, suggesting that direct negative physical effects and costs associated with the stress response were comparable. Moreover, the stress response of extracellular enzyme activities, but not that of intracellular microbial processes (for example, respiration or N mineralization), was dependent on the nutrient content of the resource through its effect on microbial physiology and community composition. Our laboratory study provides novel insights into the mechanisms of microbial functional stress responses that can serve as a basis for field studies and, in particular, illustrates the need for a closer integration of microbial C-N-P interactions into climate extremes research. PMID:28508070

  18. Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling

    PubMed Central

    Mooshammer, Maria; Wanek, Wolfgang; Hämmerle, Ieda; Fuchslueger, Lucia; Hofhansl, Florian; Knoltsch, Anna; Schnecker, Jörg; Takriti, Mounir; Watzka, Margarete; Wild, Birgit; Keiblinger, Katharina M; Zechmeister-Boltenstern, Sophie; Richter, Andreas

    2014-01-01

    Microbial nitrogen use efficiency (NUE) describes the partitioning of organic N taken up between growth and the release of inorganic N to the environment (that is, N mineralization), and is thus central to our understanding of N cycling. Here we report empirical evidence that microbial decomposer communities in soil and plant litter regulate their NUE. We find that microbes retain most immobilized organic N (high NUE), when they are N limited, resulting in low N mineralization. However, when the metabolic control of microbial decomposers switches from N to C limitation, they release an increasing fraction of organic N as ammonium (low NUE). We conclude that the regulation of NUE is an essential strategy of microbial communities to cope with resource imbalances, independent of the regulation of microbial carbon use efficiency, with significant effects on terrestrial N cycling. PMID:24739236

  19. Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling.

    PubMed

    Mooshammer, Maria; Wanek, Wolfgang; Hämmerle, Ieda; Fuchslueger, Lucia; Hofhansl, Florian; Knoltsch, Anna; Schnecker, Jörg; Takriti, Mounir; Watzka, Margarete; Wild, Birgit; Keiblinger, Katharina M; Zechmeister-Boltenstern, Sophie; Richter, Andreas

    2014-04-16

    Microbial nitrogen use efficiency (NUE) describes the partitioning of organic N taken up between growth and the release of inorganic N to the environment (that is, N mineralization), and is thus central to our understanding of N cycling. Here we report empirical evidence that microbial decomposer communities in soil and plant litter regulate their NUE. We find that microbes retain most immobilized organic N (high NUE), when they are N limited, resulting in low N mineralization. However, when the metabolic control of microbial decomposers switches from N to C limitation, they release an increasing fraction of organic N as ammonium (low NUE). We conclude that the regulation of NUE is an essential strategy of microbial communities to cope with resource imbalances, independent of the regulation of microbial carbon use efficiency, with significant effects on terrestrial N cycling.

  20. Membrane fluidity sensoring microbial fuel cell.

    PubMed

    Choi, Youngjin; Jung, Eunkyoung; Kim, Sunghyun; Jung, Seunho

    2003-04-01

    A study has been performed to examine the effect of temperature and ethanolic stresses on the coulombic efficiency of a microbial fuel cell. The conventional-type fuel cell containing Gram-negative bacteria, Proteus vulgaris, was investigated as a model system. From current output measurements, it was found that the coulombic yields were altered by environmental stresses such as temperature shock or ethanol treatment to the bacteria. While high-temperature or ethanolic shock led to a remarkable decrement in coulombic output, the low-temperature shock induced a slight increase in microbial fuel cell efficiency. These results indicate that the membrane fluidity is affected considerably by environmental stress, which in turn affects the electron transfer process through the bacterial cell membrane to and from the electrode. This interpretation was confirmed by the cyclic voltammetric study of a mediator on an electrode surface modified with the lipids extracted from the membrane of P. vulgaris under the given stress. Markedly different electrochemical behaviors were observed depending on the environmental stress. A reciprocal relationship between coulomb output and the ratio of saturation/unsaturation of fatty acids has been observed. This is the first report, to our knowledge, that the structural adaptation of membrane fatty acids in response to the environmental shock can regulate the coulombic efficiency of a microbial fuel cell.

  1. Cell cycle regulation by protein degradation.

    PubMed

    Koepp, Deanna M

    2014-01-01

    Cell division is controlled by a highly regulated program to accurately duplicate and segregate chromosomes. An important feature of the cell cycle regulatory program is that key cell cycle proteins are present and active during specific cell cycle stages but are later removed or inhibited to maintain appropriate timing. The ubiquitin-proteasome system has emerged as an important mechanism to target cell cycle proteins for degradation at critical junctures during cell division. Two key E3 ubiquitin ligase complexes that target key cell cycle proteins are the Skp1-Cul1-F-box protein complex and the anaphase-promoting complex/cyclosome. This chapter focuses on the role of these E3 ubiquitin ligases and how ubiquitin-dependent degradation of central cell cycle regulatory proteins advances the cell cycle.

  2. From microbial communities to cells

    NASA Technical Reports Server (NTRS)

    Margulis, L.

    1985-01-01

    The eukraotic cell, the unit of structure of protoctists, plants, fungi, and animals, is not at all homologous to prokaryotic cells. Instead the eukaryotic cell is homologous to communities of microorganisms such as those of the sulfuretum. This research is based on the hypothesis that at least four different interacting community members entered the original associations that, when stabilized, led to the emergence of eukaryotic cells. These are: (1) host nucleocytoplasm (thermoplasma like archaebacteria); (2) mitochrondria (paracoccus or bdellovibryo like respiring bacteria; and (3) plastids (cyanobacteria) and undulipodia. Tubulin like protein was found in the free living spirochete Spirochaeta bajacaliforniensis and in several other spirochetes. The amino acid sequence was to see if the spirochete protein is homologous to the tubulin of undulipodial and mitotic spindle microtubules.

  3. Microbially mediated transformations of phosphorus in the sea: new views of an old cycle.

    PubMed

    Karl, David M

    2014-01-01

    Phosphorus (P) is a required element for life. Its various chemical forms are found throughout the lithosphere and hydrosphere, where they are acted on by numerous abiotic and biotic processes collectively referred to as the P cycle. In the sea, microorganisms are primarily responsible for P assimilation and remineralization, including recently discovered P reduction-oxidation bioenergetic processes that add new complexity to the marine microbial P cycle. Human-induced enhancement of the global P cycle via mining of phosphate-bearing rock will likely influence the pace of P-cycle dynamics, especially in coastal marine habitats. The inextricable link between the P cycle and cycles of other bioelements predicts future impacts on, for example, nitrogen fixation and carbon dioxide sequestration. Additional laboratory and field research is required to build a comprehensive understanding of the marine microbial P cycle.

  4. Microbial Sulfur Cycling in an Acid Mine Lake

    NASA Astrophysics Data System (ADS)

    Bernier, L.; Warren, L. A.

    2004-12-01

    Geochemical dynamics of a tailings impacted lake in Northern Ontario were investigated over a three-year period, in which active pyrrhotite slurry disposal was initiated in year two. A strong seasonal trend of decreasing epilimnetic pH with significant diurnal acid production, pre-, during and post slurry deposition was observed with high rates observed compared to pre-slurry. Slurry deposition occurred at the surface of the lake and acted as a reaction stimulant for acid generation. Over the diurnal timescale investigated, the highest rates of acid production occurred not at the lake surface but within the metaliminetic region of the lake. This region was exemplified by strong decreasing oxygen gradients, and thus observed high rates of acid generation are more consistent with microbial pathways of sulfur oxidation than with abiotic, oxygen catalyzed pathways. Consistent with microbial catalysis, metalimnetic rates of acid generation were highest during June and July when microbial populations and metabolic rates were maximal. These results indicate that microbial oxidation of sulfur species play a major role in acid generation in this system. Further, observed rates of acid generation exceed those predicted by published abiotic rates of pyrrhotite oxidation, but are consistent with literature estimates of acid generation catalyzed by microbial activity. Acidithiobacilli accounted for up to 50% of the microbial community pre slurry, but were absent post slurry deposition. These results are the first to demonstrate quantitatively that microbial sulfur oxidation can play a predominant role in acid generation within mine tailings impacted systems. They further highlight the need to evaluate the more complex pathways by which microorganisms process sulfur as the conditions, controls and process rates differ from those observed for abiotic reactions.

  5. Wireless sensors powered by microbial fuel cells.

    PubMed

    Shantaram, Avinash; Beyenal, Haluk; Raajan, Raaja; Veluchamy, Angathevar; Lewandowski, Zbigniew

    2005-07-01

    Monitoring parameters characterizing water quality, such as temperature, pH, and concentrations of heavy metals in natural waters, is often followed by transmitting the data to remote receivers using telemetry systems. Such systems are commonly powered by batteries, which can be inconvenient at times because batteries have a limited lifetime and must be recharged or replaced periodically to ensure that sufficient energy is available to power the electronics. To avoid these inconveniences, a microbial fuel cell was designed to power electrochemical sensors and small telemetry systems to transmit the data acquired by the sensors to remote receivers. The microbial fuel cell was combined with low-power, high-efficiency electronic circuitry providing a stable power source for wireless data transmission. To generate enough power for the telemetry system, energy produced by the microbial fuel cell was stored in a capacitor and used in short bursts when needed. Since commercial electronic circuits require a minimum 3.3 V input and our cell was able to deliver a maximum of 2.1 V, a DC-DC converter was used to boost the potential. The DC-DC converter powered a transmitter, which gathered the data from the sensor and transmitted it wirelessly to a remote receiver. To demonstrate the utility of the system, temporal variations in temperature were measured, and the data were wirelessly transmitted to a remote receiver.

  6. [Electricity production from surplus sludge using microbial fuel cells].

    PubMed

    Jia, Bin; Liu, Zhi-Hua; Li, Xiao-Ming; Yang, Yong-Lin; Yang, Qi; Zeng, Guang-Ming; Liu, Yi-Lin; Liu, Qian-Qian; Zheng, Shi-Wen

    2009-04-15

    A single-chamber and membrane-less microbial fuel cells were successfully started up using anaerobic sludge as inoculums without any chemical substance for 20 d. The electricity generation of the microbial fuel cell using surplus sludge as fuel and the change of substrate were investigated. The results showed that the obtained maximum voltage and power density were 495 mV and 44 mW x m(-2) (fixed 1,000 Omega), and the internal resistance was about 300 Omega during steady state. In a cycle, the removal efficiency of SS and VSS were 27.3% and 28.7%, pH was 6.5-8.0. In addition, the COD increased from 617 mg x L(-1) to 1,150 mg x L(-1) and decreased afterwards with time. The change of glucose was similar to that of COD, glucose increased from 47 mg x L(-1) to 60 mg x L(-1) and decreased afterwards with time. Consequently, the microbial fuel cell can transform chemical energy of surplus sludge into the cleanest electrical energy, and it provides a new way of sludge recycling.

  7. Exoelectrogenic bacteria that power microbial fuel cells.

    PubMed

    Logan, Bruce E

    2009-05-01

    There has been an increase in recent years in the number of reports of microorganisms that can generate electrical current in microbial fuel cells. Although many new strains have been identified, few strains individually produce power densities as high as strains from mixed communities. Enriched anodic biofilms have generated power densities as high as 6.9 W per m(2) (projected anode area), and therefore are approaching theoretical limits. To understand bacterial versatility in mechanisms used for current generation, this Progress article explores the underlying reasons for exocellular electron transfer, including cellular respiration and possible cell-cell communication.

  8. Microbial fuel cell with improved anode

    DOEpatents

    Borole, Abhijeet P.

    2010-04-13

    The present invention relates to a method for preparing a microbial fuel cell, wherein the method includes: (i) inoculating an anodic liquid medium in contact with an anode of the microbial fuel cell with one or more types of microorganisms capable of functioning by an exoelectrogenic mechanism; (ii) establishing a biofilm of the microorganisms on and/or within the anode along with a substantial absence of planktonic forms of the microorganisms by substantial removal of the planktonic microorganisms during forced flow and recirculation conditions of the anodic liquid medium; and (iii) subjecting the microorganisms of the biofilm to a growth stage by incorporating one or more carbon-containing nutritive compounds in the anodic liquid medium during biofilm formation or after biofilm formation on the anode has been established.

  9. Nitrogen cycling and water pulses in semiarid grasslands: are microbial and plant processes temporally asynchronous?

    PubMed

    Dijkstra, Feike A; Augustine, David J; Brewer, Paul; von Fischer, Joseph C

    2012-11-01

    Precipitation pulses in arid ecosystems can lead to temporal asynchrony in microbial and plant processing of nitrogen (N) during drying/wetting cycles causing increased N loss. In contrast, more consistent availability of soil moisture in mesic ecosystems can synchronize microbial and plant processes during the growing season, thus minimizing N loss. We tested whether microbial N cycling is asynchronous with plant N uptake in a semiarid grassland. Using (15)N tracers, we compared rates of N cycling by microbes and N uptake by plants after water pulses of 1 and 2 cm to rates in control plots without a water pulse. Microbial N immobilization, gross N mineralization, and nitrification dramatically increased 1-3 days after the water pulses, with greatest responses after the 2-cm pulse. In contrast, plant N uptake increased more after the 1-cm than after the 2-cm pulse. Both microbial and plant responses reverted to control levels within 10 days, indicating that both microbial and plant responses were short lived. Thus, microbial and plant processes were temporally synchronous following a water pulse in this semiarid grassland, but the magnitude of the pulse substantially influenced whether plants or microbes were more effective in acquiring N. Furthermore, N loss increased after both small and large water pulses (as shown by a decrease in total (15)N recovery), indicating that changes in precipitation event sizes with future climate change could exacerbate N losses from semiarid ecosystems.

  10. [Microbial processes of the carbon and sulfur cycles in the White Sea].

    PubMed

    Savvichev, A S; Rusanov, I I; Zakharova, E E; Veslopolova, E F; Mitskevich, I N; Kravchishina, M D; Lein, A Iu; Ivanov, M V

    2008-01-01

    The present paper contains the results of our microbiological and biogeochemical investigations carried out during a series of expeditions to the White Sea in 2002-2006. The studies were conducted in the open part of the White Sea, as well as in the Onega, Dvina, and Kandalaksha bays. In August 2006, the photosynthetic productivity in the surface water layer was low (47-145 mg C m(-2) day(-1)). Quantitative characteristics of microbial numbers and activity of the the key microbial processes occurring in the water column of the White Sea were explored. Over the 5-year period of observations, the total number of bacterial cells in the surface layer of the water column varied from 50 to 600 thousand cells ml(-1). In August 2006, bacterioplankton production (BP) was estimated to be 0.26-3.3 microg C l(-1) day(-1); the P/B coefficient varied from 0.22 to 0.93. The suspended organic matter had a lighter isotope composition (from -28.0 to -30.5 per thousand) due to the predominance of terrigenous organic matter delivered by the Northern Dvina waters. The interseasonal and interannual variation coefficients for phytoplankton production and BP numbers are compared. The bacterioplankton community of the White Sea's deep water was found to be more stable than that of the surface layer. In the surface layer of bottom sediments, methane concentration was 0.2-5.2 microl dm(-3); the rate of bacterial sulfate reduction was 18-260 microg S dm(-3) day(-1); and the rates of methane production and oxidation were 24-123 and 6-13 nl CH4 dm(-3) day(-1) respectively. We demonstrated that the rates of microbial processes of the carbon and sulfur cycles occurring in the sediments of the White Sea basin were low.

  11. Sulfur Cycling and Microbial Community Structure in Cave Environment: some geomicrobiological aspects

    NASA Astrophysics Data System (ADS)

    Gulecal, Y.; Temel, M.

    2013-12-01

    In the last decade, cave microbiology has emerged as a growing interdisciplinary field. Because of caves provides a unique subsurface environment for the exploration of microbial life and their roles on biogeochemical cycling under extreme condition. Sulfidic caves form in carbonate rocks where sulfide-rich waters interact with oxygen at the water table or at subterranean springs (1). Terrestrial sulfidic caves and springs are abundant and diverse, as assessed by efforts to characterize cave microbial ecosystems and to understand large scale geochemical processes (2). In this study we examined the geochemical features, microbial community and capacity of sulfur cycling in sulfidic cave ( Kaklik Cave, Turkey ) and its two hot springs. Pyrosequencing were used to understand bacterial diversity and community structure in this study area with contrasting hydrochemial and geological properties. Environmental nucleic acids were extracted, and PCR-directed screens reveal the presence or absence of functional genes, indicating genetic capacity for sulfur cycling. The microbial community displayed a high level of microbial diversity, representing 22 phylum of the Bacteria and 5 phylum of the Archaea. Our results provide a comparative view of the microbial communities and processes involved in sulfur cycling in sulfidic cave environments. 1- Macalady et al. (2007) Extremely acidic, pendulous cave wall biofilms from the Frasassi cave system, Italy. Env.Mic. 9(6), 1402-1414 2- Rossmassler et al. Drivers of epsilonproteobacterial community composition in sulfidic caves and springs.

  12. Cell cycle regulation during viral infection.

    PubMed

    Bagga, Sumedha; Bouchard, Michael J

    2014-01-01

    To replicate their genomes in cells and generate new progeny, viruses typically require factors provided by the cells that they have infected. Subversion of the cellular machinery that controls replication of the infected host cell is a common activity of many viruses. Viruses employ different strategies to deregulate cell cycle checkpoint controls and modulate cell proliferation pathways. A number of DNA and RNA viruses encode proteins that target critical cell cycle regulators to achieve cellular conditions that are beneficial for viral replication. Many DNA viruses induce quiescent cells to enter the cell cycle; this is thought to increase pools of deoxynucleotides and thus, facilitate viral replication. In contrast, some viruses can arrest cells in a particular phase of the cell cycle that is favorable for replication of the specific virus. Cell cycle arrest may inhibit early cell death of infected cells, allow the cells to evade immune defenses, or help promote virus assembly. Although beneficial for the viral life cycle, virus-mediated alterations in normal cell cycle control mechanisms could have detrimental effects on cellular physiology and may ultimately contribute to pathologies associated with the viral infection, including cell transformation and cancer progression and maintenance. In this chapter, we summarize various strategies employed by DNA and RNA viruses to modulate the replication cycle of the virus-infected cell. When known, we describe how these virus-associated effects influence replication of the virus and contribute to diseases associated with infection by that specific virus.

  13. "Constructing" the Cell Cycle in 3D

    ERIC Educational Resources Information Center

    Koc, Isil; Turan, Merve

    2012-01-01

    The cycle of duplication and division, known as the "cell cycle," is the essential mechanism by which all living organisms reproduce. This activity allows students to develop an understanding of the main events that occur during the typical eukaryotic cell cycle mostly in the process of mitotic phase that divides the duplicated genetic material…

  14. "Constructing" the Cell Cycle in 3D

    ERIC Educational Resources Information Center

    Koc, Isil; Turan, Merve

    2012-01-01

    The cycle of duplication and division, known as the "cell cycle," is the essential mechanism by which all living organisms reproduce. This activity allows students to develop an understanding of the main events that occur during the typical eukaryotic cell cycle mostly in the process of mitotic phase that divides the duplicated genetic material…

  15. Microbial fuel cells: Their application and microbiology

    NASA Astrophysics Data System (ADS)

    He, Zhen

    The energy crisis is an urgent global issue due to the increased consumption of the finite amount of fossil fuel. As a result, looking for alternative energy sources is of critical importance. Microbial fuel cell (MFC) technology can extract electric energy from wastewater, and thus is a sustainable approach to supply energy to our electricity-based society. My research focuses on the development of a suitable MFC reactor for wastewater treatment and the understanding of the microbial function in the MFC process. First, together with colleagues, I have developed a novel MFC reactor, named upflow microbial fuel cell (UMFC), by combining upflow and MFC technologies. The power output from the UMFC was improved by 10-fold after it was modified with a U-shape cathode. The UMFC appears to be a practical reactor for continuous operation, though the output of electric power requires further improvement. In addition, a sediment MFC with a rotating cathode was also developed and its performance was examined. Second, I have adopted a human distal gut anaerobe, Bacteroides thetaiotaomicron, as the model organism to study the role of fermentative bacterium in electricity generation. When B. thetaiotaomicron grew under an applied electric potential, an electric current was generated. GeneChip data indicated that this bacterium did not alter its metabolism during this process. Although B. thetaiotaomicron may not be capable of respiration with an electrode as the electron acceptor, the experiment has demonstrated that fermentative bacteria may play an important role in electricity generation.

  16. Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

    PubMed Central

    Zhao, Mengxin; Xue, Kai; Wang, Feng; Liu, Shanshan; Bai, Shijie; Sun, Bo; Zhou, Jizhong; Yang, Yunfeng

    2014-01-01

    Despite microbes' key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO2) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling. PMID:24694714

  17. Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping.

    PubMed

    Zhao, Mengxin; Xue, Kai; Wang, Feng; Liu, Shanshan; Bai, Shijie; Sun, Bo; Zhou, Jizhong; Yang, Yunfeng

    2014-10-01

    Despite microbes' key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO2) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling.

  18. Effects of Nutrient Enrichment on Microbial Communities and Carbon Cycling in Wetland Soils

    NASA Astrophysics Data System (ADS)

    Hartman, W.; Neubauer, S. C.; Richardson, C. J.

    2013-12-01

    Soil microbial communities are responsible for catalyzing biogeochemical transformations underlying critical wetland functions, including cycling of carbon (C) and nutrients, and emissions of greenhouse gasses (GHG). Alteration of nutrient availability in wetland soils may commonly occur as the result of anthropogenic impacts including runoff from human land uses in uplands, alteration of hydrology, and atmospheric deposition. However, the impacts of altered nutrient availability on microbial communities and carbon cycling in wetland soils are poorly understood. To assess these impacts, soil microbial communities and carbon cycling were determined in replicate experimental nutrient addition plots (control, +N, +P, +NP) across several wetland types, including pocosin peat bogs (NC), freshwater tidal marshes (GA), and tidal salt marshes (SC). Microbial communities were determined by pyrosequencing (Roche 454) extracted soil DNA, targeting both bacteria (16S rDNA) and fungi (LSU) at a depth of ca. 1000 sequences per plot. Wetland carbon cycling was evaluated using static chambers to determine soil GHG fluxes, and plant inclusion chambers were used to determine ecosystem C cycling. Soil bacterial communities responded to nutrient addition treatments in freshwater and tidal marshes, while fungal communities did not respond to treatments in any of our sites. We also compared microbial communities to continuous biogeochemical variables in soil, and found that bacterial community composition was correlated only with the content and availability of soil phosphorus, while fungi responded to phosphorus stoichiometry and soil pH. Surprisingly, we did not find a significant effect of our nutrient addition treatments on most metrics of carbon cycling. However, we did find that several metrics of soil carbon cycling appeared much more related to soil phosphorus than to nitrogen or soil carbon pools. Finally, while overall microbial community composition was weakly correlated with

  19. Proton transfer in microbial electrolysis cells

    DOE PAGES

    Borole, Abhijeet P.; Lewis, Alex J.

    2017-02-15

    Proton transfer and electron transfer are of prime importance in the development of microbial electrochemical cells. While electron transfer is primarily controlled by biology, proton transfer is controlled by process engineering and cell design. To develop commercially feasible technologies around the concept of a bioelectrochemical cell, real feedstocks have to be explored and associated limitations have to be identified. Here in this study, the proton transfer rate was quantified for a microbial electrolysis cell (MEC) and its dependence on process parameters was investigated using a proton balance model. The reaction system consisted of a biomass-derived pyrolytic aqueous stream as amore » substrate producing hydrogen in a flow-through MEC. The proton transfer rate increased with anode flow rate and organic loading rate up to a maximum of 0.36 ± 0.01 moles per m2 per h, equivalent to a hydrogen production rate of 9.08 L per L per day. Higher rates of hydrogen production, reaching 11.7 ± 0.2 L per L per day were achieved, when additional protons were provided via the cathode buffer. Electrochemical impedance spectroscopy shows that proton transfer was the dominant resistance in the production of hydrogen. The quantification of proton transfer rates for MECs with potential for biorefinery application and the demonstration of high hydrogen production rates approaching those required for commercial consideration indicate the strong potential of this technology for renewable hydrogen production. Understanding the transport phenomenon in bioelectrochemical cells is of great significance since these systems have potential for wide-ranging applications including energy production, bioremediation, chemical and nanomaterial synthesis, electro-fermentation, energy storage, desalination, and produced water treatment. Electron transfer in anode biofilms has been investigated extensively, but proton transfer studies are also important, since many cathodic half reactions

  20. Cytofluorometric assessment of cell cycle progression.

    PubMed

    Vitale, Ilio; Jemaà, Mohamed; Galluzzi, Lorenzo; Metivier, Didier; Castedo, Maria; Kroemer, Guido

    2013-01-01

    One of the most prominent features of cellular senescence, a stress response that prevents the propagation of cells that have accumulated potentially oncogenic alterations, is a permanent loss of proliferative potential. Thus, at odds with quiescent cells, which resume proliferation when stimulated to do so, senescent cells cannot proceed through the cell cycle even in the presence of mitogenic factors. Here, we describe a set of cytofluorometric techniques for studying how chemical and/or physical stimuli alter the cell cycle in vitro, in both qualitative and quantitative terms. Taken together, these methods allow for the identification of bona fide cytostatic effects as well as for a refined characterization of cell cycle distributions, providing information on proliferation, DNA content as well as on the presence of cell cycle phase-specific markers. At the end of the chapter, a set of guidelines is offered to assist researchers that approach the study of the cell cycle with the interpretation of results.

  1. Cell division cycle 45 promotes papillary thyroid cancer progression via regulating cell cycle.

    PubMed

    Sun, Jing; Shi, Run; Zhao, Sha; Li, Xiaona; Lu, Shan; Bu, Hemei; Ma, Xianghua

    2017-05-01

    Cell division cycle 45 was reported to be overexpressed in some cancer-derived cell lines and was predicted to be a candidate oncogene in cervical cancer. However, the clinical and biological significance of cell division cycle 45 in papillary thyroid cancer has never been investigated. We determined the expression level and clinical significance of cell division cycle 45 using The Cancer Genome Atlas, quantitative real-time polymerase chain reaction, and immunohistochemistry. A great upregulation of cell division cycle 45 was observed in papillary thyroid cancer tissues compared with adjacent normal tissues. Furthermore, overexpression of cell division cycle 45 positively correlates with more advanced clinical characteristics. Silence of cell division cycle 45 suppressed proliferation of papillary thyroid cancer cells via G1-phase arrest and inducing apoptosis. The oncogenic activity of cell division cycle 45 was also confirmed in vivo. In conclusion, cell division cycle 45 may serve as a novel biomarker and a potential therapeutic target for papillary thyroid cancer.

  2. Soil Microbial Nitrogen Cycling Responses to Wildfire in a High Elevation Forested Catchment in Jemez Mountains, NM

    NASA Astrophysics Data System (ADS)

    Murphy, M. A.; Fairbanks, D.; Chorover, J.; Rich, V. I.; Gallery, R. E.; Boyer, J. C.

    2015-12-01

    Microbial communities mediate major ecosystem processes such as nutrient cycling, and their recovery after disturbances plays a substantial role in overall ecosystem recovery and resilience. Disturbances directly shift microbial communities and their related processes, and the severity of impact typically varies significantly with landscape position, depth, and hydrological conditions such that different conditions indicate that a specific process will be dominant. Wildfires in the southwest US are a major source of landscape-scale disturbance, and are predicted to continue increasing in size and intensity under climate change. This study investigates changing nitrogen cycling across a post-wildfire catchment within the Jemez River Basin Critical Zone Observatory. This site experienced a mixed (intermediate to high) burn severity wildfire in June 2013. Nitrogen cycling was investigated by profiling via qPCR the abundance of five key genes involved in microbial nitrogen cycling (nifH, amoA, nirS, nirK, nosZ), at points along and within the catchment. These results are being analyzed in the context of broader microbial community data (enzyme assays, microbial cell counts and biomass, and 16S rRNA gene amplicons surveys) and biogeochemical data (total organic carbon, total nitrogen, pH, graviametric water content, etc). W 22 sites along the sides of the basin (planar zones) and within the hollow (convergent zone) were sampled at 13 days, one, and two years post-fire, at six discrete depth increments from 0 to 40 cm from the surface. We attribute significance of variation in gene abundance in planar versus convergent zones, and among depths, to the strong correlation of nitrogen cycling processes (i.e., nitrification and denitrification) with specific C:N ratios, total organic carbon content, and other biogeochemical and soil edaphic parameters that vary with landscape position and wildfire. Data were also interrogated for evidence of multi-year patterns in nutrient-cycling

  3. Model Organisms for Studying the Cell Cycle.

    PubMed

    Tang, Zhaohua

    2016-01-01

    Regulation of the cell-division cycle is fundamental for the growth, development, and reproduction of all species of life. In the past several decades, a conserved theme of cell cycle regulation has emerged from research in diverse model organisms. A comparison of distinct features of several diverse model organisms commonly used in cell cycle studies highlights their suitability for various experimental approaches, and recaptures their contributions to our current understanding of the eukaryotic cell cycle. A historic perspective presents a recollection of the breakthrough upon unfolding the universal principles of cell cycle control by scientists working with diverse model organisms, thereby appreciating the discovery pathways in this field. A comprehensive understanding is necessary to address current challenging questions about cell cycle control. Advances in genomics, proteomics, quantitative methodologies, and approaches of systems biology are redefining the traditional concept of what constitutes a model organism and have established a new era for development of novel, and refinement of the established model organisms. Researchers working in the field are no longer separated by their favorite model organisms; they have become more integrated into a larger community for gaining greater insights into how a cell divides and cycles. The new technologies provide a broad evolutionary spectrum of the cell-division cycle and allow informative comparisons among different species at a level that has never been possible, exerting unimaginable impact on our comprehensive understanding of cell cycle regulation.

  4. Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods.

    PubMed

    Huhe; Borjigin, Shinchilelt; Buhebaoyin; Wu, Yanpei; Li, Minquan; Cheng, Yunxiang

    2016-01-01

    In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively). The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands.

  5. Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods

    PubMed Central

    Huhe; Borjigin, Shinchilelt; Buhebaoyin; Wu, Yanpei; Li, Minquan; Cheng, Yunxiang

    2016-01-01

    In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively). The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands. PMID:27140199

  6. The life sulfuric: microbial ecology of sulfur cycling in marine sediments

    PubMed Central

    Wasmund, Kenneth; Mußmann, Marc

    2017-01-01

    Summary Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular‐ and ecosystem‐level processes. Sulfur‐transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate‐rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep‐subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. PMID:28419734

  7. H2 cycling and microbial bioenergetics in anoxic sediments

    NASA Technical Reports Server (NTRS)

    Hoehler, Tori M.; DeVincenzi, Donald (Technical Monitor)

    2001-01-01

    The simple biochemistry of H2 is central to a large number of microbial processes, affecting the interaction of organisms with each other and with the environment. In anoxic sediments, the great majority of microbial redox processes involve H2 as a reactant, product, or potential by-product, and the thermodynamics of these processes are thus highly sensitive to fluctuations in environmental H2 concentrations. In turn, H2 concentrations are controlled by the activity of H2-consuming microorganisms, which efficiently utilize this substrate down to levels which correspond to their bioenergetic limitations. Consequently, any environmental change which impacts the thermodynamics of H2-consuming organisms is mirrored by a corresponding change in H2 concentrations. This phenomenon is illustrated in anoxic sediments from Cape Lookout Bight, NC, USA: H2 concentrations are controlled by a suite of environmental parameters (e.g., temperature, sulfate concentrations) in a fashion which can be quantitatively described by a simple thermodynamic model. These findings allow us to calculate the apparent minimum quantity of biologically useful energy in situ. We find that sulfate reducing bacteria are not active at energy yields below -18 kJ per mole sulfate, while methanogenic archaea exhibit a minimum close to -10 kJ per mole methane.

  8. H2 cycling and microbial bioenergetics in anoxic sediments

    NASA Technical Reports Server (NTRS)

    Hoehler, Tori M.; DeVincenzi, Donald (Technical Monitor)

    2001-01-01

    The simple biochemistry of H2 is central to a large number of microbial processes, affecting the interaction of organisms with each other and with the environment. In anoxic sediments, the great majority of microbial redox processes involve H2 as a reactant, product, or potential by-product, and the thermodynamics of these processes are thus highly sensitive to fluctuations in environmental H2 concentrations. In turn, H2 concentrations are controlled by the activity of H2-consuming microorganisms, which efficiently utilize this substrate down to levels which correspond to their bioenergetic limitations. Consequently, any environmental change which impacts the thermodynamics of H2-consuming organisms is mirrored by a corresponding change in H2 concentrations. This phenomenon is illustrated in anoxic sediments from Cape Lookout Bight, NC, USA: H2 concentrations are controlled by a suite of environmental parameters (e.g., temperature, sulfate concentrations) in a fashion which can be quantitatively described by a simple thermodynamic model. These findings allow us to calculate the apparent minimum quantity of biologically useful energy in situ. We find that sulfate reducing bacteria are not active at energy yields below -18 kJ per mole sulfate, while methanogenic archaea exhibit a minimum close to -10 kJ per mole methane.

  9. Exploring Viral Mediated Carbon Cycling in Thawing Permafrost Microbial Communities

    NASA Astrophysics Data System (ADS)

    Trubl, G. G.; Solonenko, N.; Moreno, M.; Sullivan, M. B.; Rich, V. I.

    2014-12-01

    Viruses are the most abundant biological entities on Earth and their impact on carbon cycling in permafrost habitats is poorly understood. Arctic C cycling is particularly important to interpret due to the rapid climate change occurring and the large amount of C stockpiled there (~1/3 of global soil C is stored in permafrost). Viruses of microbes (i.e. phages) play central roles in C cycling in the oceans, through cellular lysis (phage drive the largest ocean C flux about 150 Gt yr-1, dwarfing all others by >5-fold), production of associated DOC, as well as transport and expression during infection (1029 transduction events day-1). C cycling in thawing permafrost systems is critical in understanding the climate trajectory and phages may be as important for C cycling here as they are in the ocean. The thawed C may become a food source for microbes, producing CO2 and potentially CH4, both potent greenhouse gases. To address the potential role of phage in C cycling in these dynamic systems, we are examining phage from an arctic permafrost thaw gradient in northern Sweden. We have developed a protocol for successfully extracting phage from peat soils and are quantifying phage in 15 peat and 2 lake sediment cores, with the goal of sequencing viromes. Preliminary data suggest that phage are present at 109 g-1 across the permafrost thaw gradient (compared to the typical marine count ~105 ml-1), implying a potentially robust phage-host interaction web in these changing environments. We are examining phage from 11 depth intervals (covering the active and permafrost layer) in the cores to assess phage-host community dynamics. Phage morphology and abundance for each layer and environment are being determined using qTEM and EFM. Understanding the phage that infect bacteria and archaea in these rapidly changing habitats will provide insight into the controls on current and future CH4 and CO2 emissions in permafrost habitats.

  10. Molecular mechanisms controlling the cell cycle in embryonic stem cells.

    PubMed

    Abdelalim, Essam M

    2013-12-01

    Embryonic stem (ES) cells are originated from the inner cell mass of a blastocyst stage embryo. They can proliferate indefinitely, maintain an undifferentiated state (self-renewal), and differentiate into any cell type (pluripotency). ES cells have an unusual cell cycle structure, consists mainly of S phase cells, a short G1 phase and absence of G1/S checkpoint. Cell division and cell cycle progression are controlled by mechanisms ensuring the accurate transmission of genetic information from generation to generation. Therefore, control of cell cycle is a complicated process, involving several signaling pathways. Although great progress has been made on the molecular mechanisms involved in the regulation of ES cell cycle, many regulatory mechanisms remain unknown. This review summarizes the current knowledge about the molecular mechanisms regulating the cell cycle of ES cells and describes the relationship existing between cell cycle progression and the self-renewal.

  11. Gene copy number and cell cycle arrest

    NASA Astrophysics Data System (ADS)

    Ghosh, Bhaswar; Bose, Indrani

    2006-03-01

    The cell cycle is an orderly sequence of events which ultimately lead to the division of a single cell into two daughter cells. In the case of DNA damage by radiation or chemicals, the damage checkpoints in the G1 and G2 phases of the cell cycle are activated. This results in an arrest of the cell cycle so that the DNA damage can be repaired. Once this is done, the cell continues with its usual cycle of activity. We study a mathematical model of the DNA damage checkpoint in the G2 phase which arrests the transition from the G2 to the M (mitotic) phase of the cell cycle. The tumor suppressor protein p53 plays a key role in activating the pathways leading to cell cycle arrest in mammalian systems. If the DNA damage is severe, the p53 proteins activate other pathways which bring about apoptosis, i.e., programmed cell death. Loss of the p53 gene results in the proliferation of cells containing damaged DNA, i.e., in the growth of tumors which may ultimately become cancerous. There is some recent experimental evidence which suggests that the mutation of a single copy of the p53 gene (in the normal cell each gene has two identical copies) is sufficient to trigger the formation of tumors. We study the effect of reducing the gene copy number of the p53 and two other genes on cell cycle arrest and obtain results consistent with experimental observations.

  12. Shape recognition of microbial cells by colloidal cell imprints

    NASA Astrophysics Data System (ADS)

    Borovička, Josef; Stoyanov, Simeon D.; Paunov, Vesselin N.

    2013-08-01

    We have engineered a class of colloids which can recognize the shape and size of targeted microbial cells and selectively bind to their surfaces. These imprinted colloid particles, which we called ``colloid antibodies'', were fabricated by partial fragmentation of silica shells obtained by templating the targeted microbial cells. We successfully demonstrated the shape and size recognition between such colloidal imprints and matching microbial cells. High percentage of binding events of colloidal imprints with the size matching target particles was achieved. We demonstrated selective binding of colloidal imprints to target microbial cells in a binary mixture of cells of different shapes and sizes, which also resulted in high binding selectivity. We explored the role of the electrostatic interactions between the target cells and their colloid imprints by pre-coating both of them with polyelectrolytes. Selective binding occurred predominantly in the case of opposite surface charges of the colloid cell imprint and the targeted cells. The mechanism of the recognition is based on the amplification of the surface adhesion in the case of shape and size match due to the increased contact area between the target cell and the colloidal imprint. We also tested the selective binding for colloid imprints of particles of fixed shape and varying sizes. The concept of cell recognition by colloid imprints could be used for development of colloid antibodies for shape-selective binding of microbes. Such colloid antibodies could be additionally functionalized with surface groups to enhance their binding efficiency to cells of specific shape and deliver a drug payload directly to their surface or allow them to be manipulated using external fields. They could benefit the pharmaceutical industry in developing selective antimicrobial therapies and formulations.

  13. The microbial perspective of organic matter turnover and nutrient cycling in tropical soils

    NASA Astrophysics Data System (ADS)

    Rasche, Frank

    2017-04-01

    A primary goal of low-input small-holder farming systems in the tropics is the appropriate management of organic matter (OM) turnover and nutrient cycling via adapted agricultural practices. These emphasize the promotion of soil organic matter (SOM) turnover and carbon (C) sequestration, nutrient use efficiency and soil microbial activity. Since soil microbial communities are acknowledged as key players in the terrestrial C and nutrient (e.g., nitrogen (N), phosphorus (P)) cycles, they may respond sensitively to agricultural management with shifts in their community structure as well as functional traits (i.e., decomposition, mineralization). This may be in particular evident for tropical, agricultural soils which show an accelerated microbial decomposition activity induced by favourable climatic and unique physico-chemical soil conditions. While modern molecular techniques advanced primarily the understanding about the microbiome and their functional traits interacting closely with SOM dynamics in temperate soils, tropical soils under agricultural use have been still neglected to a great extent. The majority of available studies revealed mainly descriptive data on the structural composition of microbial communities rather than questioning if detected structural alterations of the soil microbiome influenced key processes in N and P cycling which actually maintain ecosystem functioning and soil productivity. This talk highlights latest efforts in deploying molecular techniques to study the compositional status of soil microbial decomposer communities and their functional attributes in response to land use change and OM management in tropical agro-ecosystems.

  14. Crosstalk between stem cell and cell cycle machineries.

    PubMed

    Kareta, Michael S; Sage, Julien; Wernig, Marius

    2015-12-01

    Pluripotent stem cells, defined by an unlimited self-renewal capacity and an undifferentiated state, are best typified by embryonic stem cells. These cells have a unique cell cycle compared to somatic cells as defined by a rapid progression through the cell cycle and a minimal time spent in G1. Recent reports indicate that pluripotency and cell cycle regulation are mechanistically linked. In this review, we discuss the reciprocal co-regulation of these processes, how this co-regulation may prevent differentiation, and how cellular reprogramming can re-establish the unique cell cycle regulation in induced pluripotent stem cells. Copyright © 2015. Published by Elsevier Ltd.

  15. Microbial fuel cells: From fundamentals to applications. A review.

    PubMed

    Santoro, Carlo; Arbizzani, Catia; Erable, Benjamin; Ieropoulos, Ioannis

    2017-07-15

    In the past 10-15 years, the microbial fuel cell (MFC) technology has captured the attention of the scientific community for the possibility of transforming organic waste directly into electricity through microbially catalyzed anodic, and microbial/enzymatic/abiotic cathodic electrochemical reactions. In this review, several aspects of the technology are considered. Firstly, a brief history of abiotic to biological fuel cells and subsequently, microbial fuel cells is presented. Secondly, the development of the concept of microbial fuel cell into a wider range of derivative technologies, called bioelectrochemical systems, is described introducing briefly microbial electrolysis cells, microbial desalination cells and microbial electrosynthesis cells. The focus is then shifted to electroactive biofilms and electron transfer mechanisms involved with solid electrodes. Carbonaceous and metallic anode materials are then introduced, followed by an explanation of the electro catalysis of the oxygen reduction reaction and its behavior in neutral media, from recent studies. Cathode catalysts based on carbonaceous, platinum-group metal and platinum-group-metal-free materials are presented, along with membrane materials with a view to future directions. Finally, microbial fuel cell practical implementation, through the utilization of energy output for practical applications, is described.

  16. Microbial fuel cells: From fundamentals to applications. A review

    NASA Astrophysics Data System (ADS)

    Santoro, Carlo; Arbizzani, Catia; Erable, Benjamin; Ieropoulos, Ioannis

    2017-07-01

    In the past 10-15 years, the microbial fuel cell (MFC) technology has captured the attention of the scientific community for the possibility of transforming organic waste directly into electricity through microbially catalyzed anodic, and microbial/enzymatic/abiotic cathodic electrochemical reactions. In this review, several aspects of the technology are considered. Firstly, a brief history of abiotic to biological fuel cells and subsequently, microbial fuel cells is presented. Secondly, the development of the concept of microbial fuel cell into a wider range of derivative technologies, called bioelectrochemical systems, is described introducing briefly microbial electrolysis cells, microbial desalination cells and microbial electrosynthesis cells. The focus is then shifted to electroactive biofilms and electron transfer mechanisms involved with solid electrodes. Carbonaceous and metallic anode materials are then introduced, followed by an explanation of the electro catalysis of the oxygen reduction reaction and its behavior in neutral media, from recent studies. Cathode catalysts based on carbonaceous, platinum-group metal and platinum-group-metal-free materials are presented, along with membrane materials with a view to future directions. Finally, microbial fuel cell practical implementation, through the utilization of energy output for practical applications, is described.

  17. A new method for water desalination using microbial desalination cells.

    PubMed

    Cao, Xiaoxin; Huang, Xia; Liang, Peng; Xiao, Kang; Zhou, Yingjun; Zhang, Xiaoyuan; Logan, Bruce E

    2009-09-15

    Current water desalination techniques are energy intensive and some use membranes operated at high pressures. It is shown here that water desalination can be accomplished without electrical energy input or high water pressure by using a source of organic matter as the fuel to desalinate water. A microbial fuel cell was modified by placing two membranes between the anode and cathode, creating a middle chamber for water desalination between the membranes. An anion exchange membrane was placed adjacent to the anode, and a cation exchange membrane was positioned next to the cathode. When current was produced by bacteria on the anode, ionic species in the middle chamber were transferred into the two electrode chambers, desalinating the water in the middle chamber. Proof-of-concept experiments for this approach, using what we call a microbial desalination cell (MDC), was demonstrated using water at different initial salt concentrations (5, 20, and 35 g/L) with acetate used as the substrate for the bacteria. The MDC produced a maximum of 2 W/m2 (31 W/m3) while at the same time removing about 90% of the salt in a single desalination cycle. As the salt was removed from the middle chamber the ohmic resistance of the MDC (measured using electrochemical impedance spectroscopy) increased from 25 Omega to 970 Omega at the end of the cycle. This increased resistance was reflected by a continuous decrease in the voltage produced over the cycle. These results demonstrate for the first time the possibility for a new method for water desalination and power production that uses only a source of biodegradable organic matter and bacteria.

  18. Asymmetric biocatalysis with microbial enzymes and cells.

    PubMed

    Wohlgemuth, Roland

    2010-06-01

    Microbial enzymes and cells continue to be important tools and nature's privileged chiral catalysts for performing asymmetric biocatalysis from the analytical small scale to the preparative and large scale in synthesis and degradation. The application of biocatalysts for preparing molecular asymmetry has achieved high efficiency, enantioselectivity and yield and is experiencing today a worldwide renaissance. Recent developments in the discovery, development and production of stable biocatalysts, in the design of new biocatalytic processes and in the product recovery and purification processes have made biocatalytic approaches using microbial cells and enzymes attractive choices for the synthesis of chiral compounds. The methodologies of kinetic resolution and kinetic asymmetric transformation, dynamic kinetic resolution and deracemization, desymmetrization, asymmetric synthesis with or without diastereo control and multi-step asymmetric biocatalysis are finding increasing applications in research. The ever-increasing use of hydrolytic enzymes has been accompanied by new applications of oxidoreductases, transferases and lyases. Isomerases, already used in large-scale processes, and ligases, are emerging as interesting biocatalysts for new synthetic applications. The production of a wide variety of industrial products by asymmetric biocatalysis has even become the preferred method of production. Copyright 2010 Elsevier Ltd. All rights reserved.

  19. Cell cycle control and seed development

    PubMed Central

    Dante, Ricardo A.; Larkins, Brian A.; Sabelli, Paolo A.

    2014-01-01

    Seed development is a complex process that requires coordinated integration of many genetic, metabolic, and physiological pathways and environmental cues. Different cell cycle types, such as asymmetric cell division, acytokinetic mitosis, mitotic cell division, and endoreduplication, frequently occur in sequential yet overlapping manner during the development of the embryo and the endosperm, seed structures that are both products of double fertilization. Asymmetric cell divisions in the embryo generate polarized daughter cells with different cell fates. While nuclear and cell division cycles play a key role in determining final seed cell numbers, endoreduplication is often associated with processes such as cell enlargement and accumulation of storage metabolites that underlie cell differentiation and growth of the different seed compartments. This review focuses on recent advances in our understanding of different cell cycle mechanisms operating during seed development and their impact on the growth, development, and function of seed tissues. Particularly, the roles of core cell cycle regulators, such as cyclin-dependent-kinases and their inhibitors, the Retinoblastoma-Related/E2F pathway and the proteasome-ubiquitin system, are discussed in the contexts of different cell cycle types that characterize seed development. The contributions of nuclear and cellular proliferative cycles and endoreduplication to cereal endosperm development are also discussed. PMID:25295050

  20. Cell cycle control and seed development.

    PubMed

    Dante, Ricardo A; Larkins, Brian A; Sabelli, Paolo A

    2014-01-01

    Seed development is a complex process that requires coordinated integration of many genetic, metabolic, and physiological pathways and environmental cues. Different cell cycle types, such as asymmetric cell division, acytokinetic mitosis, mitotic cell division, and endoreduplication, frequently occur in sequential yet overlapping manner during the development of the embryo and the endosperm, seed structures that are both products of double fertilization. Asymmetric cell divisions in the embryo generate polarized daughter cells with different cell fates. While nuclear and cell division cycles play a key role in determining final seed cell numbers, endoreduplication is often associated with processes such as cell enlargement and accumulation of storage metabolites that underlie cell differentiation and growth of the different seed compartments. This review focuses on recent advances in our understanding of different cell cycle mechanisms operating during seed development and their impact on the growth, development, and function of seed tissues. Particularly, the roles of core cell cycle regulators, such as cyclin-dependent-kinases and their inhibitors, the Retinoblastoma-Related/E2F pathway and the proteasome-ubiquitin system, are discussed in the contexts of different cell cycle types that characterize seed development. The contributions of nuclear and cellular proliferative cycles and endoreduplication to cereal endosperm development are also discussed.

  1. Transcriptomic evidence for microbial sulfur cycling in the eastern tropical North Pacific oxygen minimum zone

    PubMed Central

    Carolan, Molly T.; Smith, Jason M.; Beman, J. M.

    2015-01-01

    Microbial communities play central roles in ocean biogeochemical cycles, and are particularly important in in oceanic oxygen minimum zones (OMZs). However, the key carbon, nitrogen, and sulfur (S) cycling processes catalyzed by OMZ microbial communities are poorly constrained spatially, temporally, and with regard to the different microbial groups involved. Here we sample across dissolved oxygen (DO) gradients in the oceans’ largest OMZ by volume—the eastern tropical North Pacific ocean, or ETNP—and quantify 16S rRNA and functional gene transcripts to detect and constrain the activity of different S-cycling groups. Based on gene expression profiles, putative dissimilatory sulfite reductase (dsrA) genes are actively expressed within the ETNP OMZ. dsrA expression was limited almost entirely to samples with elevated nitrite concentrations, consistent with previous observations in the Eastern Tropical South Pacific OMZ. dsrA and ‘reverse’ dissimilatory sulfite reductase (rdsrA) genes are related and the associated enzymes are known to operate in either direction—reducing or oxidizing different S compounds. We found that rdsrA genes and soxB genes were expressed in the same samples, suggestive of active S cycling in the ETNP OMZ. These data provide potential thresholds for S cycling in OMZs that closely mimic recent predictions, and indicate that S cycling may be broadly relevant in OMZs. PMID:26029168

  2. The Microbial Engines That Drive Earth’s Biogeochemical Cycles

    NASA Astrophysics Data System (ADS)

    Falkowski, Paul G.; Fenchel, Tom; Delong, Edward F.

    2008-05-01

    Virtually all nonequilibrium electron transfers on Earth are driven by a set of nanobiological machines composed largely of multimeric protein complexes associated with a small number of prosthetic groups. These machines evolved exclusively in microbes early in our planet’s history yet, despite their antiquity, are highly conserved. Hence, although there is enormous genetic diversity in nature, there remains a relatively stable set of core genes coding for the major redox reactions essential for life and biogeochemical cycles. These genes created and coevolved with biogeochemical cycles and were passed from microbe to microbe primarily by horizontal gene transfer. A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales.

  3. The microbial engines that drive Earth's biogeochemical cycles.

    PubMed

    Falkowski, Paul G; Fenchel, Tom; Delong, Edward F

    2008-05-23

    Virtually all nonequilibrium electron transfers on Earth are driven by a set of nanobiological machines composed largely of multimeric protein complexes associated with a small number of prosthetic groups. These machines evolved exclusively in microbes early in our planet's history yet, despite their antiquity, are highly conserved. Hence, although there is enormous genetic diversity in nature, there remains a relatively stable set of core genes coding for the major redox reactions essential for life and biogeochemical cycles. These genes created and coevolved with biogeochemical cycles and were passed from microbe to microbe primarily by horizontal gene transfer. A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales.

  4. Soil Microbial Activity Provides Insight to Carbon Cycling in Shrub Ecotones of Sub-Arctic Sweden

    NASA Astrophysics Data System (ADS)

    Marek, E.; Kashi, N. N.; Chen, J.; Hobbie, E. A.; Schwan, M. R.; Varner, R. K.

    2015-12-01

    Shrubs are expanding in Arctic and sub-Arctic regions due to rising atmospheric temperatures. Microbial activity increases as growing temperatures cause permafrost warming and subsequent thaw, leading to a greater resource of soil nutrients enabling shrub growth. Increased carbon inputs from shrubs is predicted to result in faster carbon turnover by microbial decomposition. Further understanding of microbial activity underneath shrubs could uncover how microbes and soil processes interact to promote shrub expansion and carbon cycling. To address how higher soil carbon input from shrubs influences decomposition, soil samples were taken across a heath, shrub, and forest ecotone gradient at two sites near Abikso, Sweden. Samples were analyzed for soluble carbon and nitrogen, microbial abundance, and microbial activity of chitinase, glucosidase, and phosphatase to reflect organic matter decomposition and availability of nitrogen, carbon, and phosphate respectively. Chitinase activity positively correlated with shrub cover, suggesting microbial demands for nitrogen increase with higher shrub cover. Glucosidase activity negatively correlated with shrub cover and soluble carbon, suggesting decreased microbial demand for carbon as shrub cover and carbon stores increase. Lower glucosidase activity in areas with high carbon input from shrubs implies that microbes are decomposing carbon less readily than carbon is being put into the soil. Increasing soil carbon stores in shrub covered areas can lead to shrubs becoming a net carbon sink and a negative feedback to changing climate.

  5. Molecular Approaches to Marine Microbial Ecology and the Marine Nitrogen Cycle

    NASA Astrophysics Data System (ADS)

    Ward, Bess B.

    2005-01-01

    Microbes are recognized as important components of the Earth system, playing key roles in controlling the composition of the atmosphere and surface waters, forming the basis of the marine food web, and the cycling of chemicals in the ocean. A revolution in microbial ecology has occurred in the past 15-20 years with the advent of rapid methods for discovering and sequencing the genes of uncultivated microbes from natural environments. Initially based on sequences from the 16S rRNA gene, this revolution made it possible to identify microorganisms without first cultivating them, to discover and characterize the immense previously unsuspected diversity of the microbial world, and to reconstruct the evolutionary relationships among microbes. Subsequent focus on functional genes, those that encode enzymes that catalyze biogeochemical transformations, and current work on larger DNA fragments and entire genomes make it possible to link microbial diversity to ecosystem function. These approaches have yielded insights into the regulation of microbial activity and proof of the microbial role in biogeochemical processes previously unknown. Questions raised by the molecular revolution, which are now the focus of microbial ecology research, include the significance of microbial diversity and redundancy to biogeochemical processes and ecosystem function.

  6. Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale.

    PubMed

    Bru, D; Ramette, A; Saby, N P A; Dequiedt, S; Ranjard, L; Jolivet, C; Arrouays, D; Philippot, L

    2011-03-01

    Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. However, a landscape perspective is needed to understand the relative importance of local and regional factors and land management for the microbial communities and the ecosystem services they provide. In the most comprehensive analysis of spatial patterns of microbial communities to date, we investigated the distribution of functional microbial communities involved in N-cycling and of the total bacterial and crenarchaeal communities over 107 sites in Burgundy, a 31,500 km(2) region of France, using a 16 × 16 km(2) sampling grid. At each sampling site, the abundance of total bacteria, crenarchaea, nitrate reducers, denitrifiers- and ammonia oxidizers were estimated by quantitative PCR and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time, and soil physico-chemical properties to the spatial distribution of the different communities were analyzed by canonical variation partitioning. Our results indicate that 43-85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 739 km and used geostatistical modelling to generate predictive maps of the distribution of microbial communities at the landscape scale. The present study highlights the potential of a spatially explicit approach for microbial ecology to identify the overarching factors driving the spatial heterogeneity of microbial communities even at the landscape scale.

  7. Design of a microbial fuel cell and its transition to microbial electrolytic cell for hydrogen production by electrohydrogenesis.

    PubMed

    Gupta, Pratima; Parkhey, Piyush; Joshi, Komal; Mahilkar, Anjali

    2013-10-01

    Anaerobic bacteria were isolated from industrial wastewater and soil samples and tested for exoelectrogenic activity by current production in double chambered microbial fuel cell (MFC), which was further transitioned into a single chambered microbial electrolytic cell to test hydrogen production by electrohydrogenesis. Of all the cultures, the isolate from industrial water sample showed the maximum values for current = 0.161 mA, current density = 108.57 mA/m2 and power density = 48.85 mW/m2 with graphite electrode. Maximum voltage across the cell, however, was reported by the isolate from sewage water sample (506 mv) with copper as electrode. Tap water with KMnO4 was the best cathodic electrolyte as the highest values for all the measured MFC parameters were reported with it. Once the exoelectrogenic activity of the isolates was confirmed by current production, these were tested for hydrogen production in a single chambered microbial electrolytic cell (MEC) modified from the MFC. Hydrogen production was reported positive from co-culture of isolates of both the water samples and co-culture of one soil and one water sample. The maximum rate and yield of hydrogen production was 0.18 m3H2/m3/d and 3.2 mol H2/mol glucose respectively with total hydrogen production of 42.4 mL and energy recovery of 57.4%. Cumulative hydrogen production for a five day cycle of MEC operation was 0.16 m3H2/m3/d.

  8. Intensive cryptic microbial iron cycling in the low iron water column of the meromictic Lake Cadagno.

    PubMed

    Berg, Jasmine S; Michellod, Dolma; Pjevac, Petra; Martinez-Perez, Clara; Buckner, Caroline R T; Hach, Philipp F; Schubert, Carsten J; Milucka, Jana; Kuypers, Marcel M M

    2016-12-01

    Iron redox reactions play an important role in carbon remineralization, supporting large microbial communities in iron-rich terrestrial and aquatic sediments. Stratified water columns with comparably low iron concentrations are globally widespread, but microbial iron cycling in these systems has largely been ignored. We found evidence for unexpectedly high iron turnover rates in the low (1-2 µmol·l(-1) ) iron waters of Lake Cadagno. Light-dependent, biological iron oxidation rates (1.4-13.8 µmol·l(-1) ·d(-1) ) were even higher than in ferruginous lakes with well-studied microbial iron cycles. This photoferrotrophic iron oxidation may account for up to 10% of total primary production in the chemocline. Iron oxides could not be detected and were presumably reduced immediately by iron-reducing microorganisms. Sequences of putative iron oxidizers and reducers were retrieved from in situ 16S rRNA gene amplicon libraries and some of these bacteria were identified in our enrichment cultures supplemented with Fe(II) and FeS. Based on our results, we propose a model in which iron is oxidized by photoferrotrophs and microaerophiles, and iron oxides are immediately reduced by heterotrophic iron reducers, resulting in a cryptic iron cycle. We hypothesize that microbial iron cycling may be more prevalent in water column redoxclines, especially those within the photic zone, than previously believed. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  9. Cell cycle gene expression under clinorotation

    NASA Astrophysics Data System (ADS)

    Artemenko, Olga

    2016-07-01

    Cyclins and cyclin-dependent kinase (CDK) are main regulators of the cell cycle of eukaryotes. It's assumes a significant change of their level in cells under microgravity conditions and by other physical factors actions. The clinorotation use enables to determine the influence of gravity on simulated events in the cell during the cell cycle - exit from the state of quiet stage and promotion presynthetic phase (G1) and DNA synthesis phase (S) of the cell cycle. For the clinorotation effect study on cell proliferation activity is the necessary studies of molecular mechanisms of cell cycle regulation and development of plants under altered gravity condition. The activity of cyclin D, which is responsible for the events of the cell cycle in presynthetic phase can be controlled by the action of endogenous as well as exogenous factors, but clinorotation is one of the factors that influence on genes expression that regulate the cell cycle.These data can be used as a model for further research of cyclin - CDK complex for study of molecular mechanisms regulation of growth and proliferation. In this investigation we tried to summarize and analyze known literature and own data we obtained relatively the main regulators of the cell cycle in altered gravity condition.

  10. The peri-cell-cycle in Arabidopsis.

    PubMed

    Beeckman, T; Burssens, S; Inzé, D

    2001-03-01

    The root systems of plants proliferate via de novo formed meristems originating from differentiated pericycle cells. The identity of putative signals responsible for triggering some of the pericycle cells to re-enter the cell cycle remains unknown. Here, the cell cycle regulation in the pericycle of seedling roots of Arabidopsis thaliana (L.) HEYNH: is studied shortly after germination using various strategies. Based on the detailed analysis of the promoter-beta-glucuronidase activity of four key cell cycle regulatory genes, combined with cell length measurements, microdensitometry of DNA content, and experiments with a cell cycle-blocking agent, a model is proposed for cell cycle regulation in the pericycle at the onset of lateral root initiation. The results clearly show that before the first lateral root is initiated, the pericycle consists of dissimilar cell files in respect of their cell division history. Depending on the distance behind the root tip and on position in relation to the vascular tissue, particular pericycle cells remain in the G(2) phase of the cell cycle and are apparently more susceptible to lateral root initiation than others.

  11. Stretched cell cycle model for proliferating lymphocytes

    PubMed Central

    Dowling, Mark R.; Kan, Andrey; Heinzel, Susanne; Zhou, Jie H. S.; Marchingo, Julia M.; Wellard, Cameron J.; Markham, John F.; Hodgkin, Philip D.

    2014-01-01

    Stochastic variation in cell cycle time is a consistent feature of otherwise similar cells within a growing population. Classic studies concluded that the bulk of the variation occurs in the G1 phase, and many mathematical models assume a constant time for traversing the S/G2/M phases. By direct observation of transgenic fluorescent fusion proteins that report the onset of S phase, we establish that dividing B and T lymphocytes spend a near-fixed proportion of total division time in S/G2/M phases, and this proportion is correlated between sibling cells. This result is inconsistent with models that assume independent times for consecutive phases. Instead, we propose a stretching model for dividing lymphocytes where all parts of the cell cycle are proportional to total division time. Data fitting based on a stretched cell cycle model can significantly improve estimates of cell cycle parameters drawn from DNA labeling data used to monitor immune cell dynamics. PMID:24733943

  12. Unveiling Microbial Carbon Cycling Processes in Key U.S. Soils using ''Omics''

    SciTech Connect

    Myrold, David D.; Bottomely, Peter J.; Jumpponen, Ari; Rice, Charles W.; Zeglin, Lydia H.; David, Maude M.; Jansson, Janet K.; Prestat, Emmanuel; Hettich, Robert L.

    2014-09-17

    Soils process and store large amounts of C; however, considerable uncertainty still exists about the details of that influence microbial partitioning of C into soil C pools, and what are the main influential forces that control the fraction of the C input that is stabilized. The soil microbial community is genotypically and phenotypically diverse. Despite our ability to predict the kinds of regional environmental changes that will accompany global climate change, it is not clear how the microbial community will respond to climate-induced modification of precipitation and inter-precipitation intervals, and if this response will affect the fate of C deposited into soil by the local plant community. Part of this uncertainty lies with our ignorance of how the microbial community adapts genotypically and physiologically to changes in soil moisture brought about by shifts in precipitation. Our overarching goal is to harness the power of multiple meta-omics tools to gain greater understanding of the functioning of whole-soil microbial communities and their role in C cycling. We will do this by meeting the following three objectives: 1. Further develop and optimize a combination of meta-omics approaches to study how environmental factors affect microbially-mediated C cycling processes. 2. Determine the impacts of long-term changes in precipitation timing on microbial C cycling using an existing long-term field manipulation of a tallgrass prairie soil. 3. Conduct laboratory experiments that vary moisture and C inputs to confirm field observations of the linkages between microbial communities and C cycling processes. We took advantage of our state-of-the-art expertise in community “omics” to better understand the functioning soil C cycling within the Great Prairie ecosystem, including our ongoing Konza Prairie soil metagenome flagship project at JGI and the unique rainfall manipulation plots (RaMPs) established at this site more than a decade ago. We employed a systems

  13. Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell

    EPA Science Inventory

    Multi-anode microbial electrochemical cells (MXCs) are considered as one of the most promising configurations for scale-up of MXCs, but fundamental understanding of anode kinetics governing current density is limited in the MXCs. In this study we first assessed microbial communi...

  14. Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell

    EPA Science Inventory

    Multi-anode microbial electrochemical cells (MXCs) are considered as one of the most promising configurations for scale-up of MXCs, but fundamental understanding of anode kinetics governing current density is limited in the MXCs. In this study we first assessed microbial communi...

  15. The Epsomitic Phototrophic Microbial Mat of Hot Lake, Washington. Community Structural Responses to Seasonal Cycling

    SciTech Connect

    Lindemann, Stephen R.; Moran, James J.; Stegen, James C.; Renslow, Ryan S.; Hutchison, Janine R.; Cole, Jessica K.; Dohnalkova, Alice; Tremblay, Julien; Singh, Kanwar; Malfatti, Stephanie; Chen, Feng; Tringe, Susannah; Beyenal, Haluk; Fredrickson, Jim K.

    2013-11-13

    Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin in north-central Washington. The lake harbors a benthic, phototrophic mat that assembles each spring, disassembles each fall, and is subject to greater than tenfold variation in salinity (primarily Mg2+ and SO2-4) and irradiation over the annual cycle. We examined spatiotemporal variation in the mat community at five time points throughout the annual cycle with respect to prevailing physicochemical parameters by amplicon sequencing of the V4 region of the 16S rRNA gene coupled to near-full-length 16S RNA clone sequences. The composition of these microbial communities was relatively stable over the seasonal cycle and included dominant populations of Cyanobacteria, primarily a group IV cyanobacterium (Leptolyngbya), and Alphaproteobacteria (specifically, members of Rhodobacteraceae and Geminicoccus). Members of Gammaproteobacteria (e.g., Thioalkalivibrio and Halochromatium) and Deltaproteobacteria (e.g., Desulfofustis) that are likely to be involved in sulfur cycling peaked in summer and declined significantly by mid-fall, mirroring larger trends in mat community richness and evenness. Phylogenetic turnover analysis of abundant phylotypes employing environmental metadata suggests that seasonal shifts in light variability exert a dominant influence on the composition of Hot Lake microbial mat communities. The seasonal development and organization of these structured microbial mats provide opportunities for analysis of the temporal and physical dynamics that feed back to community function.

  16. The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling

    PubMed Central

    Lindemann, Stephen R.; Moran, James J.; Stegen, James C.; Renslow, Ryan S.; Hutchison, Janine R.; Cole, Jessica K.; Dohnalkova, Alice C.; Tremblay, Julien; Singh, Kanwar; Malfatti, Stephanie A.; Chen, Feng; Tringe, Susannah G.; Beyenal, Haluk; Fredrickson, James K.

    2013-01-01

    Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin in north-central Washington. The lake harbors a benthic, phototrophic mat that assembles each spring, disassembles each fall, and is subject to greater than tenfold variation in salinity (primarily Mg2+ and SO2−4) and irradiation over the annual cycle. We examined spatiotemporal variation in the mat community at five time points throughout the annual cycle with respect to prevailing physicochemical parameters by amplicon sequencing of the V4 region of the 16S rRNA gene coupled to near-full-length 16S RNA clone sequences. The composition of these microbial communities was relatively stable over the seasonal cycle and included dominant populations of Cyanobacteria, primarily a group IV cyanobacterium (Leptolyngbya), and Alphaproteobacteria (specifically, members of Rhodobacteraceae and Geminicoccus). Members of Gammaproteobacteria (e.g., Thioalkalivibrio and Halochromatium) and Deltaproteobacteria (e.g., Desulfofustis) that are likely to be involved in sulfur cycling peaked in summer and declined significantly by mid-fall, mirroring larger trends in mat community richness and evenness. Phylogenetic turnover analysis of abundant phylotypes employing environmental metadata suggests that seasonal shifts in light variability exert a dominant influence on the composition of Hot Lake microbial mat communities. The seasonal development and organization of these structured microbial mats provide opportunities for analysis of the temporal and physical dynamics that feed back to community function. PMID:24312082

  17. Combining microbial cultures for efficient production of electricity from butyrate in a microbial electrochemical cell.

    PubMed

    Miceli, Joseph F; Garcia-Peña, Ines; Parameswaran, Prathap; Torres, César I; Krajmalnik-Brown, Rosa

    2014-10-01

    Butyrate is an important product of anaerobic fermentation; however, it is not directly used by characterized strains of the highly efficient anode respiring bacteria (ARB) Geobacter sulfurreducens in microbial electrochemical cells. By combining a butyrate-oxidizing community with a Geobacter rich culture, we generated a microbial community which outperformed many naturally derived communities found in the literature for current production from butyrate and rivaled the highest performing natural cultures in terms of current density (∼ 11A/m(2)) and Coulombic efficiency (∼ 70%). Microbial community analyses support the shift in the microbial community from one lacking efficient ARB in the marine hydrothermal vent community to a community consisting of ∼ 80% Geobacter in the anode biofilm. This demonstrates the successful production and adaptation of a novel microbial culture for generating electrical current from butyrate with high current density and high Coulombic efficiency, by combining two mixed microbial cultures containing complementing biochemical pathways. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Engineering Robustness of Microbial Cell Factories.

    PubMed

    Gong, Zhiwei; Nielsen, Jens; Zhou, Yongjin J

    2017-08-31

    Metabolic engineering and synthetic biology offer great prospects in developing microbial cell factories capable of converting renewable feedstocks into fuels, chemicals, food ingredients, and pharmaceuticals. However, prohibitively low production rate and mass concentration remain the major hurdles in industrial processes even though the biosynthetic pathways are comprehensively optimized. These limitations are caused by a variety of factors unamenable for host cell survival, such as harsh industrial conditions, fermentation inhibitors from biomass hydrolysates, and toxic compounds including metabolic intermediates and valuable target products. Therefore, engineered microbes with robust phenotypes is essential for achieving higher yield and productivity. In this review, the recent advances in engineering robustness and tolerance of cell factories is described to cope with these issues and briefly introduce novel strategies with great potential to enhance the robustness of cell factories, including metabolic pathway balancing, transporter engineering, and adaptive laboratory evolution. This review also highlights the integration of advanced systems and synthetic biology principles toward engineering the harmony of overall cell function, more than the specific pathways or enzymes. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Microbial fuel cells meet with external resistance.

    PubMed

    Katuri, Krishna P; Scott, Keith; Head, Ian M; Picioreanu, Cristian; Curtis, Tom P

    2011-02-01

    The influence of external load on the composition of the anodic biofilm microbial community and biomass yield was investigated in a microbial fuel cell fed with glucose and domestic wastewater was used as source of electrogens. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplified 16S rRNA gene fragments revealed distinct differences in anodic bacterial communities formed at the anode of each MFC operated under a different external load. These results implied that in an MFC, electrogenic bacteria were enriched under higher current densities, i.e., low external load, and were able to sustain better current and effluent quality. The influence of the external resistance applied to the MFCs during formation of the bacterial communities from sewage wastewater was shown to have no significant effect on power performance of the MFCs nor to have a significant influence on their anodic activity with both glucose and brewery wastewater as fuel. As expected, current generation, COD removal and the biomass yield were all directly influenced by the external load. Significantly, when operated under lower external load, the biomass yield in the MFC was less than that in conventional anaerobic digestion (i.e., control). Copyright © 2010 Elsevier Ltd. All rights reserved.

  20. Protein tyrosine nitration in the cell cycle

    SciTech Connect

    Jia, Min; Mateoiu, Claudia; Souchelnytskyi, Serhiy

    2011-09-23

    Highlights: {yields} Enrichment of 3-nitrotyrosine containing proteins from cells synchronized in different phases of the cell cycle. {yields} Identification of 76 tyrosine nitrated proteins that change expression during the cell cycle. {yields} Nineteen identified proteins were previously described as regulators of cell proliferation. -- Abstract: Nitration of tyrosine residues in proteins is associated with cell response to oxidative/nitrosative stress. Tyrosine nitration is relatively low abundant post-translational modification that may affect protein functions. Little is known about the extent of protein tyrosine nitration in cells during progression through the cell cycle. Here we report identification of proteins enriched for tyrosine nitration in cells synchronized in G0/G1, S or G2/M phases of the cell cycle. We identified 27 proteins in cells synchronized in G0/G1 phase, 37 proteins in S phase synchronized cells, and 12 proteins related to G2/M phase. Nineteen of the identified proteins were previously described as regulators of cell proliferation. Thus, our data indicate which tyrosine nitrated proteins may affect regulation of the cell cycle.

  1. Lactobacillus Decelerates Cervical Epithelial Cell Cycle Progression

    PubMed Central

    Vielfort, Katarina; Weyler, Linda; Söderholm, Niklas; Engelbrecht, Mattias; Löfmark, Sonja; Aro, Helena

    2013-01-01

    We investigated cell cycle progression in epithelial cervical ME-180 cells during colonization of three different Lactobacillus species utilizing live cell microscopy, bromodeoxyuridine incorporation assays, and flow cytometry. The colonization of these ME-180 cells by L. rhamnosus and L. reuteri, originating from human gastric epithelia and saliva, respectively, was shown to reduce cell cycle progression and to cause host cells to accumulate in the G1 phase of the cell cycle. The G1 phase accumulation in L. rhamnosus-colonized cells was accompanied by the up-regulation and nuclear accumulation of p21. By contrast, the vaginal isolate L. crispatus did not affect cell cycle progression. Furthermore, both the supernatants from the lactic acid-producing L. rhamnosus colonies and lactic acid added to cell culture media were able to reduce the proliferation of ME-180 cells. In this study, we reveal the diversity of the Lactobacillus species to affect host cell cycle progression and demonstrate that L. rhamnosus and L. reuteri exert anti-proliferative effects on human cervical carcinoma cells. PMID:23675492

  2. Evidence for microbial carbon and sulfur cycling in deeply buried ridge flank basalt.

    PubMed

    Lever, Mark A; Rouxel, Olivier; Alt, Jeffrey C; Shimizu, Nobumichi; Ono, Shuhei; Coggon, Rosalind M; Shanks, Wayne C; Lapham, Laura; Elvert, Marcus; Prieto-Mollar, Xavier; Hinrichs, Kai-Uwe; Inagaki, Fumio; Teske, Andreas

    2013-03-15

    Sediment-covered basalt on the flanks of mid-ocean ridges constitutes most of Earth's oceanic crust, but the composition and metabolic function of its microbial ecosystem are largely unknown. By drilling into 3.5-million-year-old subseafloor basalt, we demonstrated the presence of methane- and sulfur-cycling microbes on the eastern flank of the Juan de Fuca Ridge. Depth horizons with functional genes indicative of methane-cycling and sulfate-reducing microorganisms are enriched in solid-phase sulfur and total organic carbon, host δ(13)C- and δ(34)S-isotopic values with a biological imprint, and show clear signs of microbial activity when incubated in the laboratory. Downcore changes in carbon and sulfur cycling show discrete geochemical intervals with chemoautotrophic δ(13)C signatures locally attenuated by heterotrophic metabolism.

  3. Evidence for microbial carbon and sulfur cycling in deeply buried ridge flank basalt

    USGS Publications Warehouse

    Lever, Mark A.; Rouxel, Olivier; Alt, Jeffrey C.; Shimizu, Nobumichi; Ono, Shuhei; Coggon, Rosalind M.; Shanks, Wayne C.; Lapham, Laura; Elvert, Marcus; Prieto-Mollar, Xavier; Hinrichs, Kai-Uwe; Inagaki, Fumio; Teske, Andreas

    2013-01-01

    Sediment-covered basalt on the flanks of mid-ocean ridges constitutes most of Earth's oceanic crust, but the composition and metabolic function of its microbial ecosystem are largely unknown. By drilling into 3.5-million-year-old subseafloor basalt, we demonstrated the presence of methane- and sulfur-cycling microbes on the eastern flank of the Juan de Fuca Ridge. Depth horizons with functional genes indicative of methane-cycling and sulfate-reducing microorganisms are enriched in solid-phase sulfur and total organic carbon, host δ13C- and δ34S-isotopic values with a biological imprint, and show clear signs of microbial activity when incubated in the laboratory. Downcore changes in carbon and sulfur cycling show discrete geochemical intervals with chemoautotrophic δ13C signatures locally attenuated by heterotrophic metabolism.

  4. Effects of freeze-thaw cycles on anaerobic microbial processes in an Arctic intertidal mud flat.

    PubMed

    Sawicka, Joanna E; Robador, Alberto; Hubert, Casey; Jørgensen, Bo Barker; Brüchert, Volker

    2010-04-01

    Insight into the effects of repeated freezing and thawing on microbial processes in sediments and soils is important for understanding sediment carbon cycling at high latitudes acutely affected by global warming. Microbial responses to repeated freeze-thaw conditions were studied in three complementary experiments using arctic sediment collected from an intertidal flat that is exposed to seasonal freeze-thaw conditions (Ymerbukta, Svalbard, Arctic Ocean). The sediment was subjected to oscillating freeze-thaw incubations, either gradual, from -5 to 4 degrees C, or abrupt, from -20 to 10 degrees C. Concentrations of low-molecular weight carboxylic acids (volatile fatty acids) were measured and sulfate reduction was assessed by measuring (35)S sulfate reduction rates (SRRs). Gradual freeze-thaw incubation decreased microbial activity in the frozen state to 0.25 % of initial levels at 4 degrees C, but activity resumed rapidly reaching >60 % of initial activity in the thawed state. Exposure of sediments to successive large temperature changes (-20 versus 10 degrees C) decreased SRR by 80% of the initial activity, suggesting that a fraction of the bacterial community recovered rapidly from extreme temperature fluctuations. This is supported by 16S rRNA gene-based denaturing gradient gel electrophoresis profiles that revealed persistence of the dominant microbial taxa under repeated freeze-thaw cycles. The fast recovery of the SRRs suggests that carbon mineralization in thawing arctic sediment can resume without delay or substantial growth of microbial populations.

  5. Convergent development of anodic bacterial communities in microbial fuel cells.

    PubMed

    Yates, Matthew D; Kiely, Patrick D; Call, Douglas F; Rismani-Yazdi, Hamid; Bibby, Kyle; Peccia, Jordan; Regan, John M; Logan, Bruce E

    2012-11-01

    Microbial fuel cells (MFCs) are often inoculated from a single wastewater source. The extent that the inoculum affects community development or power production is unknown. The stable anodic microbial communities in MFCs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wastewater treatment plant sample, and an anaerobic bog sediment. The bog-inoculated MFCs initially produced higher power densities than the wastewater-inoculated MFCs, but after 20 cycles all MFCs on average converged to similar voltages (470±20 mV) and maximum power densities (590±170 mW m(-2)). The power output from replicate bog-inoculated MFCs was not significantly different, but one wastewater-inoculated MFC (UAJA3 (UAJA, University Area Joint Authority Wastewater Treatment Plant)) produced substantially less power. Denaturing gradient gel electrophoresis profiling showed a stable exoelectrogenic biofilm community in all samples after 11 cycles. After 16 cycles the predominance of Geobacter spp. in anode communities was identified using 16S rRNA gene clone libraries (58±10%), fluorescent in-situ hybridization (FISH) (63±6%) and pyrosequencing (81±4%). While the clone library analysis for the underperforming UAJA3 had a significantly lower percentage of Geobacter spp. sequences (36%), suggesting that a predominance of this microbe was needed for convergent power densities, the lower percentage of this species was not verified by FISH or pyrosequencing analyses. These results show that the predominance of Geobacter spp. in acetate-fed systems was consistent with good MFC performance and independent of the inoculum source.

  6. Convergent development of anodic bacterial communities in microbial fuel cells

    PubMed Central

    Yates, Matthew D; Kiely, Patrick D; Call, Douglas F; Rismani-Yazdi, Hamid; Bibby, Kyle; Peccia, Jordan; Regan, John M; Logan, Bruce E

    2012-01-01

    Microbial fuel cells (MFCs) are often inoculated from a single wastewater source. The extent that the inoculum affects community development or power production is unknown. The stable anodic microbial communities in MFCs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wastewater treatment plant sample, and an anaerobic bog sediment. The bog-inoculated MFCs initially produced higher power densities than the wastewater-inoculated MFCs, but after 20 cycles all MFCs on average converged to similar voltages (470±20 mV) and maximum power densities (590±170 mW m−2). The power output from replicate bog-inoculated MFCs was not significantly different, but one wastewater-inoculated MFC (UAJA3 (UAJA, University Area Joint Authority Wastewater Treatment Plant)) produced substantially less power. Denaturing gradient gel electrophoresis profiling showed a stable exoelectrogenic biofilm community in all samples after 11 cycles. After 16 cycles the predominance of Geobacter spp. in anode communities was identified using 16S rRNA gene clone libraries (58±10%), fluorescent in-situ hybridization (FISH) (63±6%) and pyrosequencing (81±4%). While the clone library analysis for the underperforming UAJA3 had a significantly lower percentage of Geobacter spp. sequences (36%), suggesting that a predominance of this microbe was needed for convergent power densities, the lower percentage of this species was not verified by FISH or pyrosequencing analyses. These results show that the predominance of Geobacter spp. in acetate-fed systems was consistent with good MFC performance and independent of the inoculum source. PMID:22572637

  7. Methane cycling. Nonequilibrium clumped isotope signals in microbial methane.

    PubMed

    Wang, David T; Gruen, Danielle S; Lollar, Barbara Sherwood; Hinrichs, Kai-Uwe; Stewart, Lucy C; Holden, James F; Hristov, Alexander N; Pohlman, John W; Morrill, Penny L; Könneke, Martin; Delwiche, Kyle B; Reeves, Eoghan P; Sutcliffe, Chelsea N; Ritter, Daniel J; Seewald, Jeffrey S; McIntosh, Jennifer C; Hemond, Harold F; Kubo, Michael D; Cardace, Dawn; Hoehler, Tori M; Ono, Shuhei

    2015-04-24

    Methane is a key component in the global carbon cycle, with a wide range of anthropogenic and natural sources. Although isotopic compositions of methane have traditionally aided source identification, the abundance of its multiply substituted "clumped" isotopologues (for example, (13)CH3D) has recently emerged as a proxy for determining methane-formation temperatures. However, the effect of biological processes on methane's clumped isotopologue signature is poorly constrained. We show that methanogenesis proceeding at relatively high rates in cattle, surface environments, and laboratory cultures exerts kinetic control on (13)CH3D abundances and results in anomalously elevated formation-temperature estimates. We demonstrate quantitatively that H2 availability accounts for this effect. Clumped methane thermometry can therefore provide constraints on the generation of methane in diverse settings, including continental serpentinization sites and ancient, deep groundwaters.

  8. Microbial Selenite Reduction and the Selenium Biogeochemical Cycle

    NASA Astrophysics Data System (ADS)

    Stolz, J. F.; Wells, M.

    2016-12-01

    Selenium is an essential trace element utilized by many species in the three domains of life. In most Bacteria and Archaea, selenium is primarily assimilated to form selenocysteine, the 21st amino acid (Sec). Additionally selenium can be methylated, demethylated, or used as a terminal electron acceptor in dissimilatory selenate or selenite reduction. Although progress has been made on elucidating the synthesis of selenoproteins, less is known of their occurrence, diversity, and functionality, primarily due to poor genome annotation (e.g., failure to recognize UGA as a Sec and not a stop codon) and proteomics analysis (e.g., failure to detect Sec in LC/MS-MS). Furthermore important parts of the selenium biogeochemical cycle remain to be fully explored, in particular the reduction of Se(IV) to Se(O). We have examined the selenoproteome of a selenate respiring bacterium Sulfurospirillum barnesii strain SES-3, which reduces Se(VI) to Se(0) and the dissimilatory selenite reducing bacterium, Bacillus selenitireducens, strain MLS-10, which reduces Se(IV) to Se(0). Candidate selenoproteins including D-proline reductase, formate dehydrogenase, and methionine-S sulfoxide reductase have been identified in the genomes. A putative dissimilatory selenate reducase (Ser) was found in the genome of S. barnesii. More significant was the discovery of a candidate for the respiratory selenite reductase in B. selenitireducens as determined by in gel assays and LC/MS-MS. The latter has provided a hint at the potential diversity of DSiR bacteria and the development of molecular probes for investigating DSiR in the selenium biogeochemical cycle.

  9. Microbial proliferation on gill structures of juvenile European lobster ( Homarus gammarus) during a moult cycle

    NASA Astrophysics Data System (ADS)

    Middlemiss, Karen L.; Urbina, Mauricio A.; Wilson, Rod W.

    2015-12-01

    The morphology of gill-cleaning structures is not well described in European lobster ( Homarus gammarus). Furthermore, the magnitude and time scale of microbial proliferation on gill structures is unknown to date. Scanning electron microscopy was used to investigate development of setae in zoea, megalopa and juvenile stages (I-V). Microbes were classified and quantified on gill structures throughout a moult cycle from megalopa (stage IV) to juvenile (stage V). Epipodial serrulate setae, consisting of a naked proximal setal shaft with the distal portion possessing scale-like outgrowths (setules), occur only after zoea stage III. After moulting to megalopa (stage IV), gill structures were completely clean and no microbes were visible on days 1 or 5 postmoult. Microbial proliferation was first evident on day 10 postmoult, with a significant 16-fold increase from day 10 to 15. Rod-shaped bacteria were initially predominant (by day 10); however, by day 15 the microbial community was dominated by cocci-shaped bacteria. This research provides new insights into the morphology of gill-grooming structures, the timing of their development, and the magnitude, timescale and characteristics of gill microbial proliferation during a moult cycle. To some degree, the exponential growth of epibionts on gills found during a moult cycle will likely impair respiratory (gas exchange) and ion regulatory function, yet further research is needed to evaluate the physiological effects of the exponential bacterial proliferation documented here.

  10. Recovery of microbial communities and carbon cycling processes following drought manipulation in southern California

    NASA Astrophysics Data System (ADS)

    Allison, S. D.; Martiny, J. B. H.; Martiny, A.; Berlemont, R.; Treseder, K. K.; Goulden, M.; Brodie, E.

    2016-12-01

    Predicting the functioning of microbial communities under changing environmental conditions remains a key challenge in Earth system science. Metagenomics and other high-throughput molecular approaches can help address this challenge by revealing the functional potential of microbial communities. We coupled metagenomics with models and experimental manipulations to address microbial responses to drought in a California grassland ecosystem along with the consequences for carbon cycling. We developed an approach for extracting trait information from metagenomic data and asked: 1) What is the phylogenetic structure of drought response traits? 2) What is the relationship between these traits and those involved in carbohydrate degradation? 3) How do both classes of traits vary seasonally and with precipitation manipulation? 4) How resilient are these traits in the face of perturbation? We found that drought response traits are phylogenetically conserved at an equivalent of 5-8% ribosomal RNA gene sequence dissimilarity. Experimental drought treatment selected for the genetic potential to degrade starch, xylan, and mixed polysaccharides, suggesting a link between drought response and carbon cycling traits. In addition, microbial communities exposed to experimental drought showed a reduced potential to degrade plant biomass. Particularly among bacteria, seasonal drought had a larger impact on microbial composition, abundance, and carbohydrate-degrading genes compared to experimental drought. Bacterial communities were also more resilient to drought perturbation than fungal communities, which showed legacies of drought perturbation for up to three years. Altogether, these findings imply that microbial communities exhibit trait diversity that facilitates resilience but with substantial time lags and consequences for carbon turnover. This information is being used to inform new trait-based models that address the challenge of predicting microbial functioning under

  11. Nucleosome architecture throughout the cell cycle.

    PubMed

    Deniz, Özgen; Flores, Oscar; Aldea, Martí; Soler-López, Montserrat; Orozco, Modesto

    2016-01-28

    Nucleosomes provide additional regulatory mechanisms to transcription and DNA replication by mediating the access of proteins to DNA. During the cell cycle chromatin undergoes several conformational changes, however the functional significance of these changes to cellular processes are largely unexplored. Here, we present the first comprehensive genome-wide study of nucleosome plasticity at single base-pair resolution along the cell cycle in Saccharomyces cerevisiae. We determined nucleosome organization with a specific focus on two regulatory regions: transcription start sites (TSSs) and replication origins (ORIs). During the cell cycle, nucleosomes around TSSs display rearrangements in a cyclic manner. In contrast to gap (G1 and G2) phases, nucleosomes have a fuzzier organization during S and M phases, Moreover, the choreography of nucleosome rearrangements correlate with changes in gene expression during the cell cycle, indicating a strong association between nucleosomes and cell cycle-dependent gene functionality. On the other hand, nucleosomes are more dynamic around ORIs along the cell cycle, albeit with tighter regulation in early firing origins, implying the functional role of nucleosomes on replication origins. Our study provides a dynamic picture of nucleosome organization throughout the cell cycle and highlights the subsequent impact on transcription and replication activity.

  12. Nucleosome architecture throughout the cell cycle

    PubMed Central

    Deniz, Özgen; Flores, Oscar; Aldea, Martí; Soler-López, Montserrat; Orozco, Modesto

    2016-01-01

    Nucleosomes provide additional regulatory mechanisms to transcription and DNA replication by mediating the access of proteins to DNA. During the cell cycle chromatin undergoes several conformational changes, however the functional significance of these changes to cellular processes are largely unexplored. Here, we present the first comprehensive genome-wide study of nucleosome plasticity at single base-pair resolution along the cell cycle in Saccharomyces cerevisiae. We determined nucleosome organization with a specific focus on two regulatory regions: transcription start sites (TSSs) and replication origins (ORIs). During the cell cycle, nucleosomes around TSSs display rearrangements in a cyclic manner. In contrast to gap (G1 and G2) phases, nucleosomes have a fuzzier organization during S and M phases, Moreover, the choreography of nucleosome rearrangements correlate with changes in gene expression during the cell cycle, indicating a strong association between nucleosomes and cell cycle-dependent gene functionality. On the other hand, nucleosomes are more dynamic around ORIs along the cell cycle, albeit with tighter regulation in early firing origins, implying the functional role of nucleosomes on replication origins. Our study provides a dynamic picture of nucleosome organization throughout the cell cycle and highlights the subsequent impact on transcription and replication activity. PMID:26818620

  13. Microbial fuel cells and microbial electrolysis cells for the production of bioelectricity and biomaterials.

    PubMed

    Zhou, Minghua; Yang, Jie; Wang, Hongyu; Jin, Tao; Xu, Dake; Gu, Tingyue

    2013-01-01

    Today's global energy crisis requires a multifaceted solution. Bioenergy is an important part of the solution. The microbial fuel cell (MFC) technology stands out as an attractive potential technology in bioenergy. MFCs can convert energy stored in organic matter directly into bioelectricity. MFCs can also be operated in the electrolysis mode as microbial electrolysis cells to produce bioproducts such as hydrogen and ethanol. Various wastewaters containing low-grade organic carbons that are otherwise unutilized can be used as feed streams for MFCs. Despite major advances in the past decade, further improvements in MFC power output and cost reduction are needed for MFCs to be practical. This paper analysed MFC operating principles using bioenergetics and bioelectrochemistry. Several major issues were explored to improve the MFC performance. An emphasis was placed on the use of catalytic materials for MFC electrodes. Recent advances in the production of various biomaterials using MFCs were also investigated.

  14. Two stage bioethanol refining with multi litre stacked microbial fuel cell and microbial electrolysis cell.

    PubMed

    Sugnaux, Marc; Happe, Manuel; Cachelin, Christian Pierre; Gloriod, Olivier; Huguenin, Gérald; Blatter, Maxime; Fischer, Fabian

    2016-12-01

    Ethanol, electricity, hydrogen and methane were produced in a two stage bioethanol refinery setup based on a 10L microbial fuel cell (MFC) and a 33L microbial electrolysis cell (MEC). The MFC was a triple stack for ethanol and electricity co-generation. The stack configuration produced more ethanol with faster glucose consumption the higher the stack potential. Under electrolytic conditions ethanol productivity outperformed standard conditions and reached 96.3% of the theoretically best case. At lower external loads currents and working potentials oscillated in a self-synchronized manner over all three MFC units in the stack. In the second refining stage, fermentation waste was converted into methane, using the scale up MEC stack. The bioelectric methanisation reached 91% efficiency at room temperature with an applied voltage of 1.5V using nickel cathodes. The two stage bioethanol refining process employing bioelectrochemical reactors produces more energy vectors than is possible with today's ethanol distilleries.

  15. Deep sea microbial fuel cell output as a proxy for microbial activity

    NASA Astrophysics Data System (ADS)

    Richter, K.; George, R.; Hardy, K. R.

    2016-02-01

    Abstract: Microbial fuel cells (MFCs) work by providing bacteria in anaerobic sediments with an electron acceptor (anode) that stimulates metabolism of organic matter. The buried anode is connected via control circuitry to a cathode exposed to oxygen in the overlying water. During metabolism, bacteria release hydrogen ions into the sediment and transfer electrons extra-cellularly to the anode, which eventually reduce dissolved oxygen at the cathode, forming water. The current is chiefly limited by the rate of microbial metabolism at the anode and serves as a proxy for microbial activity. The Office of Naval Research has encouraged development of microbial fuel cells in the marine environment at a number of academic and naval institutions and studies of important environmental parameters that affect fuel cell performance. Earlier work in shallow sediments of San Diego Bay showed that the most important environmental parameters that control fuel cell power output in San Diego Bay were total organic carbon in the sediment and seasonal water temperature. Current MFC work at SPAWAR includes extension of microbial fuel cell tests to the deep sea environment (>4000 m) and, in parallel, testing microbial fuel cells in the laboratory under deep sea conditions. We are pursuing a field efforts to deploy a microbial fuel cell in progressively deeper water, record in situ power and temperature over several weeks, and retrieve the fuel cell along with sediment samples for analysis. We are also pursuing a laboratory effort to build a matching microbial fuel cell in a pressure vessel capable of matching the pressure and temperature of deep water, and stocking the pressure vessel with deep water sediment in order to take measurements analogous to those in the field. We also hope to determine whether bacteria growing on the anode are different from bacteria growing in the bulk sediment via DNA analysis. The current progress and results from this work at SPAWAR will be presented.

  16. Microbially-influenced Fe-Cycling within high pH serpentinizing springs of the Zambales Ophiolite, Philippines

    NASA Astrophysics Data System (ADS)

    Casar, C.; Meyer-Dombard, D. R.; Simon, A.; Cardace, D.; Arcilla, C. A.

    2014-12-01

    . This activity will increase directly with increasing cell growth, and will not be evident in abiotic control microcosms. Evidence of reduced iron mineral formation over time will be seen, and DNA sequencing will yield consistent results with microbes capable of metabolizing iron, thus demonstrating microbially-influenced iron cycling in this system.

  17. Ubiquitin ligases and cell cycle control.

    PubMed

    Teixeira, Leonardo K; Reed, Steven I

    2013-01-01

    The ubiquitin-proteasome system plays a pivotal role in the sequence of events leading to cell division known as the cell cycle. Not only does ubiquitin-mediated proteolysis constitute a critical component of the core oscillator that drives the cell cycle in all eukaryotes, it is also central to the mechanisms that ensure that the integrity of the genome is maintained. These functions are primarily carried out by two families of E3 ubiquitin ligases, the Skp/cullin/F-box-containing and anaphase-promoting complex/cyclosome complexes. However, beyond those functions associated with regulation of central cell cycle events, many peripheral cell cycle-related processes rely on ubiquitylation for signaling, homeostasis, and dynamicity, involving additional types of ubiquitin ligases and regulators. We are only beginning to understand the diversity and complexity of this regulation.

  18. Microbial Fe cycling and mineralization in sediments of an acidic, hypersaline lake (Lake Tyrell, Victoria, Australia)

    NASA Astrophysics Data System (ADS)

    Roden, E. E.; Blöthe, M.; Shelobolina, E.

    2009-12-01

    Lake Tyrrell is a variably acidic, hypersaline, Fe-rich lake located in Victoria, Australia. Terrestrial acid saline lakes like Lake Tyrrell may be analogs for ancient Martian surface environments, as well as possible extant subsurface environments. To investigate the potential for microbial Fe cycling under acidic conditions and high salt concentration, we collected sediment core samples during three field trips between 2006 and 2008 from the southern, acidic edge of the lake. Materials from the cores were used for chemical and mineralogical analyses, as well as for molecular (16S rRNA genes) and culture-based microbiological studies. Near-surface (< 1 m depth) pore fluids contained low but detectable dissolved oxygen (ca. 50 uM), significant dissolved Fe(II) (ca. 500 uM), and nearly constant pH of around 4 - conditions conducive to enzymatic Fe(II) oxidation. High concentrations of Fe(III) oxides begin accumulate at a depth of ca. 10 cm, and may reflect the starting point for formation of massive iron concretions that are evident at and beneath the sediment surface. MPN analyses revealed low (10-100 cells/mL) but detectable populations of aerobic, halophilic Fe(II)-oxidizing organisms on the sediment surface and in the near-surface ground water. With culture-dependent methods at least three different halotolerant lithoautotrophic cultures growing on Fe(II), thiosulfate, or tetrathionate from different acidic sites were obtained. Analysis of 16S rRNA gene sequences revealed that these organisms are similar to previous described gamma proteobacteria Thiobacillus prosperus (95%), Halothiobacillus kellyi (99%), Salinisphaera shabanense (95%) and a Marinobacter species. (98%). 16S rRNA gene pyrosequencing data from two different sites with a pH range between 3 and 4.5 revealed a dominance of gamma proteobacteria. 16S rRNA gene pyrosequencing libraries from both cores were dominated by sequences related to the Ectothiorhodospiraceae family, which includes the taxa

  19. Cell Cycle Deregulation in Ewing's Sarcoma Pathogenesis

    PubMed Central

    Kowalewski, Ashley A.; Randall, R. Lor; Lessnick, Stephen L.

    2011-01-01

    Ewing's sarcoma is a highly aggressive pediatric tumor of bone that usually contains the characteristic chromosomal translocation t(11;22)(q24;q12). This translocation encodes the oncogenic fusion protein EWS/FLI, which acts as an aberrant transcription factor to deregulate target genes necessary for oncogenesis. One key feature of oncogenic transformation is dysregulation of cell cycle control. It is therefore likely that EWS/FLI and other cooperating mutations in Ewing's sarcoma modulate the cell cycle to facilitate tumorigenesis. This paper will summarize current published data associated with deregulation of the cell cycle in Ewing's sarcoma and highlight important questions that remain to be answered. PMID:21052502

  20. Microbial Fuel Cells and Microbial Ecology: Applications in Ruminant Health and Production Research

    PubMed Central

    Osterstock, Jason B.; Pinchak, William E.; Ishii, Shun’ichi; Nelson, Karen E.

    2009-01-01

    Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H2) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H2in the rumen. Given the crucial role that H2 plays in ruminant digestion, it is desirable to understand the microbial relationships that control H2 partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research. PMID:20024685

  1. Microbial fuel cells and microbial ecology: applications in ruminant health and production research.

    PubMed

    Bretschger, Orianna; Osterstock, Jason B; Pinchak, William E; Ishii, Shun'ichi; Nelson, Karen E

    2010-04-01

    Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H(2)) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H(2)in the rumen. Given the crucial role that H(2) plays in ruminant digestion, it is desirable to understand the microbial relationships that control H(2) partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research.

  2. Cell cycle regulates cell type in the Arabidopsis sepal.

    PubMed

    Roeder, Adrienne H K; Cunha, Alexandre; Ohno, Carolyn K; Meyerowitz, Elliot M

    2012-12-01

    The formation of cellular patterns during development requires the coordination of cell division with cell identity specification. This coordination is essential in patterning the highly elongated giant cells, which are interspersed between small cells, in the outer epidermis of the Arabidopsis thaliana sepal. Giant cells undergo endocycles, replicating their DNA without dividing, whereas small cells divide mitotically. We show that distinct enhancers are expressed in giant cells and small cells, indicating that these cell types have different identities as well as different sizes. We find that members of the epidermal specification pathway, DEFECTIVE KERNEL1 (DEK1), MERISTEM LAYER1 (ATML1), Arabidopsis CRINKLY4 (ACR4) and HOMEODOMAIN GLABROUS11 (HDG11), control the identity of giant cells. Giant cell identity is established upstream of cell cycle regulation. Conversely, endoreduplication represses small cell identity. These results show not only that cell type affects cell cycle regulation, but also that changes in the cell cycle can regulate cell type.

  3. Programming microbial population dynamics by engineered cell-cell communication.

    PubMed

    Song, Hao; Payne, Stephen; Tan, Cheemeng; You, Lingchong

    2011-07-01

    A major aim of synthetic biology is to program novel cellular behavior using engineered gene circuits. Early endeavors focused on building simple circuits that fulfill simple functions, such as logic gates, bistable toggle switches, and oscillators. These gene circuits have primarily focused on single-cell behaviors since they operate intracellularly. Thus, they are often susceptible to cell-cell variations due to stochastic gene expression. Cell-cell communication offers an efficient strategy to coordinate cellular behavior at the population level. To this end, we review recent advances in engineering cell-cell communication to achieve reliable population dynamics, spanning from communication within single species to multispecies, from one-way sender-receiver communication to two-way communication in synthetic microbial ecosystems. These engineered systems serve as well-defined model systems to better understand design principles of their naturally occurring counterparts and to facilitate novel biotechnology applications.

  4. Programming microbial population dynamics by engineered cell-cell communication

    PubMed Central

    Song, Hao; Payne, Stephen; Tan, Cheemeng; You, Lingchong

    2013-01-01

    A major aim of synthetic biology is to program novel cellular behaviors using engineered gene circuits. Early endeavors focused on building simple circuits that fulfill simple functions, such as logic gates, bistable toggle switches, and oscillators. These gene circuits have primarily focused on single-cell behaviors since they operate intracellularly. Thus, they are often susceptible to cell-cell variations due to stochastic gene expression. Cell-cell communication offers an efficient strategy to coordinate cellular behaviors at the population level. To this end, we review recent advances in engineering cell-cell communication to achieve reliable population dynamics, spanning from communication within single species to multispecies, from one-way sender-receiver communication to two-way communication in synthetic microbial ecosystems. These engineered systems serve as well-defined model systems to better understand design principles of their naturally occurring counterparts and to facilitate novel biotechnology applications. PMID:21681967

  5. Methanogenesis in membraneless microbial electrolysis cells.

    PubMed

    Clauwaert, Peter; Verstraete, Willy

    2009-04-01

    Operation of microbial electrolysis cells (MECs) without an ion exchange membrane could help to lower the construction costs while lowering the ohmic cell resistance and improving MEC conversion rates by minimizing the pH gradient between anode and cathode. In this research, we demonstrate that membraneless MECs with plain graphite can be operated for methane production without pH adjustment and that the ohmic cell resistance could be lowered with approximately 50% by removing the cation exchange membrane. As a result, the current production increased from 66 +/- 2 to 156 +/- 1 A m(-3) MEC by removing the membrane with an applied voltage of -0.8 V. Methane was the main energetic product despite continuous operation under carbonate-limited and slightly acidified conditions (pH 6.1-6.2). Our results suggest that continuous production of hydrogen in membraneless MECs will be challenging since methane production might not be avoided easily. The electrical energy invested was not always completely recovered under the form of an energy-rich biogas; however, our results indicate that membraneless MECs might be a viable polishing step for the treatment of the effluent of anaerobic digesters as methane was produced under low organic loading conditions and at room temperature.

  6. Biological denitrification in microbial fuel cells.

    PubMed

    Clauwaert, Peter; Rabaey, Korneel; Aelterman, Peter; de Schamphelaire, Liesje; Pham, The Hai; Boeckx, Pascal; Boon, Nico; Verstraete, Willy

    2007-05-01

    Microbial fuel cells (MFCs) that remove carbon as well as nitrogen compounds out of wastewater are of special interest for practice. We developed a MFC in which microorganisms in the cathode performed a complete denitrification by using electrons supplied by microorganisms oxidizing acetate in the anode. The MFC with a cation exchange membrane was designed as a tubular reactor with an internal cathode and was able to remove up to 0.146 kg NO(3-)-N m(-3) net cathodic compartment (NCC) d(-1) (0.080 kg NO(3-)-N m(-3) total cathodic compartment d(-1) (TCC)) at a current of 58 A m(-3) NCC (32 A m(-3) TCC) and a cell voltage of 0.075 V. The highest power output in the denitrification system was 8 W m(-3) NCC (4 W m(-3) TCC) with a cell voltage of 0.214 V and a current of 35 A m(-3) NCC. The denitrification rate and the power production was limited bythe cathodic microorganisms, which only denitrified significantly at a cathodic electrode potential below 0 V versus standard hydrogen electrode (SHE). This is, to our knowledge, the first study in which a MFC has both a biological anode and cathode performing simultaneous removal of an organic substrate, power production, and complete denitrification without relying on H2-formation or external added power.

  7. Transcriptional landscape of the human cell cycle.

    PubMed

    Liu, Yin; Chen, Sujun; Wang, Su; Soares, Fraser; Fischer, Martin; Meng, Feilong; Du, Zhou; Lin, Charles; Meyer, Clifford; DeCaprio, James A; Brown, Myles; Liu, X Shirley; He, Housheng Hansen

    2017-03-28

    Steady-state gene expression across the cell cycle has been studied extensively. However, transcriptional gene regulation and the dynamics of histone modification at different cell-cycle stages are largely unknown. By applying a combination of global nuclear run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and histone-modification Chip sequencing (ChIP-seq), we depicted a comprehensive transcriptional landscape at the G0/G1, G1/S, and M phases of breast cancer MCF-7 cells. Importantly, GRO-seq and RNA-seq analysis identified different cell-cycle-regulated genes, suggesting a lag between transcription and steady-state expression during the cell cycle. Interestingly, we identified genes actively transcribed at early M phase that are longer in length and have low expression and are accompanied by a global increase in active histone 3 lysine 4 methylation (H3K4me2) and histone 3 lysine 27 acetylation (H3K27ac) modifications. In addition, we identified 2,440 cell-cycle-regulated enhancer RNAs (eRNAs) that are strongly associated with differential active transcription but not with stable expression levels across the cell cycle. Motif analysis of dynamic eRNAs predicted Kruppel-like factor 4 (KLF4) as a key regulator of G1/S transition, and this identification was validated experimentally. Taken together, our combined analysis characterized the transcriptional and histone-modification profile of the human cell cycle and identified dynamic transcriptional signatures across the cell cycle.

  8. Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersaline basin.

    PubMed

    Borin, Sara; Brusetti, Lorenzo; Mapelli, Francesca; D'Auria, Giuseppe; Brusa, Tullio; Marzorati, Massimo; Rizzi, Aurora; Yakimov, Michail; Marty, Danielle; De Lange, Gert J; Van der Wielen, Paul; Bolhuis, Henk; McGenity, Terry J; Polymenakou, Paraskevi N; Malinverno, Elisa; Giuliano, Laura; Corselli, Cesare; Daffonchio, Daniele

    2009-06-09

    Urania basin in the deep Mediterranean Sea houses a lake that is >100 m deep, devoid of oxygen, 6 times more saline than seawater, and has very high levels of methane and particularly sulfide (up to 16 mM), making it among the most sulfidic water bodies on Earth. Along the depth profile there are 2 chemoclines, a steep one with the overlying oxic seawater, and another between anoxic brines of different density, where gradients of salinity, electron donors and acceptors occur. To identify and differentiate the microbes and processes contributing to the turnover of organic matter and sulfide along the water column, these chemoclines were sampled at a high resolution. Bacterial cell numbers increased up to a hundredfold in the chemoclines as a consequence of elevated nutrient availability, with higher numbers in the upper interface where redox gradient was steeper. Bacterial and archaeal communities, analyzed by DNA fingerprinting, 16S rRNA gene libraries, activity measurements, and cultivation, were highly stratified and metabolically more active along the chemoclines compared with seawater or the uniformly hypersaline brines. Detailed analysis of 16S rRNA gene sequences revealed that in both chemoclines delta- and epsilon-Proteobacteria, predominantly sulfate reducers and sulfur oxidizers, respectively, were the dominant bacteria. In the deepest layers of the basin MSBL1, putatively responsible for methanogenesis, dominated among archaea. The data suggest that the complex microbial community is adapted to the basin's extreme chemistry, and the elevated biomass is driven largely by sulfur cycling and methanogenesis.

  9. Soil microbial communities and elk foraging intensity: implications for soil biogeochemical cycling in the sagebrush steppe.

    PubMed

    Cline, Lauren C; Zak, Donald R; Upchurch, Rima A; Freedman, Zachary B; Peschel, Anna R

    2017-02-01

    Foraging intensity of large herbivores may exert an indirect top-down ecological force on soil microbial communities via changes in plant litter inputs. We investigated the responses of the soil microbial community to elk (Cervus elaphus) winter range occupancy across a long-term foraging exclusion experiment in the sagebrush steppe of the North American Rocky Mountains, combining phylogenetic analysis of fungi and bacteria with shotgun metagenomics and extracellular enzyme assays. Winter foraging intensity was associated with reduced bacterial richness and increasingly distinct bacterial communities. Although fungal communities did not respond linearly to foraging intensity, a greater β-diversity response to winter foraging exclusion was observed. Furthermore, winter foraging exclusion increased soil cellulolytic and hemicellulolytic enzyme potential and higher foraging intensity reduced chitinolytic gene abundance. Thus, future changes in winter range occupancy may shape biogeochemical processes via shifts in microbial communities and subsequent changes to their physiological capacities to cycle soil C and N.

  10. Targeting cell cycle regulation in cancer therapy.

    PubMed

    Diaz-Moralli, Santiago; Tarrado-Castellarnau, Míriam; Miranda, Anibal; Cascante, Marta

    2013-05-01

    Cell proliferation is an essential mechanism for growth, development and regeneration of eukaryotic organisms; however, it is also the cause of one of the most devastating diseases of our era: cancer. Given the relevance of the processes in which cell proliferation is involved, its regulation is of paramount importance for multicellular organisms. Cell division is orchestrated by a complex network of interactions between proteins, metabolism and microenvironment including several signaling pathways and mechanisms of control aiming to enable cell proliferation only in response to specific stimuli and under adequate conditions. Three main players have been identified in the coordinated variation of the many molecules that play a role in cell cycle: i) The cell cycle protein machinery including cyclin-dependent kinases (CDK)-cyclin complexes and related kinases, ii) The metabolic enzymes and related metabolites and iii) The reactive-oxygen species (ROS) and cellular redox status. The role of these key players and the interaction between oscillatory and non-oscillatory species have proved essential for driving the cell cycle. Moreover, cancer development has been associated to defects in all of them. Here, we provide an overview on the role of CDK-cyclin complexes, metabolic adaptations and oxidative stress in regulating progression through each cell cycle phase and transitions between them. Thus, new approaches for the design of innovative cancer therapies targeting crosstalk between cell cycle simultaneous events are proposed. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Interplay between cell growth and cell cycle in plants.

    PubMed

    Sablowski, Robert; Carnier Dornelas, Marcelo

    2014-06-01

    The growth of organs and whole plants depends on both cell growth and cell-cycle progression, but the interaction between both processes is poorly understood. In plants, the balance between growth and cell-cycle progression requires coordinated regulation of four different processes: macromolecular synthesis (cytoplasmic growth), turgor-driven cell-wall extension, mitotic cycle, and endocycle. Potential feedbacks between these processes include a cell-size checkpoint operating before DNA synthesis and a link between DNA contents and maximum cell size. In addition, key intercellular signals and growth regulatory genes appear to target at the same time cell-cycle and cell-growth functions. For example, auxin, gibberellin, and brassinosteroid all have parallel links to cell-cycle progression (through S-phase Cyclin D-CDK and the anaphase-promoting complex) and cell-wall functions (through cell-wall extensibility or microtubule dynamics). Another intercellular signal mediated by microtubule dynamics is the mechanical stress caused by growth of interconnected cells. Superimposed on developmental controls, sugar signalling through the TOR pathway has recently emerged as a central control point linking cytoplasmic growth, cell-cycle and cell-wall functions. Recent progress in quantitative imaging and computational modelling will facilitate analysis of the multiple interconnections between plant cell growth and cell cycle and ultimately will be required for the predictive manipulation of plant growth.

  12. Performance and microbial diversity of palm oil mill effluent microbial fuel cell.

    PubMed

    Jong, B C; Liew, P W Y; Lebai Juri, M; Kim, B H; Mohd Dzomir, A Z; Leo, K W; Awang, M R

    2011-12-01

    To evaluate the bioenergy generation and the microbial community structure from palm oil mill effluent using microbial fuel cell. Microbial fuel cells enriched with palm oil mill effluent (POME) were employed to harvest bioenergy from both artificial wastewater containing acetate and complex POME. The microbial fuel cell (MFC) showed maximum power density of 3004 mW m(-2) after continuous feeding with artificial wastewater containing acetate substrate. Subsequent replacement of the acetate substrate with complex substrate of POME recorded maximum power density of 622 mW m(-2). Based on 16S rDNA analyses, relatively higher abundance of Deltaproteobacteria (88.5%) was detected in the MFCs fed with acetate artificial wastewater as compared to POME. Meanwhile, members of Gammaproteobacteria, Epsilonproteobacteria and Betaproteobacteria codominated the microbial consortium of the MFC fed with POME with 21, 20 and 18.5% abundances, respectively. Enriched electrochemically active bacteria originated from POME demonstrated potential to generate bioenergy from both acetate and complex POME substrates. Further improvements including the development of MFC systems that are able to utilize both fermentative and nonfermentative substrates in POME are needed to maximize the bioenergy generation. A better understanding of microbial structure is critical for bioenergy generation from POME using MFC. Data obtained in this study improve our understanding of microbial community structure in conversion of POME to electricity. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

  13. Metaproteogenomics reveals the soil microbial communities active in nutrient cycling processes under different tree species

    NASA Astrophysics Data System (ADS)

    Keiblinger, Katharina Maria; Masse, Jacynthe; Zühlke, Daniela; Riedel, Katharina; Zechmeister-Boltenstern, Sophie; Prescott, Cindy E.; Grayston, Sue

    2016-04-01

    Tree species exert strong effects on microbial communities in litter and soil and may alter rates of soil processes fundamental to nutrient cycling and carbon fluxes (Prescott and Grayston 2013). However, the influence of tree species on decomposition processes are still contradictory and poorly understood. An understanding of the mechanisms underlying plant influences on soil processes is important for our ability to predict ecosystem response to altered global/environmental conditions. In order to link microbial community structure and function to forest-floor nutrient cycling processes, we sampled forest floors under western redcedar (Thuja plicata), Douglas-fir (Pseudotsuga menziesii) and Sitka spruce (Picea sitchensis) grown in nutrient-poor sites in common garden experiments on Vancouver island (Canada). We measured forest-floor total N, total C, initial NH4+ and NO3- concentrations, DOC, Cmic and Nmic. Gross rates of ammonification and NH4+ consumption were measured using the 15N pool-dilution method. Organic carbon quality was assessed through FTIR analyses. Microbial community structure was analysed by a metaproteogenomic approach using 16S and ITS amplification and sequencing with MiSeq platform. Proteins were extracted and peptides characterized via LC-MS/MS on a Velos Orbitrap to assess the active microbial community. Different microbial communities were active under the three tree species and variation in process rates were observed and will be discussed. This research provides new insights on microbial processes during organic matter decomposition. The metaproteogenomic approach enables us to investigate these changes with respect to possible effects on soil C-storage at even finer taxonomic resolution.

  14. Mechanics and regulation of cell shape during the cell cycle.

    PubMed

    Clark, Andrew G; Paluch, Ewa

    2011-01-01

    Many cell types undergo dramatic changes in shape throughout the cell cycle. For individual cells, a tight control of cell shape is crucial during cell division, but also in interphase, for example during cell migration. Moreover, cell cycle-related cell shape changes have been shown to be important for tissue morphogenesis in a number of developmental contexts. Cell shape is the physical result of cellular mechanical properties and of the forces exerted on the cell. An understanding of the causes and repercussions of cell shape changes thus requires knowledge of both the molecular regulation of cellular mechanics and how specific changes in cell mechanics in turn effect global shape changes. In this chapter, we provide an overview of the current knowledge on the control of cell morphology, both in terms of general cell mechanics and specifically during the cell cycle.

  15. Microbial community analysis of a single chamber microbial fuel cell using potato wastewater.

    PubMed

    Li, Zhen; Haynes, Rishika; Sato, Eugene; Shields, Malcolm S; Fujita, Yoshiko; Sato, Chikashi

    2014-04-01

    Microbial fuel cells (MFCs) convert chemical energy to electrical energy via bio-electrochemical reactions mediated by microorganisms. This study investigated the diversity of the microbial community in an air cathode single chamber MFC that used potato-process wastewater as substrate. Terminal restriction fragment length polymorphism results indicated that the bacterial communities on the anode, cathode, control electrode, and MFC bulk fluid were similar, but differed dramatically from that of the anaerobic domestic sludge and potato wastewater inoculum. The 16S ribosomal DNA sequencing results showed that microbial species detected on the anode were predominantly within the phyla of Proteobacteria, Firmicutes, and Bacteroidetes. Fluorescent microscopy results indicated that there was a clear enhancement of biofilm formation on the anode. Results of this study could help improve understanding of the complexity of microbial communities and optimize the microbial composition for generating electricity by MFCs that use potato wastewater.

  16. Combining microbial cultures for efficient production of electricity from butyrate in a microbial electrochemical cell

    PubMed Central

    Miceli, Joseph F.; Garcia-Peña, Ines; Parameswaran, Prathap; Torres, César I.; Krajmalnik-Brown, Rosa

    2014-01-01

    Butyrate is an important product of anaerobic fermentation; however, it is not directly used by characterized strains of the highly efficient anode respiring bacteria (ARB) Geobacter sulfurreducens in microbial electrochemical cells. By combining a butyrate-oxidizing community with a Geobacter rich culture, we generated a microbial community which outperformed many naturally derived communities found in the literature for current production from butyrate and rivaled the highest performing natural cultures in terms of current density (~11 A/m2) and Coulombic efficiency (~70%). Microbial community analyses support the shift in the microbial community from one lacking efficient ARB in the marine hydrothermal vent community to a community consisting of ~80% Geobacter in the anode biofilm. This demonstrates the successful production and adaptation of a novel microbial culture for generating electrical current from butyrate with high current density and high Coulombic efficiency, by combining two mixed micro bial cultures containing complementing biochemical pathways. PMID:25048958

  17. Microbial Community Analysis of a Single Chamber Microbial Fuel Cell Using Potato Wastewater

    SciTech Connect

    Zhen Li; Rishika Haynes; Eugene Sato; Malcolm Shields; Yoshiko Fujita; Chikashi Sato

    2014-04-01

    Microbial fuel cells (MFCs) convert chemical energy to electrical energy via bioelectrochemical reactions mediated by microorganisms. We investigated the diversity of the microbial community in an air cathode single chamber MFC that utilized potato-process wastewater as substrate. Terminal Restriction Fragment Length Polymorphism (T-RFLP) results indicated that the bacterial communities on the anode, cathode, control electrode, and MFC bulk fluid were similar, but differed dramatically from that of the anaerobic domestic sludge and potato wastewater inoculum. The 16S rDNA sequencing results showed that microbial species detected on the anode were predominantly within the phyla of Proteobacteria, Firmicutes, and Bacteroidetes. Fluorescent microscopy results indicated that there was a clear enhancement of biofilm formation on the anode. Results of this study could help improve understanding of the complexity of microbial communities and optimize the microbial composition for generating electricity by MFCs that utilize potato wastewater.

  18. Soil microbial community structure and nitrogen cycling responses to agroecosystem management and carbon substrate addition

    NASA Astrophysics Data System (ADS)

    Berthrong, S. T.; Buckley, D. H.; Drinkwater, L. E.

    2011-12-01

    Fertilizer application in conventional agriculture leads to N saturation and decoupled soil C and N cycling, whereas organic practices, e.g. complex rotations and legume incorporation, often results in increased SOM and tightly coupled cycles of C and N. These legacy effects of management on soils likely affect microbial community composition and microbial process rates. This project tested if agricultural management practices led to distinct microbial communities and if those communities differed in ability to utilize labile plant carbon substrates and to produce more plant available N. We addressed several specific questions in this project. 1) Do organic and conventional management legacies on similar soils produce distinct soil bacterial and fungal community structures and abundances? 2) How do these microbial community structures change in response to carbon substrate addition? 3) How do the responses of the microbial communities influence N cycling? To address these questions we conducted a laboratory incubation of organically and conventionally managed soils. We added C-13 labelled glucose either in one large dose or several smaller pulses. We extracted genomic DNA from soils before and after incubation for TRFLP community fingerprinting. We measured C in soil pools and respiration and N in soil extracts and leachates. Management led to different compositions of bacteria and fungi driven by distinct components in organic soils. Biomass did not differ across treatments indicating that differences in cycling were due to composition rather than abundance. C substrate addition led to convergence in bacterial communities; however management still strongly influenced the difference in communities. Fungal communities were very distinct between managements and plots with substrate addition not altering this pattern. Organic soils respired 3 times more of the glucose in the first week than conventional soils (1.1% vs 0.4%). Organic soils produced twice as much

  19. Microbial Succession and Nitrogen Cycling in Cultured Biofilms as Affected by the Inorganic Nitrogen Availability.

    PubMed

    Li, Shuangshuang; Peng, Chengrong; Wang, Chun; Zheng, Jiaoli; Hu, Yao; Li, Dunhai

    2017-01-01

    Biofilms play important roles in nutrients and energy cycling in aquatic ecosystems. We hypothesized that as eutrophication could change phytoplankton community and decrease phytoplankton diversity, ambient inorganic nitrogen level will affect the microbial community and diversity of biofilms and the roles of biofilms in nutrient cycling. Biofilms were cultured using a flow incubator either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def). The results showed that the biomass and nitrogen and phosphorous accumulation of biofilms were limited by N deficiency; however, as expected, the N-def biofilms had significantly higher microbial diversity than that of N-rep biofilms. The microbial community of biofilms shifted in composition and abundance in response to ambient inorganic nitrogen level. For example, as compared between the N-def and the N-rep biofilms, the former consisted of more diazotrophs, while the latter consisted of more denitrifying bacteria. As a result of the shift of the functional microbial community, the N concentration of N-rep medium kept decreasing, while that of N-def medium showed an increasing trend in the late stage. This indicates that biofilms can serve as the source or the sink of nitrogen in aquatic ecosystems, and it depends on the inorganic nitrogen availability.

  20. Spatial distribution of N-cycling microbial communities showed complex patterns in constructed wetland sediments.

    PubMed

    Correa-Galeote, David; Marco, Diana E; Tortosa, Germán; Bru, David; Philippot, Laurent; Bedmar, Eulogio J

    2013-02-01

    Constructed wetlands are used for biological treatment of wastewater from agricultural lands carrying pollutants such as nitrates. Nitrogen removal in wetlands occurs from direct assimilation by plants and through microbial nitrification and denitrification. We investigated the spatial distribution of N-cycling microbial communities and genes involved in nitrification and denitrification in constructed wetland sediments receiving irrigation water. We used quantitative real-time PCR (qPCR) to characterize microbial communities. Geostatistical variance analysis was used to relate them with vegetation cover and biogeochemical sediment properties. The spatial distribution of the N-cycling microbial communities of sediments was heterogeneous and complex. Total communities of bacteria and crenarchaea showed different spatial distributions. Analysis of autocorrelation patterns through semivariance indicated a tendency towards a patchy distribution over scales around 10 m for genes involved in the nitrification and denitrification processes. In contrast, biogeochemical sediment properties showed diverse spatial distributions. While almost no patchiness was found for pH and moisture, patchiness at scales between 8 and 10 m was detected for carbon, nitrate and ammonia. Denitrification variables showed spatial autocorrelation at scales comparable to genes. However, denitrifying enzyme activity and potential N(2)O production showed a common spatial pattern, different from that of the N(2)O/(N(2)O + N(2)).

  1. Fuel cell and advanced turbine power cycle

    SciTech Connect

    White, D.J.

    1995-10-19

    Solar Turbines, Incorporated (Solar) has a vested interest in the integration of gas turbines and high temperature fuel cells and in particular, solid oxide fuel cells (SOFCs). Solar has identified a parallel path approach to the technology developments needed for future products. The primary approach is to move away from the simple cycle industrial machines of the past and develop as a first step more efficient recuperated engines. This move was prompted by the recognition that the simple cycle machines were rapidly approaching their efficiency limits. Improving the efficiency of simple cycle machines is and will become increasingly more costly. Each efficiency increment will be progressively more costly than the previous step.

  2. Cell cycle regulation of mitochondrial function.

    PubMed

    Lopez-Mejia, Isabel C; Fajas, Lluis

    2015-04-01

    Specific cellular functions, such as proliferation, survival, growth, or senescence, require a particular adaptive metabolic response, which is fine tuned by members of the cell cycle regulators families. Currently, proteins such as cyclins, CDKs, or E2Fs are being studied in the context of cell proliferation and survival, cell signaling, cell cycle regulation, and cancer. We show in this review that cellular, animal and molecular studies provided enough evidence to prove that these factors play, in addition, crucial roles in the control of mitochondrial function; finally resulting in a dual proliferative and metabolic response. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Over-pressurized bioreactors: application to microbial cell cultures.

    PubMed

    Lopes, Marlene; Belo, Isabel; Mota, Manuel

    2014-01-01

    In industrial biotechnology, microbial cultures are exposed to different local pressures inside bioreactors. Depending on the microbial species and strains, the increased pressure may have detrimental or beneficial effects on cellular growth and product formation. In this review, the effects of increased air pressure on various microbial cultures growing in bioreactors under moderate total pressure conditions (maximum, 15 bar) will be discussed. Recent data illustrating the diversity of increased air pressure effects at different levels in microbial cells cultivation will be presented, with particular attention to the effects of oxygen and carbon dioxide partial pressures on cellular growth and product formation, and the concomitant effect of oxygen pressure on antioxidant cellular defense mechanisms.

  4. Modeling carbon cycle responses to tree mortality: linking microbial and biogeochemical changes

    NASA Astrophysics Data System (ADS)

    Moore, D. J.; Trahan, N. A.; Dynes, E. L.; Zobitz, J. M.; Gallery, R.

    2013-12-01

    Amid a worldwide increase in tree mortality, mountain pine beetles (Dendroctonus ponderosae Hopkins) have killed billions of trees from Mexico to Alaska in the last 13 years. This mortality is predicted to influence important carbon, water and energy balance feedbacks on the Earth system. We studied changes in soil biogeochemical cycling and microbial community structure after tree mortality. We show, using a decade long chronosequence, that tree mortality causes no increase in total respiration from local to watershed scales, with corresponding changes in biogeochemical pools of nitrogen and phosphorus. We also found comparable declines in both gross primary productivity and respiration suggesting little change in net flux. We tested the mechanisms controlling these patterns using an ecosystem model; contrasting a simplified microbial subroutine with a 'dead soil' model. We coupled our modeling work with direct measurements of microbial biomass, enzyme kinetics and community structure. The transitory recovery of respiration 6-7 years after mortality was associated with increased microbial biomass, increased incorporation of leaf litter carbon into soil organic matter, and was followed by a secondary decline in respiration during years 8-10. Our findings are consistent with the mechanism of reduced input of new carbon causing a decline in microbial biomass rather than an increased output of older carbon.

  5. Anammox revisited: thermodynamic considerations in early studies of the microbial nitrogen cycle.

    PubMed

    Oren, Aharon

    2015-08-01

    This paper explores the early literature on the thermodynamics of processes in the microbial nitrogen cycle, evaluating parameters of transfer of energy which depends on the initial and final states of the system, the mechanism of the reactions involved and the rates of these reactions. Processes discussed include the anaerobic oxidation of ammonium (the anammox reaction), the use of inorganic nitrogen compounds as electron donors for anoxygenic photosynthesis, and the mechanism and bioenergetics of biological nitrogen fixation.

  6. Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

    PubMed Central

    Pan, Donald; Nolan, Jason; Williams, Kenneth H.; Robbins, Mark J.; Weber, Karrie A.

    2017-01-01

    Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Colorado River near Rifle, CO. Virus abundance ranged from 8.0 × 104 to 1.0 × 106 mL−1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 104 to 6.1 × 105 mL−1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to

  7. Assessment of soil potential for microbial nitrogen cycling using quantitative PCR

    NASA Astrophysics Data System (ADS)

    Pereg, Lily; McMillan, Mary; Aldorri, Sind

    2016-04-01

    Nitrogen is an important nutrient for the synthesis of macromolecules, such as nucleic acids and proteins, in all organisms. Nitrogen cycling is essential for the production of different forms of nitrogenous molecules used by various organisms in the soil as available nitrogen sources. While nitrogen-fixing bacteria can utilize N2 as a nitrogen source, other microbes and plants need to assimilate N from fixed forms, e.g. ammonia or nitrate. Nitrogen cycling is largely derived by microbial activity in the soil. Examples include the reduction of N2 to ammonia by nitrogen fixation, production of nitrate by nitrification and the removal of available nitrogenous compounds by denitrification. We measured the potential of agricultural soils under various management practices to cycle nitrogen by measuring the abundance of functional genes involved in the nitrogen cycle. We report on the suitability of PCR-based methods as indicators of soil function potential.

  8. Cell cycle regulated gene expression in yeasts.

    PubMed

    McInerny, Christopher J

    2011-01-01

    The regulation of gene expression through the mitotic cell cycle, so that genes are transcribed at particular cell cycle times, is widespread among eukaryotes. In some cases, it appears to be important for control mechanisms, as deregulated expression results in uncontrolled cell divisions, which can cause cell death, disease, and malignancy. In this review, I describe the current understanding of such regulated gene expression in two established simple eukaryotic model organisms, the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. In these two yeasts, the global pattern of cell cycle gene expression has been well described, and most of the transcription factors that control the various waves of gene expression, and how they are in turn themselves regulated, have been characterized. As related mechanisms occur in all other eukaryotes, including humans, yeasts offer an excellent paradigm to understand this important molecular process. Copyright © 2011 Elsevier Inc. All rights reserved.

  9. Cell cycle regulation by microRNAs in stem cells.

    PubMed

    Wang, Yangming; Blelloch, Robert

    2011-01-01

    The ability to self-renew and to differentiate into at least one-cell lineage defines a stem cell. Self-renewal is a process by which stem cells proliferate without differentiation. Proliferation is achieved through a series of highly regulated events of the cell cycle. MicroRNAs (miRNAs) are a class of short noncoding RNAs whose importance in these events is becoming increasingly appreciated. In this chapter, we discuss the role of miRNAs in regulating the cell cycle in various stem cells with a focus on embryonic stem cells. We also present the evidence indicating that cell cycle-regulating miRNAs are incorporated into a large regulatory network to control the self-renewal of stem cells by inducing or inhibiting differentiation. In addition, we discuss the function of cell cycle-regulating miRNAs in cancer.

  10. Impact of Ferrous Iron on Microbial Community of the Biofilm in Microbial Fuel Cells.

    PubMed

    Liu, Qian; Liu, Bingfeng; Li, Wei; Zhao, Xin; Zuo, Wenjing; Xing, Defeng

    2017-01-01

    The performance of microbial electrochemical cells depends upon microbial community structure and metabolic activity of the electrode biofilms. Iron as a signal affects biofilm development and enrichment of exoelectrogenic bacteria. In this study, the effect of ferrous iron on microbial communities of the electrode biofilms in microbial fuel cells (MFCs) was investigated. Voltage production showed that ferrous iron of 100 μM facilitated MFC start-up compared to 150 μM, 200 μM, and without supplement of ferrous iron. However, higher concentration of ferrous iron had an inhibitive influence on current generation after 30 days of operation. Illumina Hiseq sequencing of 16S rRNA gene amplicons indicated that ferrous iron substantially changed microbial community structures of both anode and cathode biofilms. Principal component analysis showed that the response of microbial communities of the anode biofilms to higher concentration of ferrous iron was more sensitive. The majority of predominant populations of the anode biofilms in MFCs belonged to Geobacter, which was different from the populations of the cathode biofilms. An obvious shift of community structures of the cathode biofilms occurred after ferrous iron addition. This study implied that ferrous iron influenced the power output and microbial community of MFCs.

  11. Impact of Ferrous Iron on Microbial Community of the Biofilm in Microbial Fuel Cells

    PubMed Central

    Liu, Qian; Liu, Bingfeng; Li, Wei; Zhao, Xin; Zuo, Wenjing; Xing, Defeng

    2017-01-01

    The performance of microbial electrochemical cells depends upon microbial community structure and metabolic activity of the electrode biofilms. Iron as a signal affects biofilm development and enrichment of exoelectrogenic bacteria. In this study, the effect of ferrous iron on microbial communities of the electrode biofilms in microbial fuel cells (MFCs) was investigated. Voltage production showed that ferrous iron of 100 μM facilitated MFC start-up compared to 150 μM, 200 μM, and without supplement of ferrous iron. However, higher concentration of ferrous iron had an inhibitive influence on current generation after 30 days of operation. Illumina Hiseq sequencing of 16S rRNA gene amplicons indicated that ferrous iron substantially changed microbial community structures of both anode and cathode biofilms. Principal component analysis showed that the response of microbial communities of the anode biofilms to higher concentration of ferrous iron was more sensitive. The majority of predominant populations of the anode biofilms in MFCs belonged to Geobacter, which was different from the populations of the cathode biofilms. An obvious shift of community structures of the cathode biofilms occurred after ferrous iron addition. This study implied that ferrous iron influenced the power output and microbial community of MFCs. PMID:28638368

  12. Power overshoot in two-chambered microbial fuel cell (MFC).

    PubMed

    Nien, Po-Chin; Lee, Chin-Yu; Ho, Kuo-Chuan; Adav, Sunil S; Liu, Lihong; Wang, Aijie; Ren, Nanqi; Lee, Duu-Jong

    2011-04-01

    A two-chamber microbial fuel cell was started using iron-reducing strains as inoculum and acetate as carbon sources. The tested microbial fuel cell had an open-circuit voltage of 0.67 V, and reached 1045 mA m(-2) and a power density of 486 mW m(-2) at 0.46 V before power overshoot occurred. Anodic reactions were identified as the rate-determining steps. Stirring the anolyte insignificantly increased cell performance, suggesting a minimal external mass transfer resistance from the anolyte to the anodic biofilm. Data regression analysis indicates that charge transfer resistance at the biofilm-anode junction was negligible. The order of magnitude estimation of electrical conductance indicates that electron transfer resistance had an insignificant effect on microbial fuel cell performance. Resistance in electrogens for substrate utilization is proposed to induce microbial fuel cell power overshoot.

  13. Acanthamoeba induces cell-cycle arrest in host cells.

    PubMed

    Sissons, James; Alsam, Selwa; Jayasekera, Samantha; Kim, Kwang Sik; Stins, Monique; Khan, Naveed Ahmed

    2004-08-01

    Acanthamoeba can cause fatal granulomatous amoebic encephalitis (GAE) and eye keratitis. However, the pathogenesis and pathophysiology of these emerging diseases remain unclear. In this study, the effects of Acanthamoeba on the host cell cycle using human brain microvascular endothelial cells (HBMEC) and human corneal epithelial cells (HCEC) were determined. Two isolates of Acanthamoeba belonging to the T1 genotype (GAE isolate) and T4 genotype (keratitis isolate) were used, which showed severe cytotoxicity on HBMEC and HCEC, respectively. No tissue specificity was observed in their ability to exhibit binding to the host cells. To determine the effects of Acanthamoeba on the host cell cycle, a cell-cycle-specific gene array was used. This screened for 96 genes specific for host cell-cycle regulation. It was observed that Acanthamoeba inhibited expression of genes encoding cyclins F and G1 and cyclin-dependent kinase 6, which are proteins important for cell-cycle progression. Moreover, upregulation was observed of the expression of genes such as GADD45A and p130 Rb, associated with cell-cycle arrest, indicating cell-cycle inhibition. Next, the effect of Acanthamoeba on retinoblastoma protein (pRb) phosphorylation was determined. pRb is a potent inhibitor of G1-to-S cell-cycle progression; however, its function is inhibited upon phosphorylation, allowing progression into S phase. Western blotting revealed that Acanthamoeba abolished pRb phosphorylation leading to cell-cycle arrest at the G1-to-S transition. Taken together, these studies demonstrated for the first time that Acanthamoeba inhibits the host cell cycle at the transcriptional level, as well as by modulating pRb phosphorylation using host cell-signalling mechanisms. A complete understanding of Acanthamoeba-host cell interactions may help in developing novel strategies to treat Acanthamoeba infections.

  14. Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell.

    PubMed

    Timmers, Ruud A; Rothballer, Michael; Strik, David P B T B; Engel, Marion; Schulz, Stephan; Schloter, Michael; Hartmann, Anton; Hamelers, Bert; Buisman, Cees

    2012-04-01

    The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors.

  15. Anodic and cathodic microbial communities in single chamber microbial fuel cells.

    PubMed

    Daghio, Matteo; Gandolfi, Isabella; Bestetti, Giuseppina; Franzetti, Andrea; Guerrini, Edoardo; Cristiani, Pierangela

    2015-01-25

    Microbial fuel cells (MFCs) are a rapidly growing technology for energy production from wastewater and biomasses. In a MFC, a microbial biofilm oxidizes organic matter and transfers electrons from reduced compounds to an anode as the electron acceptor by extracellular electron transfer (EET). The aim of this work was to characterize the microbial communities operating in a Single Chamber Microbial Fuel Cell (SCMFC) fed with acetate and inoculated with a biogas digestate in order to gain more insight into anodic and cathodic EET. Taxonomic characterization of the communities was carried out by Illumina sequencing of a fragment of the 16S rRNA gene. Microorganisms belonging to Geovibrio genus and purple non-sulfur (PNS) bacteria were found to be dominant in the anodic biofilm. The alkaliphilic genus Nitrincola and anaerobic microorganisms belonging to Porphyromonadaceae family were the most abundant bacteria in the cathodic biofilm.

  16. Decision for cell fate: deubiquitinating enzymes in cell cycle checkpoint.

    PubMed

    Lim, Key-Hwan; Song, Myoung-Hyun; Baek, Kwang-Hyun

    2016-04-01

    All organs consisting of single cells are consistently maintaining homeostasis in response to stimuli such as free oxygen, DNA damage, inflammation, and microorganisms. The cell cycle of all mammalian cells is regulated by protein expression in the right phase to respond to proliferation and apoptosis signals. Post-translational modifications (PTMs) of proteins by several protein-editing enzymes are associated with cell cycle regulation by their enzymatic functions. Ubiquitination, one of the PTMs, is also strongly related to cell cycle regulation by protein degradation or signal transduction. The importance of deubiquitinating enzymes (DUBs), which have a reversible function for ubiquitination, has recently suggested that the function of DUBs is also important for determining the fate of proteins during cell cycle processing. This article reviews and summarizes the diverse roles of DUBs, including DNA damage, cell cycle processing, and regulation of histone proteins, and also suggests the possibility for therapeutic targets.

  17. Cell cycle control across the eukaryotic kingdom.

    PubMed

    Harashima, Hirofumi; Dissmeyer, Nico; Schnittger, Arp

    2013-07-01

    Almost two billion years of evolution have generated a vast and amazing variety of eukaryotic life with approximately 8.7 million extant species. Growth and reproduction of all of these organisms depend on faithful duplication and distribution of their chromosomes to the newly forming daughter cells in a process called the cell cycle. However, most of what is known today about cell cycle control comes from a few model species that belong to the unikonts; that is, to only one of five 'supergroups' that comprise the eukaryotic kingdom. Recently, analyzing species from distantly related clades is providing insights into general principles of cell cycle regulation and shedding light on its evolution. Here, referring to animal and fungal as opposed to non-unikont systems, especially flowering plants from the archaeplastid supergroup, we compare the conservation of central cell cycle regulator functions, the structure of network topologies, and the evolutionary dynamics of substrates of core cell cycle kinases. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Cycle life test of secondary spacecraft cells

    NASA Technical Reports Server (NTRS)

    Harkness, J. D.

    1980-01-01

    The results of the life cycling program on rechargeable calls are reported. Information on required data, the use of which the data will be put, application details, including orbital description, charge control methods, load rquirements, etc., are given. Cycle tests were performed on 660 sealed, nickel cadmium cells. The cells consisted of seven sample classifications ranging form 3.0 to 20 amp. hours. Nickel cadmium, silver cadmium, and silver zinc sealed cells, excluding synchronous orbit and accelerated test packs were added. The capacities of the nickel cadmium cells, the silver cadmium and the silver zinc cells differed in range of amp hrs. The cells were cylced under different load, charge control, and temperature conditions. All cell packs are recharged by use of a pack voltage limit. All charging is constant current until the voltage limit is reached.

  19. Studying Microbial Mat Functioning Amidst "Unexpected Diversity": Methodological Approaches and Initial Results from Metatranscriptomes of Mats Over Diel cycles, iTags from Long Term Manipulations, and Biogeochemical Cycling in Simplified Microbial Mats Constructed from Cultures

    NASA Astrophysics Data System (ADS)

    Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Everroad, R. C.; Lee, J.; Pett-Ridge, J.; Weber, P. K.

    2014-12-01

    Microbial mats are famously amongst the most diverse microbial ecosystems on Earth, inhabiting some of the most inclement environments known, including hypersaline, dry, hot, cold, nutrient poor, and high UV environments. The high microbial diversity of microbial mats makes studies of microbial ecology notably difficult. To address this challenge, we have been using a combination of metagenomics, metatranscriptomics, iTags and culture-based simplified microbial mats to study biogeochemical cycling (H2 production, N2 fixation, and fermentation) in microbial mats collected from Elkhorn Slough, Monterey Bay, California. Metatranscriptomes of microbial mats incubated over a diel cycle have revealed that a number of gene systems activate only during the day in Cyanobacteria, while the remaining appear to be constitutive. The dominant cyanobacterium in the mat (Microcoleus chthonoplastes) expresses several pathways for nitrogen scavenging undocumented in cultured strains, as well as the expression of two starch storage and utilization cycles. Community composition shifts in response to long term manipulations of mats were assessed using iTags. Changes in community diversity were observed as hydrogen fluxes increased in response to a lowering of sulfate concentrations. To produce simplified microbial mats, we have isolated members of 13 of the 15 top taxa from our iTag libraries into culture. Simplified microbial mats and simple co-cultures and consortia constructed from these isolates reproduce many of the natural patterns of biogeochemical cycling in the parent natural microbial mats, but against a background of far lower overall diversity, simplifying studies of changes in gene expression (over the short term), interactions between community members, and community composition changes (over the longer term), in response to environmental forcing.

  20. AC power generation from microbial fuel cells

    NASA Astrophysics Data System (ADS)

    Lobo, Fernanda Leite; Wang, Heming; Forrestal, Casey; Ren, Zhiyong Jason

    2015-11-01

    Microbial fuel cells (MFCs) directly convert biodegradable substrates to electricity and carry good potential for energy-positive wastewater treatment. However, the low and direct current (DC) output from MFC is not usable for general electronics except small sensors, yet commercial DC-AC converters or inverters used in solar systems cannot be directly applied to MFCs. This study presents a new DC-AC converter system for MFCs that can generate alternating voltage in any desired frequency. Results show that AC power can be easily achieved in three different frequencies tested (1, 10, 60 Hz), and no energy storage layer such as capacitors was needed. The DC-AC converter efficiency was higher than 95% when powered by either individual MFCs or simple MFC stacks. Total harmonic distortion (THD) was used to investigate the quality of the energy, and it showed that the energy could be directly usable for linear electronic loads. This study shows that through electrical conversion MFCs can be potentially used in household electronics for decentralized off-grid communities.

  1. Quantifying the contribution of single microbial cells to nitrogen assimilation in aquatic environments

    NASA Astrophysics Data System (ADS)

    Musat, N.; Kuypers, M. M. M.

    2009-04-01

    Nitrogen is a primary productivity-limiting nutrient in the ocean. The nitrogen limitation of productivity may be overcome by organisms capable of converting dissolved N2 into fixed nitrogen available to the ecosystem. In many oceanic regions, growth of phytoplankton is nitrogen limited because fixation of N2 cannot make up for the removal of fixed inorganic nitrogen (NH4+, NO2-, NO3-) by anaerobic microbial processes. The amount of available fixed nitrogen in the ocean can be changed by the biological processes of heterotrophic denitrification, anaerobic ammonium oxidation and nitrogen fixation. For a complete understanding of nitrogen cycling in the ocean a link between the microbial and biogeochemical processes at the single cell level and their role in global biogeochemical cycles is essential. Here we report a recently developed method, Halogen In Situ Hybridization-Secondary Ion Mass Spectroscopy (HISH-SIMS) and its potential application to study the nitrogen-cycle processes in the ocean. The method allows simultaneous phylogenetic identification and quantitation of metabolic activities of single microbial cells in the environment. It uses horseradish-peroxidase-labeled oligonucleotide probes and fluorine-containing tyramides for the identification of microorganisms in combination with stable-isotope-labeling experiments for analyzing the metabolic function of single microbial cells. HISH-SIMS was successfully used to study nitrogen assimilation and nitrogen fixation by anaerobic phototrophs in a meromictic alpine lake. The HISH-SIMS method enables studies of the ecophysiology of individual, phylogenetically identified microorganisms involved in the N-cycle and allows us to track the flow of nitrogen within microbial communities.

  2. The microbial methane cycle in subsurface sediments. Final project report, July 1, 1993--August 31, 1997

    SciTech Connect

    Grossman, E.L.; Ammerman, J.W.; Suflita, J.M.

    1997-12-31

    The objectives of this study were to determine the factors controlling microbial activity and survival in the subsurface and, specifically, to determine whether microbial communities in aquitards and in aquifer microenvironments provide electron donors and/or acceptors that enhance microbial survival in aquifers. Although the original objectives were to focus on methane cycling, the authors pursued an opportunity to study sulfur cycling in aquifer systems, a process of much greater importance in microbial activity and survival, and in the mobility of metals in the subsurface. Furthermore, sulfur cycling is pertinent to the Subsurface Science Program`s study at Cerro Negro, New Mexico. The study combined field and laboratory approaches and microbiological, molecular, geochemical, and hydrogeological techniques. During drilling operations, sediments were collected aseptically and assayed for a variety of microorganisms and metabolic capabilities including total counts, viable aerobic heterotrophs, total anaerobic heterotrophs, sulfate reducing bacteria (SRB) and sulfate reduction activity (in situ and in slurries), methanogens, methanotrophs, and Fe- and S-oxidizers, among others. Geochemical analyses of sediments included organic carbon content and {sup 13}C/{sup 12}C ratio, sulfur chemistry (reduced sulfur, sulfate), {sup 34}S/{sup 32}S, {sup 13}C/{sup 12}C, {sup 14}C, tritium, etc. The authors drilled eight boreholes in the Eocene Yegua formation at four localities on the Texas A&M University campus using a hollow-stem auger drilling rig. The drilling pattern forms a T, with three well clusters along the dip direction and two along strike. Four boreholes were sampled for sediments and screened at the deepest sand interval encountered, and four boreholes were drilled to install wells in shallower sands. Boreholes range in depth from 8 to 31 m, with screened intervals ranging from 6 to 31 m. Below are the results of these field studies.

  3. Rapid prototyping of microbial cell factories via genome-scale engineering.

    PubMed

    Si, Tong; Xiao, Han; Zhao, Huimin

    2015-11-15

    Advances in reading, writing and editing genetic materials have greatly expanded our ability to reprogram biological systems at the resolution of a single nucleotide and on the scale of a whole genome. Such capacity has greatly accelerated the cycles of design, build and test to engineer microbes for efficient synthesis of fuels, chemicals and drugs. In this review, we summarize the emerging technologies that have been applied, or are potentially useful for genome-scale engineering in microbial systems. We will focus on the development of high-throughput methodologies, which may accelerate the prototyping of microbial cell factories. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Rapid Prototyping of Microbial Cell Factories via Genome-scale Engineering

    PubMed Central

    Si, Tong; Xiao, Han; Zhao, Huimin

    2014-01-01

    Advances in reading, writing and editing genetic materials have greatly expanded our ability to reprogram biological systems at the resolution of a single nucleotide and on the scale of a whole genome. Such capacity has greatly accelerated the cycles of design, build and test to engineer microbes for efficient synthesis of fuels, chemicals and drugs. In this review, we summarize the emerging technologies that have been applied, or are potentially useful for genome-scale engineering in microbial systems. We will focus on the development of high-throughput methodologies, which may accelerate the prototyping of microbial cell factories. PMID:25450192

  5. Connecting Taxon-Specific Microbial Activities to Carbon Cycling in the Rhizosphere

    NASA Astrophysics Data System (ADS)

    Hungate, B. A.; Morrissey, E.; Schwartz, E.; Dijkstra, P.; Blazewicz, S.; Pett-Ridge, J.; Koch, G. W.; Marks, J.; Koch, B.; McHugh, T. A.; Mau, R. L.; Hayer, M.

    2016-12-01

    Plant carbon inputs influence microbial growth in the rhizosphere, but the quantitative details of these effects are not well understood, nor are their consequences for carbon cycling in the rhizosphere. With a new pulse of carbon input to soil, which microbial taxa increase their growth rates, and by how much? Do any microbial taxa respond negatively? And how does the extra carbon addition alter the utilization of other resources, including other carbon sources, as well as inorganic nitrogen? This talk will present new research using quantitative stable isotope probing that reveals the distribution of growth responses among microbial taxa, from positive to neutral to negative, and how these growth responses are associated with various substrates. For example, decomposition of soil C in response to added labile carbon occurred as a phylogenetically-diverse majority of taxa shifted toward soil C use for growth. In contrast, bacteria with suppressed growth or that relied directly on glucose for growth clustered strongly by phylogeny. These results suggest that priming is a prototypical response of bacteria to sustained labile C addition, consistent with the widespread occurrence of the priming effect in nature. These results also illustrate the potential power of molecular tools and models that seek to estimate metrics directly relevant to quantitative ecology and biogeochemistry, moreso than is the standard currently in microbial ecology. Tools that estimate growth rate, mortality rate, and rates of substrate use - all quantified with the taxonomic precision afforded by modern sequencing - provide a foundation for quantifying the biogeochemical significance of microbial biodiversity, and a more complete understanding of the rich ecosystem of the rhizosphere.

  6. Metabolite recycling and bidirectional C fluxes: Revolutionizing our view on microbial C cycling in soils

    NASA Astrophysics Data System (ADS)

    Dippold, M. A.; Apostel, C.; Kuzyakov, Y.

    2016-12-01

    Biogeochemists' view on microbial C transformation in soil has rarely exceed a strongly simplified concept assuming that C gets either oxidized to CO2 via the microbial catabolism or incorporated into biomass via the anabolism. However, life in a C limited environment as challenging as soil requires microbial adaptation strategies at all levels of metabolism. By coupling of position-specific labeling of core metabolites with compound-specific isotope analysis we demonstrated that catabolic oxidation of these metabolites exists in parallel to reductive, energy consuming pathways, reducing them for anabolic purposes. Up to 55% of glucose, incorporated into the glucose derivative glucosamine, first passed glycolysis before allocated back via gluconeogenesis. Similarly, glutamate-derived C is allocated via anaplerotic pathways towards fatty acid synthesis and in parallel to its oxidation in the citric acid cycle. Furthermore, position-specific labeling of rather `cost-intensive' biomass compounds such as fatty acids revealed that intact recycling of metabolites is a crucial microbial adaptation to C scarcity in soils. Both processes are unlikely to occur in pure cultures, where constant growth conditions under high C supply allow a straight unidirectional regulation of C metabolism. However, unstable environmental conditions, C scarcity and interactions between a still unknown diversity of microorganisms in soils are likely to induce the observed metabolic diversity. To understand how microorganisms catalyze the biogeochemical fluxes in soil, a profound understanding of their metabolic adaptation strategies such as recycling or switching between bidirectional fluxes is crucial. Metabolic flux models adapted to soil microbial communities and their regulatory strategies will not only deepen our understanding on the microorganims' reactions to environmental changes but also create the prerequisits for a quantitative prediction of biogeochemical fluxes based on the

  7. Insights on the marine microbial nitrogen cycle from isotopic approaches to nitrification

    PubMed Central

    Casciotti, Karen L.; Buchwald, Carolyn

    2012-01-01

    The microbial nitrogen (N) cycle involves a variety of redox processes that control the availability and speciation of N in the environment and that are involved with the production of nitrous oxide (N2O), a climatically important greenhouse gas. Isotopic measurements of ammonium (NH+4), nitrite (NO−2), nitrate (NO−3), and N2O can now be used to track the cycling of these compounds and to infer their sources and sinks, which has lead to new and exciting discoveries. For example, dual isotope measurements of NO−3 and NO−2 have shown that there is NO−3 regeneration in the ocean's euphotic zone, as well as in and around oxygen deficient zones (ODZs), indicating that nitrification may play more roles in the ocean's N cycle than generally thought. Likewise, the inverse isotope effect associated with NO−2 oxidation yields unique information about the role of this process in NO−2 cycling in the primary and secondary NO−2 maxima. Finally, isotopic measurements of N2O in the ocean are indicative of an important role for nitrification in its production. These interpretations rely on knowledge of the isotope effects for the underlying microbial processes, in particular ammonia oxidation and nitrite oxidation. Here we review the isotope effects involved with the nitrification process and the insights provided by this information, then provide a prospectus for future work in this area. PMID:23091468

  8. Insights on the marine microbial nitrogen cycle from isotopic approaches to nitrification.

    PubMed

    Casciotti, Karen L; Buchwald, Carolyn

    2012-01-01

    The microbial nitrogen (N) cycle involves a variety of redox processes that control the availability and speciation of N in the environment and that are involved with the production of nitrous oxide (N(2)O), a climatically important greenhouse gas. Isotopic measurements of ammonium (NH(+) (4)), nitrite (NO(-) (2)), nitrate (NO(-) (3)), and N(2)O can now be used to track the cycling of these compounds and to infer their sources and sinks, which has lead to new and exciting discoveries. For example, dual isotope measurements of NO(-) (3) and NO(-) (2) have shown that there is NO(-) (3) regeneration in the ocean's euphotic zone, as well as in and around oxygen deficient zones (ODZs), indicating that nitrification may play more roles in the ocean's N cycle than generally thought. Likewise, the inverse isotope effect associated with NO(-) (2) oxidation yields unique information about the role of this process in NO(-) (2) cycling in the primary and secondary NO(-) (2) maxima. Finally, isotopic measurements of N(2)O in the ocean are indicative of an important role for nitrification in its production. These interpretations rely on knowledge of the isotope effects for the underlying microbial processes, in particular ammonia oxidation and nitrite oxidation. Here we review the isotope effects involved with the nitrification process and the insights provided by this information, then provide a prospectus for future work in this area.

  9. Cell-based detection of microbial biomaterial contaminations.

    PubMed

    Roch, Toralf; Ma, Nan; Kratz, Karl; Lendlein, Andreas

    2015-01-01

    A major challenge in biomaterial synthesis and functionalization is the prevention of microbial contaminations such as endotoxins (lipopolysaccharides (LPS)). In addition to LPS, which are exclusively expressed by Gram negative bacteria, also other microbial products derived from fungi or Gram positive bacteria can be found as contaminations in research laboratories. Typically, the Limulus amebocyte lysate (LAL)-test is used to determine the endotoxin levels of medical devices. However, this test fails to detect material-bound LPS and other microbial contaminations and, as demonstrated in this study, detects LPS from various bacterial species with different sensitivities.In this work, a cell-based assay using genetically engineered RAW macrophages, which detect not only soluble but also material-bound microbial contaminations is introduced.The sensitivity of this cell-line towards different LPS species and different heat-inactivated microbes was investigated. As proof of principle a soft hydrophobic poly(n-butyl acrylate) network (cPnBA), which may due to adhesive properties strongly bind microbes, was deliberately contaminated with heat-inactivated bacteria. While the LAL-test failed to detect the microbial contamination, the cell-based assay clearly detected material-bound microbial contaminations. Our data demonstrate that a cell-based detection system should routinely be used as supplement to the LAL-test to determine microbial contaminations of biomaterials.

  10. [Biomass energy utilization in microbial fuel cells: potentials and challenges].

    PubMed

    Huang, Liping; Cheng, Shaoan

    2010-07-01

    Microbial fuel cells (MFCs) that can harvest biomass energy from organic wastes through microbial catalysis have garnered more and more attention within the past decade due to its potential benefits to ecological environment. In this article, the updated progress in MFCs is reviewed, with a focus on frontier technologies such as chamber configurations, feedstock varieties and the integration of MFCs with microbial electrolysis cells for hydrogen production. And on the other hand, the challenges like development of cost-effective electrode materials, improvement of biomass energy recovery and power output, design and optimization of commercial MFC devices are presented.

  11. Microalgae-microbial fuel cell: A mini review.

    PubMed

    Lee, Duu-Jong; Chang, Jo-Shu; Lai, Juin-Yih

    2015-12-01

    Microalgae-microbial fuel cells (mMFCs) are a device that can convert solar energy to electrical energy via biological pathways. This mini-review lists new research and development works on microalgae processes, microbial fuel cell (MFC) processes, and their combined version, mMFC. The substantial improvement and technological advancement are highlighted, with a discussion on the challenges and prospects for possible commercialization of mMFC technologies.

  12. The Microbial Sulfur Cycle at Extremely Haloalkaline Conditions of Soda Lakes

    PubMed Central

    Sorokin, Dimitry Y.; Kuenen, J. Gijs; Muyzer, Gerard

    2011-01-01

    Soda lakes represent a unique ecosystem with extremely high pH (up to 11) and salinity (up to saturation) due to the presence of high concentrations of sodium carbonate in brines. Despite these double extreme conditions, most of the lakes are highly productive and contain a fully functional microbial system. The microbial sulfur cycle is among the most active in soda lakes. One of the explanations for that is high-energy efficiency of dissimilatory conversions of inorganic sulfur compounds, both oxidative and reductive, sufficient to cope with costly life at double extreme conditions. The oxidative part of the sulfur cycle is driven by chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria (SOB), which are unique for soda lakes. The haloalkaliphilic SOB are present in the surface sediment layer of various soda lakes at high numbers of up to 106 viable cells/cm3. The culturable forms are so far represented by four novel genera within the Gammaproteobacteria, including the genera Thioalkalivibrio, Thioalkalimicrobium, Thioalkalispira, and Thioalkalibacter. The latter two were only found occasionally and each includes a single species, while the former two are widely distributed in various soda lakes over the world. The genus Thioalkalivibrio is the most physiologically diverse and covers the whole spectrum of salt/pH conditions present in soda lakes. Most importantly, the dominant subgroup of this genus is able to grow in saturated soda brines containing 4 M total Na+ – a so far unique property for any known aerobic chemolithoautotroph. Furthermore, some species can use thiocyanate as a sole energy source and three out of nine species can grow anaerobically with nitrogen oxides as electron acceptor. The reductive part of the sulfur cycle is active in the anoxic layers of the sediments of soda lakes. The in situ measurements of sulfate reduction rates and laboratory experiments with sediment slurries using sulfate, thiosulfate, or elemental sulfur as

  13. The microbial sulfur cycle at extremely haloalkaline conditions of soda lakes.

    PubMed

    Sorokin, Dimitry Y; Kuenen, J Gijs; Muyzer, Gerard

    2011-01-01

    Soda lakes represent a unique ecosystem with extremely high pH (up to 11) and salinity (up to saturation) due to the presence of high concentrations of sodium carbonate in brines. Despite these double extreme conditions, most of the lakes are highly productive and contain a fully functional microbial system. The microbial sulfur cycle is among the most active in soda lakes. One of the explanations for that is high-energy efficiency of dissimilatory conversions of inorganic sulfur compounds, both oxidative and reductive, sufficient to cope with costly life at double extreme conditions. The oxidative part of the sulfur cycle is driven by chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria (SOB), which are unique for soda lakes. The haloalkaliphilic SOB are present in the surface sediment layer of various soda lakes at high numbers of up to 10(6) viable cells/cm(3). The culturable forms are so far represented by four novel genera within the Gammaproteobacteria, including the genera Thioalkalivibrio, Thioalkalimicrobium, Thioalkalispira, and Thioalkalibacter. The latter two were only found occasionally and each includes a single species, while the former two are widely distributed in various soda lakes over the world. The genus Thioalkalivibrio is the most physiologically diverse and covers the whole spectrum of salt/pH conditions present in soda lakes. Most importantly, the dominant subgroup of this genus is able to grow in saturated soda brines containing 4 M total Na(+) - a so far unique property for any known aerobic chemolithoautotroph. Furthermore, some species can use thiocyanate as a sole energy source and three out of nine species can grow anaerobically with nitrogen oxides as electron acceptor. The reductive part of the sulfur cycle is active in the anoxic layers of the sediments of soda lakes. The in situ measurements of sulfate reduction rates and laboratory experiments with sediment slurries using sulfate, thiosulfate, or elemental sulfur as

  14. Cell cycle regulation of Rho signaling pathways.

    PubMed

    David, Muriel; Petit, Dominique; Bertoglio, Jacques

    2012-08-15

    The dynamics of the actin cytoskeleton and its regulation by Rho GTPases are essential to maintain cell shape, to allow cell motility and are also critical during cell cycle progression and mitosis. Rho GTPases and their effectors are involved in cell rounding at mitosis onset, in chromosomes alignment and are required for contraction of the actomyosin ring that separates daughter cells at the end of mitosis. Recent studies have revealed how a number of nucleotide exchange factors and GTPase-activating proteins regulate the activity of Rho GTPases during these processes. This review will focus on how the cell cycle machinery, in turn, regulates expression of proteins in the Rho signaling pathways through transcriptional activation, ubiquitylation and proteasomal degradation and modulates their activity through phosphorylation by mitotic kinases.

  15. Modeling of Sonos Memory Cell Erase Cycle

    NASA Technical Reports Server (NTRS)

    Phillips, Thomas A.; MacLeond, Todd C.; Ho, Fat D.

    2010-01-01

    Silicon-oxide-nitride-oxide-silicon (SONOS) nonvolatile semiconductor memories (NVSMS) have many advantages. These memories are electrically erasable programmable read-only memories (EEPROMs). They utilize low programming voltages, endure extended erase/write cycles, are inherently resistant to radiation, and are compatible with high-density scaled CMOS for low power, portable electronics. The SONOS memory cell erase cycle was investigated using a nonquasi-static (NQS) MOSFET model. The SONOS floating gate charge and voltage, tunneling current, threshold voltage, and drain current were characterized during an erase cycle. Comparisons were made between the model predictions and experimental device data.

  16. Implementation of microbial fuel cell in harvesting energy using wastewater

    NASA Astrophysics Data System (ADS)

    Ramli, N. L.; Wahab, M. S. Abdul; Sharif, S. A. Md; Ramly, N. H.

    2016-02-01

    In this century, most of the companies use the electricity from the fossils fuels such as oil, gas and coal. This method will give negative impact to the environment and the fossils fuel will be run out. This project is to develop a microbial fuels cell that can produce electricity. There are several types of the microbial fuel cell, which are a single chamber, double chamber and continuous. In this paper, the double chamber microbial fuel cell was selected to investigate the effect of suspended sludge into the double chamber microbial fuels cell. The salt bridge will construct between both chambers of the double chamber microbial fuels cell. Carbon graphite rod is selected as an electrode at the cathode and anode to transfer the electron from the anode to the cathode. Electricity is generated from the anaerobic oxidation of organic matter by bacteria. At the end of this project, the microbial fuels cell was successful in generating electricity that can be used for a specific application.

  17. Microbial H2 cycling does not affect δ2H values of ground water

    USGS Publications Warehouse

    Landmeyer, J.E.; Chapelle, F.H.; Bradley, P.M.

    2000-01-01

    Stable hydrogen-isotope values of ground water (δ2H) and dissolved hydrogen concentrations (H(2(aq)) were quantified in a petroleum-hydrocarbon contaminated aquifer to determine whether the production/consumption of H2 by subsurface microorganisms affects ground water &delta2H values. The range of &delta2H observed in monitoring wells sampled (-27.8 ‰c to -15.5 ‰c) was best explained, however, by seasonal differences in recharge temperature as indicated using ground water δ18O values, rather than isotopic exchange reactions involving the microbial cycling of H2 during anaerobic petroleum-hydrocarbon biodegradation. The absence of a measurable hydrogen-isotope exchange between microbially cycled H2 and ground water reflects the fact that the amount of H2 available from the anaerobic decomposition of petroleum hydrocarbons is small relative to the amount of hydrogen present in water, even though milligram per liter concentrations of readily biodegradable contaminants are present at the study site. Additionally, isotopic fractionation calculations indicate that in order for H2 cycling processes to affect δ2H values of ground water, relatively high concentrations of H2 (>0.080 M) would have to be maintained, considerably higher than the 0.2 to 26 nM present at this site and characteristic of anaerobic conditions in general. These observations suggest that the conventional approach of using δ2H and δ18O values to determine recharge history is appropriate even for those ground water systems characterized by anaerobic conditions and extensive microbial H2 cycling.

  18. Primary Succession of Nitrogen Cycling Microbial Communities Along the Deglaciated Forelands of Tianshan Mountain, China

    PubMed Central

    Zeng, Jun; Lou, Kai; Zhang, Cui-Jing; Wang, Jun-Tao; Hu, Hang-Wei; Shen, Ju-Pei; Zhang, Li-Mei; Han, Li-Li; Zhang, Tao; Lin, Qin; Chalk, Phillip M.; He, Ji-Zheng

    2016-01-01

    Structural succession and its driving factors for nitrogen (N) cycling microbial communities during the early stages of soil development (0–44 years) were studied along a chronosequence in the glacial forelands of the Tianshan Mountain No.1 glacier in the arid and semi-arid region of central Asia. We assessed the abundance and population of functional genes affiliated with N-fixation (nifH), nitrification (bacterial and archaeal amoA), and denitrification (nirK/S and nosZ) in a glacier foreland using molecular methods. The abundance of functional genes significantly increased with soil development. N cycling community compositions were also significantly shifted within 44 years and were structured by successional age. Cyanobacterial nifH gene sequences were the most dominant N fixing bacteria and its relative abundance increased from 56.8–93.2% along the chronosequence. Ammonia-oxidizing communities shifted from the Nitrososphaera cluster (AOA-amoA) and the Nitrosospira cluster ME (AOB-aomA) in younger soils (0 and 5 years) to communities dominated by soil and sediment 1 (AOA-amoA) and Nitrosospira Cluster 2 Related (AOB-aomA) in older soils (≥17 years). Most of the denitrifers closest relatives were potential aerobic denitrifying bacteria, and some other types of denitrifying bacteria (like autotrophic nitrate-reducing, sulfide-oxidizing bacteria and denitrifying phosphorus removing bacteria) were also detected in all soil samples. The regression analysis showed that N cycling microbial communities were dominant in younger soils (0–5 years) and significantly correlated with soil total carbon, while communities that were most abundant in older soils were significantly correlated with soil total nitrogen. These results suggested that the shift of soil C and N contents during the glacial retreat significantly influenced the abundance, composition and diversity of N cycling microbial communities. PMID:27625641

  19. Primary Succession of Nitrogen Cycling Microbial Communities Along the Deglaciated Forelands of Tianshan Mountain, China.

    PubMed

    Zeng, Jun; Lou, Kai; Zhang, Cui-Jing; Wang, Jun-Tao; Hu, Hang-Wei; Shen, Ju-Pei; Zhang, Li-Mei; Han, Li-Li; Zhang, Tao; Lin, Qin; Chalk, Phillip M; He, Ji-Zheng

    2016-01-01

    Structural succession and its driving factors for nitrogen (N) cycling microbial communities during the early stages of soil development (0-44 years) were studied along a chronosequence in the glacial forelands of the Tianshan Mountain No.1 glacier in the arid and semi-arid region of central Asia. We assessed the abundance and population of functional genes affiliated with N-fixation (nifH), nitrification (bacterial and archaeal amoA), and denitrification (nirK/S and nosZ) in a glacier foreland using molecular methods. The abundance of functional genes significantly increased with soil development. N cycling community compositions were also significantly shifted within 44 years and were structured by successional age. Cyanobacterial nifH gene sequences were the most dominant N fixing bacteria and its relative abundance increased from 56.8-93.2% along the chronosequence. Ammonia-oxidizing communities shifted from the Nitrososphaera cluster (AOA-amoA) and the Nitrosospira cluster ME (AOB-aomA) in younger soils (0 and 5 years) to communities dominated by soil and sediment 1 (AOA-amoA) and Nitrosospira Cluster 2 Related (AOB-aomA) in older soils (≥17 years). Most of the denitrifers closest relatives were potential aerobic denitrifying bacteria, and some other types of denitrifying bacteria (like autotrophic nitrate-reducing, sulfide-oxidizing bacteria and denitrifying phosphorus removing bacteria) were also detected in all soil samples. The regression analysis showed that N cycling microbial communities were dominant in younger soils (0-5 years) and significantly correlated with soil total carbon, while communities that were most abundant in older soils were significantly correlated with soil total nitrogen. These results suggested that the shift of soil C and N contents during the glacial retreat significantly influenced the abundance, composition and diversity of N cycling microbial communities.

  20. Existing and emerging technologies that exploit sulfur cycling bacteria in subsurface petroleum reservoir microbial communities (Invited)

    NASA Astrophysics Data System (ADS)

    Hubert, C. R.

    2013-12-01

    Fossil fuels remain by far our most important energy resources, providing around 90% of global primary energy supply. In the coming decadal transition between petroleum reliance and a more sustainable energy future we must increasingly view our vital petroleum reserves as microbial ecosystems that can be engineered to responsibly and creatively meet the energy needs of societies worldwide. In this way, the bioenergy agenda must interface with the traditional geoenergy industry and the challenges it faces. Bioengineering and deep biosphere geomicrobiology focus on the ecophysiology and biogeography of microorganisms in subsurface habitats including marine sediments and petroleum reservoirs. Understanding microbial communities in fossil fuel deposits will allow their distribution and catalytic potential to be exploited as geobiotechnologies that target known problem areas including sulfur cycle management related to biodesulfurization of heavy oils and reservoir souring control via nitrate injection, as well as promising emerging directions such as understanding subsurface geofluid dispersal vectors that could enable microbes to be used as bio-indicators in offshore oil and gas exploration. Results related to different research themes within contemporary petroleum geomicrobiology and bioengineering at Newcastle University will be presented with a focus on microorganisms involved in sulfur cycling that are commonly detected in different oil field microbial communities including mesophilic sulfide-oxidizing Epsilonproteobacteria and thermophilic sulfate-reducers belonging to the genus Desulfotomaculum.

  1. [Microbial community abundance and diversity in typical karst ecosystem to indicate soil carbon cycle].

    PubMed

    Jin, Zhen-Jiang; Tang, Hua-Feng; Li, Min; Huang, Bing-Fu; Li, Qiang; Zhang, Jia-Yu; Li, Gui-Wen

    2014-11-01

    The soil microbial characteristics were detected to clarify their indications in organic carbon cycle in karst system. Soil samples from three karst types (saddle, depression and slop) at 0-10 cm, 10-20 cm and 20-30 cm layers were collected in the Yaji Karst Experimental Site, a typical karst ecosystem. The microbial diversity and abundance were assayed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and fluorescence quantitative PCR. The data showed that the highest abundance of 16S rRNA and 18S rRNA were in depression with 1.32 x 10(11) copies x g(-1) and in saddle with 1.12 x 10(10) copies x g(-1), respectively. The abundance of 16S rRNA in saddle and depression decreased from top to bottom, while that of 18S rRNA in three karst forms decreased, which showed that the abundance changed consistently with soil organic carbon (SOC). The 3 diversity indices of 16S rRNA and 6 diversity indices of 18S rRNA increased from top to bottom in soil profiles of three karst forms. These results showed that microbial diversity changed conversely with the abundance and SOC in soil profile. It can be concluded that the abundance was more important than the diversity index for soil carbon cycle in karst system.

  2. Parvovirus infection-induced cell death and cell cycle arrest

    PubMed Central

    Chen, Aaron Yun; Qiu, Jianming

    2011-01-01

    The cytopathic effects induced during parvovirus infection have been widely documented. Parvovirus infection-induced cell death is often directly associated with disease outcomes (e.g., anemia resulting from loss of erythroid progenitors during parvovirus B19 infection). Apoptosis is the major form of cell death induced by parvovirus infection. However, nonapoptotic cell death, namely necrosis, has also been reported during infection of the minute virus of mice, parvovirus H-1 and bovine parvovirus. Recent studies have revealed multiple mechanisms underlying the cell death during parvovirus infection. These mechanisms vary in different parvoviruses, although the large nonstructural protein (NS)1 and the small NS proteins (e.g., the 11 kDa of parvovirus B19), as well as replication of the viral genome, are responsible for causing infection-induced cell death. Cell cycle arrest is also common, and contributes to the cytopathic effects induced during parvovirus infection. While viral NS proteins have been indicated to induce cell cycle arrest, increasing evidence suggests that a cellular DNA damage response triggered by an invading single-stranded parvoviral genome is the major inducer of cell cycle arrest in parvovirus-infected cells. Apparently, in response to infection, cell death and cell cycle arrest of parvovirus-infected cells are beneficial to the viral cell lifecycle (e.g., viral DNA replication and virus egress). In this article, we will discuss recent advances in the understanding of the mechanisms underlying parvovirus infection-induced cell death and cell cycle arrest. PMID:21331319

  3. Analysis of oxygen reduction and microbial community of air-diffusion biocathode in microbial fuel cells.

    PubMed

    Wang, Zejie; Zheng, Yue; Xiao, Yong; Wu, Song; Wu, Yicheng; Yang, Zhaohui; Zhao, Feng

    2013-09-01

    Microbes play irreplaceable role in oxygen reduction reaction of biocathode in microbial fuel cells (MFCs). In this study, air-diffusion biocathode MFCs were set up for accelerating oxygen reduction and microbial community analysis. Linear sweep voltammetry and Tafel curve confirmed the function of cathode biofilm to catalyze oxygen reduction. Microbial community analysis revealed higher diversity and richness of community in plankton than in biofilm. Proteobacteria was the shared predominant phylum in both biofilm and plankton (39.9% and 49.8%) followed by Planctomycetes (29.9%) and Bacteroidetes (13.3%) in biofilm, while Bacteroidetes (28.2%) in plankton. Minor fraction (534, 16.4%) of the total operational taxonomic units (3252) was overlapped demonstrating the disproportionation of bacterial distribution in biofilm and plankton. Pseudomonadales, Rhizobiales and Sphingobacteriales were exoelectrogenic orders in the present study. The research obtained deep insight of microbial community and provided more comprehensive information on uncultured rare bacteria.

  4. Rapid detection of microbial cell abundance in aquatic systems

    DOE PAGES

    Rocha, Andrea M.; Yuan, Quan; Close, Dan M.; ...

    2016-06-01

    The detection and quantification of naturally occurring microbial cellular densities is an essential component of environmental systems monitoring. While there are a number of commonly utilized approaches for monitoring microbial abundance, capacitance-based biosensors represent a promising approach because of their low-cost and label-free detection of microbial cells, but are not as well characterized as more traditional methods. Here, we investigate the applicability of enhanced alternating current electrokinetics (ACEK) capacitive sensing as a new application for rapidly detecting and quantifying microbial cellular densities in cultured and environmentally sourced aquatic samples. ACEK capacitive sensor performance was evaluated using two distinct and dynamicmore » systems the Great Australian Bight and groundwater from the Oak Ridge Reservation in Oak Ridge, TN. Results demonstrate that ACEK capacitance-based sensing can accurately determine microbial cell counts throughout cellular concentrations typically encountered in naturally occurring microbial communities (103 – 106 cells/mL). A linear relationship was observed between cellular density and capacitance change correlations, allowing a simple linear curve fitting equation to be used for determining microbial abundances in unknown samples. As a result, this work provides a foundation for understanding the limits of capacitance-based sensing in natural environmental samples and supports future efforts focusing on evaluating the robustness ACEK capacitance-based within aquatic environments.« less

  5. Rapid detection of microbial cell abundance in aquatic systems.

    PubMed

    Rocha, Andrea M; Yuan, Quan; Close, Dan M; O'Dell, Kaela B; Fortney, Julian L; Wu, Jayne; Hazen, Terry C

    2016-11-15

    The detection and quantification of naturally occurring microbial cellular densities is an essential component of environmental systems monitoring. While there are a number of commonly utilized approaches for monitoring microbial abundance, capacitance-based biosensors represent a promising approach because of their low-cost and label-free detection of microbial cells, but are not as well characterized as more traditional methods. Here, we investigate the applicability of enhanced alternating current electrokinetics (ACEK) capacitive sensing as a new application for rapidly detecting and quantifying microbial cellular densities in cultured and environmentally sourced aquatic samples. ACEK capacitive sensor performance was evaluated using two distinct and dynamic systems - the Great Australian Bight and groundwater from the Oak Ridge Reservation in Oak Ridge, TN. Results demonstrate that ACEK capacitance-based sensing can accurately determine microbial cell counts throughout cellular concentrations typically encountered in naturally occurring microbial communities (10(3)-10(6) cells/mL). A linear relationship was observed between cellular density and capacitance change correlations, allowing a simple linear curve fitting equation to be used for determining microbial abundances in unknown samples. This work provides a foundation for understanding the limits of capacitance-based sensing in natural environmental samples and supports future efforts focusing on evaluating the robustness ACEK capacitance-based within aquatic environments. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  6. SAFT nickel hydrogen cell cycling status

    NASA Technical Reports Server (NTRS)

    Borthomieu, Yannick; Duquesne, Didier

    1994-01-01

    An overview of the NiH2 cell development is given. The NiH2 SAFT system is an electrochemical (single or dual) stack (IPV). The stack is mounted in an hydroformed Inconel 718 vessel operating at high pressure, equipped with 'rabbit ears' ceramic brazed electrical feedthroughs. The cell design is described: positive electrode, negative electrode, and stack configuration. Overviews of low earth orbit and geostationary earth orbit cyclings are provided. DPA results are also provided. The cycling and DPA results demonstrate that SAFT NiH2 is characterized by high reliability and very stable performances.

  7. Natural flavonoids targeting deregulated cell cycle progression in cancer cells.

    PubMed

    Singh, Rana Pratap; Agarwal, Rajesh

    2006-03-01

    The prolonged duration requiring alteration of multi-genetic and epigenetic molecular events for cancer development provides a strong rationale for cancer prevention, which is developing as a potential strategy to arrest or reverse carcinogenic changes before the appearance of the malignant disease. Cell cycle progression is an important biological event having controlled regulation in normal cells, which almost universally becomes aberrant or deregulated in transformed and neoplastic cells. In this regard, targeting deregulated cell cycle progression and its modulation by various natural and synthetic agents are gaining widespread attention in recent years to control the unchecked growth and proliferation in cancer cells. In fact, a vast number of experimental studies convincingly show that many phytochemicals halt uncontrolled cell cycle progression in cancer cells. Among these phytochemicals, natural flavonoids have been identified as a one of the major classes of natural anticancer agents exerting antineoplastic activity via cell cycle arrest as a major mechanism in various types of cancer cells. This review is focused at the modulatory effects of natural flavonoids on cell cycle regulators including cyclin-dependent kinases and their inhibitors, cyclins, p53, retinoblastoma family of proteins, E2Fs, check-point kinases, ATM/ATR and survivin controlling G1/S and G2/M check-point transitions in cell cycle progression, and discusses how these molecular changes could contribute to the antineoplastic effects of natural flavonoids.

  8. An efficient magnetically modified microbial cell biocomposite for carbazole biodegradation

    PubMed Central

    2013-01-01

    Magnetic modification of microbial cells enables to prepare smart biocomposites in bioremediation. In this study, we constructed an efficient biocomposite by assembling Fe3O4 nanoparticles onto the surface of Sphingomonas sp. XLDN2-5 cells. The average particle size of Fe3O4 nanoparticles was about 20 nm with 45.5 emu g-1 saturation magnetization. The morphology of Sphingomonas sp. XLDN2-5 cells before and after Fe3O4 nanoparticle loading was verified by scanning electron microscopy and transmission electronic microscopy. Compared with free cells, the microbial cell/Fe3O4 biocomposite had the same biodegradation activity but exhibited remarkable reusability. The degradation activity of the microbial cell/Fe3O4 biocomposite increased gradually during recycling processes. Additionally, the microbial cell/Fe3O4 biocomposite could be easily separated and recycled by an external magnetic field due to the super-paramagnetic properties of Fe3O4 nanoparticle coating. These results indicated that magnetically modified microbial cells provide a promising technique for improving biocatalysts used in the biodegradation of hazardous compounds. PMID:24330511

  9. An efficient magnetically modified microbial cell biocomposite for carbazole biodegradation

    NASA Astrophysics Data System (ADS)

    Li, Yufei; Du, Xiaoyu; Wu, Chao; Liu, Xueying; Wang, Xia; Xu, Ping

    2013-12-01

    Magnetic modification of microbial cells enables to prepare smart biocomposites in bioremediation. In this study, we constructed an efficient biocomposite by assembling Fe3O4 nanoparticles onto the surface of Sphingomonas sp. XLDN2-5 cells. The average particle size of Fe3O4 nanoparticles was about 20 nm with 45.5 emu g-1 saturation magnetization. The morphology of Sphingomonas sp. XLDN2-5 cells before and after Fe3O4 nanoparticle loading was verified by scanning electron microscopy and transmission electronic microscopy. Compared with free cells, the microbial cell/Fe3O4 biocomposite had the same biodegradation activity but exhibited remarkable reusability. The degradation activity of the microbial cell/Fe3O4 biocomposite increased gradually during recycling processes. Additionally, the microbial cell/Fe3O4 biocomposite could be easily separated and recycled by an external magnetic field due to the super-paramagnetic properties of Fe3O4 nanoparticle coating. These results indicated that magnetically modified microbial cells provide a promising technique for improving biocatalysts used in the biodegradation of hazardous compounds.

  10. Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change

    PubMed Central

    Nazaries, Loïc; Pan, Yao; Bodrossy, Levente; Baggs, Elizabeth M.; Millard, Peter; Murrell, J. Colin

    2013-01-01

    Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles. PMID:23624469

  11. Size and Carbon Content of Sub-seafloor Microbial Cells at Landsort Deep, Baltic Sea.

    PubMed

    Braun, Stefan; Morono, Yuki; Littmann, Sten; Kuypers, Marcel; Aslan, Hüsnü; Dong, Mingdong; Jørgensen, Bo B; Lomstein, Bente Aa

    2016-01-01

    The discovery of a microbial ecosystem in ocean sediments has evoked interest in life under extreme energy limitation and its role in global element cycling. However, fundamental parameters such as the size and the amount of biomass of sub-seafloor microbial cells are poorly constrained. Here we determined the volume and the carbon content of microbial cells from a marine sediment drill core retrieved by the Integrated Ocean Drilling Program (IODP), Expedition 347, at Landsort Deep, Baltic Sea. To determine their shape and volume, cells were separated from the sediment matrix by multi-layer density centrifugation and visualized via epifluorescence microscopy (FM) and scanning electron microscopy (SEM). Total cell-carbon was calculated from amino acid-carbon, which was analyzed by high-performance liquid chromatography (HPLC) after cells had been purified by fluorescence-activated cell sorting (FACS). The majority of microbial cells in the sediment have coccoid or slightly elongated morphology. From the sediment surface to the deepest investigated sample (~60 m below the seafloor), the cell volume of both coccoid and elongated cells decreased by an order of magnitude from ~0.05 to 0.005 μm(3). The cell-specific carbon content was 19-31 fg C cell(-1), which is at the lower end of previous estimates that were used for global estimates of microbial biomass. The cell-specific carbon density increased with sediment depth from about 200 to 1000 fg C μm(-3), suggesting that cells decrease their water content and grow small cell sizes as adaptation to the long-term subsistence at very low energy availability in the deep biosphere. We present for the first time depth-related data on the cell volume and carbon content of sedimentary microbial cells buried down to 60 m below the seafloor. Our data enable estimates of volume- and biomass-specific cellular rates of energy metabolism in the deep biosphere and will improve global estimates of microbial biomass.

  12. Electricity generation in a microbial fuel cell with a microbially catalyzed cathode.

    PubMed

    Zhang, Jin-Na; Zhao, Qing-Liang; Aelterman, Peter; You, Shi-Jie; Jiang, Jun-Qiu

    2008-10-01

    A microbial fuel cell using aerobic microorganisms as the cathodic catalysts is described. By using anaerobic sludge in the anode and aerobic sludge in the cathode as inocula, the microbial fuel cell could be started up after a short lag time of 9 days, generating a stable voltage of 0.324 V (R (ex) = 500 Omega). At an aeration rate of 300 ml min(-1) in the cathode, a maximum volumetric power density of up to 24.7 W m(-3) (117.2 A m(-3)) was reached. This research demonstrates an economic system for recovering electrical energy from organic compounds.

  13. Determination of Microbial Diversity and Nitrogen Cycling from Kizildere Geothermal Field with Next Generation Sequencing

    NASA Astrophysics Data System (ADS)

    Gulecal, Y.; Dilek, Y.

    2012-12-01

    The deep terrestrial subsurface biosphere represents an emerging frontier for studies of biodiversity, the physiological limits to life, microbial mechanisms of adaptation, and potentially analogous environments for extraterrestrial life (1). Last decade, researches of deep boreholes in the United States, Finland, Sweden, Japan and South Africa, using molecular tools, have shown an an active biosphere composed of diverse groups of microorganisms. The microbial communities reported from different subsurface communities vary widely; such differences are due to different host rock types and varied water origins and chemistry, as well as geography. Furthermore, nitrogen cycling is studied intensely in hot springs for instance in situ nifH expression in Yellowstone National Park, is a new upper temperature limit for nitrogen fixation in alkaline, terrestrial hydrothermal environments (2). This study explores the genetic diversity of microbial communities and genes of nitrogen cycling in Kizildere Geothermal Field, Turkey. The Kizildere thermal waters are located in the northern part of the Büyük Menderes rift zone. The hydrothermal alteration includes phyllic, argillic, silicic,hematitized, and carbonatized alteration zones. The surface temperatures of Kizildere thermal waters in drill holes range from 95 to100°C and pH 9.0-9.5. Microbial communities were examined using culture independent methods, next generation sequencing. Nitrogen fixation, the diversity of nifH, ammonia oxidation (amoA), narG, nosZ genes are investigated in deeply-sourced fluids. We present field observations and interpret new data, establishing a geobiological baseline for previously undescribed sitres of subsurface ecosystems. (1)Fredrickson et al. 2006. Geomicrobial processes and biodiversity in the deep terrestrial subsurface. Geomicrobiology J. 23:345-356. (2) Loiacono et al. 2012. Evidence for high-temperature in situ nifH transcription in an alkaline hot spring of Lower Geyser Basin

  14. qPCR analysis of carbon, nitrogen, and arsenic cycling in Zetaproteobacteria-dominated microbial mats

    NASA Astrophysics Data System (ADS)

    Jesser, K. J.; Fullerton, H.; Hilton, T. S.; Kimber, J.; Hager, K.; Moyer, C. L.

    2013-12-01

    The recently discovered Zetaproteobacteria represent a novel class of Proteobacteria which oxidize Fe(II) to Fe(III) to fix CO2 at hydrothermal vents. Zetaproteobacteria were first discovered at Lo'ihi Seamount, located 35 km southeast of the big island of Hawai'i and characterized by low-temperature diffuse hydrothermal vents. The hydrothermal vents at Lo'ihi are surrounded by luxuriant iron-rich microbial mats dominated by Zetaproteobacteria. We aim to use real-time quantitative PCR (qPCR) to quantify functional genes associated with the microbial carbon, nitrogen, and arsenic cycles in complex Zetaproteobacteria- dominated iron mat communities. Unique qPCR primer sets have been developed based on Illumina next-generation sequence data from an iron mat collected in 2009 at Lo'ihi. These primers target the sequences for arsenate reductase and nitrite reductase, genes associated with arsenic detoxification and denitrification, respectively. Additionally, we are utilizing published primer sets to quantify genes associated with autotrophic carbon and nitrogen fixation pathways. Genomic DNA was isolated from microbial mats at multiple vent sites with varying temperatures and fluid flow during our 2013 expedition to Lo'ihi. The qPCR data for these samples can be used to draw correlations among fine scale mat structures and nutrient cycling processes across diverse mat morphologies, as previous research has identified unique microbial communities and metabolic strategies associated with distinct mat morphologies. This work will enable us to better identify samples for further molecular analysis, and may provide insights into the evolutionary history and metabolic functionality of various mat morphotypes. We hypothesize that Zetaproteobacteria act as ecosystem engineers, driving the structure and function of iron mat ecosystems.

  15. The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils

    PubMed Central

    Zhou, Xue; Fornara, Dario; Ikenaga, Makoto; Akagi, Isao; Zhang, Ruifu; Jia, Zhongjun

    2016-01-01

    Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations

  16. Productivity Estimation of Hypersaline Microbial Mat Communities - Diurnal Cycles of Dissolved Oxygen

    NASA Astrophysics Data System (ADS)

    Less, G.; Cohen, Y.; Luz, B.; Lazar, B.

    2002-05-01

    Hypersaline microbial mat communities (MMC) are the modern equivalents of the Archean stromatolities, the first photosynthetic organisms on Earth. An estimate of their oxygen production rate is important to the understanding of oxygen evolution on Earth ca. 2 b.y.b.p. Here we use the diurnal cycle of dissolved oxygen, O2/Ar ratio and the isotopic composition of dissolved oxygen to calculate net and gross primary productivity of MMC growing in a large scale (80 m2) experimental pan. The pan is inoculated with MMC taken from the Solar Lake, Sinai, Egypt and filled with 90\\permil evaporated Red Sea water brine up to a depth of ca. 0.25 m. It is equipped with computerized flow through system that is programmed to pump pan water at selected time intervals into a sampling cell fitted with dissolved oxygen, pH, conductivity and temperature sensors connected to a datalogger. Manual brine samples were taken for calibrating the sensors, mass spectrometric analyses and for measurements of additional relevant parameters. Dissolved oxygen concentrations fluctuate during the diurnal cycle being highly supersaturated except for the end of the night. The O2 curve varies seasonally and has a typical "shark fin" shape due to the MMC metabolic response to the shape of the diurnal light curve. The dissolved oxygen data were fitted to a smooth curve that its time derivative (dO2 /dt) is defined as: Z dO2 /dt=GP-R-k(O2(meas)- O2(sat)) where z is the depth (m); GP and R are the MMC gross production and respiration (mol m-2 d-1), respectively; k is the gas exchange coefficient (m d-1); O2(meas) and O2(sat) (mol L-1) are the measured and equilibrium dissolved oxygen concentrations, respectively. The high resolution sampling of the automated system produces O2 curves that enable the calculation of smooth and reliable time derivatives. The calculations yield net production values that vary between 1,000 10-6 to -100 10-6 mol O2 m-2 h-1 and day respiration rates between 60 10-6 to 30 10

  17. Enrichment of microbial electrolysis cell biocathodes from sediment microbial fuel cell bioanodes.

    PubMed

    Pisciotta, John M; Zaybak, Zehra; Call, Douglas F; Nam, Joo-Youn; Logan, Bruce E

    2012-08-01

    Electron-accepting (electrotrophic) biocathodes were produced by first enriching graphite fiber brush electrodes as the anodes in sediment-type microbial fuel cells (sMFCs) using two different marine sediments and then electrically inverting the anodes to function as cathodes in two-chamber bioelectrochemical systems (BESs). Electron consumption occurred at set potentials of -439 mV and -539 mV (versus the potential of a standard hydrogen electrode) but not at -339 mV in minimal media lacking organic sources of energy. Results at these different potentials were consistent with separate linear sweep voltammetry (LSV) scans that indicated enhanced activity (current consumption) below only ca. -400 mV. MFC bioanodes not originally acclimated at a set potential produced electron-accepting (electrotrophic) biocathodes, but bioanodes operated at a set potential (+11 mV) did not. CO(2) was removed from cathode headspace, indicating that the electrotrophic biocathodes were autotrophic. Hydrogen gas generation, followed by loss of hydrogen gas and methane production in one sample, suggested hydrogenotrophic methanogenesis. There was abundant microbial growth in the biocathode chamber, as evidenced by an increase in turbidity and the presence of microorganisms on the cathode surface. Clone library analysis of 16S rRNA genes indicated prominent sequences most similar to those of Eubacterium limosum (Butyribacterium methylotrophicum), Desulfovibrio sp. A2, Rhodococcus opacus, and Gemmata obscuriglobus. Transfer of the suspension to sterile cathodes made of graphite plates, carbon rods, or carbon brushes in new BESs resulted in enhanced current after 4 days, demonstrating growth by these microbial communities on a variety of cathode substrates. This report provides a simple and effective method for enriching autotrophic electrotrophs by the use of sMFCs without the need for set potentials, followed by the use of potentials more negative than -400 mV.

  18. Enrichment of Microbial Electrolysis Cell Biocathodes from Sediment Microbial Fuel Cell Bioanodes

    SciTech Connect

    Pisciotta, JM; Zaybak, Z; Call, DF; Nam, JY; Logan, BE

    2012-07-18

    Electron-accepting (electrotrophic) biocathodes were produced by first enriching graphite fiber brush electrodes as the anodes in sediment-type microbial fuel cells (sMFCs) using two different marine sediments and then electrically inverting the anodes to function as cathodes in two-chamber bioelectrochemical systems (BESs). Electron consumption occurred at set potentials of -439 mV and -539 mV (versus the potential of a standard hydrogen electrode) but not at -339 mV in minimal media lacking organic sources of energy. Results at these different potentials were consistent with separate linear sweep voltammetry (LSV) scans that indicated enhanced activity (current consumption) below only ca. -400 mV. MFC bioanodes not originally acclimated at a set potential produced electron-accepting (electrotrophic) biocathodes, but bioanodes operated at a set potential (+11 mV) did not. CO, was removed from cathode headspace, indicating that the electrotrophic biocathodes were autotrophic. Hydrogen gas generation, followed by loss of hydrogen gas and methane production in one sample, suggested hydrogenotrophic methanogenesis. There was abundant microbial growth in the biocathode chamber, as evidenced by an increase in turbidity and the presence of microorganisms on the cathode surface. Clone library analysis of 16S rRNA genes indicated prominent sequences most similar to those of Eubacterium limosum (Butyribacterium methylotrophicum), Desulfovibrio sp. A2, Rhodococcus opacus, and Gemmata obscuriglobus. Transfer of the suspension to sterile cathodes made of graphite plates, carbon rods, or carbon brushes in new BESs resulted in enhanced current after 4 days, demonstrating growth by these microbial communities on a variety of cathode substrates. This report provides a simple and effective method for enriching autotrophic electrotrophs by the use of sMFCs without the need for set potentials, followed by the use of potentials more negative than -400 mV.

  19. Enrichment of Microbial Electrolysis Cell Biocathodes from Sediment Microbial Fuel Cell Bioanodes

    PubMed Central

    Pisciotta, John M.; Zaybak, Zehra; Call, Douglas F.; Nam, Joo-Youn

    2012-01-01

    Electron-accepting (electrotrophic) biocathodes were produced by first enriching graphite fiber brush electrodes as the anodes in sediment-type microbial fuel cells (sMFCs) using two different marine sediments and then electrically inverting the anodes to function as cathodes in two-chamber bioelectrochemical systems (BESs). Electron consumption occurred at set potentials of −439 mV and −539 mV (versus the potential of a standard hydrogen electrode) but not at −339 mV in minimal media lacking organic sources of energy. Results at these different potentials were consistent with separate linear sweep voltammetry (LSV) scans that indicated enhanced activity (current consumption) below only ca. −400 mV. MFC bioanodes not originally acclimated at a set potential produced electron-accepting (electrotrophic) biocathodes, but bioanodes operated at a set potential (+11 mV) did not. CO2 was removed from cathode headspace, indicating that the electrotrophic biocathodes were autotrophic. Hydrogen gas generation, followed by loss of hydrogen gas and methane production in one sample, suggested hydrogenotrophic methanogenesis. There was abundant microbial growth in the biocathode chamber, as evidenced by an increase in turbidity and the presence of microorganisms on the cathode surface. Clone library analysis of 16S rRNA genes indicated prominent sequences most similar to those of Eubacterium limosum (Butyribacterium methylotrophicum), Desulfovibrio sp. A2, Rhodococcus opacus, and Gemmata obscuriglobus. Transfer of the suspension to sterile cathodes made of graphite plates, carbon rods, or carbon brushes in new BESs resulted in enhanced current after 4 days, demonstrating growth by these microbial communities on a variety of cathode substrates. This report provides a simple and effective method for enriching autotrophic electrotrophs by the use of sMFCs without the need for set potentials, followed by the use of potentials more negative than −400 mV. PMID:22610438

  20. Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir.

    PubMed

    Freedman, Adam J E; Tan, BoonFei; Thompson, Janelle R

    2017-06-01

    Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO2 -water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  1. Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir

    PubMed Central

    Freedman, Adam J.E.; Tan, BoonFei

    2017-01-01

    Summary Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long‐term fate of sequestered scCO2, harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO2‐water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling. PMID:28229521

  2. Control of cell cycle and cell growth by molecular chaperones.

    PubMed

    Aldea, Martí; Garí, Eloi; Colomina, Neus

    2007-11-01

    Cells adapt their size to both intrinsic and extrinsic demands and, among them, those that stem from growth and proliferation rates are crucial for cell size homeostasis. Here we revisit mechanisms that regulate cell cycle and cell growth in budding yeast. Cyclin Cln3, the most upstream activator of Start, is retained at the endoplasmic reticulum in early G(1) and released by specific chaperones in late G(1) to initiate the cell cycle. On one hand, these chaperones are rate-limiting for release of Cln3 and cell cycle entry and, on the other hand, they are required for key biosynthetic processes. We propose a model whereby the competition for specialized chaperones between growth and cycle machineries could gauge biosynthetic rates and set a critical size threshold at Start.

  3. B cell-helping functions of gut microbial metabolites

    PubMed Central

    Kim, Chang H.

    2016-01-01

    Commensal microflora profoundly affects the host immune system. It has long been observed that commensal bacteria enhance antibody production in the host by producing antigens for B cell receptors (BCR) and ligands for Toll-like receptors (TLR). We recently reported that the microbial metabolites short-chain fatty acids (SCFAs) regulate the metabolism and gene expression in B cells to promote antibody production (Kim et al. Gut Microbial Metabolites Fuel Host Antibody Responses. Cell Host & Microbe. 2016; 20(2):202-14). The B-cell helping function of SCFAs and its implication in the host immune system are discussed in this article. PMID:28357321

  4. B cell-helping functions of gut microbial metabolites.

    PubMed

    Kim, Chang H

    2016-09-23

    Commensal microflora profoundly affects the host immune system. It has long been observed that commensal bacteria enhance antibody production in the host by producing antigens for B cell receptors (BCR) and ligands for Toll-like receptors (TLR). We recently reported that the microbial metabolites short-chain fatty acids (SCFAs) regulate the metabolism and gene expression in B cells to promote antibody production (Kim et al. Gut Microbial Metabolites Fuel Host Antibody Responses. Cell Host & Microbe. 2016; 20(2):202-14). The B-cell helping function of SCFAs and its implication in the host immune system are discussed in this article.

  5. Size and Carbon Content of Sub-seafloor Microbial Cells at Landsort Deep, Baltic Sea

    PubMed Central

    Braun, Stefan; Morono, Yuki; Littmann, Sten; Kuypers, Marcel; Aslan, Hüsnü; Dong, Mingdong; Jørgensen, Bo B.; Lomstein, Bente Aa.

    2016-01-01

    The discovery of a microbial ecosystem in ocean sediments has evoked interest in life under extreme energy limitation and its role in global element cycling. However, fundamental parameters such as the size and the amount of biomass of sub-seafloor microbial cells are poorly constrained. Here we determined the volume and the carbon content of microbial cells from a marine sediment drill core retrieved by the Integrated Ocean Drilling Program (IODP), Expedition 347, at Landsort Deep, Baltic Sea. To determine their shape and volume, cells were separated from the sediment matrix by multi-layer density centrifugation and visualized via epifluorescence microscopy (FM) and scanning electron microscopy (SEM). Total cell-carbon was calculated from amino acid-carbon, which was analyzed by high-performance liquid chromatography (HPLC) after cells had been purified by fluorescence-activated cell sorting (FACS). The majority of microbial cells in the sediment have coccoid or slightly elongated morphology. From the sediment surface to the deepest investigated sample (~60 m below the seafloor), the cell volume of both coccoid and elongated cells decreased by an order of magnitude from ~0.05 to 0.005 μm3. The cell-specific carbon content was 19–31 fg C cell−1, which is at the lower end of previous estimates that were used for global estimates of microbial biomass. The cell-specific carbon density increased with sediment depth from about 200 to 1000 fg C μm−3, suggesting that cells decrease their water content and grow small cell sizes as adaptation to the long-term subsistence at very low energy availability in the deep biosphere. We present for the first time depth-related data on the cell volume and carbon content of sedimentary microbial cells buried down to 60 m below the seafloor. Our data enable estimates of volume- and biomass-specific cellular rates of energy metabolism in the deep biosphere and will improve global estimates of microbial biomass. PMID:27630628

  6. Sulfur-Oxidizing Bacteria Mediate Microbial Community Succession and Element Cycling in Launched Marine Sediment

    PubMed Central

    Ihara, Hideyuki; Hori, Tomoyuki; Aoyagi, Tomo; Takasaki, Mitsuru; Katayama, Yoko

    2017-01-01

    A large amount of marine sediment was launched on land by the Great East Japan earthquake. Here, we employed both on-site and laboratory studies on the launched marine sediment to investigate the succession of microbial communities and its effects on geochemical properties of the sediment. Twenty-two-month on-site survey showed that microbial communities at the uppermost layer (0–2 mm depth) of the sediment changed significantly with time, whereas those at the deeper layer (20–40 mm depth) remained nearly unchanged and kept anaerobic microbial communities. Nine months after the incidence, various sulfur-oxidizing bacteria (SOB) prevailed in the uppermost layer, in which afterwards diverse chemoorganotrophic bacteria predominated. Geochemical analyses indicated that the concentration of metals other than Fe was lower in the uppermost layer than that in the deeper layer. Laboratory study was carried out by incubating the sediment for 57 days, and clearly indicated the dynamic transition of microbial communities in the uppermost layer exposed to atmosphere. SOB affiliated in the class Epsilonproteobacteria rapidly proliferated and dominated at the uppermost layer during the first 3 days, after that Fe(II)-oxidizing bacteria and chemoorganotrophic bacteria were sequentially dominant. Furthermore, the concentration of sulfate ion increased and the pH decreased. Consequently, SOB may have influenced the mobilization of heavy metals in the sediment by metal-bound sulfide oxidation and/or sediment acidification. These results demonstrate that SOB initiated the dynamic shift from the anaerobic to aerobic microbial communities, thereby playing a critical role in element cycling in the marine sediment. PMID:28217124

  7. Growing Rocks: Implications of Lithification for Microbial Communities and Nutrient Cycling

    NASA Astrophysics Data System (ADS)

    Corman, J. R.; Poret-Peterson, A. T.; Elser, J. J.

    2014-12-01

    Lithifying microbial communities ("microbialites") have left their signature on Earth's rock record for over 3.4 billion years and are regarded as important players in paleo-biogeochemical cycles. In this project, we study extant microbialites to understand the interactions between lithification and resource availability. All microbes need nutrients and energy for growth; indeed, nutrients are often a factor limiting microbial growth. We hypothesize that calcium carbonate deposition can sequester bioavailable phosphorus (P) and expect the growth of microbialites to be P-limited. To test our hypothesis, we first compared nutrient limitation in lithifying and non-lithifying microbial communities in Río Mesquites, Cuatro Ciénegas. Then, we experimentally manipulated calcification rates in the Río Mesquites microbialites. Our results suggest that lithifying microbialites are indeed P-limited, while non-lithifying, benthic microbial communities tend towards co-limitation by nitrogen (N) and P. Indeed, in microbialites, photosynthesis and aerobic respiration responded positively to P additions (P<0.05). Organic carbon (OC) additions caused shifts in bacterial community composition based on analysis of 16S rRNA genes. Unexpectedly, calcification rates increased with OC additions (P<0.05), but not with P additions, suggesting that sulfate reduction may be an important pathway for calcification. Experimental reductions in calcification rates caused changes to microbial biomass OC and P concentrations (P<0.01 and P<0.001, respectively), although shifts depended on whether calcification was decreased abiotically or biotically. These results show that resource availability does influence microbialite formation and that lithification may promote phosphorus limitation; however, further investigation is required to understand the mechanism by which the later occurs.

  8. Contribution of Microbial Activities To Carbon Cycle In A Deep Sea Ionian Area

    NASA Astrophysics Data System (ADS)

    Zaccone, R.; Caruso, G.; Azzaro, F.; Azzaro, M.; Decembrini, F.; La Ferla, R.; Leonardi, M.

    Main biological process which sustain life in deep environments is the microbial uti- lization of particulated matter. Despite the well known importance of bacterial role in biogeochemical cycles, the rates of microbial processes on organic matter in the Mediterranean Sea, and in particular in the Ionian Sea, are still poorly understood. During winter 1999, water samples were collected at different depths (0-3300m) from six stations along a costal-offshore transect located at 60 miles off Cape Passero (SE Sicily) in the Ionian Sea. Measurements of chlorophyll a, bacterial abundance, ATP and POC enabled the estimation of autotrophic and bacterial contribution to the pool of particulate organic matter. Estimates of microbial leucine-aminopeptidase (LAP) and respiration rates (ETSa) were compared with different water masses identified ac- cording to temperature, salinity and nutrients. Results showed that bacterial biomass contributed to particulated carbon in percentage ranging from 4.57% in surface waters (ISW) to 1.29% in EMDW. Microbial hydrolysis of POC showed higher percentage also in ISW reaching 1.81% and potentially liberating 0.73µg C/l/h (mean values), bioavailable for bacterial growth. The lowest rates of LAP mean values (0.06µg C/l/h) were observed in EMDW with 0.16% of POC potentially hydrolysed. These hydroly- sis rates confirm that during sinking a greater amount of organic matter can not be uti- lized by bacteria and may become refractory. Respiratory rates ranged from 0.118µg C/l/h in MAW to 0.003 µg C/l/h in CDW, with a decreasing trend with depth, indicat- ing low respiration rates with respect to precedent data recorded in deep Mediterranean zones. This research tried of evaluating the carbon flux through the microbial commu- nity and contributed to study some steps of degradative process of organic matter and mineralization to CO2 in relation to the different hydrological characteristics in the Mediterranean changing environment.

  9. Sulfur-Oxidizing Bacteria Mediate Microbial Community Succession and Element Cycling in Launched Marine Sediment.

    PubMed

    Ihara, Hideyuki; Hori, Tomoyuki; Aoyagi, Tomo; Takasaki, Mitsuru; Katayama, Yoko

    2017-01-01

    A large amount of marine sediment was launched on land by the Great East Japan earthquake. Here, we employed both on-site and laboratory studies on the launched marine sediment to investigate the succession of microbial communities and its effects on geochemical properties of the sediment. Twenty-two-month on-site survey showed that microbial communities at the uppermost layer (0-2 mm depth) of the sediment changed significantly with time, whereas those at the deeper layer (20-40 mm depth) remained nearly unchanged and kept anaerobic microbial communities. Nine months after the incidence, various sulfur-oxidizing bacteria (SOB) prevailed in the uppermost layer, in which afterwards diverse chemoorganotrophic bacteria predominated. Geochemical analyses indicated that the concentration of metals other than Fe was lower in the uppermost layer than that in the deeper layer. Laboratory study was carried out by incubating the sediment for 57 days, and clearly indicated the dynamic transition of microbial communities in the uppermost layer exposed to atmosphere. SOB affiliated in the class Epsilonproteobacteria rapidly proliferated and dominated at the uppermost layer during the first 3 days, after that Fe(II)-oxidizing bacteria and chemoorganotrophic bacteria were sequentially dominant. Furthermore, the concentration of sulfate ion increased and the pH decreased. Consequently, SOB may have influenced the mobilization of heavy metals in the sediment by metal-bound sulfide oxidation and/or sediment acidification. These results demonstrate that SOB initiated the dynamic shift from the anaerobic to aerobic microbial communities, thereby playing a critical role in element cycling in the marine sediment.

  10. Tumor cell "dead or alive": caspase and survivin regulate cell death, cell cycle and cell survival.

    PubMed

    Suzuki, A; Shiraki, K

    2001-04-01

    Cell death and cell cycle progression are two sides of the same coin, and these two different phenomenons are regulated moderately to maintain the cellular homeostasis. Tumor is one of the disease states produced as a result of the disintegrated regulation and is characterized as cells showing an irreversible progression of cell cycle and a resistance to cell death signaling. Several investigations have been performed for the understanding of cell death or cell cycle, and cell death research has remarkably progressed in these 10 years. Caspase is a nomenclature referring to ICE/CED-3 cysteine proteinase family and plays a central role during cell death. Recently, several investigations raised some possible hypotheses that caspase is also involved in cell cycle regulation. In this issue, therefore, we review the molecular basis of cell death and cell cycle regulated by caspase in tumor, especially hepatocellular carcinoma cells.

  11. Microbial communities involved in electricity generation from sulfide oxidation in a microbial fuel cell.

    PubMed

    Sun, Min; Tong, Zhong-Hua; Sheng, Guo-Ping; Chen, Yong-Zhen; Zhang, Feng; Mu, Zhe-Xuan; Wang, Hua-Lin; Zeng, Raymond J; Liu, Xian-Wei; Yu, Han-Qing; Wei, Li; Ma, Fang

    2010-10-15

    Simultaneous electricity generation and sulfide removal can be achieved in a microbial fuel cell (MFC). In electricity harvesting from sulfide oxidation in such an MFC, various microbial communities are involved. It is essential to elucidate the microbial communities and their roles in the sulfide conversion and electricity generation. In this work, an MFC was constructed to enrich a microbial consortium, which could harvest electricity from sulfide oxidation. Electrochemical analysis demonstrated that microbial catalysis was involved in electricity output in the sulfide-fed MFC. The anode-attached and planktonic communities could perform catalysis independently, and synergistic interactions occurred when the two communities worked together. A 16S rRNA clone library analysis was employed to characterize the microbial communities in the MFC. The anode-attached and planktonic communities shared similar richness and diversity, while the LIBSHUFF analysis revealed that the two community structures were significantly different. The exoelectrogenic, sulfur-oxidizing and sulfate-reducing bacteria were found in the MFC anodic chamber. The discovery of these bacteria was consistent with the community characteristics for electricity generation from sulfide oxidation. The exoelectrogenic bacteria were found both on the anode and in the solution. The sulfur-oxidizing bacteria were present in greater abundance on the anode than in the solution, while the sulfate-reducing bacteria preferably lived in the solution.

  12. Carbon Cycling in Restored Wisconsin Grasslands: Examining Linkages Between Plant Diversity, Microbial Communities and Ecosystem Processes

    NASA Astrophysics Data System (ADS)

    Cahill, K. N.; Kucharik, C. J.; Balser, T. C.; Foley, J. A.

    2002-12-01

    It is important to characterize the variability of carbon (C) fluxes and stocks and the relationship between biotic and abiotic factors and C sequestration, a proposed strategy to help mitigate climate change. An observation site to study C cycling was established on land enrolled in the USDA Conservation Reserve Program in southwestern Wisconsin in spring 2002 on silt-loam soil. The site was converted from intensive row-crop agriculture in 1987 to three adjacent land cover types: an assortment of native C4 grasses, two C3 grasses and a nitrogen-fixer, and a disk planted, no-tillage food plot rotation of maize and soybeans. Key goals of the study were to characterize the effect of plant species composition and microbial community characteristics on carbon cycling in an attempt to link above- and below-ground processes. Measurements of soil surface CO2 efflux were made on a near-weekly basis during the growing season using a LICOR-6400, concurrently with soil surface moisture adjacent to the CO2 collars. Thermocouples were installed to record hourly average air temperature and soil temperature at 5 depths, from 2 to 70 cm, and water content sensors made hourly average measurements at 15 and 30 cm. Leaf area index measurements were made weekly, aboveground vegetation biomass was collected monthly, and belowground root biomass was collected bimonthly. Monthly microbial measurements included an assessment of community physiological profiles using BiOLOG, and assays of community composition (lipid analysis) and activity. Preliminary results suggest that land cover types significantly altered carbon cycling and microbial community structure and function, leading to different rates of C sequestration.

  13. Source and Cycling of Trace Metals and Nutrients in a Microbial Coalbed Methane System

    NASA Astrophysics Data System (ADS)

    Earll, M. M.; Barnhart, E. P.; Ritter, D.; Vinson, D. S.; Orem, W. H.; Vengosh, A.; McIntosh, J. C.

    2015-12-01

    The source and cycling of trace metals and nutrients in coalbed methane (CBM) systems are controlled by both geochemical processes, such as dissolution or precipitation, and biological mediation by microbial communities. CBM production by the microbes is influenced by trace metals and macronutrients such as nitrogen (N) and phosphate (P). Previous studies have shown the importance of these nutrients to both enhance and inhibit methane production; however, it's not clear whether they are sourced from coal via in-situ biodegradation of organic matter or transported into the seams with groundwater recharge. To address this knowledge gap, trace metal and nutrient geochemistry and the organic content of solid coal and associated groundwater will be investigated across a hydrologic gradient in CBM wells in the Powder River Basin, MT. Sequential dissolution experiments (chemical extraction of organic and inorganic constituents) using 8 core samples of coal and sandstone will provide insight into the presence of trace metals and nutrients in coalbeds, the associated minerals present, and their mobilization. If significant concentrations of N, P, and trace metals are present in core samples, in-situ sourcing of nutrients by microbes is highly probable. The biogeochemical evolution of groundwater, as it relates to trace metal and nutrient cycling by microbial consortia, will be investigated by targeting core-associated coal seams from shallow wells in recharge areas to depths of at least 165 m and across a 28 m vertical profile that include overburden, coal, and underburden. If microbial-limiting trace metals and nutrients are transported into coal seams with groundwater recharge, we would expect to see higher concentrations of trace metals and nutrients in recharge areas compared to deeper coalbeds. The results of this study will provide novel understanding of where trace metals and nutrients are sourced and how they are cycled in CBM systems.

  14. Cell cycle regulation of glucocorticoid receptor function.

    PubMed Central

    Hsu, S C; Qi, M; DeFranco, D B

    1992-01-01

    Glucocorticoid receptor (GR) nuclear translocation, transactivation and phosphorylation were examined during the cell cycle in mouse L cell fibroblasts. Glucocorticoid-dependent transactivation of the mouse mammary tumor virus promoter was observed in G0 and S phase synchronized L cells, but not in G2 synchronized cells. G2 effects were selective on the glucocorticoid hormone signal transduction pathway, since glucocorticoid but not heavy metal induction of the endogenous Metallothionein-1 gene was also impaired in G2 synchronized cells. GRs that translocate to the nucleus of G2 synchronized cells in response to dexamethasone treatment were not efficiently retained there and redistributed to the cytoplasmic compartment. In contrast, GRs bound by the glucocorticoid antagonist RU486 were efficiently retained within nuclei of G2 synchronized cells. Inefficient nuclear retention was observed for both dexamethasone- and RU486-bound GRs in L cells that actively progress through G2 following release from an S phase arrest. Finally, site-specific alterations in GR phosphorylation were observed in G2 synchronized cells suggesting that cell cycle regulation of specific protein kinases and phosphatases could influence nuclear retention, recycling and transactivation activity of the GR. Images PMID:1505524

  15. Control points within the cell cycle

    SciTech Connect

    Van't Hof, J.

    1984-01-01

    Evidence of the temporal order of chromosomal DNA replication argues favorably for the view that the cell cycle is controlled by genes acting in sequence whose time of expression is determined by mitosis and the amount of nuclear DNA (2C vs 4C) in the cell. Gl and G2 appear to be carbohydrate dependent in that cells starved of either carbohydrate of phosphate fail to make these transitions. Cells deprived of nitrate, however, fail only at Gl to S transition indicating that the controls that operate in G1 differ from those that operate in G2. 46 references, 5 figures.

  16. Cell cycle regulation of human endometrial stromal cells during decidualization.

    PubMed

    Logan, Philip C; Steiner, Michael; Ponnampalam, Anna P; Mitchell, Murray D

    2012-08-01

    Differentiation of endometrial stromal cells into decidual cells is crucial for optimal endometrial receptivity. Data from our previous microarray study implied that expression of many cell cycle regulators are changed during decidualization and inhibition of DNA methylation in vitro. In this study, we hypothesized that both the classic progestin treatment and DNA methylation inhibition would inhibit stromal cell proliferation and cell cycle transition. The human endometrial stromal cell line (HESC) was treated from 2 days to 18 days with the DNA methylation inhibitor, 5-aza-2'-deoxycytidine (AZA), a mixture of estradiol/progestin/cyclic adenosine monophosphate ([cAMP]; medroxy-progesterone acetate [MPA mix]) or both. Cell growth was measured by cell counting, cell cycle transition and apoptosis were analyzed by flow cytometry, expression of cell cycle regulators were analyzed by quantitative polymerase chain reaction (qPCR) and Western blotting, and change in DNA methylation profiles were detected by methylation-specific PCR. Both AZA and MPA mix inhibited the proliferation of HESC for at least 7 days. Treatment with MPA mix resulted in an early G0/G1 inhibition followed by G2/M phase inhibition at 18 days. In contrast, AZA treatment inhibited cell cycle progression at the G2/M phase throughout. The protein levels of p21(Cip1)and 14-3-3σ were increased with both AZA and MPA mix treatments without any change in the DNA methylation profiles of the genes. Our data imply that the decidualization of HESC is associated with cell cycle arrest at G0/G1 phase initially and G2/M phase at later stages. Our results also suggest that p53 pathway members play a role in the cell cycle regulation of endometrial stromal cells.

  17. Modeling of Sustainable Base Production by Microbial Electrolysis Cell.

    PubMed

    Blatter, Maxime; Sugnaux, Marc; Comninellis, Christos; Nealson, Kenneth; Fischer, Fabian

    2016-07-07

    A predictive model for the microbial/electrochemical base formation from wastewater was established and compared to experimental conditions within a microbial electrolysis cell. A Na2 SO4 /K2 SO4 anolyte showed that model prediction matched experimental results. Using Shewanella oneidensis MR-1, a strong base (pH≈13) was generated using applied voltages between 0.3 and 1.1 V. Due to the use of bicarbonate, the pH value in the anolyte remained unchanged, which is required to maintain microbial activity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Electricity production from municipal solid waste using microbial fuel cells.

    PubMed

    Chiu, H Y; Pai, T Y; Liu, M H; Chang, C A; Lo, F C; Chang, T C; Lo, H M; Chiang, C F; Chao, K P; Lo, W Y; Lo, S W; Chu, Y L

    2016-07-01

    The organic content of municipal solid waste has long been an attractive source of renewable energy, mainly as a solid fuel in waste-to-energy plants. This study focuses on the potential to use microbial fuel cells to convert municipal solid waste organics into energy using various operational conditions. The results showed that two-chamber microbial fuel cells with carbon felt and carbon felt allocation had a higher maximal power density (20.12 and 30.47 mW m(-2) for 1.5 and 4 L, respectively) than those of other electrode plate allocations. Most two-chamber microbial fuel cells (1.5 and 4 L) had a higher maximal power density than single-chamber ones with corresponding electrode plate allocations. Municipal solid waste with alkali hydrolysis pre-treatment and K3Fe(CN)6 as an electron acceptor improved the maximal power density to 1817.88 mW m(-2) (~0.49% coulomb efficiency, from 0.05-0.49%). The maximal power density from experiments using individual 1.5 and 4 L two-chamber microbial fuel cells, and serial and parallel connections of 1.5 and 4 L two-chamber microbial fuel cells, was found to be in the order of individual 4 L (30.47 mW m(-2)) > serial connection of 1.5 and 4 L (27.75) > individual 1.5 L (20.12) > parallel connection of 1.5 and 4 L (17.04) two-chamber microbial fuel cells . The power density using municipal solid waste microbial fuel cells was compared with information in the literature and discussed. © The Author(s) 2016.

  19. Mitochondrial dynamics and the cell cycle

    USDA-ARS?s Scientific Manuscript database

    Nuclear-mitochondrial (NM) communication impacts many aspects of plant development including vigor, sterility and viability. Dynamic changes in mitochondrial number, shape, size, and cellular location takes place during the cell cycle possibly impacting the process itself and leading to distribution...

  20. Dynamic ubiquitin signaling in cell cycle regulation.

    PubMed

    Gilberto, Samuel; Peter, Matthias

    2017-08-07

    The cell division cycle is driven by a collection of enzymes that coordinate DNA duplication and separation, ensuring that genomic information is faithfully and perpetually maintained. The activity of the effector proteins that perform and coordinate these biological processes oscillates by regulated expression and/or posttranslational modifications. Ubiquitylation is a cardinal cellular modification and is long known for driving cell cycle transitions. In this review, we emphasize emerging concepts of how ubiquitylation brings the necessary dynamicity and plasticity that underlie the processes of DNA replication and mitosis. New studies, often focusing on the regulation of chromosomal proteins like DNA polymerases or kinetochore kinases, are demonstrating that ubiquitylation is a versatile modification that can be used to fine-tune these cell cycle events, frequently through processes that do not involve proteasomal degradation. Understanding how the increasing variety of identified ubiquitin signals are transduced will allow us to develop a deeper mechanistic perception of how the multiple factors come together to faithfully propagate genomic information. Here, we discuss these and additional conceptual challenges that are currently under study toward understanding how ubiquitin governs cell cycle regulation. © 2017 Gilberto and Peter.

  1. Solar energy powered microbial fuel cell with a reversible bioelectrode.

    PubMed

    Strik, David P B T B; Hamelers, Hubertus V M; Buisman, Cees J N

    2010-01-01

    The solar energy powered microbial fuel cell is an emerging technology for electricity generation via electrochemically active microorganisms fueled by solar energy via in situ photosynthesized metabolites from algae, cyanobacteria, or living higher plants. A general problem with microbial fuel cells is the pH membrane gradient which reduces cell voltage and power output. This problem is caused by acid production at the anode, alkaline production at the cathode, and the nonspecific proton exchange through the membrane. Here we report a solution for a new kind of solar energy powered microbial fuel cell via development of a reversible bioelectrode responsible for both biocatalyzed anodic and cathodic electron transfer. Anodic produced protons were used for the cathodic reduction reaction which held the formation of a pH membrane gradient. The microbial fuel cell continuously generated electricity and repeatedly reversed polarity dependent on aeration or solar energy exposure. Identified organisms within biocatalyzing biofilm of the reversible bioelectrode were algae, (cyano)bacteria and protozoa. These results encourage application of solar energy powered microbial fuel cells.

  2. Linking the Cell Cycle to Cell Fate Decisions.

    PubMed

    Dalton, Stephen

    2015-10-01

    Pluripotent stem cells (PSCs) retain the ability to differentiate into a wide range of cell types while undergoing self-renewal. They also exhibit an unusual mode of cell cycle regulation, reflected by a cell cycle structure where G1 and G2 phases are truncated. When individual PSCs are exposed to specification cues, they activate developmental programs and remodel the cell cycle so that the length of G1 and overall cell division times increase. The response of individual stem cells to pro-differentiation signals is strikingly heterogeneous, resulting in asynchronous differentiation. Recent evidence indicates that this phenomenon is due to cell cycle-dependent mechanisms that restrict the initial activation of developmental genes to the G1 phase. This suggests a broad biological mechanism where multipotent cells are 'primed' to initiate cell fate decisions during their transition through G1. Here, I discuss mechanisms underpinning the commitment towards the differentiated state and its relation to the cell cycle. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Challenges in microbial fuel cell development and operation.

    PubMed

    Kim, Byung Hong; Chang, In Seop; Gadd, Geoffrey M

    2007-09-01

    A microbial fuel cell (MFC) is a device that converts chemical energy into electricity through the catalytic activities of microorganisms. Although there is great potential of MFCs as an alternative energy source, novel wastewater treatment process, and biosensor for oxygen and pollutants, extensive optimization is required to exploit the maximum microbial potential. In this article, the main limiting factors of MFC operation are identified and suggestions are made to improve performance.

  4. The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation

    PubMed Central

    Yazdani Foshtomi, Maryam; Braeckman, Ulrike; Derycke, Sofie; Sapp, Melanie; Van Gansbeke, Dirk; Sabbe, Koen; Willems, Anne; Vincx, Magda; Vanaverbeke, Jan

    2015-01-01

    Objectives The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea. Spatio-Temporal Patterns of the Microbial Communities Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices. Macrofauna, Microbes and the Benthic N-Cycle Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided

  5. FUEL CELL/MICRO-TURBINE COMBINED CYCLE

    SciTech Connect

    Larry J. Chaney; Mike R. Tharp; Tom W. Wolf; Tim A. Fuller; Joe J. Hartvigson

    1999-12-01

    A wide variety of conceptual design studies have been conducted that describe ultra-high efficiency fossil power plant cycles. The most promising of these ultra-high efficiency cycles incorporate high temperature fuel cells with a gas turbine. Combining fuel cells with a gas turbine increases overall cycle efficiency while reducing per kilowatt emissions. This study has demonstrated that the unique approach taken to combining a fuel cell and gas turbine has both technical and economic merit. The approach used in this study eliminates most of the gas turbine integration problems associated with hybrid fuel cell turbine systems. By using a micro-turbine, and a non-pressurized fuel cell the total system size (kW) and complexity has been reduced substantially from those presented in other studies, while maintaining over 70% efficiency. The reduced system size can be particularly attractive in the deregulated electrical generation/distribution environment where the market may not demand multi-megawatt central stations systems. The small size also opens up the niche markets to this high efficiency, low emission electrical generation option.

  6. Microbial Mercury Cycling in San Francisco Bay Sediments: From Regions to the Rhizosphere

    NASA Astrophysics Data System (ADS)

    Evans, V. A.; Mann, A.; Romeis, J.; Marvin-Dipasquale, M. C.; Agee, J. L.; Kieu, L. H.; Harms, H. A.

    2004-05-01

    The San Francisco Bay (SFB) estuary is hydrodynamically diverse ecosystem with extensive mercury contamination associated with historic gold and mercury mining wastes, and in a region with an unprecedented number of wetland restoration projects planned or ongoing. Wetlands are known to be active areas for the microbial transformation of Hg(II) to methylmercury (MeHg), which bioaccumulates in the food web. A better understanding of this microbial process, in these restored wetlands and other sub-habitats, is critical if Hg contamination is to be successfully managed in this system. An examination of MeHg production and degradation in sediments has been conducted at multiple spatial scales throughout the SFB estuary and its tributaries over the past four years. At the regional scale, we will present data from the brackish Bay, the delta, and rivers and reservoirs in tributary watersheds. Within the freshwater delta and river regions, a new project is focusing on emergent marsh, non-vegetated open water, and submerged-macrophyte zones. At the smallest scale, we consider microbial Hg cycling in the root zone (rhizosphere) of dominant wetland plants and propose a conceptual model of the key biogoechemical reactions that may make this transitional zone one of the most important with respect to Hg(II)-methylation.

  7. Modeling of SONOS Memory Cell Erase Cycle

    NASA Technical Reports Server (NTRS)

    Phillips, Thomas A.; MacLeod, Todd C.; Ho, Fat H.

    2011-01-01

    Utilization of Silicon-Oxide-Nitride-Oxide-Silicon (SONOS) nonvolatile semiconductor memories as a flash memory has many advantages. These electrically erasable programmable read-only memories (EEPROMs) utilize low programming voltages, have a high erase/write cycle lifetime, are radiation hardened, and are compatible with high-density scaled CMOS for low power, portable electronics. In this paper, the SONOS memory cell erase cycle was investigated using a nonquasi-static (NQS) MOSFET model. Comparisons were made between the model predictions and experimental data.

  8. Solid oxide fuel cell combined cycles

    SciTech Connect

    Bevc, F.P.; Lundberg, W.L.; Bachovchin, D.M.

    1996-12-31

    The integration of the solid oxide fuel cell and combustion turbine technologies can result in combined-cycle power plants, fueled with natural gas, that have high efficiencies and clean gaseous emissions. Results of a study are presented in which conceptual designs were developed for 3 power plants based upon such an integration, and ranging in rating from 3 to 10 MW net ac. The plant cycles are described and characteristics of key components summarized. Also, plant design-point efficiency estimates are presented as well as values of other plant performance parameters.

  9. Cell Cycle Progression of Human Cells Cultured in Rotating Bioreactor

    NASA Technical Reports Server (NTRS)

    Parks, Kelsey

    2009-01-01

    Space flight has been shown to alter the astronauts immune systems. Because immune performance is complex and reflects the influence of multiple organ systems within the host, scientists sought to understand the potential impact of microgravity alone on the cellular mechanisms critical to immunity. Lymphocytes and their differentiated immature form, lymphoblasts, play an important and integral role in the body's defense system. T cells, one of the three major types of lymphocytes, play a central role in cell-mediated immunity. They can be distinguished from other lymphocyte types, such as B cells and natural killer cells by the presence of a special receptor on their cell surface called T cell receptors. Reported studies have shown that spaceflight can affect the expression of cell surface markers. Cell surface markers play an important role in the ability of cells to interact and to pass signals between different cells of the same phenotype and cells of different phenotypes. Recent evidence suggests that cell-cycle regulators are essential for T-cell function. To trigger an effective immune response, lymphocytes must proliferate. The objective of this project is to investigate the changes in growth of human cells cultured in rotating bioreactors and to measure the growth rate and the cell cycle distribution for different human cell types. Human lymphocytes and lymphoblasts will be cultured in a bioreactor to simulate aspects of microgravity. The bioreactor is a cylindrical culture vessel that incorporates the aspects of clinostatic rotation of a solid fluid body around a horizontal axis at a constant speed, and compensates gravity by rotation and places cells within the fluid body into a sustained free-fall. Cell cycle progression and cell proliferation of the lymphocytes will be measured for a number of days. In addition, RNA from the cells will be isolated for expression of genes related in cell cycle regulations.

  10. Cell Cycle Progression of Human Cells Cultured in Rotating Bioreactor

    NASA Technical Reports Server (NTRS)

    Parks, Kelsey

    2009-01-01

    Space flight has been shown to alter the astronauts immune systems. Because immune performance is complex and reflects the influence of multiple organ systems within the host, scientists sought to understand the potential impact of microgravity alone on the cellular mechanisms critical to immunity. Lymphocytes and their differentiated immature form, lymphoblasts, play an important and integral role in the body's defense system. T cells, one of the three major types of lymphocytes, play a central role in cell-mediated immunity. They can be distinguished from other lymphocyte types, such as B cells and natural killer cells by the presence of a special receptor on their cell surface called T cell receptors. Reported studies have shown that spaceflight can affect the expression of cell surface markers. Cell surface markers play an important role in the ability of cells to interact and to pass signals between different cells of the same phenotype and cells of different phenotypes. Recent evidence suggests that cell-cycle regulators are essential for T-cell function. To trigger an effective immune response, lymphocytes must proliferate. The objective of this project is to investigate the changes in growth of human cells cultured in rotating bioreactors and to measure the growth rate and the cell cycle distribution for different human cell types. Human lymphocytes and lymphoblasts will be cultured in a bioreactor to simulate aspects of microgravity. The bioreactor is a cylindrical culture vessel that incorporates the aspects of clinostatic rotation of a solid fluid body around a horizontal axis at a constant speed, and compensates gravity by rotation and places cells within the fluid body into a sustained free-fall. Cell cycle progression and cell proliferation of the lymphocytes will be measured for a number of days. In addition, RNA from the cells will be isolated for expression of genes related in cell cycle regulations.

  11. Cell cycle nucleic acids, polypeptides and uses thereof

    DOEpatents

    Gordon-Kamm, William J.; Lowe, Keith S.; Larkins, Brian A.; Dilkes, Brian R.; Sun, Yuejin

    2007-08-14

    The invention provides isolated nucleic acids and their encoded proteins that are involved in cell cycle regulation. The invention further provides recombinant expression cassettes, host cells, transgenic plants, and antibody compositions. The present invention provides methods and compositions relating to altering cell cycle protein content, cell cycle progression, cell number and/or composition of plants.

  12. Impact of volatile fatty acids on microbial electrolysis cell performance.

    PubMed

    Yang, Nan; Hafez, Hisham; Nakhla, George

    2015-10-01

    This study investigated the performance of microbial electrolysis cells (MECs) fed with three common fermentation products: acetate, butyrate, and propionate. Each substrate was fed to the reactor for three consecutive-batch cycles. The results showed high current densities for acetate, but low current densities for butyrate and propionate (maximum values were 6.0 ± 0.28, 2.5 ± 0.06, 1.6 ± 0.14 A/m(2), respectively). Acetate also showed a higher coulombic efficiency of 87 ± 5.7% compared to 72 ± 2.0 and 51 ± 6.4% for butyrate and propionate, respectively. This paper also revealed that acetate could be easily oxidized by anode respiring bacteria in MEC, while butyrate and propionate could not be oxidized to the same degree. The utilization rate of the substrates in MEC followed the order: acetate > butyrate > propionate. The ratio of suspended biomass to attached biomass was approximately 1:4 for all the three substrates.

  13. Nanoparticle Facilitated Extracellular Electron Transfer in Microbial Fuel Cells

    DTIC Science & Technology

    2014-10-13

    KEYWORDS: Bacteria , facilitated electron transport, electrochemically active, iron sulfide, Shewanella Microbial fuel cells (MFCs) are capable of...to MFC technology is the unique capability of electrochemically active bacteria , such as Shewanella and Geobacter, to divert electrons from the...finger electrode by reactive ion etching. The electrochemical measurements were Figure 1. Current and cell morphology changes at early stage of

  14. Impact of catch crop mixtures and soils on microbial diversity and nitrogen cycling communities in agroecosystems

    NASA Astrophysics Data System (ADS)

    Burbano, Claudia S.; Große, Julia; Hurek, Thomas; Reinhold-Hurek, Barbara

    2017-04-01

    In light of the projected world's population growth, food supplies will necessary have to increase. Soils are an essential component for achieving this expansion and its quality and fertility are crucial for bio-economic productivity. Catch crops can be an option to preserve or even improve soil productivity because of their effect on soil fertility and health. A long-term field experiment of the CATCHY project (Catch-cropping as an agrarian tool for continuing soil health and yield-increase) with two contrasting crop rotations was established in two different locations in Northern and Southern Germany. Single catch crops (white mustard, Egyptian clover, phacelia and bristle oat), catch crop mixtures (a mixture of the above and a commercial mixture) and main crops (wheat and maize) have been grown. To investigate how catch crops can affect the microbial diversity and particularly the microbial nitrogen cycling communities, we are studying first the short-term effect of different catch crop mixtures on the microbiomes associated with soils and roots. We compared these microbiomes with wheat plants, representing the microbial community before a catch crop treatment. Roots, rhizosphere and bulk soils were collected from representative samples of wheat plants from one field. The same compartments were also sampled from one fallow treatment and three catch crops variants from three fields each. The variants consisted of white mustard and the two catch crop mixtures. All fields were sampled by triplicate. Quantitative analyses were carried out by qPCR based on key functional marker genes for mineralization (ureC), nitrification (amoA), dissimilatory nitrate and nitrite reduction to ammonium -DNRA- (nrfA), denitrification (nirK, nirS, nosZ), and nitrogen fixation (nifH). These genes were targeted at the DNA and RNA level for the characterization of the microbial population and the actual transcription activity, respectively. We detected the presence and activity of

  15. Biochar impacts soil microbial community composition and nitrogen cycling in an acidic soil planted with rape.

    PubMed

    Xu, Hui-Juan; Wang, Xiao-Hui; Li, Hu; Yao, Huai-Ying; Su, Jian-Qiang; Zhu, Yong-Guan

    2014-08-19

    Biochar has been suggested to improve acidic soils and to mitigate greenhouse gas emissions. However, little has been done on the role of biochar in ameliorating acidified soils induced by overuse of nitrogen fertilizers. In this study, we designed a pot trial with an acidic soil (pH 4.48) in a greenhouse to study the interconnections between microbial community, soil chemical property changes, and N2O emissions after biochar application. The results showed that biochar increased plant growth, soil pH, total carbon, total nitrogen, C/N ratio, and soil cation exchange capacity. The results of high-throughput sequencing showed that biochar application increased α-diversity significantly and changed the relative abundances of some microbes that are related with carbon and nitrogen cycling at the family level. Biochar amendment stimulated both nitrification and denitrification processes, while reducing N2O emissions overall. Results of redundancy analysis indicated biochar could shift the soil microbial community by changing soil chemical properties, which modulate N-cycling processes and soil N2O emissions. The significantly increased nosZ transcription suggests that biochar decreased soil N2O emissions by enhancing its further reduction to N2.

  16. The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments

    DOE PAGES

    Scott, Nicole M.; Hess, Matthias; Bouskill, Nick J.; ...

    2014-03-25

    During hydrocarbon exposure, the composition and functional dynamics of marine microbial communities are altered, favoring bacteria that can utilize this rich carbon source. Initial exposure of high levels of hydrocarbons in aerobic surface sediments can enrich growth of heterotrophic microorganisms having hydrocarbon degradation capacity. As a result, there can be a localized reduction in oxygen potential within the surface layer of marine sediments causing anaerobic zones. We hypothesized that increasing exposure to elevated hydrocarbon concentrations would positively correlate with an increase in denitrification processes and the net accumulation of dinitrogen. This hypothesis was tested by comparing the relative abundance ofmore » genes associated with nitrogen metabolism and nitrogen cycling identified in 6 metagenomes from sediments contaminated by polyaromatic hydrocarbons from the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico, and 3 metagenomes from sediments associated with natural oil seeps in the Santa Barbara Channel. An additional 8 metagenomes from uncontaminated sediments from the Gulf of Mexico were analyzed for comparison. We predicted relative changes in metabolite turnover as a function of the differential microbial gene abundances, which showed predicted accumulation of metabolites associated with denitrification processes, including anammox, in the contaminated samples compared to uncontaminated sediments, with the magnitude of this change being positively correlated to the hydrocarbon concentration and exposure duration. Furthermore, these data highlight the potential impact of hydrocarbon inputs on N cycling processes in marine sediments and provide information relevant for system scale models of nitrogen metabolism in affected ecosystems.« less

  17. The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments

    SciTech Connect

    Scott, Nicole M.; Hess, Matthias; Bouskill, Nick J.; Mason, Olivia U.; Jansson, Janet K.; Gilbert, Jack A.

    2014-03-25

    During hydrocarbon exposure, the composition and functional dynamics of marine microbial communities are altered, favoring bacteria that can utilize this rich carbon source. Initial exposure of high levels of hydrocarbons in aerobic surface sediments can enrich growth of heterotrophic microorganisms having hydrocarbon degradation capacity. As a result, there can be a localized reduction in oxygen potential within the surface layer of marine sediments causing anaerobic zones. We hypothesized that increasing exposure to elevated hydrocarbon concentrations would positively correlate with an increase in denitrification processes and the net accumulation of dinitrogen. This hypothesis was tested by comparing the relative abundance of genes associated with nitrogen metabolism and nitrogen cycling identified in 6 metagenomes from sediments contaminated by polyaromatic hydrocarbons from the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico, and 3 metagenomes from sediments associated with natural oil seeps in the Santa Barbara Channel. An additional 8 metagenomes from uncontaminated sediments from the Gulf of Mexico were analyzed for comparison. We predicted relative changes in metabolite turnover as a function of the differential microbial gene abundances, which showed predicted accumulation of metabolites associated with denitrification processes, including anammox, in the contaminated samples compared to uncontaminated sediments, with the magnitude of this change being positively correlated to the hydrocarbon concentration and exposure duration. Furthermore, these data highlight the potential impact of hydrocarbon inputs on N cycling processes in marine sediments and provide information relevant for system scale models of nitrogen metabolism in affected ecosystems.

  18. The microbial nitrogen cycling potential in marine sediments is impacted by polyaromatic hydrocarbon pollution

    DOE PAGES

    Gilbert, Jack A.

    2014-03-25

    During hydrocarbon exposure, the composition and functional dynamics of marine microbial communities are altered, favoring bacteria that can utilize this rich carbon source. Initial exposure of high levels of hydrocarbons in aerobic surface sediments can enrich growth of heterotrophic microorganisms having hydrocarbon degradation capacity. As a result, there can be a localized reduction in oxygen potential within the surface layer of marine sediments causing anaerobic zones. We hypothesized that increasing exposure to elevated hydrocarbon concentrations would positively correlate with an increase in denitrification processes and the net accumulation of dinitrogen. This hypothesis was tested by comparing the relative abundance ofmore » genes associated with nitrogen metabolism and nitrogen cycling identified in 6 metagenomes from sediments contaminated by polyaromatic hydrocarbons from the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico, and 3 metagenomes from sediments associated with natural oil seeps in the Santa Barbara Channel. An additional 8 metagenomes from uncontaminated sediments from the Gulf of Mexico were analyzed for comparison. We predicted relative changes in metabolite turnover as a function of the differential microbial gene abundances, which showed predicted accumulation of metabolites associated with denitrification processes, including anammox, in the contaminated samples compared to uncontaminated sediments, with the magnitude of this change being positively correlated to the hydrocarbon concentration and exposure duration. These data highlight the potential impact of hydrocarbon inputs on N cycling processes in marine sediments and provide information relevant for system scale models of nitrogen metabolism in affected ecosystems.« less

  19. The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments

    SciTech Connect

    Scott, Nicole M.; Hess, Matthias; Bouskill, Nick; Mason, Olivia U; Jansson, Janet K; Gilbert, Jack A.

    2014-03-25

    During hydrocarbon exposure, the composition and functional dynamics of marine microbial communities are altered, favoring bacteria that can utilize this rich carbon source. Initial exposure of high levels of hydrocarbons in aerobic surface sediments can enrich growth of heterotrophic microorganisms having hydrocarbon degradation capacity. As a result, there can be a localized reduction in oxygen potential within the surface layer of marine sediments causing anaerobic zones. We hypothesized that increasing exposure to elevated hydrocarbon concentrations would positively correlate with an increase in denitrification processes and the net accumulation of dinitrogen. This hypothesis was tested by comparing the relative abundance of genes associated with nitrogen metabolism and nitrogen cycling identified in 6 metagenomes from sediments contaminated by polyaromatic hydrocarbons from the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico, and 3 metagenomes from sediments associated with natural oil seeps in the Santa Barbara Channel. An additional 8 metagenomes from uncontaminated sediments from the Gulf of Mexico were analyzed for comparison. We predicted relative changes in metabolite turnover as a function of the differential microbial gene abundances, which showed predicted accumulation of metabolites associated with denitrification processes, including anammox, in the contaminated samples compared to uncontaminated sediments, with the magnitude of this change being positively correlated to the hydrocarbon concentration and exposure duration. These data highlight the potential impact of hydrocarbon inputs on N cycling processes in marine sediments and provide information relevant for system scale models of nitrogen metabolism in affected ecosystems

  20. The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments.

    PubMed

    Scott, Nicole M; Hess, Matthias; Bouskill, Nick J; Mason, Olivia U; Jansson, Janet K; Gilbert, Jack A

    2014-01-01

    During hydrocarbon exposure, the composition and functional dynamics of marine microbial communities are altered, favoring bacteria that can utilize this rich carbon source. Initial exposure of high levels of hydrocarbons in aerobic surface sediments can enrich growth of heterotrophic microorganisms having hydrocarbon degradation capacity. As a result, there can be a localized reduction in oxygen potential within the surface layer of marine sediments causing anaerobic zones. We hypothesized that increasing exposure to elevated hydrocarbon concentrations would positively correlate with an increase in denitrification processes and the net accumulation of dinitrogen. This hypothesis was tested by comparing the relative abundance of genes associated with nitrogen metabolism and nitrogen cycling identified in 6 metagenomes from sediments contaminated by polyaromatic hydrocarbons from the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico, and 3 metagenomes from sediments associated with natural oil seeps in the Santa Barbara Channel. An additional 8 metagenomes from uncontaminated sediments from the Gulf of Mexico were analyzed for comparison. We predicted relative changes in metabolite turnover as a function of the differential microbial gene abundances, which showed predicted accumulation of metabolites associated with denitrification processes, including anammox, in the contaminated samples compared to uncontaminated sediments, with the magnitude of this change being positively correlated to the hydrocarbon concentration and exposure duration. These data highlight the potential impact of hydrocarbon inputs on N cycling processes in marine sediments and provide information relevant for system scale models of nitrogen metabolism in affected ecosystems.

  1. Municipal solid waste landfill leachate treatment and electricity production using microbial fuel cells.

    PubMed

    Damiano, Lisa; Jambeck, Jenna R; Ringelberg, David B

    2014-05-01

    Microbial fuel cells were designed and operated to treat landfill leachate while simultaneously producing electricity. Two designs were tested in batch cycles using landfill leachate as a substrate without inoculation (908 to 3,200 mg/L chemical oxygen demand (COD)): Circle (934 mL) and large-scale microbial fuel cells (MFC) (18.3 L). A total of seven cycles were completed for the Circle MFC and two cycles for the larger-scale MFC. Maximum power densities of 24 to 31 mW/m(2) (653 to 824 mW/m(3)) were achieved using the Circle MFC, and a maximum voltage of 635 mV was produced using the larger-scale MFC. In the Circle MFC, COD, biological oxygen demand (BOD), total organic carbon (TOC), and ammonia were removed at an average of 16%, 62%, 23%, and 20%, respectively. The larger-scale MFC achieved an average of 74% BOD removal, 27% TOC removal, and 25% ammonia reduction while operating over 52 days. Analysis of the microbial characteristics of the leachate indicates that there might be both supportive and inhibiting bacteria in landfill leachate for operation of an MFC. Issues related to scale-up and heterogeneity of a mixed substrate remain.

  2. Microbial diversity and population dynamics of activated sludge microbial communities participating in electricity generation in microbial fuel cells.

    PubMed

    Ki, D; Park, J; Lee, J; Yoo, K

    2008-01-01

    In this study, we performed microbial community analysis to examine microbial diversity and community structure in microbial fuel cells (MFCs) seeded with activated sludge from a municipal wastewater treatment plant in South Korea. Because anode-attached biofilm populations are particularly important in electricity transfer, the ecological characteristics of anode-attached biofilm microbes were explored and compared with those of microbes grown in suspension in an anode chamber. 16S rDNA-based community analysis showed that the degree of diversity in anode-attached biofilms was greater than that of the originally seeded activated sludge as well as that of the suspension-grown microbes in the anode bottle. In addition, Bacteroidetes and Clostridia grew preferentially during MFC electricity generation. Further phylogenetic analysis revealed that the anode biofilm populations described in this work are phylogenetically distant from previously characterized MFC anode biofilm microbes. These findings suggest that a phylogenetically diverse set of microbes can be involved in the electricity generation of MFC anode compartments, and that increased microbial diversity in anode biofilms may help to stabilize electricity production in the MFC. Copyright (c) IWA Publishing 2008.

  3. Organo-mineral complexation alters carbon and nitrogen cycling in stream microbial assemblages

    NASA Astrophysics Data System (ADS)

    Hunter, William Ross; Wanek, Wolfgang; Prommer, Judith; Mooshammer, Maria; Battin, Tom

    2014-05-01

    Inland waters are of global biogeochemical importance receiving carbon inputs of ~ 4.8 Pg C y-1. Of this 12 % is buried, 18 % transported to the oceans, and 70 % supports aquatic secondary production. However, the mechanisms that determine the fate of organic matter (OM) in these systems are poorly defined. One important aspect is the formation of organo-mineral complexes in aquatic systems and their potential as a route for OM transport and burial vs. microbial utilization as organic carbon (C) and nitrogen (N) sources. Organo-mineral particles form by sorption of dissolved OM to freshly eroded mineral surfaces and may contribute to ecosystem-scale particulate OM fluxes. We tested the availability of mineral-sorbed OM as a C & N source for streamwater microbial assemblages and streambed biofilms. Organo-mineral particles were constructed in vitro by sorption of 13C:15N-labelled amino acids to hydrated kaolin particles, and microbial degradation of these particles compared with equivalent doses of 13C:15N-labelled free amino acids. Experiments were conducted in 120 ml mesocosms over 7 days using biofilms and streamwater sampled from the Oberer Seebach stream (Austria), tracing assimilation and mineralization of 13C and 15N labels from mineral-sorbed and dissolved amino acids. Here we present data on the effects of organo-mineral sorption upon amino acid mineralization and its C:N stoichiometry. Organo-mineral sorption had a significant effect upon microbial activity, restricting C and N mineralization by both the biofilm and streamwater treatments. Distinct differences in community response were observed, with both dissolved and mineral-stabilized amino acids playing an enhanced role in the metabolism of the streamwater microbial community. Mineral-sorption of amino acids differentially affected C & N mineralization and reduced the C:N ratio of the dissolved amino acid pool. The present study demonstrates that organo-mineral complexes restrict microbial degradation

  4. Microbial electrodialysis cell for simultaneous water desalination and hydrogen gas production.

    PubMed

    Mehanna, Maha; Kiely, Patrick D; Call, Douglas F; Logan, Bruce E

    2010-12-15

    A new approach to water desalination is to use exoelectrogenic bacteria to generate electrical power from the biodegradation of organic matter, moving charged ions from a middle chamber between two membranes in a type of microbial fuel cell called a microbial desalination cell. Desalination efficiency using this approach is limited by the voltage produced by the bacteria. Here we examine an alternative strategy based on boosting the voltage produced by the bacteria to achieve hydrogen gas evolution from the cathode using a three-chambered system we refer to as a microbial electrodialysis cell (MEDC). We examined the use of the MEDC process using two different initial NaCl concentrations of 5 g/L and 20 g/L. Conductivity in the desalination chamber was reduced by up to 68 ± 3% in a single fed-batch cycle, with electrical energy efficiencies reaching 231 ± 59%, and maximum hydrogen production rates of 0.16 ± 0.05 m(3) H(2)/m(3) d obtained at an applied voltage of 0.55 V. The advantage of this system compared to a microbial fuel cell approach is that the potentials between the electrodes can be better controlled, and the hydrogen gas that is produced can be used to recover energy to make the desalination process self-sustaining with respect to electrical power requirements.

  5. Westinghouse fuel cell combined cycle systems

    SciTech Connect

    Veyo, S.

    1996-12-31

    Efficiency (voltage) of the solid oxide fuel cell (SOFC) should increase with operating pressure, and a pressurized SOFC could function as the heat addition process in a Brayton cycle gas turbine (GT) engine. An overall cycle efficiency of 70% should be possible. In cogeneration, half of the waste heat from a PSOFC/GT should be able to be captured in process steam and hot water, leading to a fuel effectiveness of about 85%. In order to make the PSOFC/GT a commercial reality, satisfactory operation of the SOFC at elevated pressure must be verified, a pressurized SOFC generator module must be designed, built, and tested, and the combined cycle and parameters must be optimized. A prototype must also be demonstrated. This paper describes progress toward making the PSOFC/GT a reality.

  6. Pyrosequencing evidence for iron-cycling microbial communities in sediments of the Skagerrak and Bothnian Bay

    NASA Astrophysics Data System (ADS)

    Reyes, Carolina; Dellwig, Olaf; Noriega-Ortega, Beatriz; Dähnke, Kirstin; Gehre, Matthias; Böttcher, Michael E.; Friedrich, Michael W.

    2015-04-01

    The diversity and metabolic pathways of microorganisms linked to Fe cycling in marine sediments are still poorly understood. Marine microorganisms in general are difficult to isolate and those that have been successfully isolated may not represent the main endogenous population. Various culture-independent techniques have been applied to characterize marine microbial communities, but only recently, has high throughput pyrosequencing been applied in marine sediment studies. Initial results are promising in capturing the full complexity of microbial communities in sediments. We performed a pyrosequencing-based study in marine and brackish sediments of the Baltic Sea; to our knowledge this is the first pyrosequencing study focused on the zone of Fe cycling. The goal of this study was to determine the bacterial and archaeal community composition near the sediment surface showing ongoing Fe cycling as a first step in characterizing the microorganisms potentially involved in Fe cycling. Two 35-cm-cores were sampled from ferruginous sediments in the Skagerrak, SK, North-Baltic Sea and the Bothnian Bay, BB, Northern Baltic Sea. Porewater (Fe2+, Mn2+, SO42-) and solid phase (Fe, Mn, total S) concentrations were measured and 16S rRNA genes were analysed using 454-pyrosequencing. Additionally, stable S and O isotope signatures of dissolved sulfate were measured at SK site. Sediment biogeochemistry indicated an intense suboxic zone with accumulation of dissolved Fe in the top 30 cm but only minor net sulfate (SO42-) reduction at both sites. Pore water profiles showed Fe2+ and Mn2+ levels of ~140-150 µM throughout the core below a 6 cm thick oxidized surface layer in SK sediments and ~300 µM below a 2 cm thick surface layer in BB sediments. Dissolved sulfide levels were below the detection limit in both sediments. Stable S and O isotope signatures suggest only minor net sulfate reduction. Fe reduction in the studied sediments is dominated by microbial dissimilatory Fe

  7. Linking Sediment Microbial Communities to Carbon Cycling in High-Latitude Lakes

    NASA Astrophysics Data System (ADS)

    Emerson, J. B.; Varner, R. K.; Johnson, J. E.; Owusu-Dommey, A.; Binder, M.; Woodcroft, B. J.; Wik, M.; Freitas, N. L.; Boyd, J. A.; Crill, P. M.; Saleska, S. R.; Tyson, G. W.; Rich, V. I.

    2015-12-01

    It is well recognized that thawing permafrost peatlands are likely to provide a positive feedback to climate change via CH4 and CO2 emissions. High-latitude lakes in these landscapes have also been identified as sources of CH4 and CO2 loss to the atmosphere. To investigate microbial contributions to carbon loss from high-latitude lakes, we characterized sediment geochemistry and microbiota via cores collected from deep and shallow regions of two lakes (Inre Harrsjön and Mellersta Harrsjön) in Arctic Sweden in July, 2012. These lakes are within the Stordalen Mire long-term ecological area, a focal site for investigating the impacts of climate change-related permafrost thaw, and the lakes in this area are responsible for ~55% of the CH4 loss from this hydrologically interconnected system. Across 40 samples from 4 to 40 cm deep within four sediment cores, Illumina 16S rRNA gene sequencing revealed that the sedimentary microbiota was dominated by candidate phyla OP9 and OP8 (Atribacteria and Aminicenantes, respectively, including putative fermenters and anaerobic respirers), predicted methanotrophic Gammaproteobacteria, and predicted methanogenic archaea from the Thermoplasmata Group E2 clade. We observed some overlap in community structure with nearby peatlands, which tend to be dominated by methanogens and Acidobacteria. Sediment microbial communities differed significantly between lakes, by overlying lake depth (shallow vs. deep), and by depth within a core, with each trend corresponding to parallel differences in biogeochemical measurements. Overall, our results support the potential for significant microbial controls on carbon cycling in high-latitude lakes associated with thawing permafrost, and ongoing metagenomic analyses of focal samples will yield further insight into the functional potential of these microbial communities and their dominant members.

  8. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community

    SciTech Connect

    Handley, KM; Verberkmoes, Nathan C; Steefel, Carl I; Sharon, I; Williams, Ken; Miller, CS; Frischkorn, Kyle C; Chourey, Karuna; Thomas, Brian; Shah, Manesh B; Long, Phil; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2013-01-01

    Stimulation of subsurface microorganisms to induce reductive immobilization of metals is a promising approach for bioremediation, yet the overall microbial community response is typically poorly understood. Here we used community proteogenomics to test the hypothesis that excess input of acetate activates syntrophic interactions among autotrophs and heterotrophs. A flow-through sediment column was incubated in a groundwater well of an acetate-amended aquifer. Genomic sequences from the community recovered during microbial sulfate reduction were used to econstruct, de novo, near-complete genomes for Desulfobacter (Deltaproteobacteria) and relatives of Sulfurovum and Sulfurimonas (Epsilonproteobacteria), and Bacteroidetes. Partial genomes were obtained for Clostridiales (Firmicutes) and Desulfuromonadales-like Deltaproteobacteria. The majority of proteins identified by mass spectrometry corresponded to Desulfobacter-like species, and demonstrate the role of this organism in sulfate reduction (Dsr and APS), nitrogen-fixation (Nif) and acetate oxidation to CO2 during amendment. Results suggest less abundant Desulfuromonadales and Bacteroidetes also actively contributed to CO2 production via the TCA cycle. Proteomic data indicate that sulfide was partially re-oxidized by Epsilonproteobacteria through nitrate-dependent sulfide oxidation (using Nap, Nir, Nos, SQR and Sox), with CO2 fixed using the reverse TCA cycle. Modeling shows that this reaction was thermodynamically possible, and kinetically favorable relative to acetate-dependent denitrification. We conclude that high-levels of carbon amendment aimed to stimulate anaerobic heterotrophy led to carbon fixation in co-dependent chemoautotrophs. These results have implications for understanding complex ecosystem behavior, and show that high levels of organic carbon supplementation can expand the range of microbial functionalities accessible for ecosystem manipulation.

  9. Microbial Iron Oxidation in the Arctic Tundra and Its Implications for Biogeochemical Cycling

    PubMed Central

    Scott, Jarrod J.; Benes, Joshua; Bowden, William B.

    2015-01-01

    The role that neutrophilic iron-oxidizing bacteria play in the Arctic tundra is unknown. This study surveyed chemosynthetic iron-oxidizing communities at the North Slope of Alaska near Toolik Field Station (TFS) at Toolik Lake (lat 68.63, long −149.60). Microbial iron mats were common in submerged habitats with stationary or slowly flowing water, and their greatest areal extent is in coating plant stems and sediments in wet sedge meadows. Some Fe-oxidizing bacteria (FeOB) produce easily recognized sheath or stalk morphotypes that were present and dominant in all the mats we observed. The cool water temperatures (9 to 11°C) and reduced pH (5.0 to 6.6) at all sites kinetically favor microbial iron oxidation. A microbial survey of five sites based on 16S rRNA genes found a predominance of Proteobacteria, with Betaproteobacteria and members of the family Comamonadaceae being the most prevalent operational taxonomic units (OTUs). In relative abundance, clades of lithotrophic FeOB composed 5 to 10% of the communities. OTUs related to cyanobacteria and chloroplasts accounted for 3 to 25% of the communities. Oxygen profiles showed evidence for oxygenic photosynthesis at the surface of some mats, indicating the coexistence of photosynthetic and FeOB populations. The relative abundance of OTUs belonging to putative Fe-reducing bacteria (FeRB) averaged around 11% in the sampled iron mats. Mats incubated anaerobically with 10 mM acetate rapidly initiated Fe reduction, indicating that active iron cycling is likely. The prevalence of iron mats on the tundra might impact the carbon cycle through lithoautotrophic chemosynthesis, anaerobic respiration of organic carbon coupled to iron reduction, and the suppression of methanogenesis, and it potentially influences phosphorus dynamics through the adsorption of phosphorus to iron oxides. PMID:26386054

  10. Microbial iron oxidation in the Arctic tundra and its implications for biogeochemical cycling.

    PubMed

    Emerson, David; Scott, Jarrod J; Benes, Joshua; Bowden, William B

    2015-12-01

    The role that neutrophilic iron-oxidizing bacteria play in the Arctic tundra is unknown. This study surveyed chemosynthetic iron-oxidizing communities at the North Slope of Alaska near Toolik Field Station (TFS) at Toolik Lake (lat 68.63, long -149.60). Microbial iron mats were common in submerged habitats with stationary or slowly flowing water, and their greatest areal extent is in coating plant stems and sediments in wet sedge meadows. Some Fe-oxidizing bacteria (FeOB) produce easily recognized sheath or stalk morphotypes that were present and dominant in all the mats we observed. The cool water temperatures (9 to 11°C) and reduced pH (5.0 to 6.6) at all sites kinetically favor microbial iron oxidation. A microbial survey of five sites based on 16S rRNA genes found a predominance of Proteobacteria, with Betaproteobacteria and members of the family Comamonadaceae being the most prevalent operational taxonomic units (OTUs). In relative abundance, clades of lithotrophic FeOB composed 5 to 10% of the communities. OTUs related to cyanobacteria and chloroplasts accounted for 3 to 25% of the communities. Oxygen profiles showed evidence for oxygenic photosynthesis at the surface of some mats, indicating the coexistence of photosynthetic and FeOB populations. The relative abundance of OTUs belonging to putative Fe-reducing bacteria (FeRB) averaged around 11% in the sampled iron mats. Mats incubated anaerobically with 10 mM acetate rapidly initiated Fe reduction, indicating that active iron cycling is likely. The prevalence of iron mats on the tundra might impact the carbon cycle through lithoautotrophic chemosynthesis, anaerobic respiration of organic carbon coupled to iron reduction, and the suppression of methanogenesis, and it potentially influences phosphorus dynamics through the adsorption of phosphorus to iron oxides.

  11. Batteryless, wireless sensor powered by a sediment microbial fuel cell.

    PubMed

    Donovan, Conrad; Dewan, Alim; Heo, Deukhyoun; Beyenal, Haluk

    2008-11-15

    Sediment microbial fuel cells (SMFCs) are considered to be an alternative renewable power source for remote monitoring. There are two main challenges to using SMFCs as power sources: 1) a SMFC produces a low potential at which most sensor electronics do not operate, and 2) a SMFC cannot provide continuous power, so energy from the SMFC must be stored and then used to repower sensor electronics intermittently. In this study, we developed a SMFC and a power management system (PMS) to power a batteryless, wireless sensor. A SMFC operating with a microbial anode and cathode, located in the Palouse River, Pullman, Washington, U.S.A., was used to demonstrate the utility of the developed system. The designed PMS stored microbial energy and then started powering the wireless sensor when the SMFC potential reached 320 mV. It continued powering until the SMFC potential dropped below 52 mV. The system was repowered when the SMFC potential increased to 320 mV, and this repowering continued as long as microbial reactions continued. We demonstrated that a microbial fuel cell with a microbial anode and cathode can be used as an effective renewable power source for remote monitoring using custom-designed electronics.

  12. Electricity generation and microbial community changes in microbial fuel cells packed with different anodic materials.

    PubMed

    Sun, Yanmei; Wei, Jincheng; Liang, Peng; Huang, Xia

    2011-12-01

    Four materials, carbon felt cube (CFC), granular graphite (GG), granular activated carbon (GAC) and granular semicoke (GS) were tested as packed anodic materials to seek a potentially practical material for microbial fuel cells (MFCs). The microbial community and its correlation with the electricity generation performance of MFCs were explored. The maximum power density was found in GAC, followed by CFC, GG and GS. In GAC and CFC packed MFCs, Geobacter was the dominating genus, while Azospira was the most populous group in GG. Results further indicated that GAC was the most favorable for Geobacter adherence and growth, and the maximum power densities had positive correlation with the total biomass and the relative abundance of Geobacter, but without apparent correlation with the microbial diversity. Due to the low content of Geobacter in GS, power generated in this system may be attributed to other microorganisms such as Synergistes, Bacteroidetes and Castellaniella.

  13. Microbial community structure of different electrode materials in constructed wetland incorporating microbial fuel cell.

    PubMed

    Wang, Junfeng; Song, Xinshan; Wang, Yuhui; Abayneh, Befkadu; Ding, Yi; Yan, Denghua; Bai, Junhong

    2016-12-01

    The microbial fuel cell coupled with constructed wetland (CW-MFC) microcosms were operated under fed-batch mode for evaluating the effect of electrode materials on bioelectricity generation and microbial community composition. Experimental results indicated that the bioenergy output in CW-MFC increased with the substrate concentration; maximum average voltage (177mV) was observed in CW-MFC with carbon fiber felt (CFF). In addition, the four different materials resulted in the formation of significantly different microbial community distribution around the anode electrode. The relative abundance of Proteobacteria in CFF and foamed nickel (FN) was significantly higher than that in stainless steel mesh (SSM) and graphite rod (GR) samples. Notably, the findings indicate that CW-MFC utilizing FN anode electrode could apparently improve relative abundance of Dechloromonas, which has been regarded as a denitrifying and phosphate accumulating microorganism.

  14. Simultaneous microbial and electrochemical reductions of vanadium (V) with bioelectricity generation in microbial fuel cells.

    PubMed

    Zhang, Baogang; Tian, Caixing; Liu, Ying; Hao, Liting; Liu, Ye; Feng, Chuanping; Liu, Yuqian; Wang, Zhongli

    2015-03-01

    Simultaneous microbial and electrochemical reductions of vanadium (V) with bioelectricity generation were realized in microbial fuel cells (MFCs). With initial V(V) concentrations of 75 mg/l and 150 mg/l in anolyte and catholyte, respectively, stable power output of 419±11 mW/m(2) was achieved. After 12h operation, V(V) concentration in the catholyte decreased to the value similar to that of the initial one in the anolyte, meanwhile it was nearly reduced completely in the anolyte. V(IV) was the main reduction product, which subsequently precipitated, acquiring total vanadium removal efficiencies of 76.8±2.9%. Microbial community analysis revealed the emergence of the new species of Deltaproteobacteria and Bacteroidetes as well as the enhanced Spirochaetes mainly functioned in the anode. This study opens new pathways to successful remediation of vanadium contamination. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Microbially-reduced graphene scaffolds to facilitate extracellular electron transfer in microbial fuel cells.

    PubMed

    Yuan, Yong; Zhou, Shungui; Zhao, Bo; Zhuang, Li; Wang, Yueqiang

    2012-07-01

    A one-pot method is exploited by adding graphene oxide (GO) and acetate into an microbial fuel cell (MFC) in which GO is microbially reduced, leading to in situ construction of a bacteria/graphene network in the anode. The obtained microbially reduced graphene (MRG) exhibits comparable conductivity and physical characteristics to the chemically reduced graphene. Electrochemical measurements reveal that the number of exoelectrogens involved in extracellular electron transfer (EET) to the solid electrode, increases due to the presence of graphene scaffolds, and the EET is facilitated in terms of electron transfer kinetics. As a result, the maximum power density of the MFC is enhanced by 32% (from 1440 to 1905 mW m(-2)) and the coulombic efficiency is improved by 80% (from 30 to 54%). The results demonstrate that the construction of the bacteria/graphene network is an effective alternative to improve the MFC performance. Copyright © 2012 Elsevier Ltd. All rights reserved.

  16. Cell shape dynamics during the staphylococcal cell cycle

    PubMed Central

    Monteiro, João M.; Fernandes, Pedro B.; Vaz, Filipa; Pereira, Ana R.; Tavares, Andreia C.; Ferreira, Maria T.; Pereira, Pedro M.; Veiga, Helena; Kuru, Erkin; VanNieuwenhze, Michael S.; Brun, Yves V.; Filipe, Sérgio R.; Pinho, Mariana G.

    2015-01-01

    Staphylococcus aureus is an aggressive pathogen and a model organism to study cell division in sequential orthogonal planes in spherical bacteria. However, the small size of staphylococcal cells has impaired analysis of changes in morphology during the cell cycle. Here we use super-resolution microscopy and determine that S. aureus cells are not spherical throughout the cell cycle, but elongate during specific time windows, through peptidoglycan synthesis and remodelling. Both peptidoglycan hydrolysis and turgor pressure are required during division for reshaping the flat division septum into a curved surface. In this process, the septum generates less than one hemisphere of each daughter cell, a trait we show is common to other cocci. Therefore, cell surface scars of previous divisions do not divide the cells in quadrants, generating asymmetry in the daughter cells. Our results introduce a need to reassess the models for division plane selection in cocci. PMID:26278781

  17. Population dynamics of electrogenic microbial communities in microbial fuel cells started with three different inoculum sources.

    PubMed

    Ishii, Shun'ichi; Suzuki, Shino; Yamanaka, Yuko; Wu, Angela; Nealson, Kenneth H; Bretschger, Orianna

    2017-10-01

    Microbial fuel cells (MFCs) are one of the bioelectrochemical systems that exploit microorganisms as biocatalysts to degrade organic matters and recover energy as electric power. Here, we explored how the established electrogenic microbial communities were influenced by three different inoculum sources; anaerobic sludge of the wastewater plant, rice paddy field soil, and coastal lagoon sediment. We periodically characterized both electricity generation with sucrose consumption and 16S rRNA-basis microbial community composition. The electrochemical features of MFCs were slightly different among three inocula, and the lagoon sediment-inoculated MFC showed the highest performance in terms of the treatment time. Meanwhile, although the inoculated microbial communities were highly diverse and quite different, only twelve genera affiliated with δ-Proteobacteria, γ-Proteobacteria, Bacilli, Clostridia/Negativicutes or Bacteroidetes were abundantly enriched in all MFC anode communities. Within them, several fermentative genera were clearly different due to the inocula, while the inocula-specific phylotypes were identified in an electrogenic genus Geobacter. The relative abundances of phylotypes closely-related to Geobacter metallireducens were increased in later stages of all the sucrose-fed MFCs. These results indicate that key microbial members for the functional electrogenic community widely exist in natural ecosystems, but the community members presenting in inoculum sources affected the MFC performances. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Cell cycle regulation of hematopoietic stem or progenitor cells.

    PubMed

    Hao, Sha; Chen, Chen; Cheng, Tao

    2016-05-01

    The highly regulated process of blood production is achieved through the hierarchical organization of hematopoietic stem cell (HSC) subsets and their progenies, which differ in self-renewal and differentiation potential. Genetic studies in mice have demonstrated that cell cycle is tightly controlled by the complex interplay between extrinsic cues and intrinsic regulatory pathways involved in HSC self-renewal and differentiation. Deregulation of these cellular programs may transform HSCs or hematopoietic progenitor cells (HPCs) into disease-initiating stem cells, and can result in hematopoietic malignancies such as leukemia. While previous studies have shown roles for some cell cycle regulators and related signaling pathways in HSCs and HPCs, a more complete picture regarding the molecular mechanisms underlying cell cycle regulation in HSCs or HPCs is lacking. Based on accumulated studies in this field, the present review introduces the basic components of the cell cycle machinery and discusses their major cellular networks that regulate the dormancy and cell cycle progression of HSCs. Knowledge on this topic would help researchers and clinicians to better understand the pathogenesis of relevant blood disorders and to develop new strategies for therapeutic manipulation of HSCs.

  19. Protozoan grazing reduces the current output of microbial fuel cells.

    PubMed

    Holmes, Dawn E; Nevin, Kelly P; Snoeyenbos-West, Oona L; Woodard, Trevor L; Strickland, Justin N; Lovley, Derek R

    2015-10-01

    Several experiments were conducted to determine whether protozoan grazing can reduce current output from sediment microbial fuel cells. When marine sediments were amended with eukaryotic inhibitors, the power output from the fuel cells increased 2-5-fold. Quantitative PCR showed that Geobacteraceae sequences were 120 times more abundant on anodes from treated fuel cells compared to untreated fuel cells, and that Spirotrichea sequences in untreated fuel cells were 200 times more abundant on anode surfaces than in the surrounding sediments. Defined studies with current-producing biofilms of Geobacter sulfurreducens and pure cultures of protozoa demonstrated that protozoa that were effective in consuming G. sulfurreducens reduced current production up to 91% when added to G. sulfurreducens fuel cells. These results suggest that anode biofilms are an attractive food source for protozoa and that protozoan grazing can be an important factor limiting the current output of sediment microbial fuel cells. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. 4D chromatin dynamics in cycling cells

    PubMed Central

    Strickfaden, Hilmar; Zunhammer, Andreas; van Koningsbruggen, Silvana; Köhler, Daniela

    2010-01-01

    This live cell study of chromatin dynamics in four dimensions (space and time) in cycling human cells provides direct evidence for three hypotheses first proposed by Theodor Boveri in seminal studies of fixed blastomeres from Parascaris equorum embryos: (I) Chromosome territory (CT) arrangements are stably maintained during interphase. (II) Chromosome proximity patterns change profoundly during prometaphase. (III) Similar CT proximity patterns in pairs of daughter nuclei reflect symmetrical chromosomal movements during anaphase and telophase, but differ substantially from the arrangement in mother cell nucleus. Hypothesis I could be confirmed for the majority of interphase cells. A minority, however, showed complex, rotational movements of CT assemblies with large-scale changes of CT proximity patterns, while radial nuclear arrangements were maintained. A new model of chromatin dynamics is proposed. It suggests that long-range DNA-DNA interactions in cell nuclei may depend on a combination of rotational CT movements and locally constrained chromatin movements. PMID:21327076

  1. Recognition of Microbial Glycolipids by Natural Killer T Cells

    PubMed Central

    Zajonc, Dirk M.; Girardi, Enrico

    2015-01-01

    T cells can recognize microbial antigens when presented by dedicated antigen-presenting molecules. While peptides are presented by classical members of the major histocompatibility complex (MHC) family (MHC I and II), lipids, glycolipids, and lipopeptides can be presented by the non-classical MHC member, CD1. The best studied subset of lipid-reactive T cells are type I natural killer T (iNKT) cells that recognize a variety of different antigens when presented by the non-classical MHCI homolog CD1d. iNKT cells have been shown to be important for the protection against various microbial pathogens, including B. burgdorferi, the causative agents of Lyme disease, and S. pneumoniae, which causes pneumococcal meningitis and community-acquired pneumonia. Both pathogens carry microbial glycolipids that can trigger the T cell antigen receptor (TCR), leading to iNKT cell activation. iNKT cells have an evolutionary conserved TCR alpha chain, yet retain the ability to recognize structurally diverse glycolipids. They do so using a conserved recognition mode, in which the TCR enforces a conserved binding orientation on CD1d. TCR binding is accompanied by structural changes within the TCR binding site of CD1d, as well as the glycolipid antigen itself. In addition to direct recognition of microbial antigens, iNKT cells can also be activated by a combination of cytokines (IL-12/IL-18) and TCR stimulation. Many microbes carry TLR antigens, and microbial infections can lead to TLR activation. The subsequent cytokine response in turn lower the threshold of TCR-mediated iNKT cell activation, especially when weak microbial or even self-antigens are presented during the cause of the infection. In summary, iNKT cells can be directly activated through TCR triggering of strong antigens, while cytokines produced by the innate immune response may be necessary for TCR triggering and iNKT cell activation in the presence of weak antigens. Here, we will review the molecular basis of iNKT cell

  2. Molecular regulation of the diatom cell cycle.

    PubMed

    Huysman, Marie J J; Vyverman, Wim; De Veylder, Lieven

    2014-06-01

    Accounting for almost one-fifth of the primary production on Earth, the unicellular eukaryotic group of diatoms plays a key ecological and biogeochemical role in our contemporary oceans. Furthermore, as producers of various lipids and pigments, and characterized by their finely ornamented silica cell wall, diatoms hold great promise for different industrial fields, including biofuel production, nanotechnology, and pharmaceutics. However, in spite of their major ecological importance and their high commercial value, little is known about the mechanisms that control the diatom life and cell cycle. To date, both microscopic and genomic analyses have revealed that diatoms exhibit specific and unique mechanisms of cell division compared with those found in the classical model organisms. Here, we review the structural peculiarities of diatom cell proliferation, highlight the regulation of their major cell cycle checkpoints by environmental factors, and discuss recent progress in molecular cell division research. © The Author 2013. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  3. Potential climate change impacts on microbial distribution and carbon cycling in the Australian Southern Ocean

    NASA Astrophysics Data System (ADS)

    Evans, Claire; Thomson, Paul G.; Davidson, Andrew T.; Bowie, Andrew R.; van den Enden, Rick; Witte, Harry; Brussaard, Corina P. D.

    2011-11-01

    increased production by smaller cells, increased significance of the microbial loop and viral lysis. These changes would promote carbon recycling within the photic zone, thereby potentially decreasing the capacity of the future SAZ to absorb CO 2.

  4. A thermodynamic cycle for the solar cell

    NASA Astrophysics Data System (ADS)

    Alicki, Robert; Gelbwaser-Klimovsky, David; Jenkins, Alejandro

    2017-03-01

    A solar cell is a heat engine, but textbook treatments are not wholly satisfactory from a thermodynamic standpoint, since they present solar cells as directly converting the energy of light into electricity, and the current in the circuit as maintained by an electrostatic potential. We propose a thermodynamic cycle in which the gas of electrons in the p phase serves as the working substance. The interface between the p and n phases acts as a self-oscillating piston that modulates the absorption of heat from the photons so that it may perform a net positive work during a complete cycle of its motion, in accordance with the laws of thermodynamics. We draw a simple hydrodynamical analogy between this model and the ;putt-putt; engine of toy boats, in which the interface between the water's liquid and gas phases serves as the piston. We point out some testable consequences of this model.

  5. A metabolic thermodynamic theory of cell cycle

    NASA Astrophysics Data System (ADS)

    Kummer, A.; Ocone, R.

    2003-08-01

    Due to its intrinsic complexity, a complete mathematical description of the cell cycle appears a difficult task. Nevertheless, a preliminary analysis, based on molecular biology, can help in clarifying what are the reliable tools for a quantitative approach. In a previous paper [Physica A 321 (3-4) (2003) 587], the steps to be followed to formulate a metabolic statistical thermodynamics have been established. Here we present a simple mathematical model for the interaction of CyclinB and Cdh1 [The Cell Cycle. An Introduction, Oxford University Press, New York, 1993], with the aim of analysing the properties of the system from a thermodynamic viewpoint. The model is shown to define the Gibbs phase integral of the system and the general Gibbs energy function is obtained. This, together with the analogue of the temperature, defines the working tools indispensable for the formulation of a metabolic statistical thermodynamic-like theory.

  6. Cell cycle regulation in human embryonic stem cells: links to adaptation to cell culture.

    PubMed

    Barta, Tomas; Dolezalova, Dasa; Holubcova, Zuzana; Hampl, Ales

    2013-03-01

    Cell cycle represents not only a tightly orchestrated mechanism of cell replication and cell division but it also plays an important role in regulation of cell fate decision. Particularly in the context of pluripotent stem cells or multipotent progenitor cells, regulation of cell fate decision is of paramount importance. It has been shown that human embryonic stem cells (hESCs) show unique cell cycle characteristics, such as short doubling time due to abbreviated G1 phase; these properties change with the onset of differentiation. This review summarizes the current understanding of cell cycle regulation in hESCs. We discuss cell cycle properties as well as regulatory machinery governing cell cycle progression of undifferentiated hESCs. Additionally, we provide evidence that long-term culture of hESCs is accompanied by changes in cell cycle properties as well as configuration of several cell cycle regulatory molecules.

  7. Gold-FISH: A correlative approach to microscopic imaging of single microbial cells in environmental samples

    NASA Astrophysics Data System (ADS)

    Schmidt, Hannes; Seki, David; Woebken, Dagmar; Eickhorst, Thilo

    2017-04-01

    Fluorescence in situ hybridization (FISH) is routinely used for the phylogenetic identification, detection, and quantification of single microbial cells environmental microbiology. Oligonucleotide probes that match the 16S rRNA sequence of target organisms are generally applied and the resulting signals are visualized via fluorescence microscopy. Consequently, the detection of the microbial cells of interest is limited by the resolution and the sensitivity of light microscopy where objects smaller than 0.2 µm can hardly be represented. Visualizing microbial cells at magnifications beyond light microscopy, however, can provide information on the composition and potential complexity of microbial habitats - the actual sites of nutrient cycling in soil and sediments. We present a recently developed technique that combines (1) the phylogenetic identification and detection of individual microorganisms by epifluorescence microscopy, with (2) the in situ localization of gold-labelled target cells on an ultrastructural level by SEM. Based on 16S rRNA targeted in situ hybridization combined with catalyzed reporter deposition, a streptavidin conjugate labeled with a fluorescent dye and nanogold particles is introduced into whole microbial cells. A two-step visualization process including an autometallographic enhancement of nanogold particles then allows for either fluorescence or electron microscopy, or a correlative application thereof. We will present applications of the Gold-FISH protocol to samples of marine sediments, agricultural soils, and plant roots. The detection and enumeration of bacterial cells in soil and sediment samples was comparable to CARD-FISH applications via fluorescence microscopy. Examples of microbe-surface interaction analysis will be presented on the basis of bacteria colonizing the rhizoplane of rice roots. In principle, Gold-FISH can be performed on any material to give a snapshot of microbe-surface interactions and provides a promising tool for

  8. Targeting cell cycle regulators in hematologic malignancies

    PubMed Central

    Aleem, Eiman; Arceci, Robert J.

    2015-01-01

    Hematologic malignancies represent the fourth most frequently diagnosed cancer in economically developed countries. In hematologic malignancies normal hematopoiesis is interrupted by uncontrolled growth of a genetically altered stem or progenitor cell (HSPC) that maintains its ability of self-renewal. Cyclin-dependent kinases (CDKs) not only regulate the mammalian cell cycle, but also influence other vital cellular processes, such as stem cell renewal, differentiation, transcription, epigenetic regulation, apoptosis, and DNA repair. Chromosomal translocations, amplification, overexpression and altered CDK activities have been described in different types of human cancer, which have made them attractive targets for pharmacological inhibition. Mouse models deficient for one or more CDKs have significantly contributed to our current understanding of the physiological functions of CDKs, as well as their roles in human cancer. The present review focuses on selected cell cycle kinases with recent emerging key functions in hematopoiesis and in hematopoietic malignancies, such as CDK6 and its role in MLL-rearranged leukemia and acute lymphocytic leukemia, CDK1 and its regulator WEE-1 in acute myeloid leukemia (AML), and cyclin C/CDK8/CDK19 complexes in T-cell acute lymphocytic leukemia. The knowledge gained from gene knockout experiments in mice of these kinases is also summarized. An overview of compounds targeting these kinases, which are currently in clinical development in various solid tumors and hematopoietic malignances, is presented. These include the CDK4/CDK6 inhibitors (palbociclib, LEE011, LY2835219), pan-CDK inhibitors that target CDK1 (dinaciclib, flavopiridol, AT7519, TG02, P276-00, terampeprocol and RGB 286638) as well as the WEE-1 kinase inhibitor, MK-1775. The advantage of combination therapy of cell cycle inhibitors with conventional chemotherapeutic agents used in the treatment of AML, such as cytarabine, is discussed. PMID:25914884

  9. Targeting cell cycle regulators in hematologic malignancies.

    PubMed

    Aleem, Eiman; Arceci, Robert J

    2015-01-01

    Hematologic malignancies represent the fourth most frequently diagnosed cancer in economically developed countries. In hematologic malignancies normal hematopoiesis is interrupted by uncontrolled growth of a genetically altered stem or progenitor cell (HSPC) that maintains its ability of self-renewal. Cyclin-dependent kinases (CDKs) not only regulate the mammalian cell cycle, but also influence other vital cellular processes, such as stem cell renewal, differentiation, transcription, epigenetic regulation, apoptosis, and DNA repair. Chromosomal translocations, amplification, overexpression and altered CDK activities have been described in different types of human cancer, which have made them attractive targets for pharmacological inhibition. Mouse models deficient for one or more CDKs have significantly contributed to our current understanding of the physiological functions of CDKs, as well as their roles in human cancer. The present review focuses on selected cell cycle kinases with recent emerging key functions in hematopoiesis and in hematopoietic malignancies, such as CDK6 and its role in MLL-rearranged leukemia and acute lymphocytic leukemia, CDK1 and its regulator WEE-1 in acute myeloid leukemia (AML), and cyclin C/CDK8/CDK19 complexes in T-cell acute lymphocytic leukemia. The knowledge gained from gene knockout experiments in mice of these kinases is also summarized. An overview of compounds targeting these kinases, which are currently in clinical development in various solid tumors and hematopoietic malignances, is presented. These include the CDK4/CDK6 inhibitors (palbociclib, LEE011, LY2835219), pan-CDK inhibitors that target CDK1 (dinaciclib, flavopiridol, AT7519, TG02, P276-00, terampeprocol and RGB 286638) as well as the WEE-1 kinase inhibitor, MK-1775. The advantage of combination therapy of cell cycle inhibitors with conventional chemotherapeutic agents used in the treatment of AML, such as cytarabine, is discussed.

  10. The cell cycle as a brake for β-cell regeneration from embryonic stem cells.

    PubMed

    El-Badawy, Ahmed; El-Badri, Nagwa

    2016-01-13

    The generation of insulin-producing β cells from stem cells in vitro provides a promising source of cells for cell transplantation therapy in diabetes. However, insulin-producing cells generated from human stem cells show deficiency in many functional characteristics compared with pancreatic β cells. Recent reports have shown molecular ties between the cell cycle and the differentiation mechanism of embryonic stem (ES) cells, assuming that cell fate decisions are controlled by the cell cycle machinery. Both β cells and ES cells possess unique cell cycle machinery yet with significant contrasts. In this review, we compare the cell cycle control mechanisms in both ES cells and β cells, and highlight the fundamental differences between pluripotent cells of embryonic origin and differentiated β cells. Through critical analysis of the differences of the cell cycle between these two cell types, we propose that the cell cycle of ES cells may act as a brake for β-cell regeneration. Based on these differences, we discuss the potential of modulating the cell cycle of ES cells for the large-scale generation of functionally mature β cells in vitro. Further understanding of the factors that modulate the ES cell cycle will lead to new approaches to enhance the production of functional mature insulin-producing cells, and yield a reliable system to generate bona fide β cells in vitro.

  11. Plasmonic cell nanocoating: a new concept for rapid microbial screening.

    PubMed

    Xu, Ke; Bui, Minh-Phuong N; Fang, Aiqin; Abbas, Abdennour

    2017-09-13

    Nanocoating of single microbial cells with gold nanostructures can confer optical, electrical, thermal, and mechanical properties to microorganisms, thus enabling new avenues for their control, study, application, and detection. Cell nanocoating is often performed using layer-by-layer (LbL) deposition. LbL is time-consuming and relies on nonspecific electrostatic interactions, which limit potential applications for microbial diagnostics. Here, we show that, by taking advantage of surface molecules densely present in the microbial outer layers, cell nanocoating with gold nanoparticles can be achieved within seconds using surface molecules, including disulfide- bond-containing (Dsbc) proteins and chitin. A simple activation of these markers and their subsequent interaction with gold nanoparticles allow specific microbial screening and quantification of bacteria and fungi within 5 and 30 min, respectively. The use of plasmonics and fluorescence as transduction methods offers a limit of detection below 35 cfu mL(-1) for E. coli bacteria and 1500 cfu mL(-1) for M. circinelloides fungi using a hand-held fluorescent reader. Graphical abstract A new concept for rapid microbial screening by targeting disulfide - bond-containing (Dsbc) proteins and chitin with reducing agents and gold nanoparticles.

  12. Ionizing radiation damage to cells: effects of cell cycle redistribution.

    PubMed

    Chen, P L; Brenner, D J; Sachs, R K

    1995-04-01

    If a population of cycling cells is exposed to a fixed dose of ionizing radiation delivered over time T, it is sometimes observed that increasing T increases the amount of cell killing. This is essentially because at first the radiation preferentially kills cells in a sensitive portion of the cycle and the surviving, more resistant cells then have time to reach more sensitive stages. We refer to this effect as population resensitization, caused by redistribution within the cell cycle. We investigate the effect theoretically by employing the McKendrick-von Foerster equation for age-structured proliferating cell populations, generalized by introducing a radiation damage term. Within our formalism, we show that population resensitization occurs whenever: (a) prior to irradiation the cell population has the stable age-distribution approached asymptotically by an unirradiated population, and (b) T is sufficiently small. Examples and other cases are outlined. The methods of Volterra integral equations, renewal theory, and positive semigroup theory are applied. The effect of varying T is evaluated by considering the ultimate amplitude of the stable age-distribution population at times much greater than both the irradiation duration and the average cell-cycle time. The main biological limitations of the formalism are the following: considering only radiation damage which is not subject to enzymatic repair or quadratic misrepair, using an overly naive method of ensuring loss of cell cycle synchrony, neglecting nonlinear effects such as density inhibition of growth, and neglecting radiatively induced perturbations of the cell cycle. Possible methods for removing these limitations are briefly discussed.

  13. Reprogramming the Cell Cycle for Endoreduplication in Rodent Trophoblast Cells

    PubMed Central

    MacAuley, Alasdair; Cross, James C.; Werb, Zena

    1998-01-01

    Differentiation of trophoblast giant cells in the rodent placenta is accompanied by exit from the mitotic cell cycle and onset of endoreduplication. Commitment to giant cell differentiation is under developmental control, involving down-regulation of Id1 and Id2, concomitant with up-regulation of the basic helix-loop-helix factor Hxt and acquisition of increased adhesiveness. Endoreduplication disrupts the alternation of DNA synthesis and mitosis that maintains euploid DNA content during proliferation. To determine how the mammalian endocycle is regulated, we examined the expression of the cyclins and cyclin-dependent kinases during the transition from replication to endoreduplication in the Rcho-1 rat choriocarcinoma cell line. We cultured these cells under conditions that gave relatively synchronous endoreduplication. This allowed us to study the events that occur during the transition from the mitotic cycle to the first endocycle. With giant cell differentiation, the cells switched cyclin D isoform expression from D3 to D1 and altered several checkpoint functions, acquiring a relative insensitivity to DNA-damaging agents and a coincident serum independence. The initiation of S phase during endocycles appeared to involve cycles of synthesis of cyclins E and A, and termination of S was associated with abrupt loss of cyclin A and E. Both cyclins were absent from gap phase cells, suggesting that their degradation may be necessary to allow reinitiation of the endocycle. The arrest of the mitotic cycle at the onset of endoreduplication was associated with a failure to assemble cyclin B/p34cdk1 complexes during the first endocycle. In subsequent endocycles, cyclin B expression was suppressed. Together these data suggest several points at which cell cycle regulation could be targeted to shift cells from a mitotic to an endoreduplicative cycle. PMID:9529378

  14. Anodic microbial community diversity as a predictor of the power output of microbial fuel cells.

    PubMed

    Stratford, James P; Beecroft, Nelli J; Slade, Robert C T; Grüning, André; Avignone-Rossa, Claudio

    2014-03-01

    The relationship between the diversity of mixed-species microbial consortia and their electrogenic potential in the anodes of microbial fuel cells was examined using different diversity measures as predictors. Identical microbial fuel cells were sampled at multiple time-points. Biofilm and suspension communities were analysed by denaturing gradient gel electrophoresis to calculate the number and relative abundance of species. Shannon and Simpson indices and richness were examined for association with power using bivariate and multiple linear regression, with biofilm DNA as an additional variable. In simple bivariate regressions, the correlation of Shannon diversity of the biofilm and power is stronger (r=0.65, p=0.001) than between power and richness (r=0.39, p=0.076), or between power and the Simpson index (r=0.5, p=0.018). Using Shannon diversity and biofilm DNA as predictors of power, a regression model can be constructed (r=0.73, p<0.001). Ecological parameters such as the Shannon index are predictive of the electrogenic potential of microbial communities.

  15. Production Strategies and Applications of Microbial Single Cell Oils

    PubMed Central

    Ochsenreither, Katrin; Glück, Claudia; Stressler, Timo; Fischer, Lutz; Syldatk, Christoph

    2016-01-01

    Polyunsaturated fatty acids (PUFAs) of the ω-3 and ω-6 class (e.g., α-linolenic acid, linoleic acid) are essential for maintaining biofunctions in mammalians like humans. Due to the fact that humans cannot synthesize these essential fatty acids, they must be taken up from different food sources. Classical sources for these fatty acids are porcine liver and fish oil. However, microbial lipids or single cell oils, produced by oleaginous microorganisms such as algae, fungi and bacteria, are a promising source as well. These single cell oils can be used for many valuable chemicals with applications not only for nutrition but also for fuels and are therefore an ideal basis for a bio-based economy. A crucial point for the establishment of microbial lipids utilization is the cost-effective production and purification of fuels or products of higher value. The fermentative production can be realized by submerged (SmF) or solid state fermentation (SSF). The yield and the composition of the obtained microbial lipids depend on the type of fermentation and the particular conditions (e.g., medium, pH-value, temperature, aeration, nitrogen source). From an economical point of view, waste or by-product streams can be used as cheap and renewable carbon and nitrogen sources. In general, downstream processing costs are one of the major obstacles to be solved for full economic efficiency of microbial lipids. For the extraction of lipids from microbial biomass cell disruption is most important, because efficiency of cell disruption directly influences subsequent downstream operations and overall extraction efficiencies. A multitude of cell disruption and lipid extraction methods are available, conventional as well as newly emerging methods, which will be described and discussed in terms of large scale applicability, their potential in a modern biorefinery and their influence on product quality. Furthermore, an overview is given about applications of microbial lipids or derived fatty

  16. Production Strategies and Applications of Microbial Single Cell Oils.

    PubMed

    Ochsenreither, Katrin; Glück, Claudia; Stressler, Timo; Fischer, Lutz; Syldatk, Christoph

    2016-01-01

    Polyunsaturated fatty acids (PUFAs) of the ω-3 and ω-6 class (e.g., α-linolenic acid, linoleic acid) are essential for maintaining biofunctions in mammalians like humans. Due to the fact that humans cannot synthesize these essential fatty acids, they must be taken up from different food sources. Classical sources for these fatty acids are porcine liver and fish oil. However, microbial lipids or single cell oils, produced by oleaginous microorganisms such as algae, fungi and bacteria, are a promising source as well. These single cell oils can be used for many valuable chemicals with applications not only for nutrition but also for fuels and are therefore an ideal basis for a bio-based economy. A crucial point for the establishment of microbial lipids utilization is the cost-effective production and purification of fuels or products of higher value. The fermentative production can be realized by submerged (SmF) or solid state fermentation (SSF). The yield and the composition of the obtained microbial lipids depend on the type of fermentation and the particular conditions (e.g., medium, pH-value, temperature, aeration, nitrogen source). From an economical point of view, waste or by-product streams can be used as cheap and renewable carbon and nitrogen sources. In general, downstream processing costs are one of the major obstacles to be solved for full economic efficiency of microbial lipids. For the extraction of lipids from microbial biomass cell disruption is most important, because efficiency of cell disruption directly influences subsequent downstream operations and overall extraction efficiencies. A multitude of cell disruption and lipid extraction methods are available, conventional as well as newly emerging methods, which will be described and discussed in terms of large scale applicability, their potential in a modern biorefinery and their influence on product quality. Furthermore, an overview is given about applications of microbial lipids or derived fatty

  17. Spatial colonization of microbial cells on the rhizoplane.

    NASA Astrophysics Data System (ADS)

    Raynaud, Xavier; Eickhorst, Thilo; Nunan, Naoise; Kaiser, Christina; Woebken, Dagmar; Schmidt, Hannes

    2017-04-01

    The rhizoplane is the region where the root surface is in contact with soil and corresponds to the inner limit of the rhizosphere. At the rhizoplane level, plants exchange elements with the surrounding soil and the rhizoplane can therefore be considered as the region that drives nutrient movement and transformation in the rhizosphere. The rhizoplane differs in many respects from the bulk soil due to the far larger supply of substrates derived from the roots, with far greater microbial cell densities and reduced levels of diversity (Philippot et al., 2013). This is likely to result in completely different interaction profiles among microorganisms which may affect rhizosphere biogeochemistry. While the diversity of microorganisms associated with the rhizosphere and on the rhizoplane is getting increasing attention, knowledge on the spatial organisation of this diversity is still scarce. We therefore aimed at investigating the spatial arrangement of microbial rhizoplane colonization to increase our understanding of potential interaction dynamics within soil-microbe-plant interfaces. To study the spatial distribution of microbial cells on roots we cultivated rice plants in water-logged paddy soil. Root samples were taken three months after germination. After removing adhering rhizosphere soil the root samples were chemically fixed and prepared for CARD-FISH (Schmidt & Eickhorst, 2014). For hybridization, the oligonucleotide probes EUB I-III (Daims et al., 1999) were applied to cover the majority of bacteria colonizing the rhizoplane. Root segments were then subjected to confocal laser scanning microscopy where triplicate image stacks of 10 µm thickness (0.5 µm layer distance) were acquired per region of interest (ROI). ROIs were defined as distances from the root tip (0, 5, 10, 15 mm) and corresponded to the root tip, elongation zone, and zone of maturation. Image stacks were processed using ImageJ software to extract microbial cells spatial coordinates, as well as

  18. Enhanced product formation in continuous fermentations with microbial cell recycle

    SciTech Connect

    Bull, D.N.; Young, M.D.

    1981-02-01

    The effect of partial recycle of microbial cells on the operation of a chemostat has been investigated for two fermentations. Stable steady states with and without partial cell recycle were obtained for the conversion of d-sorbitol to L-sorbose by Gluconobacter oxydans subsp. suboxydans 1916B and for the conversion of glucose to 2-ketogluconic acid by Serratia marcescens NRRl B-486. The employment of partial cell recycle dramatically increased product formation rates for both fermentations.

  19. Recent advances in microbial single cell genomics technology and applications

    NASA Astrophysics Data System (ADS)

    Stepanauskas, R.

    2015-12-01

    Single cell genomics is increasingly utilized as a powerful tool to decipher the metabolic potential, evolutionary histories and in situ interactions of environmental microorganisms. I will present several new developments of this exciting technology, which improve genomic data recovery from individual cells and allow its integration with cell's phenotypic properties. I will also demonstrate how these new technical capabilities help understanding the biology of the "microbial dark matter" inhabiting marine and terrestrial subsurface environments.

  20. Microbial anaerobic methane cycling in the subseafloor at the Von Damm hydrothermal vent field, Mid-Cayman Rise

    NASA Astrophysics Data System (ADS)

    Huber, J. A.; Reveillaud, J. C.; Stepanauskas, R.; McDermott, J. M.; Sylva, S. P.; Seewald, J.

    2013-12-01

    The Mid-Cayman Rise (MCR) is Earth's deepest and slowest spreading mid-ocean ridge located in the western Caribbean. With an axial rift valley floor at a depth of ~4200-6500 m, it represents one of the deepest sections of ridge crest worldwide. In 2009, the world's deepest hydrothermal vents (Piccard at 4960 m) and an ultramafic-influenced system only 20 km away on top of an oceanic core complex (Von Damm at 2350 m) were discovered along the MCR. Each site is hosted in a distinct geologic setting with different thermal and chemical regimes. The Von Damm site is a particularly interesting location to examine chemolithoautotrophic subseafloor microbial communities due to the abundant hydrogen, methane, and organic compounds in the venting fluids. Here, we used a combination of stable isotope tracing, next-generation sequencing, and single cell techniques to determine the identity, activity, and genomic repertoire of subseafloor anaerobic archaea involved in methane cycling in hydrothermal fluids venting at the Von Damm site. Molecular sequencing of phylogenetic marker genes revealed the presence of diverse archaea that both generate and consume methane across a geochemical and thermal spectrum of vents. Stable isotope tracing experiments were used to detect biological utilization of formate and dissolved inorganic carbon, and methane generation at 70 °C under anaerobic conditions. Results indicate that methanogenesis with formate as a substrate is occurring at 70 °C at two Von Damm sites, Ginger Castle and the Main Orifice. The results are consistent with thermodynamic predictions for carbon speciation at the temperatures encountered at the ultramafic-hosted Von Damm, where formate is predicted to be thermodynamically stable, and may thus serve as a an important source of carbon. Diverse thermophilic methanogenic archaea belonging to the genera Methanothermococcus were detected at all vent sites with both 16S rRNA tag sequencing and single cell sorting. Other

  1. Cell cycle regulation of Golgi membrane dynamics

    PubMed Central

    Tang, Danming; Wang, Yanzhuang

    2013-01-01

    The Golgi apparatus is a membranous organelle in the cell that plays essential roles in protein and lipid trafficking, sorting, processing and modification. Its basic structure is a stack of closely aligned flattened cisternae. In mammalian cells, dozens of Golgi stacks are often laterally linked into a ribbon-like structure. Biogenesis of the Golgi during cell division occurs through a sophisticated disassembly and reassembly process that can be divided into three distinct but cooperative steps, including the deformation and reformation of the Golgi cisternae, stacks and ribbon. Here, we review our current understanding of the protein machineries that control these three steps in the cycle of mammalian cell division: GRASP65 and GRASP55 in Golgi stack and ribbon formation; ubiquitin and AAA ATPases in post-mitotic Golgi membrane fusion; and golgins and cytoskeleton in Golgi ribbon formation. PMID:23453991

  2. Fuel cell and advanced turbine power cycle

    SciTech Connect

    White, D.J.

    1996-12-31

    Solar has a vested interest in integration of gas turbines and high temperature fuels (particularly solid oxide fuel cells[SOFC]); this would be a backup for achieving efficiencies on the order of 60% with low exhaust emissions. Preferred cycle is with the fuel cell as a topping system to the gas turbine; bottoming arrangements (fuel cells using the gas turbine exhaust as air supply) would likely be both larger and less efficient unless complex steam bottoming systems are added. The combined SOFC and gas turbine will have an advantage because it will have lower NOx emissions than any heat engine system. Market niche for initial product entry will be the dispersed or distributed power market in nonattainment areas. First entry will be of 1-2 MW units between the years 2000 and 2004. Development requirements are outlined for both the fuel cell and the gas turbine.

  3. Segregation of the Anodic Microbial Communities in a Microbial Fuel Cell Cascade.

    PubMed

    Hodgson, Douglas M; Smith, Ann; Dahale, Sonal; Stratford, James P; Li, Jia V; Grüning, André; Bushell, Michael E; Marchesi, Julian R; Avignone Rossa, C

    2016-01-01

    Metabolic interactions within microbial communities are essential for the efficient degradation of complex organic compounds, and underpin natural phenomena driven by microorganisms, such as the recycling of carbon-, nitrogen-, and sulfur-containing molecules. These metabolic interactions ultimately determine the function, activity and stability of the community, and therefore their understanding would be essential to steer processes where microbial communities are involved. This is exploited in the design of microbial fuel cells (MFCs), bioelectrochemical devices that convert the chemical energy present in substrates into electrical energy through the metabolic activity of microorganisms, either single species or communities. In this work, we analyzed the evolution of the microbial community structure in a cascade of MFCs inoculated with an anaerobic microbial community and continuously fed with a complex medium. The analysis of the composition of the anodic communities revealed the establishment of different communities in the anodes of the hydraulically connected MFCs, with a decrease in the abundance of fermentative taxa and a concurrent increase in respiratory taxa along the cascade. The analysis of the metabolites in the anodic suspension showed a metabolic shift between the first and last MFC, confirming the segregation of the anodic communities. Those results suggest a metabolic interaction mechanism between the predominant fermentative bacteria at the first stages of the cascade and the anaerobic respiratory electrogenic population in the latter stages, which is reflected in the observed increase in power output. We show that our experimental system represents an ideal platform for optimization of processes where the degradation of complex substrates is involved, as well as a potential tool for the study of metabolic interactions in complex microbial communities.

  4. Segregation of the Anodic Microbial Communities in a Microbial Fuel Cell Cascade

    PubMed Central

    Hodgson, Douglas M.; Smith, Ann; Dahale, Sonal; Stratford, James P.; Li, Jia V.; Grüning, André; Bushell, Michael E.; Marchesi, Julian R.; Avignone Rossa, C.

    2016-01-01

    Metabolic interactions within microbial communities are essential for the efficient degradation of complex organic compounds, and underpin natural phenomena driven by microorganisms, such as the recycling of carbon-, nitrogen-, and sulfur-containing molecules. These metabolic interactions ultimately determine the function, activity and stability of the community, and therefore their understanding would be essential to steer processes where microbial communities are involved. This is exploited in the design of microbial fuel cells (MFCs), bioelectrochemical devices that convert the chemical energy present in substrates into electrical energy through the metabolic activity of microorganisms, either single species or communities. In this work, we analyzed the evolution of the microbial community structure in a cascade of MFCs inoculated with an anaerobic microbial community and continuously fed with a complex medium. The analysis of the composition of the anodic communities revealed the establishment of different communities in the anodes of the hydraulically connected MFCs, with a decrease in the abundance of fermentative taxa and a concurrent increase in respiratory taxa along the cascade. The analysis of the metabolites in the anodic suspension showed a metabolic shift between the first and last MFC, confirming the segregation of the anodic communities. Those results suggest a metabolic interaction mechanism between the predominant fermentative bacteria at the first stages of the cascade and the anaerobic respiratory electrogenic population in the latter stages, which is reflected in the observed increase in power output. We show that our experimental system represents an ideal platform for optimization of processes where the degradation of complex substrates is involved, as well as a potential tool for the study of metabolic interactions in complex microbial communities. PMID:27242723

  5. [Detection of toxic substances in microbial fuel cells].

    PubMed

    Wang, Jiefu; Niu, Hao; Wu, Wenguo

    2017-05-25

    Microbial fuel cells (MFCs) is a highly promising bioelectrochemical technology and uses microorganisms as catalyst to convert chemical energy directly to electrical energy. Microorganisms in the anodic chamber of MFC oxidize the substrate and generate electrons. The electrons are absorbed by the anode and transported through an external circuit to the cathode for corresponding reduction. The flow of electrons is measured as current. This current is a linear measure of the activity of microorganisms. If a toxic event occurs, microbial activity will change, most likely decrease. Hence, fewer electrons are transported and current decreases as well. In this way, a microbial fuel cell-based biosensor provides a direct measure to detect toxicity for samples. This paper introduces the detection of antibiotics, heavy metals, organic pollutants and acid in MFCs. The existing problems and future application of MFCs are also analyzed.

  6. Microbial and Isotopic Evidence for Methane Cycling in Hydrocarbon-Containing Groundwater from the Pennsylvania Region

    PubMed Central

    Vigneron, Adrien; Bishop, Andrew; Alsop, Eric B.; Hull, Kellie; Rhodes, Ileana; Hendricks, Robert; Head, Ian M.; Tsesmetzis, Nicolas

    2017-01-01

    The Pennsylvania region hosts numerous oil and gas reservoirs and the presence of hydrocarbons in groundwater has been locally observed. However, these methane-containing freshwater ecosystems remain poorly explored despite their potential importance in the carbon cycle. Methane isotope analysis and analysis of low molecular weight hydrocarbon gases from 18 water wells indicated that active methane cycling may be occurring in methane-containing groundwater from the Pennsylvania region. Consistent with this observation, multigenic qPCR and gene sequencing (16S rRNA genes, mcrA, and pmoA genes) indicated abundant populations of methanogens, ANME-2d (average of 1.54 × 104 mcrA gene per milliliter of water) and bacteria associated with methane oxidation (NC10, aerobic methanotrophs, methylotrophs; average of 2.52 × 103 pmoA gene per milliliter of water). Methane cycling therefore likely represents an important process in these hydrocarbon-containing aquifers. The microbial taxa and functional genes identified and geochemical data suggested that (i) methane present is at least in part due to methanogens identified in situ; (ii) Potential for aerobic and anaerobic methane oxidation is important in groundwater with the presence of lineages associated with both anaerobic an aerobic methanotrophy; (iii) the dominant methane oxidation process (aerobic or anaerobic) can vary according to prevailing conditions (oxic or anoxic) in the aquifers; (iv) the methane cycle is closely associated with the nitrogen cycle in groundwater methane seeps with methane and/or methanol oxidation coupled to denitrification or nitrate and nitrite reduction. PMID:28424678

  7. A mechanistic soil biogeochemistry model with explicit representation of microbial and macrofaunal activities and nutrient cycles

    NASA Astrophysics Data System (ADS)

    Fatichi, Simone; Manzoni, Stefano; Or, Dani; Paschalis, Athanasios

    2016-04-01

    The potential of a given ecosystem to store and release carbon is inherently linked to soil biogeochemical processes. These processes are deeply connected to the water, energy, and vegetation dynamics above and belowground. Recently, it has been advocated that a mechanistic representation of soil biogeochemistry require: (i) partitioning of soil organic carbon (SOC) pools according to their functional role; (ii) an explicit representation of microbial dynamics; (iii) coupling of carbon and nutrient cycles. While some of these components have been introduced in specialized models, they have been rarely implemented in terrestrial biosphere models and tested in real cases. In this study, we combine a new soil biogeochemistry model with an existing model of land-surface hydrology and vegetation dynamics (T&C). Specifically the soil biogeochemistry component explicitly separates different litter pools and distinguishes SOC in particulate, dissolved and mineral associated fractions. Extracellular enzymes and microbial pools are explicitly represented differentiating the functional roles of bacteria, saprotrophic and mycorrhizal fungi. Microbial activity depends on temperature, soil moisture and litter or SOC stoichiometry. The activity of macrofauna is also modeled. Nutrient dynamics include the cycles of nitrogen, phosphorous and potassium. The model accounts for feedbacks between nutrient limitations and plant growth as well as for plant stoichiometric flexibility. In turn, litter input is a function of the simulated vegetation dynamics. Root exudation and export to mycorrhiza are computed based on a nutrient uptake cost function. The combined model is tested to reproduce respiration dynamics and nitrogen cycle in few sites where data were available to test plausibility of results across a range of different metrics. For instance in a Swiss grassland ecosystem, fine root, bacteria, fungal and macrofaunal respiration account for 40%, 23%, 33% and 4% of total belowground

  8. Mir-33 regulates cell proliferation and cell cycle progression

    PubMed Central

    Allen, Ryan M; Salerno, Alessandro G; Ramírez, Cristina M; Chamorro-Jorganes, Aránzazu; Wanschel, Amarylis C; Lasunción, Miguel A; Morales-Ruiz, Manuel; Suárez, Yajaira; Baldán, Ángel; Esplugues, Enric

    2012-01-01

    Cholesterol metabolism is tightly regulated at the cellular level and is essential for cellular growth. MicroRNAs (miRNAs), a class of noncoding RNAs, have emerged as critical regulators of gene expression, acting predominantly at the posttranscriptional level. Recent work from our group and others has shown that hsa-miR-33a and hsa-miR-33b, miRNAs located within intronic sequences of the Srebp genes, regulate cholesterol and fatty acid metabolism in concert with their host genes. Here, we show that hsa-miR-33 family members modulate the expression of genes involved in cell cycle regulation and cell proliferation. MiR-33 inhibits the expression of the cyclin-dependent kinase 6 (CDK6) and cyclin D1 (CCND1), thereby reducing cell proliferation and cell cycle progression. Overexpression of miR-33 induces a significant G1 cell cycle arrest in Huh7 and A549 cell lines. Most importantly, inhibition of miR-33 expression using 2′fluoro/methoxyethyl-modified (2′F/MOE-modified) phosphorothioate backbone antisense oligonucleotides improves liver regeneration after partial hepatectomy (PH) in mice, suggesting an important role for miR-33 in regulating hepatocyte proliferation during liver regeneration. Altogether, these results suggest that Srebp/miR-33 locus may cooperate to regulate cell proliferation and cell cycle progression and may also be relevant to human liver regeneration. PMID:22333591

  9. Mir-33 regulates cell proliferation and cell cycle progression.

    PubMed

    Cirera-Salinas, Daniel; Pauta, Montse; Allen, Ryan M; Salerno, Alessandro G; Ramírez, Cristina M; Chamorro-Jorganes, Aranzazu; Wanschel, Amarylis C; Lasuncion, Miguel A; Morales-Ruiz, Manuel; Suarez, Yajaira; Baldan, Ángel; Esplugues, Enric; Fernández-Hernando, Carlos

    2012-03-01

    Cholesterol metabolism is tightly regulated at the cellular level and is essential for cellular growth. microRNAs (miRNAs), a class of noncoding RNAs, have emerged as critical regulators of gene expression, acting predominantly at posttranscriptional level. Recent work from our group and others has shown that hsa-miR-33a and hsa-miR-33b, miRNAs located within intronic sequences of the Srebp genes, regulate cholesterol and fatty acid metabolism in concert with their host genes. Here, we show that hsa-miR-33 family members modulate the expression of genes involved in cell cycle regulation and cell proliferation. MiR-33 inhibits the expression of the cyclin-dependent kinase 6 (CDK6) and cyclin D1 (CCND1), thereby reducing cell proliferation and cell cycle progression. Overexpression of miR-33 induces a significant G 1 cell cycle arrest in Huh7 and A549 cell lines. Most importantly, inhibition of miR-33 expression using 2'fluoro/methoxyethyl-modified (2'F/MOE-modified) phosphorothioate backbone antisense oligonucleotides improves liver regeneration after partial hepatectomy (PH) in mice, suggesting an important role for miR-33 in regulating hepatocyte proliferation during liver regeneration. Altogether, these results suggest that Srebp/miR-33 locus may cooperate to regulate cell proliferation, cell cycle progression and may also be relevant to human liver regeneration.

  10. The Candida albicans transcription factor Cas5 couples stress responses, drug resistance and cell cycle regulation.

    PubMed

    Xie, Jinglin L; Qin, Longguang; Miao, Zhengqiang; Grys, Ben T; Diaz, Jacinto De La Cruz; Ting, Kenneth; Krieger, Jonathan R; Tong, Jiefei; Tan, Kaeling; Leach, Michelle D; Ketela, Troy; Moran, Michael F; Krysan, Damian J; Boone, Charles; Andrews, Brenda J; Selmecki, Anna; Ho Wong, Koon; Robbins, Nicole; Cowen, Leah E

    2017-09-11

    The capacity to coordinate environmental sensing with initiation of cellular responses underpins microbial survival and is crucial for virulence and stress responses in microbial pathogens. Here we define circuitry that enables the fungal pathogen Candida albicans to couple cell cycle dynamics with responses to cell wall stress induced by echinocandins, a front-line class of antifungal drugs. We discover that the C. albicans transcription factor Cas5 is crucial for proper cell cycle dynamics and responses to echinocandins, which inhibit β-1,3-glucan synthesis. Cas5 has distinct transcriptional targets under basal and stress conditions, is activated by the phosphatase Glc7, and can regulate the expression of target genes in concert with the transcriptional regulators Swi4 and Swi6. Thus, we illuminate a mechanism of transcriptional control that couples cell wall integrity with cell cycle regulation, and uncover circuitry governing antifungal drug resistance.Cas5 is a transcriptional regulator of responses to cell wall stress in the fungal pathogen Candida albicans. Here, Xie et al. show that Cas5 also modulates cell cycle dynamics and responses to antifungal drugs.

  11. Abundances and potential activities of nitrogen cycling microbial communities along a chronosequence of a glacier forefield

    PubMed Central

    Brankatschk, Robert; Töwe, Stefanie; Kleineidam, Kristina; Schloter, Michael; Zeyer, Josef

    2011-01-01

    Glacier forefields are ideal ecosystems to study the development of nutrient cycles as well as single turnover processes during soil development. In this study, we examined the ecology of the microbial nitrogen (N) cycle in bulk soil samples from a chronosequence of the Damma glacier, Switzerland. Major processes of the N cycle were reconstructed on the genetic as well as the potential enzyme activity level at sites of the chronosequence that have been ice-free for 10, 50, 70, 120 and 2000 years. In our study, we focused on N fixation, mineralization (chitinolysis and proteolysis), nitrification and denitrification. Our results suggest that mineralization, mainly the decomposition of deposited organic material, was the main driver for N turnover in initial soils, that is, ice-free for 10 years. Transient soils being ice-free for 50 and 70 years were characterized by a high abundance of N fixing microorganisms. In developed soils, ice-free for 120 and 2000 years, significant rates of nitrification and denitrification were measured. Surprisingly, copy numbers of the respective functional genes encoding the corresponding enzymes were already high in the initial phase of soil development. This clearly indicates that the genetic potential is not the driver for certain functional traits in the initial phase of soil formation but rather a well-balanced expression of the respective genes coding for selected functions. PMID:21124490

  12. Abundances and potential activities of nitrogen cycling microbial communities along a chronosequence of a glacier forefield.

    PubMed

    Brankatschk, Robert; Töwe, Stefanie; Kleineidam, Kristina; Schloter, Michael; Zeyer, Josef

    2011-06-01

    Glacier forefields are ideal ecosystems to study the development of nutrient cycles as well as single turnover processes during soil development. In this study, we examined the ecology of the microbial nitrogen (N) cycle in bulk soil samples from a chronosequence of the Damma glacier, Switzerland. Major processes of the N cycle were reconstructed on the genetic as well as the potential enzyme activity level at sites of the chronosequence that have been ice-free for 10, 50, 70, 120 and 2000 years. In our study, we focused on N fixation, mineralization (chitinolysis and proteolysis), nitrification and denitrification. Our results suggest that mineralization, mainly the decomposition of deposited organic material, was the main driver for N turnover in initial soils, that is, ice-free for 10 years. Transient soils being ice-free for 50 and 70 years were characterized by a high abundance of N fixing microorganisms. In developed soils, ice-free for 120 and 2000 years, significant rates of nitrification and denitrification were measured. Surprisingly, copy numbers of the respective functional genes encoding the corresponding enzymes were already high in the initial phase of soil development. This clearly indicates that the genetic potential is not the driver for certain functional traits in the initial phase of soil formation but rather a well-balanced expression of the respective genes coding for selected functions.

  13. Magnetic studies of ferrofluid-modified microbial cells.

    PubMed

    Mosiniewicz-Szablewska, Ewa; Safarikova, Mirka; Safarik, Ivo

    2010-04-01

    Microbial cells (Kluyveromyces fragilis and Chlorella vulgaris) efficiently interacted with maghemite nanoparticles stabilized as low-pH ionic magnetic fluid, leading to the formation of magnetically labeled cells. This simple procedure allows to use the prepared materials as new cheap and easy to get magnetic affinity adsorbents to the removal of water-soluble dyes from polluted water sources using magnetic separation techniques. Magnetically modified cells were investigated by means of electron spin resonance spectroscopy and conventional magnetic methods over the temperature range 4-300 K. The magnetic behavior of these materials was dominated by the superparamagnetic relaxation of isolated single domain maghemite particles although a little amount of agglomerates was also present on the cell surface. However, these agglomerates were sufficiently small to show at static conditions the superparamagnetic behavior at room temperature. Therefore, the ferrofluid-modified microbial cells represent new interesting magnetic affinity adsorbents which could be applied for large-scale magnetic separation processes.

  14. Proliferation and cell cycle dynamics in the developing stellate ganglion.

    PubMed

    Gonsalvez, David G; Cane, Kylie N; Landman, Kerry A; Enomoto, Hideki; Young, Heather M; Anderson, Colin R

    2013-04-03

    Cell proliferation during nervous system development is poorly understood outside the mouse neocortex. We measured cell cycle dynamics in the embryonic mouse sympathetic stellate ganglion, where neuroblasts continue to proliferate following neuronal differentiation. At embryonic day (E) 9.5, when neural crest-derived cells were migrating and coalescing into the ganglion primordium, all cells were cycling, cell cycle length was only 10.6 h, and S-phase comprised over 65% of the cell cycle; these values are similar to those previously reported for embryonic stem cells. At E10.5, Sox10(+) cells lengthened their cell cycle to 38 h and reduced the length of S-phase. As cells started to express the neuronal markers Tuj1 and tyrosine hydroxylase (TH) at E10.5, they exited the cell cycle. At E11.5, when >80% of cells in the ganglion were Tuj1(+)/TH(+) neuroblasts, all cells were again cycling. Neuroblast cell cycle length did not change significantly after E11.5, and 98% of Sox10(-)/TH(+) cells had exited the cell cycle by E18.5. The cell cycle length of Sox10(+)/TH(-) cells increased during late embryonic development, and ∼25% were still cycling at E18.5. Loss of Ret increased neuroblast cell cycle length at E16.5 and decreased the number of neuroblasts at E18.5. A mathematical model generated from our data successfully predicted the relative change in proportions of neuroblasts and non-neuroblasts in wild-type mice. Our results show that, like other neurons, sympathetic neuron differentiation is associated with exit from the cell cycle; sympathetic neurons are unusual in that they then re-enter the cell cycle before later permanently exiting.

  15. Carbon and sulfur cycling by microbial communities in a gypsum-treated oil sands tailings pond.

    PubMed

    Ramos-Padrón, Esther; Bordenave, Sylvain; Lin, Shiping; Bhaskar, Iyswarya Mani; Dong, Xiaoli; Sensen, Christoph W; Fournier, Joseph; Voordouw, Gerrit; Gieg, Lisa M

    2011-01-15

    Oil sands tailings ponds receive and store the solid and liquid waste from bitumen extraction and are managed to promote solids densification and water recycling. The ponds are highly stratified due to increasing solids content as a function of depth but can be impacted by tailings addition and removal and by convection due to microbial gas production. We characterized the microbial communities in relation to microbial activities as a function of depth in an active tailings pond routinely treated with gypsum (CaSO(4)·2H(2)O) to accelerate densification. Pyrosequencing of 16S rDNA gene sequences indicated that the aerobic surface layer, where the highest level of sulfate (6 mM) but no sulfide was detected, had a very different community profile than the rest of the pond. Deeper anaerobic layers were dominated by syntrophs (Pelotomaculum, Syntrophus, and Smithella spp.), sulfate- and sulfur-reducing bacteria (SRB, Desulfocapsa and Desulfurivibrio spp.), acetate- and H(2)-using methanogens, and a variety of other anaerobes that have been implicated in hydrocarbon utilization or iron and sulfur cycling. The SRB were most abundant from 10 to 14 mbs, bracketing the zone where the sulfate reduction rate was highest. Similarly, the most abundant methanogens and syntrophs identified as a function of depth closely mirrored the fluctuating methanogenesis rates. Methanogenesis was inhibited in laboratory incubations by nearly 50% when sulfate was supplied at pond-level concentrations suggesting that in situ sulfate reduction can substantially minimize methane emissions. Based on our data, we hypothesize that the emission of sulfide due to SRB activity in the gypsum treated pond is also limited due to its high solubility and oxidation in surface waters.

  16. Microbial cycling, oxidative weathering, and the triple oxygen isotope consequences for marine sulfate

    NASA Astrophysics Data System (ADS)

    Johnston, D. T.; Cowie, B.; Turchyn, A. V.; Antler, G.; Gill, B. C.; Berelson, W.

    2015-12-01

    Microorganisms are responsible for most geochemical sulfur cycling in the ocean. On both modern and geological time scales, stable isotope ratios often serve as a mechanism to track conspicuous or coupled microbial processes, which in turn inform burial fluxes. The most common example of this approach is the use of sulfur isotopes in sulfate and sulfide (both aqueous and in mineral form) to track everything from rates of microbial processes through to the presence/absence of certain metabolic processes in a given environment. The use of oxygen isotope ratios in sulfate has developed in a similar fashion, providing complementary information to that of sulfur isotopes. Through our current work, we will extend the application of oxygen isotopes to include the trace stable oxygen isotope, 17O. These data are facilitated by a new laser F2 fluorination technique running at Harvard, and accompanied by the calibration of a suite of common sulfate standards. At first blush, 16O - 17O - 18O systematics should carry mass-dependent microbial fractionations with process-specific mass laws that are resolvable at the level of our analytical precision. We look to calibrate these biogeochemical effects through the integrated picture captured in marine pore water sulfate profiles, where the 18O/16O is known to evolve. In compliment, riverine sulfate (the sulfate input to the ocean) is an oxidative weathering product and is posited to carry a memory effect of tropospheric O2. Interestingly, the 17O/16O of that O2 carries a mass-independent signal reflecting the balance between stratospheric reactions and Earth surface biospheric fluxes. Through this presentation, we look to calibrate the controls on the balance between biospheric and atmospheric contributions to the marine sulfate reservoir. This is enabled by a series of isotope mass-balance models and with the ultimate goal of developing the geological triple oxygen isotope records of sulfate as a new environmental proxy for paleo

  17. Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones

    PubMed Central

    Glass, Jennifer B.; Kretz, Cecilia B.; Ganesh, Sangita; Ranjan, Piyush; Seston, Sherry L.; Buck, Kristen N.; Landing, William M.; Morton, Peter L.; Moffett, James W.; Giovannoni, Stephen J.; Vergin, Kevin L.; Stewart, Frank J.

    2015-01-01

    Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO3−, NO2−, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu. PMID:26441925

  18. Cell cycle of globose basal cells in rat olfactory epithelium.

    PubMed

    Huard, J M; Schwob, J E

    1995-05-01

    The olfactory epithelium of adult mammals has the unique property of generating olfactory sensory neurons throughout life. Cells of the basal compartment, which include horizontal and globose basal cells, are responsible for the ongoing process of neurogenesis in this system. We report here that the globose basal cells in olfactory epithelium of rats, as in mice, are the predominant type of proliferating cell, and account for 97.6% of the actively dividing cells in the basal compartment of the normal epithelium. Globose basal cells have not been fully characterized in terms of their proliferative properties, and the dynamic aspects of neurogenesis are not well understood. As a consequence, it is uncertain whether cell kinetic properties are under any regulation that could affect the rate of neurogenesis. To address this gap in our knowledge, we have determined the duration of both the synthesis phase (S-phase) and the full cell cycle of globose basal cells in adult rats. The duration of the S-phase was found to be 9 hr in experiments utilizing sequential injections of either IdU followed by BrdU or 3H-thy followed by BrdU. The duration of the cell cycle was determined by varying the time interval between the injections of 3H-thy and BrdU and tracking the set of cells that exit S shortly after the first injection. With this paradigm, the interval required for these cells to traverse G2, M, G1, and a second S-phase, is equivalent to the duration of one mitotic cycle and equals 17 hr. These observations serve as the foundation to assess whether the cell cycle duration is subject to regulation in response to experimental injury, and whether such regulation is partly responsible for changes in the rate of neurogenesis in such settings.

  19. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

    NASA Astrophysics Data System (ADS)

    Maslov, Sergei; Sneppen, Kim

    2017-01-01

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity.

  20. [Sulfate reduction and microbial processes of the methane cycle in the sediments of the Sevastopol bay].

    PubMed

    Pimenov, N V; Egorov, V N; Kanapatskiĭ, T A; Malakhova, T V; Artemov, Iu G; Sigalevich, P A; Malakhova, L V

    2013-01-01

    The rates of microbial processes of sulfate reduction and of the methane cycle were measured in the bottom sediments of the Sevastopol basin, where seeps of gaseous methane have been previously found. Typically for marine environments, sulfate reduction played the major role in the terminal phase of decomposition of organic matter (OM) in reduced sediments of this area. The rate of this process depended on the amount of available OM. The rate of methanogenesis in the sediments increased with depth, peaking in the subsurface horizons, where decreased sulfate concentration was detected in the pore water. The highest rates of sulfate-dependent anaerobic methane oxidation were found close to the methane-sulfate transition zone as is typical of most investigated marine sediments. The data on the carbon isotopic composition of gaseous methane from the seeps and dissolved CH4 from the bottom sediments, as well as on the rates of microbial methanogenesis and methane oxidation indicate that the activity of the methane seeps results from accumulation of biogenic methane in the cavities of the underlying geological structures with subsequent periodic release of methane bubbles into the water column.

  1. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

    PubMed Central

    Maslov, Sergei; Sneppen, Kim

    2017-01-01

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity. PMID:28051127

  2. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems.

    PubMed

    Maslov, Sergei; Sneppen, Kim

    2017-01-04

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity.

  3. The first self-sustainable microbial fuel cell stack.

    PubMed

    Ledezma, Pablo; Stinchcombe, Andrew; Greenman, John; Ieropoulos, Ioannis

    2013-02-21

    This study reports for the first time on the development of a self-sustainable microbial fuel cell stack capable of self-maintenance (feeding, hydration, sensing & reporting). Furthermore, the stack system is producing excess energy, which can be used for improved functionality. The self-maintenance is performed by the stack powering single and multi-channel peristaltic pumps.

  4. Microbial Fuel Cell Performance with a Pressurized Cathode Chamber

    USDA-ARS?s Scientific Manuscript database

    Microbial fuel cell (MFC) power densities are often constrained by the oxygen reduction reaction rate on the cathode electrode. One important factor for this is the normally low solubility of oxygen in the aqueous cathode solution creating mass transport limitations, which hinder oxygen reduction a...

  5. The Microbial Fuel Cell as an Education Tool

    ERIC Educational Resources Information Center

    Dewan, Alim; Van Wie, Bernard; Beyenal, Haluk; Lewandowski, Zbigniew

    2010-01-01

    Many chemical engineering programs offer courses from a variety of disciplines to teach their students multidisciplinary concepts, but often these courses lack appropriate tools for linking newly learned concepts to principles learned in the core courses. This paper describes our experience of incorporating a microbial fuel cell education module…

  6. Oxygen - Enemy or Friend for Microbial Fuel Cell Anode Performance?

    USDA-ARS?s Scientific Manuscript database

    Until recently, scientists and engineers have held a strong belief that oxygen intrusion into the anode chamber of a bioelectrochemical system (BES) is detrimental to microbial fuel cell (MFC) performance because oxygen acts as an alternate electron acceptor. This would, according to recent beliefs...

  7. The Microbial Fuel Cell as an Education Tool

    ERIC Educational Resources Information Center

    Dewan, Alim; Van Wie, Bernard; Beyenal, Haluk; Lewandowski, Zbigniew

    2010-01-01

    Many chemical engineering programs offer courses from a variety of disciplines to teach their students multidisciplinary concepts, but often these courses lack appropriate tools for linking newly learned concepts to principles learned in the core courses. This paper describes our experience of incorporating a microbial fuel cell education module…

  8. Mitochondrial Regulation of Cell Cycle and Proliferation

    PubMed Central

    Antico Arciuch, Valeria Gabriela; Elguero, María Eugenia; Poderoso, Juan José

    2012-01-01

    Abstract Eukaryotic mitochondria resulted from symbiotic incorporation of α-proteobacteria into ancient archaea species. During evolution, mitochondria lost most of the prokaryotic bacterial genes and only conserved a small fraction including those encoding 13 proteins of the respiratory chain. In this process, many functions were transferred to the host cells, but mitochondria gained a central role in the regulation of cell proliferation and apoptosis, and in the modulation of metabolism; accordingly, defective organelles contribute to cell transformation and cancer, diabetes, and neurodegenerative diseases. Most cell and transcriptional effects of mitochondria depend on the modulation of respiratory rate and on the production of hydrogen peroxide released into the cytosol. The mitochondrial oxidative rate has to remain depressed for cell proliferation; even in the presence of O2, energy is preferentially obtained from increased glycolysis (Warburg effect). In response to stress signals, traffic of pro- and antiapoptotic mitochondrial proteins in the intermembrane space (B-cell lymphoma-extra large, Bcl-2-associated death promoter, Bcl-2 associated X-protein and cytochrome c) is modulated by the redox condition determined by mitochondrial O2 utilization and mitochondrial nitric oxide metabolism. In this article, we highlight the traffic of the different canonical signaling pathways to mitochondria and the contributions of organelles to redox regulation of kinases. Finally, we analyze the dynamics of the mitochondrial population in cell cycle and apoptosis. Antioxid. Redox Signal. 16, 1150–1180. PMID:21967640

  9. Microbial community dynamics in continuous microbial fuel cells fed with synthetic wastewater and pig slurry.

    PubMed

    Sotres, Ana; Tey, Laura; Bonmatí, August; Viñas, Marc

    2016-10-01

    Two-chambered microbial fuel cells (MFCs) operating with synthetic wastewater and pig slurry were assessed. Additionally, the use of 2-bromoethanesulfonate (BES-Inh) was studied. The synthetic wastewater-fed MFC (MFCSW) showed a maximum power density (PDmax) of 2138mWm(-3), and the addition of BES-Inh (10mM) did not show any improvement in its performance (PDmax=2078mWm(-3)). When pig slurry was used as feed (MFCPS), PDmax increased up to 5623mWm(-3). The microbial community composition was affected by the type of substrate used. While, Pseudomonadaceae and Clostridiaceae were the most representative families within the acetate-based medium, Flavobacteriaceae, Chitinophagaceae, Comamonadaceae and Nitrosomonadaceae were predominant when pig slurry was used as feed. Otherwise, only the Eubacterial microbial community composition was strongly modified when adding BES-Inh, thus leading to an enrichment of the Bacteroidetes phylum. Oppositely, the Archaeal community was less affected by the addition of BES-Inh, and Methanosarcina sp., arose as the predominant family in both situations. Despite all the differences in microbial communities, 6 operational taxonomic units (OTUs) belonging to Bacteroidetes (Porphyromonadaceae and Marinilabiaceae) and Firmicutes (Clostridiales) were found to be common to both MFCs, also for different contents of COD and N-NH4(+), and therefore could be considered as the bioanode core microbiome.

  10. High shear enrichment improves the performance of the anodophilic microbial consortium in a microbial fuel cell

    PubMed Central

    Pham, Hai The; Boon, Nico; Aelterman, Peter; Clauwaert, Peter; De Schamphelaire, Liesje; Van Oostveldt, Patrick; Verbeken, Kim; Rabaey, Korneel; Verstraete, Willy

    2008-01-01

    Summary In many microbial bioreactors, high shear rates result in strong attachment of microbes and dense biofilms. In this study, high shear rates were applied to enrich an anodophilic microbial consortium in a microbial fuel cell (MFC). Enrichment at a shear rate of about 120 s−1 resulted in the production of a current and power output two to three times higher than those in the case of low shear rates (around 0.3 s−1). Biomass and biofilm analyses showed that the anodic biofilm from the MFC enriched under high shear rate conditions, in comparison with that under low shear rate conditions, had a doubled average thickness and the biomass density increased with a factor 5. The microbial community of the former, as analysed by DGGE, was significantly different from that of the latter. The results showed that enrichment by applying high shear rates in an MFC can result in a specific electrochemically active biofilm that is thicker and denser and attaches better, and hence has a better performance. PMID:21261869

  11. [Cell cycle, mitosis and therapeutic applications].

    PubMed

    Levy, Antonin; Albiges-Sauvin, Laurence; Massard, Christophe; Soria, Jean-Charles; Deutsch, Eric

    2011-10-01

    Genomic DNA is constantly under stress of endogenous and exogenous DNA damaging agents. Without proper care, the DNA damage causes an alteration of the genomic structure and can lead to cell death or the occurrence of mutations involved in tumorigenesis. During the process of evolution, organisms have acquired a series of response mechanisms and repair of DNA damage, thereby ensuring the maintenance of genome stability and faithful transmission of genetic information. The checkpoints are the major mechanisms by which a cell can respond to DNA damage, either by actively stopping the cell cycle or by induction of apoptosis. Two parallel signalling pathways, ATM and ATR respond to genotoxic stress by activating their downstream target proteins including the two effectors kinases CHK1 and CHK2. Promising preliminary data render these proteins potential targets for therapeutic development against cancer.

  12. Microbial Fe(III) oxide reduction and Fe cycling in iron-rich freshwater wetland sediments

    SciTech Connect

    Roden, E.E.

    1995-12-31

    The dynamics of Fe cycling and the interaction between microbial Fe(III) oxide reduction and other anaerobic microbial respiratory processes were examined in Fe-rich, sulfate-poor freshwater wetland sediments. Sediment incubation experiments demonstrated that reduction of Fe(III) oxides (amorphous, soluble in dilute HCl) dominated anaerobic carbon mineralization at Fe(III) concentrations in excess of 10 mmol per liter wet sediment. The kinetics of Fe(III) reduction were found to be first-order with respect to the concentration of Fe(III) oxide, although estimated first-order rate constants varied in relation to the absolute rates of Fe(III) reduction, suggesting a co-dependency on the concentration of easily degradable organic carbon. High concentrations of amorphous Fe(III) oxides (10-100 mmol L wet sed {sup -1}) were found in surface sediments (0-3 cm) of unvegetated zones of the wetland and in the rhizosphere (0-10 cm) of emergent aquatic plants, sufficient (based on sediment incubation experiments) to allow Fe(III)-reducing bacteria (FeRB) to dominate anaerobic carbon mineralization. A rapid redox cycling of Fe is apparent in these localized zones based on observed rates of Fe(III) reduction and the abundance/depth distribution of Fe(Ill) oxides. Preliminary culture enrichment studies indicate that FeRB present in these sediments are capable of metabolizing a range of both natural and contaminant aromatic hydrocarbons, which suggests a potential for utilization of natural and/or artificial Fe-rich wetland systems for organic contaminant bioremediation.

  13. Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments.

    PubMed

    Hunter, Evan M; Mills, Heath J; Kostka, Joel E

    2006-09-01

    Though a large fraction of primary production and organic matter cycling in the oceans occurs on continental shelves dominated by sandy deposits, the microbial communities associated with permeable shelf sediments remain poorly characterized. Therefore, in this study, we provide the first detailed characterization of microbial diversity in marine sands of the South Atlantic Bight through parallel analyses of small-subunit (SSU) rRNA gene (Bacteria), nosZ (denitrifying bacteria), and amoA (ammonia-oxidizing bacteria) sequences. Communities were analyzed by parallel DNA extractions and clone library construction from both sediment core material and manipulated sediment within column experiments designed for geochemical rate determinations. Rapid organic-matter degradation and coupled nitrification-denitrification were observed in column experiments at flow rates resembling in situ conditions over a range of oxygen concentrations. Numerous SSU rRNA phylotypes were affiliated with the phyla Proteobacteria (classes Alpha-, Delta-, and Gammaproteobacteria), Planctomycetes, Cyanobacteria, Chloroflexi, and Bacteroidetes. Detectable sequence diversity of nosZ and SSU rRNA genes increased in stratified redox-stabilized columns compared to in situ sediments, with the Alphaproteobacteria comprising the most frequently detected group. Alternatively, nitrifier communities showed a relatively low and stable diversity that did not covary with the other gene targets. Our results elucidate predominant phylotypes that are likely to catalyze carbon and nitrogen cycling in marine sands. Although overall diversity increased in response to redox stabilization and stratification in column experiments, the major phylotypes remained the same in all of our libraries, indicating that the columns sufficiently mimic in situ conditions.

  14. Bacterial sulfur cycling shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field.

    PubMed

    Schauer, Regina; Røy, Hans; Augustin, Nico; Gennerich, Hans-Hermann; Peters, Marc; Wenzhoefer, Frank; Amann, Rudolf; Meyerdierks, Anke

    2011-10-01

    The ultramafic-hosted Logatchev hydrothermal field (LHF) is characterized by vent fluids, which are enriched in dissolved hydrogen and methane compared with fluids from basalt-hosted systems. Thick sediment layers in LHF are partly covered by characteristic white mats. In this study, these sediments were investigated in order to determine biogeochemical processes and key organisms relevant for primary production. Temperature profiling at two mat-covered sites showed a conductive heating of the sediments. Elemental sulfur was detected in the overlying mat and metal-sulfides in the upper sediment layer. Microprofiles revealed an intensive hydrogen sulfide flux from deeper sediment layers. Fluorescence in situ hybridization showed that filamentous and vibrioid, Arcobacter-related Epsilonproteobacteria dominated the overlying mats. This is in contrast to sulfidic sediments in basalt-hosted fields where mats of similar appearance are composed of large sulfur-oxidizing Gammaproteobacteria. Epsilonproteobacteria (7-21%) and Deltaproteobacteria (20-21%) were highly abundant in the surface sediment layer. The physiology of the closest cultivated relatives, revealed by comparative 16S rRNA sequence analysis, was characterized by the capability to metabolize sulfur components. High sulfate reduction rates as well as sulfide depleted in (34)S further confirmed the importance of the biogeochemical sulfur cycle. In contrast, methane was found to be of minor relevance for microbial life in mat-covered surface sediments. Our data indicate that in conductively heated surface sediments microbial sulfur cycling is the driving force for bacterial biomass production although ultramafic-hosted systems are characterized by fluids with high levels of dissolved methane and hydrogen. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  15. Linking Microbial Community Structure, Activity and Carbon Cycling in Biological Soil Crust

    NASA Astrophysics Data System (ADS)

    Swenson, T.; Karaoz, U.; Swenson, J.; Bowen, B.; Northen, T.

    2016-12-01

    Soils play a key role in the global carbon cycle, but the relationships between soil microbial communities and metabolic pathways are poorly understood. In this study, biological soil crusts (biocrusts) from the Colorado Plateau are being used to develop soil metabolomics methods and statistical models to link active microbes to the abundance and turnover of soil metabolites and to examine the detailed substrate and product profiles of individual soil bacteria isolated from biocrust. To simulate a pulsed activity (wetting) event and to analyze the subsequent correlations between soil metabolite dynamics, community structure and activity, biocrusts were wetup with water and samples (porewater and DNA) were taken at various timepoints up to 49.5 hours post-wetup. DNA samples were sequenced using the HiSeq sequencing platform and porewater metabolites were analyzed using untargeted liquid chromatography/ mass spectrometry. Exometabolite analysis revealed the release of a breadth of metabolites including sugars, amino acids, fatty acids, dicarboxylic acids, nucleobases and osmolytes. In general, many metabolites (e.g. amino acids and nucleobases) immediately increased in abundance following wetup and then steadily decreased. However, a few continued to increase over time (e.g. xanthine). Interestingly, in a previous study exploring utilization of soil metabolites by sympatric bacterial isolates from biocrust, we observed xanthine to be released by some Bacilli sp. Furthermore, our current metagenomics data show that members of the Paenibacillaceae family increase in abundance in late wetup samples. Previous 16S amplicon data also show a "Firmicutes bloom" following wetup with the new metagenomic data resolving this at genome-level. Our continued metagenome and exometabolome analyses are allowing us to examine complex pulsed-activity events in biocrust microbial communities specifically by correlating the abundance of microbes to the release of soil metabolites

  16. Electricity production and microbial biofilm characterization in cellulose-fed microbial fuel cells.

    PubMed

    Ren, Z; Steinberg, L M; Regan, J M

    2008-01-01

    Converting biodegradable materials into electricity, microbial fuel cells (MFCs) present a promising technology for renewable energy production in specific applications. Unlike typical soluble substrates that have been used as electron donors in MFC studies, cellulose is unique because it requires a microbial consortium that can metabolize both an insoluble electron donor (cellulose) and electron acceptor (electrode). In this study, electricity generation and the microbial ecology of cellulose-fed MFCs were analyzed using a defined co-culture of Clostridium cellulolyticum and Geobacter sulfurreducens. Fluorescent in situ hybridization and quantitative PCR showed that when particulate MN301 cellulose was used as sole substrate, most Clostridium cells were found adhered to cellulose particles in suspension, while most Geobacter cells were attached to the electrode. By comparison, both bacteria resided in suspension and biofilm samples when soluble carboxymethyl cellulose was used. This distinct function-related distribution of the bacteria suggests an opportunity to optimize reactor operation by settling cellulose and decanting supernatant to extend cellulose hydrolysis and improve cellulose-electricity conversion. (c) IWA Publishing 2008.

  17. Reconstructing the Genetic Potential of the Microbially-Mediated Nitrogen Cycle in a Salt Marsh Ecosystem

    PubMed Central

    Dini-Andreote, Francisco; Brossi, Maria Julia de L.; van Elsas, Jan Dirk; Salles, Joana F.

    2016-01-01

    Coastal ecosystems are considered buffer zones for the discharge of land-derived nutrients without accounting for potential negative side effects. Hence, there is an urgent need to better understand the ecological assembly and dynamics of the microorganisms that are involved in nitrogen (N) cycling in such systems. Here, we employed two complementary methodological approaches (i.e., shotgun metagenomics and quantitative PCR) to examine the distribution and abundance of selected microbial genes involved in N transformations. We used soil samples collected along a well-established pristine salt marsh soil chronosequence that spans over a century of ecosystem development at the island of Schiermonnikoog, The Netherlands. Across the examined soil successional stages, the structure of the populations of genes involved in N cycling processes was strongly related to (shifts in the) soil nitrogen levels (i.e., NO3−, NH4+), salinity and pH (explaining 73.8% of the total variation, R2 = 0.71). Quantification of the genes used as proxies for N fixation, nitrification and denitrification revealed clear successional signatures that corroborated the taxonomic assignments obtained by metagenomics. Notably, we found strong evidence for niche partitioning, as revealed by the abundance and distribution of marker genes for nitrification (ammonia-oxidizing bacteria and archaea) and denitrification (nitrite reductase nirK, nirS and nitrous oxide reductase nosZ clades I and II). This was supported by a distinct correlation between these genes and soil physico-chemical properties, such as soil physical structure, pH, salinity, organic matter, total N, NO3−, NH4+ and SO42−, across four seasonal samplings. Overall, this study sheds light on the successional trajectories of microbial N cycle genes along a naturally developing salt marsh ecosystem. The data obtained serve as a foundation to guide the formulation of ecological models that aim to effectively monitor and manage pristine

  18. The cell cycle rallies the transcription cycle: Cdc28/Cdk1 is a cell cycle-regulated transcriptional CDK.

    PubMed

    Chymkowitch, Pierre; Enserink, Jorrit M

    2013-01-01

    In the budding yeast Saccharomyces cerevisiae, the cyclin-dependent kinases (CDKs) Kin28, Bur1 and Ctk1 regulate basal transcription by phosphorylating the carboxyl-terminal domain (CTD) of RNA polymerase II. However, very little is known about the involvement of the cell cycle CDK Cdc28 in the transcription process. We have recently shown that, upon cell cycle entry, Cdc28 kinase activity boosts transcription of a subset of genes by directly stimulating the basal transcription machinery. Here, we discuss the biological significance of this finding and give our view of the kinase-dependent role of Cdc28 in regulation of RNA polymerase II.

  19. Metabolic Differences in Microbial Cell Populations Revealed by Nanophotonic Ionization

    SciTech Connect

    Walker, Bennett; Antonakos, Cory; Retterer, Scott T; Vertes, Akos

    2013-01-01

    ellular differences are linked to cell differentiation, the proliferation of cancer and to the development of drug resistance in microbial infections. Due to sensitivity limitations, however, large- scale metabolic analysis at the single cell level is only available for cells significantly larger in volume than Saccharomyces cerevisiae (~30 fL). Here we demonstrate that by a nanophotonic ionization platform and mass spectrometry, over one hundred up to 108 metabolites, or up to 18% of the known S. cerevisiae metabolome, can be identified in very small cell populations (n < 100). Under ideal conditions, r Relative quantitation of up to 4% of the metabolites is achieved at the single cell level.

  20. Microbial fuel cell treatment of fuel process wastewater

    DOEpatents

    Borole, Abhijeet P; Tsouris, Constantino

    2013-12-03

    The present invention is directed to a method for cleansing fuel processing effluent containing carbonaceous compounds and inorganic salts, the method comprising contacting the fuel processing effluent with an anode of a microbial fuel ell, the anode containing microbes thereon which oxidatively degrade one or more of the carbonaceous compounds while producing electrical energy from the oxidative degradation, and directing the produced electrical energy to drive an electrosorption mechanism that operates to reduce the concentration of one or more inorganic salts in the fuel processing effluent, wherein the anode is in electrical communication with a cathode of the microbial fuel cell. The invention is also directed to an apparatus for practicing the method.

  1. The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

    PubMed Central

    Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

    2016-01-01

    Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system. PMID:27698381

  2. The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system.

    PubMed

    Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J D; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

    2016-10-04

    Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S(0) oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S(0) and Fe(2+), which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

  3. The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

    NASA Astrophysics Data System (ADS)

    Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

    2016-10-01

    Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

  4. Subsurface Nitrogen-Cycling Microbial Communities at Uranium Contaminated Sites in the Colorado River Basin

    NASA Astrophysics Data System (ADS)

    Cardarelli, E.; Bargar, J.; Williams, K. H.; Dam, W. L.; Francis, C.

    2015-12-01

    Throughout the Colorado River Basin (CRB), uranium (U) persists as a relic contaminant of former ore processing activities. Elevated solid-phase U levels exist in fine-grained, naturally-reduced zone (NRZ) sediments intermittently found within the subsurface floodplain alluvium of the following Department of Energy-Legacy Management sites: Rifle, CO; Naturita, CO; and Grand Junction, CO. Coupled with groundwater fluctuations that alter the subsurface redox conditions, previous evidence from Rifle, CO suggests this resupply of U may be controlled by microbially-produced nitrite and nitrate. Nitrification, the two-step process of archaeal and bacterial ammonia-oxidation followed by bacterial nitrite oxidation, generates nitrate under oxic conditions. Our hypothesis is that when elevated groundwater levels recede and the subsurface system becomes anoxic, the nitrate diffuses into the reduced interiors of the NRZ and stimulates denitrification, the stepwise anaerobic reduction of nitrate/nitrite to dinitrogen gas. Denitrification may then be coupled to the oxidation of sediment-bound U(IV) forming mobile U(VI), allowing it to resupply U into local groundwater supplies. A key step in substantiating this hypothesis is to demonstrate the presence of nitrogen-cycling organisms in U-contaminated, NRZ sediments from the upper CRB. Here we investigate how the diversity and abundances of nitrifying and denitrifying microbial populations change throughout the NRZs of the subsurface by using functional gene markers for ammonia-oxidation (amoA, encoding the α-subunit of ammonia monooxygenase) and denitrification (nirK, nirS, encoding nitrite reductase). Microbial diversity has been assessed via clone libraries, while abundances have been determined through quantitative polymerase chain reaction (qPCR), elucidating how relative numbers of nitrifiers (amoA) and denitrifiers (nirK, nirS) vary with depth, vary with location, and relate to uranium release within NRZs in sediment

  5. Effects of Snowpack on Biogeochemical Cycling and Microbial Activity in Prairie Soils

    NASA Astrophysics Data System (ADS)

    Schade, J. D.; Lynch, L. M.; Lapo, K. E.; Brownlee, A.

    2012-12-01

    A central prediction of current climate change models is a shift towards less frequent, more intense precipitation events and a shorter and smaller snowpack period in many regions, including the upper Midwest. Previous work in Arctic ecosystems and forests of the northeastern US have shown strong impacts of changes in the depth of snow on soil respiration and biogeochemical cycling. In spite of this, we still lack enough information on ecosystem processes during winter months to claim a general understanding of the impacts of changes in snowpack and precipitation patterns on ecosystem structure and function. Our objective was to investigate seasonal patterns in soil microbial activity and carbon and nitrogen cycling and the impact of snow accumulation on these patterns in restored tall grass prairies in Minnesota. To meet these objectives we experimentally manipulated snowpack depth in replicate plots in two restored prairies in southern Minnesota. In all plots, we measured soil temperature and respiration in the field once in October and November 2010 and every 7-10 days between January and September 2011. Soil samples were collected from each plot 10 times between Oct 2010 and November 2011 and analyzed for extracellular enzyme activity (EEA), extractable C, N, and P (phosphorus), and microbial biomass C, N, and P. In July of 2011, we also collected plant samples to assess differences in plant community composition and biomass. Soil temperatures under ambient snow were slightly above freezing and remained very stable throughout the winter, while in snow removal plots, temperature was highly variable and remained below freezing, often as low as -10 degrees C. Soil respiration in the winter was significantly higher under ambient snow. During spring thaw in March, respiration increased in all plots for roughly three weeks, after which rates dropped back to low levels. This increase was significantly higher in snow removal plots in both fields. We also observed

  6. Yeast surface display of dehydrogenases in microbial fuel-cells.

    PubMed

    Gal, Idan; Schlesinger, Orr; Amir, Liron; Alfonta, Lital

    2016-12-01

    Two dehydrogenases, cellobiose dehydrogenase from Corynascus thermophilus and pyranose dehydrogenase from Agaricus meleagris, were displayed for the first time on the surface of Saccharomyces cerevisiae using the yeast surface display system. Surface displayed dehydrogenases were used in a microbial fuel cell and generated high power outputs. Surface displayed cellobiose dehydrogenase has demonstrated a midpoint potential of -28mV (vs. Ag/AgCl) at pH=6.5 and was used in a mediator-less anode compartment of a microbial fuel cell producing a power output of 3.3μWcm(-2) using lactose as fuel. Surface-displayed pyranose dehydrogenase was used in a microbial fuel cell and generated high power outputs using different substrates, the highest power output that was achieved was 3.9μWcm(-2) using d-xylose. These results demonstrate that surface displayed cellobiose dehydrogenase and pyranose dehydrogenase may successfully be used in microbial bioelectrochemical systems. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. [Microbial fuel cells as an alternative power supply].

    PubMed

    Il'in, V K; Smirnov, I A; Soldatov, P É; Korshunov, D V; Tiurin-Kuz'min, A Iu; Starkova, L V; Chumakov, P E; Emel'ianova, L K; Novikova, L M; Debabov, V G; Voeĭkova, T A

    2012-01-01

    Purpose of the work was designing and prototyping of microbial fuel cells (MFC) and comparative evaluation of the electrogenic activity of wastewater autochthonous microorganisms as well as bacterial monocultures. Objects were model electrogenic strain Shewanella oneidensis MR-1, and an Ochrobactrum sp. strain isolated from the active anode biofilm of MFC composed as an electricity generating system. The study employed the methods typically used for aerobic and anaerobic strains, current measurement, identification of new electrogenic strains in microbial association of wastewater sludge and species definition by rRNA 16-S. As a result, two MFCs prototypes were tried out. Besides, it was shown that electrogenic activity of S. oneidensis MR-1 and Ochrobactrum sp. monocultures is similar but differs from that of the microbial association of the anode biofilm.

  8. Identifying the microbial communities and operational conditions for optimized wastewater treatment in microbial fuel cells.

    PubMed

    Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M; Wu, Angela; Yamanaka, Yuko; Nealson, Kenneth H; Bretschger, Orianna

    2013-12-01

    Microbial fuel cells (MFCs) are devices that exploit microorganisms as "biocatalysts" to recover energy from organic matter in the form of electricity. MFCs have been explored as possible energy neutral wastewater treatment systems; however, fundamental knowledge is still required about how MFC-associated microbial communities are affected by different operational conditions and can be optimized for accelerated wastewater treatment rates. In this study, we explored how electricity-generating microbial biofilms were established at MFC anodes and responded to three different operational conditions during wastewater treatment: 1) MFC operation using a 750 Ω external resistor (0.3 mA current production); 2) set-potential (SP) operation with the anode electrode potentiostatically controlled to +100 mV vs SHE (4.0 mA current production); and 3) open circuit (OC) operation (zero current generation). For all reactors, primary clarifier effluent collected from a municipal wastewater plant was used as the sole carbon and microbial source. Batch operation demonstrated nearly complete organic matter consumption after a residence time of 8-12 days for the MFC condition, 4-6 days for the SP condition, and 15-20 days for the OC condition. These results indicate that higher current generation accelerates organic matter degradation during MFC wastewater treatment. The microbial community analysis was conducted for the three reactors using 16S rRNA gene sequencing. Although the inoculated wastewater was dominated by members of Epsilonproteobacteria, Gammaproteobacteria, and Bacteroidetes species, the electricity-generating biofilms in MFC and SP reactors were dominated by Deltaproteobacteria and Bacteroidetes. Within Deltaproteobacteria, phylotypes classified to family Desulfobulbaceae and Geobacteraceae increased significantly under the SP condition with higher current generation; however those phylotypes were not found in the OC reactor. These analyses suggest that species

  9. Programmed Cell Death and Complexity in Microbial Systems.

    PubMed

    Durand, Pierre M; Sym, Stuart; Michod, Richard E

    2016-07-11

    Programmed cell death (PCD) is central to organism development and for a long time was considered a hallmark of multicellularity. Its discovery, therefore, in unicellular organisms presents compelling questions. Why did PCD evolve? What is its ecological effect on communities? To answer these questions, one is compelled to consider the impacts of PCD beyond the cell, for death obviously lowers the fitness of the cell. Here, we examine the ecological effects of PCD in different microbial scenarios and conclude that PCD can increase biological complexity. In mixed microbial communities, the mode of death affects the microenvironment, impacting the interactions between taxa. Where the population comprises groups of relatives, death has a more explicit effect. Death by lysis or other means can be harmful, while PCD can evolve by providing advantages to relatives. The synchronization of death between individuals suggests a group level property is being maintained and the mode of death also appears to have had an impact during the origin of multicellularity. PCD can result in the export of fitness from the cell to the group level via re-usable resources and PCD may also provide a mechanism for how groups beget new groups comprising kin. Furthermore, PCD is a means for solving a central problem of group living - the toxic effects of death - by making resources in dying cells beneficial to others. What emerges from the data reviewed here is that while PCD carries an obvious cost to the cell, it can be a driver of complexity in microbial communities.

  10. [Microbial processes of the carbon and sulfur cycles in the Chukchi Sea].

    PubMed

    Savvichev, A S; Rusanov, I I; Pimenov, N V; Zakharova, E E; Veslopolova, E F; Lein, A Iu; Crane, K; Ivanov, M V

    2007-01-01

    The research performed in August 2004 within the framework of the Russian-American Long-term Census of the Arctic (RUSALCA) resulted in the first data concerning the rates of the key microbial processes in the water column and bottom sediments of the Bering strait and the Chukchi Sea. The total bacterial counts in the water column varied from 30 x 10(3) cells ml(-1) in the northern and eastern parts to 245 x 10(3) cells ml(-1) in the southern part. The methane content in the water column of the Chukchi sea varied from 8 nmol CH4 l(-1) in the eastern part of the sea to 31 nmol CH4 l(-1) in the northern part of the Herald Canyon. Active microbial processes occurred in the upper 0-3 cm of the bottom sediments; the methane formation rate varied from 0.25 to 16 nmol CH4 dm(-3) day(-1). The rates of methane oxidation varied from 1.61 to 14.7 nmol CH4 dm(-3) day(-1). The rates of sulfate reduction varied from 1.35 to 16.2 micromol SO4(2-) dm(-3) day(-1). The rate of methane formation in the sediments increased with depth, while sulfate reduction rates decreased (less than 1 micromol SO4(2-) dm(-3) day(-1)). These high concentrations of biogenic elements and high rates of microbial processes in the upper sediment layers suggest a specific type of trophic chain in the Chukchi Sea. The approximate calculated balance of methane emission from the water column into the atmosphere is from 5.4 to 57.3 micromol CH4 m(-2) day(-1).

  11. Microbial activity and biogeochemical cycling in first-order Russian Arctic streams

    NASA Astrophysics Data System (ADS)

    Rhoades, R. E.; Lynch, L. M.; Ortega, J. C.; Holmes, R. M.; Mann, P. J.; Vonk, J. E.; Schade, J. D.

    2011-12-01

    Global climate change is strongly impacting Arctic ecosystems and is predicted to lead to thawing of permafrost soils. These soils are rich in organic matter and other nutrients and influence biogeochemical cycling in terrestrial and aquatic ecosystems. Small arctic streams are likely to be the first aquatic ecosystems to receive materials exported as soils warm. These first-order streams are characterized by strong interactions between the water column and stream bottom and have the potential to affect nutrient flux. Previous studies suggest that phosphorous availability limits biological productivity in many first-order arctic streams, however, they remain understudied, particularly in the Russian Arctic. Our objective was to assess microbial activity and biogeochemical cycling among arctic streams. We used three approaches to meet our objectives, including a survey of 9 streams, intensive longitudinal sampling in 5 streams, and nutrient pulse addition experiments in 4 streams, designed to assess the potential for limitation by N or P. We measured pH, temperature, dissolved oxygen, NH4, SRP, DOC, and TDN at all sampling sites. We also conducted biological oxygen demand (BOD) incubations designed to assess DOC lability, and correlated these measurements with background nutrient concentrations. We found a strong positive linear correlation between BOD and phosphate concentration, suggesting P limitation of production and/or consumption of labile DOC. To complement ambient stream measurements, we conducted whole stream nutrient addition experiments to calculate N and P uptake lengths, which we then used to infer whether N or P is more likely to limit biological processes, and the degree of coupling between N and P cycling. Results from the nutrient addition experiments suggest both N and P limitation among streams depending on stream location and characteristics. In addition, these experiments suggest a significant, but complex interaction between N and P cycles

  12. Quantifying Rates of Complete Microbial Iron Redox Cycling in Acidic Hot Springs

    NASA Astrophysics Data System (ADS)

    St Clair, B.; Pottenger, J. W.; Shock, E.

    2013-12-01

    concentrations of ferrous iron. Experimental design allowed us to measure biological and abiological rates independently. Results indicate a relatively consistent rate of biological iron oxidation between 20-100 ng Fe2+(gm wet sediment)-1 (second)-1 where oxide accumulations occur. Abiological oxidation rates increase significantly with increasing pH, and greatly limit soluble ferrous iron above a pH of 3.5 at high temperatures. Rates of biological iron reduction are typically comparable to oxidation, and can often double oxidation rates when supplemented with organic carbon. Abiological iron reduction rates are inconsequential when the pH is greater than 2, but increase sharply below this point. Results indicate that comparable rates of microbial oxidation and reduction are common in springs where biogenic iron oxide accumulates. It appears that the interplay of temperature, oxygen availability, and supply of organic carbon determines the extent and history of iron oxide accumulation. Taken together, our results show that complete microbial iron redox cycles are active in acidic hot springs wherever biogenic iron oxides accumulate.

  13. Microbial evidence for sulfur cycling in the deep subsurface of the Witwatersrand Basin, South Africa

    NASA Astrophysics Data System (ADS)

    Morgan, L. E.; Gihring, T. M.; Moser, D. P.; Dollhopf, M.; Balkwill, D. L.; Davidson, M. M.; Onstott, T. C.; Pfiffner, S. M.; Macalady, J. L.

    2004-05-01

    The continental deep subsurface harbors a heterogeneous community of microorganisms that have yet to be well understood. The gold mines of the Witwatersrand Basin in South Africa provide relatively easy access to this environment and have been integral to recent attempts to characterize subsurface microbiology. Molecular evidence for the biogeochemical cycling of sulfur has been detected in fissure water from Merriespruit and Driefontein mines. PCR amplification, cloning, and sequencing of adenosine-5'-phosphosulfate reductase (APS) and 16S rRNA genes were used to assess the composition of sulfur metabolizing microbial populations. Sequences closely related to APS reductase genes of the sulfur-oxidizing bacterium Allochromatium vinosum were detected in the Merriespruit Mine sample. APS reductase gene libraries from the Driefontein Mine sample were dominated by sequences with high identity to known sulfate-reducing bacteria. Phylogenetic analyses of 16S rRNA sequences indicated the presence of Thiobacillus-related species (known S-oxidizing organisms) in the Merriespruit sample, while Driefontein 16S rRNA clone libraries were dominated by sequences with high identity to known sulfate-reducing organisms in the delta-Proteobacteria and Firmicutes lineages. This study provides some of the first environmental APS sequences from sulfur-oxidizing bacteria and sheds new light on the organisms participating in sulfur-cycling in the deep subsurface.

  14. T Cell Receptor-induced Activation and Apoptosis In Cycling Human T Cells Occur throughout the Cell Cycle

    PubMed Central

    Karas, Michael; Zaks, Tal Z.; JL, Liu; LeRoith, Derek

    1999-01-01

    Previous studies have found conflicting associations between susceptibility to activation-induced cell death and the cell cycle in T cells. However, most of the studies used potentially toxic pharmacological agents for cell cycle synchronization. A panel of human melanoma tumor-reactive T cell lines, a CD8+ HER-2/neu-reactive T cell clone, and the leukemic T cell line Jurkat were separated by centrifugal elutriation. Fractions enriched for the G0–G1, S, and G2–M phases of the cell cycle were assayed for T cell receptor-mediated activation as measured by intracellular Ca2+ flux, cytolytic recognition of tumor targets, and induction of Fas ligand mRNA. Susceptibility to apoptosis induced by recombinant Fas ligand and activation-induced cell death were also studied. None of the parameters studied was specific to a certain phase of the cell cycle, leading us to conclude that in nontransformed human T cells, both activation and apoptosis through T cell receptor activation can occur in all phases of the cell cycle. PMID:10588669

  15. Interactions between microbial iron reduction and metal geochemistry: effect of redox cycling on transition metal speciation in iron bearing sediments.

    PubMed

    Cooper, D Craig; Picardal, Flynn F; Coby, Aaron J

    2006-03-15

    Microbial iron reduction is an important biogeochemical process that can affect metal geochemistry in sediments through direct and indirect mechanisms. With respectto Fe(III) (hydr)oxides bearing sorbed divalent metals, recent reports have indicated that (1) microbial reduction of goethite/ferrihydrite mixtures preferentially removes ferrihydrite, (2) this process can incorporate previously sorbed Zn(II) into an authigenic crystalline phase that is insoluble in 0.5 M HCl, (3) this new phase is probably goethite, and (4) the presence of nonreducible minerals can inhibit this transformation. This study demonstrates that a range of sorbed transition metals can be selectively sequestered into a 0.5 M HCl insoluble phase and that the process can be stimulated through sequential steps of microbial iron reduction and air oxidation. Microbial reduction experiments with divalent Cd, Co, Mn, Ni, Pb, and Zn indicate that all metals save Mn experienced some sequestration, with the degree of metal incorporation into the 0.5 M HCl insoluble phase correlating positively with crystalline ionic radius at coordination number = 6. Redox cycling experiments with Zn adsorbed to synthetic goethite/ferrihydrite or iron-bearing natural sediments indicate that redox cycling from iron reducing to iron oxidizing conditions sequesters more Zn within authigenic minerals than microbial iron reduction alone. In addition, the process is more effective in goethite/ferrihydrite mixtures than in iron-bearing natural sediments. Microbial reduction alone resulted in a -3x increase in 0.5 M HCl insoluble Zn and increased aqueous Zn (Zn-aq) in goethite/ferrihydrite, but did not significantly affect Zn speciation in natural sediments. Redox cycling enhanced the Zn sequestration by approximately 12% in both goethite/ferrihydrite and natural sediments and reduced Zn-aq to levels equal to the uninoculated control in goethite/ferrihydrite and less than the uninoculated control in natural sediments. These

  16. Electricity generation from food wastes and microbial community structure in microbial fuel cells.

    PubMed

    Jia, Jianna; Tang, Yu; Liu, Bingfeng; Wu, Di; Ren, Nanqi; Xing, Defeng

    2013-09-01

    Microbial fuel cell (MFC) was studied as an alternate and a novel way to dispose food wastes (FWs) in a waste-to-energy form. Different organic loading rate obviously affected the performance of MFCs fed with FWs. The maximum power density of ~18 W/m(3) (~556 mW/m(2)) was obtained at COD of 3200±400 mg/L and the maximum coulombic efficiency (CE) was ~27.0% at COD of 4900±350 mg/L. The maximum removals of COD, total carbohydrate (TC) and total nitrogen (TN) were ~86.4%, ~95.9% and ~16.1%, respectively. Microbial community analysis using 454 pyrosequencing of 16S rRNA gene demonstrated the combination of the dominant genera of the exoelectrogenic Geobacter and fermentative Bacteroides effectively drove highly efficient and reliable MFC systems with functions of organic matters degradation and electricity generation.

  17. Microbial community structure accompanied with electricity production in a constructed wetland plant microbial fuel cell.

    PubMed

    Lu, Lu; Xing, Defeng; Ren, Zhiyong Jason

    2015-11-01

    This study reveals the complex structure of bacterial and archaeal communities associated with a Canna indica plant microbial fuel cell (PMFC) and its electricity production. The PMFC produced a maximum current of 105 mA/m(2) by utilizing rhizodeposits as the sole electron donor without any external nutrient or buffer supplements, which demonstrates the feasibility of PMFCs in practical oligotrophic conditions with low solution conductivity. The microbial diversity was significantly higher in the PMFC than non-plant controls or sediment-only controls, and pyrosequencing and clone library reveal that rhizodeposits conversion to current were carried out by syntrophic interactions between fermentative bacteria (e.g., Anaerolineaceae) and electrochemically active bacteria (e.g., Geobacter). Denitrifying bacteria and acetotrophic methanogens play a minor role in organics degradation, but abundant hydrogenotrophic methanogens and thermophilic archaea are likely main electron donor competitors.

  18. Fungal Cell Cycle: A Unicellular versus Multicellular Comparison.

    PubMed

    Dörter, Ilkay; Momany, Michelle

    2016-12-01

    All cells must accurately replicate DNA and partition it to daughter cells. The basic cell cycle machinery is highly conserved among eukaryotes. Most of the mechanisms that control the cell cycle were worked out in fungal cells, taking advantage of their powerful genetics and rapid duplication times. Here we describe the cell cycles of the unicellular budding yeast Saccharomyces cerevisiae and the multicellular filamentous fungus Aspergillus nidulans. We compare and contrast morphological landmarks of G1, S, G2, and M phases, molecular mechanisms that drive cell cycle progression, and checkpoints in these model unicellular and multicellular fungal systems.

  19. The cell-cycle state of stem cells determines cell fate propensity.

    PubMed

    Pauklin, Siim; Vallier, Ludovic

    2013-09-26

    Self-renewal and differentiation of stem cells are fundamentally associated with cell-cycle progression to enable tissue specification, organ homeostasis, and potentially tumorigenesis. However, technical challenges have impaired the study of the molecular interactions coordinating cell fate choice and cell-cycle progression. Here, we bypass these limitations by using the FUCCI reporter system in human pluripotent stem cells and show that their capacity of differentiation varies during the progression of their cell cycle. These mechanisms are governed by the cell-cycle regulators cyclin D1-3 that control differentiation signals such as the TGF-β-Smad2/3 pathway. Conversely, cell-cycle manipulation using a small molecule directs differentiation of hPSCs and provides an approach to generate cell types with a clinical interest. Our results demonstrate that cell fate decisions are tightly associated with the cell-cycle machinery and reveal insights in the mechanisms synchronizing differentiation and proliferation in developing tissues.

  20. Cell Cycle Regulators during Human Atrial Development

    PubMed Central

    Kim, Won Ho; Joo, Chan Uhng; Ku, Ja Hong; Ryu, Chul Hee; Koh, Keum Nim; Koh, Gou Young; Ko, Jae Ki

    1998-01-01

    Objectives The molecular mechanisms that regulate cardiomyocyte cell cycle and terminal differentiation in humans remain largely unknown. To determine which cyclins, cyclin dependent kinases (CDKs) and cyclin kinase inhibitors (CKIs) are important for cardiomyocyte proliferation, we have examined protein levels of cyclins, CDKs and CKIs during normal atrial development in humans. Methods Atrial tissues were obtained in the fetus from inevitable abortion and in the adult during surgery, Cyclin and CDK proteins were determined by Western blot analysis, CDK activities were determined by phosphorylation amount using specific substrate. Results Most cyclins and CDKs were high during the fetal period and their levels decreased at different rates during the adult period. While the protein levels of cyclin D1, cyclin D3, CDK4, CDK6 and CDK2 were still detectable in adult atria, the protein levels of cyclin E, cyclin A, cyclin B, cdc2 and PCNA were not detectable. Interestingly, p27KIP 1 protein increased markedly in the adult period, while p21C IP 1 protein in atria was detectable only in the fetal period. While the activities of CDK6, CDK2 and cdc2 decreased markedly, the activity of CDK4 did not change from the fetal period to the adult period. Conclusion These findings indicate that marked reduction of protein levels and activities of cyclins and CDKs, and marked induction of p27KIP 1 in atria, are associated with the withdrawal of cardiac cell cycle in adult humans. PMID:9735660

  1. Microbial fuel cell (MFC) for bioelectricity generation from organic wastes.

    PubMed

    Moqsud, M Azizul; Omine, Kiyoshi; Yasufuku, Noriyuki; Hyodo, Masayuki; Nakata, Yukio

    2013-11-01

    Microbial fuel cells (MFCs) have gained a lot of attention recently as a mode of converting organic matter into electricity. In this study, a compost-based microbial fuel cell that generates bioelectricity by biodegradation of organic matter is developed. Grass cuttings, along with leaf mold, rice bran, oil cake (from mustard plants) and chicken droppings (waste from chickens) were used as organic waste. The electric properties of the MFC under anaerobic fermentation condition were investigated along with the influence of different types of membranes, the mixing of fly ash, and different types of electrode materials. It is observed that the maximum voltage was increased by mixing fly ash. Cellophane showed the highest value of voltage (around 350mV). Bamboo charcoal is good for anode material; however carbon fiber is better for the cathode material in terms of optimization of power generated. This developed MFC is a simple cell to generate electricity from organic waste.

  2. Alteration of cell cycle progression by Sindbis virus infection

    SciTech Connect

    Yi, Ruirong; Saito, Kengo; Isegawa, Naohisa; Shirasawa, Hiroshi

    2015-07-10

    We examined the impact of Sindbis virus (SINV) infection on cell cycle progression in a cancer cell line, HeLa, and a non-cancerous cell line, Vero. Cell cycle analyses showed that SINV infection is able to alter the cell cycle progression in both HeLa and Vero cells, but differently, especially during the early stage of infection. SINV infection affected the expression of several cell cycle regulators (CDK4, CDK6, cyclin E, p21, cyclin A and cyclin B) in HeLa cells and caused HeLa cells to accumulate in S phase during the early stage of infection. Monitoring SINV replication in HeLa and Vero cells expressing cell cycle indicators revealed that SINV which infected HeLa cells during G{sub 1} phase preferred to proliferate during S/G{sub 2} phase, and the average time interval for viral replication was significantly shorter in both HeLa and Vero cells infected during G{sub 1} phase than in cells infected during S/G{sub 2} phase. - Highlights: • SINV infection was able to alter the cell cycle progression of infected cancer cells. • SINV infection can affect the expression of cell cycle regulators. • SINV infection exhibited a preference for the timing of viral replication among the cell cycle phases.

  3. Cell cycle regulation by long non-coding RNAs.

    PubMed

    Kitagawa, Masatoshi; Kitagawa, Kyoko; Kotake, Yojiro; Niida, Hiroyuki; Ohhata, Tatsuya

    2013-12-01

    The mammalian cell cycle is precisely controlled by cyclin-dependent kinases (CDKs) and related pathways such as the RB and p53 pathways. Recent research on long non-coding RNAs (lncRNAs) indicates that many lncRNAs are involved in the regulation of critical cell cycle regulators such as the cyclins, CDKs, CDK inhibitors, pRB, and p53. These lncRNAs act as epigenetic regulators, transcription factor regulators, post-transcription regulators, and protein scaffolds. These cell cycle-regulated lncRNAs mainly control cellular levels of cell cycle regulators via various mechanisms, and may provide diversity and reliability to the general cell cycle. Interestingly, several lncRNAs are induced by DNA damage and participate in cell cycle arrest or induction of apoptosis as DNA damage responses. Therefore, deregulations of these cell cycle regulatory lncRNAs may be involved in tumorigenesis, and they are novel candidate molecular targets for cancer therapy and diagnosis.

  4. Cell cycle proliferation decisions: the impact of single cell analyses.

    PubMed

    Matson, Jacob P; Cook, Jeanette G

    2017-02-01

    Cell proliferation is a fundamental requirement for organismal development and homeostasis. The mammalian cell division cycle is tightly controlled to ensure complete and precise genome duplication and segregation of replicated chromosomes to daughter cells. The onset of DNA replication marks an irreversible commitment to cell division, and the accumulated efforts of many decades of molecular and cellular studies have probed this cellular decision, commonly called the restriction point. Despite a long-standing conceptual framework of the restriction point for progression through G1 phase into S phase or exit from G1 phase to quiescence (G0), recent technical advances in quantitative single cell analysis of mammalian cells have provided new insights. Significant intercellular heterogeneity revealed by single cell studies and the discovery of discrete subpopulations in proliferating cultures suggests the need for an even more nuanced understanding of cell proliferation decisions. In this review, we describe some of the recent developments in the cell cycle field made possible by quantitative single cell experimental approaches. © 2016 Federation of European Biochemical Societies.

  5. Metabolism, cell growth and the bacterial cell cycle

    PubMed Central

    Wang, Jue D.; Levin, Petra A.

    2010-01-01

    Adaptation to fluctuations in nutrient availability is a fact of life for single-celled organisms in the ‘wild’. A decade ago our understanding of how bacteria adjust cell cycle parameters to accommodate changes in nutrient availability stemmed almost entirely from elegant physiological studies completed in the 1960s. In this Opinion article we summarize recent groundbreaking work in this area and discuss potential mechanisms by which nutrient availability and metabolic status are coordinated with cell growth, chromosome replication and cell division. PMID:19806155

  6. Microbial mechanisms coupling carbon and phosphorus cycles in phosphorus-limited northern Adriatic Sea.

    PubMed

    Malfatti, F; Turk, V; Tinta, T; Mozetič, P; Manganelli, M; Samo, T J; Ugalde, J A; Kovač, N; Stefanelli, M; Antonioli, M; Fonda-Umani, S; Del Negro, P; Cataletto, B; Hozić, A; Ivošević Denardis, N; Zutić, V; Svetličić, V; Mišić Radić, T; Radić, T; Fuks, D; Azam, F

    2014-02-01

    The coastal northern Adriatic Sea receives pulsed inputs of riverine nutrients, causing phytoplankton blooms and seasonally sustained dissolved organic carbon (DOC) accumulation-hypothesized to cause episodes of massive mucilage. The underlying mechanisms regulating P and C cycles and their coupling are unclear. Extensive biogeochemical parameters, processes and community composition were measured in a 64-day mesocosms deployed off Piran, Slovenia. We followed the temporal trends of C and P fluxes in P-enriched (P+) and unenriched (P-) mesocosms. An intense diatom bloom developed then crashed; however, substantial primary production was maintained throughout, supported by tightly coupled P regeneration by bacteria and phytoplankton. Results provide novel insights on post-bloom C and P dynamics and mechanisms. 1) Post-bloom DOC accumulation to 186 μM remained elevated despite high bacterial carbon demand. Presumably, a large part of DOC accumulated due to the bacterial ectohydrolytic processing of primary productivity that adventitiously generated slow-to-degrade DOC; 2) bacteria heavily colonized post-bloom diatom aggregates, rendering them microscale hotspots of P regeneration due to locally intense bacterial ectohydrolase activities; 3) Pi turnover was rapid thus suggesting high P flux through the DOP pool (dissolved organic phosphorus) turnover; 4) Alpha- and Gamma-proteobacteria dominated the bacterial communities despite great differences of C and P pools and fluxes in both mesocosms. However, minor taxa showed dramatic changes in community compositions. Major OTUs were presumably generalists adapted to diverse productivity regimes.We suggest that variation in bacterial ectohydrolase activities on aggregates, regulating the rates of POM→DOM transition as well as dissolved polymer hydrolysis, could become a bottleneck in P regeneration. This could be another regulatory step, in addition to APase, in the microbial regulation of P cycle and the coupling

  7. The role of FeS(aq) molecular clusters in microbial redox cycling and iron mineralization.

    NASA Astrophysics Data System (ADS)

    Druschel, G.; Oduro, H.; Sperling, J.; Johnson, C.

    2008-12-01

    Iron sulfide molecular clusters, FeS(aq), are a group of polynuclear Fe-S complexes varying in size between a few and a few hundred molecules that occur in many environments and are critical parts of cycling between soluble iron and iron sulfide minerals. These clusters react uniquely with voltammetric Au-amalgam electrodes, and the signal for these molecules has now been observed in many terrestrial and marine aquatic settings. FeS(aq) clusters form when aqueous sulfide and iron(II) interact, but the source of those ions can come from abiotic or microbial sulfate and iron reduction or from the abiotic non-oxidative dissolution of iron sulfide minerals. Formation of iron sulfide minerals, principally mackinawite as the first solid nanocrystalline phase in many settings, is necessarily preceeded by formation and evolution of these molecular clusters as mineralization proceeds, and the clusters have been suggested to additionally be part of the pyritization process (Rickard and Luther, 1997; Luther and Rickard, 2005). In several systems, we have also observed FeS(aq) clusters to be the link between Fe-S mineral dissolution and oxidation of iron and sulfide, with important implications for changes to the overall oxidation pathway. Microorganisms can clearly be involved in the formation of FeS(aq) through iron and sulfate reduction, but it is not clear to date if organisms can utilize these clusters either as metabolic components or as anabolic 'building blocks' for enzyme production. Cycling of iron in the Fe-S system linked to FeS(aq) would clearly be a critical part of understanding iron isotope dynamics preserved in iron sulfide minerals. We will review ongoing work towards understanding the role of FeS(aq) in iron cycling and isotope fractionation as well as the measurement and characterization of this key class of iron complexes using environmental voltammetry.

  8. Deployable Microbial Fuel Cell and Methods

    DTIC Science & Technology

    2011-09-08

    cells and batteries and in particular to cathodes which are suitable for use in galvanic cells that use an oxidant dissolved in the electrolyte as...is preferably dried so the battery is activated when liquid contacts the electrolyte and separator layer. Water swellable particles are included...required divers to install graphite plates in the marine sediment. As noted above, this is a costly and time consuming process. In addition, the graphite

  9. Phylogenetic and Metagenomic Analyses of Substrate-Dependent Bacterial Temporal Dynamics in Microbial Fuel Cells

    PubMed Central

    Zhang, Husen; Chen, Xi; Braithwaite, Daniel; He, Zhen

    2014-01-01

    Understanding the microbial community structure and genetic potential of anode biofilms is key to improve extracellular electron transfers in microbial fuel cells. We investigated effect of substrate and temporal dynamics of anodic biofilm communities using phylogenetic and metagenomic approaches in parallel with electrochemical characterizations. The startup non-steady state anodic bacterial structures were compared for a simple substrate, acetate, and for a complex substrate, landfill leachate, using a single-chamber air-cathode microbial fuel cell. Principal coordinate analysis showed that distinct community structures were formed with each substrate type. The bacterial diversity measured as Shannon index decreased with time in acetate cycles, and was restored with the introduction of leachate. The change of diversity was accompanied by an opposite trend in the relative abundance of Geobacter-affiliated phylotypes, which were acclimated to over 40% of total Bacteria at the end of acetate-fed conditions then declined in the leachate cycles. The transition from acetate to leachate caused a decrease in output power density from 243±13 mW/m2 to 140±11 mW/m2, accompanied by a decrease in Coulombic electron recovery from 18±3% to 9±3%. The leachate cycles selected protein-degrading phylotypes within phylum Synergistetes. Metagenomic shotgun sequencing showed that leachate-fed communities had higher cell motility genes including bacterial chemotaxis and flagellar assembly, and increased gene abundance related to metal resistance, antibiotic resistance, and quorum sensing. These differentially represented genes suggested an altered anodic biofilm community in response to additional substrates and stress from the complex landfill leachate. PMID:25202990

  10. Capacity fade of Sony 18650 cells cycled at elevated temperatures. Part I. Cycling performance

    NASA Astrophysics Data System (ADS)

    Ramadass, P.; Haran, Bala; White, Ralph; Popov, Branko N.

    The capacity fade of Sony 18650 Li-ion cells increases with increase in temperature. After 800 cycles, the cells cycled at RT and 45 °C showed a capacity fade of 30 and 36%, respectively. The cell cycled at 55 °C showed a capacity loss of about 70% after 490 cycles. The rate capability of the cells continues to decrease with cycling. Impedance measurements showed an overall increase in the cell resistance with cycling and temperature. Impedance studies of the electrode materials showed an increased positive electrode resistance when compared to that of the negative electrode for cells cycled at RT and 45 °C. However, cells cycled at 50 and 55 °C exhibit higher negative electrode resistance. The increased capacity fade for the cells cycled at high temperatures can be explained by taking into account the repeated film formation over the surface of anode, which results in increased rate of lithium loss and also in a drastic increase in the negative electrode resistance with cycling.

  11. Dose-dependent regulation of microbial activity on sinking particles by polyunsaturated aldehydes: Implications for the carbon cycle.

    PubMed

    Edwards, Bethanie R; Bidle, Kay D; Van Mooy, Benjamin A S

    2015-05-12

    Diatoms and other phytoplankton play a crucial role in the global carbon cycle, fixing CO2 into organic carbon, which may then be exported to depth via sinking particles. The molecular diversity of this organic carbon is vast and many highly bioactive molecules have been identified. Polyunsaturated aldehydes (PUAs) are bioactive on various levels of the marine food web, and yet the potential for these molecules to affect the fate of organic carbon produced by diatoms remains an open question. In this study, the effects of PUAs on the natural microbial assemblages associated with sinking particles were investigated. Sinking particles were collected from 150 m in the water column and exposed to varying concentrations of PUAs in dark incubations over 24 h. PUA doses ranging from 1 to 10 µM stimulated respiration, organic matter hydrolysis, and cell growth by bacteria associated with sinking particles. PUA dosages near 100 µM appeared to be toxic, resulting in decreased bacterial cell abundance and metabolism, as well as pronounced shifts in bacterial community composition. Sinking particles were hot spots for PUA production that contained concentrations within the stimulatory micromolar range in contrast to previously reported picomolar concentrations of these compounds in bulk seawater. This suggests PUAs produced in situ stimulate the remineralization of phytoplankton-derived sinking organic matter, decreasing carbon export efficiency, and shoaling the average depths of nutrient regeneration. Our results are consistent with a "bioactivity hypothesis" for explaining variations in carbon export efficiency in the oceans.

  12. Dose-dependent regulation of microbial activity on sinking particles by polyunsaturated aldehydes: Implications for the carbon cycle

    PubMed Central

    Edwards, Bethanie R.; Bidle, Kay D.; Van Mooy, Benjamin A. S.

    2015-01-01

    Diatoms and other phytoplankton play a crucial role in the global carbon cycle, fixing CO2 into organic carbon, which may then be exported to depth via sinking particles. The molecular diversity of this organic carbon is vast and many highly bioactive molecules have been identified. Polyunsaturated aldehydes (PUAs) are bioactive on various levels of the marine food web, and yet the potential for these molecules to affect the fate of organic carbon produced by diatoms remains an open question. In this study, the effects of PUAs on the natural microbial assemblages associated with sinking particles were investigated. Sinking particles were collected from 150 m in the water column and exposed to varying concentrations of PUAs in dark incubations over 24 h. PUA doses ranging from 1 to 10 µM stimulated respiration, organic matter hydrolysis, and cell growth by bacteria associated with sinking particles. PUA dosages near 100 µM appeared to be toxic, resulting in decreased bacterial cell abundance and metabolism, as well as pronounced shifts in bacterial community composition. Sinking particles were hot spots for PUA production that contained concentrations within the stimulatory micromolar range in contrast to previously reported picomolar concentrations of these compounds in bulk seawater. This suggests PUAs produced in situ stimulate the remineralization of phytoplankton-derived sinking organic matter, decreasing carbon export efficiency, and shoaling the average depths of nutrient regeneration. Our results are consistent with a “bioactivity hypothesis” for explaining variations in carbon export efficiency in the oceans. PMID:25918397

  13. Dose-dependent regulation of microbial activity on sinking particles by polyunsaturated aldehydes: Implications for the carbon cycle

    NASA Astrophysics Data System (ADS)

    Edwards, Bethanie R.; Bidle, Kay D.; Van Mooy, Benjamin A. S.

    2015-05-01

    Diatoms and other phytoplankton play a crucial role in the global carbon cycle, fixing CO2 into organic carbon, which may then be exported to depth via sinking particles. The molecular diversity of this organic carbon is vast and many highly bioactive molecules have been identified. Polyunsaturated aldehydes (PUAs) are bioactive on various levels of the marine food web, and yet the potential for these molecules to affect the fate of organic carbon produced by diatoms remains an open question. In this study, the effects of PUAs on the natural microbial assemblages associated with sinking particles were investigated. Sinking particles were collected from 150 m in the water column and exposed to varying concentrations of PUAs in dark incubations over 24 h. PUA doses ranging from 1 to 10 µM stimulated respiration, organic matter hydrolysis, and cell growth by bacteria associated with sinking particles. PUA dosages near 100 µM appeared to be toxic, resulting in decreased bacterial cell abundance and metabolism, as well as pronounced shifts in bacterial community composition. Sinking particles were hot spots for PUA production that contained concentrations within the stimulatory micromolar range in contrast to previously reported picomolar concentrations of these compounds in bulk seawater. This suggests PUAs produced in situ stimulate the remineralization of phytoplankton-derived sinking organic matter, decreasing carbon export efficiency, and shoaling the average depths of nutrient regeneration. Our results are consistent with a "bioactivity hypothesis" for explaining variations in carbon export efficiency in the oceans.

  14. Characterization of microbial fuel cells at microbially and electrochemically meaningful time scales.

    PubMed

    Ren, Zhiyong; Yan, Hengjing; Wang, Wei; Mench, Matthew M; Regan, John M

    2011-03-15

    The variable biocatalyst density in a microbial fuel cell (MFC) anode biofilm is a unique feature of MFCs relative to other electrochemical systems, yet performance characterizations of MFCs typically involve analyses at electrochemically relevant time scales that are insufficient to account for these variable biocatalyst effects. This study investigated the electrochemical performance and the development of anode biofilm architecture under different external loadings, with duplicate acetate-fed single-chamber MFCs stabilized at each resistance for microbially relevant time scales. Power density curves from these steady-state reactors generally showed comparable profiles despite the fact that anode biofilm architectures and communities varied considerably, showing that steady-state biofilm differences had little influence on electrochemical performance until the steady-state external loading was much larger than the reactor internal resistance. Filamentous bacteria were dominant on the anodes under high external resistances (1000 and 5000 Ω), while more diverse rod-shaped cells formed dense biofilms under lower resistances (10, 50, and 265 Ω). Anode charge transfer resistance decreased with decreasing fixed external resistances, but was consistently 2 orders of magnitude higher than the resistance at the cathode. Cell counting showed an inverse exponential correlation between cell numbers and external resistances. This direct link of MFC anode biofilm evolution with external resistance and electricity production offers several operational strategies for system optimization.

  15. Cell cycle dysregulation in pituitary oncogenesis.

    PubMed

    Muşat, Madalina; Vax, Vladimir V; Borboli, Ninetta; Gueorguiev, Maria; Bonner, Sarah; Korbonits, Márta; Grossman, Ashley B

    2004-01-01

    The cell cycle is the process by which cells grow, replicate their genome and divide. The cell cycle control system is a cyclically-operating biochemical device constructed from a set of interacting proteins that induce and coordinate proper progression through the cycle, and includes cyclins, cyclin-dependent kinases (CDK) and their inhibitors (CDKI). There are mainly two families of CDKI, the INK family (INK4a/p16; INK4b/p15; INK4c/p18 and INK4d/p19) and the WAF/KIP family (WAF1/p21; KIP1/p27; KIP2/p57). Progression through the cell cycle is mainly dependent on fluctuations in the concentration of cyclins and CDKI achieved through the programmed degradation of these proteins by proteolysis within the ubiquitin-proteasome system. There is also a transcriptional regulation of cyclin expression, probably dependent on CDK phosphorylation. The p53 family--p53, p63 and p73--function as transcription factors that play a major role in regulating the response of mammalian cells to stressors and damage, in part through the transcriptional activation of genes involved in cell cycle control (e.g. p21), DNA repair, senescence, angiogenesis and apoptosis. Essential for the maintenance of euploidy during mitosis is human securin, identical to the product of the pituitary tumour-transforming gene (PTTG). Loss of regulation at the G1/S transition appears to be a common event among virtually all types of human tumours. Aberrations of one or more components of the pRb/p16/cyclin D1/CDK4 pathway seem to be a frequent event (80%) in pituitary tumours. The role of p27 is rather that of a haploinsufficient gene. p27-/- mice show an increased growth rate, due to increased cellularity, testicular and ovarian cell hyperplasia and infertility, and hyperplasia of the pituitary intermediate lobe with nearly 100% mortality caused by such a benign pituitary tumour. Although the p27 gene was not found to be mutated in human pituitary tumours and its mRNA expression was similar in tumour samples

  16. Temporal Microbial Community Dynamics in Microbial Electrolysis Cells – Influence of Acetate and Propionate Concentration

    PubMed Central

    Hari, Ananda Rao; Venkidusamy, Krishnaveni; Katuri, Krishna P.; Bagchi, Samik; Saikaly, Pascal E.

    2017-01-01

    Microbial electrolysis cells (MECs) are widely considered as a next generation wastewater treatment system. However, fundamental insight on the temporal dynamics of microbial communities associated with MEC performance under different organic types with varied loading concentrations is still unknown, nevertheless this knowledge is essential for optimizing this technology for real-scale applications. Here, the temporal dynamics of anodic microbial communities associated with MEC performance was examined at low (0.5 g COD/L) and high (4 g COD/L) concentrations of acetate or propionate, which are important intermediates of fermentation of municipal wastewaters and sludge. The results showed that acetate-fed reactors exhibited higher performance in terms of maximum current density (I: 4.25 ± 0.23 A/m2), coulombic efficiency (CE: 95 ± 8%), and substrate degradation rate (98.8 ± 1.2%) than propionate-fed reactors (I: 2.7 ± 0.28 A/m2; CE: 68 ± 9.5%; substrate degradation rate: 84 ± 13%) irrespective of the concentrations tested. Despite of the repeated sampling of the anodic biofilm over time, the high-concentration reactors demonstrated lower and stable performance in terms of current density (I: 1.1 ± 0.14 to 4.2 ± 0.21 A/m2), coulombic efficiency (CE: 44 ± 4.1 to 103 ± 7.2%) and substrate degradation rate (64.9 ± 6.3 to 99.7 ± 0.5%), while the low-concentration reactors produced higher and dynamic performance (I: 1.1 ± 0.12 to 4.6 ± 0.1 A/m2; CE: 52 ± 2.5 to 105 ± 2.7%; substrate degradation rate: 87.2 ± 0.2 to 99.9 ± 0.06%) with the different substrates tested. Correlating reactor’s performance with temporal dynamics of microbial communities showed that relatively similar anodic microbial community composition but with varying relative abundances was observed in all the reactors despite differences in the substrate and concentrations tested. Particularly, Geobacter was the predominant bacteria on the anode biofilm of all MECs over time suggesting

  17. Carbon and nitrogen assimilation in deep subseafloor microbial cells.

    PubMed

    Morono, Yuki; Terada, Takeshi; Nishizawa, Manabu; Ito, Motoo; Hillion, François; Takahata, Naoto; Sano, Yuji; Inagaki, Fumio

    2011-11-08

    Remarkable numbers of microbial cells have been observed in global shallow to deep subseafloor sediments. Accumulating evidence indicates that deep and ancient sediments harbor living microbial life, where the flux of nutrients and energy are extremely low. However, their physiology and energy requirements remain largely unknown. We used stable isotope tracer incubation and nanometer-scale secondary ion MS to investigate the dynamics of carbon and nitrogen assimilation activities in individual microbial cells from 219-m-deep lower Pleistocene (460,000 y old) sediments from the northwestern Pacific off the Shimokita Peninsula of Japan. Sediment samples were incubated in vitro with (13)C- and/or (15)N-labeled glucose, pyruvate, acetate, bicarbonate, methane, ammonium, and amino acids. Significant incorporation of (13)C and/or (15)N and growth occurred in response to glucose, pyruvate, and amino acids (∼76% of total cells), whereas acetate and bicarbonate were incorporated without fostering growth. Among those substrates, a maximum substrate assimilation rate was observed at 67 × 10(-18) mol/cell per d with bicarbonate. Neither carbon assimilation nor growth was evident in response to methane. The atomic ratios between nitrogen incorporated from ammonium and the total cellular nitrogen consistently exceeded the ratios of carbon, suggesting that subseafloor microbes preferentially require nitrogen assimilation for the recovery in vitro. Our results showed that the most deeply buried subseafloor sedimentary microbes maintain potentials for metabolic activities and that growth is generally limited by energy but not by the availability of C and N compounds.

  18. Analysis of Cell Cycle Switches in Drosophila Oogenesis.

    PubMed

    Jia, Dongyu; Huang, Yi-Chun; Deng, Wu-Min

    2015-01-01

    The study of Drosophila oogenesis provides invaluable information about signaling pathway regulation and cell cycle programming. During Drosophila oogenesis, a string of egg chambers in each ovariole progressively develops toward maturity. Egg chamber development consists of 14 stages. From stage 1 to stage 6 (mitotic cycle), main-body follicle cells undergo mitotic divisions. From stage 7 to stage 10a (endocycle), follicle cells cease mitosis but continue three rounds of endoreduplication. From stage 10b to stage 13 (gene amplification), instead of whole genome duplication, follicle cells selectively amplify specific genomic regions, mostly for chorion production. So far, Drosophila oogenesis is one of the most well studied model systems used to understand cell cycle switches, which furthers our knowledge about cell cycle control machinery and sheds new light on potential cancer treatments. Here, we give a brief summary of cell cycle switches, the associated signaling pathways and factors, and the detailed experimental procedures used to study the cell cycle switches.

  19. S and O Isotope Studies of Microbial S Cycling in the Deep Biosphere of Marine Sediments: Eastern Equatorial Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Blake, R. E.; Bottcher, M. E.; Surkov, A. V.; Ferdelman, T. G.; Jorgensen, B. B.

    2004-12-01

    We have determined the oxygen (18O/16O) and sulfur (34S/32S) isotope ratios of porewater sulfate to depths of over 400 mbsf in sediments from open-ocean and upwelling sites in the Eastern Equatorial Pacific ocean. Sulfate δ 18O ranges from near-normal seawater values (9.5 permil) at organic-poor open-ocean sites, to approximately 30 permil at sites with higher organic matter content and higher associated microbial activity. Depth-correlative trends of δ 18O, δ 34S, alkalinity, methane, ammonium and the presence of sulfide, indicate significant oxidation of sedimentary organic matter by sulfate-reducing microbial populations as well as anaerobic oxidation of methane. δ 18O-SO4 values at low-activity sites reveal the presence of significant microbial sulfur-cycling activity despite relatively flat sulfate concentration and δ 34S profiles. This activity may include contributions from several processes including: enzyme-catalyzed equilibration between oxygen in sulfate and water superimposed upon microbial sulfate reduction, sulfide oxidation, and bacterial disproportionation of sulfur intermediates. Large isotope enrichment factors observed at low-activity sites (40-80 permil) likely reflect concurrent processes of: kinetic isotope fractionation, equilibrium fractionation between sulfate and water, and sulfide oxidation at low rates of sulfate reduction. Results of this study indicate that coupled measurements of S and O isotope ratios of porewater sulfate are a powerful tool for tracing microbial activity and sulfur cycling in marine sediments.

  20. The role of microbial communities in phosphorus cycling during litter decomposition in a tropical forest

    NASA Astrophysics Data System (ADS)

    Lloret Sevilla, E.; Brodie, E.; Bouskill, N.; Hao, Z.

    2016-12-01

    Phosphorus is an essential nutrient with a reduced availability in tropical forests. In these ecosystems, P is recycled highly efficiently through resorption and mineralization and P immobilization in the microbial biomass prevents its loss through occlusion in the soil mineral fraction. To improve models of ecosystem response to global change, further studies of the above and belowground plant and microbial traits related to P availability and uptake, are required. In tropical forests, high temperature and rainfall lead to some of the highest rates of litter decomposition on earth. Litter decomposition is a complex process mediated by a range of trophic groups: meso and microfauna initiate litter turnover through litter fragmentation facilitating colonization by fungi, and bacteria mediate the mineralization of organic matter and release of nutrients. To determine the important functional traits of these players in the efficient cycling of P in soils with low P availability, we are performing a leaf litter decomposition experiment in a humid tropical forest in Puerto Rico. Nylon litterbags with three mesh sizes (2mm, 20 μm and 0.45 μm) containing litter with different chemistry (tabonuco and palm) will be deployed on soil surface and sampled 6 times throughout 12 months. The use of different mesh sizes will allow us to identify the leading roles in litter turnover by physical allowance and/or exclusion of the decomposers. The 2 mm bags allow meso and microfauna, roots, fungi and bacteria. 20 μm bags will exclude fauna and roots and 0.45 μm only allow some bacteria. We hypothesize that fungi will dominate over bacteria in earlier stages of the decomposition with a higher production of extracellular hydrolytic enzymes. On the other hand, bacterial biomass is expected to increase with time. Qualitative changes in both fungal and bacterial communities along the decomposition process are also expected leading to changes in enzyme activity. We also postulate an

  1. Microbial communities change in an anaerobic digestion after application of microbial electrolysis cells.

    PubMed

    Lee, Beom; Park, Jun-Gyu; Shin, Won-Beom; Tian, Dong-Jie; Jun, Hang-Bae

    2017-06-01

    Microbial electrolysis cells (MECs) are being studied to improve the efficiency of anaerobic digesters and biogas production. In the present study, we investigated the effects of electrochemical reactions in AD-MEC (anaerobic digester combined with MECs) on changes in the microbial communities of bulk sludge through 454-pyrosequencing analysis, as well as the effect of these changes on anaerobic digestion. Methanobacterium beijingense and Methanobacterium petrolearium were the dominant archaeal species in AD, while Methanosarcina thermophila and Methanobacterium formicicum were dominant in AD-MEC at steady-state. There were no substantial differences in dominant bacterial species. Clostridia class was more abundant than Bacteroidia class in both reactors. Compared to AD, AD-MEC showed a 40% increase in overall bacterial population, increasing the removal of organic matters and the conversion of volatile fatty acids (VFAs). Thus, the MEC reaction more effectively converts organic matters to VFAs and activates microbial communities favorable for methane production. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Effect of electricity on microbial community of microbial fuel cell simultaneously treating sulfide and nitrate

    NASA Astrophysics Data System (ADS)

    Cai, Jing; Zheng, Ping; Xing, Yajuan; Qaisar, Mahmood

    2015-05-01

    The effect of electric current on microbial community is explored in Microbial Fuel Cells (MFCs) simultaneously treating sulfide and nitrate. The MFCs are operated under four different conditions which exhibited different characteristics of electricity generation. In batch mode, MFCs generate intermittently high current pulses in the beginning, and the current density is instable subsequently, while the current density of MFCs in continuous mode is relatively stable. All operational parameters show good capacity for substrate removal, and nitrogen and sulfate were the main reaction products. Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analysis is employed to obtain profiles of the bacterial communities present in inoculum and suspension of four MFCs. Based on the community diversity indices and Spearman correlation analyses, significant correlation exists between Richness of the community of anode chamber and the electricity generated, while no strong correlation is evident between other indexes (Shannon index, Simpson index and Equitability index) and the electricity. Additionally, the results of Principal Component Analysis (PCA) suggest that MFCs suffering from current shock have similar suspension communities, while the others have diverse microbial communities.

  3. Enhanced microbial reduction of vanadium (V) in groundwater with bioelectricity from microbial fuel cells

    NASA Astrophysics Data System (ADS)

    Hao, Liting; Zhang, Baogang; Tian, Caixing; Liu, Ye; Shi, Chunhong; Cheng, Ming; Feng, Chuanping

    2015-08-01

    Bioelectricity generated from the microbial fuel cell (MFC) is applied to the bioelectrical reactor (BER) directly to enhance microbial reduction of vanadium (V) (V(V)) in groundwater. With the maximum power density of 543.4 mW m-2 from the MFC, V(V) removal is accelerated with efficiency of 93.6% during 12 h operation. Higher applied voltage can facilitate this process. V(V) removals decrease with the increase of initial V(V) concentration, while extra addition of chemical oxygen demand (COD) has little effect on performance improvement. Microbial V(V) reduction is enhanced and then suppressed with the increase of conductivity. High-throughput 16S rRNA gene pyrosequencing analysis implies the accumulated Enterobacter and Lactococcus reduce V(V) with products from fermentative microorganisms such as Macellibacteroides. The presentation of electrochemically active bacteria as Enterobacter promotes electron transfers. This study indicates that application of bioelectricity from MFCs is a promising strategy to improve the efficiency of in-situ bioremediation of V(V) polluted groundwater.

  4. Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell

    NASA Astrophysics Data System (ADS)

    Dhar, Bipro Ranjan; Ryu, Hodon; Santo Domingo, Jorge W.; Lee, Hyung-Sool

    2016-11-01

    Multi-anode microbial electrochemical cells (MxCs) are considered as one of the most promising configurations for scale-up of MxCs, but understanding of anode kinetics in multiple anodes is limited in the MxCs. In this study we assessed microbial community and electrochemical kinetic parameters for biofilms on individual anodes in a multi-anode MxC to better comprehend anode fundamentals. Microbial community analysis targeting 16S rRNA Illumina sequencing showed that Geobacter genus was abundant (87%) only on the biofilm anode closest to a reference electrode (low ohmic energy loss) in which current density was the highest among three anodes. In comparison, Geobacter populations were less than 1% for biofilms on other two anodes distant from the reference electrode (high ohmic energy loss), generating small current density. Half-saturation anode potential (EKA) was the lowest at -0.251 to -0.242 V (vs. standard hydrogen electrode) for the closest biofilm anode to the reference electrode, while EKA was as high as -0.134 V for the farthest anode. Our study proves that electric potential of individual anodes changed by ohmic energy loss shifts biofilm communities on individual anodes and consequently influences electron transfer kinetics on each anode in the multi-anode MxC.

  5. Investigational cell cycle inhibitors in clinical trials for bladder cancer.

    PubMed

    Yun, Seok Joong; Moon, Sung-Kwon; Kim, Wun-Jae

    2013-03-01

    Cancer-related cell cycle defects are often mediated by alterations in activity of diverse cell cycle regulators. The development of cell cycle inhibitors has undergone a gradual evolution, and new investigational drugs have been extensively tested as a single agent or combination with conventional chemotherapeutic drugs. This review covers a broad perspective of how the cell cycle is deregulated in bladder cancer and discusses the clinical trials of cell cycle inhibitors. Although diverse cell cycle inhibitors have been considered as relevant drug candidates for cancer therapy owing to their potential role in restoring control of the cell cycle, these inhibitors have not been yet widely tested in human bladder cancer. Numerous studies already reported that deregulation of cell cycle controls has been commonly observed in bladder cancer cells, thus warranting clinical trials of these inhibitors in advanced bladder cancer patients. In addition, nonmuscle invasive bladder cancer (NMIBC) and muscle invasive bladder cancer (MIBC) show different clinical and molecular biological characteristics, although ∼ 10 - 20% of NMIBC will progress to MIBC. Therefore, adequate cell cycle inhibitors have to be chosen for bladder cancer treatment based on the different genetic features between NMIBC and MIBC related to cell cycle regulators.

  6. Microbial community structures differentiated in a single-chamber air-cathode microbial fuel cell fueled with rice straw hydrolysate.

    PubMed

    Wang, Zejie; Lee, Taekwon; Lim, Bongsu; Choi, Chansoo; Park, Joonhong

    2014-01-17

    The microbial fuel cell represents a novel technology to simultaneously generate electric power and treat wastewater. Both pure organic matter and real wastewater can be used as fuel to generate electric power and the substrate type can influence the microbial community structure. In the present study, rice straw, an important feedstock source in the world, was used as fuel after pretreatment with diluted acid method for a microbial fuel cell to obtain electric power. Moreover, the microbial community structures of anodic and cathodic biofilm and planktonic culturewere analyzed and compared to reveal the effect of niche on microbial community structure. The microbial fuel cell produced a maximum power density of 137.6 ± 15.5 mW/m2 at a COD concentration of 400 mg/L, which was further increased to 293.33 ± 7.89 mW/m2 through adjusting the electrolyte conductivity from 5.6 mS/cm to 17 mS/cm. Microbial community analysis showed reduction of the microbial diversities of the anodic biofilm and planktonic culture, whereas diversity of the cathodic biofilm was increased. Planktonic microbial communities were clustered closer to the anodic microbial communities compared to the cathodic biofilm. The differentiation in microbial community structure of the samples was caused by minor portion of the genus. The three samples shared the same predominant phylum of Proteobacteria. The abundance of exoelectrogenic genus was increased with Desulfobulbus as the shared most abundant genus; while the most abundant exoelectrogenic genus of Clostridium in the inoculum was reduced. Sulfate reducing bacteria accounted for large relative abundance in all the samples, whereas the relative abundance varied in different samples. The results demonstrated that rice straw hydrolysate can be used as fuel for microbial fuel cells; microbial community structure differentiated depending on niches after microbial fuel cell operation; exoelectrogens were enriched; sulfate from rice straw

  7. Microbial cell retention in a melting High Arctic snowpack, Svalbard

    NASA Astrophysics Data System (ADS)

    Zarsky, Jakub; Björkman, Mats; Kühnel, Rafael; Hell, Katherina; Hodson, Andy; Sattler, Birgit; Psenner, Roland

    2014-05-01

    Introduction The melting snow pack represents a highly dynamic system not only for chemical compounds but also for bacterial cells. Microbial activity was found at subzero temperatures in ice veins when liquid water persists due to high concentration of ions on the surface of snow crystals and brine channels between large ice crystals in ice. Several observations also suggest microbial activity under subzero temperatures in seasonal snow. Even with regard to the spatial and temporal relevance of snow ecosystems, microbial activity in such an extreme habitat represents a relatively small proportion in the carbon flux of the global ecosystem and even of the glacial ecosystems specifically. On the other hand, it represents a remarkable piece of mosaic of the microbial activity in glacial ecosystems because the snow pack represents the first contact between the atmosphere and cryosphere. This topic also embodies vital crossovers to biogeochemistry and ecotoxicology, offering a quantitative view of utilization of various substrates relevant for downstream ecosystems. Here we present our study of the dynamics of both solvents and cells suspended in meltwater of the melting snowpack on a high arctic glacier to demonstrate the spatio-temporal constraint of interaction between solvent and bacterial cells in this environment. Method We used 6 lysimeters inserted into the bottom of the snowpack to collect replicated samples of melt water before it comes into contact with basal ice or slush layer at the base of the snow pack. The sampling site was chosen at Midre Lovénbreen (Svalbard, Kongsfjorden, MLB stake 6) where the snow pack showed melting on the surface but the basal ice was still dry. Sampling was conducted in June 2010 for a period of 10 days once per day and the snow profile was sampled according to distinguished layers in the profile at the beginning of the field mission and as bulk at its end. The height of snow above the lysimeters dropped from the initial 74 cm

  8. Composite materials for polymer electrolyte membrane microbial fuel cells.

    PubMed

    Antolini, Ermete

    2015-07-15

    Recently, the feasibility of using composite metal-carbon, metal-polymer, polymer-carbon, polymer-polymer and carbon-carbon materials in microbial fuel cells (MFCs) has been investigated. These materials have been tested as MFC anode catalyst (microorganism) supports, cathode catalysts and membranes. These hybrid materials, possessing the properties of each component, or even with a synergistic effect, would present improved characteristics with respect to the bare components. In this paper we present an overview of the use of these composite materials in microbial fuel cells. The characteristics of the composite materials as well as their effect on MFC performance were compared with those of the individual component and/or the conventionally used materials.

  9. Produced Water Treatment Using Microbial Fuel Cell Technology

    SciTech Connect

    Borole, A. P.; Campbell, R.

    2011-05-20

    ORNL has developed a treatment for produced water using a combination of microbial fuel cells and electrosorption. A collaboration between Campbell Applied Physics and ORNL was initiated to further investigate development of the technology and apply it to treatment of field produced water. The project successfully demonstrated the potential of microbial fuel cells to generate electricity from organics in produced water. A steady voltage was continuously generated for several days using the system developed in this study. In addition to the extraction of electrical energy from the organic contaminants, use of the energy at the representative voltage was demonstrated for salts removal or desalination of the produced water. Thus, the technology has potential to remove organic as well as ionic contaminants with minimal energy input using this technology. This is a novel energy-efficient method to treat produced water. Funding to test the technology at larger scale is being pursued to enable application development.

  10. Recent developments in microbial fuel cell technologies for sustainable bioenergy.

    PubMed

    Watanabe, Kazuya

    2008-12-01

    Microbial fuel cells (MFCs) are devices that exploit microbial catabolic activities to generate electricity from a variety of materials, including complex organic waste and renewable biomass. These sources provide MFCs with a great advantage over chemical fuel cells that can utilize only purified reactive fuels (e.g., hydrogen). A developing primary application of MFCs is its use in the production of sustainable bioenergy, e.g., organic waste treatment coupled with electricity generation, although further technical developments are necessary for its practical use. In this article, recent advances in MFC technologies that can become fundamentals for future practical MFC developments are summarized. Results of recent studies suggest that MFCs will be of practical use in the near future and will become a preferred option among sustainable bioenergy processes.

  11. Profiling Hyporheic Microbial Community Nitrogen Cycle and Carbohydrate Active Enzyme Gene Abundances across Seasons

    NASA Astrophysics Data System (ADS)

    Nelson, W. C.; Graham, E.; Stegen, J.

    2016-12-01

    The hyporheic zone (HZ) is the permanently inundated sediment layer between a surface channel and adjacent groundwater-saturated sediments. It has been hypothesized to play a major role in macronutrient (C, N, P) cycling in rivers. The correlation between community taxonomic composition dynamics and functional gene representation is poorly understood for hyporheic communities. To explore how microbial communities respond to temporal changes in environmental conditions, metagenomes were derived from communities captured in sterile sandpacks deployed within the HZ of the Columbia River. HMM databases were used to enumerate protein families present. Functional classification of reads allowed a general assessment of community function over time, while targeted assembly of specific genes enabled investigation of the diversity of organisms encoding these functions. Preliminary analysis of nitrogen cycle pathways shows most gene families examined to have quite steady representation across seasons, with most observed changes being less than an order of magnitude. Analysis of ammonia oxidation genes showed bacterial ammonia oxidizers (AOB) to be stably present across the year, while the archaeal amoA gene increased in late summer, peaking sharply in November, mirroring results from 16S rRNA amplicon analysis which showed an increase in Thaumarcheal OTUs during that same period. Most glycosyl hydrolase GH families had low representation. Highly abundant classes of GH included the GH94 (beta-glucosidase), GH95 (1-2-alpha-L-fucosidase) and GH103 (lytic transglycosylase) families, suggesting activity on plant, fungus and insect polysaccharides and peptidoglycans. Further work is investigating the taxonomy of the sequences identified, to determine how changes in the community composition contribute to the stable gene family profiles observed. These results are intended to work towards a greater understanding of the role of species diversity and functional redundancy in the

  12. Classic "broken cell" techniques and newer live cell methods for cell cycle assessment.

    PubMed

    Henderson, Lindsay; Bortone, Dante S; Lim, Curtis; Zambon, Alexander C

    2013-05-15

    Many common, important diseases are either caused or exacerbated by hyperactivation (e.g., cancer) or inactivation (e.g., heart failure) of the cell division cycle. A better understanding of the cell cycle is critical for interpreting numerous types of physiological changes in cells. Moreover, new insights into how to control it will facilitate new therapeutics for a variety of diseases and new avenues in regenerative medicine. The progression of cells through the four main phases of their division cycle [G(0)/G(1), S (DNA synthesis), G(2), and M (mitosis)] is a highly conserved process orchestrated by several pathways (e.g., transcription, phosphorylation, nuclear import/export, and protein ubiquitination) that coordinate a core cell cycle pathway. This core pathway can also receive inputs that are cell type and cell niche dependent. "Broken cell" methods (e.g., use of labeled nucleotide analogs) to assess for cell cycle activity have revealed important insights regarding the cell cycle but lack the ability to assess living cells in real time (longitudinal studies) and with single-cell resolution. Moreover, such methods often require cell synchronization, which can perturb the pathway under study. Live cell cycle sensors can be used at single-cell resolution in living cells, intact tissue, and whole animals. Use of these more recently available sensors has the potential to reveal physiologically relevant insights regarding the normal and perturbed cell division cycle.

  13. USE OF THE COMPOSITION AND STABLE CARBONIISOTOPE RATIO OF MICROBIAL FATTY ACIDS TO STUDY CARBON CYCLING

    EPA Science Inventory

    We use measurements of the concentration and stable carbon isotopic ratio (*13C) of individual microbial phospholipid fatty acids (PLFAs) in soils and sediments as indicators of live microbial biomass levels and microbial carbon source. For studies of soil organic matter (SOM) cy...

  14. USE OF THE COMPOSITION AND STABLE CARBONIISOTOPE RATIO OF MICROBIAL FATTY ACIDS TO STUDY CARBON CYCLING

    EPA Science Inventory

    We use measurements of the concentration and stable carbon isotopic ratio (*13C) of individual microbial phospholipid fatty acids (PLFAs) in soils and sediments as indicators of live microbial biomass levels and microbial carbon source. For studies of soil organic matter (SOM) cy...

  15. A deregulated intestinal cell cycle program disrupts tissue homeostasis without affecting longevity in Drosophila.

    PubMed

    Petkau, Kristina; Parsons, Brendon D; Duggal, Aashna; Foley, Edan

    2014-10-10

    Recent studies illuminate a complex relationship between the control of stem cell division and intestinal tissue organization in the model system Drosophila melanogaster. Host and microbial signals drive intestinal proliferation to maintain an effective epithelial barrier. Although it is widely assumed that proliferation induces dysplasia and shortens the life span of the host, the phenotypic consequences of deregulated intestinal proliferation for an otherwise healthy host remain unexplored. To address this question, we genetically isolated and manipulated the cell cycle programs of adult stem cells and enterocytes. Our studies revealed that cell cycle alterations led to extensive cell death and morphological disruptions. Despite the extensive tissue damage, we did not observe an impact on longevity, suggesting a remarkable degree of plasticity in intestinal function.

  16. The Cell Cycle Switch Computes Approximate Majority

    NASA Astrophysics Data System (ADS)

    Cardelli, Luca; Csikász-Nagy, Attila

    2012-09-01

    Both computational and biological systems have to make decisions about switching from one state to another. The `Approximate Majority' computational algorithm provides the asymptotically fastest way to reach a common decision by all members of a population between two possible outcomes, where the decision approximately matches the initial relative majority. The network that regulates the mitotic entry of the cell-cycle in eukaryotes also makes a decision before it induces early mitotic processes. Here we show that the switch from inactive to active forms of the mitosis promoting Cyclin Dependent Kinases is driven by a system that is related to both the structure and the dynamics of the Approximate Majority computation. We investigate the behavior of these two switches by deterministic, stochastic and probabilistic methods and show that the steady states and temporal dynamics of the two systems are similar and they are exchangeable as components of oscillatory networks.

  17. Local circadian clock gates cell cycle progression of transient amplifying cells during regenerative hair cycling

    PubMed Central

    Plikus, Maksim V.; Vollmers, Christopher; de la Cruz, Damon; Chaix, Amandine; Ramos, Raul; Panda, Satchidananda; Chuong, Cheng-Ming

    2013-01-01

    Regenerative cycling of hair follicles offers an unique opportunity to explore the role of circadian clock in physiological tissue regeneration. We focused on the role of circadian clock in actively proliferating transient amplifying cells, as opposed to quiescent stem cells. We identified two key sites of peripheral circadian clock activity specific to regenerating anagen hair follicles, namely epithelial matrix and mesenchymal dermal papilla. We showed that peripheral circadian clock in epithelial matrix cells generates prominent daily mitotic rhythm. As a consequence of this mitotic rhythmicity, hairs grow faster in the morning than in the evening. Because cells are the most susceptible to DNA damage during mitosis, this cycle leads to a remarkable time-of-day–dependent sensitivity of growing hair follicles to genotoxic stress. Same doses of γ-radiation caused dramatic hair loss in wild-type mice when administered in the morning, during mitotic peak, compared with the evening, when hair loss is minimal. This diurnal radioprotective effect becomes lost in circadian mutants, consistent with asynchronous mitoses in their hair follicles. Clock coordinates cell cycle progression with genotoxic stress responses by synchronizing Cdc2/Cyclin B-mediated G2/M checkpoint. Our results uncover diurnal mitotic gating as the essential protective mechanism in highly proliferative hair follicles and offer strategies for minimizing or maximizing cytotoxicity of radiation therapies. PMID:23690597

  18. New insights in Microbial Fuel Cells: novel solid phase anolyte

    NASA Astrophysics Data System (ADS)

    Tommasi, Tonia; Salvador, Gian Paolo; Quaglio, Marzia

    2016-07-01

    For the development of long lasting portable microbial fuel cells (MFCs) new strategies are necessary to overcome critical issues such as hydraulic pump system and the biochemical substrate retrieval overtime to sustain bacteria metabolism. The present work proposes the use of a synthetic solid anolyte (SSA), constituted by agar, carbonaceous and nitrogen sources dissolved into diluted seawater. Results of a month-test showed the potential of the new SSA-MFC as a long lasting low energy consuming system.

  19. New insights in Microbial Fuel Cells: novel solid phase anolyte

    PubMed Central

    Tommasi, Tonia; Salvador, Gian Paolo; Quaglio, Marzia

    2016-01-01

    For the development of long lasting portable microbial fuel cells (MFCs) new strategies are necessary to overcome critical issues such as hydraulic pump system and the biochemical substrate retrieval overtime to sustain bacteria metabolism. The present work proposes the use of a synthetic solid anolyte (SSA), constituted by agar, carbonaceous and nitrogen sources dissolved into diluted seawater. Results of a month-test showed the potential of the new SSA-MFC as a long lasting low energy consuming system. PMID:27375205

  20. New insights in Microbial Fuel Cells: novel solid phase anolyte.

    PubMed

    Tommasi, Tonia; Salvador, Gian Paolo; Quaglio, Marzia

    2016-07-04

    For the development of long lasting portable microbial fuel cells (MFCs) new strategies are necessary to overcome critical issues such as hydraulic pump system and the biochemical substrate retrieval overtime to sustain bacteria metabolism. The present work proposes the use of a synthetic solid anolyte (SSA), constituted by agar, carbonaceous and nitrogen sources dissolved into diluted seawater. Results of a month-test showed the potential of the new SSA-MFC as a long lasting low energy consuming system.

  1. Enzyme Amplified Detection of Microbial Cell Wall Components

    NASA Technical Reports Server (NTRS)

    Wainwright, Norman R.

    2004-01-01

    This proposal is MBL's portion of NASA's Johnson Space Center's Astrobiology Center led by Principal Investigator, Dr. David McKay, entitled: 'Institute for the Study of Biomarkers in Astromaterials.' Dr. Norman Wainwright is the principal investigator at MBL and is responsible for developing methods to detect trace quantities of microbial cell wall chemicals using the enzyme amplification system of Limulus polyphemus and other related methods.

  2. Enzyme Amplified Detection of Microbial Cell Wall Components

    NASA Technical Reports Server (NTRS)

    Wainwright, Norman R.

    2004-01-01

    This proposal is MBL's portion of NASA's Johnson Space Center's Astrobiology Center led by Principal Investigator, Dr. David McKay, entitled: 'Institute for the Study of Biomarkers in Astromaterials.' Dr. Norman Wainwright is the principal investigator at MBL and is responsible for developing methods to detect trace quantities of microbial cell wall chemicals using the enzyme amplification system of Limulus polyphemus and other related methods.

  3. Turnover of microbial groups and cell components in soil: 13C analysis of cellular biomarkers

    NASA Astrophysics Data System (ADS)

    Gunina, Anna; Dippold, Michaela; Glaser, Bruno; Kuzyakov, Yakov

    2017-01-01

    Microorganisms regulate the carbon (C) cycle in soil, controlling the utilization and recycling of organic substances. To reveal the contribution of particular microbial groups to C utilization and turnover within the microbial cells, the fate of 13C-labelled glucose was studied under field conditions. Glucose-derived 13C was traced in cytosol, amino sugars and phospholipid fatty acid (PLFA) pools at intervals of 3, 10 and 50 days after glucose addition into the soil. 13C enrichment in PLFAs ( ˜ 1.5 % of PLFA C at day 3) was an order of magnitude greater than in cytosol, showing the importance of cell membranes for initial C utilization. The 13C enrichment in amino sugars of living microorganisms at day 3 accounted for 0.57 % of total C pool; as a result, we infer that the replacement of C in cell wall components is 3 times slower than that of cell membranes. The C turnover time in the cytosol (150 days) was 3 times longer than in PLFAs (47 days). Consequently, even though the cytosol pool has the fastest processing rates compared to other cellular compartments, intensive recycling of components here leads to a long C turnover time. Both PLFA and amino-sugar profiles indicated that bacteria dominated in glucose utilization. 13C enrichment decreased with time for bacterial cell membrane components, but it remained constant or even increased for filamentous microorganisms. 13C enrichment of muramic acid was the 3.5 times greater than for galactosamine, showing a more rapid turnover of bacterial cell wall components compared to fungal. Thus, bacteria utilize a greater proportion of low-molecular-weight organic substances, whereas filamentous microorganisms are responsible for further C transformations. Thus, tracing 13C in cellular compounds with contrasting turnover rates elucidated the role of microbial groups and their cellular compartments in C utilization and recycling in soil. The results also reflect that microbial C turnover is not restricted to the death or

  4. Electricity generation from synthesis gas by microbial processes: CO fermentation and microbial fuel cell technology.

    PubMed

    Kim, Daehee; Chang, In Seop

    2009-10-01

    A microbiological process was established to harvest electricity from the carbon monoxide (CO). A CO fermenter was enriched with CO as the sole carbon source. The DGGE/DNA sequencing results showed that Acetobacterium spp. were enriched from the anaerobic digester fluid. After the fermenter was operated under continuous mode, the products were then continuously fed to the microbial fuel cell (MFC) to generate electricity. Even though the conversion yield was quite low, this study proved that synthesis gas (syn-gas) can be converted to electricity with the aid of microbes that do not possess the drawbacks of metal catalysts of conventional methods.

  5. Stable Isotope Phenotyping via Cluster Analysis of NanoSIMS Data As a Method for Characterizing Distinct Microbial Ecophysiologies and Sulfur-Cycling in the Environment

    PubMed Central

    Dawson, Katherine S.; Scheller, Silvan; Dillon, Jesse G.; Orphan, Victoria J.

    2016-01-01

    Stable isotope probing (SIP) is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS), allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH) microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with 13C-acetate, 15N-ammonium, and 33S-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope (13C/12C, 15N/14N, and 33S/32S) and elemental ratio (C/CN and S/CN) profiles, our analysis partitioned ~2200 cellular regions of interest (ROIs) into five distinct groups. These isotope phenotype groupings are reflective of the variation in labeled substrate uptake by cells in a multispecies metabolic network dominated by Gamma- and Deltaproteobacteria. Populations independently grouped by isotope phenotype were subsequently compared with paired FISH data, demonstrating a single coherent deltaproteobacterial cluster and multiple gammaproteobacterial groups, highlighting the distinct ecophysiologies of spatially-associated microbes within the sulfur-cycling biofilm from White Point Beach, CA. PMID:27303371

  6. Stable isotope phenotyping via cluster analysis of NanoSIMS data as a method for characterizing distinct microbial ecophysiologies and sulfur-cycling in the environment

    NASA Astrophysics Data System (ADS)

    Dawson, K.; Scheller, S.; Dillon, J. G.; Orphan, V. J.

    2016-12-01

    Stable isotope probing (SIP) is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS), allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH) microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with 13C-acetate, 15N-ammonium, and 33S-sulfate. Using a cluster analysis