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Sample records for yeast population dynamics

  1. Yeast population dynamics during prefermentative cold soak of Cabernet Sauvignon and Malbec wines.

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    Maturano, Y Paola; Mestre, M Victoria; Esteve-Zarzoso, Braulio; Nally, María Cristina; Lerena, María Cecilia; Toro, María Eugenia; Vazquez, Fabio; Combina, Mariana

    2015-04-16

    Prefermentative cold soak is a widely used technique in red wine production, but the impact on the development of native yeast species is hardly described. The aim of this work was to analyse the dynamics and diversity of yeast populations during prefermentative cold soak in red wines. Three different temperatures (14 ± 1 °C; 8 ± 1 °C and 2.5 ± 1 °C) were used for prefermentative cold soak in Cabernet Sauvignon and Malbec grape musts. Saccharomyces and non-Saccharomyces populations during cold soak and alcoholic fermentation were analysed. In addition, the impact on chemical and sensory properties of the wines was examined. Yeast dynamics during prefermentative cold soak were temperature dependent. At 14 ± 1 °C, the total yeast population progressively increased throughout the cold soak period. Conversely, at 2.5 ± 1 °C, the yeast populations maintained stable during the same period. Prefermentative cold soak conducted at 14±1°C favoured development of Hanseniospora uvarum and Candida zemplinina, whereas cold soak conducted at 8 ± 1 °C favoured growth of Saccharomyces cerevisiae. At 2.5 ± 1 °C, no changes in yeast species were recorded. Acidity and bitterness, two sensory descriptors, appear to be related to wines produced with prefermentative cold soak carried out at 14 ± 1 °C. This fact could be associated with the increase in non-Saccharomyces during the prefermentation stage. Our results emphasise the importance of the temperature as a determinant factor to allow an increase in non-Saccharomyces population during prefermentative cold soak and consequently to modify sensorial attributes of wines as well as their sensorial impact. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Yeast Population Dynamics in Spontaneous and Inoculated Alcoholic Fermentations of Zametovka Must

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    Franc Cus

    2002-01-01

    Full Text Available Inoculated fermentations, which are more rapid and more reliable than spontaneous fermentations, and assure predictable wine quality, are nowadays prevalent in Slovenia’s large-scale wine production. However, spontaneous fermentation strengthens local characteristics of wine and offers opportunities for technological innovation. In the 1999 vintage, spontaneous and inoculated fermentations of Zametovka (Vitis vinifera grape must were studied. Zametovka is the main red variety in production of traditional Slovene red blend wine, Cvicek. The diversity of yeast species and strains in both of the investigated fermentations was determined by molecular and traditional identification methods. The outset of alcoholic fermentation, yeast growth kinetics, and yeast population dynamics presents the main differences between the examined fermentations. Yeast population diversity was higher in the spontaneous process. Dominant yeast isolates from spontaneous fermentation were identified as Candida stellata, Hanseniaspora uvarum and Saccharomyces cerevisiae; whereas Saccharomyces bayanus, Pichia kluyveri, Pichia membranifaciens and Torulaspora delbrueckiim were found less frequently. Dominant species in the inoculated fermentation was Saccharomyces cerevisiae; other species found in smaller numbers were Candida stellata, Hanseniaspora uvarum and Debaryomyces hansenii var. hansenii. Using PFGE, we were able to distinguish among 15 different Saccharomyces cerevisiae strains and three different Saccharomyces bayanus strains isolated from spontaneous fermentation, whereas, in the case of inoculated fermentation, only two Saccharomyces cerevisiae strains were found. Their chromosomal patterns coincide with the chromosomal patterns of the starter culture strains.

  3. Population dynamics of mixed cultures of yeast and lactic acid bacteria in cider conditions

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    Leila Roseli Dierings

    2013-10-01

    Full Text Available The objective of this work was to study the malolactic bioconversion in low acidity cider, according Brazilian conditions. The apple must was inoculated with Saccharomyces cerevisiae or S. cerevisiae with Oenococcus oeni. The control contained the indigenous microorganisms. Fermentation assays were carried out with clarified apple must from the Gala variety. At the beginning of fermentation, there was a fast growth of the non-Saccharomyces yeast population. Competitive inhibition occurred in all the assays, either with inoculated or indigenous populations of the yeast. The lactic acid bacteria count was ca. 1.41·10²CFU/mL at the beginning and 10(6CFU/mL after yeast cells autolysis. The lactic bacteria O. oeni reached the highest population (10(7CFU/mL when added to the apple must after the decline of the yeast. The malic acid was totally consumed during the alcoholic fermentation period (80.0 to 95.5 % and lactic acid was still synthesized during the 35 days of malolactic fermentation. These results could be important in order to achieve a high quality brut, or sec cider obtained from the dessert apple must.

  4. The Rise and Fall of a Yeast Community, An Environmental Investigation into the Dynamics of Population Growth.

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    Minnesota Environmental Sciences Foundation, Inc., Minneapolis.

    In this unit students study populations by observing some of the activities that go on in one particular population. Specifically, yeast plants are examined and some of the effects which various environmental factors have on yeast plant populations are investigated. A population curve is developed showing how easily it is affected by the…

  5. Yeast population dynamics reveal a potential 'collaboration' between Metschnikowia pulcherrima and Saccharomyces uvarum for the production of reduced alcohol wines during Shiraz fermentation.

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    Contreras, A; Curtin, C; Varela, C

    2015-02-01

    The wine sector is actively seeking strategies and technologies that facilitate the production of wines with lower alcohol content. One of the simplest approaches to achieve this aim would be the use of wine yeast strains which are less efficient at transforming grape sugars into ethanol; however, commercial wine yeasts have very similar ethanol yields. We recently demonstrated that Metschnikowia pulcherrima AWRI1149 was able to produce wine with reduced alcohol concentration when used in sequential inoculation with a wine strain of Saccharomyces cerevisiae. Here, different inoculation regimes were explored to study the effect of yeast population dynamics and potential yeast interactions on the metabolism of M. pulcherrima AWRI1149 during fermentation of non-sterile Shiraz must. Of all inoculation regimes tested, only ferments inoculated with M. pulcherrima AWRI1149 showed reduced ethanol concentration. Population dynamics revealed the presence of several indigenous yeast species and one of these, Saccharomyces uvarum (AWRI 2846), was able to produce wine with reduced ethanol concentration in sterile conditions. Both strains however, were inhibited when a combination of three non-Saccharomyces strains, Hanseniaspora uvarum AWRI863, Pichia kluyveri AWRI1896 and Torulaspora delbrueckii AWRI2845 were inoculated into must, indicating that the microbial community composition might impact on the growth of M. pulcherrima AWRI1149 and S. uvarum AWRI 2846. Our results indicate that mixed cultures of M. pulcherrima AWRI1149 and S. uvarum AWRI2846 enable an additional reduction of wine ethanol concentration compared to the same must fermented with either strain alone. This work thus provides a foundation to develop inoculation regimes for the successful application of non-cerevisiae yeast to the production of wines with reduced alcohol.

  6. Dynamics of Cocoa Bean Pulp Degradation during Cocoa Bean Fermentation: Effects of Yeast Starter Culture Addition

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    Laras Cempaka

    2014-07-01

    Full Text Available Fermentation is a crucial step in the post-harvest processing of cocoa beans. This process comprises mixed culture microbial activities on the cocoa bean pulp, producing metabolites that act as important precursors for cocoa flavour development. Variations in the microbial population dynamics during the fermentation process may induce changes in the overall process. Thus, the introduction of a specific microbial starter culture may improve the quality of the fermentation. This article discusses the effects ofthe addition of Saccharomyces cerevisae var. Chevalieri starter culture on cocoa bean fermentation. The dynamics in the yeast concentration, sugary pulp compounds and metabolic products were measured during fermentation. The alterations in the dynamic metabolite profile were significant, although only a slight difference was observed in the yeast population. A higher fermentation index was measured for the cocoa bean fermentation with yeast starter culture, 1.13 compared to 0.84. In conclusion, this method can potentially be applied to shorten the cocoa bean fermentation time.

  7. Outcrossed sex allows a selfish gene to invade yeast populations.

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    Goddard, M. R.; Greig, D.; Burt, A.

    2001-01-01

    Homing endonuclease genes (HEGs) in eukaryotes are optional genes that have no obvious effect on host phenotype except for causing chromosomes not containing a copy of the gene to be cut, thus causing them to be inherited at a greater than Mendelian rate via gene conversion. These genes are therefore expected to increase in frequency in outcrossed populations, but not in obligately selfed populations. In order to test this idea, we compared the dynamics of the VDE HEG in six replicate outcrossed and inbred populations of yeast (Saccharomyces cerevisiae). VDE increased in frequency from 0.21 to 0.55 in four outcrossed generations, but showed no change in frequency in the inbred populations. The absence of change in the inbred populations indicates that any effect of VDE on mitotic replication rates is less than 1%. The data from the outcrossed populations best fit a model in which 82% of individuals are derived from outcrossing and VDE is inherited by 74% of the meiotic products from heterozygotes (as compared with 50% for Mendelian genes). These results empirically demonstrate how a host mating system plays a key role in determining the population dynamics of a selfish gene. PMID:11749707

  8. Outcrossed sex allows a selfish gene to invade yeast populations.

    Science.gov (United States)

    Goddard, M R; Greig, D; Burt, A

    2001-12-22

    Homing endonuclease genes (HEGs) in eukaryotes are optional genes that have no obvious effect on host phenotype except for causing chromosomes not containing a copy of the gene to be cut, thus causing them to be inherited at a greater than Mendelian rate via gene conversion. These genes are therefore expected to increase in frequency in outcrossed populations, but not in obligately selfed populations. In order to test this idea, we compared the dynamics of the VDE HEG in six replicate outcrossed and inbred populations of yeast (Saccharomyces cerevisiae). VDE increased in frequency from 0.21 to 0.55 in four outcrossed generations, but showed no change in frequency in the inbred populations. The absence of change in the inbred populations indicates that any effect of VDE on mitotic replication rates is less than 1%. The data from the outcrossed populations best fit a model in which 82% of individuals are derived from outcrossing and VDE is inherited by 74% of the meiotic products from heterozygotes (as compared with 50% for Mendelian genes). These results empirically demonstrate how a host mating system plays a key role in determining the population dynamics of a selfish gene.

  9. Yeast dynamics during spontaneous fermentation of mawe and tchoukoutou, two traditional products from Benin

    DEFF Research Database (Denmark)

    Greppi, Anna; Rantisou, Kalliopi; Padonou, Wilfrid

    2013-01-01

    Mawe and tchoukoutou are two traditional fermented foods largely consumed in Benin, West Africa. Their preparations remain as a house art and they are the result of spontaneous fermentation processes. In this study, dynamics of the yeast populations occurring during spontaneous fermentations...... of mawe and tchoukoutou were investigated using both culture-dependent and -independent approaches. For each product, two productions were followed. Samples were taken at different fermentation times and yeasts were isolated, resulting in the collection of 177 isolates. They were identified by the PCR......-DGGE technique followed by the sequencing of the D1/D2 domain of the 26S rRNA gene. The predominant yeast species identified were typed by rep-PCR. Candida krusei was the predominant yeast species in mawe fermentation followed by Candida glabrata and Kluyveromyces marxianus. Other yeast species were detected...

  10. Occurrence of Killer Yeast Strains in Fruit and Berry Wine Yeast Populations

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    Gintare Gulbiniene

    2004-01-01

    Full Text Available Apple, cranberry, chokeberry and Lithuanian red grape wine yeast populations were used for the determination of killer yeast occurrence. According to the tests of the killer characteristics and immunity the isolated strains were divided into seven groups. In this work the activity of killer toxins purified from some typical strains was evaluated. The analysed strains produced different amounts of active killer toxin and some of them possessed new industrially significant killer properties. Total dsRNA extractions in 11 killer strains of yeast isolated from spontaneous fermentations revealed that the molecular basis of the killer phenomenon was not only dsRNAs, but also unidentified genetic determinants.

  11. Game dynamic model for yeast development.

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    Huang, Yuanyuan; Wu, Zhijun

    2012-07-01

    Game theoretic models, along with replicator equations, have been applied successfully to the study of evolution of populations of competing species, including the growth of a population, the reaching of the population to an equilibrium state, and the evolutionary stability of the state. In this paper, we analyze a game model proposed by Gore et al. (Nature 456:253-256, 2009) in their recent study on the co-development of two mixed yeast strains. We examine the mathematical properties of this model with varying experimental parameters. We simulate the growths of the yeast strains and compare them with the experimental results. We also compute and analyze the equilibrium state of the system and prove that it is asymptotically and evolutionarily stable.

  12. Measuring mitotic spindle dynamics in budding yeast

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    Plumb, Kemp

    In order to carry out its life cycle and produce viable progeny through cell division, a cell must successfully coordinate and execute a number of complex processes with high fidelity, in an environment dominated by thermal noise. One important example of such a process is the assembly and positioning of the mitotic spindle prior to chromosome segregation. The mitotic spindle is a modular structure composed of two spindle pole bodies, separated in space and spanned by filamentous proteins called microtubules, along which the genetic material of the cell is held. The spindle is responsible for alignment and subsequent segregation of chromosomes into two equal parts; proper spindle positioning and timing ensure that genetic material is appropriately divided amongst mother and daughter cells. In this thesis, I describe fluorescence confocal microscopy and automated image analysis algorithms, which I have used to observe and analyze the real space dynamics of the mitotic spindle in budding yeast. The software can locate structures in three spatial dimensions and track their movement in time. By selecting fluorescent proteins which specifically label the spindle poles and cell periphery, mitotic spindle dynamics have been measured in a coordinate system relevant to the cell division. I describe how I have characterised the accuracy and precision of the algorithms by simulating fluorescence data for both spindle poles and the budding yeast cell surface. In this thesis I also describe the construction of a microfluidic apparatus that allows for the measurement of long time-scale dynamics of individual cells and the development of a cell population. The tools developed in this thesis work will facilitate in-depth quantitative analysis of the non-equilibrium processes in living cells.

  13. Population FBA predicts metabolic phenotypes in yeast.

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    Piyush Labhsetwar

    2017-09-01

    Full Text Available Using protein counts sampled from single cell proteomics distributions to constrain fluxes through a genome-scale model of metabolism, Population flux balance analysis (Population FBA successfully described metabolic heterogeneity in a population of independent Escherichia coli cells growing in a defined medium. We extend the methodology to account for correlations in protein expression arising from the co-regulation of genes and apply it to study the growth of independent Saccharomyces cerevisiae cells in two different growth media. We find the partitioning of flux between fermentation and respiration predicted by our model agrees with recent 13C fluxomics experiments, and that our model largely recovers the Crabtree effect (the experimentally known bias among certain yeast species toward fermentation with the production of ethanol even in the presence of oxygen, while FBA without proteomics constraints predicts respirative metabolism almost exclusively. The comparisons to the 13C study showed improvement upon inclusion of the correlations and motivated a technique to systematically identify inconsistent kinetic parameters in the literature. The minor secretion fluxes for glycerol and acetate are underestimated by our method, which indicate a need for further refinements to the metabolic model. For yeast cells grown in synthetic defined (SD medium, the calculated broad distribution of growth rates matches experimental observations from single cell studies, and we characterize several metabolic phenotypes within our modeled populations that make use of diverse pathways. Fast growing yeast cells are predicted to perform significant amount of respiration, use serine-glycine cycle and produce ethanol in mitochondria as opposed to slow growing cells. We use a genetic algorithm to determine the proteomics constraints necessary to reproduce the growth rate distributions seen experimentally. We find that a core set of 51 constraints are essential but

  14. Evolutionary Dynamics and Diversity in Microbial Populations

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    Thompson, Joel; Fisher, Daniel

    2013-03-01

    Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

  15. Characterization, Ecological Distribution, and Population Dynamics of Saccharomyces Sensu Stricto Killer Yeasts in the Spontaneous Grape Must Fermentations of Southwestern Spain

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    Maqueda, Matilde; Zamora, Emiliano; Álvarez, María L.

    2012-01-01

    Killer yeasts secrete protein toxins that are lethal to sensitive strains of the same or related yeast species. Among the four types of Saccharomyces killer yeasts already described (K1, K2, K28, and Klus), we found K2 and Klus killer yeasts in spontaneous wine fermentations from southwestern Spain. Both phenotypes were encoded by medium-size double-stranded RNA (dsRNA) viruses, Saccharomyces cerevisiae virus (ScV)-M2 and ScV-Mlus, whose genome sizes ranged from 1.3 to 1.75 kb and from 2.1 to 2.3 kb, respectively. The K2 yeasts were found in all the wine-producing subareas for all the vintages analyzed, while the Klus yeasts were found in the warmer subareas and mostly in the warmer ripening/harvest seasons. The middle-size isotypes of the M2 dsRNA were the most frequent among K2 yeasts, probably because they encoded the most intense K2 killer phenotype. However, the smallest isotype of the Mlus dsRNA was the most frequent for Klus yeasts, although it encoded the least intense Klus killer phenotype. The killer yeasts were present in most (59.5%) spontaneous fermentations. Most were K2, with Klus being the minority. The proportion of killer yeasts increased during fermentation, while the proportion of sensitive yeasts decreased. The fermentation speed, malic acid, and wine organoleptic quality decreased in those fermentations where the killer yeasts replaced at least 15% of a dominant population of sensitive yeasts, while volatile acidity and lactic acid increased, and the amount of bacteria in the tumultuous and the end fermentation stages also increased in an unusual way. PMID:22101056

  16. Dynamical analysis of yeast protein interaction network during the sake brewing process.

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    Mirzarezaee, Mitra; Sadeghi, Mehdi; Araabi, Babak N

    2011-12-01

    Proteins interact with each other for performing essential functions of an organism. They change partners to get involved in various processes at different times or locations. Studying variations of protein interactions within a specific process would help better understand the dynamic features of the protein interactions and their functions. We studied the protein interaction network of Saccharomyces cerevisiae (yeast) during the brewing of Japanese sake. In this process, yeast cells are exposed to several stresses. Analysis of protein interaction networks of yeast during this process helps to understand how protein interactions of yeast change during the sake brewing process. We used gene expression profiles of yeast cells for this purpose. Results of our experiments revealed some characteristics and behaviors of yeast hubs and non-hubs and their dynamical changes during the brewing process. We found that just a small portion of the proteins (12.8 to 21.6%) is responsible for the functional changes of the proteins in the sake brewing process. The changes in the number of edges and hubs of the yeast protein interaction networks increase in the first stages of the process and it then decreases at the final stages.

  17. Mitogen-activated protein kinase (MAPK) dynamics determine cell fate in the yeast mating response.

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    Li, Yang; Roberts, Julie; AkhavanAghdam, Zohreh; Hao, Nan

    2017-12-15

    In the yeast Saccharomyces cerevisiae , the exposure to mating pheromone activates a prototypic mitogen-activated protein kinase (MAPK) cascade and triggers a dose-dependent differentiation response. Whereas a high pheromone dose induces growth arrest and formation of a shmoo-like morphology in yeast cells, lower pheromone doses elicit elongated cell growth. Previous population-level analysis has revealed that the MAPK Fus3 plays an important role in mediating this differentiation switch. To further investigate how Fus3 controls the fate decision process at the single-cell level, we developed a specific translocation-based reporter for monitoring Fus3 activity in individual live cells. Using this reporter, we observed strikingly different dynamic patterns of Fus3 activation in single cells differentiated into distinct fates. Cells committed to growth arrest and shmoo formation exhibited sustained Fus3 activation. In contrast, most cells undergoing elongated growth showed either a delayed gradual increase or pulsatile dynamics of Fus3 activity. Furthermore, we found that chemically perturbing Fus3 dynamics with a specific inhibitor could effectively redirect the mating differentiation, confirming the causative role of Fus3 dynamics in driving cell fate decisions. MAPKs mediate proliferation and differentiation signals in mammals and are therapeutic targets in many cancers. Our results highlight the importance of MAPK dynamics in regulating single-cell responses and open up the possibility that MAPK signaling dynamics could be a pharmacological target in therapeutic interventions. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations

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    Sanchez, Alvaro; Gore, Jeff

    2013-01-01

    The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50–100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators “spiral” to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the demographic fate

  19. feedback between population and evolutionary dynamics determines the fate of social microbial populations.

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    Alvaro Sanchez

    Full Text Available The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50-100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators "spiral" to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the

  20. Accelerating Yeast Prion Biology using Droplet Microfluidics

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    Ung, Lloyd; Rotem, Assaf; Jarosz, Daniel; Datta, Manoshi; Lindquist, Susan; Weitz, David

    2012-02-01

    Prions are infectious proteins in a misfolded form, that can induce normal proteins to take the misfolded state. Yeast prions are relevant, as a model of human prion diseases, and interesting from an evolutionary standpoint. Prions may also be a form of epigenetic inheritance, which allow yeast to adapt to stressful conditions at rates exceeding those of random mutations and propagate that adaptation to their offspring. Encapsulation of yeast in droplet microfluidic devices enables high-throughput measurements with single cell resolution, which would not be feasible using bulk methods. Millions of populations of yeast can be screened to obtain reliable measurements of prion induction and loss rates. The population dynamics of clonal yeast, when a fraction of the cells are prion expressing, can be elucidated. Furthermore, the mechanism by which certain strains of bacteria induce yeast to express prions in the wild can be deduced. Integrating the disparate fields of prion biology and droplet microfluidics reveals a more complete picture of how prions may be more than just diseases and play a functional role in yeast.

  1. Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation

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    2016-02-11

    unlimited. Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation The views, opinions and...into Dynamics and Regulation of Yeast Translation Report Title Ribosome-footprint profiling provides genome-wide snapshots of translation, but...tend to slow translation. With the improved mRNA measurements, the variation attributable to translational control in exponentially growing yeast was

  2. Development of Yeast Populations during Processing and Ripening of Blue Veined Cheese

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    Alison M. Knox

    2003-01-01

    Full Text Available Varieties of blue veined cheese were analyzed regularly during different stages of manufacturing and ripening to determine the origin of contaminating the yeasts present in them, their population diversity and development until the end of the storage. Yeast diversity and development in the inner and outer core of the cheeses during ripening were also compared. Air samples revealed few if any yeasts whereas the samples in contact with the equipment and the surroundings revealed high number of yeasts, implicating it as the possible main source of post-pasteurization contamination, as very few yeasts were isolated from the milk and cheese making process itself. Samples from the inner and outer core of the maturing cheeses had typical survival curves. The number of yeasts on the outer core was about a 100-fold more than of those in the inner core. The most abundant yeasts isolated from the environment and ripening cheeses were identified as Debaryomyces hansenii, Saccharomyces cerevisiae, Torulaspora delbrueckii, Trichosporon beigelii, Candida versatilis and Cryptococcus albidus, while the yeasts Candida zeylanoides and Dekkera anomala were additionally isolated from the environment. Yeasts were present in high number, making their occurrence in blue-veined cheeses meaningful.

  3. Impact of oxygenation on the performance of three non-Saccharomyces yeasts in co-fermentation with Saccharomyces cerevisiae.

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    Shekhawat, Kirti; Bauer, Florian F; Setati, Mathabatha E

    2017-03-01

    The sequential or co-inoculation of grape must with non-Saccharomyces yeast species and Saccharomyces cerevisiae wine yeast strains has recently become a common practice in winemaking. The procedure intends to enhance unique aroma and flavor profiles of wine. The extent of the impact of non-Saccharomyces strains depends on their ability to produce biomass and to remain metabolically active for a sufficiently long period. However, mixed-culture wine fermentations tend to become rapidly dominated by S. cerevisiae, reducing or eliminating the non-Saccharomyces yeast contribution. For an efficient application of these yeasts, it is therefore essential to understand the environmental factors that modulate the population dynamics of such ecosystems. Several environmental parameters have been shown to influence population dynamics, but their specific effect remains largely uncharacterized. In this study, the population dynamics in co-fermentations of S. cerevisiae and three non-Saccharomyces yeast species: Torulaspora delbrueckii, Lachancea thermotolerans, and Metschnikowia pulcherrima, was investigated as a function of oxygen availability. In all cases, oxygen availability strongly influenced population dynamics, but clear species-dependent differences were observed. Our data show that L. thermotolerans required the least oxygen, followed by T. delbrueckii and M. pulcherrima. Distinct species-specific chemical volatile profiles correlated in all cases with increased persistence of non-Saccharomyces yeasts, in particular increases in some higher alcohols and medium chain fatty acids. The results highlight the role of oxygen in regulating the succession of yeasts during wine fermentations and suggests that more stringent aeration strategies would be necessary to support the persistence of non-Saccharomyces yeasts in real must fermentations.

  4. Yeast species associated with the spontaneous fermentation of cider.

    OpenAIRE

    Suárez, Belén; Pando, Rosa; Fernández, Norman; Querol, Amparo; Rodríguez, Roberto

    2018-01-01

    This paper reports the influence of cider-making technology (pneumatic and traditional pressing) on the dynamics of wild yeast populations. Yeast colonies isolated from apple juice before and throughout fermentation at a cider cellar of Asturias (Spain), during two consecutive years were studied. The yeast strains were identified by restriction fragment length polymorphism analysis of the 5.8S rRNA gene and the two flanking internal transcribed sequences (ITS). The musts obtained by ...

  5. Presence and changes in populations of yeasts on raw and processed poultry products stored at refrigeration temperature.

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    Ismail, S A; Deak, T; El-Rahman, H A; Yassien, M A; Beuchat, L R

    2000-12-05

    A study was undertaken to determine populations and profiles of yeast species on fresh and processed poultry products upon purchase from retail supermarkets and after storage at 5 degrees C until shelf life expiration, and to assess the potential role of these yeasts in product spoilage. Fifty samples representing 15 commercial raw, marinated, smoked, or roasted chicken and turkey products were analyzed. Yeast populations were determined by plating on dichloran rose bengal chloramphenicol (DRBC) agar and tryptone glucose yeast extract (TGY) agar. Proteolytic activity was determined using caseinate and gelatin agars and lipolytic activity was determined on plate count agar supplemented with tributyrin. Populations of aerobic microorganisms were also determined. Initial populations of yeasts (log10 cfu/g) ranged from less than 1 (detection limit) to 2.89, and increased by the expiration date to 0.37-5.06, indicating the presence of psychrotrophic species. Highest initial populations were detected in raw chicken breast, wings, and ground chicken, as well as in turkey necks and legs, whereas roasted chicken and turkey products contained less than 1 log10 cfu/g. During storage, yeast populations increased significantly (P chicken, ground chicken, liver, heart and gizzard, and in ground turkey and turkey sausage. Isolates (152 strains) of yeasts from poultry products consisted of 12 species. Yarrowia lipolytica and Candida zeylanoides were predominant, making up 39 and 26% of the isolates, respectively. Six different species of basidiomycetous yeasts representing 24% of the isolates were identified. Most Y. lipolytica strains showed strong proteolytic and lipolytic activities, whereas C. zeylanoides was weakly lipolytic. Results suggest that yeasts, particularly Y. lipolytica, may play a more prominent role than previously recognized in the spoilage of fresh and processed poultry stored at 5 degrees C.

  6. Isolation and Identification of the Indigenous Yeast Population during Spontaneous Fermentation of Isabella (Vitis labrusca L.) Grape Must

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    Raymond Eder, María L.; Reynoso, Cristina; Lauret, Santiago C.; Rosa, Alberto L.

    2017-01-01

    Grape must harbors a complex community of yeast species responsible for spontaneous alcoholic fermentation. Although there are detailed studies on the microbiota of Vitis vinifera L. grapes, less is known about the diversity and behavior of yeast communities present on fermenting grape must from other species of Vitis. In this work, we used a culture-dependent method to study the identity and dynamics of the indigenous yeast population present during the spontaneous fermentation of Isabella (Vitis labrusca L.) grape must. Alcoholic fermentation was conducted using standard enological practices, and the associated non-Saccharomyces and S. cerevisiae yeast community was analyzed using selective growth media and 5.8-ITS DNA sequencing. Candida californica, Candida hellenica, Starmerella bacillaris (synonym Candida zemplinina), Hanseniaspora uvarum, and Hanseniaspora vineae were the main non-Saccharomyces species identified on Isabella fermenting must. Issatchenkia hanoiensis, a yeast species rarely found on Vitis vinifera L. grapes, was also recognized on Isabella grape must. Candida azymoides, Candida californica and Pichia cecembensis, identified in this work on Isabella fermenting must, have not previously been found on Vitis vinifera L. grape must. Interestingly, C. azymoides, I. hanoiensis and P. cecembensis have recently been isolated from the surface of Vitis labrusca L. grapes from vineyards in the Azores archipelago, suggesting that specific Vitis-yeast species associations are formed independently of geographic origin. We suggest that C. azymoides, C. californica, and P. cecembensis are yeast species preferentially associated with Vitis labrusca L. grapes. Specific biological interactions between grapevines and yeast species may underlie the assembly of differential Vitis-microbial communities. PMID:28424672

  7. Cell mass and cell cycle dynamics of an asynchronous budding yeast population

    DEFF Research Database (Denmark)

    Lencastre Fernandes, Rita; Carlquist, Magnus; Lundin, Luisa

    2013-01-01

    of model predictions for cell property distributions against experimental data is scarce. This study focuses on the experimental and mathematical description of the dynamics of cell size and cell cycle position distributions, of a population of Saccharomyces cerevisiae, in response to the substrate...

  8. Yeast cells contain a heterogeneous population of peroxisomes that segregate asymmetrically during cell division

    NARCIS (Netherlands)

    Kumar, Sanjeev; de Boer, Rinse; van der Klei, Ida J

    2018-01-01

    Here we used fluorescence microscopy and a peroxisome-targeted tandem fluorescent protein timer to determine the relative age of peroxisomes in yeast. Our data indicate that yeast cells contain a heterogeneous population of relatively old and younger peroxisomes. During budding the peroxisome

  9. Decoherence in yeast cell populations and its implications for genome-wide expression noise.

    Science.gov (United States)

    Briones, M R S; Bosco, F

    2009-01-20

    Gene expression "noise" is commonly defined as the stochastic variation of gene expression levels in different cells of the same population under identical growth conditions. Here, we tested whether this "noise" is amplified with time, as a consequence of decoherence in global gene expression profiles (genome-wide microarrays) of synchronized cells. The stochastic component of transcription causes fluctuations that tend to be amplified as time progresses, leading to a decay of correlations of expression profiles, in perfect analogy with elementary relaxation processes. Measuring decoherence, defined here as a decay in the auto-correlation function of yeast genome-wide expression profiles, we found a slowdown in the decay of correlations, opposite to what would be expected if, as in mixing systems, correlations decay exponentially as the equilibrium state is reached. Our results indicate that the populational variation in gene expression (noise) is a consequence of temporal decoherence, in which the slow decay of correlations is a signature of strong interdependence of the transcription dynamics of different genes.

  10. Engineering 1-Alkene Biosynthesis and Secretion by Dynamic Regulation in Yeast

    DEFF Research Database (Denmark)

    Zhou, Yongjin J.; Hu, Yating; Zhu, Zhiwei

    2018-01-01

    strategy to control the expression of membrane enzyme and 1-alkene production and cell growth by relieving the possible toxicity of overexpressed membrane proteins. With these efforts, the engineered yeast cell factory produced 35.3 mg/L 1-alkenes with more than 80% being secreted. This represents a 10...... product secretion. Here, we engineered the budding yeast Saccharomyces cerevisiae to produce and secrete 1-alkenes by manipulation of the fatty acid metabolism, enzyme selection, engineering the electron transfer system and expressing a transporter. Furthermore, we implemented a dynamic regulation...

  11. Population analysis of biofilm yeasts during fino sherry wine aging in the Montilla-Moriles D.O. region.

    Science.gov (United States)

    Marin-Menguiano, Miriam; Romero-Sanchez, Sandra; Barrales, Ramón R; Ibeas, Jose I

    2017-03-06

    Fino is the most popular sherry wine produced in southern Spain. Fino is matured by biological aging under a yeast biofilm constituted of Saccharomyces cerevisiae yeasts. Although different S. cerevisiae strains can be identified in such biofilms, their diversity and contribution to wine character have been poorly studied. In this work, we analyse the flor yeast population in five different wineries from the Montilla-Moriles D.O. (Denominación de Origen) in southern Spain. Yeasts present in wines of different ages were identified using two different culture-dependent molecular techniques. From 2000 individual yeast isolates, five different strains were identified with one of them dominating in four out of the five wineries analysed, and representing 76% of all the yeast isolates collected. Surprisingly, this strain is similar to the predominant strain isolated twenty years ago in Jerez D.O. wines, suggesting that this yeast is particularly able to adapt to such a stressful environment. Fino wine produced with pure cultures of three of the isolated strains resulted in different levels of acetaldehyde. Because acetaldehyde levels are a distinctive characteristic of fino wines and an indicator of fino aging, the use of molecular techniques for yeast identification and management of yeast populations may be of interest for fino wine producers looking to control one of the main features of this wine. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. A population study of killer viruses reveals different evolutionary histories of two closely related Saccharomyces sensu stricto yeasts.

    Science.gov (United States)

    Chang, Shang-Lin; Leu, Jun-Yi; Chang, Tien-Hsien

    2015-08-01

    Microbes have evolved ways of interference competition to gain advantage over their ecological competitors. The use of secreted killer toxins by yeast cells through acquiring double-stranded RNA viruses is one such prominent example. Although the killer behaviour has been well studied in laboratory yeast strains, our knowledge regarding how killer viruses are spread and maintained in nature and how yeast cells co-evolve with viruses remains limited. We investigated these issues using a panel of 81 yeast populations belonging to three Saccharomyces sensu stricto species isolated from diverse ecological niches and geographic locations. We found that killer strains are rare among all three species. In contrast, killer toxin resistance is widespread in Saccharomyces paradoxus populations, but not in Saccharomyces cerevisiae or Saccharomyces eubayanus populations. Genetic analyses revealed that toxin resistance in S. paradoxus is often caused by dominant alleles that have independently evolved in different populations. Molecular typing identified one M28 and two types of M1 killer viruses in those killer strains. We further showed that killer viruses of the same type could lead to distinct killer phenotypes under different host backgrounds, suggesting co-evolution between the viruses and hosts in different populations. Taken together, our data suggest that killer viruses vary in their evolutionary histories even within closely related yeast species. © 2015 John Wiley & Sons Ltd.

  13. Expanding a dynamic flux balance model of yeast fermentation to genome-scale

    Science.gov (United States)

    2011-01-01

    Background Yeast is considered to be a workhorse of the biotechnology industry for the production of many value-added chemicals, alcoholic beverages and biofuels. Optimization of the fermentation is a challenging task that greatly benefits from dynamic models able to accurately describe and predict the fermentation profile and resulting products under different genetic and environmental conditions. In this article, we developed and validated a genome-scale dynamic flux balance model, using experimentally determined kinetic constraints. Results Appropriate equations for maintenance, biomass composition, anaerobic metabolism and nutrient uptake are key to improve model performance, especially for predicting glycerol and ethanol synthesis. Prediction profiles of synthesis and consumption of the main metabolites involved in alcoholic fermentation closely agreed with experimental data obtained from numerous lab and industrial fermentations under different environmental conditions. Finally, fermentation simulations of genetically engineered yeasts closely reproduced previously reported experimental results regarding final concentrations of the main fermentation products such as ethanol and glycerol. Conclusion A useful tool to describe, understand and predict metabolite production in batch yeast cultures was developed. The resulting model, if used wisely, could help to search for new metabolic engineering strategies to manage ethanol content in batch fermentations. PMID:21595919

  14. Aging and differentiation in yeast populations: elders with different properties and functions.

    Science.gov (United States)

    Palková, Zdena; Wilkinson, Derek; Váchová, Libuše

    2014-02-01

    Over the past decade, it has become evident that similarly to cells forming metazoan tissues, yeast cells have the ability to differentiate and form specialized cell types. Examples of yeast cellular differentiation have been identified both in yeast liquid cultures and within multicellular structures occupying solid surfaces. Most current knowledge on different cell types comes from studies of the spatiotemporal internal architecture of colonies developing on various media. With a few exceptions, yeast cell differentiation often concerns nongrowing, stationary-phase cells and leads to the formation of cell subpopulations differing in stress resistance, cell metabolism, respiration, ROS production, and others. These differences can affect longevity of particular subpopulations. In contrast to liquid cultures, where various cell types are dispersed within stationary-phase populations, cellular differentiation depends on the specific position of particular cells within multicellular colonies. Differentiated colonies, thus, resemble primitive multicellular organisms, in which the gradients of certain compounds and the position of cells within the structure affect cellular differentiation. In this review, we summarize and compare the properties of diverse types of differentiated chronologically aging yeast cells that have been identified in colonies growing on different media, as well as of those found in liquid cultures. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  15. Dispersal, density dependence, and population dynamics of a fungal microbe on leaf surfaces.

    Science.gov (United States)

    Woody, Scott T; Ives, Anthony R; Nordheim, Erik V; Andrews, John H

    2007-06-01

    Despite the ubiquity and importance of microbes in nature, little is known about their natural population dynamics, especially for those that occupy terrestrial habitats. Here we investigate the dynamics of the yeast-like fungus Aureobasidium pullulans (Ap) on apple leaves in an orchard. We asked three questions. (1) Is variation in fungal population density among leaves caused by variation in leaf carrying capacities and strong density-dependent population growth that maintains densities near carrying capacity? (2) Do resident populations have competitive advantages over immigrant cells? (3) Do Ap dynamics differ at different times during the growing season? To address these questions, we performed two experiments at different times in the growing season. Both experiments used a 2 x 2 factorial design: treatment 1 removed fungal cells from leaves to reveal density-dependent population growth, and treatment 2 inoculated leaves with an Ap strain engineered to express green fluorescent protein (GFP), which made it possible to track the fate of immigrant cells. The experiments showed that natural populations of Ap vary greatly in density due to sustained differences in carrying capacities among leaves. The maintenance of populations close to carrying capacities indicates strong density-dependent processes. Furthermore, resident populations are strongly competitive against immigrants, while immigrants have little impact on residents. Finally, statistical models showed high population growth rates of resident cells in one experiment but not in the other, suggesting that Ap experiences relatively "good" and "bad" periods for population growth. This picture of Ap dynamics conforms to commonly held, but rarely demonstrated, expectations of microbe dynamics in nature. It also highlights the importance of local processes, as opposed to immigration, in determining the abundance and dynamics of microbes on surfaces in terrestrial systems.

  16. Separation of selenium compounds by CE-ICP-MS in dynamically coated capillaries applied to selenized yeast samples

    DEFF Research Database (Denmark)

    Bendahl, Lars; Gammelgaard, Bente

    2004-01-01

    The selenium species in nutritional supplement tablets, based on selenized yeast, were separated by capillary zone electrophoresis using capillaries coated dynamically with poly(vinyl sulfonate) and detected by ICP-MS. Sample pre-treatment consisted of cold-water extraction by sonication and subs......The selenium species in nutritional supplement tablets, based on selenized yeast, were separated by capillary zone electrophoresis using capillaries coated dynamically with poly(vinyl sulfonate) and detected by ICP-MS. Sample pre-treatment consisted of cold-water extraction by sonication...

  17. Co-Flocculation of Yeast Species, a New Mechanism to Govern Population Dynamics in Microbial Ecosystems.

    Directory of Open Access Journals (Sweden)

    Debra Rossouw

    Full Text Available Flocculation has primarily been studied as an important technological property of Saccharomyces cerevisiae yeast strains in fermentation processes such as brewing and winemaking. These studies have led to the identification of a group of closely related genes, referred to as the FLO gene family, which controls the flocculation phenotype. All naturally occurring S. cerevisiae strains assessed thus far possess at least four independent copies of structurally similar FLO genes, namely FLO1, FLO5, FLO9 and FLO10. The genes appear to differ primarily by the degree of flocculation induced by their expression. However, the reason for the existence of a large family of very similar genes, all involved in the same phenotype, has remained unclear. In natural ecosystems, and in wine production, S. cerevisiae growth together and competes with a large number of other Saccharomyces and many more non-Saccharomyces yeast species. Our data show that many strains of such wine-related non-Saccharomyces species, some of which have recently attracted significant biotechnological interest as they contribute positively to fermentation and wine character, were able to flocculate efficiently. The data also show that both flocculent and non-flocculent S. cerevisiae strains formed mixed species flocs (a process hereafter referred to as co-flocculation with some of these non-Saccharomyces yeasts. This ability of yeast strains to impact flocculation behaviour of other species in mixed inocula has not been described previously. Further investigation into the genetic regulation of co-flocculation revealed that different FLO genes impact differently on such adhesion phenotypes, favouring adhesion with some species while excluding other species from such mixed flocs. The data therefore strongly suggest that FLO genes govern the selective association of S. cerevisiae with specific species of non-Saccharomyces yeasts, and may therefore be drivers of ecosystem organisational

  18. What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast.

    Directory of Open Access Journals (Sweden)

    Artémis Llamosi

    2016-02-01

    Full Text Available Significant cell-to-cell heterogeneity is ubiquitously observed in isogenic cell populations. Consequently, parameters of models of intracellular processes, usually fitted to population-averaged data, should rather be fitted to individual cells to obtain a population of models of similar but non-identical individuals. Here, we propose a quantitative modeling framework that attributes specific parameter values to single cells for a standard model of gene expression. We combine high quality single-cell measurements of the response of yeast cells to repeated hyperosmotic shocks and state-of-the-art statistical inference approaches for mixed-effects models to infer multidimensional parameter distributions describing the population, and then derive specific parameters for individual cells. The analysis of single-cell parameters shows that single-cell identity (e.g. gene expression dynamics, cell size, growth rate, mother-daughter relationships is, at least partially, captured by the parameter values of gene expression models (e.g. rates of transcription, translation and degradation. Our approach shows how to use the rich information contained into longitudinal single-cell data to infer parameters that can faithfully represent single-cell identity.

  19. The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection.

    Science.gov (United States)

    Payen, Celia; Di Rienzi, Sara C; Ong, Giang T; Pogachar, Jamie L; Sanchez, Joseph C; Sunshine, Anna B; Raghuraman, M K; Brewer, Bonita J; Dunham, Maitreya J

    2014-03-20

    Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity, and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining quantitative polymerase chain reaction, array comparative genomic hybridization, restriction digestion and contour-clamped homogeneous electric field gel electrophoresis, and whole-genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. During a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that were driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolved under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared with single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another.

  20. Effects of seven diets on the population dynamics of laboratory cultured Tisbe holothuriae Humes (Copepoda, Harpacticoida)

    Science.gov (United States)

    Miliou, H.; Moraïtou-Apostolopoulou, M.

    1991-09-01

    The harpacticoid copepod Tisbe holothuriae was collected from Saronicos Gulf (Greece) and reared under constant laboratory conditions. In order to study the effects of food on the population dynamics, seven diets were tested: the seaweed Ulva; five artificial compound feeds: the liquid Fryfood® (Waterlife), a powder of Mytilus, yeast, soya and Spirulina, respectively; and a mixed diet consisting of Ulva and Fryfood. The life cycle parameters (mortality, sex ratio, generation time, offspring production) were measured, and the demographic variables [mean generation time (T), net reproductive rate (Ro), and intrinsic rate of natural increase (rm)] were determined. As to their efficiency regarding population dynamics, the diets ranked as follows: (1) Ulva+Fryfood, (2), Ulva, (3) Fryfood, (4) Mytilus, (5) soya, (6) yeast, and (7) Spirulina. In this order they cause a progressive increase of both larval mortality and generation time, a progressive decrease of sex ratio, number of offspring per egg sac, number of egg sacs per female and, consequently, of Ro and rm. The observed differences between diets were most pronounced with respect to offspring production. Of the compound diets, those containing animal extracts were more efficient than those containing vegetable materials. Ulva plays an important role in the nutrition of T. holothuriae, favouring offspring production as well as larval survival, development and pigmentation. Ulva in combination with Fryfood led to a greater copepodid survival and offspring production. This mixed diet proved to be the most favourable for rearing the Greek population of t. holothuriae, resulting in an efficient intrinsic rate of natural increase (rm=0.304) of the population.

  1. The Hidden Complexity of Mendelian Traits across Natural Yeast Populations

    Directory of Open Access Journals (Sweden)

    Jing Hou

    2016-07-01

    Full Text Available Mendelian traits are considered to be at the lower end of the complexity spectrum of heritable phenotypes. However, more than a century after the rediscovery of Mendel’s law, the global landscape of monogenic variants, as well as their effects and inheritance patterns within natural populations, is still not well understood. Using the yeast Saccharomyces cerevisiae, we performed a species-wide survey of Mendelian traits across a large population of isolates. We generated offspring from 41 unique parental pairs and analyzed 1,105 cross/trait combinations. We found that 8.9% of the cases were Mendelian. Further tracing of causal variants revealed background-specific expressivity and modified inheritances, gradually transitioning from Mendelian to complex traits in 30% of the cases. In fact, when taking into account the natural population diversity, the hidden complexity of traits could be substantial, confounding phenotypic predictability even for simple Mendelian traits.

  2. A long term field study of the effect of fungicides penconazole and sulfur on yeasts in the vineyard.

    Science.gov (United States)

    Cordero-Bueso, Gustavo; Arroyo, Teresa; Valero, Eva

    2014-10-17

    This research deals with how two fungicide treatments against powdery mildew, penconazole as a systematic fungicide and sulfur as an inorganic broad-spectrum fungicide, affect the diversity and density of wine yeasts associated with grape berry surfaces and subsequent spontaneous fermentations. Unlike other studies in this area, this work aims to evaluate this effect on the population dynamics in the environment, the conditions of which are not reproducible in the laboratory. A long term (three year) sampling plan was thus devised. A minimum inhibitory concentration assay was also carried out in the laboratory in order to prove the influence of these antifungals on yeast populations. While both antifungal treatments (penconazole and sulfur) were similarly effective against powdery mildew, each had a very different effect on yeast populations. Penconazole showed the most negative effect on biodiversity in the vineyard and was the fungicide to which the isolated yeasts showed the greatest sensitivity. This study therefore evidences the suitability of treatment with sulfur, in both conventional and organic viticulture, to preserve the yeast population associated with grape berries, in particular the Saccharomyces cerevisiae species. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments.

    Science.gov (United States)

    Gorter, Florien A; Aarts, Mark G M; Zwaan, Bas J; de Visser, J Arjan G M

    2018-01-01

    The fitness landscape is a concept that is widely used for understanding and predicting evolutionary adaptation. The topography of the fitness landscape depends critically on the environment, with potentially far-reaching consequences for evolution under changing conditions. However, few studies have assessed directly how empirical fitness landscapes change across conditions, or validated the predicted consequences of such change. We previously evolved replicate yeast populations in the presence of either gradually increasing, or constant high, concentrations of the heavy metals cadmium (Cd), nickel (Ni), and zinc (Zn), and analyzed their phenotypic and genomic changes. Here, we reconstructed the local fitness landscapes underlying adaptation to each metal by deleting all repeatedly mutated genes both by themselves and in combination. Fitness assays revealed that the height, and/or shape, of each local fitness landscape changed considerably across metal concentrations, with distinct qualitative differences between unconditionally (Cd) and conditionally toxic metals (Ni and Zn). This change in topography had particularly crucial consequences in the case of Ni, where a substantial part of the individual mutational fitness effects changed in sign across concentrations. Based on the Ni landscape analyses, we made several predictions about which mutations had been selected when during the evolution experiment. Deep sequencing of population samples from different time points generally confirmed these predictions, demonstrating the power of landscape reconstruction analyses for understanding and ultimately predicting evolutionary dynamics, even under complex scenarios of environmental change. Copyright © 2018 by the Genetics Society of America.

  4. Yeast species associated with the spontaneous fermentation of cider.

    Science.gov (United States)

    Valles, Belén Suárez; Bedriñana, Rosa Pando; Tascón, Norman Fernández; Simón, Amparo Querol; Madrera, Roberto Rodríguez

    2007-02-01

    This paper reports the influence of cider-making technology (pneumatic and traditional pressing) on the dynamics of wild yeast populations. Yeast colonies isolated from apple juice before and throughout fermentation at a cider cellar of Asturias (Spain), during two consecutive years were studied. The yeast strains were identified by restriction fragment length polymorphism analysis of the 5.8S rRNA gene and the two flanking internal transcribed sequences (ITS). The musts obtained by pneumatic pressing were dominated by non-Saccharomyces yeasts (Hanseniaspora genus and Metschnikowia pulcherrima) whereas in the apple juices obtained by traditional pressing Saccharomyces together with non-Saccharomyces, were always present. The species Saccharomyces present were S. cerevisiae and S. bayanus. Apparently S. bayanus, was the predominant species at the beginning and the middle fermentation steps of the fermentation process, reaching a percentage of isolation between 33% and 41%, whereas S. cerevisiae took over the process in the final stages of fermentation. During the 2001 harvest, with independence of cider-making technology, the species Hanseniaspora valbyensis was always isolated at the end of fermentations.

  5. Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature

    Science.gov (United States)

    Ma, Zhanshan (Sam)

    In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three

  6. Oxygen availability and strain combination modulate yeast growth dynamics in mixed culture fermentations of grape must with Starmerella bacillaris and Saccharomyces cerevisiae.

    Science.gov (United States)

    Englezos, Vasileios; Cravero, Francesco; Torchio, Fabrizio; Rantsiou, Kalliopi; Ortiz-Julien, Anne; Lambri, Milena; Gerbi, Vincenzo; Rolle, Luca; Cocolin, Luca

    2018-02-01

    Starmerella bacillaris (synonym Candida zemplinina) is a non-Saccharomyces yeast that has been proposed as a co-inoculant of selected Saccharomyces cerevisiae strains in mixed culture fermentations to enhance the analytical composition of the wines. In order to acquire further knowledge on the metabolic interactions between these two species, in this study we investigated the impact of oxygen addition and combination of Starm. bacillaris with S. cerevisiae strains on the microbial growth and metabolite production. Fermentations were carried out under two different conditions of oxygen availability. Oxygen availability and strain combination clearly influenced the population dynamics throughout the fermentation. Oxygen concentration increased the survival time of Starm. bacillaris and decreased the growth rate of S. cerevisiae strains in mixed culture fermentations, whereas it did not affect the growth of the latter in pure culture fermentations. This study reveals new knowledge about the influence of oxygen availability on the successional evolution of yeast species during wine fermentation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Population dynamics

    Directory of Open Access Journals (Sweden)

    Cooch, E. G.

    2004-06-01

    Full Text Available Increases or decreases in the size of populations over space and time are, arguably, the motivation for much of pure and applied ecological research. The fundamental model for the dynamics of any population is straightforward: the net change over time in the abundance of some population is the simple difference between the number of additions (individuals entering the population minus the number of subtractions (individuals leaving the population. Of course, the precise nature of the pattern and process of these additions and subtractions is often complex, and population biology is often replete with fairly dense mathematical representations of both processes. While there is no doubt that analysis of such abstract descriptions of populations has been of considerable value in advancing our, there has often existed a palpable discomfort when the ‘beautiful math’ is faced with the often ‘ugly realities’ of empirical data. In some cases, this attempted merger is abandoned altogether, because of the paucity of ‘good empirical data’ with which the theoretician can modify and evaluate more conceptually–based models. In some cases, the lack of ‘data’ is more accurately represented as a lack of robust estimates of one or more parameters. It is in this arena that methods developed to analyze multiple encounter data from individually marked organisms has seen perhaps the greatest advances. These methods have rapidly evolved to facilitate not only estimation of one or more vital rates, critical to population modeling and analysis, but also to allow for direct estimation of both the dynamics of populations (e.g., Pradel, 1996, and factors influencing those dynamics (e.g., Nichols et al., 2000. The interconnections between the various vital rates, their estimation, and incorporation into models, was the general subject of our plenary presentation by Hal Caswell (Caswell & Fujiwara, 2004. Caswell notes that although interest has traditionally

  8. Modeling diauxic glycolytic oscillations in yeast

    DEFF Research Database (Denmark)

    Hald, Bjørn Olav; Sørensen, Preben Graae

    2010-01-01

    for investigations of central metabolism dynamics of yeast cells. We have previously proposed a model for the open system comprised of the primary fermentative reactions in yeast that quantitatively describes the oscillatory dynamics. However, this model fails to describe the transient behavior of metabolic......Glycolytic oscillations in a stirred suspension of starved yeast cells is an excellent model system for studying the dynamics of metabolic switching in living systems. In an open-flow system the oscillations can be maintained indefinitely at a constant operating point where they can....... Experimental and computational results strongly suggest that regulation of acetaldehyde explains the observed behavior. We have extended the original model with regulation of pyruvate decarboxylase, a reversible alcohol dehydrogenase, and drainage of pyruvate. Using the method of time rescaling in the extended...

  9. Schizosaccharomyces japonicus: the fission yeast is a fusion of yeast and hyphae.

    Science.gov (United States)

    Niki, Hironori

    2014-03-01

    The clade of Schizosaccharomyces includes 4 species: S. pombe, S. octosporus, S. cryophilus, and S. japonicus. Although all 4 species exhibit unicellular growth with a binary fission mode of cell division, S. japonicus alone is dimorphic yeast, which can transit from unicellular yeast to long filamentous hyphae. Recently it was found that the hyphal cells response to light and then synchronously activate cytokinesis of hyphae. In addition to hyphal growth, S. japonicas has many properties that aren't shared with other fission yeast. Mitosis of S. japonicas is referred to as semi-open mitosis because dynamics of nuclear membrane is an intermediate mode between open mitosis and closed mitosis. Novel genetic tools and the whole genomic sequencing of S. japonicas now provide us with an opportunity for revealing unique characters of the dimorphic yeast. © 2013 The Author. Yeast Published by John Wiley & Sons Ltd.

  10. Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts.

    Science.gov (United States)

    Gonçalves, Margarida; Pontes, Ana; Almeida, Pedro; Barbosa, Raquel; Serra, Marta; Libkind, Diego; Hutzler, Mathias; Gonçalves, Paula; Sampaio, José Paulo

    2016-10-24

    Beer is one of the oldest alcoholic beverages and is produced by the fermentation of sugars derived from starches present in cereal grains. Contrary to lager beers, made by bottom-fermenting strains of Saccharomyces pastorianus, a hybrid yeast, ale beers are closer to the ancient beer type and are fermented by S. cerevisiae, a top-fermenting yeast. Here, we use population genomics to investigate (1) the closest relatives of top-fermenting beer yeasts; (2) whether top-fermenting yeasts represent an independent domestication event separate from those already described; (3) whether single or multiple beer yeast domestication events can be inferred; and (4) whether top-fermenting yeasts represent non-recombinant or recombinant lineages. Our results revealed that top-fermenting beer yeasts are polyphyletic, with a main clade composed of at least three subgroups, dominantly represented by the German, British, and wheat beer strains. Other beer strains were phylogenetically close to sake, wine, or bread yeasts. We detected genetic signatures of beer yeast domestication by investigating genes previously linked to brewing and using genome-wide scans. We propose that the emergence of the main clade of beer yeasts is related with a domestication event distinct from the previously known cases of wine and sake yeast domestication. The nucleotide diversity of the main beer clade more than doubled that of wine yeasts, which might be a consequence of fundamental differences in the modes of beer and wine yeast domestication. The higher diversity of beer strains could be due to the more intense and different selection regimes associated to brewing. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Yeast ecology of Kombucha fermentation.

    Science.gov (United States)

    Teoh, Ai Leng; Heard, Gillian; Cox, Julian

    2004-09-01

    Kombucha is a traditional fermentation of sweetened tea, involving a symbiosis of yeast species and acetic acid bacteria. Despite reports of different yeast species being associated with the fermentation, little is known of the quantitative ecology of yeasts in Kombucha. Using oxytetracycline-supplemented malt extract agar, yeasts were isolated from four commercially available Kombucha products and identified using conventional biochemical and physiological tests. During the fermentation of each of the four products, yeasts were enumerated from both the cellulosic pellicle and liquor of the Kombucha. The number and diversity of species varied between products, but included Brettanomyces bruxellensis, Candida stellata, Schizosaccharomyces pombe, Torulaspora delbrueckii and Zygosaccharomyces bailii. While these yeast species are known to occur in Kombucha, the enumeration of each species present throughout fermentation of each of the four Kombucha cultures demonstrated for the first time the dynamic nature of the yeast ecology. Kombucha fermentation is, in general, initiated by osmotolerant species, succeeded and ultimately dominated by acid-tolerant species.

  12. Microbial dynamics during azo dye degradation in a UASB reactor supplied with yeast extract.

    Science.gov (United States)

    Silva, S Q; Silva, D C; Lanna, M C S; Baeta, B E L; Aquino, S F

    2014-01-01

    The present work aimed to investigate the microbial dynamics during the anaerobic treatment of the azo dye blue HRFL in bench scale upflow anaerobic sludge bed (UASB) reactor operated at ambient temperature. Sludge samples were collected under distinct operational phases, when the reactor were stable (low variation of color removal), to assess the effect of glucose and yeast extract as source of carbon and redox mediators, respectively. Reactors performance was evaluated based on COD (chemical oxygen demand) and color removal. The microbial dynamics were investigated by PCR-DGGE (Polimerase Chain Reaction - Denaturing Gradient of Gel Electrophoresis) technique by comparing the 16S rDNA profiles among samples. The results suggest that the composition of microorganisms changed from the beginning to the end of the reactor operation, probably in response to the presence of azo dye and/or its degradation byproducts. Despite the highest efficiency of color removal was observed in the presence of 500 mg/L of yeast extract (up to 93%), there were no differences regarding the microbial profiles that could indicate a microbial selection by the yeast extract addition. On the other hand Methosarcina barkeri was detected only in the end of operation when the best efficiencies on color removal occurred. Nevertheless the biomass selection observed in the last stages of UASB operation is probably a result of the washout of the sludge in response of accumulation of aromatic amines which led to tolerant and very active biomass that contributed to high efficiencies on color removal.

  13. Dynamic Changes in Yeast Phosphatase Families Allow for Specialization in Phosphate and Thiamine Starvation.

    Science.gov (United States)

    Nahas, John V; Iosue, Christine L; Shaik, Noor F; Selhorst, Kathleen; He, Bin Z; Wykoff, Dennis D

    2018-05-10

    Convergent evolution is often due to selective pressures generating a similar phenotype. We observe relatively recent duplications in a spectrum of Saccharomycetaceae yeast species resulting in multiple phosphatases that are regulated by different nutrient conditions - thiamine and phosphate starvation. This specialization is both transcriptional and at the level of phosphatase substrate specificity. In Candida glabrata , loss of the ancestral phosphatase family was compensated by the co-option of a different histidine phosphatase family with three paralogs. Using RNA-seq and functional assays, we identify one of these paralogs, CgPMU3 , as a thiamine phosphatase. We further determine that the 81% identical paralog CgPMU2 does not encode thiamine phosphatase activity; however, both are capable of cleaving the phosphatase substrate, 1-napthyl-phosphate. We functionally demonstrate that members of this family evolved novel enzymatic functions for phosphate and thiamine starvation, and are regulated transcriptionally by either nutrient condition, and observe similar trends in other yeast species. This independent, parallel evolution involving two different families of histidine phosphatases suggests that there were likely similar selective pressures on multiple yeast species to recycle thiamine and phosphate. In this work, we focused on duplication and specialization, but there is also repeated loss of phosphatases, indicating that the expansion and contraction of the phosphatase family is dynamic in many Ascomycetes. The dynamic evolution of the phosphatase gene families is perhaps just one example of how gene duplication, co-option, and transcriptional and functional specialization together allow species to adapt to their environment with existing genetic resources. Copyright © 2018, G3: Genes, Genomes, Genetics.

  14. Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Hussmann

    2015-12-01

    Full Text Available Ribosome profiling produces snapshots of the locations of actively translating ribosomes on messenger RNAs. These snapshots can be used to make inferences about translation dynamics. Recent ribosome profiling studies in yeast, however, have reached contradictory conclusions regarding the average translation rate of each codon. Some experiments have used cycloheximide (CHX to stabilize ribosomes before measuring their positions, and these studies all counterintuitively report a weak negative correlation between the translation rate of a codon and the abundance of its cognate tRNA. In contrast, some experiments performed without CHX report strong positive correlations. To explain this contradiction, we identify unexpected patterns in ribosome density downstream of each type of codon in experiments that use CHX. These patterns are evidence that elongation continues to occur in the presence of CHX but with dramatically altered codon-specific elongation rates. The measured positions of ribosomes in these experiments therefore do not reflect the amounts of time ribosomes spend at each position in vivo. These results suggest that conclusions from experiments in yeast using CHX may need reexamination. In particular, we show that in all such experiments, codons decoded by less abundant tRNAs were in fact being translated more slowly before the addition of CHX disrupted these dynamics.

  15. ODE, RDE and SDE models of cell cycle dynamics and clustering in yeast.

    Science.gov (United States)

    Boczko, Erik M; Gedeon, Tomas; Stowers, Chris C; Young, Todd R

    2010-07-01

    Biologists have long observed periodic-like oxygen consumption oscillations in yeast populations under certain conditions, and several unsatisfactory explanations for this phenomenon have been proposed. These ‘autonomous oscillations’ have often appeared with periods that are nearly integer divisors of the calculated doubling time of the culture. We hypothesize that these oscillations could be caused by a form of cell cycle synchronization that we call clustering. We develop some novel ordinary differential equation models of the cell cycle. For these models, and for random and stochastic perturbations, we give both rigorous proofs and simulations showing that both positive and negative growth rate feedback within the cell cycle are possible agents that can cause clustering of populations within the cell cycle. It occurs for a variety of models and for a broad selection of parameter values. These results suggest that the clustering phenomenon is robust and is likely to be observed in nature. Since there are necessarily an integer number of clusters, clustering would lead to periodic-like behaviour with periods that are nearly integer divisors of the period of the cell cycle. Related experiments have shown conclusively that cell cycle clustering occurs in some oscillating yeast cultures.

  16. Indigenous and inoculated yeast fermentation of gabiroba (Campomanesia pubescens) pulp for fruit wine production.

    Science.gov (United States)

    Duarte, Whasley Ferreira; Dias, Disney Ribeiro; de Melo Pereira, Gilberto Vinicius; Gervásio, Ivani Maria; Schwan, Rosane Freitas

    2009-04-01

    The objectives of this study were to evaluate the potential of gabiroba Campomanesia pubescens (DC) O. Berg in the production of a beverage fermented using selected and wild yeasts from indigenous fermentation, analyze the volatile compounds profile present during the process of fermentation, and evaluate the sensory quality of the final beverage produced. Throughout the process of fermentation, when Saccharomyces cerevisiae UFLA CA 1162 was inoculated, there were stable viable populations around 9 log cells ml(-1). During indigenous fermentation, yeast population increased from 3.7 log CFU ml(-1) to 8.1 log CFU ml(-1) after 14 days. The diversity and dynamics of the yeast population during indigenous fermentation observed by PFGE analysis showed five different karyotyping profiles in the first days of fermentation. After the seventh day, there was a higher frequency of a similar S. cerevisiae profile. The yeast non-Saccharomyces were identified by sequencing of the ITS region as Candida quercitrusa and Issatchenkia terricola. Inoculated fermentations yielded a higher amount of alcohol than indigenous ones, indicating the efficiency of selected strains. There was also a greater concentration of higher alcohols, which are usually responsible for the flavor found in alcoholic beverages. Based on the characteristics of the pulp and acceptance in the sensory analysis, gabiroba fruits showed good potential for use in the production of fermented beverage.

  17. Divergence of iron metabolism in wild Malaysian yeast.

    Science.gov (United States)

    Lee, Hana N; Mostovoy, Yulia; Hsu, Tiffany Y; Chang, Amanda H; Brem, Rachel B

    2013-12-09

    Comparative genomic studies have reported widespread variation in levels of gene expression within and between species. Using these data to infer organism-level trait divergence has proven to be a key challenge in the field. We have used a wild Malaysian population of S. cerevisiae as a test bed in the search to predict and validate trait differences based on observations of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron. Malaysian yeast also showed a hyperactive regulatory response during culture in the presence of excess iron and had a unique growth defect in conditions of high iron. Molecular validation experiments pinpointed the iron metabolism factors AFT1, CCC1, and YAP5 as contributors to these molecular and cellular phenotypes; in genome-scale sequence analyses, a suite of iron toxicity response genes showed evidence for rapid protein evolution in Malaysian yeast. Our findings support a model in which iron metabolism has diverged in Malaysian yeast as a consequence of a change in selective pressure, with Malaysian alleles shifting the dynamic range of iron response to low-iron concentrations and weakening resistance to extreme iron toxicity. By dissecting the iron scarcity specialist behavior of Malaysian yeast, our work highlights the power of expression divergence as a signpost for biologically and evolutionarily relevant variation at the organismal level. Interpreting the phenotypic relevance of gene expression variation is one of the primary challenges of modern genomics.

  18. Yeast diversity and dynamics in the production processes of Norwegian dry-cured meat products.

    Science.gov (United States)

    Asefa, Dereje T; Møretrø, Trond; Gjerde, Ragnhild O; Langsrud, Solveig; Kure, Cathrine F; Sidhu, Maan S; Nesbakken, Truls; Skaar, Ida

    2009-07-31

    This study investigate the diversity and dynamics of yeasts in the production processes of one unsmoked and two smoked dry-cured meat products of a Norwegian dry-cured meat production facility. A longitudinal observational study was performed to collect 642 samples from the meat, production materials, room installations and indoor and outdoor air of the production facility. Nutrient rich agar media were used to isolate the yeasts. Morphologically different isolates were re-cultivated in their pure culture forms. Both classical and molecular methods were employed for species identification. Totally, 401 yeast isolates belonging to 10 species of the following six genera were identified: Debaryomyces, Candida, Rhodotorula, Rhodosporidium, Cryptococcus and Sporidiobolus. Debaryomyces hansenii and Candida zeylanoides were dominant and contributed by 63.0% and 26.4% respectively to the total isolates recovered from both smoked and unsmoked products. The yeast diversity was higher at the pre-salting production processes with C. zeylanoides being the dominant. Later at the post-salting stages, D. hansenii occurred frequently. Laboratory studies showed that D. hansenii was more tolerant to sodium chloride and nitrite than C. zeylanoides. Smoking seems to have a killing or a temporary growth inhibiting effect on yeasts that extend to the start of the drying process. Yeasts were isolated only from 31.1% of the environmental samples. They belonged to six different species of which five of them were isolated from the meat samples too. Debaryomyces hansenii and Rhodotorula glutinis were dominant with a 62.6% and 22.0% contribution respectively. As none of the air samples contained D. hansenii, the production materials and room installations used in the production processes were believed to be the sources of contamination. The dominance of D. hansenii late in the production process replacing C. zeylanoides should be considered as a positive change both for the quality and safety

  19. The genomics of wild yeast populations sheds light on the domestication of man's best (micro) friend.

    Science.gov (United States)

    Eberlein, Chris; Leducq, Jean-Baptiste; Landry, Christian R

    2015-11-01

    The domestication of plants, animals and microbes by humans are the longest artificial evolution experiments ever performed. The study of these long-term experiments can teach us about the genomics of adaptation through the identification of the genetic bases underlying the traits favoured by humans. In laboratory evolution, the characterization of the molecular changes that evolved specifically in some lineages is straightforward because the ancestors are readily available, for instance in the freezer. However, in the case of domesticated species, the ancestor is often missing, which leads to the necessity of going back to nature in order to infer the most likely ancestral state. Significant and relatively recent examples of this approach include wolves as the closest wild relative to domestic dogs (Axelsson et al. 2013) and teosinte as the closest relative to maize (reviewed in Hake & Ross-Ibarra 2015). In both cases, the joint analysis of domesticated lineages and their wild cousins has been key in reconstructing the molecular history of their domestication. While the identification of closest wild relatives has been done for many plants and animals, these comparisons represent challenges for micro-organisms. This has been the case for the budding yeast Saccharomyces cerevisiae, whose natural ecological niche is particularly challenging to define. For centuries, this unicellular fungus has been the cellular factory for wine, beer and bread crafting, and currently for bioethanol and drug production. While the recent development of genomics has lead to the identification of many genetic elements associated with important wine characteristics, the historical origin of some of the domesticated wine strains has remained elusive due to the lack of knowledge of their close wild relatives. In this issue of Molecular Ecology, Almeida et al. (2015) identified what is to date the closest known wild population of the wine yeast. This population is found associated with

  20. Digital Image Analysis of Yeast Single Cells Growing in Two Different Oxygen Concentrations to Analyze the Population Growth and to Assist Individual-Based Modeling.

    Science.gov (United States)

    Ginovart, Marta; Carbó, Rosa; Blanco, Mónica; Portell, Xavier

    2017-01-01

    Nowadays control of the growth of Saccharomyces to obtain biomass or cellular wall components is crucial for specific industrial applications. The general aim of this contribution is to deal with experimental data obtained from yeast cells and from yeast cultures to attempt the integration of the two levels of information, individual and population, to progress in the control of yeast biotechnological processes by means of the overall analysis of this set of experimental data, and to assist in the improvement of an individual-based model, namely, INDISIM- Saccha . Populations of S. cerevisiae growing in liquid batch culture, in aerobic and microaerophilic conditions, were studied. A set of digital images was taken during the population growth, and a protocol for the treatment and analyses of the images obtained was established. The piecewise linear model of Buchanan was adjusted to the temporal evolutions of the yeast populations to determine the kinetic parameters and changes of growth phases. In parallel, for all the yeast cells analyzed, values of direct morphological parameters, such as area, perimeter, major diameter, minor diameter, and derived ones, such as circularity and elongation, were obtained. Graphical and numerical methods from descriptive statistics were applied to these data to characterize the growth phases and the budding state of the yeast cells in both experimental conditions, and inferential statistical methods were used to compare the diverse groups of data achieved. Oxidative metabolism of yeast in a medium with oxygen available and low initial sugar concentration can be taken into account in order to obtain a greater number of cells or larger cells. Morphological parameters were analyzed statistically to identify which were the most useful for the discrimination of the different states, according to budding and/or growth phase, in aerobic and microaerophilic conditions. The use of the experimental data for subsequent modeling work was then

  1. An Algorithm to Automate Yeast Segmentation and Tracking

    Science.gov (United States)

    Doncic, Andreas; Eser, Umut; Atay, Oguzhan; Skotheim, Jan M.

    2013-01-01

    Our understanding of dynamic cellular processes has been greatly enhanced by rapid advances in quantitative fluorescence microscopy. Imaging single cells has emphasized the prevalence of phenomena that can be difficult to infer from population measurements, such as all-or-none cellular decisions, cell-to-cell variability, and oscillations. Examination of these phenomena requires segmenting and tracking individual cells over long periods of time. However, accurate segmentation and tracking of cells is difficult and is often the rate-limiting step in an experimental pipeline. Here, we present an algorithm that accomplishes fully automated segmentation and tracking of budding yeast cells within growing colonies. The algorithm incorporates prior information of yeast-specific traits, such as immobility and growth rate, to segment an image using a set of threshold values rather than one specific optimized threshold. Results from the entire set of thresholds are then used to perform a robust final segmentation. PMID:23520484

  2. A Nonlinear Mixed Effects Approach for Modeling the Cell-To-Cell Variability of Mig1 Dynamics in Yeast.

    Directory of Open Access Journals (Sweden)

    Joachim Almquist

    Full Text Available The last decade has seen a rapid development of experimental techniques that allow data collection from individual cells. These techniques have enabled the discovery and characterization of variability within a population of genetically identical cells. Nonlinear mixed effects (NLME modeling is an established framework for studying variability between individuals in a population, frequently used in pharmacokinetics and pharmacodynamics, but its potential for studies of cell-to-cell variability in molecular cell biology is yet to be exploited. Here we take advantage of this novel application of NLME modeling to study cell-to-cell variability in the dynamic behavior of the yeast transcription repressor Mig1. In particular, we investigate a recently discovered phenomenon where Mig1 during a short and transient period exits the nucleus when cells experience a shift from high to intermediate levels of extracellular glucose. A phenomenological model based on ordinary differential equations describing the transient dynamics of nuclear Mig1 is introduced, and according to the NLME methodology the parameters of this model are in turn modeled by a multivariate probability distribution. Using time-lapse microscopy data from nearly 200 cells, we estimate this parameter distribution according to the approach of maximizing the population likelihood. Based on the estimated distribution, parameter values for individual cells are furthermore characterized and the resulting Mig1 dynamics are compared to the single cell times-series data. The proposed NLME framework is also compared to the intuitive but limited standard two-stage (STS approach. We demonstrate that the latter may overestimate variabilities by up to almost five fold. Finally, Monte Carlo simulations of the inferred population model are used to predict the distribution of key characteristics of the Mig1 transient response. We find that with decreasing levels of post-shift glucose, the transient

  3. Natural Selection in Large Populations

    Science.gov (United States)

    Desai, Michael

    2011-03-01

    I will discuss theoretical and experimental approaches to the evolutionary dynamics and population genetics of natural selection in large populations. In these populations, many mutations are often present simultaneously, and because recombination is limited, selection cannot act on them all independently. Rather, it can only affect whole combinations of mutations linked together on the same chromosome. Methods common in theoretical population genetics have been of limited utility in analyzing this coupling between the fates of different mutations. In the past few years it has become increasingly clear that this is a crucial gap in our understanding, as sequence data has begun to show that selection appears to act pervasively on many linked sites in a wide range of populations, including viruses, microbes, Drosophila, and humans. I will describe approaches that combine analytical tools drawn from statistical physics and dynamical systems with traditional methods in theoretical population genetics to address this problem, and describe how experiments in budding yeast can help us directly observe these evolutionary dynamics.

  4. Selection of Yeast Strains for Tequila Fermentation Based on Growth Dynamics in Combined Fructose and Ethanol Media.

    Science.gov (United States)

    Aldrete-Tapia, J A; Miranda-Castilleja, D E; Arvizu-Medrano, S M; Hernández-Iturriaga, M

    2018-02-01

    The high concentration of fructose in agave juice has been associated with reduced ethanol tolerance of commercial yeasts used for tequila production and low fermentation yields. The selection of autochthonous strains, which are better adapted to agave juice, could improve the process. In this study, a 2-step selection process of yeasts isolated from spontaneous fermentations for tequila production was carried out based on analysis of the growth dynamics in combined conditions of high fructose and ethanol. First, yeast isolates (605) were screened to identify strains tolerant to high fructose (20%) and to ethanol (10%), yielding 89 isolates able to grow in both conditions. From the 89 isolates, the growth curves under 8 treatments of combined fructose (from 20% to 5%) and ethanol (from 0% to 10%) were obtained, and the kinetic parameters were analyzed with principal component analysis and k-means clustering. The resulting yeast strain groups corresponded to the fast, medium and slow growers. A second clustering of only the fast growers led to the selection of 3 Saccharomyces strains (199, 230, 231) that were able to grow rapidly in 4 out of the 8 conditions evaluated. This methodology differentiated strains phenotypically and could be further used for strain selection in other processes. A method to select yeast strains for fermentation taking into account the natural differences of yeast isolates. This methodology is based on the cell exposition to combinations of sugar and ethanol, which are the most important stress factors in fermentation. This strategy will help to identify the most tolerant strain that could improve ethanol yield and reduce fermentation time. © 2018 Institute of Food Technologists®.

  5. Dynamic Metabolic Footprinting Reveals the Key Components of Metabolic Network in Yeast Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Chumnanpuen, Pramote; Hansen, Michael Adsetts Edberg; Smedsgaard, Jørn

    2014-01-01

    relies on analysis at a single time point. Using direct infusion-mass spectrometry (DI-MS), we could observe the dynamic metabolic footprinting in yeast S. cerevisiae BY4709 (wild type) cultured on 3 different C-sources (glucose, glycerol, and ethanol) and sampled along 10 time points with 5 biological...... replicates. In order to analyze the dynamic mass spectrometry data, we developed the novel analysis methods that allow us to perform correlation analysis to identify metabolites that significantly correlate over time during growth on the different carbon sources. Both positive and negative electrospray...... reconstructed an interaction map that provides information of how different metabolic pathways have correlated patterns during growth on the different carbon sources....

  6. An algorithm to automate yeast segmentation and tracking.

    Directory of Open Access Journals (Sweden)

    Andreas Doncic

    Full Text Available Our understanding of dynamic cellular processes has been greatly enhanced by rapid advances in quantitative fluorescence microscopy. Imaging single cells has emphasized the prevalence of phenomena that can be difficult to infer from population measurements, such as all-or-none cellular decisions, cell-to-cell variability, and oscillations. Examination of these phenomena requires segmenting and tracking individual cells over long periods of time. However, accurate segmentation and tracking of cells is difficult and is often the rate-limiting step in an experimental pipeline. Here, we present an algorithm that accomplishes fully automated segmentation and tracking of budding yeast cells within growing colonies. The algorithm incorporates prior information of yeast-specific traits, such as immobility and growth rate, to segment an image using a set of threshold values rather than one specific optimized threshold. Results from the entire set of thresholds are then used to perform a robust final segmentation.

  7. Cell dualism: presence of cells with alternative membrane potentials in growing populations of bacteria and yeasts.

    Science.gov (United States)

    Ivanov, Volodymyr; Rezaeinejad, Saeid; Chu, Jian

    2013-10-01

    It is considered that all growing cells, for exception of acidophilic bacteria, have negatively charged inside cytoplasmic membrane (Δψ⁻-cells). Here we show that growing populations of microbial cells contain a small portion of cells with positively charged inside cytoplasmic membrane (Δψ⁺-cells). These cells were detected after simultaneous application of the fluorescent probes for positive membrane potential (anionic dye DIBAC⁻) and membrane integrity (propidium iodide, PI). We found in exponentially growing cell populations of Escherichia coli and Saccharomyces cerevisiae that the content of live Δψ⁻-cells was 93.6 ± 1.8 % for bacteria and 90.4 ± 4.0 % for yeasts and the content of live Δψ⁺-cells was 0.9 ± 0.3 % for bacteria and 2.4 ± 0.7 % for yeasts. Hypothetically, existence of Δψ⁺-cells could be due to short-term, about 1 min for bacteria and 5 min for yeasts, change of membrane potential from negative to positive value during the cell cycle. This change has been shown by the reversions of K⁺, Na⁺, and Ca²⁺ ions fluxes across the cell membrane during synchronous yeast culture. The transformation of Δψ(⁻-cells to Δψ⁺-cells can be explained by slow influx of K⁺ ions into Δψ⁻-cell to the trigger level of K⁺ concentration ("compression of potassium spring"), which is forming "alternative" Δψ⁺-cell for a short period, following with fast efflux of K⁺ ions out of Δψ⁺-cell ("release of potassium spring") returning cell to normal Δψ⁻ state. We anticipate our results to be a starting point to reveal the biological role of cell dualism in form of Δψ⁻- and Δψ⁺- cells.

  8. Yeast community associated with the solid state fermentation of traditional Chinese Maotai-flavor liquor.

    Science.gov (United States)

    Wu, Qun; Chen, Liangqiang; Xu, Yan

    2013-09-02

    Yeasts are the most important group of microorganisms contributing to liquor quality in the solid-state fermentation process of Chinese Maotai-flavor liquor. There occurred a complex yeast community structure during this process, including stages of Daqu (the starter) making, stacking fermentation on the ground and liquor fermentation in the pits. In the Daqu making stage, few yeast strains accumulated. However, the stacking fermentation stage accumulated nine yeast species with different physio-biochemical characteristics. But only four species kept dominant until liquor fermentation, which were Zygosaccharomyces bailii, Saccharomyces cerevisiae, Pichia membranifaciens, and Schizosaccharomyces pombe, implying their important functions in liquor making. The four species tended to inhabit in different locations of the stack and pits during stacking and liquor fermentation, due to the condition heterogeneity of the solid-state fermentation, including the different fermentation temperature profiles and oxygen density in different locations. Moreover, yeast population was much larger in the upper layer than that in the middle and bottom layers in liquor fermentation, which was in accordance with the profile of reducing sugar consumption and ethanol production. This was a systematical investigation of yeast community structure dynamics in the Maotai-flavor liquor fermentation process. It would be of help to understand the fermentative mechanism in solid-state fermentation for Maotai-flavor liquor. © 2013.

  9. Lactic acid bacteria population dynamics during spontaneous fermentation of radish (Raphanus sativus L.) roots in brine.

    Science.gov (United States)

    Pardali, Eleni; Paramithiotis, Spiros; Papadelli, Marina; Mataragas, Marios; Drosinos, Eleftherios H

    2017-06-01

    The aim of the present study was to assess the microecosystem development and the dynamics of the lactic acid bacteria population during spontaneous fermentation of radish (Raphanus sativus L.) roots in brine at 20 and 30 °C. In both temperatures, lactic acid bacteria prevailed the fermentation; as a result, the pH value was reduced to ca. 3.6 and total titrable acidity increased to ca. 0.4% lactic acid. Enterococci population increased and formed a secondary microbiota while pseudomonads, Enterobacteriaceae and yeasts/molds populations were below enumeration limit already before the middle of fermentation. Pediococcus pentosaceus dominated during the first days, followed by Lactobacillus plantarum that prevailed the fermentation until the end. Lactobacillus brevis was also detected during the final days of fermentation. A succession at sub-species level was revealed by the combination of RAPD-PCR and rep-PCR analyses. Glucose and fructose were the main carbohydrates detected in brine and were metabolized into lactic acid, acetic acid and ethanol.

  10. Yeast Biodiversity from DOQ Priorat Uninoculated Fermentations.

    Science.gov (United States)

    Padilla, Beatriz; García-Fernández, David; González, Beatriz; Izidoro, Iara; Esteve-Zarzoso, Braulio; Beltran, Gemma; Mas, Albert

    2016-01-01

    Climate, soil, and grape varieties are the primary characteristics of terroir and lead to the definition of various appellations of origin. However, the microbiota associated with grapes are also affected by these conditions and can leave a footprint in a wine that will be part of the characteristics of terroir. Thus, a description of the yeast microbiota within a vineyard is of interest not only to provide a better understanding of the winemaking process, but also to understand the source of microorganisms that maintain a microbial footprint in wine from the examined vineyard. In this study, two typical grape varieties, Grenache and Carignan, have been sampled from four different vineyards in the DOQ Priorat winegrowing region. Afterward, eight spontaneous alcoholic fermentations containing only grapes from one sampling point and of one variety were conducted at laboratory scale. The fermentation kinetics and yeast population dynamics within each fermentation experiment were evaluated. Yeast identification was performed by RFLP-PCR of the 5.8S-ITS region and by sequencing D1/D2 of the 26S rRNA gene of the isolates. The fermentation kinetics did not indicate clear differences between the two varieties of grapes or among vineyards. Approximately 1,400 isolates were identified, exhibiting high species richness in some fermentations. Of all the isolates studied, approximately 60% belong to the genus Hanseniaspora, 16% to Saccharomyces, and 11% to Candida. Other minor genera, such as Hansenula, Issatchenkia, Kluyveromyces, Saccharomycodes, and Zygosaccharomyces, were also found. The distribution of the identified yeast throughout the fermentation process was studied, and Saccharomyces cerevisiae was found to be present mainly at the end of the fermentation process, while Aureobasidium pullulans was isolated primarily during the first days of fermentation in three of the eight spontaneous fermentations. This work highlights the complexity and diversity of the vineyard

  11. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.

    Directory of Open Access Journals (Sweden)

    Raffi Tonikian

    2009-10-01

    Full Text Available SH3 domains are peptide recognition modules that mediate the assembly of diverse biological complexes. We scanned billions of phage-displayed peptides to map the binding specificities of the SH3 domain family in the budding yeast, Saccharomyces cerevisiae. Although most of the SH3 domains fall into the canonical classes I and II, each domain utilizes distinct features of its cognate ligands to achieve binding selectivity. Furthermore, we uncovered several SH3 domains with specificity profiles that clearly deviate from the two canonical classes. In conjunction with phage display, we used yeast two-hybrid and peptide array screening to independently identify SH3 domain binding partners. The results from the three complementary techniques were integrated using a Bayesian algorithm to generate a high-confidence yeast SH3 domain interaction map. The interaction map was enriched for proteins involved in endocytosis, revealing a set of SH3-mediated interactions that underlie formation of protein complexes essential to this biological pathway. We used the SH3 domain interaction network to predict the dynamic localization of several previously uncharacterized endocytic proteins, and our analysis suggests a novel role for the SH3 domains of Lsb3p and Lsb4p as hubs that recruit and assemble several endocytic complexes.

  12. Fish population dynamics

    National Research Council Canada - National Science Library

    Gulland, J. A

    1977-01-01

    This book describes how the dynamics of fish populations can be analysed in terms of the factors affecting their rates of growth, mortality and reproduction, with particular emphasis on the effects of fishing...

  13. Oral yeast carriage in HIV-infected and non-infected populations in Rosario, Argentina.

    Science.gov (United States)

    Luque, A G; Biasoli, M S; Tosello, M E; Binolfi, A; Lupo, S; Magaró, H M

    2009-01-01

    The objectives of the present study were: (i) to assess the frequency of oral colonisation by Candida species in HIV-positive patients and to compare it with a population of HIV-negative individuals, (ii) to determine the prevalence of C. dubliniensis in both populations and (iii) to determine the susceptibility of C. dubliniensis and other Candida species isolated from HIV-positive patients to the most commonly used antifungal agents. Oral samples were obtained from 101 HIV-positive and 108 HIV-negative subjects. For yeast identification, we used morphology in cornmeal agar, the API 20C Aux, growth at 45 degrees C, d-xylose assimilation, morphology in sunflower seed agar and PCR. The frequency of isolation of Candida in HIV-positive patients was: C. albicans, 60.7%; C. dubliniensis, 20.2%; C. glabrata, 5.6%; C. krusei, 5.6%; C. tropicalis, 4.5%; others, <5%. The frequency of isolation of Candida in HIV-negative patients was: C. albicans, 73.9%; C. tropicalis, 15.5%; C. dubliniensis, 2.1%; C. glabrata, 2.1%; C. parapsilosis, 2.1%; others, <5%. The oral colonisation by yeast in the HIV-positive patients was higher than that in the HIV-negative subjects. The susceptibilities of 42 Candida isolates to three antifungal agents were determined. All isolates of C. dubliniensis were susceptible to fluconazole, although several individuals had been previously treated with this drug. Out of the 42 Candida isolates, 10 presented resistance to fluconazole and 10 to itraconazole. The presence of Candida species, resistant to commonly used antifungal agents, represents a potential risk in immunocompromised patients.

  14. Population dynamics at high Reynolds number

    NARCIS (Netherlands)

    Perlekar, P.; Benzi, R.; Nelson, D.R.; Toschi, F.

    2010-01-01

    We study the statistical properties of population dynamics evolving in a realistic two-dimensional compressible turbulent velocity field. We show that the interplay between turbulent dynamics and population growth and saturation leads to quasi-localization and a remarkable reduction in the carrying

  15. [The homogeneity of a population of yeasts from Camembert cheeses].

    Science.gov (United States)

    Schmidt, J L; Daudin, J J

    1983-01-01

    Yeasts are found to a large extent in cheeses, more particularly in soft cheeses such as Camembert. The proximity between two species previously identified by standard methods was studied using a factorial discriminant analysis on 326 strains. Twenty-three fermentation and assimilation tests (discriminant variables) gave a fairly good discrimination between species. This treatment has allowed us to confirm the present tendencies noticed in yeast classification and has also enabled us to group some of the species.

  16. Dynamical systems in population biology

    CERN Document Server

    Zhao, Xiao-Qiang

    2017-01-01

    This research monograph provides an introduction to the theory of nonautonomous semiflows with applications to population dynamics. It develops dynamical system approaches to various evolutionary equations such as difference, ordinary, functional, and partial differential equations, and pays more attention to periodic and almost periodic phenomena. The presentation includes persistence theory, monotone dynamics, periodic and almost periodic semiflows, basic reproduction ratios, traveling waves, and global analysis of prototypical population models in ecology and epidemiology. Research mathematicians working with nonlinear dynamics, particularly those interested in applications to biology, will find this book useful. It may also be used as a textbook or as supplementary reading for a graduate special topics course on the theory and applications of dynamical systems. Dr. Xiao-Qiang Zhao is a University Research Professor at Memorial University of Newfoundland, Canada. His main research interests involve applied...

  17. Kinesin-8 effects on mitotic microtubule dynamics contribute to spindle function in fission yeast

    Science.gov (United States)

    Gergely, Zachary R.; Crapo, Ammon; Hough, Loren E.; McIntosh, J. Richard; Betterton, Meredith D.

    2016-01-01

    Kinesin-8 motor proteins destabilize microtubules. Their absence during cell division is associated with disorganized mitotic chromosome movements and chromosome loss. Despite recent work studying effects of kinesin-8s on microtubule dynamics, it remains unclear whether the kinesin-8 mitotic phenotypes are consequences of their effect on microtubule dynamics, their well-established motor activity, or additional, unknown functions. To better understand the role of kinesin-8 proteins in mitosis, we studied the effects of deletion of the fission yeast kinesin-8 proteins Klp5 and Klp6 on chromosome movements and spindle length dynamics. Aberrant microtubule-driven kinetochore pushing movements and tripolar mitotic spindles occurred in cells lacking Klp5 but not Klp6. Kinesin-8–deletion strains showed large fluctuations in metaphase spindle length, suggesting a disruption of spindle length stabilization. Comparison of our results from light microscopy with a mathematical model suggests that kinesin-8–induced effects on microtubule dynamics, kinetochore attachment stability, and sliding force in the spindle can explain the aberrant chromosome movements and spindle length fluctuations seen. PMID:27146110

  18. Allee effects on population dynamics with delay

    International Nuclear Information System (INIS)

    Celik, C.; Merdan, H.; Duman, O.; Akin, O.

    2008-01-01

    In this paper, we study the stability analysis of equilibrium points of population dynamics with delay when the Allee effect occurs at low population density. Mainly, our mathematical results and numerical simulations point to the stabilizing effect of the Allee effects on population dynamics with delay

  19. Structural stability of nonlinear population dynamics.

    Science.gov (United States)

    Cenci, Simone; Saavedra, Serguei

    2018-01-01

    In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

  20. Structural stability of nonlinear population dynamics

    Science.gov (United States)

    Cenci, Simone; Saavedra, Serguei

    2018-01-01

    In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

  1. Gene expression dynamics in the oxidative stress response of fission yeast

    DEFF Research Database (Denmark)

    Papadakis, Emmanouil

    Changes in the environment continuously challenge living organisms during their lifetime. A cell’s survival depends on its ability to coordinate a rapid and successful stress response when exposed to acute doses of damaging agents. Oxidative stress caused by an excess of reactive oxygen species......, especially using model organisms. The fission yeast Schizosaccharomyces pombe is a unicellular eukaryotic organism that possesses genome features and molecular pathways that are highly conserved in humans. Moreover, the limited redundancy of its genome make S. pombe well suited for phenotypic studies...... (HP, 0.5 mM). The applied experimental design allowed us to measure both the activation and recovery phases of the response at a sufficiently high time resolution to model transcription and translation dynamics. Absolute expression levels (copies per cell) and time-resolved expression profiles for 4...

  2. Yeast species associated with wine grapes in China.

    Science.gov (United States)

    Li, Shuang-Shi; Cheng, Chao; Li, Zheng; Chen, Jing-Yu; Yan, Bin; Han, Bei-Zhong; Reeves, Malcolm

    2010-03-31

    Having more information on the yeast ecology of grapes is important for wine-makers to produce wine with high quality and typical attributes. China is a significant wine-consuming country and is becoming a serious wine-producer, but little has been reported about the yeast ecology of local ecosystems. This study provides the first step towards the exploitation of the yeast wealth in China's vine-growing regions. The aim of this study was to investigate the yeast population density and diversity on three grape varieties cultivated in four representative vine-growing regions of China. Yeast species diversity was evaluated by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and sequence analysis of the 5.8S internal transcribed spacer (ITS) ribosomal DNA (rDNA) region of cultivable yeasts. The grapes harbored yeast populations at 10(2)-10(6)CFU/mL, consisting mostly of non-Saccharomyces species. Seventeen different yeast species belonging to eight genera were detected on the grape samples tested, including Hanseniaspora uvarum, Cryptococcus flavescens, Pichia fermentans, Candida zemplinina, Cryptococcus carnescens, Candida inconpicua, Zygosaccharomyces fermentati, Issatchenkia terricola, Candida quercitrusa, Hanseniaspora guilliermondii, Candida bombi, Zygosaccharomyces bailii, Sporidiobolus pararoseus, Cryptococcus magnus, Metschnikowia pulcherrima, Issatchenkia orientalis and Pichia guilliermondii. H. uvarum and C. flavescens were the dominant species present on the grapes. For the first time Sporidiobolus pararoseus was discovered as an inhabitant of the grape ecosystem. The yeast community on grape berries was influenced by the grape chemical composition, vine-variety and vine-growing region. This study is the first to identify the yeast communities associated with grapes in China using molecular methods. The results enrich our knowledge of wine-related microorganisms, and can be used to promote the development of the local wine

  3. Lager Yeast Comes of Age

    Science.gov (United States)

    2014-01-01

    Alcoholic fermentations have accompanied human civilizations throughout our history. Lager yeasts have a several-century-long tradition of providing fresh beer with clean taste. The yeast strains used for lager beer fermentation have long been recognized as hybrids between two Saccharomyces species. We summarize the initial findings on this hybrid nature, the genomics/transcriptomics of lager yeasts, and established targets of strain improvements. Next-generation sequencing has provided fast access to yeast genomes. Its use in population genomics has uncovered many more hybridization events within Saccharomyces species, so that lager yeast hybrids are no longer the exception from the rule. These findings have led us to propose network evolution within Saccharomyces species. This “web of life” recognizes the ability of closely related species to exchange DNA and thus drain from a combined gene pool rather than be limited to a gene pool restricted by speciation. Within the domesticated lager yeasts, two groups, the Saaz and Frohberg groups, can be distinguished based on fermentation characteristics. Recent evidence suggests that these groups share an evolutionary history. We thus propose to refer to the Saaz group as Saccharomyces carlsbergensis and to the Frohberg group as Saccharomyces pastorianus based on their distinct genomes. New insight into the hybrid nature of lager yeast will provide novel directions for future strain improvement. PMID:25084862

  4. Population dynamics on heterogeneous bacterial substrates

    Science.gov (United States)

    Mobius, Wolfram; Murray, Andrew W.; Nelson, David R.

    2012-02-01

    How species invade new territories and how these range expansions influence the population's genotypes are important questions in the field of population genetics. The majority of work addressing these questions focuses on homogeneous environments. Much less is known about the population dynamics and population genetics when the environmental conditions are heterogeneous in space. To better understand range expansions in two-dimensional heterogeneous environments, we employ a system of bacteria and bacteriophage, the viruses of bacteria. Thereby, the bacteria constitute the environment in which a population of bacteriophages expands. The spread of phage constitutes itself in lysis of bacteria and thus formation of clear regions on bacterial lawns, called plaques. We study the population dynamics and genetics of the expanding page for various patterns of environments.

  5. Interactions between Drosophila and its natural yeast symbionts-Is Saccharomyces cerevisiae a good model for studying the fly-yeast relationship?

    Science.gov (United States)

    Hoang, Don; Kopp, Artyom; Chandler, James Angus

    2015-01-01

    Yeasts play an important role in the biology of the fruit fly, Drosophila melanogaster. In addition to being a valuable source of nutrition, yeasts affect D. melanogaster behavior and interact with the host immune system. Most experiments investigating the role of yeasts in D. melanogaster biology use the baker's yeast, Saccharomyces cerevisiae. However, S. cerevisiae is rarely found with natural populations of D. melanogaster or other Drosophila species. Moreover, the strain of S. cerevisiae used most often in D. melanogaster experiments is a commercially and industrially important strain that, to the best of our knowledge, was not isolated from flies. Since disrupting natural host-microbe interactions can have profound effects on host biology, the results from D. melanogaster-S. cerevisiae laboratory experiments may not be fully representative of host-microbe interactions in nature. In this study, we explore the D. melanogaster-yeast relationship using five different strains of yeast that were isolated from wild Drosophila populations. Ingested live yeasts have variable persistence in the D. melanogaster gastrointestinal tract. For example, Hanseniaspora occidentalis persists relative to S. cerevisiae, while Brettanomyces naardenensis is removed. Despite these differences in persistence relative to S. cerevisiae, we find that all yeasts decrease in total abundance over time. Reactive oxygen species (ROS) are an important component of the D. melanogaster anti-microbial response and can inhibit S. cerevisiae growth in the intestine. To determine if sensitivity to ROS explains the differences in yeast persistence, we measured yeast growth in the presence and absence of hydrogen peroxide. We find that B. naardenesis is completely inhibited by hydrogen peroxide, while H. occidentalis is not, which is consistent with yeast sensitivity to ROS affecting persistence within the D. melanogaster gastrointestinal tract. We also compared the feeding preference of D

  6. Population dynamics in variable environments

    CERN Document Server

    Tuljapurkar, Shripad

    1990-01-01

    Demography relates observable facts about individuals to the dynamics of populations. If the dynamics are linear and do not change over time, the classical theory of Lotka (1907) and Leslie (1945) is the central tool of demography. This book addresses the situation when the assumption of constancy is dropped. In many practical situations, a population will display unpredictable variation over time in its vital rates, which must then be described in statistical terms. Most of this book is concerned with the theory of populations which are subject to random temporal changes in their vital rates, although other kinds of variation (e. g. , cyclical) are also dealt with. The central questions are: how does temporal variation work its way into a population's future, and how does it affect our interpretation of a population's past. The results here are directed at demographers of humans and at popula­ tion biologists. The uneven mathematical level is dictated by the material, but the book should be accessible to re...

  7. Population dynamical responses to climate change

    DEFF Research Database (Denmark)

    Forchhammer, Mads; Schmidt, Niels Martin; Høye, Toke Thomas

    2008-01-01

    approaches, we analyse concurrently the influence of climatic variability and trophic interactions on the temporal population dynamics of species in the terrestrial vertebrate community at Zackenberg. We describe and contrast the population dynamics of three predator species (arctic fox Alopex lagopus, stoat...... of arctic fox were not significantly related to changes in lemming abundance, both the stoat and the breeding of long-tailed skua were mainly related to lemming dynamics. The predator-prey system at Zackenberg differentiates from previously described systems in high-arctic Greenland, which, we suggest...

  8. Impact of Commercial Strain Use on Saccharomyces cerevisiae Population Structure and Dynamics in Pinot Noir Vineyards and Spontaneous Fermentations of a Canadian Winery.

    Directory of Open Access Journals (Sweden)

    Jonathan T Martiniuk

    Full Text Available Wine is produced by one of two methods: inoculated fermentation, where a commercially-produced, single Saccharomyces cerevisiae (S. cerevisiae yeast strain is used; or the traditional spontaneous fermentation, where yeast present on grape and winery surfaces carry out the fermentative process. Spontaneous fermentations are characterized by a diverse succession of yeast, ending with one or multiple strains of S. cerevisiae dominating the fermentation. In wineries using both fermentation methods, commercial strains may dominate spontaneous fermentations. We elucidate the impact of the winery environment and commercial strain use on S. cerevisiae population structure in spontaneous fermentations over two vintages by comparing S. cerevisiae populations in aseptically fermented grapes from a Canadian Pinot Noir vineyard to S. cerevisiae populations in winery-conducted fermentations of grapes from the same vineyard. We also characterize the vineyard-associated S. cerevisiae populations in two other geographically separate Pinot Noir vineyards farmed by the same winery. Winery fermentations were not dominated by commercial strains, but by a diverse number of strains with genotypes similar to commercial strains, suggesting that a population of S. cerevisiae derived from commercial strains is resident in the winery. Commercial and commercial-related yeast were also identified in the three vineyards examined, although at a lower frequency. There is low genetic differentiation and S. cerevisiae population structure between vineyards and between the vineyard and winery that persisted over both vintages, indicating commercial yeast are a driver of S. cerevisiae population structure. We also have evidence of distinct and persistent populations of winery and vineyard-associated S. cerevisiae populations unrelated to commercial strains. This study is the first to characterize S. cerevisiae populations in Canadian vineyards.

  9. Impact of Commercial Strain Use on Saccharomyces cerevisiae Population Structure and Dynamics in Pinot Noir Vineyards and Spontaneous Fermentations of a Canadian Winery.

    Science.gov (United States)

    Martiniuk, Jonathan T; Pacheco, Braydon; Russell, Gordon; Tong, Stephanie; Backstrom, Ian; Measday, Vivien

    2016-01-01

    Wine is produced by one of two methods: inoculated fermentation, where a commercially-produced, single Saccharomyces cerevisiae (S. cerevisiae) yeast strain is used; or the traditional spontaneous fermentation, where yeast present on grape and winery surfaces carry out the fermentative process. Spontaneous fermentations are characterized by a diverse succession of yeast, ending with one or multiple strains of S. cerevisiae dominating the fermentation. In wineries using both fermentation methods, commercial strains may dominate spontaneous fermentations. We elucidate the impact of the winery environment and commercial strain use on S. cerevisiae population structure in spontaneous fermentations over two vintages by comparing S. cerevisiae populations in aseptically fermented grapes from a Canadian Pinot Noir vineyard to S. cerevisiae populations in winery-conducted fermentations of grapes from the same vineyard. We also characterize the vineyard-associated S. cerevisiae populations in two other geographically separate Pinot Noir vineyards farmed by the same winery. Winery fermentations were not dominated by commercial strains, but by a diverse number of strains with genotypes similar to commercial strains, suggesting that a population of S. cerevisiae derived from commercial strains is resident in the winery. Commercial and commercial-related yeast were also identified in the three vineyards examined, although at a lower frequency. There is low genetic differentiation and S. cerevisiae population structure between vineyards and between the vineyard and winery that persisted over both vintages, indicating commercial yeast are a driver of S. cerevisiae population structure. We also have evidence of distinct and persistent populations of winery and vineyard-associated S. cerevisiae populations unrelated to commercial strains. This study is the first to characterize S. cerevisiae populations in Canadian vineyards.

  10. Clonality, genetic diversity and support for the diversifying selection hypothesis in natural populations of a flower-living yeast.

    Science.gov (United States)

    Herrera, C M; Pozo, M I; Bazaga, P

    2011-11-01

    Vast amounts of effort have been devoted to investigate patterns of genetic diversity and structuring in plants and animals, but similar information is scarce for organisms of other kingdoms. The study of the genetic structure of natural populations of wild yeasts can provide insights into the ecological and genetic correlates of clonality, and into the generality of recent hypotheses postulating that microbial populations lack the potential for genetic divergence and allopatric speciation. Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain were DNA fingerprinted using amplified fragment length polymorphism (AFLP) markers. Genetic diversity and structuring was investigated with band-based methods and model- and nonmodel-based clustering. Linkage disequilibrium tests were used to assess reproduction mode. Microsite-dependent, diversifying selection was tested by comparing genetic characteristics of isolates from bumble bee vectors and different floral microsites. AFLP polymorphism (91%) and genotypic diversity were very high. Genetic diversity was spatially structured, as shown by amova (Φ(st)  = 0.155) and clustering. The null hypothesis of random mating was rejected, clonality seeming the prevailing reproductive mode in the populations studied. Genetic diversity of isolates declined from bumble bee mouthparts to floral microsites, and frequency of five AFLP markers varied significantly across floral microsites, thus supporting the hypothesis of diversifying selection on clonal lineages. Wild populations of clonal fungal microbes can exhibit levels of genetic diversity and spatial structuring that are not singularly different from those shown by sexually reproducing plants or animals. Microsite-dependent, divergent selection can maintain high local and regional genetic diversity in microbial populations despite extensive clonality. © 2011 Blackwell Publishing Ltd.

  11. Market Squid Population Dynamics

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains population dynamics data on paralarvae, juvenile and adult market squid collected off California and the US Pacific Northwest. These data were...

  12. Population dynamics and population control of Galium aparine L.

    NARCIS (Netherlands)

    Weide, van der R.Y.

    1993-01-01

    The population biology of Galium aparine L. needs to be better understood, in order to be able to rationalize decisions about the short- and long-term control of this weed species for different cropping practices.

    A population dynamics model was developed to

  13. Population genetics inside a cell: Mutations and mitochondrial genome maintenance

    Science.gov (United States)

    Goyal, Sidhartha; Shraiman, Boris; Gottschling, Dan

    2012-02-01

    In realistic ecological and evolutionary systems natural selection acts on multiple levels, i.e. it acts on individuals as well as on collection of individuals. An understanding of evolutionary dynamics of such systems is limited in large part due to the lack of experimental systems that can challenge theoretical models. Mitochondrial genomes (mtDNA) are subjected to selection acting on cellular as well as organelle levels. It is well accepted that mtDNA in yeast Saccharomyces cerevisiae is unstable and can degrade over time scales comparable to yeast cell division time. We utilize a recent technology designed in Gottschling lab to extract DNA from populations of aged yeast cells and deep sequencing to characterize mtDNA variation in a population of young and old cells. In tandem, we developed a stochastic model that includes the essential features of mitochondrial biology that provides a null model for expected mtDNA variation. Overall, we find approximately 2% of the polymorphic loci that show significant increase in frequency as cells age providing direct evidence for organelle level selection. Such quantitative study of mtDNA dynamics is absolutely essential to understand the propagation of mtDNA mutations linked to a spectrum of age-related diseases in humans.

  14. Solving the puzzle of yeast survival in ephemeral nectar systems: exponential growth is not enough.

    Science.gov (United States)

    Hausmann, Sebastian L; Tietjen, Britta; Rillig, Matthias C

    2017-12-01

    Flower nectar is a sugar-rich ephemeral habitat for microorganisms. Nectar-borne yeasts are part of the microbial community and can affect pollination by changing nectar chemistry, attractiveness to pollinators or flower temperature if yeast population densities are high. Pollinators act as dispersal agents in this system; however, pollination events lead potentially to shrinking nectar yeast populations. We here examine how sufficiently high cell densities of nectar yeast can develop in a flower. In laboratory experiments, we determined the remaining fraction of nectar yeast cells after nectar removal, and used honeybees to determine the number of transmitted yeast cells from one flower to the next. The results of these experiments directly fed into a simulation model providing an insight into movement and colonization ecology of nectar yeasts. We found that cell densities only reached an ecologically relevant size for an intermediate pollination probability. Too few pollination events reduce yeast inoculation rate and too many reduce yeast population size strongly. In addition, nectar yeasts need a trait combination of at least an intermediate growth rate and an intermediate remaining fraction to compensate for highly frequent decimations. Our results can be used to predict nectar yeast dispersal, growth and consequently their ecological effects. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Specific features of the dynamics of epiphytic and soil yeast communities in the thickets of Indian balsam on mucky gley soil

    Science.gov (United States)

    Glushakova, A. M.; Kachalkin, A. V.; Chernov, I. Yu.

    2011-08-01

    The annual dynamics of the number and taxonomic composition of yeast communities were studied in the phyllosphere, on the flowers, and on the roots of Indian balsam ( Impatiens glandulifera Royle) and in the mucky gley soil under the thickets of this plant. It was shown that typical phyllosphere yeast communities with a predominance of the red-pigmented species Rhodotorula mucilaginosa and Rhodotorula glutinis and the typical epiphyte Cryptococcus magnus are formed on the leaves of this annual hygrophyte. However, yeast groups with a predominance of the ascosporous species Saccharomyces paradoxus, Kazachstania barnettii, and Torulaspora delbrueckii, which are not typical of soils at all, were found in the mucky gley soil under the thickets of Indian balsam. Thus, the epiphytic and soil yeast complexes under the thickets of Indian balsam are represented by two entirely discrete communities without common species. In other biogeocenoses of the forest zone, the rearrangement of the structure of yeast communities in passing from the aboveground substrates to the soil proceeds gradually, and most of the species can be isolated both from the aboveground parts of plants and from the soil. The strong difference between the yeast communities in the phyllosphere of Indian balsam and in the soil under its thickets is apparently related to the fact that the annual hygrophytes are decomposed very quickly (during several days after the first frosts). Because of this, an intermediate layer between the phyllosphere and the soil (the litter layer), in which epiphytic microorganisms can develop, is not formed under these plants.

  16. Evolutionary dynamics of cooperation in neutral populations

    Science.gov (United States)

    Szolnoki, Attila; Perc, Matjaž

    2018-01-01

    Cooperation is a difficult proposition in the face of Darwinian selection. Those that defect have an evolutionary advantage over cooperators who should therefore die out. However, spatial structure enables cooperators to survive through the formation of homogeneous clusters, which is the hallmark of network reciprocity. Here we go beyond this traditional setup and study the spatiotemporal dynamics of cooperation in a population of populations. We use the prisoner's dilemma game as the mathematical model and show that considering several populations simultaneously gives rise to fascinating spatiotemporal dynamics and pattern formation. Even the simplest assumption that strategies between different populations are payoff-neutral with one another results in the spontaneous emergence of cyclic dominance, where defectors of one population become prey of cooperators in the other population, and vice versa. Moreover, if social interactions within different populations are characterized by significantly different temptations to defect, we observe that defectors in the population with the largest temptation counterintuitively vanish the fastest, while cooperators that hang on eventually take over the whole available space. Our results reveal that considering the simultaneous presence of different populations significantly expands the complexity of evolutionary dynamics in structured populations, and it allows us to understand the stability of cooperation under adverse conditions that could never be bridged by network reciprocity alone.

  17. Regulation of ER-Golgi Transport Dynamics by GTPases in Budding Yeast

    Directory of Open Access Journals (Sweden)

    Yasuyuki Suda

    2018-01-01

    Full Text Available A large number of proteins are synthesized de novo in the endoplasmic reticulum (ER. They are transported through the Golgi apparatus and then delivered to their proper destinations. The ER and the Golgi play a central role in protein processing and sorting and show dynamic features in their forms. Ras super family small GTPases mediate the protein transport through and between these organelles. The ER-localized GTPase, Sar1, facilitates the formation of COPII transport carriers at the ER exit sites (ERES on the ER for the transport of cargo proteins from the ER to the Golgi. The Golgi-localized GTPase, Arf1, controls intra-Golgi, and Golgi-to-ER transport of cargo proteins by the formation of COPI carriers. Rab GTPases localized at the Golgi, which are responsible for fusion of membranes, are thought to establish the identities of compartments. Recent evidence suggests that these small GTPases regulate not only discrete sites for generation/fusion of transport carriers, but also membrane dynamics of the organelles where they locate to ensure the integrity of transport. Here we summarize the current understandings about the membrane traffic between these organelles and highlight the cutting-edge advances from super-resolution live imaging of budding yeast, Saccharomyces cerevisiae.

  18. Dynamics of yeast cell populations

    DEFF Research Database (Denmark)

    Sørensen, Preben Graae; Hynne, Finn; Danø, Sune

    2000-01-01

    Proceedings of the 5th International Conference on Fundamental and Applied Aspects of Physical Chemistry......Proceedings of the 5th International Conference on Fundamental and Applied Aspects of Physical Chemistry...

  19. Synchronization of glycolytic oscillations in a yeast cell population

    DEFF Research Database (Denmark)

    Dano, S.; Hynne, F.; De Monte, Silvia

    2001-01-01

    The mechanism of active phase synchronization in a suspension of oscillatory yeast cells has remained a puzzle for almost half a century. The difficulty of the problem stems from the fact that the synchronization phenomenon involves the entire metabolic network of glycolysis and fermentation, and...

  20. Simultaneous cell growth and ethanol production from cellulose by an engineered yeast consortium displaying a functional mini-cellulosome

    Directory of Open Access Journals (Sweden)

    Madan Bhawna

    2011-11-01

    Full Text Available Abstract Background The recalcitrant nature of cellulosic materials and the high cost of enzymes required for efficient hydrolysis are the major impeding steps to their practical usage for ethanol production. Ideally, a recombinant microorganism, possessing the capability to utilize cellulose for simultaneous growth and ethanol production, is of great interest. We have reported recently the use of a yeast consortium for the functional presentation of a mini-cellulosome structure onto the yeast surface by exploiting the specific interaction of different cohesin-dockerin pairs. In this study, we engineered a yeast consortium capable of displaying a functional mini-cellulosome for the simultaneous growth and ethanol production on phosphoric acid swollen cellulose (PASC. Results A yeast consortium composed of four different populations was engineered to display a functional mini-cellulosome containing an endoglucanase, an exoglucanase and a β-glucosidase. The resulting consortium was demonstrated to utilize PASC for growth and ethanol production. The final ethanol production of 1.25 g/L corresponded to 87% of the theoretical value and was 3-fold higher than a similar yeast consortium secreting only the three cellulases. Quantitative PCR was used to enumerate the dynamics of each individual yeast population for the two consortia. Results indicated that the slight difference in cell growth cannot explain the 3-fold increase in PASC hydrolysis and ethanol production. Instead, the substantial increase in ethanol production is consistent with the reported synergistic effect on cellulose hydrolysis using the displayed mini-cellulosome. Conclusions This report represents a significant step towards the goal of cellulosic ethanol production. This engineered yeast consortium displaying a functional mini-cellulosome demonstrated not only the ability to grow on the released sugars from PASC but also a 3-fold higher ethanol production than a similar yeast

  1. Yeast Colonies: A Model for Studies of Aging, Environmental Adaptation, and Longevity

    Directory of Open Access Journals (Sweden)

    Libuše Váchová

    2012-01-01

    Full Text Available When growing on solid surfaces, yeast, like other microorganisms, develops organized multicellular populations (colonies and biofilms that are composed of differentiated cells with specialized functions. Life within these populations is a prevalent form of microbial existence in natural settings that provides the cells with capabilities to effectively defend against environmental attacks as well as efficiently adapt and survive long periods of starvation and other stresses. Under such circumstances, the fate of an individual yeast cell is subordinated to the profit of the whole population. In the past decade, yeast colonies, with their complicated structure and high complexity that are also developed under laboratory conditions, have become an excellent model for studies of various basic cellular processes such as cell interaction, signaling, and differentiation. In this paper, we summarize current knowledge on the processes related to chronological aging, adaptation, and longevity of a colony cell population and of its differentiated cell constituents. These processes contribute to the colony ability to survive long periods of starvation and mostly differ from the survival strategies of individual yeast cells.

  2. Strongly Deterministic Population Dynamics in Closed Microbial Communities

    Directory of Open Access Journals (Sweden)

    Zak Frentz

    2015-10-01

    Full Text Available Biological systems are influenced by random processes at all scales, including molecular, demographic, and behavioral fluctuations, as well as by their interactions with a fluctuating environment. We previously established microbial closed ecosystems (CES as model systems for studying the role of random events and the emergent statistical laws governing population dynamics. Here, we present long-term measurements of population dynamics using replicate digital holographic microscopes that maintain CES under precisely controlled external conditions while automatically measuring abundances of three microbial species via single-cell imaging. With this system, we measure spatiotemporal population dynamics in more than 60 replicate CES over periods of months. In contrast to previous studies, we observe strongly deterministic population dynamics in replicate systems. Furthermore, we show that previously discovered statistical structure in abundance fluctuations across replicate CES is driven by variation in external conditions, such as illumination. In particular, we confirm the existence of stable ecomodes governing the correlations in population abundances of three species. The observation of strongly deterministic dynamics, together with stable structure of correlations in response to external perturbations, points towards a possibility of simple macroscopic laws governing microbial systems despite numerous stochastic events present on microscopic levels.

  3. How Resource Phenology Affects Consumer Population Dynamics.

    Science.gov (United States)

    Bewick, Sharon; Cantrell, R Stephen; Cosner, Chris; Fagan, William F

    2016-02-01

    Climate change drives uneven phenology shifts across taxa, and this can result in changes to the phenological match between interacting species. Shifts in the relative phenology of partner species are well documented, but few studies have addressed the effects of such changes on population dynamics. To explore this, we develop a phenologically explicit model describing consumer-resource interactions. Focusing on scenarios for univoltine insects, we show how changes in resource phenology can be reinterpreted as transformations in the year-to-year recursion relationships defining consumer population dynamics. This perspective provides a straightforward path for interpreting the long-term population consequences of phenology change. Specifically, by relating the outcome of phenological shifts to species traits governing recursion relationships (e.g., consumer fecundity or competitive scenario), we demonstrate how changes in relative phenology can force systems into different dynamical regimes, with major implications for resource management, conservation, and other areas of applied dynamics.

  4. Replenishment and mobilization of intracellular nitrogen pools decouples wine yeast nitrogen uptake from growth

    OpenAIRE

    SANCHO FORNER, MARTA; Alicia Gutiérrez; BELTRAN CASELLAS, GEMMA; José Manuel Guillamon; Jonas Warringer

    2016-01-01

    Wine yeast capacity to take up nitrogen from the environment and catabolize it to support population growth, fermentation, and aroma production is critical to wine production. Under nitrogen restriction, yeast nitrogen uptake is believed to be intimately coupled to reproduction with nitrogen catabolite repression (NCR) suggested mediating this link. We provide a time- and strain-resolved view of nitrogen uptake, population growth, and NCR activity in wine yeasts. Nitrogen uptake was found to ...

  5. Modelling the Dynamics of an Aedes albopictus Population

    Directory of Open Access Journals (Sweden)

    Thomas Anung Basuki

    2010-08-01

    Full Text Available We present a methodology for modelling population dynamics with formal means of computer science. This allows unambiguous description of systems and application of analysis tools such as simulators and model checkers. In particular, the dynamics of a population of Aedes albopictus (a species of mosquito and its modelling with the Stochastic Calculus of Looping Sequences (Stochastic CLS are considered. The use of Stochastic CLS to model population dynamics requires an extension which allows environmental events (such as changes in the temperature and rainfalls to be taken into account. A simulator for the constructed model is developed via translation into the specification language Maude, and used to compare the dynamics obtained from the model with real data.

  6. Made for Each Other: Ascomycete Yeasts and Insects.

    Science.gov (United States)

    Blackwell, Meredith

    2017-06-01

    Fungi and insects live together in the same habitats, and many species of both groups rely on each other for success. Insects, the most successful animals on Earth, cannot produce sterols, essential vitamins, and many enzymes; fungi, often yeast-like in growth form, make up for these deficits. Fungi, however, require constantly replenished substrates because they consume the previous ones, and insects, sometimes lured by volatile fungal compounds, carry fungi directly to a similar, but fresh, habitat. Yeasts associated with insects include Ascomycota (Saccharomycotina, Pezizomycotina) and a few Basidiomycota. Beetles, homopterans, and flies are important associates of fungi, and in turn the insects carry yeasts in pits, specialized external pouches, and modified gut pockets. Some yeasts undergo sexual reproduction within the insect gut, where the genetic diversity of the population is increased, while others, well suited to their stable environment, may never mate. The range of interactions extends from dispersal of yeasts on the surface of insects (e.g., cactus- Drosophila -yeast and ephemeral flower communities, ambrosia beetles, yeasts with holdfasts) to extremely specialized associations of organisms that can no longer exist independently, as in the case of yeast-like symbionts of planthoppers. In a few cases yeast-like fungus-insect associations threaten butterflies and other species with extinction. Technical advances improve discovery and identification of the fungi but also inform our understanding of the evolution of yeast-insect symbioses, although there is much more to learn.

  7. Stochastic population dynamics in populations of western terrestrial garter snakes with divergent life histories.

    Science.gov (United States)

    Miller, David A; Clark, William R; Arnold, Stevan J; Bronikowski, Anne M

    2011-08-01

    Comparative evaluations of population dynamics in species with temporal and spatial variation in life-history traits are rare because they require long-term demographic time series from multiple populations. We present such an analysis using demographic data collected during the interval 1978-1996 for six populations of western terrestrial garter snakes (Thamnophis elegans) from two evolutionarily divergent ecotypes. Three replicate populations from a slow-living ecotype, found in mountain meadows of northeastern California, were characterized by individuals that develop slowly, mature late, reproduce infrequently with small reproductive effort, and live longer than individuals of three populations of a fast-living ecotype found at lakeshore locales. We constructed matrix population models for each of the populations based on 8-13 years of data per population and analyzed both deterministic dynamics based on mean annual vital rates and stochastic dynamics incorporating annual variation in vital rates. (1) Contributions of highly variable vital rates to fitness (lambda(s)) were buffered against the negative effects of stochastic variation, and this relationship was consistent with differences between the meadow (M-slow) and lakeshore (L-fast) ecotypes. (2) Annual variation in the proportion of gravid females had the greatest negative effect among all vital rates on lambda(s). The magnitude of variation in the proportion of gravid females and its effect on lambda(s) was greater in M-slow than L-fast populations. (3) Variation in the proportion of gravid females, in turn, depended on annual variation in prey availability, and its effect on lambda(s) was 4 23 times greater in M-slow than L-fast populations. In addition to differences in stochastic dynamics between ecotypes, we also found higher mean mortality rates across all age classes in the L-fast populations. Our results suggest that both deterministic and stochastic selective forces have affected the evolution of

  8. Aerobic Stability and Effects of Yeasts during Deterioration of Non-fermented and Fermented Total Mixed Ration with Different Moisture Levels

    Directory of Open Access Journals (Sweden)

    W. Hao

    2015-06-01

    Full Text Available The present experiment evaluated the influence of moisture level and anaerobic fermentation on aerobic stability of total mixed ration (TMR. The dynamic changes in chemical composition and microbial population that occur after air exposure were examined, and the species of yeast associated with the deterioration process were also identified in both non-fermented and fermented TMR to deepen the understanding of aerobic deterioration. The moisture levels of TMR in this experiment were adjusted to 400 g/kg (low moisture level, LML, 450 g/kg (medium moisture level, MML, and 500 g/kg (high moisture level, HML, and both non-fermented and 56-d-fermented TMR were subjected to air exposure to determine aerobic stability. Aerobic deterioration resulted in high losses of nutritional components and largely reduced dry matter digestibility. Non-fermented TMR deteriorated during 48 h of air exposure and the HML treatment was more aerobically unstable. On dry matter (DM basis, yeast populations significantly increased from 107 to 1010 cfu/g during air exposure, and Candida ethanolica was the predominant species during deterioration in non-fermented TMR. Fermented TMR exhibited considerable resistance to aerobic deterioration. Spoilage was only observed in the HML treatment and its yeast population increased dramatically to 109 cfu/g DM when air exposure progressed to 30 d. Zygosaccharomyces bailii was the sole yeast species isolated when spoilage occurred. These results confirmed that non-fermented and fermented TMR with a HML are more prone to spoilage, and fermented TMR has considerable resistance to aerobic deterioration. Yeasts can trigger aerobic deterioration in both non-fermented and fermented TMR. C. ethanolica may be involved in the spoilage of non-fermented TMR and the vigorous growth of Z. bailii can initiate aerobic deterioration in fermented TMR.

  9. Aerobic Stability and Effects of Yeasts during Deterioration of Non-fermented and Fermented Total Mixed Ration with Different Moisture Levels.

    Science.gov (United States)

    Hao, W; Wang, H L; Ning, T T; Yang, F Y; Xu, C C

    2015-06-01

    The present experiment evaluated the influence of moisture level and anaerobic fermentation on aerobic stability of total mixed ration (TMR). The dynamic changes in chemical composition and microbial population that occur after air exposure were examined, and the species of yeast associated with the deterioration process were also identified in both non-fermented and fermented TMR to deepen the understanding of aerobic deterioration. The moisture levels of TMR in this experiment were adjusted to 400 g/kg (low moisture level, LML), 450 g/kg (medium moisture level, MML), and 500 g/kg (high moisture level, HML), and both non-fermented and 56-d-fermented TMR were subjected to air exposure to determine aerobic stability. Aerobic deterioration resulted in high losses of nutritional components and largely reduced dry matter digestibility. Non-fermented TMR deteriorated during 48 h of air exposure and the HML treatment was more aerobically unstable. On dry matter (DM) basis, yeast populations significantly increased from 10(7) to 10(10) cfu/g during air exposure, and Candida ethanolica was the predominant species during deterioration in non-fermented TMR. Fermented TMR exhibited considerable resistance to aerobic deterioration. Spoilage was only observed in the HML treatment and its yeast population increased dramatically to 10(9) cfu/g DM when air exposure progressed to 30 d. Zygosaccharomyces bailii was the sole yeast species isolated when spoilage occurred. These results confirmed that non-fermented and fermented TMR with a HML are more prone to spoilage, and fermented TMR has considerable resistance to aerobic deterioration. Yeasts can trigger aerobic deterioration in both non-fermented and fermented TMR. C. ethanolica may be involved in the spoilage of non-fermented TMR and the vigorous growth of Z. bailii can initiate aerobic deterioration in fermented TMR.

  10. Evolutionary dynamics with fluctuating population sizes and strong mutualism

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David R.

    2015-08-01

    Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

  11. Evolutionary dynamics with fluctuating population sizes and strong mutualism.

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David R

    2015-08-01

    Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

  12. Replication dynamics of the yeast genome.

    Science.gov (United States)

    Raghuraman, M K; Winzeler, E A; Collingwood, D; Hunt, S; Wodicka, L; Conway, A; Lockhart, D J; Davis, R W; Brewer, B J; Fangman, W L

    2001-10-05

    Oligonucleotide microarrays were used to map the detailed topography of chromosome replication in the budding yeast Saccharomyces cerevisiae. The times of replication of thousands of sites across the genome were determined by hybridizing replicated and unreplicated DNAs, isolated at different times in S phase, to the microarrays. Origin activations take place continuously throughout S phase but with most firings near mid-S phase. Rates of replication fork movement vary greatly from region to region in the genome. The two ends of each of the 16 chromosomes are highly correlated in their times of replication. This microarray approach is readily applicable to other organisms, including humans.

  13. Occurrence of mycotoxins and yeasts and moulds identification in corn silages in tropical climate.

    Science.gov (United States)

    Carvalho, B F; Ávila, C L S; Krempser, P M; Batista, L R; Pereira, M N; Schwan, R F

    2016-05-01

    This study was aimed to identify yeasts and moulds as well as to detect mycotoxin in corn silages in southern Minas Gerais, Brazil. Corn silages from 36 farms were sampled to analyse dry matter, crude protein, ether extract, ash, neutral detergent fibre, nonfibre carbohydrates and mycotoxins contents, yeasts and moulds population, pH and temperature values. The mycotoxins found in high frequency were aflatoxin in 77·7% of analysed samples, ochratoxin (33·3%) and zearalenone (22·2%). There was no significant correlation between the mycotoxin concentration and the presence of moulds. The pH was negatively correlated with ochratoxin concentration. Aspergillus fumigatus was identified in all silages that presented growth of moulds. Ten different yeast species were identified using the culture-dependent method: Candida diversa, Candida ethanolica, Candida rugosa, Issatchenkia orientalis, Kluyveromyces marxianus, Pichia manshurica, Pichia membranifaciens, Saccharomyces cerevisiae, Trichosporon asahii and Trichosporon japonicum. Another six different yeast species were identified using the culture-independent method. A high mycotoxin contamination rate (91·6% of the analysed silages) was observed. The results indicated that conventional culturing and PCR-DGGE should be combined to optimally describe the microbiota associated with corn silage. This study provides information about the corn silage fermentation dynamics and our findings are relevant to optimization of this silage fermentation. © 2016 The Society for Applied Microbiology.

  14. Allee effects on population dynamics in continuous (overlapping) case

    International Nuclear Information System (INIS)

    Merdan, H.; Duman, O.; Akin, O.; Celik, C.

    2009-01-01

    This paper presents the stability analysis of equilibrium points of a continuous population dynamics with delay under the Allee effect which occurs at low population density. The mathematical results and numerical simulations show the stabilizing role of the Allee effects on the stability of the equilibrium point of this population dynamics.

  15. Consolidated Bio-Processing of Cellulosic Biomass for Efficient Biofuel Production Using Yeast Consortium

    Science.gov (United States)

    Goyal, Garima

    composed of four yeast populations. These yeast populations include: one displaying scaffoldin on its surface and three populations secreting three different cellulases in the medium to hydrolyze the cellulose. The modular nature of the consortium system allows for the fine-tuning of each population by changing their initial inoculum ratio, thereby optimizing the cellulose hydrolysis and hence ethanol production. When comparing the optimized consortium with equal ratio consortium, the optimized one produced almost double the amount of ethanol (1.87 g/l) with a yield of 0.475 g ethanol/g cellulose. To further evaluate the feasibility of using consortium for CBP, it was grown at very low optical density (OD) under anaerobic conditions. Under stressful conditions like low OD and no oxygen, the consortium system was proficient in assembling the cellulosome on its surface and growing on the PAS-avicel as sole carbon source and concomitantly producing ethanol with a yield of 87% of the theoretical value. For the dynamic study of yeast consortium system, quantitative real time PCR was used to enumerate the individual yeast population in the mixed culture. At the end of the cultivation, ratios of each population in this consortium maintained similar number as the initial inoculums ratios, which further confirms the consortium system is suitable for the application of CBP.

  16. Analysis of Population Dynamics in World Economy

    OpenAIRE

    Martin, Gress

    2011-01-01

    Population dynamics is an important topic in current world economy. The size and growth of population have an impact on economic growth and development of individual countries and vice versa, economic development influences demographic variables in a country. The aim of the article is to analyze historical development of world population, population stock change and relations between population stock change and economic development.

  17. Rapid evolution leads to differential population dynamics and top-down control in resurrected Daphnia populations.

    Science.gov (United States)

    Goitom, Eyerusalem; Kilsdonk, Laurens J; Brans, Kristien; Jansen, Mieke; Lemmens, Pieter; De Meester, Luc

    2018-01-01

    There is growing evidence of rapid genetic adaptation of natural populations to environmental change, opening the perspective that evolutionary trait change may subsequently impact ecological processes such as population dynamics, community composition, and ecosystem functioning. To study such eco-evolutionary feedbacks in natural populations, however, requires samples across time. Here, we capitalize on a resurrection ecology study that documented rapid and adaptive evolution in a natural population of the water flea Daphnia magna in response to strong changes in predation pressure by fish, and carry out a follow-up mesocosm experiment to test whether the observed genetic changes influence population dynamics and top-down control of phytoplankton. We inoculated populations of the water flea D. magna derived from three time periods of the same natural population known to have genetically adapted to changes in predation pressure in replicate mesocosms and monitored both Daphnia population densities and phytoplankton biomass in the presence and absence of fish. Our results revealed differences in population dynamics and top-down control of algae between mesocosms harboring populations from the time period before, during, and after a peak in fish predation pressure caused by human fish stocking. The differences, however, deviated from our a priori expectations. An S-map approach on time series revealed that the interactions between adults and juveniles strongly impacted the dynamics of populations and their top-down control on algae in the mesocosms, and that the strength of these interactions was modulated by rapid evolution as it occurred in nature. Our study provides an example of an evolutionary response that fundamentally alters the processes structuring population dynamics and impacts ecosystem features.

  18. Cooperation, cheating, and collapse in microbial populations

    Science.gov (United States)

    Gore, Jeff

    2012-02-01

    Natural populations can suffer catastrophic collapse in response to small changes in environmental conditions, and recovery after such a collapse can be exceedingly difficult. We have used laboratory yeast populations to study proposed early warning signals of impending extinction. Yeast cooperatively breakdown the sugar sucrose, meaning that there is a minimum number of cells required to sustain the population. We have demonstrated experimentally that the fluctuations in the population size increase in magnitude and become slower as the population approaches collapse. The cooperative nature of yeast growth on sucrose suggests that the population may be susceptible to cheater cells, which do not contribute to the public good and instead merely take advantage of the cooperative cells. We have confirmed this possibility experimentally by using a cheater yeast strain that lacks the gene encoding the cooperative behavior [1]. However, recent results in the lab demonstrate that the presence of a bacterial competitor may drive cooperation within the yeast population.[4pt] [1] Gore et al, Nature 459, 253 -- 256 (2009)

  19. The ecology of the Drosophila-yeast mutualism in wineries

    Science.gov (United States)

    2018-01-01

    The fruit fly, Drosophila melanogaster, is preferentially found on fermenting fruits. The yeasts that dominate the microbial communities of these substrates are the primary food source for developing D. melanogaster larvae, and adult flies manifest a strong olfactory system-mediated attraction for the volatile compounds produced by these yeasts during fermentation. Although most work on this interaction has focused on the standard laboratory yeast Saccharomyces cerevisiae, a wide variety of other yeasts naturally ferment fallen fruit. Here we address the open question of whether D. melanogaster preferentially associates with distinct yeasts in different, closely-related environments. We characterized the spatial and temporal dynamics of Drosophila-associated fungi in Northern California wineries that use organic grapes and natural fermentation using high-throughput, short-amplicon sequencing. We found that there is nonrandom structure in the fungal communities that are vectored by flies both between and within vineyards. Within wineries, the fungal communities associated with flies in cellars, fermentation tanks, and pomace piles are distinguished by varying abundances of a small number of yeast species. To investigate the origins of this structure, we assayed Drosophila attraction to, oviposition on, larval development in, and longevity when consuming the yeasts that distinguish vineyard microhabitats from each other. We found that wild fly lines did not respond differentially to the yeast species that distinguish winery habitats in habitat specific manner. Instead, this subset of yeast shares traits that make them attractive to and ensure their close association with Drosophila. PMID:29768432

  20. The occurrence and growth of yeasts in Camembert and blue-veined cheeses.

    Science.gov (United States)

    Roostita, R; Fleet, G H

    1996-01-01

    Yeast populations greater than 10(6) cfu/g were found in approximately 54% and 36%, respectively in surface samples of retail Camembert (85 samples) and Blue-veined (45 samples) cheeses. The most predominant species isolated were Debaryomyces hansenii, Candida catenulata, C. lipolytica, C. kefyr, C. intermedia, Saccharomyces cerevisiae, Cryptococcus albidus and Kluyveromyces marxianus. The salt concentration of the surface samples of the cheeses varied between 2.5-5.5% (w/w) (Camembert) and 7.5-8.3 (Blue-veined), depending upon brand, and influenced the yeast ecology, especially the presence of S. cerevisiae. Yeasts grew to populations of 10(6)-10(8) cfu/g when cheeses were stored at either 25 degrees C or 10 degrees C. These populations decreased on continued storage at 25 degrees C, but such decreases were not so evident on storage at 10 degrees C. The properties of yeasts influencing their occurrence and growth in cheese were: fermentation/assimilation of lactose; production of extracellular lipolytic and proteolytic enzymes, utilisation of lactic and citric acids; and growth at 10 degrees C.

  1. Influence of cyanide on diauxic oscillations in yeast

    DEFF Research Database (Denmark)

    Hald, Bjørn Olav; Smrcinova, Miroslava; Sørensen, Preben Graae

    2012-01-01

    Coherent glycolytic oscillations in Saccharomyces cerevisiae are a multicellular property induced by addition of glucose to a starved cell population of sufficient density. However, initiation of oscillations requires an additional perturbation, usually addition of cyanide. The fate of cyanide...... during glycolytic oscillations has not previously been studied, and is the subject of the present paper. Using a cyanide electrode, a substantial decrease in cyanide concentration was observed. In the pH range 6-7, we found experimentally that the electrode behaves reasonably well, provided changes in p......H are taken into account. To our knowledge, use of a cyanide electrode to study cyanide dynamics in living biological systems is new. Cyanide was found to enter starving yeast cells in only negligible amounts, and did not react significantly with glucose. Thus, cyanide consumption must be explained...

  2. Stage-Structured Population Dynamics of AEDES AEGYPTI

    Science.gov (United States)

    Yusoff, Nuraini; Budin, Harun; Ismail, Salemah

    Aedes aegypti is the main vector in the transmission of dengue fever, a vector-borne disease affecting world population living in tropical and sub-tropical countries. Better understanding of the dynamics of its population growth will help in the efforts of controlling the spread of this disease. In looking at the population dynamics of Aedes aegypti, this paper explored the stage-structured modeling of the population growth of the mosquito using the matrix population model. The life cycle of the mosquito was divided into five stages: eggs, larvae, pupae, adult1 and adult2. Developmental rates were obtained for the average Malaysian temperature and these were used in constructing the transition matrix for the matrix model. The model, which was based only on temperature, projected that the population of Aedes aegypti will blow up with time, which is not realistic. For further work, other factors need to be taken into account to obtain a more realistic result.

  3. Perturbation analysis of transient population dynamics using matrix projection models

    DEFF Research Database (Denmark)

    Stott, Iain

    2016-01-01

    Non-stable populations exhibit short-term transient dynamics: size, growth and structure that are unlike predicted long-term asymptotic stable, stationary or equilibrium dynamics. Understanding transient dynamics of non-stable populations is important for designing effective population management...... these methods to know exactly what is being measured. Despite a wealth of existing methods, I identify some areas that would benefit from further development....

  4. Stochastic population dynamics of a montane ground-dwelling squirrel.

    Science.gov (United States)

    Hostetler, Jeffrey A; Kneip, Eva; Van Vuren, Dirk H; Oli, Madan K

    2012-01-01

    Understanding the causes and consequences of population fluctuations is a central goal of ecology. We used demographic data from a long-term (1990-2008) study and matrix population models to investigate factors and processes influencing the dynamics and persistence of a golden-mantled ground squirrel (Callospermophilus lateralis) population, inhabiting a dynamic subalpine habitat in Colorado, USA. The overall deterministic population growth rate λ was 0.94±SE 0.05 but it varied widely over time, ranging from 0.45±0.09 in 2006 to 1.50±0.12 in 2003, and was below replacement (λbounce back from low densities and prevented extinction. These results suggest that dynamics and persistence of our study population are determined synergistically by density-dependence, stochastic forces, and immigration.

  5. Phenotypic and metabolic traits of commercial Saccharomyces cerevisiae yeasts.

    Science.gov (United States)

    Barbosa, Catarina; Lage, Patrícia; Vilela, Alice; Mendes-Faia, Arlete; Mendes-Ferreira, Ana

    2014-01-01

    Currently, pursuing yeast strains that display both a high potential fitness for alcoholic fermentation and a favorable impact on quality is a major goal in the alcoholic beverage industry. This considerable industrial interest has led to many studies characterizing the phenotypic and metabolic traits of commercial yeast populations. In this study, 20 Saccharomyces cerevisiae strains from different geographical origins exhibited high phenotypic diversity when their response to nine biotechnologically relevant conditions was examined. Next, the fermentation fitness and metabolic traits of eight selected strains with a unique phenotypic profile were evaluated in a high-sugar synthetic medium under two nitrogen regimes. Although the strains exhibited significant differences in nitrogen requirements and utilization rates, a direct relationship between nitrogen consumption, specific growth rate, cell biomass, cell viability, acetic acid and glycerol formation was only observed under high-nitrogen conditions. In contrast, the strains produced more succinic acid under the low-nitrogen regime, and a direct relationship with the final cell biomass was established. Glucose and fructose utilization patterns depended on both yeast strain and nitrogen availability. For low-nitrogen fermentation, three strains did not fully degrade the fructose. This study validates phenotypic and metabolic diversity among commercial wine yeasts and contributes new findings on the relationship between nitrogen availability, yeast cell growth and sugar utilization. We suggest that measuring nitrogen during the stationary growth phase is important because yeast cells fermentative activity is not exclusively related to population size, as previously assumed, but it is also related to the quantity of nitrogen consumed during this growth phase.

  6. Saccharomyces cerevisiae: a sexy yeast with a prion problem.

    Science.gov (United States)

    Kelly, Amy C; Wickner, Reed B

    2013-01-01

    Yeast prions are infectious proteins that spread exclusively by mating. The frequency of prions in the wild therefore largely reflects the rate of spread by mating counterbalanced by prion growth slowing effects in the host. We recently showed that the frequency of outcross mating is about 1% of mitotic doublings with 23-46% of total matings being outcrosses. These findings imply that even the mildest forms of the [PSI+], [URE3] and [PIN+] prions impart > 1% growth/survival detriment on their hosts. Our estimate of outcrossing suggests that Saccharomyces cerevisiae is far more sexual than previously thought and would therefore be more responsive to the adaptive effects of natural selection compared with a strictly asexual yeast. Further, given its large effective population size, a growth/survival detriment of > 1% for yeast prions should strongly select against prion-infected strains in wild populations of Saccharomyces cerevisiae.

  7. Some Metabolites Act as Second Messengers in Yeast Chronological Aging

    Directory of Open Access Journals (Sweden)

    Karamat Mohammad

    2018-03-01

    Full Text Available The concentrations of some key metabolic intermediates play essential roles in regulating the longevity of the chronologically aging yeast Saccharomyces cerevisiae. These key metabolites are detected by certain ligand-specific protein sensors that respond to concentration changes of the key metabolites by altering the efficiencies of longevity-defining cellular processes. The concentrations of the key metabolites that affect yeast chronological aging are controlled spatially and temporally. Here, we analyze mechanisms through which the spatiotemporal dynamics of changes in the concentrations of the key metabolites influence yeast chronological lifespan. Our analysis indicates that a distinct set of metabolites can act as second messengers that define the pace of yeast chronological aging. Molecules that can operate both as intermediates of yeast metabolism and as second messengers of yeast chronological aging include reduced nicotinamide adenine dinucleotide phosphate (NADPH, glycerol, trehalose, hydrogen peroxide, amino acids, sphingolipids, spermidine, hydrogen sulfide, acetic acid, ethanol, free fatty acids, and diacylglycerol. We discuss several properties that these second messengers of yeast chronological aging have in common with second messengers of signal transduction. We outline how these second messengers of yeast chronological aging elicit changes in cell functionality and viability in response to changes in the nutrient, energy, stress, and proliferation status of the cell.

  8. Dynamic Analysis of Bioethanol Production from Corn Stover and Immobilized Yeast

    Directory of Open Access Journals (Sweden)

    Shuang-Qi Tian

    2016-05-01

    Full Text Available The use of low cost and abundant corn stover in yeast fermentation can reduce product costs. In this study, bioethanol was produced from a hydrolysate of corn stover using immobilized yeast. A kinetic model was established for the total reducing sugar consumption and the production of bioethanol. The parameter estimation for kinetic modeling considered the main process variables during bioethanol production from corn stover. Total reducing sugar concentrations decreased exponentially in the bioethanol fermentation for 6 h; consumption was more than 90%. To use kinetic modelling of yeast growth for bioethanol fermentation, the value of μmax reached 0.2891 h-1, and the matrix inhibition constant (KIS and production inhibition constant (KIP were 8.9154 g/dm3 and 0.00676 g/dm3, respectively. To use kinetic modelling of fermentation time on bioethanol, the maximum ratio of bioethanol production rate (qmax reached 1.427 g/g•L. However, KIS was 2.813 g/dm3, and KIP was 0.0149 g/dm3.

  9. Central-marginal population dynamics in species invasions

    Directory of Open Access Journals (Sweden)

    Qinfeng eGuo

    2014-06-01

    Full Text Available The species’ range limits and associated central-marginal (C-M; i.e., from species range center to margin population dynamics continue to draw increasing attention because of their importance for current emerging issues such as biotic invasions and epidemic diseases under global change. Previous studies have mainly focused on species borders and C-M process in natural settings for native species. More recently, growing efforts are devoted to examine the C-M patterns and process for invasive species partly due to their relatively short history, highly dynamic populations, and management implications. Here I examine recent findings and information gaps related to (1 the C-M population dynamics linked to species invasions, and (2 the possible effects of climate change and land use on the C-M patterns and processes. Unlike most native species that are relatively stable (some even having contracting populations or ranges, many invasive species are still spreading fast and form new distribution or abundance centers. Because of the strong nonlinearity of population demographic or vital rates (i.e. birth, death, immigration and emigration across the C-M gradients and the increased complexity of species ranges due to habitat fragmentation, multiple introductions, range-wide C-M comparisons and simulation involving multiple vital rates are needed in the future.

  10. Nonlinear Relaxation in Population Dynamics

    Science.gov (United States)

    Cirone, Markus A.; de Pasquale, Ferdinando; Spagnolo, Bernardo

    We analyze the nonlinear relaxation of a complex ecosystem composed of many interacting species. The ecological system is described by generalized Lotka-Volterra equations with a multiplicative noise. The transient dynamics is studied in the framework of the mean field theory and with random interaction between the species. We focus on the statistical properties of the asymptotic behaviour of the time integral of the ith population and on the distribution of the population and of the local field.

  11. In vivo 31P NMR studies on the role of the vacuole in phosphate metabolism in yeasts

    NARCIS (Netherlands)

    Nicolaij, K.; Scheffers, W.A.; Bruinenberg, P.M.; Kaptein, R.

    1983-01-01

    31P NMR was used to study the dynamics of phosphate pools during substrate utilization by aerobic and anaerobic suspensions of the yeast Candida utilis and by aerobic suspensions of the yeast Brettanomyces intermedius. In both yeast, the cytoplasmic pH was monitored; in C. utilis also the vacuolar

  12. Apoptosis at inflection point in liquid culture of budding yeasts.

    Directory of Open Access Journals (Sweden)

    Toshiyuki Hagiwara

    Full Text Available Budding yeasts are highly suitable for aging studies, because the number of bud scars (stage proportionally correlates with age. Its maximum stages are known to reach at 20-30 stages on an isolated agar medium. However, their stage dynamics in a liquid culture is virtually unknown. We investigate the population dynamics by counting scars in each cell. Here one cell division produces one new cell and one bud scar. This simple rule leads to a conservation law: "The total number of bud scars is equal to the total number of cells." We find a large discrepancy: extremely fewer cells with over 5 scars than expected. Almost all cells with 6 or more scars disappear within a short period of time in the late log phase (corresponds to the inflection point. This discrepancy is confirmed directly by the microscopic observations of broken cells. This finding implies apoptosis in older cells (6 scars or more.

  13. A microfluidic system for studying ageing and dynamic single-cell responses in budding yeast.

    Directory of Open Access Journals (Sweden)

    Matthew M Crane

    Full Text Available Recognition of the importance of cell-to-cell variability in cellular decision-making and a growing interest in stochastic modeling of cellular processes has led to an increased demand for high density, reproducible, single-cell measurements in time-varying surroundings. We present ALCATRAS (A Long-term Culturing And TRApping System, a microfluidic device that can quantitatively monitor up to 1000 cells of budding yeast in a well-defined and controlled environment. Daughter cells are removed by fluid flow to avoid crowding allowing experiments to run for over 60 hours, and the extracellular media may be changed repeatedly and in seconds. We illustrate use of the device by measuring ageing through replicative life span curves, following the dynamics of the cell cycle, and examining history-dependent behaviour in the general stress response.

  14. Population and evolutionary dynamics in spatially structured seasonally varying environments.

    Science.gov (United States)

    Reid, Jane M; Travis, Justin M J; Daunt, Francis; Burthe, Sarah J; Wanless, Sarah; Dytham, Calvin

    2018-03-25

    Increasingly imperative objectives in ecology are to understand and forecast population dynamic and evolutionary responses to seasonal environmental variation and change. Such population and evolutionary dynamics result from immediate and lagged responses of all key life-history traits, and resulting demographic rates that affect population growth rate, to seasonal environmental conditions and population density. However, existing population dynamic and eco-evolutionary theory and models have not yet fully encompassed within-individual and among-individual variation, covariation, structure and heterogeneity, and ongoing evolution, in a critical life-history trait that allows individuals to respond to seasonal environmental conditions: seasonal migration. Meanwhile, empirical studies aided by new animal-tracking technologies are increasingly demonstrating substantial within-population variation in the occurrence and form of migration versus year-round residence, generating diverse forms of 'partial migration' spanning diverse species, habitats and spatial scales. Such partially migratory systems form a continuum between the extreme scenarios of full migration and full year-round residence, and are commonplace in nature. Here, we first review basic scenarios of partial migration and associated models designed to identify conditions that facilitate the maintenance of migratory polymorphism. We highlight that such models have been fundamental to the development of partial migration theory, but are spatially and demographically simplistic compared to the rich bodies of population dynamic theory and models that consider spatially structured populations with dispersal but no migration, or consider populations experiencing strong seasonality and full obligate migration. Second, to provide an overarching conceptual framework for spatio-temporal population dynamics, we define a 'partially migratory meta-population' system as a spatially structured set of locations that can

  15. Aerobic Stability and Effects of Yeasts during Deterioration of Non-fermented and Fermented Total Mixed Ration with Different Moisture Levels

    OpenAIRE

    W. Hao; H. L. Wang; T. T. Ning; F. Y. Yang; C. C. Xu

    2015-01-01

    The present experiment evaluated the influence of moisture level and anaerobic fermentation on aerobic stability of total mixed ration (TMR). The dynamic changes in chemical composition and microbial population that occur after air exposure were examined, and the species of yeast associated with the deterioration process were also identified in both non-fermented and fermented TMR to deepen the understanding of aerobic deterioration. The moisture levels of TMR in this experiment were adjusted...

  16. Effects of an invasive plant on population dynamics in toads.

    Science.gov (United States)

    Greenberg, Daniel A; Green, David M

    2013-10-01

    When populations decline in response to unfavorable environmental change, the dynamics of their population growth shift. In populations that normally exhibit high levels of variation in recruitment and abundance, as do many amphibians, declines may be difficult to identify from natural fluctuations in abundance. However, the onset of declines may be evident from changes in population growth rate in sufficiently long time series of population data. With data from 23 years of study of a population of Fowler's toad (Anaxyrus [ = Bufo] fowleri) at Long Point, Ontario (1989-2011), we sought to identify such a shift in dynamics. We tested for trends in abundance to detect a change point in population dynamics and then tested among competing population models to identify associated intrinsic and extrinsic factors. The most informative models of population growth included terms for toad abundance and the extent of an invasive marsh plant, the common reed (Phragmites australis), throughout the toads' marshland breeding areas. Our results showed density-dependent growth in the toad population from 1989 through 2002. After 2002, however, we found progressive population decline in the toads associated with the spread of common reeds and consequent loss of toad breeding habitat. This resulted in reduced recruitment and population growth despite the lack of significant loss of adult habitat. Our results underscore the value of using long-term time series to identify shifts in population dynamics coincident with the advent of population decline. © 2013 Society for Conservation Biology.

  17. Mutant allele of rna14 in fission yeast affects pre-mRNA splicing

    Indian Academy of Sciences (India)

    transcript. Rna14 protein in budding yeast has been implicated in cleavage and ... Subsequently, genetic interaction of Rna14 with prp1 and physical .... molecular yeast techniques as described by Moreno et al. ..... To elucidate the role of Rna14 in splicing, RT-PCR analysis ..... design principles of a dynamic RNP machine.

  18. The role of mitochondria in yeast programmed cell death

    International Nuclear Information System (INIS)

    Guaragnella, Nicoletta; Ždralević, Maša; Antonacci, Lucia; Passarella, Salvatore; Marra, Ersilia; Giannattasio, Sergio

    2012-01-01

    Mammalian apoptosis and yeast programmed cell death (PCD) share a variety of features including reactive oxygen species production, protease activity and a major role played by mitochondria. In view of this, and of the distinctive characteristics differentiating yeast and multicellular organism PCD, the mitochondrial contribution to cell death in the genetically tractable yeast Saccharomyces cerevisiae has been intensively investigated. In this mini-review we report whether and how yeast mitochondrial function and proteins belonging to oxidative phosphorylation, protein trafficking into and out of mitochondria, and mitochondrial dynamics, play a role in PCD. Since in PCD many processes take place over time, emphasis will be placed on an experimental model based on acetic acid-induced PCD (AA-PCD) which has the unique feature of having been investigated as a function of time. As will be described there are at least two AA-PCD pathways each with a multifaceted role played by mitochondrial components, in particular by cytochrome c.

  19. Dynamical community structure of populations evolving on genotype networks

    International Nuclear Information System (INIS)

    Capitán, José A.; Aguirre, Jacobo; Manrubia, Susanna

    2015-01-01

    Neutral evolutionary dynamics of replicators occurs on large and heterogeneous networks of genotypes. These networks, formed by all genotypes that yield the same phenotype, have a complex architecture that conditions the molecular composition of populations and their movements on genome spaces. Here we consider as an example the case of populations evolving on RNA secondary structure neutral networks and study the community structure of the network revealed through dynamical properties of the population at equilibrium and during adaptive transients. We unveil a rich hierarchical community structure that, eventually, can be traced back to the non-trivial relationship between RNA secondary structure and sequence composition. We demonstrate that usual measures of modularity that only take into account the static, topological structure of networks, cannot identify the community structure disclosed by population dynamics

  20. The effect of newly induced mutations on the fitness of genotypes and populations of yeast (Saccharomyces cerevisiae).

    Science.gov (United States)

    Orthen, E; Lange, P; Wöhrmann, K

    1984-12-01

    This paper analyses the fate of artificially induced mutations and their importance to the fitness of populations of the yeast, Saccharomyces cerevisiae, an increasingly important model organism in population genetics. Diploid strains, treated with UV and EMS, were cultured asexually for approximately 540 generations and under conditions where the asexual growth was interrupted by a sexual phase. Growth rates of 100 randomly sampled diploid clones were estimated at the beginning and at the end of the experiment. After the induction of sporulation the growth rates of 100 randomly sampled spores were measured. UV and EMS treatment decreases the average growth rate of the clones significantly but increases the variability in comparison to the untreated control. After selection over approximately 540 generations, variability in growth rates was reduced to that of the untreated control. No increase in mean population fitness was observed. However, the results show that after selection there still exists a large amount of hidden genetic variability in the populations which is revealed when the clones are cultivated in environments other than those in which selection took place. A sexual phase increased the reduction of the induced variability.

  1. Dynamics of a physiologically structured population in a time-varying environment

    DEFF Research Database (Denmark)

    Heilmann, Irene Louise Torpe; Starke, Jens; Andersen, Ken Haste

    2016-01-01

    Physiologically structured population models have become a valuable tool to model the dynamics of populations. In a stationary environment such models can exhibit equilibrium solutions as well as periodic solutions. However, for many organisms the environment is not stationary, but varies more...... or less regularly. In order to understand the interaction between an external environmental forcing and the internal dynamics in a population, we examine the response of a physiologically structured population model to a periodic variation in the food resource. We explore the addition of forcing in two...... cases: (A) where the population dynamics is in equilibrium in a stationary environment, and (B) where the population dynamics exhibits a periodic solution in a stationary environment. When forcing is applied in case A, the solutions are mainly periodic. In case B the forcing signal interacts...

  2. Changes in the relative population size of selected ruminal bacteria following an induced episode of acidosis in beef heifers receiving viable and non-viable active dried yeast.

    Science.gov (United States)

    Mohammed, R; Vyas, D; Yang, W Z; Beauchemin, K A

    2017-06-01

    To characterize the changes in the relative population size (RPS) of select ruminal bacteria and rumen fermentation variables in beef heifers supplemented with a strain of Saccharomyces cerevisiae as viable active dried (ADY) or killed dried (KDY) yeast following an induced episode of ruminal acidosis. Six ruminally cannulated beef heifers fed a diet consisting of 50% forage and 50% grain (dry matter basis) were used in a replicated 3 × 3 Latin square design with three 28-day periods. Treatments were: (i) control (CTRL; no yeast); (ii) ADY (4 g day -1 providing 10 10  CFU per g; AB Vista, UK); and (iii) KDY (4 g day -1 autoclaved ADY). The acidosis challenge was induced on day 22 and rumen samples were collected on day 15 (baseline; BASE), day 22 (challenge day; CHAL), and on day 29 (168th hour post acid challenge or recovery, REC) of each period. Over the study, duration of pH Yeast supplementation, irrespective of its viability, showed beneficial effects on ruminal pH variables in animals more susceptible to acidosis. Rumen microbial population was altered with the induction of severe acidosis. Most of the changes reverted back to baseline values during the recovery phase. Yeast supplementation reduced subacute rumen acidosis in the most susceptible cattle, but failed to attenuate severe acidosis induced by a grain challenge. The study provided valuable insight into the mechanism by which acidosis affects cattle performance. Individual animal variation in ruminal fermentation partly explained the variability in response to yeast supplementation in the study. © 2017 Her Majesty the Queen in Right of Canada. Journal of Applied Microbiology © 2017 The Society for Applied Microbiology.

  3. Ecological structuring of yeasts associated with trees around Hamilton, Ontario, Canada.

    Science.gov (United States)

    Maganti, Harinad; Bartfai, David; Xu, Jianping

    2012-02-01

    This study seeks to determine the distribution and diversity of yeasts in and around the Hamilton area in Canada. In light of the increasing number of fungal infections along with rising morbidity and mortality rates, especially among the immunocompromised, understanding the diversity and distribution of yeasts in natural environments close to human habitations has become an increasingly relevant topic. In this study, we analyzed 1110 samples obtained from the hollows of trees, shrubs and avian droppings at 8 geographical sites in and around Hamilton, Ontario, Canada. A total of 88 positive yeast strains were isolated and identified belonging to 20 yeast species. Despite the relative proximity of the sampling sites, our DNA fingerprinting results showed that the yeast populations were highly heterogenous. Among the 14 tree species sampled, cedar, cottonwood and basswood hollows had relatively high yeast colonization rates. Interestingly, Candida parapsilosis was isolated almost exclusively from Pine trees only. Our results are consistent with microgeographic and ecological differentiation of yeast species in and around an urban environment. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  4. Population dynamics of minimally cognitive individuals. Part 2: Dynamics of time-dependent knowledge

    Energy Technology Data Exchange (ETDEWEB)

    Schmieder, R.W.

    1995-07-01

    The dynamical principle for a population of interacting individuals with mutual pairwise knowledge, presented by the author in a previous paper for the case of constant knowledge, is extended to include the possibility that the knowledge is time-dependent. Several mechanisms are presented by which the mutual knowledge, represented by a matrix K, can be altered, leading to dynamical equations for K(t). The author presents various examples of the transient and long time asymptotic behavior of K(t) for populations of relatively isolated individuals interacting infrequently in local binary collisions. Among the effects observed in the numerical experiments are knowledge diffusion, learning transients, and fluctuating equilibria. This approach will be most appropriate to small populations of complex individuals such as simple animals, robots, computer networks, agent-mediated traffic, simple ecosystems, and games. Evidence of metastable states and intermittent switching leads them to envision a spectroscopy associated with such transitions that is independent of the specific physical individuals and the population. Such spectra may serve as good lumped descriptors of the collective emergent behavior of large classes of populations in which mutual knowledge is an important part of the dynamics.

  5. An individual-based model of Zebrafish population dynamics accounting for energy dynamics

    DEFF Research Database (Denmark)

    Beaudouin, Remy; Goussen, Benoit; Piccini, Benjamin

    2015-01-01

    Developing population dynamics models for zebrafish is crucial in order to extrapolate from toxicity data measured at the organism level to biological levels relevant to support and enhance ecological risk assessment. To achieve this, a dynamic energy budget for individual zebrafish (DEB model...

  6. Population dynamics of active and total ciliate populations in arable soil amended with wheat

    DEFF Research Database (Denmark)

    Ekelund, F.; Frederiksen, Helle B.; Ronn, R.

    2002-01-01

    of the population may be encysted. The factors governing the dynamics of active and encysted cells in the soil are not well understood. Our objective was to determine the dynamics of active and encysted populations of ciliates during the decomposition of freshly added organic material. We monitored, in soil...... microcosms, the active and total populations of ciliates, their potential prey (bacteria and small protozoa), their potential competitors (amoebae, flagellates, and nematodes), and their potential predators (nematodes). We sampled with short time intervals (2 to 6 days) and generated a data set, suitable...

  7. Occurrence and identification of yeast species in fermented liquid feed for piglets

    DEFF Research Database (Denmark)

    Gori, Klaus; Bjørklund, Marina Kryger; Canibe, Nuria

    2011-01-01

    The major objective of the present study was to investigate the occurrence and identity of yeast species in fermented liquid feed (FLF) used for feeding piglets. In total, 40 different Danish farms were included in the analysis. The preparation and composition of FLF was found to be very...... heterogeneous with high variations in both yeast counts and yeast species composition. The yeast population varied between 6.0 × 10(3) and 4.2 × 10(7) cfug(-1) with an average yeast count of 8.7 × 10(6) ± 1.1 × 10(7) cfug(-1). A total of 766 yeasts were isolated and identified by conventional and/or molecular...... typing techniques. The predominant yeast species in the FLF samples were found to be Candida milleri (58.4%), Kazachstania exigua (17.5%), Candida pararugosa (6.40%) and Kazachstania bulderi (5.09%). No clear separation between isolates of C. milleri and Candida humilis could be obtained based...

  8. Estimating Traveler Populations at Airport and Cruise Terminals for Population Distribution and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Jochem, Warren C [ORNL; Sims, Kelly M [ORNL; Bright, Eddie A [ORNL; Urban, Marie L [ORNL; Rose, Amy N [ORNL; Coleman, Phil R [ORNL; Bhaduri, Budhendra L [ORNL

    2013-01-01

    In recent years, uses of high-resolution population distribution databases are increasing steadily for environmental, socioeconomic, public health, and disaster-related research and operations. With the development of daytime population distribution, temporal resolution of such databases has been improved. However, the lack of incorporation of transitional population, namely business and leisure travelers, leaves a significant population unaccounted for within the critical infrastructure networks, such as at transportation hubs. This paper presents two general methodologies for estimating passenger populations in airport and cruise port terminals at a high temporal resolution which can be incorporated into existing population distribution models. The methodologies are geographically scalable and are based on, and demonstrate how, two different transportation hubs with disparate temporal population dynamics can be modeled utilizing publicly available databases including novel data sources of flight activity from the Internet which are updated in near-real time. The airport population estimation model shows great potential for rapid implementation for a large collection of airports on a national scale, and the results suggest reasonable accuracy in the estimated passenger traffic. By incorporating population dynamics at high temporal resolutions into population distribution models, we hope to improve the estimates of populations exposed to or at risk to disasters, thereby improving emergency planning and response, and leading to more informed policy decisions.

  9. Extraction of the number of peroxisomes in yeast cells by automated image analysis.

    Science.gov (United States)

    Niemistö, Antti; Selinummi, Jyrki; Saleem, Ramsey; Shmulevich, Ilya; Aitchison, John; Yli-Harja, Olli

    2006-01-01

    An automated image analysis method for extracting the number of peroxisomes in yeast cells is presented. Two images of the cell population are required for the method: a bright field microscope image from which the yeast cells are detected and the respective fluorescent image from which the number of peroxisomes in each cell is found. The segmentation of the cells is based on clustering the local mean-variance space. The watershed transformation is thereafter employed to separate cells that are clustered together. The peroxisomes are detected by thresholding the fluorescent image. The method is tested with several images of a budding yeast Saccharomyces cerevisiae population, and the results are compared with manually obtained results.

  10. DYNAMICS OF Cercospora zeina POPULATIONS IN MAIZE-BASED ...

    African Journals Online (AJOL)

    ACSS

    DYNAMICS OFCercospora zeina POPULATIONS IN MAIZE-BASED AGRO- ..... Population differentiation of Cercospora zeina in three districts of Uganda based on analysis of molecular variance ..... interactions: The example of the Erysiphe.

  11. Structural differences between yeast and mammalian microtubules revealed by cryo-EM

    Energy Technology Data Exchange (ETDEWEB)

    Howes, Stuart C. [Univ. of California, Berkeley, CA (United States). Biophysics Graduate Group; Geyer, Elisabeth A. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biophysics; Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry; LaFrance, Benjamin [Univ. of California, Berkeley, CA (United States). Molecular and Cell Biology Graduate Program; Zhang, Rui [Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst.; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Kellogg, Elizabeth H. [Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst.; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Westermann, Stefan [Univ. of Duisburg-Essen, Essen (Germany). Dept. of Molecular Genetics, Center for Medical Biotechnology; Rice, Luke M. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biophysics; Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry; Nogales, Eva [Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst.; Univ. of California, Berkeley, CA (United States). Dept. of Molecular Biology and California Inst. for Quantitative Biosciences; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division

    2017-06-26

    Microtubules are polymers of αβ-tubulin heterodimers essential for all eukaryotes. Despite sequence conservation, there are significant structural differences between microtubules assembled in vitro from mammalian or budding yeast tubulin. Yeast MTs were not observed to undergo compaction at the interdimer interface as seen for mammalian microtubules upon GTP hydrolysis. Lack of compaction might reflect slower GTP hydrolysis or a different degree of allosteric coupling in the lattice. The microtubule plus end–tracking protein Bim1 binds yeast microtubules both between αβ-tubulin heterodimers, as seen for other organisms, and within tubulin dimers, but binds mammalian tubulin only at interdimer contacts. At the concentrations used in cryo-electron microscopy, Bim1 causes the compaction of yeast microtubules and induces their rapid disassembly. In conclusion, our studies demonstrate structural differences between yeast and mammalian microtubules that likely underlie their differing polymerization dynamics. These differences may reflect adaptations to the demands of different cell size or range of physiological growth temperatures.

  12. Prions in yeast

    OpenAIRE

    Bezdíčka, Martin

    2013-01-01

    The thesis describes yeast prions and their biological effects on yeast in general. It defines the basic characteristics of yeast prions, that distinguish prions from other proteins. The thesis introduces various possibilities of prion formation, and propagation as well as specific types of yeast prions, including various functions of most studied types of prions. The thesis also focuses on chaperones that affect the state of yeast prions in cells. Lastly, the thesis indicates similarities be...

  13. Biodiversity of Yeasts During Plum Wegierka Zwykla Spontaneous Fermentation

    Directory of Open Access Journals (Sweden)

    Tadeusz Tuszynski

    2005-01-01

    Full Text Available The study comprises an analysis of the yeast microbiota that participated in the spontaneous fermentation of crushed Wegierka Zwykla plum fruit, which is the raw material for slivovitz production in the mountain region in the south of Poland. Saccharomyces cerevisiae yeast strains were differentiated by means of the killer sensitivity analysis related to a killer reference panel of 9 well-known killer yeast strains. The first phase of the fermentation was dominated by the representatives of Kloeckera apiculata and Candida pulcherrima species, which reached their maximum concentration (1.4·106 CFU/mL after 48 h of the process. Almost all yeasts isolated during the following days were classified as S. cerevisiae and the killer sensitivity analysis revealed a high population diversity of this species and the presence of 14 different strains that changed quantitatively and qualitatively throughout the fermentation period.

  14. POPULATION DYNAMICS OF PSEUDO-NITZSCHIA SPECIES ...

    African Journals Online (AJOL)

    nb

    current study aimed at assessing the population dynamics of Pseudo-nitzschia ... and to the developing aquaculture industry ... B. Hotel. Pangani Island. Bongoyo Island. Mbudya Island. Msasani Bay ... Salinity values did not show clear trends.

  15. The finite state projection approach to analyze dynamics of heterogeneous populations

    Science.gov (United States)

    Johnson, Rob; Munsky, Brian

    2017-06-01

    Population modeling aims to capture and predict the dynamics of cell populations in constant or fluctuating environments. At the elementary level, population growth proceeds through sequential divisions of individual cells. Due to stochastic effects, populations of cells are inherently heterogeneous in phenotype, and some phenotypic variables have an effect on division or survival rates, as can be seen in partial drug resistance. Therefore, when modeling population dynamics where the control of growth and division is phenotype dependent, the corresponding model must take account of the underlying cellular heterogeneity. The finite state projection (FSP) approach has often been used to analyze the statistics of independent cells. Here, we extend the FSP analysis to explore the coupling of cell dynamics and biomolecule dynamics within a population. This extension allows a general framework with which to model the state occupations of a heterogeneous, isogenic population of dividing and expiring cells. The method is demonstrated with a simple model of cell-cycle progression, which we use to explore possible dynamics of drug resistance phenotypes in dividing cells. We use this method to show how stochastic single-cell behaviors affect population level efficacy of drug treatments, and we illustrate how slight modifications to treatment regimens may have dramatic effects on drug efficacy.

  16. Permeation of iodide from iodine-enriched yeast through porcine intestine.

    Science.gov (United States)

    Ryszka, Florian; Dolińska, Barbara; Zieliński, Michał; Chyra, Dagmara; Dobrzański, Zbigniew

    2013-01-01

    Iodine deficiency is a common phenomenon, threatening the whole global human population. Recommended daily intake of iodine is 150 μg for adults and 250 μg for pregnant and breastfeeding women. About 50% of human population can be at risk of moderate iodine deficiency. Due to this fact, increased iodine supplementation is recommended, through intake of iodized mineral water and salt iodization. The aim of this study was to investigate permeation and absorption of iodide from iodine bioplex (experimental group) in comparison with potassium iodide (controls). Permeation and absorption processes were investigated in vitro using a porcine intestine. The experimental model was based on a standard Franz diffusion cell (FD-Cell). The iodine bioplex was produced using Saccharomyces cerevisiae yeast and whey powder: iodine content - 388 μg/g, total protein - 28.5%, total fat - 0.9%., glutamic acid - 41.2%, asparaginic acid - 29.4%, lysine - 24.8%; purchased from: F.Z.N.P. Biochefa, Sosnowiec, Poland. Potassium iodide was used as controls, at 388 μg iodine concentration, which was the same as in iodine-enriched yeast bioplex. A statistically significant increase in iodide permeation was observed for iodine-enriched yeast bioplex in comparison with controls - potassium iodide. After 5h the total amount of permeated iodide from iodine-enriched yeast bioplex was 85%, which is ~ 2-fold higher than controls - 37%. Iodide absorption was by contrast statistically significantly higher in controls - 7.3%, in comparison with 4.5% in experimental group with iodine-enriched yeast bioplex. Presented results show that iodide permeation process dominates over absorption in case of iodine-enriched yeast bioplex.

  17. Critical dynamics in population vaccinating behavior.

    Science.gov (United States)

    Pananos, A Demetri; Bury, Thomas M; Wang, Clara; Schonfeld, Justin; Mohanty, Sharada P; Nyhan, Brendan; Salathé, Marcel; Bauch, Chris T

    2017-12-26

    Vaccine refusal can lead to renewed outbreaks of previously eliminated diseases and even delay global eradication. Vaccinating decisions exemplify a complex, coupled system where vaccinating behavior and disease dynamics influence one another. Such systems often exhibit critical phenomena-special dynamics close to a tipping point leading to a new dynamical regime. For instance, critical slowing down (declining rate of recovery from small perturbations) may emerge as a tipping point is approached. Here, we collected and geocoded tweets about measles-mumps-rubella vaccine and classified their sentiment using machine-learning algorithms. We also extracted data on measles-related Google searches. We find critical slowing down in the data at the level of California and the United States in the years before and after the 2014-2015 Disneyland, California measles outbreak. Critical slowing down starts growing appreciably several years before the Disneyland outbreak as vaccine uptake declines and the population approaches the tipping point. However, due to the adaptive nature of coupled behavior-disease systems, the population responds to the outbreak by moving away from the tipping point, causing "critical speeding up" whereby resilience to perturbations increases. A mathematical model of measles transmission and vaccine sentiment predicts the same qualitative patterns in the neighborhood of a tipping point to greatly reduced vaccine uptake and large epidemics. These results support the hypothesis that population vaccinating behavior near the disease elimination threshold is a critical phenomenon. Developing new analytical tools to detect these patterns in digital social data might help us identify populations at heightened risk of widespread vaccine refusal. Copyright © 2017 the Author(s). Published by PNAS.

  18. The impact of rapid evolution on population dynamics in the wild: experimental test of eco-evolutionary dynamics.

    Science.gov (United States)

    Turcotte, Martin M; Reznick, David N; Hare, J Daniel

    2011-11-01

    Rapid evolution challenges the assumption that evolution is too slow to impact short-term ecological dynamics. This insight motivates the study of 'Eco-Evolutionary Dynamics' or how evolution and ecological processes reciprocally interact on short time scales. We tested how rapid evolution impacts concurrent population dynamics using an aphid (Myzus persicae) and an undomesticated host (Hirschfeldia incana) in replicated wild populations. We manipulated evolvability by creating non-evolving (single clone) and potentially evolving (two-clone) aphid populations that contained genetic variation in intrinsic growth rate. We observed significant evolution in two-clone populations whether or not they were exposed to predators and competitors. Evolving populations grew up to 42% faster and attained up to 67% higher density, compared with non-evolving control populations but only in treatments exposed to competitors and predators. Increased density also correlates with relative fitness of competing clones suggesting a full eco-evolutionary dynamic cycle defined as reciprocal interactions between evolution and density. © 2011 Blackwell Publishing Ltd/CNRS.

  19. Membrane bioreactor wastewater treatment plants reveal diverse yeast and protist communities of potential significance in biofouling.

    Science.gov (United States)

    Liébana, Raquel; Arregui, Lucía; Belda, Ignacio; Gamella, Luis; Santos, Antonio; Marquina, Domingo; Serrano, Susana

    2015-01-01

    The yeast community was studied in a municipal full-scale membrane bioreactor wastewater treatment plant (MBR-WWTP). The unexpectedly high diversity of yeasts indicated that the activated sludge formed a suitable environment for them to proliferate, with cellular concentrations of 2.2 ± 0.8 × 10(3) CFU ml(-1). Sixteen species of seven genera were present in the biological reactor, with Ascomycetes being the most prevalent group (93%). Most isolates were able to grow in a synthetic wastewater medium, adhere to polyethylene surfaces, and develop biofilms of variable complexity. The relationship between yeast populations and the protists in the MBR-WWTP was also studied, revealing that some protist species preyed on and ingested yeasts. These results suggest that yeast populations may play a role in the food web of a WWTP and, to some extent, contribute to membrane biofouling in MBR systems.

  20. Delay differential systems for tick population dynamics.

    Science.gov (United States)

    Fan, Guihong; Thieme, Horst R; Zhu, Huaiping

    2015-11-01

    Ticks play a critical role as vectors in the transmission and spread of Lyme disease, an emerging infectious disease which can cause severe illness in humans or animals. To understand the transmission dynamics of Lyme disease and other tick-borne diseases, it is necessary to investigate the population dynamics of ticks. Here, we formulate a system of delay differential equations which models the stage structure of the tick population. Temperature can alter the length of time delays in each developmental stage, and so the time delays can vary geographically (and seasonally which we do not consider). We define the basic reproduction number [Formula: see text] of stage structured tick populations. The tick population is uniformly persistent if [Formula: see text] and dies out if [Formula: see text]. We present sufficient conditions under which the unique positive equilibrium point is globally asymptotically stable. In general, the positive equilibrium can be unstable and the system show oscillatory behavior. These oscillations are primarily due to negative feedback within the tick system, but can be enhanced by the time delays of the different developmental stages.

  1. Radiation stimulation of yeast crops for increasing output of alcohol and baker yeasts

    International Nuclear Information System (INIS)

    Vlad, E.; Marsheu, P.

    1974-01-01

    The purpose of this study was to stimulate by gamma radiation the existing commercial types of yeast so as to obtain yeasts that would better reflect the substrate and have improved reproductive capacity. The experiments were conducted under ordinary conditions using commercial yeasts received from one factory producing alcohol and bakery yeasts and isolated as pure cultures. Irradiating yeast cultures with small doses (up to 10 krad) was found to stimulate the reproduction and fermenting activity of yeast cells as manifested in increased accumulation of yeast biomass and greater yield of ethyl alcohol. (E.T.)

  2. In situ rheology of yeast biofilms.

    Science.gov (United States)

    Brugnoni, Lorena I; Tarifa, María C; Lozano, Jorge E; Genovese, Diego

    2014-01-01

    The aim of the present work was to investigate the in situ rheological behavior of yeast biofilms growing on stainless steel under static and turbulent flow. The species used (Rhodototula mucilaginosa, Candida krusei, Candida kefyr and Candida tropicalis) were isolated from a clarified apple juice industry. The flow conditions impacted biofilm composition over time, with a predominance of C. krusei under static and turbulent flow. Likewise, structural variations occurred, with a tighter appearance under dynamic flow. Under turbulent flow there was an increase of 112 μm in biofilm thickness at 11 weeks (p < 0.001) and cell morphology was governed by hyphal structures and rounded cells. Using the in situ growth method introduced here, yeast biofilms were determined to be viscoelastic materials with a predominantly solid-like behavior, and neither this nor the G'0 values were significantly affected by the flow conditions or the growth time, and at large deformations their weak structure collapsed beyond a critical strain of about 1.5-5%. The present work could represent a starting point for developing in situ measurements of yeast rheology and contribute to a thin body of knowledge about fungal biofilm formation.

  3. Modeling the population dynamics of Pacific yew.

    Science.gov (United States)

    Richard T. Busing; Thomas A. Spies

    1995-01-01

    A study of Pacific yew (Taxus brevifolia Nutt.) population dynamics in the mountains of western Oregon and Washington was based on a combination of long-term population data and computer modeling. Rates of growth and mortality were low in mature and old-growth forest stands. Diameter growth at breast height ranged from 0 to 3 centimeters per decade...

  4. Stochastic population dynamic models as probability networks

    Science.gov (United States)

    M.E. and D.C. Lee. Borsuk

    2009-01-01

    The dynamics of a population and its response to environmental change depend on the balance of birth, death and age-at-maturity, and there have been many attempts to mathematically model populations based on these characteristics. Historically, most of these models were deterministic, meaning that the results were strictly determined by the equations of the model and...

  5. Estimating spatio-temporal dynamics of size-structured populations

    DEFF Research Database (Denmark)

    Kristensen, Kasper; Thygesen, Uffe Høgsbro; Andersen, Ken Haste

    2014-01-01

    with simple stock dynamics, to estimate simultaneously how size distributions and spatial distributions develop in time. We demonstrate the method for a cod population sampled by trawl surveys. Particular attention is paid to correlation between size classes within each trawl haul due to clustering...... of individuals with similar size. The model estimates growth, mortality and reproduction, after which any aspect of size-structure, spatio-temporal population dynamics, as well as the sampling process can be probed. This is illustrated by two applications: 1) tracking the spatial movements of a single cohort...

  6. Computer simulation of population dynamics inside the urban environment

    Science.gov (United States)

    Andreev, A. S.; Inovenkov, I. N.; Echkina, E. Yu.; Nefedov, V. V.; Ponomarenko, L. S.; Tikhomirov, V. V.

    2017-12-01

    In this paper using a mathematical model of the so-called “space-dynamic” approach we investigate the problem of development and temporal dynamics of different urban population groups. For simplicity we consider an interaction of only two population groups inside a single urban area with axial symmetry. This problem can be described qualitatively by a system of two non-stationary nonlinear differential equations of the diffusion type with boundary conditions of the third type. The results of numerical simulations show that with a suitable choice of the diffusion coefficients and interaction functions between different population groups we can receive different scenarios of population dynamics: from complete displacement of one population group by another (originally more “aggressive”) to the “peaceful” situation of co-existence of them together.

  7. Methods for Synchronization and Analysis of the Budding Yeast Cell Cycle.

    Science.gov (United States)

    Rosebrock, Adam P

    2017-01-03

    Like other eukaryotes, budding yeast temporally separate cell growth and division. DNA synthesis is distinct from chromosome segregation. Storage carbohydrates are accumulated slowly and then rapidly liquidated once per cycle. Cyclin-dependent kinase associates with multiple different transcriptionally and posttranslationally regulated cyclins to drive the cell cycle. These and other crucial events of cellular growth and division are limited to narrow windows of the cell cycle. Many experiments in the yeast laboratory treat a culture of cells as a homogeneous mixture. Measurements of asynchronous cultures are, however, confounded by the presence of cells in various cell cycle stages; measuring a population average in unsynchronized cells provides at best a decreased signal and at worst an artifactual result. A number of experimentally tractable methods have been developed to generate populations of yeast cells that are synchronized with respect to cell cycle phase. Robust methods for determining cell cycle position have also been developed. These methods are introduced here. © 2017 Cold Spring Harbor Laboratory Press.

  8. Data Driven Approach for High Resolution Population Distribution and Dynamics Models

    Energy Technology Data Exchange (ETDEWEB)

    Bhaduri, Budhendra L [ORNL; Bright, Eddie A [ORNL; Rose, Amy N [ORNL; Liu, Cheng [ORNL; Urban, Marie L [ORNL; Stewart, Robert N [ORNL

    2014-01-01

    High resolution population distribution data are vital for successfully addressing critical issues ranging from energy and socio-environmental research to public health to human security. Commonly available population data from Census is constrained both in space and time and does not capture population dynamics as functions of space and time. This imposes a significant limitation on the fidelity of event-based simulation models with sensitive space-time resolution. This paper describes ongoing development of high-resolution population distribution and dynamics models, at Oak Ridge National Laboratory, through spatial data integration and modeling with behavioral or activity-based mobility datasets for representing temporal dynamics of population. The model is resolved at 1 km resolution globally and describes the U.S. population for nighttime and daytime at 90m. Integration of such population data provides the opportunity to develop simulations and applications in critical infrastructure management from local to global scales.

  9. Independent Origins of Yeast Associated with Coffee and Cacao Fermentation.

    Science.gov (United States)

    Ludlow, Catherine L; Cromie, Gareth A; Garmendia-Torres, Cecilia; Sirr, Amy; Hays, Michelle; Field, Colburn; Jeffery, Eric W; Fay, Justin C; Dudley, Aimée M

    2016-04-04

    Modern transportation networks have facilitated the migration and mingling of previously isolated populations of plants, animals, and insects. Human activities can also influence the global distribution of microorganisms. The best-understood example is yeasts associated with winemaking. Humans began making wine in the Middle East over 9,000 years ago [1, 2]. Selecting favorable fermentation products created specialized strains of Saccharomyces cerevisiae [3, 4] that were transported along with grapevines. Today, S. cerevisiae strains residing in vineyards around the world are genetically similar, and their population structure suggests a common origin that followed the path of human migration [3-7]. Like wine, coffee and cacao depend on microbial fermentation [8, 9] and have been globally dispersed by humans. Theobroma cacao originated in the Amazon and Orinoco basins of Colombia and Venezuela [10], was cultivated in Central America by Mesoamerican peoples, and was introduced to Europeans by Hernán Cortés in 1530 [11]. Coffea, native to Ethiopia, was disseminated by Arab traders throughout the Middle East and North Africa in the 6(th) century and was introduced to European consumers in the 17(th) century [12]. Here, we tested whether the yeasts associated with coffee and cacao are genetically similar, crop-specific populations or genetically diverse, geography-specific populations. Our results uncovered populations that, while defined by niche and geography, also bear signatures of admixture between major populations in events independent of the transport of the plants. Thus, human-associated fermentation and migration may have affected the distribution of yeast involved in the production of coffee and chocolate. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. LIVE/DEAD YEAST VIABILITY STAINING AS A TOOL FOR IMPROVING ARTISANAL PILSNER BEER PRODUCTION

    Directory of Open Access Journals (Sweden)

    Benedetta Bottari

    2014-10-01

    Full Text Available The production of an artisanal beer, made by brewers using traditional practices on a small scale, is founded on the empirical adjustment of parameters, including yeasts handling and serial repitching. The aim of this study was to monitor yeast viability during different stages of artisanal beer productions through the Live/Dead Yeast viability staining and to correlate it with fermentation dynamics in order to increase process standardization and to maintain the quality of final products. Yeast viability and fermentation activities were evaluated during seven fermentation cycles of an artisanal pilsner beer. Yeast inoculated with higher viability performed generally better in fermentation, resulting in faster sugar consumption, faster ethanol production and stability. Handling yeast and serial repitching based on Live/Dead viability measurements, could be the key way to ensure reliable manufacture of high quality beer and to improve process standardization particularly for microbreweries, where variability of production can be a challenging point.

  11. Yeast Methylotrophy and Autophagy in a Methanol-Oscillating Environment on Growing Arabidopsis thaliana Leaves

    Science.gov (United States)

    Kawaguchi, Kosuke; Yurimoto, Hiroya; Oku, Masahide; Sakai, Yasuyoshi

    2011-01-01

    The yeast Candida boidinii capable of growth on methanol proliferates and survives on the leaves of Arabidopsis thaliana. The local methanol concentration at the phyllosphere of growing A. thaliana exhibited daily periodicity, and yeast cells responded by altering both the expression of methanol-inducible genes and peroxisome proliferation. Even under these dynamically changing environmental conditions, yeast cells proliferated 3 to 4 times in 11 days. Among the C1-metabolic enzymes, enzymes in the methanol assimilation pathway, but not formaldehyde dissimilation or anti-oxidizing enzymes, were necessary for yeast proliferation at the phyllosphere. Furthermore, both peroxisome assembly and pexophagy, a selective autophagy pathway that degrades peroxisomes, were necessary for phyllospheric proliferation. Thus, the present study sheds light on the life cycle and physiology of yeast in the natural environment at both the molecular and cellular levels. PMID:21966472

  12. Bread, beer and wine: yeast domestication in the Saccharomyces sensu stricto complex.

    Science.gov (United States)

    Sicard, Delphine; Legras, Jean-Luc

    2011-03-01

    Yeasts of the Saccharomyces sensu stricto species complex are able to convert sugar into ethanol and CO(2) via fermentation. They have been used for thousands years by mankind for fermenting food and beverages. In the Neolithic times, fermentations were probably initiated by naturally occurring yeasts, and it is unknown when humans started to consciously add selected yeast to make beer, wine or bread. Interestingly, such human activities gave rise to the creation of new species in the Saccharomyces sensu stricto complex by interspecies hybridization or polyploidization. Within the S. cerevisiae species, they have led to the differentiation of genetically distinct groups according to the food process origin. Although the evolutionary history of wine yeast populations has been well described, the histories of other domesticated yeasts need further investigation. Copyright © 2011 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  13. Population Dynamics and Cost-Benefit Analysis. An Attempt to Relate Population Dynamics via Lifetime Reproductive Success to Short-Term Decisions

    NARCIS (Netherlands)

    Tinbergen, J.M.; Balen, J.H. van; Drent, P.J.; Cavé, A.J.; Mertens, J.A.L.; Boer-Hazewinkel, J. den

    1987-01-01

    1. The aim of this article is to explore whether cost-benefit analysis of behaviour may help to understand the population dynamics of a species. The Great Tit is taken as an example. 2. The lifetime reproductive success in different populations of Great Tits amounts from 0.7 (Hoge Veluwe, Wytham) to

  14. Particle algorithms for population dynamics in flows

    International Nuclear Information System (INIS)

    Perlekar, Prasad; Toschi, Federico; Benzi, Roberto; Pigolotti, Simone

    2011-01-01

    We present and discuss particle based algorithms to numerically study the dynamics of population subjected to an advecting flow condition. We discuss few possible variants of the algorithms and compare them in a model compressible flow. A comparison against appropriate versions of the continuum stochastic Fisher equation (sFKPP) is also presented and discussed. The algorithms can be used to study populations genetics in fluid environments.

  15. Fatty acids from oleaginous yeasts and yeast-like fungi and their potential applications.

    Science.gov (United States)

    Xue, Si-Jia; Chi, Zhe; Zhang, Yu; Li, Yan-Feng; Liu, Guang-Lei; Jiang, Hong; Hu, Zhong; Chi, Zhen-Ming

    2018-02-01

    Oleaginous yeasts, fatty acids biosynthesis and regulation in the oleaginous yeasts and the fatty acids from the oleaginous yeasts and their applications are reviewed in this article. Oleaginous yeasts such as Rhodosporidium toruloides, Yarrowia lipolytica, Rhodotorula mucilaginosa, and Aureobasidium melanogenum, which can accumulate over 50% lipid of their cell dry weight, have many advantages over other oleaginous microorganisms. The fatty acids from the oleaginous yeasts have many potential applications. Many oleaginous yeasts have now been genetically modified to over-produce fatty acids and their derivatives. The most important features of the oleaginous yeasts are that they have special enzymatic systems for enhanced biosynthesis and regulation of fatty acids in their lipid particles. Recently, some oleaginous yeasts such as R. toruloides have been found to have a unique fatty acids synthetase and other oleaginous yeasts such as A. melanogenum have a unique highly reducing polyketide synthase (HR-PKS) involved in the biosynthesis of hydroxyl fatty acids. It is necessary to further enhance lipid biosynthesis using metabolic engineering and explore new applications of fatty acids in biotechnology.

  16. Prion-based memory of heat stress in yeast.

    Science.gov (United States)

    Chernova, Tatiana A; Chernoff, Yury O; Wilkinson, Keith D

    2017-05-04

    Amyloids and amyloid-based prions are self-perpetuating protein aggregates which can spread by converting a normal protein of the same sequence into a prion form. They are associated with diseases in humans and mammals, and control heritable traits in yeast and other fungi. Some amyloids are implicated in biologically beneficial processes. As prion formation generates reproducible memory of a conformational change, prions can be considered as molecular memory devices.  We have demonstrated that in yeast, stress-inducible cytoskeleton-associated protein Lsb2 forms a metastable prion in response to high temperature. This prion promotes conversion of other proteins into prions and can persist in a fraction of cells for a significant number of cell generations after stress, thus maintaining the memory of stress in a population of surviving cells. Acquisition of an amino acid substitution required for Lsb2 to form a prion coincides with acquisition of increased thermotolerance in the evolution of Saccharomyces yeast. Thus the ability to form an Lsb2 prion in response to stress coincides with yeast adaptation to growth at higher temperatures. These findings intimately connect prion formation to the cellular response to environmental stresses.

  17. Population dynamics of rural Ethiopia.

    Science.gov (United States)

    Bariabagar, H

    1978-01-01

    2 rounds of the national sample surveys, conducted by the central statistical office of Ethiopia during 1964-1967 and 1969-1971, provide the only comprehensive demographic data for the country and are the basis for this discussion of rural Ethiopia's population dynamics. The population of Ethiopia is predominantly rural. Agglomerations of 2000 and over inhabitants constitute about 14% of the population, and this indicates that Ethiopia has a low level of urbanization. In rural Ethiopia, international migration was negligent in the 1970's and the age structure can be assumed to be the results of past trends of fertility and mortality conditions. The reported crude birthrate (38.2), crude death rate (12.3) and infant mortality rate (90) of rural Ethiopia fall short of the averages for African countries. Prospects of population growth of rural Ethiopia would be immense. At the rate of natural increase of between 2.4 and 3.0% per annum, the population would double in 24-29 years. Regarding population issues, the programs of the National Democratic Revolution of Ethiopia faces the following main challenging problems: 1) carrying out national population censuses in order to obtain basic information for socialist planning; 2) minimizing or curtailing the existing high urban growth rates; 3) reducing rapidly growing population; and 5) mobilizing Ethiopian women to participate in the social, economic and political life of the country in order to create favorable conditions for future fertility reduction.

  18. Genomic signatures of adaptation to wine biological ageing conditions in biofilm-forming flor yeasts.

    Science.gov (United States)

    Coi, A L; Bigey, F; Mallet, S; Marsit, S; Zara, G; Gladieux, P; Galeote, V; Budroni, M; Dequin, S; Legras, J L

    2017-04-01

    The molecular and evolutionary processes underlying fungal domestication remain largely unknown despite the importance of fungi to bioindustry and for comparative adaptation genomics in eukaryotes. Wine fermentation and biological ageing are performed by strains of S. cerevisiae with, respectively, pelagic fermentative growth on glucose and biofilm aerobic growth utilizing ethanol. Here, we use environmental samples of wine and flor yeasts to investigate the genomic basis of yeast adaptation to contrasted anthropogenic environments. Phylogenetic inference and population structure analysis based on single nucleotide polymorphisms revealed a group of flor yeasts separated from wine yeasts. A combination of methods revealed several highly differentiated regions between wine and flor yeasts, and analyses using codon-substitution models for detecting molecular adaptation identified sites under positive selection in the high-affinity transporter gene ZRT1. The cross-population composite likelihood ratio revealed selective sweeps at three regions, including in the hexose transporter gene HXT7, the yapsin gene YPS6 and the membrane protein coding gene MTS27. Our analyses also revealed that the biological ageing environment has led to the accumulation of numerous mutations in proteins from several networks, including Flo11 regulation and divalent metal transport. Together, our findings suggest that the tuning of FLO11 expression and zinc transport networks are a distinctive feature of the genetic changes underlying the domestication of flor yeasts. Our study highlights the multiplicity of genomic changes underlying yeast adaptation to man-made habitats and reveals that flor/wine yeast lineage can serve as a useful model for studying the genomics of adaptive divergence. © 2017 John Wiley & Sons Ltd.

  19. The Response of Ω-Loop D Dynamics to Truncation of Trimethyllysine 72 of Yeast Iso-1-cytochrome c Depends on the Nature of Loop Deformation

    Science.gov (United States)

    McClelland, Levi J.; Seagraves, Sean M.; Khan, Khurshid Alam; Cherney, Melisa M.; Bandi, Swati; Culbertson, Justin E.; Bowler, Bruce E.

    2015-01-01

    Trimethyllysine 72 (tmK72) has been suggested to play a role in sterically constraining the heme crevice dynamics of yeast iso-1-cytochrome c mediated by the Ω-loop D cooperative substructure (residues 70 to 85). A tmK72A mutation causes a gain in peroxidase activity, a function of cytochrome c that is important early in apoptosis. More than one higher energy state is accessible for the Ω-loop D substructure via tier 0 dynamics. Two of these are alkaline conformers mediated by Lys73 and Lys79. In the current work, the effect of the tmK72A mutation on the thermodynamic and kinetic properties of wild type iso-1-cytochrome c (yWT versus WT*) and on variants carrying a K73H mutation (yWT/K73H versus WT*/K73H) is studied. Whereas the tmK72A mutation confers increased peroxidase activity in wild type yeast iso-1-cytochrome c and increased dynamics for formation of a previously studied His79-heme alkaline conformer, the tmK72A mutation speeds return of the His73-heme alkaline conformer to the native state through destabilization of the His73-heme alkaline conformer relative to the native conformer. These opposing behaviors demonstrate that the response of the dynamics of a protein substructure to mutation depends on the nature of the perturbation to the substructure. For a protein substructure which mediates more than one function of a protein through multiple non-native structures, a mutation could change the partitioning between these functions. The current results suggest that the tier 0 dynamics of Ω-loop D that mediates peroxidase activity has similarities to the tier 0 dynamics required to form the His79-heme alkaline conformer. PMID:25948392

  20. Genomics and Biochemistry of Saccharomyces cerevisiae Wine Yeast Strains.

    Science.gov (United States)

    Eldarov, M A; Kishkovskaia, S A; Tanaschuk, T N; Mardanov, A V

    2016-12-01

    Saccharomyces yeasts have been used for millennia for the production of beer, wine, bread, and other fermented products. Long-term "unconscious" selection and domestication led to the selection of hundreds of strains with desired production traits having significant phenotypic and genetic differences from their wild ancestors. This review summarizes the results of recent research in deciphering the genomes of wine Saccharomyces strains, the use of comparative genomics methods to study the mechanisms of yeast genome evolution under conditions of artificial selection, and the use of genomic and postgenomic approaches to identify the molecular nature of the important characteristics of commercial wine strains of Saccharomyces. Succinctly, data concerning metagenomics of microbial communities of grapes and wine and the dynamics of yeast and bacterial flora in the course of winemaking is provided. A separate section is devoted to an overview of the physiological, genetic, and biochemical features of sherry yeast strains used to produce biologically aged wines. The goal of the review is to convince the reader of the efficacy of new genomic and postgenomic technologies as tools for developing strategies for targeted selection and creation of new strains using "classical" and modern techniques for improving winemaking technology.

  1. Coupling population dynamics with earth system models: the POPEM model.

    Science.gov (United States)

    Navarro, Andrés; Moreno, Raúl; Jiménez-Alcázar, Alfonso; Tapiador, Francisco J

    2017-09-16

    Precise modeling of CO 2 emissions is important for environmental research. This paper presents a new model of human population dynamics that can be embedded into ESMs (Earth System Models) to improve climate modeling. Through a system dynamics approach, we develop a cohort-component model that successfully simulates historical population dynamics with fine spatial resolution (about 1°×1°). The population projections are used to improve the estimates of CO 2 emissions, thus transcending the bulk approach of existing models and allowing more realistic non-linear effects to feature in the simulations. The module, dubbed POPEM (from Population Parameterization for Earth Models), is compared with current emission inventories and validated against UN aggregated data. Finally, it is shown that the module can be used to advance toward fully coupling the social and natural components of the Earth system, an emerging research path for environmental science and pollution research.

  2. Yeast vitality during cider fermentation: assessment by energy metabolism.

    Science.gov (United States)

    Dinsdale, M G; Lloyd, D; McIntyre, P; Jarvis, B

    1999-03-15

    In an apple juice-based medium, an ethanol-tolerant Australian wine-yeast used for cider manufacture produced more than 10% ethanol over a 5 week period. Growth of the inoculum (10(6) organisms ml(-1)) occurred to a population of 3.1 x 10(7) ml(-1) during the first few days; at the end of the fermentation only 5 x 10(5) yeasts ml(-1) could be recovered as colony-forming units on plates. Respiratory and fermentative activities were measured by mass spectrometric measurements (O2 consumption and CO2 and ethanol production) of washed yeast suspensions taken from the cider fermentation at intervals. Both endogenous and glucose-supported energy-yielding metabolism declined, especially during the first 20 days. Levels of adenine nucleotides also showed decreases after day 1, as did adenylate energy charge, although in a prolonged (16.5 week) fermentation the lowest value calculated was 0.55. AMP was released into the medium. 31P-NMR spectra showed that by comparison with aerobically grown yeast, that from the later stages of the cider fermentation showed little polyphosphate. However, as previously concluded from studies of 'acidification power' and fluorescent oxonol dye exclusion (Dinsdale et al., 1995), repitching of yeast indicated little loss of viability despite considerable loss of vitality.

  3. Dynamics of Population on the Verge of Extinction

    OpenAIRE

    Oborny, B.; Meszena, G.; Szabo, G.

    2005-01-01

    Theoretical considerations suggest that extinction in dispersal-limited populations is necessarily a threshold-like process that is analogous to a critical phase transition in physics. We use this analogy to find robust, common features in the dynamics of extinctions, and suggest early warning signals which may indicate that a population is endangered. As the critical threshold of extinction is approached, the population spontaneously fragments into discrete subpopulations and, consequently, ...

  4. Yeast for virus research

    Science.gov (United States)

    Zhao, Richard Yuqi

    2017-01-01

    Budding yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe) are two popular model organisms for virus research. They are natural hosts for viruses as they carry their own indigenous viruses. Both yeasts have been used for studies of plant, animal and human viruses. Many positive sense (+) RNA viruses and some DNA viruses replicate with various levels in yeasts, thus allowing study of those viral activities during viral life cycle. Yeasts are single cell eukaryotic organisms. Hence, many of the fundamental cellular functions such as cell cycle regulation or programed cell death are highly conserved from yeasts to higher eukaryotes. Therefore, they are particularly suited to study the impact of those viral activities on related cellular activities during virus-host interactions. Yeasts present many unique advantages in virus research over high eukaryotes. Yeast cells are easy to maintain in the laboratory with relative short doubling time. They are non-biohazardous, genetically amendable with small genomes that permit genome-wide analysis of virologic and cellular functions. In this review, similarities and differences of these two yeasts are described. Studies of virologic activities such as viral translation, viral replication and genome-wide study of virus-cell interactions in yeasts are highlighted. Impacts of viral proteins on basic cellular functions such as cell cycle regulation and programed cell death are discussed. Potential applications of using yeasts as hosts to carry out functional analysis of small viral genome and to develop high throughput drug screening platform for the discovery of antiviral drugs are presented. PMID:29082230

  5. Stochastic population dynamics of a montane ground-dwelling squirrel.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Hostetler

    Full Text Available Understanding the causes and consequences of population fluctuations is a central goal of ecology. We used demographic data from a long-term (1990-2008 study and matrix population models to investigate factors and processes influencing the dynamics and persistence of a golden-mantled ground squirrel (Callospermophilus lateralis population, inhabiting a dynamic subalpine habitat in Colorado, USA. The overall deterministic population growth rate λ was 0.94±SE 0.05 but it varied widely over time, ranging from 0.45±0.09 in 2006 to 1.50±0.12 in 2003, and was below replacement (λ<1 for 9 out of 18 years. The stochastic population growth rate λ(s was 0.92, suggesting a declining population; however, the 95% CI on λ(s included 1.0 (0.52-1.60. Stochastic elasticity analysis showed that survival of adult females, followed by survival of juvenile females and litter size, were potentially the most influential vital rates; analysis of life table response experiments revealed that the same three life history variables made the largest contributions to year-to year changes in λ. Population viability analysis revealed that, when the influences of density dependence and immigration were not considered, the population had a high (close to 1.0 in 50 years probability of extinction. However, probability of extinction declined to as low as zero when density dependence and immigration were considered. Destabilizing effects of stochastic forces were counteracted by regulating effects of density dependence and rescue effects of immigration, which allowed our study population to bounce back from low densities and prevented extinction. These results suggest that dynamics and persistence of our study population are determined synergistically by density-dependence, stochastic forces, and immigration.

  6. [The dynamics of heath indicators of population of industrial town].

    Science.gov (United States)

    Kalinkin, D E; Karpov, A B; Takhauov, R M; Samoĭlova, Iu A

    2013-01-01

    The article presents the results of analysis of dynamics of health indicators of population of industrial town (medical demographic indicators, disability, morbidity of social hygienically important diseases) during 1970-2010. The classified administrative territorial municipality of Seversk constructed near the Siberian chemical industrial center, the internationally first-rate complex of nuclear industry enterprises was used as a research base. It is demonstrated that dynamics of health indicators of studied population had such negative tendencies as rapid population ageing, population loss due to decrease of natality and increase of mortality (population of able-bodied age included), prevalence of cardio-vascular diseases, malignant neoplasms and external causes, chronization of diseases. The established tendencies are to be considered in management decision making targeted to support and promote population health in industrial towns.

  7. A Theoretical Approach to Understanding Population Dynamics with Seasonal Developmental Durations

    Science.gov (United States)

    Lou, Yijun; Zhao, Xiao-Qiang

    2017-04-01

    There is a growing body of biological investigations to understand impacts of seasonally changing environmental conditions on population dynamics in various research fields such as single population growth and disease transmission. On the other side, understanding the population dynamics subject to seasonally changing weather conditions plays a fundamental role in predicting the trends of population patterns and disease transmission risks under the scenarios of climate change. With the host-macroparasite interaction as a motivating example, we propose a synthesized approach for investigating the population dynamics subject to seasonal environmental variations from theoretical point of view, where the model development, basic reproduction ratio formulation and computation, and rigorous mathematical analysis are involved. The resultant model with periodic delay presents a novel term related to the rate of change of the developmental duration, bringing new challenges to dynamics analysis. By investigating a periodic semiflow on a suitably chosen phase space, the global dynamics of a threshold type is established: all solutions either go to zero when basic reproduction ratio is less than one, or stabilize at a positive periodic state when the reproduction ratio is greater than one. The synthesized approach developed here is applicable to broader contexts of investigating biological systems with seasonal developmental durations.

  8. Network evolution induced by the dynamical rules of two populations

    Science.gov (United States)

    Platini, Thierry; Zia, R. K. P.

    2010-10-01

    We study the dynamical properties of a finite dynamical network composed of two interacting populations, namely extrovert (a) and introvert (b). In our model, each group is characterized by its size (Na and Nb) and preferred degree (κa and \\kappa_b\\ll \\kappa_a ). The network dynamics is governed by the competing microscopic rules of each population that consist of the creation and destruction of links. Starting from an unconnected network, we give a detailed analysis of the mean field approach which is compared to Monte Carlo simulation data. The time evolution of the restricted degrees langkbbrang and langkabrang presents three time regimes and a non-monotonic behavior well captured by our theory. Surprisingly, when the population sizes are equal Na = Nb, the ratio of the restricted degree θ0 = langkabrang/langkbbrang appears to be an integer in the asymptotic limits of the three time regimes. For early times (defined by t introverts remains constant while the number of connections increases linearly in the extrovert population. Finally, due to the competing dynamics, the network presents a frustrated stationary state characterized by a ratio θ0 = 3.

  9. L-arabinose fermenting yeast

    Science.gov (United States)

    Zhang, Min; Singh, Arjun; Suominen, Pirkko; Knoshaug, Eric; Franden, Mary Ann; Jarvis, Eric

    2013-02-12

    An L-arabinose utilizing yeast strain is provided for the production of ethanol by introducing and expressing bacterial araA, araB and araD genes. L-arabinose transporters are also introduced into the yeast to enhance the uptake of arabinose. The yeast carries additional genomic mutations enabling it to consume L-arabinose, even as the only carbon source, and to produce ethanol. A yeast strain engineered to metabolize arabinose through a novel pathway is also disclosed. Methods of producing ethanol include utilizing these modified yeast strains.

  10. Bounds on the dynamics of sink populations with noisy immigration.

    Science.gov (United States)

    Eager, Eric Alan; Guiver, Chris; Hodgson, Dave; Rebarber, Richard; Stott, Iain; Townley, Stuart

    2014-03-01

    Sink populations are doomed to decline to extinction in the absence of immigration. The dynamics of sink populations are not easily modelled using the standard framework of per capita rates of immigration, because numbers of immigrants are determined by extrinsic sources (for example, source populations, or population managers). Here we appeal to a systems and control framework to place upper and lower bounds on both the transient and future dynamics of sink populations that are subject to noisy immigration. Immigration has a number of interpretations and can fit a wide variety of models found in the literature. We apply the results to case studies derived from published models for Chinook salmon (Oncorhynchus tshawytscha) and blowout penstemon (Penstemon haydenii). Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Population dynamics model for plasmid bearing and plasmid lacking ...

    African Journals Online (AJOL)

    Streptokinase production in bioreactor is well associated to cell population dynamics. It is an established fact that two types of cell populations are found to emerge from the initial pool of recombinant cell population. This phenomenon leads to an undesired loss in yield of the product. Primary metabolites, like acetic acid etc ...

  12. Polyhexamethyl biguanide can eliminate contaminant yeasts from fuel-ethanol fermentation process.

    Science.gov (United States)

    Elsztein, Carolina; de Menezes, João Assis Scavuzzi; de Morais, Marcos Antonio

    2008-09-01

    Industrial ethanol fermentation is a non-sterile process and contaminant microorganisms can lead to a decrease in industrial productivity and significant economic loss. Nowadays, some distilleries in Northeastern Brazil deal with bacterial contamination by decreasing must pH and adding bactericides. Alternatively, contamination can be challenged by adding a pure batch of Saccharomyces cerevisiae-a time-consuming and costly process. A better strategy might involve the development of a fungicide that kills contaminant yeasts while preserving S. cerevisiae cells. Here, we show that polyhexamethyl biguanide (PHMB) inhibits and kills the most important contaminant yeasts detected in the distilleries of Northeastern Brazil without affecting the cell viability and fermentation capacity of S. cerevisiae. Moreover, some physiological data suggest that PHMB acts through interaction with the yeast membrane. These results support the development of a new strategy for controlling contaminant yeast population whilst keeping industrial yields high.

  13. Passivity analysis of higher order evolutionary dynamics and population games

    KAUST Repository

    Mabrok, Mohamed

    2017-01-05

    Evolutionary dynamics describe how the population composition changes in response to the fitness levels, resulting in a closed-loop feedback system. Recent work established a connection between passivity theory and certain classes of population games, namely so-called “stable games”. In particular, it was shown that a combination of stable games and (an analogue of) passive evolutionary dynamics results in stable convergence to Nash equilibrium. This paper considers the converse question of necessary conditions for evolutionary dynamics to exhibit stable behaviors for all generalized stable games. Using methods from robust control analysis, we show that if an evolutionary dynamic does not satisfy a passivity property, then it is possible to construct a generalized stable game that results in instability. The results are illustrated on selected evolutionary dynamics with particular attention to replicator dynamics, which are also shown to be lossless, a special class of passive systems.

  14. Electron beam radiation of dried fruits and nuts to reduce yeast and mold bioburden.

    Science.gov (United States)

    Ic, Erhan; Kottapalli, Bala; Maxim, Joseph; Pillai, Suresh D

    2007-04-01

    Dried fruits and nuts make up a significant portion of the commodities traded globally, and the presence of yeasts and molds on dried fruits and nuts can be a public health risk because of the potential for exposure to toxigenic fungi. Since current postharvest treatment technologies are rather limited for dried fruits and nuts, electron beam (E-beam) radiation experiments were performed to determine the doses required to reduce the yeast and mold bioburden of raisins, walnuts, and dates. The indigenous yeast and mold bioburden on a select number of commodities sold at retail ranged from 10(2) to 10(3) CFU/g. E-beam inactivation kinetics based on the linear model suggest that the decimal reduction dose required to eliminate 90% of the microbial population (D10-value) of these indigenous fungal populations ranges from 1.09 to 1.59 kGy. Some samples, however, exhibited inactivation kinetics that were better modeled by a quadratic model. The results indicate that different commodities can contain molds and yeasts of varying resistance to ionizing radiation. It is thus essential for the dried fruit and nut industry to determine empirically the minimum E-beam dose that is capable of reducing or eliminating the bioburden of yeasts and molds in their specific commodities.

  15. Population dynamics of Pseudo-nitzschia species ...

    African Journals Online (AJOL)

    The genus Pseudo-nitzschia is a chain-forming diatom comprising about 30 species some of which are known to produce domoic acid (DA) that causes amnesic shellfish poisoning (ASP). The current study aimed at assessing the population dynamics of Pseudo-nitzschia in the near shore waters of Dar es Salaam. Samples ...

  16. Aging and differentiation in yeast populations: elders with different properties and functions

    Czech Academy of Sciences Publication Activity Database

    Palková, Z.; Wilkinson, D.; Váchová, Libuše

    2014-01-01

    Roč. 14, č. 1 (2014), s. 96-108 ISSN 1567-1356 R&D Projects: GA ČR GA13-08605S Institutional support: RVO:61388971 Keywords : yeast colonies * stationary-phase liquid cultures * comparison of differentiated cell subpopulations Subject RIV: EE - Microbiology, Virology Impact factor: 2.818, year: 2014

  17. Effects of demographic structure on key properties of stochastic density-independent population dynamics.

    Science.gov (United States)

    Vindenes, Yngvild; Sæther, Bernt-Erik; Engen, Steinar

    2012-12-01

    The development of stochastic demography has largely been based on age structured populations, although other types of demographic structure, especially permanent and dynamic heterogeneity, are likely common in natural populations. The combination of stochasticity and demographic structure is a challenge for analyses of population dynamics and extinction risk, because the population structure will fluctuate around the stable structure and the population size shows transient fluctuations. However, by using a diffusion approximation for the total reproductive value, density-independent dynamics of structured populations can be described with only three population parameters: the expected population growth rate, the environmental variance and the demographic variance. These parameters depend on population structure via the state-specific vital rates and transition rates. Once they are found, the diffusion approximation represents a substantial reduction in model complexity. Here, we review and compare the key population parameters across a wide range of demographic structure, from the case of no structure to the most general case of dynamic heterogeneity, and for both discrete and continuous types. We focus on the demographic variance, but also show how environmental stochasticity can be included. This study brings together results from recent models, each considering a specific type of population structure, and places them in a general framework for structured populations. Comparison across different types of demographic structure reveals that the reproductive value is an essential concept for understanding how population structure affects stochastic dynamics and extinction risk. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. Aspiration dynamics of multi-player games in finite populations.

    Science.gov (United States)

    Du, Jinming; Wu, Bin; Altrock, Philipp M; Wang, Long

    2014-05-06

    On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics.

  19. Radiosensitivity of continuous cultures: experiments with diploid yeast

    International Nuclear Information System (INIS)

    Kiefer, J.; Wagner, E.

    1975-01-01

    To study the influence of systems parameters on the radiosensitivity of cell populations, stationary chemostat cultures of diploid yeast with different dilution rates were γ-irradiated. Proliferation and budding kinetics were investigated and the doses necessary to eliminate the entire population determined as a function of dilution rate. It was found that this killing dose decreases with dilution rate in a linear manner. The radiosensitivity of the cells was shown to depend on the dilution rate which is presumably due to differing compositions of the population. (U.S.)

  20. On the population dynamics of the malaria vector

    International Nuclear Information System (INIS)

    Ngwa, G.A.

    2005-10-01

    A deterministic differential equation model for the population dynamics of the human malaria vector is derived and studied. Conditions for the existence and stability of a non-zero steady state vector population density are derived. These reveal that a threshold parameter, the vectorial basic reproduction number, exist and the vector can establish itself in the community if and only if this parameter exceeds unity. When a non-zero steady state population density exists, it can be stable but it can also be driven to instability via a Hopf Bifurcation to periodic solutions, as a parameter is varied in parameter space. By considering a special case, an asymptotic perturbation analysis is used to derive the amplitude of the oscillating solutions for the full non-linear system. The present modelling exercise and results show that it is possible to study the population dynamics of disease vectors, and hence oscillatory behaviour as it is often observed in most indirectly transmitted infectious diseases of humans, without recourse to external seasonal forcing. (author)

  1. High population variability and source-sink dynamics in a solitary bee species.

    Science.gov (United States)

    Franzén, Markus; Nilsson, Sven G

    2013-06-01

    Although solitary bees are considered to play key roles in ecosystem functions, surprisingly few studies have explored their population dynamics. We investigated the population dynamics of a rare, declining, solitary bee (Andrena humilis) in a landscape of 80 km2 in southern Sweden from 2003 to 2011. Only one population was persistent throughout all years studied; most likely this population supplied the surrounding landscape with 11 smaller, temporary local populations. Despite stable pollen availability, the size of the persistent population fluctuated dramatically in a two-year cycle over the nine years, with 490-1230 nests in odd-numbered years and 21-48 nests in even-numbered years. These fluctuations were not significantly related to climatic variables or pollen availability. Nineteen colonization and 14 extinction events were recorded. Occupancy decreased with distance from the persistent population and increased with increasing resource (pollen) availability. There were significant positive correlations between the size of the persistent population and patch occupancy and colonization. Colonizations were generally more common in patches closer to the persistent population, whereas extinctions were independent of distance from the persistent population. Our results highlight the complex population dynamics that exist for this solitary bee species, which could be due to source-sink dynamics, a prolonged diapause, or can represent a bet-hedging strategy to avoid natural enemies and survive in small habitat patches. If large fluctuations in solitary bee populations prove to be widespread, it will have important implications for interpreting ecological relationships, bee conservation, and pollination.

  2. Bridging the Timescales of Single-Cell and Population Dynamics

    Science.gov (United States)

    Jafarpour, Farshid; Wright, Charles S.; Gudjonson, Herman; Riebling, Jedidiah; Dawson, Emma; Lo, Klevin; Fiebig, Aretha; Crosson, Sean; Dinner, Aaron R.; Iyer-Biswas, Srividya

    2018-04-01

    How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a data-validated theoretical framework that accounts for observables at both single-cell and population scales. We derive exact analytical complete time-dependent solutions to cell-age distributions and population growth rates as functionals of the underlying interdivision time distributions, for symmetric and asymmetric cell division. These results provide insights into the surprising implications of stochastic single-cell dynamics for population growth. Using our results for asymmetric division, we deduce the time to transition from the reproductively quiescent (swarmer) to the replication-competent (stalked) stage of the Caulobacter crescentus life cycle. Remarkably, population numbers can spontaneously oscillate with time. We elucidate the physics leading to these population oscillations. For C. crescentus cells, we show that a simple measurement of the population growth rate, for a given growth condition, is sufficient to characterize the condition-specific cellular unit of time and, thus, yields the mean (single-cell) growth and division timescales, fluctuations in cell division times, the cell-age distribution, and the quiescence timescale.

  3. Diversity and adaptive evolution of Saccharomyces wine yeast: a review

    Science.gov (United States)

    Marsit, Souhir; Dequin, Sylvie

    2015-01-01

    Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole-genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary history of wine yeasts. Comparisons between S. cerevisiae isolates from various origins have indicated that a variety of mechanisms, including heterozygosity, nucleotide and structural variations, introgressions, horizontal gene transfer and hybridization, contribute to the genetic and phenotypic diversity of S. cerevisiae. This review will summarize the current knowledge on the diversity and evolutionary history of wine yeasts, focusing on the domestication fingerprints identified in these strains. PMID:26205244

  4. Neural Population Dynamics during Reaching Are Better Explained by a Dynamical System than Representational Tuning.

    Science.gov (United States)

    Michaels, Jonathan A; Dann, Benjamin; Scherberger, Hansjörg

    2016-11-01

    Recent models of movement generation in motor cortex have sought to explain neural activity not as a function of movement parameters, known as representational models, but as a dynamical system acting at the level of the population. Despite evidence supporting this framework, the evaluation of representational models and their integration with dynamical systems is incomplete in the literature. Using a representational velocity-tuning based simulation of center-out reaching, we show that incorporating variable latency offsets between neural activity and kinematics is sufficient to generate rotational dynamics at the level of neural populations, a phenomenon observed in motor cortex. However, we developed a covariance-matched permutation test (CMPT) that reassigns neural data between task conditions independently for each neuron while maintaining overall neuron-to-neuron relationships, revealing that rotations based on the representational model did not uniquely depend on the underlying condition structure. In contrast, rotations based on either a dynamical model or motor cortex data depend on this relationship, providing evidence that the dynamical model more readily explains motor cortex activity. Importantly, implementing a recurrent neural network we demonstrate that both representational tuning properties and rotational dynamics emerge, providing evidence that a dynamical system can reproduce previous findings of representational tuning. Finally, using motor cortex data in combination with the CMPT, we show that results based on small numbers of neurons or conditions should be interpreted cautiously, potentially informing future experimental design. Together, our findings reinforce the view that representational models lack the explanatory power to describe complex aspects of single neuron and population level activity.

  5. Generic sorting of raft lipids into secretory vesicles in yeast

    DEFF Research Database (Denmark)

    Surma, Michal A; Klose, Christian; Klemm, Robin W

    2011-01-01

    Previous work has showed that ergosterol and sphingolipids become sorted to secretory vesicles immunoisolated using a chimeric, artificial raft membrane protein as bait. In this study, we have extended this analysis to three populations of secretory vesicles isolated using natural yeast plasma...... a complete lipid overview of the yeast late secretory pathway. We could show that vesicles captured with different baits carry the same cargo and have almost identical lipid compositions; being highly enriched in ergosterol and sphingolipids. This finding indicates that lipid raft sorting is a generic...

  6. Field Assessment of Yeast- and Oxalic Acid-generated Carbon Dioxide for Mosquito Surveillance

    Science.gov (United States)

    2014-12-01

    SentinelTM, Centers for Disease Control and Prevention light trap, sugar- fermenting yeast, electrolyzed oxalic acid INTRODUCTION Successful vector-borne...and Eisen 2008). Population data from trap surveil- lance provide key information for the develop- ment of disease risk assessment models (Diuk- Wasser...generated by a fermentation chamber, in which yeast metabolized sucrose. This source had been shown to attract various mosquito species in field and

  7. Influence of fenamidone, indoxacarb, pyraclostrobin, and deltamethrin on the population of natural yeast microflora during winemaking of two sardinian grape cultivars.

    Science.gov (United States)

    Zara, Severino; Caboni, Pierluigi; Orro, Davide; Farris, Giovanni Antonio; Pirisi, Filippo; Angioni, Alberto

    2011-01-01

    The influence of fenamidone ((S)-1-anilino-4-methyl-2-methylthio-4-phenylimidazolin-5-one), pyraclostrobin (methyl 2-[1-(4-chlorophenyl)pyrazol-3-yloxymethyl]-N-methoxycarbanilate), indoxacarb (methyl 7-Chloro-2,5-dihydro-2-[[(methoxycarbonyl) [4- (trifluoromethoxy) phenyl] amino] carbonyl] indeno[1,2-e][1,3,4] oxadiazine-4a(3H)-carboxylate), and deltamethrin ([cyano-[3-(phenoxy)phenyl]methyl] 3-(2,2-dibromoethenyl)-2,2-dimethylcyclopropane-1-carboxylate) on spontaneous fermentation carried out by natural yeast grapes microflora, was studied during the wine-making process. Aliquots of pesticide standard solutions were added to the grapes before crushing, to reach a concentration equal or half the maximum residue limit (MRL). Vinifications were performed, with maceration (R), or without maceration (W). During the wine-making process, samples were taken at the beginning (one hour after grapes crushing), at the middle and at the end of the spontaneous fermentation process. At half the MRL concentration, deltamethrin affected Pichia sp. population with a decrease of almost 50 %, while fenamidone decreased Candida sp., Candida stellata at 83, and 36%, respectively. Metschnikowia pulcherrima population decreased in all samples when compared to the control. Experiments at MRL levels showed a strong reduction for all non-Saccharomyces yeast species, when grapes had been treated with pyraclostrobin, fenamidone, and deltamethrine, except for Candida sp. which was found to have been affected only by fenamidone residues. Growth zone inhibition test showed only an in vitro activity of pyraclostrobin over Kloeckera spp., C. stellata, and M. pulcherrima. Microvinification experiments produced wines with no differences concerning S. cerevisiae population as well as production of ethanol and residual sugars. Experiments showed that at the end of the fermentation process pesticides were adsorbed by the lees and grape skins, and no pesticides residue was detectable in wine.

  8. Starvation-associated genome restructuring can lead to reproductive isolation in yeast.

    Directory of Open Access Journals (Sweden)

    Evgueny Kroll

    Full Text Available Knowledge of the mechanisms that lead to reproductive isolation is essential for understanding population structure and speciation. While several models have been advanced to explain post-mating reproductive isolation, experimental data supporting most are indirect. Laboratory investigations of this phenomenon are typically carried out under benign conditions, which result in low rates of genetic change unlikely to initiate reproductive isolation. Previously, we described an experimental system using the yeast Saccharomyces cerevisiae where starvation served as a proxy to any stress that decreases reproduction and/or survivorship. We showed that novel lineages with restructured genomes quickly emerged in starved populations, and that these survivors were more fit than their ancestors when re-starved. Here we show that certain yeast lineages that survive starvation have become reproductively isolated from their ancestor. We further demonstrate that reproductive isolation arises from genomic rearrangements, whose frequency in starving yeast is several orders of magnitude greater than an unstarved control. By contrast, the frequency of point mutations is less than 2-fold greater. In a particular case, we observe that a starved lineage becomes reproductively isolated as a direct result of the stress-related accumulation of a single chromosome. We recapitulate this result by demonstrating that introducing an extra copy of one or several chromosomes into naïve, i.e. unstarved, yeast significantly diminishes their fertility. This type of reproductive barrier, whether arising spontaneously or via genetic manipulation, can be removed by making a lineage euploid for the altered chromosomes. Our model provides direct genetic evidence that reproductive isolation can arise frequently in stressed populations via genome restructuring without the precondition of geographic isolation.

  9. Monitoring the Diversity of the Yeasts Population which are Present in the Musts Obtained from the Grapes Harvested in Iordana-Apold, Riesling Italian –Blaj, Royal Feteasca Jidvei and Hárslevelű – Tokaj

    Directory of Open Access Journals (Sweden)

    Enikő Gaspar

    2011-05-01

    Full Text Available The paper’s aim is to emphasize the variety of the yeasts populations which are present in the musts from inland and Tokaj areas. The study is based on the alcoholic fermentation on the four strains which were selected for this purpose, the isolation of the specific yeasts and the quantification of the obtained results through in the data base. From the fermentative dynamics’ point of view, the differences occur depending on the growing environment and on the strain types which were considered.The minerals play an important role in increasing the biotechnological properties of the wine yeasts Saccharomyces bayanus, Saccharomyces ellipsoideus regarding the fermentative activity and multiplication speed.

  10. The essence of yeast quiescence.

    Science.gov (United States)

    De Virgilio, Claudio

    2012-03-01

    Like all microorganisms, yeast cells spend most of their natural lifetime in a reversible, quiescent state that is primarily induced by limitation for essential nutrients. Substantial progress has been made in defining the features of quiescent cells and the nutrient-signaling pathways that shape these features. A view that emerges from the wealth of new data is that yeast cells dynamically configure the quiescent state in response to nutritional challenges by using a set of key nutrient-signaling pathways, which (1) regulate pathway-specific effectors, (2) converge on a few regulatory nodes that bundle multiple inputs to communicate unified, graded responses, and (3) mutually modulate their competences to transmit signals. Here, I present an overview of our current understanding of the architecture of these pathways, focusing on how the corresponding core signaling protein kinases (i.e. PKA, TORC1, Snf1, and Pho85) are wired to ensure an adequate response to nutrient starvation, which enables cells to tide over decades, if not centuries, of famine. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  11. A new ODE tumor growth modeling based on tumor population dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Oroji, Amin; Omar, Mohd bin [Institute of Mathematical Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia amin.oroji@siswa.um.edu.my, mohd@um.edu.my (Malaysia); Yarahmadian, Shantia [Mathematics Department Mississippi State University, USA Syarahmadian@math.msstate.edu (United States)

    2015-10-22

    In this paper a new mathematical model for the population of tumor growth treated by radiation is proposed. The cells dynamics population in each state and the dynamics of whole tumor population are studied. Furthermore, a new definition of tumor lifespan is presented. Finally, the effects of two main parameters, treatment parameter (q), and repair mechanism parameter (r) on tumor lifespan are probed, and it is showed that the change in treatment parameter (q) highly affects the tumor lifespan.

  12. A new ODE tumor growth modeling based on tumor population dynamics

    International Nuclear Information System (INIS)

    Oroji, Amin; Omar, Mohd bin; Yarahmadian, Shantia

    2015-01-01

    In this paper a new mathematical model for the population of tumor growth treated by radiation is proposed. The cells dynamics population in each state and the dynamics of whole tumor population are studied. Furthermore, a new definition of tumor lifespan is presented. Finally, the effects of two main parameters, treatment parameter (q), and repair mechanism parameter (r) on tumor lifespan are probed, and it is showed that the change in treatment parameter (q) highly affects the tumor lifespan

  13. Biocontrol activity of a cold-adapted yeast from Tibet against gray mold in cherry tomato and its action mechanism.

    Science.gov (United States)

    Hu, Hao; Wisniewski, Michael E; Abdelfattah, Ahmed; Zheng, Xiaodong

    2017-07-01

    Cold-adapted biocontrol yeast was selected from four yeast isolates from Tibet against gray mold of cherry tomato in cold storage. The strain numbered LB2 showed the best biocontrol activity and identified as Cryptococcus laurentii. Competition for nutrient, space, and induced fruit resistance was also its antagonistic mechanism. Compared with C. laurentii from sea-level place, the reason why LB2 had a better biocontrol activity was studied. More trehalose and proline in cell of LB2 made it exhibit a better cellular activity at low temperature, such as higher population dynamics in the wounds of cherry tomato and more biocontrol-related enzyme secretion, chitinase and β-glucanase. The better oxidative stress tolerance was another characteristic of LB2. Maybe because of the ideal culture condition, there was no obvious difference between these two yeasts in the growth in vitro test at low temperature. Although the same phenomenon existed in the low pH stress test, LB2 still had higher cell concentration under this stress. Comparative transcriptomics method was also applied to analyze the cell activity of LB2 and C. laurentii at different temperatures. The results showed that more active response in the intracellular structure and intracellular metabolic process to cold temperature made LB2 had a better activity. The present study indicated a possibility to select cold-adapted biocontrol yeast from Tibet and also showed its primary action mechanism.

  14. Calculating evolutionary dynamics in structured populations.

    Directory of Open Access Journals (Sweden)

    Charles G Nathanson

    2009-12-01

    Full Text Available Evolution is shaping the world around us. At the core of every evolutionary process is a population of reproducing individuals. The outcome of an evolutionary process depends on population structure. Here we provide a general formula for calculating evolutionary dynamics in a wide class of structured populations. This class includes the recently introduced "games in phenotype space" and "evolutionary set theory." There can be local interactions for determining the relative fitness of individuals, but we require global updating, which means all individuals compete uniformly for reproduction. We study the competition of two strategies in the context of an evolutionary game and determine which strategy is favored in the limit of weak selection. We derive an intuitive formula for the structure coefficient, sigma, and provide a method for efficient numerical calculation.

  15. Methods to Measure Lipophagy in Yeast.

    Science.gov (United States)

    Cristobal-Sarramian, A; Radulovic, M; Kohlwein, S D

    2017-01-01

    Maintenance of cellular and organismal lipid homeostasis is critical for life, and any deviation from a balanced equilibrium between fat uptake and degradation may have deleterious consequences, resulting in severe lipid-associated disorders. Excess fat is typically stored in cytoplasmic organelles termed "lipid droplets" (LDs); to adjust for a constantly fluctuating supply of and demand for cellular fat, these organelles are metabolically highly dynamic and subject to multiple levels of regulation. In addition to a well-described cytosolic lipid degradation pathway, recent evidence underscores the importance of "lipophagy" in cellular lipid homeostasis, i.e., the degradation of LD by autophagy in the lysosome/vacuole. Pioneering work in yeast mutant models has unveiled the requirement of key components of the autophagy machinery, providing evidence for a highly conserved process of lipophagy from yeast to man. However, further work is required to unveil the intricate metabolic interaction between LD metabolism and autophagy to sustain membrane homeostasis and cellular survival. © 2017 Elsevier Inc. All rights reserved.

  16. Yeast Flocculation—Sedimentation and Flotation

    Directory of Open Access Journals (Sweden)

    Graham G. Stewart

    2018-04-01

    Full Text Available Unlike most fermentation alcohol beverage production processes, brewers recycle their yeast. This is achieved by employing a yeast culture’s: flocculation, adhesion, sedimentation, flotation, and cropping characteristics. As a consequence of yeast recycling, the quality of the cropped yeast culture’s characteristics is critical. However, the other major function of brewer’s yeast is to metabolise wort into ethanol, carbon dioxide, glycerol, and other fermentation products, many of which contribute to beer’s overall flavour characteristics. This review will only focus on brewer’s yeast flocculation characteristics.

  17. Yeast cell differentiation: Lessons from pathogenic and non-pathogenic yeasts.

    Science.gov (United States)

    Palková, Zdena; Váchová, Libuše

    2016-09-01

    Yeasts, historically considered to be single-cell organisms, are able to activate different differentiation processes. Individual yeast cells can change their life-styles by processes of phenotypic switching such as the switch from yeast-shaped cells to filamentous cells (pseudohyphae or true hyphae) and the transition among opaque, white and gray cell-types. Yeasts can also create organized multicellular structures such as colonies and biofilms, and the latter are often observed as contaminants on surfaces in industry and medical care and are formed during infections of the human body. Multicellular structures are formed mostly of stationary-phase or slow-growing cells that diversify into specific cell subpopulations that have unique metabolic properties and can fulfill specific tasks. In addition to the development of multiple protective mechanisms, processes of metabolic reprogramming that reflect a changed environment help differentiated individual cells and/or community cell constituents to survive harmful environmental attacks and/or to escape the host immune system. This review aims to provide an overview of differentiation processes so far identified in individual yeast cells as well as in multicellular communities of yeast pathogens of the Candida and Cryptococcus spp. and the Candida albicans close relative, Saccharomyces cerevisiae. Molecular mechanisms and extracellular signals potentially involved in differentiation processes are also briefly mentioned. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. L-arabinose fermenting yeast

    Science.gov (United States)

    Zhang, Min; Singh, Arjun; Knoshaug, Eric; Franden, Mary Ann; Jarvis, Eric; Suominen, Pirkko

    2010-12-07

    An L-arabinose utilizing yeast strain is provided for the production of ethanol by introducing and expressing bacterial araA, araB and araD genes. L-arabinose transporters are also introduced into the yeast to enhance the uptake of arabinose. The yeast carries additional genomic mutations enabling it to consume L-arabinose, even as the only carbon source, and to produce ethanol. Methods of producing ethanol include utilizing these modified yeast strains. ##STR00001##

  19. Nitrile Metabolizing Yeasts

    Science.gov (United States)

    Bhalla, Tek Chand; Sharma, Monica; Sharma, Nitya Nand

    Nitriles and amides are widely distributed in the biotic and abiotic components of our ecosystem. Nitrile form an important group of organic compounds which find their applications in the synthesis of a large number of compounds used as/in pharmaceutical, cosmetics, plastics, dyes, etc>. Nitriles are mainly hydro-lyzed to corresponding amide/acid in organic chemistry. Industrial and agricultural activities have also lead to release of nitriles and amides into the environment and some of them pose threat to human health. Biocatalysis and biotransformations are increasingly replacing chemical routes of synthesis in organic chemistry as a part of ‘green chemistry’. Nitrile metabolizing organisms or enzymes thus has assumed greater significance in all these years to convert nitriles to amides/ acids. The nitrile metabolizing enzymes are widely present in bacteria, fungi and yeasts. Yeasts metabolize nitriles through nitrilase and/or nitrile hydratase and amidase enzymes. Only few yeasts have been reported to possess aldoxime dehydratase. More than sixty nitrile metabolizing yeast strains have been hither to isolated from cyanide treatment bioreactor, fermented foods and soil. Most of the yeasts contain nitrile hydratase-amidase system for metabolizing nitriles. Transformations of nitriles to amides/acids have been carried out with free and immobilized yeast cells. The nitrilases of Torulopsis candida>and Exophiala oligosperma>R1 are enantioselec-tive and regiospecific respectively. Geotrichum>sp. JR1 grows in the presence of 2M acetonitrile and may have potential for application in bioremediation of nitrile contaminated soil/water. The nitrilase of E. oligosperma>R1 being active at low pH (3-6) has shown promise for the hydroxy acids. Immobilized yeast cells hydrolyze some additional nitriles in comparison to free cells. It is expected that more focus in future will be on purification, characterization, cloning, expression and immobilization of nitrile metabolizing

  20. MIPS: a database for protein sequences, homology data and yeast genome information.

    Science.gov (United States)

    Mewes, H W; Albermann, K; Heumann, K; Liebl, S; Pfeiffer, F

    1997-01-01

    The MIPS group (Martinsried Institute for Protein Sequences) at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, collects, processes and distributes protein sequence data within the framework of the tripartite association of the PIR-International Protein Sequence Database (,). MIPS contributes nearly 50% of the data input to the PIR-International Protein Sequence Database. The database is distributed on CD-ROM together with PATCHX, an exhaustive supplement of unique, unverified protein sequences from external sources compiled by MIPS. Through its WWW server (http://www.mips.biochem.mpg.de/ ) MIPS permits internet access to sequence databases, homology data and to yeast genome information. (i) Sequence similarity results from the FASTA program () are stored in the FASTA database for all proteins from PIR-International and PATCHX. The database is dynamically maintained and permits instant access to FASTA results. (ii) Starting with FASTA database queries, proteins have been classified into families and superfamilies (PROT-FAM). (iii) The HPT (hashed position tree) data structure () developed at MIPS is a new approach for rapid sequence and pattern searching. (iv) MIPS provides access to the sequence and annotation of the complete yeast genome (), the functional classification of yeast genes (FunCat) and its graphical display, the 'Genome Browser' (). A CD-ROM based on the JAVA programming language providing dynamic interactive access to the yeast genome and the related protein sequences has been compiled and is available on request. PMID:9016498

  1. Modeling structured population dynamics using data from unmarked individuals

    Science.gov (United States)

    Grant, Evan H. Campbell; Zipkin, Elise; Thorson, James T.; See, Kevin; Lynch, Heather J.; Kanno, Yoichiro; Chandler, Richard; Letcher, Benjamin H.; Royle, J. Andrew

    2014-01-01

    The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark–recapture data. We extended recently developed N-mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders (Desmognathus fuscus) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark–recapture) and extensive (e.g., counts) data sources.

  2. Mutational meltdown in laboratory yeast populations

    NARCIS (Netherlands)

    Zeyl, C.; Mizesko, M.; Visser, de J.A.G.M.

    2001-01-01

    In small or repeatedly bottlenecked populations, mutations are expected to accumulate by genetic drift, causing fitness declines. In mutational meltdown models, such fitness declines further reduce population size, thus accelerating additional mutation accumulation and leading to extinction. Because

  3. Drosophila Regulate Yeast Density and Increase Yeast Community Similarity in a Natural Substrate

    OpenAIRE

    Stamps, Judy A.; Yang, Louie H.; Morales, Vanessa M.; Boundy-Mills, Kyria L.

    2012-01-01

    Drosophila melanogaster adults and larvae, but especially larvae, had profound effects on the densities and community structure of yeasts that developed in banana fruits. Pieces of fruit exposed to adult female flies previously fed fly-conditioned bananas developed higher yeast densities than pieces of the same fruits that were not exposed to flies, supporting previous suggestions that adult Drosophila vector yeasts to new substrates. However, larvae alone had dramatic effects on yeast densit...

  4. Population dynamics and distribution of the coffee berry borer ...

    African Journals Online (AJOL)

    Population dynamics and distribution of coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Scolytidae) were studied on Coffea arabica L. in southwestern region of Ethiopia. Thirty coffee trees were sampled at weekly intervals from 2000 to 2001. Findings of this study showed that coffee berry borer population ...

  5. [Population dynamics and armed violence in Colombia, 1985-2010].

    Science.gov (United States)

    Salaya, Hernán Eduardo; Rodríguez, Jesús

    2014-09-01

    Describe changes in the population structure of Colombia's municipalities in relation to internal displacement in response to armed violence. A descriptive ecological study was carried out. Secondary sources were consulted, taken from the Consolidated Registry of Displaced Population and from the National Administrative Department of Statistics, to calculate expulsion and reception rates for population displaced by violence from 2002 to 2010. Based on these rates, four groups were created of municipalities in the extreme quartile for each rate during the entire period, which were classified as high expulsion, low expulsion, high reception, and low reception. Subsequently, population pyramids and structure indicators were constructed for each group of municipalities for two comparative reference years (1985 and 2010). Municipalities with high expulsion or reception rates experienced a slower epidemiological transition, with lower mean ages and aging indices. The high expulsion group had the least regression, based on the Sundbärg index. In the high reception group, the masculinity ratio decreased the most, especially among the economically active population, and it had the highest population growth. Population dynamics in Colombia have been affected by armed violence and changes in these dynamics are not uniform across the country, leading to important social, economic, and cultural consequences. This study is useful for decision-making and public policy making.

  6. Regulation of activity of the yeast TATA-binding protein through intra ...

    Indian Academy of Sciences (India)

    Unknown

    Abbreviations used: BMH, Bismaleimidohexane; TBP, TATA-binding protein; yTBP, yeast TBP. J. Biosci. | Vol. ... Therefore for full-length TBP, intra-molecular interactions can regulate its activity via a similar ..... simulations (Miaskeiwicz and Ornstein 1996). .... box binding protein (TBP): A molecular dynamics computa-.

  7. Homogenization techniques for population dynamics in strongly heterogeneous landscapes.

    Science.gov (United States)

    Yurk, Brian P; Cobbold, Christina A

    2018-12-01

    An important problem in spatial ecology is to understand how population-scale patterns emerge from individual-level birth, death, and movement processes. These processes, which depend on local landscape characteristics, vary spatially and may exhibit sharp transitions through behavioural responses to habitat edges, leading to discontinuous population densities. Such systems can be modelled using reaction-diffusion equations with interface conditions that capture local behaviour at patch boundaries. In this work we develop a novel homogenization technique to approximate the large-scale dynamics of the system. We illustrate our approach, which also generalizes to multiple species, with an example of logistic growth within a periodic environment. We find that population persistence and the large-scale population carrying capacity is influenced by patch residence times that depend on patch preference, as well as movement rates in adjacent patches. The forms of the homogenized coefficients yield key theoretical insights into how large-scale dynamics arise from the small-scale features.

  8. Effect of Red Yeast Rice and Coconut, Rice Bran or Sunflower Oil Combination in Rats on Hypercholesterolemic Diet.

    Science.gov (United States)

    Govindarajan, Sumitra; Vellingiri, Kishore

    2016-04-01

    Dietary supplements provide a novel population based health approach for treating hyperlipidemias. Red yeast rice is known to have lipid lowering effects. Combination of red yeast rice with various oils is taken by different population around the world. In this present work, we aimed to compare the effects of red yeast rice with different oil (coconut, rice bran and sunflower oil) supplementations on lipid levels and oxidative stress in rats fed on hypercholesterolemic diet. A Randomized controlled study was conducted on 28 male Sprague Dawley rats. It included 4 arms-Control arm (hypercholesterolemic diet), Test arm A (hypercholesterolemic diet +Red yeast rice + Rice bran oil), arm B (hypercholesterolemic diet +Red yeast rice + Coconut oil) and arm C (hypercholesterolemic diet +Red yeast rice + Sunflower oil). At the end of one month, serum cholesterol, triglycerides, MDA and paraoxonase was measured. The mean values of analytes between the different groups were compared using student 't-' test. The rats fed with red yeast rice and rice bran oil combination showed significantly lower levels of serum cholesterol, triglycerides and MDA when compared to the controls. The serum paraoxonase levels were significantly higher in this group when compared to the controls. The rats fed with red yeast rice and coconut oil combination showed significantly lower serum cholesterol and MDA levels when compared to the controls. The mean triglyceride and paraoxonase levels did not show any statistically significant difference from the controls. The rats on red yeast rice and sunflower oil combination did not show any statistically significant difference in the lipid levels and oxidative stress parameters. The food combination which had best outcome in preventing the development of hyperlipidemia and oxidative stress in rats fed with hypercholesterolemic diet was red yeast rice and rice bran oil. Combining red yeast rice with coconut oil and sunflower oil gave suboptimal benefits.

  9. Understanding long-term fruit fly (Diptera: Tephritidae) population dynamics: implications for areawide management.

    Science.gov (United States)

    Aluja, Martín; Ordano, Mariano; Guillén, Larissa; Rull, Juan

    2012-06-01

    Fruit flies (Diptera: Tephritidae) are devastating agricultural pests worldwide but studies on their long-term population dynamics are sparse. Our aim was to determine the mechanisms driving long-term population dynamics as a prerequisite for ecologically based areawide pest management. The population density of three pestiferous Anastrepha species [Anastrepha ludens (Loew), Anastrepha obliqua (Macquart), and Anastrepha serpentina (Wiedemann)] was determined in grapefruit (Citrus x paradisi Macfad.), mango (Mangifera indica L.), and sapodilla [Manilkara zapota (L.) P. Royen] orchards in central Veracruz, México, on a weekly basis over an 11-yr period. Fly populations exhibited relatively stable dynamics over time. Population dynamics were mainly driven by a direct density-dependent effect and a seasonal feedback process. We discovered direct and delayed influences that were correlated with both local (rainfall and air temperature) and global climatic variation (El Niño Southern Oscillation [ENSO] and North Atlantic Oscillation [NAO]), and detected differences among species and location of orchards with respect to the magnitude and nature (linear or nonlinear) of the observed effects, suggesting that highly mobile pest outbreaks become uncertain in response to significant climatic events at both global and local levels. That both NAO and ENSO affected Anastrepha population dynamics, coupled with the high mobility of Anastrepha adults and the discovery that when measured as rate of population change, local population fluctuations exhibited stable dynamics over time, suggests potential management scenarios for the species studied lie beyond the local scale and should be approached from an areawide perspective. Localized efforts, from individual growers will probably prove ineffective, and nonsustainable.

  10. Passivity analysis of higher order evolutionary dynamics and population games

    KAUST Repository

    Mabrok, Mohamed; Shamma, Jeff S.

    2017-01-01

    Evolutionary dynamics describe how the population composition changes in response to the fitness levels, resulting in a closed-loop feedback system. Recent work established a connection between passivity theory and certain classes of population

  11. Social Information Links Individual Behavior to Population and Community Dynamics.

    Science.gov (United States)

    Gil, Michael A; Hein, Andrew M; Spiegel, Orr; Baskett, Marissa L; Sih, Andrew

    2018-05-07

    When individual animals make decisions, they routinely use information produced intentionally or unintentionally by other individuals. Despite its prevalence and established fitness consequences, the effects of such social information on ecological dynamics remain poorly understood. Here, we synthesize results from ecology, evolutionary biology, and animal behavior to show how the use of social information can profoundly influence the dynamics of populations and communities. We combine recent theoretical and empirical results and introduce simple population models to illustrate how social information use can drive positive density-dependent growth of populations and communities (Allee effects). Furthermore, social information can shift the nature and strength of species interactions, change the outcome of competition, and potentially increase extinction risk in harvested populations and communities. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Network evolution induced by the dynamical rules of two populations

    International Nuclear Information System (INIS)

    Platini, Thierry; Zia, R K P

    2010-01-01

    We study the dynamical properties of a finite dynamical network composed of two interacting populations, namely extrovert (a) and introvert (b). In our model, each group is characterized by its size (N a and N b ) and preferred degree (κ a and κ b a ). The network dynamics is governed by the competing microscopic rules of each population that consist of the creation and destruction of links. Starting from an unconnected network, we give a detailed analysis of the mean field approach which is compared to Monte Carlo simulation data. The time evolution of the restricted degrees (k bb ) and (k ab ) presents three time regimes and a non-monotonic behavior well captured by our theory. Surprisingly, when the population sizes are equal N a = N b , the ratio of the restricted degree θ 0 = (k ab )/(k bb ) appears to be an integer in the asymptotic limits of the three time regimes. For early times (defined by t 1 = κ b ) the total number of links presents a linear evolution, where the two populations are indistinguishable and where θ 0 = 1. Interestingly, in the intermediate time regime (defined for t 1 2 ∝κ a and for which θ 0 = 5), the system reaches a transient stationary state, where the number of contacts among introverts remains constant while the number of connections increases linearly in the extrovert population. Finally, due to the competing dynamics, the network presents a frustrated stationary state characterized by a ratio θ 0 = 3

  13. Sharing the cell's bounty - organelle inheritance in yeast.

    Science.gov (United States)

    Knoblach, Barbara; Rachubinski, Richard A

    2015-02-15

    Eukaryotic cells replicate and partition their organelles between the mother cell and the daughter cell at cytokinesis. Polarized cells, notably the budding yeast Saccharomyces cerevisiae, are well suited for the study of organelle inheritance, as they facilitate an experimental dissection of organelle transport and retention processes. Much progress has been made in defining the molecular players involved in organelle partitioning in yeast. Each organelle uses a distinct set of factors - motor, anchor and adaptor proteins - that ensures its inheritance by future generations of cells. We propose that all organelles, regardless of origin or copy number, are partitioned by the same fundamental mechanism involving division and segregation. Thus, the mother cell keeps, and the daughter cell receives, their fair and equitable share of organelles. This mechanism of partitioning moreover facilitates the segregation of organelle fragments that are not functionally equivalent. In this Commentary, we describe how this principle of organelle population control affects peroxisomes and other organelles, and outline its implications for yeast life span and rejuvenation. © 2015. Published by The Company of Biologists Ltd.

  14. A general modeling framework for describing spatially structured population dynamics

    Science.gov (United States)

    Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

    2017-01-01

    Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance

  15. The population dynamical implications of male-biased parasitism in different mating systems.

    Directory of Open Access Journals (Sweden)

    Martin R Miller

    2007-07-01

    Full Text Available Although there is growing evidence that males tend to suffer higher levels of parasitism than females, the implications of this for the population dynamics of the host population are not yet understood. Here we build on an established 'two-sex' model and investigate how increased susceptibility to infection in males affects the dynamics, under different mating systems. We investigate the effect of pathogenic disease at different case mortalities, under both monogamous and polygynous mating systems. If the case mortality is low, then male-biased parasitism appears similar to unbiased parasitism in terms of its effect on the population dynamics. At higher case mortalities, we identified significant differences between male-biased and unbiased parasitism. A host population may therefore be differentially affected by male-biased and unbiased parasitism. The dynamical outcome is likely to depend on a complex interaction between the host's mating system and demography, and the parasite virulence.

  16. New yeasts-new brews: modern approaches to brewing yeast design and development.

    Science.gov (United States)

    Gibson, B; Geertman, J-M A; Hittinger, C T; Krogerus, K; Libkind, D; Louis, E J; Magalhães, F; Sampaio, J P

    2017-06-01

    The brewing industry is experiencing a period of change and experimentation largely driven by customer demand for product diversity. This has coincided with a greater appreciation of the role of yeast in determining the character of beer and the widespread availability of powerful tools for yeast research. Genome analysis in particular has helped clarify the processes leading to domestication of brewing yeast and has identified domestication signatures that may be exploited for further yeast development. The functional properties of non-conventional yeast (both Saccharomyces and non-Saccharomyces) are being assessed with a view to creating beers with new flavours as well as producing flavoursome non-alcoholic beers. The discovery of the psychrotolerant S. eubayanus has stimulated research on de novo S. cerevisiae × S. eubayanus hybrids for low-temperature lager brewing and has led to renewed interest in the functional importance of hybrid organisms and the mechanisms that determine hybrid genome function and stability. The greater diversity of yeast that can be applied in brewing, along with an improved understanding of yeasts' evolutionary history and biology, is expected to have a significant and direct impact on the brewing industry, with potential for improved brewing efficiency, product diversity and, above all, customer satisfaction. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Vaginal yeast infection

    Science.gov (United States)

    Yeast infection - vagina; Vaginal candidiasis; Monilial vaginitis ... Most women have a vaginal yeast infection at some time. Candida albicans is a common type of fungus. It is often found in small amounts ...

  18. Chronological aging-induced apoptosis in yeast

    OpenAIRE

    Fabrizio, Paola; Longo, Valter D.

    2008-01-01

    Saccharomyces cerevisiae is the simplest among the major eukaryotic model organisms for aging and diseases. Longevity in the chronological life span paradigm is measured as the mean and maximum survival period of populations of non-dividing yeast. This paradigm has been used successfully to identify several life-regulatory genes and three evolutionary conserved pro-aging pathways. More recently, Schizosaccharomyces pombe has been shown to age chronologically in a manner that resembles that of...

  19. Effects of wind farms on harbour porpoise behaviour and population dynamics

    DEFF Research Database (Denmark)

    Nabe-Nielsen, Jacob; Tougaard, Jakob; Teilmann, Jonas

    We developed an individual-based simulation model in order to study the cumulative impacts of wind farms and ship traffic on the long-term survival and population dynamics of the harbour porpoise (Phocoena phocoena) in Kattegat and the Belt Seas. The model is based on knowl- edge of the porpoises...... at distances >1 km. Our simulations suggest that operating wind farms and wind farms under construction do not affect the size or dynamics of the harbour porpoise population in Kattegat. Ship traffic may, in contrast, cause the population size to decrease....

  20. Learning to Estimate Dynamical State with Probabilistic Population Codes.

    Directory of Open Access Journals (Sweden)

    Joseph G Makin

    2015-11-01

    Full Text Available Tracking moving objects, including one's own body, is a fundamental ability of higher organisms, playing a central role in many perceptual and motor tasks. While it is unknown how the brain learns to follow and predict the dynamics of objects, it is known that this process of state estimation can be learned purely from the statistics of noisy observations. When the dynamics are simply linear with additive Gaussian noise, the optimal solution is the well known Kalman filter (KF, the parameters of which can be learned via latent-variable density estimation (the EM algorithm. The brain does not, however, directly manipulate matrices and vectors, but instead appears to represent probability distributions with the firing rates of population of neurons, "probabilistic population codes." We show that a recurrent neural network-a modified form of an exponential family harmonium (EFH-that takes a linear probabilistic population code as input can learn, without supervision, to estimate the state of a linear dynamical system. After observing a series of population responses (spike counts to the position of a moving object, the network learns to represent the velocity of the object and forms nearly optimal predictions about the position at the next time-step. This result builds on our previous work showing that a similar network can learn to perform multisensory integration and coordinate transformations for static stimuli. The receptive fields of the trained network also make qualitative predictions about the developing and learning brain: tuning gradually emerges for higher-order dynamical states not explicitly present in the inputs, appearing as delayed tuning for the lower-order states.

  1. Building the bridge between animal movement and population dynamics.

    Science.gov (United States)

    Morales, Juan M; Moorcroft, Paul R; Matthiopoulos, Jason; Frair, Jacqueline L; Kie, John G; Powell, Roger A; Merrill, Evelyn H; Haydon, Daniel T

    2010-07-27

    While the mechanistic links between animal movement and population dynamics are ecologically obvious, it is much less clear when knowledge of animal movement is a prerequisite for understanding and predicting population dynamics. GPS and other technologies enable detailed tracking of animal location concurrently with acquisition of landscape data and information on individual physiology. These tools can be used to refine our understanding of the mechanistic links between behaviour and individual condition through 'spatially informed' movement models where time allocation to different behaviours affects individual survival and reproduction. For some species, socially informed models that address the movements and average fitness of differently sized groups and how they are affected by fission-fusion processes at relevant temporal scales are required. Furthermore, as most animals revisit some places and avoid others based on their previous experiences, we foresee the incorporation of long-term memory and intention in movement models. The way animals move has important consequences for the degree of mixing that we expect to find both within a population and between individuals of different species. The mixing rate dictates the level of detail required by models to capture the influence of heterogeneity and the dynamics of intra- and interspecific interaction.

  2. The failure rate dynamics in heterogeneous populations

    International Nuclear Information System (INIS)

    Cha, Ji Hwan; Finkelstein, Maxim

    2013-01-01

    Most populations encountered in real world are heterogeneous. In reliability applications, the mixture (observed) failure rate, obviously, can be considered as a measure of ‘average’ quality in these populations. However, in addition to this average measure, some variability characteristics for failure rates can be very helpful in describing the time-dependent changes in quality of heterogeneous populations. In this paper, we discuss variance and the coefficient of variation of the corresponding random failure rate as variability measures for items in heterogeneous populations. Furthermore, there is often a risk that items of poor quality are selected for important missions. Therefore, along with the ‘average quality’ of a population, more ‘conservative’ quality measures should be also defined and studied. For this purpose, we propose the percentile and the tail-mixture of the failure rates as the corresponding conservative measures. Some illustrative examples are given. -- Highlights: ► This paper provides the insight on the variability measures in heterogeneous populations. ► The conservative quality measures in heterogeneous populations are defined. ► The utility of these measures is illustrated by meaningful examples. ► This paper provides a better understanding of the dynamics in heterogeneous populations

  3. SIR dynamics in structured populations with heterogeneous connectivity

    OpenAIRE

    Volz, Erik

    2005-01-01

    Most epidemic models assume equal mixing among members of a population. An alternative approach is to model a population as random network in which individuals may have heterogeneous connectivity. This paper builds on previous research by describing the exact dynamical behavior of epidemics as they occur in random networks. A system of nonlinear differential equations is presented which describes the behavior of epidemics spreading through random networks with arbitrary degree distributions. ...

  4. An age-structured population balance model for microbial dynamics

    Directory of Open Access Journals (Sweden)

    Duarte M.V.E.

    2003-01-01

    Full Text Available This work presents an age-structured population balance model (ASPBM for a bioprocess in a continuous stirred-tank fermentor. It relates the macroscopic properties and dynamic behavior of biomass to the operational parameters and microscopic properties of cells. Population dynamics is governed by two time- and age-dependent density functions for living and dead cells, accounting for the influence of substrate and dissolved oxygen concentrations on cell division, aging and death processes. The ASPBM described biomass and substrate oscillations in aerobic continuous cultures as experimentally observed. It is noteworthy that a small data set consisting of nonsegregated measurements was sufficient to adjust a complex segregated mathematical model.

  5. GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.

    Science.gov (United States)

    Liachko, Ivan; Youngblood, Rachel A; Tsui, Kyle; Bubb, Kerry L; Queitsch, Christine; Raghuraman, M K; Nislow, Corey; Brewer, Bonita J; Dunham, Maitreya J

    2014-03-01

    The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins--a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation.

  6. Population Dynamics of Early Human Migration in Britain.

    Directory of Open Access Journals (Sweden)

    Mayank N Vahia

    Full Text Available Early human migration is largely determined by geography and human needs. These are both deterministic parameters when small populations move into unoccupied areas where conflicts and large group dynamics are not important. The early period of human migration into the British Isles provides such a laboratory which, because of its relative geographical isolation, may allow some insights into the complex dynamics of early human migration and interaction.We developed a simulation code based on human affinity to habitable land, as defined by availability of water sources, altitude, and flatness of land, in choosing the path of migration. Movement of people on the British island over the prehistoric period from their initial entry points was simulated on the basis of data from the megalithic period. Topographical and hydro-shed data from satellite databases was used to define habitability, based on distance from water bodies, flatness of the terrain, and altitude above sea level. We simulated population movement based on assumptions of affinity for more habitable places, with the rate of movement tempered by existing populations. We compared results of our computer simulations with genetic data and show that our simulation can predict fairly accurately the points of contacts between different migratory paths. Such comparison also provides more detailed information about the path of peoples' movement over ~2000 years before the present era.We demonstrate an accurate method to simulate prehistoric movements of people based upon current topographical satellite data. Our findings are validated by recently-available genetic data. Our method may prove useful in determining early human population dynamics even when no genetic information is available.

  7. How Large Asexual Populations Adapt

    Science.gov (United States)

    Desai, Michael

    2007-03-01

    We often think of beneficial mutations as being rare, and of adaptation as a sequence of selected substitutions: a beneficial mutation occurs, spreads through a population in a selective sweep, then later another beneficial mutation occurs, and so on. This simple picture is the basis for much of our intuition about adaptive evolution, and underlies a number of practical techniques for analyzing sequence data. Yet many large and mostly asexual populations -- including a wide variety of unicellular organisms and viruses -- live in a very different world. In these populations, beneficial mutations are common, and frequently interfere or cooperate with one another as they all attempt to sweep simultaneously. This radically changes the way these populations adapt: rather than an orderly sequence of selective sweeps, evolution is a constant swarm of competing and interfering mutations. I will describe some aspects of these dynamics, including why large asexual populations cannot evolve very quickly and the character of the diversity they maintain. I will explain how this changes our expectations of sequence data, how sex can help a population adapt, and the potential role of ``mutator'' phenotypes with abnormally high mutation rates. Finally, I will discuss comparisons of these predictions with evolution experiments in laboratory yeast populations.

  8. Genetic and phenotypic diversity of autochthonous cider yeasts in a cellar from Asturias.

    Science.gov (United States)

    Pando Bedriñana, R; Querol Simón, A; Suárez Valles, B

    2010-06-01

    This paper analyses yeast diversity and dynamics during the production of Asturian cider. Yeasts were isolated from apple juice and at different stages of fermentation in a cellar in Villaviciosa during two Asturian cider-apple harvests. The species identified by ITS-RFLP corresponded to Hanseniaspora valbyensis, Hanseniaspora uvarum, Metschnikowia pulcherrima, Pichia guilliermondii, Candida parapsilosis, Saccharomyces cerevisiae and Saccharomyces bayanus/Saccharomyces pastorianus/Saccharomyces kudriavzevii/Saccharomyces mikatae. The species C. parapsilosis is reported here for the first time in cider. The analysis of Saccharomyces mtDNA patterns showed great diversity, sequential substitution and the presence of a small number of yeast patterns (up to 8), present in both harvests. Killer (patterns nos. 22' and 47), sensitive (patterns nos. 12, 15, 33 and 61) and neutral phenotypes were found among the S. cerevisiae isolates. The detection of beta-glucosidase activity, with arbutin as the sole carbon source, allowed two S. cerevisiae strains (patterns nos. 3' and 19') to be differentiated by means of this enzymatic activity. Yeast strains producing the killer toxin or with beta-glucosidase activity are reported for the first time in autochthonous cider yeasts. 2009 Elsevier Ltd. All rights reserved.

  9. Identification and Characterization of Yeast Isolates from Pharmaceutical Waste Water

    Directory of Open Access Journals (Sweden)

    Marjeta Recek

    2002-01-01

    Full Text Available In order to develop an efficient an system for waste water pretreatment, the isolation of indigenous population of microorganisms from pharmaceutical waste water was done. We obtained pure cultures of 16 yeast isolates that differed slightly in colony morphology. Ten out of 16 isolates efficiently reduced COD in pharmaceutical waste water. Initial physiological characterization failed to match the 10 yeast isolates to either Pichia anomala or Pichia ciferrii. Restriction analysis of rDNA (rDNA-RFLP using three different restriction enzymes: HaeIII, MspI and CfoI, showed identical patterns of the isolates and Pichia anomala type strain. Separation of chromosomal DNAs of yeast isolates by the pulsed field gel electrophoresis revealed that the 10 isolates could be grouped into 6 karyotypes. Growth characteristics of the 6 isolates with distinct karyotypes were then studied in batch cultivation in pharmaceutical waste water for 80 hours.

  10. Geography, European colonization, and past population dynamics in Africa

    OpenAIRE

    Vaz Silva, Luis

    2005-01-01

    Past population dynamics in Africa have remained largely elusive due to the lack of demographic data. Researchers are understandably deterred from trying to explain what is not known and African historical population estimates suffer from this lack of interest. In this paper I explain present day African population densities using mostly ecological factors as explanatory variables. I find evidence supporting the view that ecological factors deeply affected precolonial patterns of human settle...

  11. Effects of constant immigration on the dynamics and persistence of stable and unstable Drosophila populations

    Science.gov (United States)

    Dey, Snigdhadip; Joshi, Amitabh

    2013-01-01

    Constant immigration can stabilize population size fluctuations but its effects on extinction remain unexplored. We show that constant immigration significantly reduced extinction in fruitfly populations with relatively stable or unstable dynamics. In unstable populations with oscillations of amplitude around 1.5 times the mean population size, persistence and constancy were unrelated. Low immigration enhanced persistence without affecting constancy whereas high immigration increased constancy without enhancing persistence. In relatively stable populations with erratic fluctuations of amplitude close to the mean population size, both low and high immigration enhanced persistence. In these populations, the amplitude of fluctuations relative to mean population size went down due to immigration, and their dynamics were altered to low-period cycles. The effects of immigration on the population size distribution and intrinsic dynamics of stable versus unstable populations differed considerably, suggesting that the mechanisms by which immigration reduced extinction risk depended on underlying dynamics in complex ways. PMID:23470546

  12. Nonlinear dynamics of interacting populations

    CERN Document Server

    Bazykin, Alexander D

    1998-01-01

    This book contains a systematic study of ecological communities of two or three interacting populations. Starting from the Lotka-Volterra system, various regulating factors are considered, such as rates of birth and death, predation and competition. The different factors can have a stabilizing or a destabilizing effect on the community, and their interplay leads to increasingly complicated behavior. Studying and understanding this path to greater dynamical complexity of ecological systems constitutes the backbone of this book. On the mathematical side, the tool of choice is the qualitative the

  13. Stochastic population dynamics in spatially extended predator-prey systems

    Science.gov (United States)

    Dobramysl, Ulrich; Mobilia, Mauro; Pleimling, Michel; Täuber, Uwe C.

    2018-02-01

    Spatially extended population dynamics models that incorporate demographic noise serve as case studies for the crucial role of fluctuations and correlations in biological systems. Numerical and analytic tools from non-equilibrium statistical physics capture the stochastic kinetics of these complex interacting many-particle systems beyond rate equation approximations. Including spatial structure and stochastic noise in models for predator-prey competition invalidates the neutral Lotka-Volterra population cycles. Stochastic models yield long-lived erratic oscillations stemming from a resonant amplification mechanism. Spatially extended predator-prey systems display noise-stabilized activity fronts that generate persistent correlations. Fluctuation-induced renormalizations of the oscillation parameters can be analyzed perturbatively via a Doi-Peliti field theory mapping of the master equation; related tools allow detailed characterization of extinction pathways. The critical steady-state and non-equilibrium relaxation dynamics at the predator extinction threshold are governed by the directed percolation universality class. Spatial predation rate variability results in more localized clusters, enhancing both competing species’ population densities. Affixing variable interaction rates to individual particles and allowing for trait inheritance subject to mutations induces fast evolutionary dynamics for the rate distributions. Stochastic spatial variants of three-species competition with ‘rock-paper-scissors’ interactions metaphorically describe cyclic dominance. These models illustrate intimate connections between population dynamics and evolutionary game theory, underscore the role of fluctuations to drive populations toward extinction, and demonstrate how space can support species diversity. Two-dimensional cyclic three-species May-Leonard models are characterized by the emergence of spiraling patterns whose properties are elucidated by a mapping onto a complex

  14. An Empirical Study of AI Population Dynamics with Million-agent Reinforcement Learning

    OpenAIRE

    Yang, Yaodong; Yu, Lantao; Bai, Yiwei; Wang, Jun; Zhang, Weinan; Wen, Ying; Yu, Yong

    2017-01-01

    In this paper, we conduct an empirical study on discovering the ordered collective dynamics obtained by a population of artificial intelligence (AI) agents. Our intention is to put AI agents into a simulated natural context, and then to understand their induced dynamics at the population level. In particular, we aim to verify if the principles developed in the real world could also be used in understanding an artificially-created intelligent population. To achieve this, we simulate a large-sc...

  15. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  16. [Onychomycosis by yeast not common in diabetics of a health center].

    Science.gov (United States)

    Imbert, J L; G Gomez, J V; Escudero, R B; Blasco, J L

    2016-10-01

    Mexican diabetic population frequently presents mycosis under foot hyperkeratosis; however, in another type of onychomycosis as the ones that is assumed Candida albicans is the causal agent, it is unknown the frequency, the prevalence and if another Candida species or other yeasts are found. Evaluate the frequency of yeasts causing onychomycosis in diabetic patients looked after in public institutions of health of the State of Hidalgo, Mexico, and its association with clinical epidemiological variables. An observational, descriptive and transversal study was made on 261 patients, from which one nail sample of each one was obtained, used to isolate and identify dermatophytes and yeasts; the results were statistically correlated with 24 epidemiological parameters. The clinical study was done through interrogation and by medical exploration in order to evaluate Tinea pedis and onychomycosis. Onychomycosis were caused by Candida guilliermondii, Candida parapsilosis, Candida glabrata, Candida krusei, Candida spp., Kodamaea ohmeri, Prototheca wickerhamii and unidentified yeasts. The prevalence for general onychomycosis, by dermatophytes, mixed onychomycosis and by yeasts were: 24.1, 19.5, 2.3 and 14.6%, respectively. Patients with significant probability to be diagnosed as having onychomycosis by yeasts are those wearing open shoes (2.59%); technicians and professionals (10.49%) and alcohol drinkers (3.72%). The fact that Candida albicans is not present in this study as causal agent of onychomycosis, and emerging and non-common yeasts were indeed isolated, creates new challenges. It is remarked the clinical criterion that when onychomycosis is suspected in diabetics, the diagnosis for culturing dermatophytes and yeasts should be included. Copyright © 2015 Sociedad Española de Médicos de Atención Primaria (SEMERGEN). Publicado por Elsevier España, S.L.U. All rights reserved.

  17. The Geographic Distribution of Saccharomyces cerevisiae Isolates within three Italian Neighboring Winemaking Regions Reveals Strong Differences in Yeast Abundance, Genetic Diversity and Industrial Strain Dissemination

    Directory of Open Access Journals (Sweden)

    Alessia Viel

    2017-08-01

    Full Text Available In recent years the interest for natural fermentations has been re-evaluated in terms of increasing the wine terroir and managing more sustainable winemaking practices. Therefore, the level of yeast genetic variability and the abundance of Saccharomyces cerevisiae native populations in vineyard are becoming more and more crucial at both ecological and technological level. Among the factors that can influence the strain diversity, the commercial starter release that accidentally occur in the environment around the winery, has to be considered. In this study we led a wide scale investigation of S. cerevisiae genetic diversity and population structure in the vineyards of three neighboring winemaking regions of Protected Appellation of Origin, in North-East of Italy. Combining mtDNA RFLP and microsatellite markers analyses we evaluated 634 grape samples collected over 3 years. We could detect major differences in the presence of S. cerevisiae yeasts, according to the winemaking region. The population structures revealed specificities of yeast microbiota at vineyard scale, with a relative Appellation of Origin area homogeneity, and transition zones suggesting a geographic differentiation. Surprisingly, we found a widespread industrial yeast dissemination that was very high in the areas where the native yeast abundance was low. Although geographical distance is a key element involved in strain distribution, the high presence of industrial strains in vineyard reduced the differences between populations. This finding indicates that industrial yeast diffusion it is a real emergency and their presence strongly interferes with the natural yeast microbiota.

  18. The demographic drivers of local population dynamics in two rare migratory birds.

    Science.gov (United States)

    Schaub, Michael; Reichlin, Thomas S; Abadi, Fitsum; Kéry, Marc; Jenni, Lukas; Arlettaz, Raphaël

    2012-01-01

    The exchange of individuals among populations can have strong effects on the dynamics and persistence of a given population. Yet, estimation of immigration rates remains one of the greatest challenges for animal demographers. Little empirical knowledge exists about the effects of immigration on population dynamics. New integrated population models fitted using Bayesian methods enable simultaneous estimation of fecundity, survival and immigration, as well as the growth rate of a population of interest. We applied this novel analytical framework to the demography of two populations of long-distance migratory birds, hoopoe Upupa epops and wryneck Jynx torquilla, in a study area in south-western Switzerland. During 2002-2010, the hoopoe population increased annually by 11%, while the wryneck population remained fairly stable. Apparent juvenile and adult survival probability was nearly identical in both species, but fecundity and immigration were slightly higher in the hoopoe. Hoopoe population growth rate was strongly correlated with juvenile survival, fecundity and immigration, while that of wrynecks strongly correlated only with immigration. This indicates that demographic components impacting the arrival of new individuals into the populations were more important for their dynamics than demographic components affecting the loss of individuals. The finding that immigration plays a crucial role in the population growth rates of these two rare species emphasizes the need for a broad rather than local perspective for population studies, and the development of wide-scale conservation actions.

  19. NetPhosYeast: prediction of protein phosphorylation sites in yeast

    DEFF Research Database (Denmark)

    Ingrell, C.R.; Miller, Martin Lee; Jensen, O.N.

    2007-01-01

    sites compared to those in humans, suggesting the need for an yeast-specific phosphorylation site predictor. NetPhosYeast achieves a correlation coefficient close to 0.75 with a sensitivity of 0.84 and specificity of 0.90 and outperforms existing predictors in the identification of phosphorylation sites...

  20. Causes and consequences of complex population dynamics in an annual plant, Cardamine pensylvanica

    Energy Technology Data Exchange (ETDEWEB)

    Crone, E.E.

    1995-11-08

    The relative importance of density-dependent and density-independent factors in determining the population dynamics of plants has been widely debated with little resolution. In this thesis, the author explores the effects of density-dependent population regulation on population dynamics in Cardamine pensylvanica, an annual plant. In the first chapter, she shows that experimental populations of C. pensylvanica cycled from high to low density in controlled constant-environment conditions. These cycles could not be explained by external environmental changes or simple models of direct density dependence (N{sub t+1} = f[N{sub t}]), but they could be explained by delayed density dependence (N{sub t+1} = f[N{sub t}, N{sub t+1}]). In the second chapter, she shows that the difference in the stability properties of population growth models with and without delayed density dependence is due to the presence of Hopf as well as slip bifurcations from stable to chaotic population dynamics. She also measures delayed density dependence due to effects of parental density on offspring quality in C. pensylvanica and shows that this is large enough to be the cause of the population dynamics observed in C. pensylvanica. In the third chapter, the author extends her analyses of density-dependent population growth models to include interactions between competing species. In the final chapter, she compares the effects of fixed spatial environmental variation and variation in population size on the evolutionary response of C. pensylvanica populations.

  1. Nonequilibrium population dynamics of phenotype conversion of cancer cells.

    Directory of Open Access Journals (Sweden)

    Joseph Xu Zhou

    Full Text Available Tumorigenesis is a dynamic biological process that involves distinct cancer cell subpopulations proliferating at different rates and interconverting between them. In this paper we proposed a mathematical framework of population dynamics that considers both distinctive growth rates and intercellular transitions between cancer cell populations. Our mathematical framework showed that both growth and transition influence the ratio of cancer cell subpopulations but the latter is more significant. We derived the condition that different cancer cell types can maintain distinctive subpopulations and we also explain why there always exists a stable fixed ratio after cell sorting based on putative surface markers. The cell fraction ratio can be shifted by changing either the growth rates of the subpopulations (Darwinism selection or by environment-instructed transitions (Lamarckism induction. This insight can help us to understand the dynamics of the heterogeneity of cancer cells and lead us to new strategies to overcome cancer drug resistance.

  2. Reconstructing the regulatory circuit of cell fate determination in yeast mating response.

    Science.gov (United States)

    Shao, Bin; Yuan, Haiyu; Zhang, Rongfei; Wang, Xuan; Zhang, Shuwen; Ouyang, Qi; Hao, Nan; Luo, Chunxiong

    2017-07-01

    Massive technological advances enabled high-throughput measurements of proteomic changes in biological processes. However, retrieving biological insights from large-scale protein dynamics data remains a challenging task. Here we used the mating differentiation in yeast Saccharomyces cerevisiae as a model and developed integrated experimental and computational approaches to analyze the proteomic dynamics during the process of cell fate determination. When exposed to a high dose of mating pheromone, the yeast cell undergoes growth arrest and forms a shmoo-like morphology; however, at intermediate doses, chemotropic elongated growth is initialized. To understand the gene regulatory networks that control this differentiation switch, we employed a high-throughput microfluidic imaging system that allows real-time and simultaneous measurements of cell growth and protein expression. Using kinetic modeling of protein dynamics, we classified the stimulus-dependent changes in protein abundance into two sources: global changes due to physiological alterations and gene-specific changes. A quantitative framework was proposed to decouple gene-specific regulatory modes from the growth-dependent global modulation of protein abundance. Based on the temporal patterns of gene-specific regulation, we established the network architectures underlying distinct cell fates using a reverse engineering method and uncovered the dose-dependent rewiring of gene regulatory network during mating differentiation. Furthermore, our results suggested a potential crosstalk between the pheromone response pathway and the target of rapamycin (TOR)-regulated ribosomal biogenesis pathway, which might underlie a cell differentiation switch in yeast mating response. In summary, our modeling approach addresses the distinct impacts of the global and gene-specific regulation on the control of protein dynamics and provides new insights into the mechanisms of cell fate determination. We anticipate that our

  3. GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.

    Directory of Open Access Journals (Sweden)

    Ivan Liachko

    2014-03-01

    Full Text Available The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins--a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation.

  4. The basic approach to age-structured population dynamics models, methods and numerics

    CERN Document Server

    Iannelli, Mimmo

    2017-01-01

    This book provides an introduction to age-structured population modeling which emphasises the connection between mathematical theory and underlying biological assumptions. Through the rigorous development of the linear theory and the nonlinear theory alongside numerics, the authors explore classical equations that describe the dynamics of certain ecological systems. Modeling aspects are discussed to show how relevant problems in the fields of demography, ecology, and epidemiology can be formulated and treated within the theory. In particular, the book presents extensions of age-structured modelling to the spread of diseases and epidemics while also addressing the issue of regularity of solutions, the asymptotic behaviour of solutions, and numerical approximation. With sections on transmission models, non-autonomous models and global dynamics, this book fills a gap in the literature on theoretical population dynamics. The Basic Approach to Age-Structured Population Dynamics will appeal to graduate students an...

  5. Potential impact of harvesting on the population dynamics of two epiphytic bromeliads

    Science.gov (United States)

    Toledo-Aceves, Tarin; Hernández-Apolinar, Mariana; Valverde, Teresa

    2014-08-01

    Large numbers of epiphytes are extracted from cloud forests for ornamental use and illegal trade in Latin America. We examined the potential effects of different harvesting regimes on the population dynamics of the epiphytic bromeliads Tillandsia multicaulis and Tillandsia punctulata. The population dynamics of these species were studied over a 2-year period in a tropical montane cloud forest in Veracruz, Mexico. Prospective and retrospective analyses were used to identify which demographic processes and life-cycle stages make the largest relative contribution to variation in population growth rate (λ). The effect of simulated harvesting levels on population growth rates was analysed for both species. λ of both populations was highly influenced by survival (stasis), to a lesser extent by growth, and only slightly by fecundity. Vegetative growth played a central role in the population dynamics of these organisms. The λ value of the studied populations did not differ significantly from unity: T. multicaulis λ (95% confidence interval) = 0.982 (0.897-1.060) and T. punctulata λ = 0.967 (0.815-1.051), suggesting population stability. However, numerical simulation of different levels of extraction showed that λ would drop substantially even under very low (2%) harvesting levels. Matrix analysis revealed that T. multicaulis and T. punctulata populations are likely to decline and therefore commercial harvesting would be unsustainable. Based on these findings, management recommendations are outlined.

  6. Differences between flocculating yeast and regular industrial yeast in transcription and metabolite profiling during ethanol fermentation

    Directory of Open Access Journals (Sweden)

    Lili Li

    2017-03-01

    Full Text Available Objectives: To improve ethanolic fermentation performance of self-flocculating yeast, difference between a flocculating yeast strain and a regular industrial yeast strain was analyzed by transcriptional and metabolic approaches. Results: The number of down-regulated (industrial yeast YIC10 vs. flocculating yeast GIM2.71 and up-regulated genes were 4503 and 228, respectively. It is the economic regulation for YIC10 that non-essential genes were down-regulated, and cells put more “energy” into growth and ethanol production. Hexose transport and phosphorylation were not the limiting-steps in ethanol fermentation for GIM2.71 compared to YIC10, whereas the reaction of 1,3-disphosphoglycerate to 3-phosphoglycerate, the decarboxylation of pyruvate to acetaldehyde and its subsequent reduction to ethanol were the most limiting steps. GIM2.71 had stronger stress response than non-flocculating yeast and much more carbohydrate was distributed to other bypass, such as glycerol, acetate and trehalose synthesis. Conclusions: Differences between flocculating yeast and regular industrial yeast in transcription and metabolite profiling will provide clues for improving the fermentation performance of GIM2.71.

  7. Linking individual phenotype to density-dependent population growth: the influence of body size on the population dynamics of malaria vectors

    Science.gov (United States)

    Russell, Tanya L.; Lwetoijera, Dickson W.; Knols, Bart G. J.; Takken, Willem; Killeen, Gerry F.; Ferguson, Heather M.

    2011-01-01

    Understanding the endogenous factors that drive the population dynamics of malaria mosquitoes will facilitate more accurate predictions about vector control effectiveness and our ability to destabilize the growth of either low- or high-density insect populations. We assessed whether variation in phenotypic traits predict the dynamics of Anopheles gambiae sensu lato mosquitoes, the most important vectors of human malaria. Anopheles gambiae dynamics were monitored over a six-month period of seasonal growth and decline. The population exhibited density-dependent feedback, with the carrying capacity being modified by rainfall (97% wAICc support). The individual phenotypic expression of the maternal (p = 0.0001) and current (p = 0.040) body size positively influenced population growth. Our field-based evidence uniquely demonstrates that individual fitness can have population-level impacts and, furthermore, can mitigate the impact of exogenous drivers (e.g. rainfall) in species whose reproduction depends upon it. Once frontline interventions have suppressed mosquito densities, attempts to eliminate malaria with supplementary vector control tools may be attenuated by increased population growth and individual fitness. PMID:21389034

  8. Tolerant industrial yeast Saccharomyces cerevisiae posses a more robust cell wall integrity signaling pathway against 2-furaldehyde and 5-(hydroxymethyl)-2-furaldehyde

    Science.gov (United States)

    Cell wall integrity signaling pathway in Saccharomyces cerevisiae is a conserved function for detecting and responding to cell stress conditions but less understood for industrial yeast. We dissected gene expression dynamics for a tolerant industrial yeast strain NRRL Y-50049 in response to challeng...

  9. Population dynamics of light-limited phytoplankton : Microcosm experiments

    NARCIS (Netherlands)

    Huisman, Jef

    This paper investigates the extent to which the predictions of an elementary model for light-limited growth are matched by laboratory experiments with light-limited phytoplankton. The model and experiments link the population dynamics of phytoplankton species with changes in the light gradient

  10. Distribution of yeast species associated with oral lesions in HIV-infected patients in Southwest Uganda.

    LENUS (Irish Health Repository)

    Agwu, Ezera

    2012-04-01

    Oropharyngeal candidiasis remains a significant clinical problem in HIV-infected and AIDS patients in regions of Africa where anti-retroviral therapy isn\\'t readily available. In this study we identified the yeast populations associated with oral lesions in HIV-infected patients in Southwest Uganda who were receiving treatment with nystatin and topical clotrimazole. Samples were taken from 605 patients and 316 (52%) of these yielded yeast growth following incubation on Sabouraud dextrose agar. Samples were subsequently re-plated on CHROMagar Candida medium to facilitate identification of the yeast species present. The majority (56%) of culture-positive samples yielded a mix of two or more species. Candida albicans was present in 87% (274\\/316) of patient samples and accounted for 87% (120\\/138) of single species samples. Candida glabrata, Candida tropicalis and Candida norvegensis were also found in cultures that yielded a single species. No Candida dubliniensis isolates were identified in this population.

  11. Distribution of yeast species associated with oral lesions in HIV-infected patients in Southwest Uganda.

    Science.gov (United States)

    Agwu, Ezera; Ihongbe, John C; McManus, Brenda A; Moran, Gary P; Coleman, David C; Sullivan, Derek J

    2012-04-01

    Oropharyngeal candidiasis remains a significant clinical problem in HIV-infected and AIDS patients in regions of Africa where anti-retroviral therapy isn't readily available. In this study we identified the yeast populations associated with oral lesions in HIV-infected patients in Southwest Uganda who were receiving treatment with nystatin and topical clotrimazole. Samples were taken from 605 patients and 316 (52%) of these yielded yeast growth following incubation on Sabouraud dextrose agar. Samples were subsequently re-plated on CHROMagar Candida medium to facilitate identification of the yeast species present. The majority (56%) of culture-positive samples yielded a mix of two or more species. Candida albicans was present in 87% (274/316) of patient samples and accounted for 87% (120/138) of single species samples. Candida glabrata, Candida tropicalis and Candida norvegensis were also found in cultures that yielded a single species. No Candida dubliniensis isolates were identified in this population.

  12. Rethinking the logistic approach for population dynamics of mutualistic interactions.

    Science.gov (United States)

    García-Algarra, Javier; Galeano, Javier; Pastor, Juan Manuel; Iriondo, José María; Ramasco, José J

    2014-12-21

    Mutualistic communities have an internal structure that makes them resilient to external perturbations. Late research has focused on their stability and the topology of the relations between the different organisms to explain the reasons of the system robustness. Much less attention has been invested in analyzing the systems dynamics. The main population models in use are modifications of the r-K formulation of logistic equation with additional terms to account for the benefits produced by the interspecific interactions. These models have shortcomings as the so-called r-K formulation diverges under some conditions. In this work, we introduce a model for population dynamics under mutualism that preserves the original logistic formulation. It is mathematically simpler than the widely used type II models, although it shows similar complexity in terms of fixed points and stability of the dynamics. We perform an analytical stability analysis and numerical simulations to study the model behavior in general interaction scenarios including tests of the resilience of its dynamics under external perturbations. Despite its simplicity, our results indicate that the model dynamics shows an important richness that can be used to gain further insights in the dynamics of mutualistic communities. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Direct characterization of chaotic and stochastic dynamics in a population model with strong periodicity

    International Nuclear Information System (INIS)

    Tung Wenwen; Qi Yan; Gao, J.B.; Cao Yinhe; Billings, Lora

    2005-01-01

    In recent years it has been increasingly recognized that noise and determinism may have comparable but different influences on population dynamics. However, no simple analysis methods have been introduced into ecology which can readily characterize those impacts. In this paper, we study a population model with strong periodicity and both with and without noise. The noise-free model generates both quasi-periodic and chaotic dynamics for certain parameter values. Due to the strong periodicity, however, the generated chaotic dynamics have not been satisfactorily described. The dynamics becomes even more complicated when there is noise. Characterizing the chaotic and stochastic dynamics in this model thus represents a challenging problem. Here we show how the chaotic dynamics can be readily characterized by the direct dynamical test for deterministic chaos developed by [Gao JB, Zheng ZM. Europhys. Lett. 1994;25:485] and how the influence of noise on quasi-periodic motions can be characterized as asymmetric diffusions wandering along the quasi-periodic orbit. It is hoped that the introduced methods will be useful in studying other population models as well as population time series obtained both in field and laboratory experiments

  14. Efficient characterisation of large deviations using population dynamics

    Science.gov (United States)

    Brewer, Tobias; Clark, Stephen R.; Bradford, Russell; Jack, Robert L.

    2018-05-01

    We consider population dynamics as implemented by the cloning algorithm for analysis of large deviations of time-averaged quantities. We use the simple symmetric exclusion process with periodic boundary conditions as a prototypical example and investigate the convergence of the results with respect to the algorithmic parameters, focussing on the dynamical phase transition between homogeneous and inhomogeneous states, where convergence is relatively difficult to achieve. We discuss how the performance of the algorithm can be optimised, and how it can be efficiently exploited on parallel computing platforms.

  15. Yeasts and yeast-like organisms associated with fruits and blossoms of different fruit trees.

    Science.gov (United States)

    Vadkertiová, Renáta; Molnárová, Jana; Vránová, Dana; Sláviková, Elena

    2012-12-01

    Yeasts are common inhabitants of the phyllosphere, but our knowledge of their diversity in various plant organs is still limited. This study focused on the diversity of yeasts and yeast-like organisms associated with matured fruits and fully open blossoms of apple, plum, and pear trees, during 2 consecutive years at 3 localities in southwest Slovakia. The occurrence of yeasts and yeast-like organisms in fruit samples was 2½ times higher and the yeast community more diverse than that in blossom samples. Only 2 species (Aureobasidium pullulans and Metschnikowia pulcherrima) occurred regularly in the blossom samples, whereas Galactomyces candidus, Hanseniaspora guilliermondii, Hanseniaspora uvarum, M. pulcherrima, Pichia kluyveri, Pichia kudriavzevii, and Saccharomyces cerevisiae were the most frequently isolated species from the fruit samples. The ratio of the number of samples where only individual species were present to the number of samples where 2 or more species were found (consortium) was counted. The occurrence of individual species in comparison with consortia was much higher in blossom samples than in fruit samples. In the latter, consortia predominated. Aureobasidium pullulans, M. pulcherrima, and S. cerevisiae, isolated from both the fruits and blossoms, can be considered as resident yeast species of various fruit tree species cultivated in southwest Slovakia localities.

  16. Cell wall trapping of autocrine peptides for human G-protein-coupled receptors on the yeast cell surface.

    Directory of Open Access Journals (Sweden)

    Jun Ishii

    Full Text Available G-protein-coupled receptors (GPCRs regulate a wide variety of physiological processes and are important pharmaceutical targets for drug discovery. Here, we describe a unique concept based on yeast cell-surface display technology to selectively track eligible peptides with agonistic activity for human GPCRs (Cell Wall Trapping of Autocrine Peptides (CWTrAP strategy. In our strategy, individual recombinant yeast cells are able to report autocrine-positive activity for human GPCRs by expressing a candidate peptide fused to an anchoring motif. Following expression and activation, yeast cells trap autocrine peptides onto their cell walls. Because captured peptides are incapable of diffusion, they have no impact on surrounding yeast cells that express the target human GPCR and non-signaling peptides. Therefore, individual yeast cells can assemble the autonomous signaling complex and allow single-cell screening of a yeast population. Our strategy may be applied to identify eligible peptides with agonistic activity for target human GPCRs.

  17. Ruffed grouse population dynamics in the central and southern Appalachians

    Science.gov (United States)

    John M. Giuliano Tirpak; C. Allan Miller; Thomas J. Allen; Steve Bittner; David A. Buehler; John W. Edwards; Craig A. Harper; William K. Igo; Gary W. Norman; M. Seamster; Dean F. Stauffer

    2006-01-01

    Ruffed grouse (Bonasa urnbellus; hereafter grouse) populations in the central and southern Appalachians are in decline. However, limited information on the dynamics of these populations prevents the development of effective management strategies to reverse these trends. We used radiotelemetry data collected on grouse to parameterize 6 models of...

  18. Enumeration and rapid identification of yeasts during extraction processes of extra virgin olive oil in Tuscany.

    Science.gov (United States)

    Mari, Eleonora; Guerrini, Simona; Granchi, Lisa; Vincenzini, Massimo

    2016-06-01

    The aim of this study was to evaluate the occurrence of yeast populations during different olive oil extraction processes, carried out in three consecutive years in Tuscany (Italy), by analysing crushed pastes, kneaded pastes, oil from decanter and pomaces. The results showed yeast concentrations ranging between 10(3) and 10(5) CFU/g or per mL. Seventeen dominant yeast species were identified by random amplified polymorphic DNA with primer M13 and their identification was confirmed by restriction fragments length polymorphism of ribosomal internal transcribed spacer and sequencing rRNA genes. The isolation frequencies of each species in the collected samples pointed out that the occurrence of the various yeast species in olive oil extraction process was dependent not only on the yeasts contaminating the olives but also on the yeasts colonizing the plant for oil extraction. In fact, eleven dominant yeast species were detected from the washed olives, but only three of them were also found in oil samples at significant isolation frequency. On the contrary, the most abundant species in oil samples, Yamadazyma terventina, did not occur in washed olive samples. These findings suggest a phenomenon of contamination of the plant for oil extraction that selects some yeast species that could affect the quality of olive oil.

  19. Interaction Between Yeasts and Zinc

    Science.gov (United States)

    Nicola, Raffaele De; Walker, Graeme

    Zinc is an essential trace element in biological systems. For example, it acts as a cellular membrane stabiliser, plays a critical role in gene expression and genome modification and activates nearly 300 enzymes, including alcohol dehydrogenase. The present chapter will be focused on the influence of zinc on cell physiology of industrial yeast strains of Saccharomyces cerevisiae, with special regard to the uptake and subsequent utilisation of this metal. Zinc uptake by yeast is metabolism-dependent, with most of the available zinc translocated very quickly into the vacuole. At cell division, zinc is distributed from mother to daughter cells and this effectively lowers the individual cellular zinc concentration, which may become zinc depleted at the onset of the fermentation. Zinc influences yeast fermentative performance and examples will be provided relating to brewing and wine fermentations. Industrial yeasts are subjected to several stresses that may impair fermentation performance. Such stresses may also impact on yeast cell zinc homeostasis. This chapter will discuss the practical implications for the correct management of zinc bioavailability for yeast-based biotechnologies aimed at improving yeast growth, viability, fermentation performance and resistance to environmental stresses

  20. Nectar yeasts in the tall Larkspur Delphinium barbeyi (Ranunculaceae and effects on components of pollinator foraging behavior.

    Directory of Open Access Journals (Sweden)

    Robert N Schaeffer

    Full Text Available Microorganisms frequently colonize the nectar of angiosperm species. Though capable of altering a suite of traits important for pollinator attraction, few studies exist that test the degree to which they mediate pollinator foraging behavior. The objective of our study was to fill this gap by assessing the abundance and diversity of yeasts associated with the perennial larkspur Delphinium barbeyi (Ranunculaceae and testing whether their presence affected components of pollinator foraging behavior. Yeasts frequently colonized D. barbeyi nectar, populating 54-77% of flowers examined depending on site. Though common, the yeast community was species-poor, represented by a single species, Metschnikowia reukaufii. Female-phase flowers of D. barbeyi were more likely to have higher densities of yeasts in comparison to male-phase flowers. Pollinators were likely vectors of yeasts, as virgin (unvisited flowers rarely contained yeasts compared to flowers open to pollinator visitation, which were frequently colonized. Finally, pollinators responded positively to the presence of yeasts. Bombus foragers both visited and probed more flowers inoculated with yeasts in comparison to uninoculated controls. Taken together, our results suggest that variation in the occurrence and density of nectar-inhabiting yeasts have the potential to alter components of pollinator foraging behavior linked to pollen transfer and plant fitness.

  1. Nectar Yeasts in the Tall Larkspur Delphinium barbeyi (Ranunculaceae) and Effects on Components of Pollinator Foraging Behavior

    Science.gov (United States)

    Schaeffer, Robert N.; Phillips, Cody R.; Duryea, M. Catherine; Andicoechea, Jonathan; Irwin, Rebecca E.

    2014-01-01

    Microorganisms frequently colonize the nectar of angiosperm species. Though capable of altering a suite of traits important for pollinator attraction, few studies exist that test the degree to which they mediate pollinator foraging behavior. The objective of our study was to fill this gap by assessing the abundance and diversity of yeasts associated with the perennial larkspur Delphinium barbeyi (Ranunculaceae) and testing whether their presence affected components of pollinator foraging behavior. Yeasts frequently colonized D. barbeyi nectar, populating 54–77% of flowers examined depending on site. Though common, the yeast community was species-poor, represented by a single species, Metschnikowia reukaufii. Female-phase flowers of D. barbeyi were more likely to have higher densities of yeasts in comparison to male-phase flowers. Pollinators were likely vectors of yeasts, as virgin (unvisited) flowers rarely contained yeasts compared to flowers open to pollinator visitation, which were frequently colonized. Finally, pollinators responded positively to the presence of yeasts. Bombus foragers both visited and probed more flowers inoculated with yeasts in comparison to uninoculated controls. Taken together, our results suggest that variation in the occurrence and density of nectar-inhabiting yeasts have the potential to alter components of pollinator foraging behavior linked to pollen transfer and plant fitness. PMID:25272164

  2. Modelling population dynamics model formulation, fitting and assessment using state-space methods

    CERN Document Server

    Newman, K B; Morgan, B J T; King, R; Borchers, D L; Cole, D J; Besbeas, P; Gimenez, O; Thomas, L

    2014-01-01

    This book gives a unifying framework for estimating the abundance of open populations: populations subject to births, deaths and movement, given imperfect measurements or samples of the populations.  The focus is primarily on populations of vertebrates for which dynamics are typically modelled within the framework of an annual cycle, and for which stochastic variability in the demographic processes is usually modest. Discrete-time models are developed in which animals can be assigned to discrete states such as age class, gender, maturity,  population (within a metapopulation), or species (for multi-species models). The book goes well beyond estimation of abundance, allowing inference on underlying population processes such as birth or recruitment, survival and movement. This requires the formulation and fitting of population dynamics models.  The resulting fitted models yield both estimates of abundance and estimates of parameters characterizing the underlying processes.  

  3. Population dynamics of potato cyst nematodes and associated damage to potato

    NARCIS (Netherlands)

    Schans, J.

    1993-01-01

    Population dynamics of potato cyst nematodes (PCN; Globoderarostochiensis (Woll.) Skarbilovich and G. pallida Stone) and their interactions with potato plants are insufficiently understood to explain variations of population

  4. Population dynamics of bowfin in a south Georgia reservoir: latitudinal comparisons of population structure, growth, and mortality

    Science.gov (United States)

    Porter, Nicholas J.; Bonvechio, Timothy F.; McCormick, Joshua L.; Quist, Michael

    2014-01-01

    The objectives of this study were to evaluate the population dynamics of bowfin (Amia calva) in Lake Lindsay Grace, Georgia, and to compare those dynamics to other bowfin populations. Relative abundance of bowfin sampled in 2010 in Lake Lindsay Grace was low and variable (mean±SD; 2.7±4.7 fish per hour of electrofishing). Total length (TL) of bowfin collected in Lake Lindsay Grace varied from 233–683 mm. Age of bowfin in Lake Lindsay Grace varied from 0–5 yr. Total annual mortality (A) was estimated at 68%. Both sexes appeared to be fully mature by age 2 with gonadosomatic index values above 8 for females and close to 1 for males. The majority of females were older, longer, and heavier than males. Bowfin in Lake Lindsay Grace had fast growth up to age 4 and higher total annual mortality than the other populations examined in this study. A chi-square test indicated that size structure of bowfin from Lake Lindsay Grace was different than those of a Louisiana population and two bowfin populations from the upper Mississippi River. To further assess bowfin size structure, we proposed standard length (i.e., TL) categories: stock (200 mm, 8 inches), quality (350 mm, 14 inches), preferred (460 mm, 18 inches), memorable (560 mm, 22, inches), and trophy (710 mm, 28 inches). Because our knowledge of bowfin ecology is limited, additional understanding of bowfin population dynamics provides important insight that can be used in management of bowfin across their distribution.

  5. Cooperation, cheating, and collapse in biological populations

    Science.gov (United States)

    Gore, Jeff

    2014-03-01

    Natural populations can collapse suddenly in response to small changes in environmental conditions, and recovery from such a collapse can be difficult. We have used laboratory microbial ecosystems to directly measure theoretically proposed early warning signals of impending population collapse. Yeast cooperatively break down the sugar sucrose, meaning that below a critical size the population cannot sustain itself. We have demonstrated experimentally that changes in the fluctuations of the population size can serve as an early warning signal that the population is close to collapse. The cooperative nature of yeast growth on sucrose suggests that the population may be susceptible to ``cheater'' cells, which do not contribute to the public good and instead merely take advantage of the cooperative cells. We confirm this possibility experimentally and find that such social parasitism decreases the resilience of the population.

  6. Boom or bust? A comparative analysis of transient population dynamics in plants

    DEFF Research Database (Denmark)

    Stott, Iain; Franco, Miguel; Carslake, David

    2010-01-01

    researchers as further possible effectors of complicated dynamics. Previously published methods of transient analysis have tended to require knowledge of initial population structure. However, this has been overcome by the recent development of the parametric Kreiss bound (which describes how large...... a population must become before reaching its maximum possible transient amplification following a disturbance) and the extension of this and other transient indices to simultaneously describe both amplified and attenuated transient dynamics. We apply the Kreiss bound and other transient indices to a data base...... worrying artefact of basic model parameterization. Synthesis. Transient indices describe how big or how small plant populations can get, en route to long-term stable rates of increase or decline. The patterns we found in the potential for transient dynamics, across many species of plants, suggest...

  7. Entropy analysis in yeast DNA

    International Nuclear Information System (INIS)

    Kim, Jongkwang; Kim, Sowun; Lee, Kunsang; Kwon, Younghun

    2009-01-01

    In this article, we investigate the language structure in yeast 16 chromosomes. In order to find it, we use the entropy analysis for codons (or amino acids) of yeast 16 chromosomes, developed in analysis of natural language by Montemurro et al. From the analysis, we can see that there exists a language structure in codons (or amino acids) of yeast 16 chromosomes. Also we find that the grammar structure of amino acids of yeast 16 chromosomes has a deep relationship with secondary structure of protein.

  8. Genetic diversity and pectinolytic activity of epiphytic yeasts from grape carposphere.

    Science.gov (United States)

    Filho, M Cilião; Bertéli, M B D; Valle, J S; Paccola-Meirelles, L D; Linde, G A; Barcellos, F G; Colauto, N B

    2017-06-20

    The genetic diversity of epiphytic yeasts from grape carposphere is susceptible to environmental variations that determine the predominant carposphere microbiota. Understanding the diversity of yeasts that inhabit grape carposphere in different environments and their pectinolytic activity is a way to understand the biotechnological potential that surrounds us and help improve winemaking. Therefore, this study aimed to evaluate the pectinolytic activity and characterize the genetic diversity of isolated epiphytic yeasts from grape carposphere. Grapes of the Bordeaux cultivar were collected from different regions of Paraná and Rio Grande do Sul States, in Brazil, and the yeasts were isolated from these grape carpospheres. Monosporic isolates were morphologically and genetically characterized on potato dextrose agar medium and by PCR-RFLP and rep-PCR (BOX-PCR) in the ITS1-5.8S-ITS2 region of rDNA. The index of pectinolytic activity of isolates was also evaluated estimating the ratio between the halo diameter of enzymatic degradation and the diameter of the colony when the isolates were grown in cultivation medium containing 10 g/L pectin, 5 g/L yeast extract, 15 g/L agar, 0.12% (w/v) Congo red, and pH 6.2. We observed that the grape carposphere is an environment with a great genetic diversity of epiphytic yeasts of the following genera: Cryptococcus (31.25%), Pichia (25.0%), Candida (25.0%), Dekkera (12.5%), and Saccharomyces (6.25%). The PCR-RFLP technique allowed analyzing existing polymorphism among individuals of a population based on a more restrict and evolutionarily preserved region, mostly utilized to differentiate isolates at the genus level. Approximately 33% of yeast isolates presented pectinolytic activity with potential biotechnological for wine and fruit juice production. This great genetic variability found indicated that it is a potential reservoir of genes to be applied in viniculture improvement programs.

  9. Yeast flocculation: New story in fuel ethanol production.

    Science.gov (United States)

    Zhao, X Q; Bai, F W

    2009-01-01

    Yeast flocculation has been used in the brewing industry to facilitate biomass recovery for a long time, and thus its mechanism of yeast flocculation has been intensively studied. However, the application of flocculating yeast in ethanol production garnered attention mainly in the 1980s and 1990s. In this article, updated research progress in the molecular mechanism of yeast flocculation and the impact of environmental conditions on yeast flocculation are reviewed. Construction of flocculating yeast strains by genetic approach and utilization of yeast flocculation for ethanol production from various feedstocks were presented. The concept of self-immobilized yeast cells through their flocculation is revisited through a case study of continuous ethanol fermentation with the flocculating yeast SPSC01, and their technical and economic advantages are highlighted by comparing with yeast cells immobilized with supporting materials and regular free yeast cells as well. Taking the flocculating yeast SPSC01 as an example, the ethanol tolerance of the flocculating yeast was also discussed.

  10. An individual-based probabilistic model for simulating fisheries population dynamics

    Directory of Open Access Journals (Sweden)

    Jie Cao

    2016-12-01

    Full Text Available The purpose of stock assessment is to support managers to provide intelligent decisions regarding removal from fish populations. Errors in assessment models may have devastating impacts on the population fitness and negative impacts on the economy of the resource users. Thus, accuracte estimations of population size, growth rates are critical for success. Evaluating and testing the behavior and performance of stock assessment models and assessing the consequences of model mis-specification and the impact of management strategies requires an operating model that accurately describe the dynamics of the target species, and can resolve spatial and seasonal changes. In addition, the most thorough evaluations of assessment models use an operating model that takes a different form than the assessment model. This paper presents an individual-based probabilistic model used to simulate the complex dynamics of populations and their associated fisheries. Various components of population dynamics are expressed as random Bernoulli trials in the model and detailed life and fishery histories of each individual are tracked over their life span. The simulation model is designed to be flexible so it can be used for different species and fisheries. It can simulate mixing among multiple stocks and link stock-recruit relationships to environmental factors. Furthermore, the model allows for flexibility in sub-models (e.g., growth and recruitment and model assumptions (e.g., age- or size-dependent selectivity. This model enables the user to conduct various simulation studies, including testing the performance of assessment models under different assumptions, assessing the impacts of model mis-specification and evaluating management strategies.

  11. Metastable states and quasicycles in a stochastic Wilson-Cowan model of neuronal population dynamics

    KAUST Repository

    Bressloff, Paul C.

    2010-01-01

    We analyze a stochastic model of neuronal population dynamics with intrinsic noise. In the thermodynamic limit N→∞, where N determines the size of each population, the dynamics is described by deterministic Wilson-Cowan equations. On the other hand

  12. Biology as population dynamics: heuristics for transmission risk.

    Science.gov (United States)

    Keebler, Daniel; Walwyn, David; Welte, Alex

    2013-02-01

    Population-type models, accounting for phenomena such as population lifetimes, mixing patterns, recruitment patterns, genetic evolution and environmental conditions, can be usefully applied to the biology of HIV infection and viral replication. A simple dynamic model can explore the effect of a vaccine-like stimulus on the mortality and infectiousness, which formally looks like fertility, of invading virions; the mortality of freshly infected cells; and the availability of target cells, all of which impact on the probability of infection. Variations on this model could capture the importance of the timing and duration of different key events in viral transmission, and hence be applied to questions of mucosal immunology. The dynamical insights and assumptions of such models are compatible with the continuum of between- and within-individual risks in sexual violence and may be helpful in making sense of the sparse data available on the association between HIV transmission and sexual violence. © 2012 John Wiley & Sons A/S.

  13. An age structured model for obesity prevalence dynamics in populations

    Directory of Open Access Journals (Sweden)

    Gilberto González Parra

    2010-08-01

    Full Text Available Objective. Modeling the correlation of the development of obesity in a population with age and time and predict the dynamics of the correlation of the development of obesity in a population with age and time under different scenarios in Valencia (Spain. Materials and methods. An age structured mathematical model is used to describe the future dynamics of obesity prevalence for different ages in human population with excess weight. Simulation of the model with parameters estimated using the Health Survey of the Region of Valencia 2000 (4.319 interviews and Health Survey of the Region of Valencia 2005 (4.012 interviews. The model considers only overweight and obese populations since these subpopulations are the most relevant on obesity health concern. Results. The model allows predicting and studying the prevalence of obesity for each age. Results showed an increasing trend of obesity in the following years in well accordance with the trend observed in several countries. Conclusions. Based on the numerical simulations it is possible to conclude that the age structured mathematical model is suitable to forecast the obesity epidemic in each age group in different countries. Additionally, this type of models may be applied to study other characteristics of other populations such animal populations.

  14. Brewing characteristics of piezosensitive sake yeasts

    Science.gov (United States)

    Nomura, Kazuki; Hoshino, Hirofumi; Igoshi, Kazuaki; Onozuka, Haruka; Tanaka, Erika; Hayashi, Mayumi; Yamazaki, Harutake; Takaku, Hiroaki; Iguchi, Akinori; Shigematsu, Toru

    2018-04-01

    Application of high hydrostatic pressure (HHP) treatment to food processing is expected as a non-thermal fermentation regulation technology that supresses over fermentation. However, the yeast Saccharomyces cerevisiae used for Japanese rice wine (sake) brewing shows high tolerance to HHP. Therefore, we aimed to generate pressure-sensitive (piezosensitive) sake yeast strains by mating sake with piezosensitive yeast strains to establish an HHP fermentation regulation technology and extend the shelf life of fermented foods. The results of phenotypic analyses showed that the generated yeast strains were piezosensitive and exhibited similar fermentation ability compared with the original sake yeast strain. In addition, primary properties of sake brewed using these strains, such as ethanol concentration, sake meter value and sake flavor compounds, were almost equivalent to those obtained using the sake yeast strain. These results suggest that the piezosensitive strains exhibit brewing characteristics essentially equivalent to those of the sake yeast strain.

  15. Use of Mobile Device Data To Better Estimate Dynamic Population Size for Wastewater-Based Epidemiology.

    Science.gov (United States)

    Thomas, Kevin V; Amador, Arturo; Baz-Lomba, Jose Antonio; Reid, Malcolm

    2017-10-03

    Wastewater-based epidemiology is an established approach for quantifying community drug use and has recently been applied to estimate population exposure to contaminants such as pesticides and phthalate plasticizers. A major source of uncertainty in the population weighted biomarker loads generated is related to estimating the number of people present in a sewer catchment at the time of sample collection. Here, the population quantified from mobile device-based population activity patterns was used to provide dynamic population normalized loads of illicit drugs and pharmaceuticals during a known period of high net fluctuation in the catchment population. Mobile device-based population activity patterns have for the first time quantified the high degree of intraday, week, and month variability within a specific sewer catchment. Dynamic population normalization showed that per capita pharmaceutical use remained unchanged during the period when static normalization would have indicated an average reduction of up to 31%. Per capita illicit drug use increased significantly during the monitoring period, an observation that was only possible to measure using dynamic population normalization. The study quantitatively confirms previous assessments that population estimates can account for uncertainties of up to 55% in static normalized data. Mobile device-based population activity patterns allow for dynamic normalization that yields much improved temporal and spatial trend analysis.

  16. Experimental evolution in budding yeast

    Science.gov (United States)

    Murray, Andrew

    2012-02-01

    I will discuss our progress in analyzing evolution in the budding yeast, Saccharomyces cerevisiae. We take two basic approaches. The first is to try and examine quantitative aspects of evolution, for example by determining how the rate of evolution depends on the mutation rate and the population size or asking whether the rate of mutation is uniform throughout the genome. The second is to try to evolve qualitatively novel, cell biologically interesting phenotypes and track the mutations that are responsible for the phenotype. Our efforts include trying to alter cell morphology, evolve multicellularity, and produce a biological oscillator.

  17. Periodic matrix models for seasonal dynamics of structured populations with application to a seabird population.

    Science.gov (United States)

    Cushing, J M; Henson, Shandelle M

    2018-02-03

    For structured populations with an annual breeding season, life-stage interactions and behavioral tactics may occur on a faster time scale than that of population dynamics. Motivated by recent field studies of the effect of rising sea surface temperature (SST) on within-breeding-season behaviors in colonial seabirds, we formulate and analyze a general class of discrete-time matrix models designed to account for changes in behavioral tactics within the breeding season and their dynamic consequences at the population level across breeding seasons. As a specific example, we focus on egg cannibalism and the daily reproductive synchrony observed in seabirds. Using the model, we investigate circumstances under which these life history tactics can be beneficial or non-beneficial at the population level in light of the expected continued rise in SST. Using bifurcation theoretic techniques, we study the nature of non-extinction, seasonal cycles as a function of environmental resource availability as they are created upon destabilization of the extinction state. Of particular interest are backward bifurcations in that they typically create strong Allee effects in population models which, in turn, lead to the benefit of possible (initial condition dependent) survival in adverse environments. We find that positive density effects (component Allee effects) due to increased adult survival from cannibalism and the propensity of females to synchronize daily egg laying can produce a strong Allee effect due to a backward bifurcation.

  18. Interacting trophic forcing and the population dynamics of herring

    DEFF Research Database (Denmark)

    Lindegren, Martin; Ostman, Orjan; Gardmark, Anna

    2011-01-01

    -up nor top-down, but rather through multiple external and internal drivers. While in many studies single drivers have been identified, potential synergies of multiple factors, as well as their relative importance in regulating population dynamics of small pelagic fish, is a largely unresolved issue....... Using a statistical, age-structured modeling approach, we demonstrate the relative importance and influence of bottom-up (e.g., climate, zooplankton availability) and top-down (i.e., fishing and predation) factors on the population dynamics of Bothnian Sea herring (Clupea harengus) throughout its life...... cycle. Our results indicate significant bottom-up effects of zooplankton and interspecific competition from sprat (Sprattus sprattus), particularly on younger age classes of herring. Although top-down forcing through fishing and predation by grey seals (Halichoerus grypus) and Atlantic cod (Gadus morhua...

  19. Molecular Characterization of Yeast Strains Isolated from Different Sources by Restriction Fragment Length Polymorphism

    International Nuclear Information System (INIS)

    Ali, M. S.; Latif, Z.

    2016-01-01

    Various molecular techniques like analysis of the amplified rDNA internal transcribed spacers (ITS), intragenic spacers and total ITS region analysis by restriction fragment length polymorphism (RFLP) has been introduced for yeast identification but there are limited databases to identify yeast species on the basis of 5.8S rDNA. In this study, twenty nine yeast strains from various sources including spoiled fruits, vegetables, foodstuffs, and concentrated juices were characterized by PCR-RFLP. PCR-RFLP has been used to characterize yeasts present in different spoiled food samples after isolation of the yeasts. By using this technique, the isolated yeast strains were characterized by direct 5.8S-ITS rDNA region amplification. RFLP analysis was applied to each of the amplification products (varied from 400bp to 800bp) detected, and the corresponding yeast identifications were made according to each specific restriction patterns obtained after treatment with two endonucleases TaqI and HaeIII which yielded a specific banding pattern for each species. For further confirmation amplified products of eleven selected isolates were sequenced and blast on NCBI. Both RFLP and sequence analyses of the strains with accession nos. KF472163, KF472164, KF472165, KF472166, KF472167, KF472168, KF472169, KF472170, KF472171, KF472172, KF472173 gave significantly similar results. The isolates were found to belong five different yeast species including; Candida spp., Pichia spp., Kluyveromyces spp., Clavispora spp. and Hanseniaspora spp. This method provides a fast, easy, reliable and authentic way for determining yeast population present in different type of samples, as compared to traditional characterization technique. (author)

  20. Production of Food Grade Yeasts

    Directory of Open Access Journals (Sweden)

    Argyro Bekatorou

    2006-01-01

    Full Text Available Yeasts have been known to humans for thousands of years as they have been used in traditional fermentation processes like wine, beer and bread making. Today, yeasts are also used as alternative sources of high nutritional value proteins, enzymes and vitamins, and have numerous applications in the health food industry as food additives, conditioners and flavouring agents, for the production of microbiology media and extracts, as well as livestock feeds. Modern scientific advances allow the isolation, construction and industrial production of new yeast strains to satisfy the specific demands of the food industry. Types of commercial food grade yeasts, industrial production processes and raw materials are highlighted. Aspects of yeast metabolism, with respect to carbohydrate utilization, nutritional aspects and recent research advances are also discussed.

  1. Effects of different protein concentrations on longevity and feeding behavior of two adult populations of Ceratitis capitata Wiedemann (Diptera: Tephritidae)

    International Nuclear Information System (INIS)

    Placido-Silva, Maria do Carmo; Silva Neto, Alberto M. da; Joachim-Bravo, Iara S.; Zucoloto, Fernando S.

    2006-01-01

    The effects of protein intake on two adult male and female populations of Ceratitis capitata Wiedemann were assessed. One population consisted of flies reared for twenty years in the laboratory (Lab-pop); the other population consisted both of flies reared in the laboratory for approximately fifteen years and of the periodically introduced wild flies (Hybrid-pop). Three diets were tested: a no-yeast diet and two diets containing yeast (protein source) at the concentrations 6.5 g or 1.5 g per 100 ml diet. The parameters analyzed were: adult longevity, diet intake with and without yeast, and discrimination threshold for yeast. Protein intake increased Lab-pop adult longevity and did not affect longevity of the Hybrid-pop. Longevity in each population was similar for males and females fed on the same diet. Food behavior were similar for male and female adults of both populations; all preferred diets containing protein (yeast). Males and females in both populations ingested similar amounts of each diet. The discrimination threshold for yeast was similar for all males (0.5 g yeast/100 ml diet); Lab-pop females were able to detect the presence of smaller quantities of yeast in their diet, thus having a higher discrimination capacity (0.4 g/100 ml diet) as compared to the Hybrid-pop females (0.6 g/ 100 ml diet). (author)

  2. Sourdough microbial community dynamics: An analysis during French organic bread-making processes.

    Science.gov (United States)

    Lhomme, Emilie; Urien, Charlotte; Legrand, Judith; Dousset, Xavier; Onno, Bernard; Sicard, Delphine

    2016-02-01

    Natural sourdoughs are commonly used in bread-making processes, especially for organic bread. Despite its role in bread flavor and dough rise, the stability of the sourdough microbial community during and between bread-making processes is debated. We investigated the dynamics of lactic acid bacteria (LAB) and yeast communities in traditional organic sourdoughs of five French bakeries during the bread-making process and several months apart using classical and molecular microbiology techniques. Sourdoughs were sampled at four steps of the bread-making process with repetition. The analysis of microbial density over 68 sourdough/dough samples revealed that both LAB and yeast counts changed along the bread-making process and between bread-making runs. The species composition was less variable. A total of six LAB and nine yeast species was identified from 520 and 1675 isolates, respectively. The dominant LAB species was Lactobacillus sanfranciscensis, found for all bakeries and each bread-making run. The dominant yeast species changed only once between bread-making processes but differed between bakeries. They mostly belonged to the Kazachstania clade. Overall, this study highlights the change of population density within the bread-making process and between bread-making runs and the relative stability of the sourdough species community during bread-making process. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Alterations in Phosphatidylcholine and Phosphatidylethanolamine Content During Fermentative Metabolism in Saccharomyces cerevisiae Brewer’s Yeast

    Directory of Open Access Journals (Sweden)

    Gordana Čanadi Jurešić

    2009-01-01

    Full Text Available During beer production and serial recycling, brewer’s yeasts are exposed to various stress factors that, overpowering the cellular defence mechanisms, can impair yeast growth and fermentation performance. It is well known that yeast cells acclimatize to stress conditions in part by changing the lipid composition of their membranes. The main focus of this study is the effect of stressful fermentation conditions on two phospholipid species, phosphatidylcholine (PtdCho and phosphatidylethanolamine (PtdEtn, in Saccharomyces cerevisiae bottom-fermenting brewer’s yeast. For this purpose the content and fatty acid profile of these major classes of phospholipids have been compared, as well as their ratio in the whole cells of the starter culture, non-stressed yeast population, and the first three recycled yeast generations. The stressed yeast generations showed an increased mass fraction of PtdCho and a decreased mass fraction of PtdEtn, which led to an increased PtdCho/PtdEtn ratio in the recycled cells as compared to the non-stressed yeast culture. The most pronounced variation of PtdCho/PtdEtn ratio was found in the second yeast generation, yielding a 78 % increase with respect to the starter culture. Variations in the content of both, PtdCho and PtdEtn, were accompanied by a higher mass fraction of unsaturated fatty acids in both phospholipid species (palmitoleic acid in PtdCho, and palmitoleic and oleic in PtdEtn and by the increased ratio of C16/C18 acids in PtdCho. The results suggest that both phospholipid species, including their fatty acids, are highly involved in the adaptation of brewer’s yeast to stressful fermentation conditions.

  4. Some Practical Aspects of Sugar Fermentation by Baker's Yeast (Saccharomyces cerevisiae)

    Science.gov (United States)

    Freeland, P. W.

    1973-01-01

    Describes simple quantitative determinations for ethanol and carbon dioxide, together with techniques for examining the effects of a number of environmental factors on their production. The experimental work centers around the growth of a cell population of yeast, and is suitable for senior high school students. (JR)

  5. Drivers of waterfowl population dynamics: from teal to swans

    Science.gov (United States)

    Koons, David N.; Gunnarsson, Gunnar; Schmutz, Joel A.; Rotella, Jay J.

    2014-01-01

    Waterfowl are among the best studied and most extensively monitored species in the world. Given their global importance for sport and subsistence hunting, viewing and ecosystem functioning, great effort has been devoted since the middle part of the 20th century to understanding both the environmental and demographic mechanisms that influence waterfowl population and community dynamics. Here we use comparative approaches to summarise and contrast our understanding ofwaterfowl population dynamics across species as short-lived as the teal Anas discors and A.crecca to those such as the swans Cygnus sp. which have long life-spans. Specifically, we focus on population responses to vital rate perturbations across life history strategies, discuss bottom-up and top-down responses of waterfowlpopulations to global change, and summarise our current understanding of density dependence across waterfowl species. We close by identifying research needs and highlight ways to overcome the challenges of sustainably managing waterfowl populations in the 21st century.

  6. The Genomic Landscape and Evolutionary Resolution of Antagonistic Pleiotropy in Yeast

    Directory of Open Access Journals (Sweden)

    Wenfeng Qian

    2012-11-01

    Full Text Available Antagonistic pleiotropy (AP, or genetic tradeoff, is an important concept that is frequently invoked in theories of aging, cancer, genetic disease, and other common phenomena. However, the prevalence of AP, which genes are subject to AP, and to what extent and how AP may be resolved remain unclear. By measuring the fitness difference between the wild-type and null alleles of ∼5,000 nonessential genes in yeast, we found that in any given environment, yeast expresses hundreds of genes that harm rather than benefit the organism, demonstrating widespread AP. Nonetheless, under sufficient selection, AP is often resolvable through regulatory evolution, primarily by trans-acting changes, although in one case we also detected a cis-acting change and localized its causal mutation. However, AP is resolved more slowly in smaller populations, predicting more unresolved AP in multicellular organisms than in yeast. These findings provide an empirical foundation for AP-dependent theories and have broad biomedical and evolutionary implications.

  7. Not your ordinary yeast: non-Saccharomyces yeasts in wine production uncovered.

    Science.gov (United States)

    Jolly, Neil P; Varela, Cristian; Pretorius, Isak S

    2014-03-01

    Saccharomyces cerevisiae and grape juice are 'natural companions' and make a happy wine marriage. However, this relationship can be enriched by allowing 'wild' non-Saccharomyces yeast to participate in a sequential manner in the early phases of grape must fermentation. However, such a triangular relationship is complex and can only be taken to 'the next level' if there are no spoilage yeast present and if the 'wine yeast' - S. cerevisiae - is able to exert its dominance in time to successfully complete the alcoholic fermentation. Winemakers apply various 'matchmaking' strategies (e.g. cellar hygiene, pH, SO2 , temperature and nutrient management) to keep 'spoilers' (e.g. Dekkera bruxellensis) at bay, and allow 'compatible' wild yeast (e.g. Torulaspora delbrueckii, Pichia kluyveri, Lachancea thermotolerans and Candida/Metschnikowia pulcherrima) to harmonize with potent S. cerevisiae wine yeast and bring the best out in wine. Mismatching can lead to a 'two is company, three is a crowd' scenario. More than 40 of the 1500 known yeast species have been isolated from grape must. In this article, we review the specific flavour-active characteristics of those non-Saccharomyces species that might play a positive role in both spontaneous and inoculated wine ferments. We seek to present 'single-species' and 'multi-species' ferments in a new light and a new context, and we raise important questions about the direction of mixed-fermentation research to address market trends regarding so-called 'natural' wines. This review also highlights that, despite the fact that most frontier research and technological developments are often focussed primarily on S. cerevisiae, non-Saccharomyces research can benefit from the techniques and knowledge developed by research on the former. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  8. Cooperation guided by the coexistence of imitation dynamics and aspiration dynamics in structured populations

    Science.gov (United States)

    Xu, Kuangyi; Li, Kun; Cong, Rui; Wang, Long

    2017-02-01

    In the framework of the evolutionary game theory, two fundamentally different mechanisms, the imitation process and the aspiration-driven dynamics, can be adopted by players to update their strategies. In the former case, individuals imitate the strategy of a more successful peer, while in the latter case individuals change their strategies based on a comparison of payoffs they collect in the game to their own aspiration levels. Here we explore how cooperation evolves for the coexistence of these two dynamics. Intriguingly, cooperation reaches its lowest level when a certain moderate fraction of individuals pick aspiration-level-driven rule while the others choose pairwise comparison rule. Furthermore, when individuals can adjust their update rules besides their strategies, either imitation dynamics or aspiration-driven dynamics will finally take over the entire population, and the stationary cooperation level is determined by the outcome of competition between these two dynamics. We find that appropriate synergetic effects and moderate aspiration level boost the fixation probability of aspiration-driven dynamics most effectively. Our work may be helpful in understanding the cooperative behavior induced by the coexistence of imitation dynamics and aspiration dynamics in the society.

  9. Nectar sugars and bird visitation define a floral niche for basidiomycetous yeast on the Canary Islands.

    Science.gov (United States)

    Mittelbach, Moritz; Yurkov, Andrey M; Nocentini, Daniele; Nepi, Massimo; Weigend, Maximilian; Begerow, Dominik

    2015-02-01

    Studies on the diversity of yeasts in floral nectar were first carried out in the late 19th century. A narrow group of fermenting, osmophilous ascomycetes were regarded as exclusive specialists able to populate this unique and species poor environment. More recently, it became apparent that microorganisms might play an important role in the process of plant pollination. Despite the importance of these nectar dwelling yeasts, knowledge of the factors that drive their diversity and species composition is scarce. In this study, we linked the frequencies of yeast species in floral nectars from various host plants on the Canary Islands to nectar traits and flower visitors. We estimated the structuring impact of pollination syndromes (nectar volume, sugar concentration and sugar composition) on yeast diversity.The observed total yeast diversity was consistent with former studies, however, the present survey yielded additional basidiomycetous yeasts in unexpectedly high numbers. Our results show these basidiomycetes are significantly associated with ornithophilous flowers. Specialized ascomycetes inhabit sucrose-dominant nectars, but are surprisingly rare in nectar dominated by monosaccharides. There are two conclusions from this study: (i) a shift of floral visitors towards ornithophily alters the likelihood of yeast inoculation in flowers, and (ii) low concentrated hexose-dominant nectar promotes colonization of flowers by basidiomycetes. In the studied floral system, basidiomycete yeasts are acknowledged as regular members of nectar. This challenges the current understanding that nectar is an ecological niche solely occupied by ascomycetous yeasts.

  10. Missing cycles: Effect of climate change on population dynamics

    Indian Academy of Sciences (India)

    population dynamics of the larch budmoth – an insect pest which causes massive defoliation of entire larch forests ... hypothesized that global warming has led to the collapse of the cycles ... When temperatures increase after winter, and the.

  11. Impact of environmental colored noise in single-species population dynamics

    Science.gov (United States)

    Spanio, Tommaso; Hidalgo, Jorge; Muñoz, Miguel A.

    2017-10-01

    Variability on external conditions has important consequences for the dynamics and the organization of biological systems. In many cases, the characteristic timescale of environmental changes as well as their correlations play a fundamental role in the way living systems adapt and respond to it. A proper mathematical approach to understand population dynamics, thus, requires approaches more refined than, e.g., simple white-noise approximations. To shed further light onto this problem, in this paper we propose a unifying framework based on different analytical and numerical tools available to deal with "colored" environmental noise. In particular, we employ a "unified colored noise approximation" to map the original problem into an effective one with white noise, and then we apply a standard path integral approach to gain analytical understanding. For the sake of specificity, we present our approach using as a guideline a variation of the contact process—which can also be seen as a birth-death process of the Malthus-Verhulst class—where the propagation or birth rate varies stochastically in time. Our approach allows us to tackle in a systematic manner some of the relevant questions concerning population dynamics under environmental variability, such as determining the stationary population density, establishing the conditions under which a population may become extinct, and estimating extinction times. We focus on the emerging phase diagram and its possible phase transitions, underlying how these are affected by the presence of environmental noise time-correlations.

  12. Population dynamics of Aphis gossypii Glover and in sole and intercropping systems of cotton and cowpea.

    Science.gov (United States)

    Fernandes, Francisco S; Godoy, Wesley A C; Ramalho, Francisco S; Garcia, Adriano G; Santos, Bárbara D B; Malaquias, José B

    2018-01-01

    Population dynamics of aphids have been studied in sole and intercropping systems. These studies have required the use of more precise analytical tools in order to better understand patterns in quantitative data. Mathematical models are among the most important tools to explain the dynamics of insect populations. This study investigated the population dynamics of aphids Aphis gossypii and Aphis craccivora over time, using mathematical models composed of a set of differential equations as a helpful analytical tool to understand the population dynamics of aphids in arrangements of cotton and cowpea. The treatments were sole cotton, sole cowpea, and three arrangements of cotton intercropped with cowpea (t1, t2 and t3). The plants were infested with two aphid species and were evaluated at 7, 14, 28, 35, 42, and 49 days after the infestations. Mathematical models were used to fit the population dynamics of two aphid species. There were good fits for aphid dynamics by mathematical model over time. The highest population peak of both species A. gossypii and A. craccivora was found in the sole crops, and the lowest population peak was found in crop system t2. These results are important for integrated management programs of aphids in cotton and cowpea.

  13. Glycerol production by Oenococcus oeni during sequential and simultaneous cultures with wine yeast strains.

    Science.gov (United States)

    Ale, Cesar E; Farías, Marta E; Strasser de Saad, Ana M; Pasteris, Sergio E

    2014-07-01

    Growth and fermentation patterns of Saccharomyces cerevisiae, Kloeckera apiculata, and Oenococcus oeni strains cultured in grape juice medium were studied. In pure, sequential and simultaneous cultures, the strains reached the stationary growth phase between 2 and 3 days. Pure and mixed K. apiculata and S. cerevisiae cultures used mainly glucose, producing ethanol, organic acids, and 4.0 and 0.1 mM glycerol, respectively. In sequential cultures, O. oeni achieved about 1 log unit at 3 days using mainly fructose and L-malic acid. Highest sugars consumption was detected in K. apiculata supernatants, lactic acid being the major end-product. 8.0 mM glycerol was found in 6-day culture supernatants. In simultaneous cultures, total sugars and L-malic acid were used at 3 days and 98% of ethanol and glycerol were detected. This study represents the first report of the population dynamics and metabolic behavior of yeasts and O. oeni in sequential and simultaneous cultures and contributes to the selection of indigenous strains to design starter cultures for winemaking, also considering the inclusion of K. apiculata. The sequential inoculation of yeasts and O. oeni would enhance glycerol production, which confers desirable organoleptic characteristics to wines, while organic acids levels would not affect their sensory profile. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Characterization of volatile fraction of typical Irpinian wines fermented with a new starter yeast.

    Science.gov (United States)

    Calabretti, A; La Cara, F; Sorrentino, A; Di Stasio, M; Santomauro, F; Rastrelli, L; Gabrielli, L; Limone, F; Volpe, M G

    2012-04-01

    Non-Saccharomyces yeasts are microorganisms that play an important role in the fermentation dynamics, compositions and flavour of wine. The aromatic compounds responsible for varietal aroma in wine are mainly terpenes, of which the most important group are the monoterpenes because of their volatility and odour if present in a free form. In fact, some terpenyl-glycosides do not contribute to the aroma unless they are hydrolysed. The glycosylated form of terpenes can be converted by hydrolysis with β-glycosidases produced by yeasts during the winemaking process, into aromatic compounds. In this study we utilized a non-Saccharomyces yeast, with a high extra-cellular glycosidase activity, isolated from grapes of cultivars typical of Irpinia region. This strain, identified as a Rhodotorula mucillaginosa (strain WLR12), was used to carry out an experimental winemaking process and the results were compared with those obtained with a commercial yeast starter. Chemical and sensorial analysis demonstrated that the wines produced with WLR12 strain had a more floral aroma and some sweet and ripened fruit notes compared to those obtained with commercial yeast. The data also showed an increasing of the free terpenes fraction that, however, did not significatively modify the bouquet of the wines.

  15. Effect of yeast storage temperature and flour composition on fermentative activities of baker's yeast

    Directory of Open Access Journals (Sweden)

    Pejin Dušanka J.

    2009-01-01

    Full Text Available Baker's yeast is a set of living cells of Saccharomyces cerevisiae. It contains around 70-72% of water, 42-45% of proteins, around 40% of carbohydrates, around 7.5% of lipids (based on dry matter, and vitamin B-complex. On the basis of yeast cell analysis it can be concluded that yeast is a complex biological system which changes in time. The intensity of the changes depends on temperature. Yeast sample was stored at 4°C i 24°C for 12 days. During storage at 4°C, the content of total carbohydrates decreased from 48.81% to 37.50% (dry matter, whereas carbohydrate loss ranged from 40.81% to 29.28% at 24°C. The content of trehalose was 12.33% in the yeast sample stored at 4°C and 0.24% at 24°C. Loss of fermentative activity was 81.76% in the sample stored at 24°C for 12 days. The composition of five samples of 1st category flour was investigated. It was found that flours containing more reducing sugars and maltose enable higher fermentation activities. The flours with higher ash content (in the range 0.5-0.94% had higher contents of phytic acid. Higher ash and phytic contents in flour increased the yeast fermentative efficiency. In bakery industry, a range of ingredients has been applied to improve the product's quality such as surface active substances (emulsifiers, enzymes, sugars and fats. In the paper, the effect of some ingredients added to dough (margarine, saccharose, sodium chloride and malted barley on the yeast fermentative activity was studied. The mentioned ingredients were added to dough at different doses: 0.5, 1.0, 1.5 and 2.0%, flour basis. It was found that the investigated ingredients affected the fermentative activity of yeast and improved the bread quality.

  16. Nonlinear dynamics in a business-cycle model with logistic population growth

    International Nuclear Information System (INIS)

    Brianzoni, Serena; Mammana, Cristiana; Michetti, Elisabetta

    2009-01-01

    We consider a discrete-time growth model of the Solow type where workers and shareholders have different but constant saving rates and the population growth dynamics is described by the logistic equation able to exhibit complicated dynamics. We show conditions for the resulting system having a compact global attractor and we describe its structure. We also perform a mainly numerical analysis using the critical lines method able to describe the strange attractor and the absorbing area, in order to show how cyclical or complex fluctuations may be produced in a business-cycle model. We study the dynamic behaviour of the model under different ranges of the main parameters, i.e. the elasticity of substitution between the two production factors and the one in the logistic equation (namely μ). We prove the existence of complex dynamics when the elasticity of substitution between production factors drops below one (so that capital income declines) or μ increases (so that the amplitude of movements in the population growth rate increases).

  17. Emergent Patterns of Diversity and Dynamics in Natural Populations of Planktonic Vibrio Bacteria

    Science.gov (United States)

    2005-06-01

    1973. Ecology of Vibrio parahemolyticus in mixed-template amplifications: formation, consequences and elimination by Chesapeake Bay. J. Bacteriol. 113...Science 1930 and Engineering DOCTORAL DISSERTATION Emergent Patterns of Diversity and Dynamics in Natural Populations of Planktonic Vibrio Bacteria by...DYNAMICS IN NATURAL POPULATIONS OF PLANKTONIC VIBRIO BACTERIA by Janelle Ren6e Thompson B.S. Biological Sciences, Stanford University 1998 M.S

  18. Growth of Nile tilapia Oreochromis niloticus fed with different levels of alcohol yeast.

    Science.gov (United States)

    Medri, V; Pereira, G V; Leonhardt, J H

    2000-02-01

    Two hundred and forty 45-day-old fingerlings of Nile tilapia (Oreochromis niloticus), sexually reverted with an initial average weight of 1.25 +/- 0.14 g, distributed in a totally casualized delineation, during 330 days. The effect of the substitution of 10%, 20% and 30% of the ration by distillery yeast (Saccharomiyces cerevisae) in balanced experimental rations on the development in the breeding of tilapias did not show a harmful effect up to the maximum tested level of 30%, showing that the choice of the yeast in the ration for these fishes depends on the availability and occasional cost. The yeast provides fish with good resistance to unfavorable environmental conditions, which could be verified since there were no statistical differences among the treatments with different levels of yeast and the witness. The long growth rate in terms of length and weight can be attributed to the little available space for each specimen, not obeying the limit of populational density, as well as reduction of food ingestion, which coincide with the winter season, above of the absence of natural feeding.

  19. Yeast strains and methods of use thereof

    OpenAIRE

    Goddard, Matthew Robert; Gardner, Richard Clague; Anfang, Nicole

    2013-01-01

    The present invention relates to yeast strains and, in particular, to yeast stains for use in fermentation processes. The invention also relates to methods of fermentation using the yeast strains of the invention either alone or in combination with other yeast strains. The invention thither relates to methods for the selection of yeast strains suitable for fermentation cultures by screening for various metabolic products and the use of specific nutrient sources.

  20. Demography of the Early Neolithic Population in Central Balkans: Population Dynamics Reconstruction Using Summed Radiocarbon Probability Distributions.

    Directory of Open Access Journals (Sweden)

    Marko Porčić

    Full Text Available The Central Balkans region is of great importance for understanding the spread of the Neolithic in Europe but the Early Neolithic population dynamics of the region is unknown. In this study we apply the method of summed calibrated probability distributions to a set of published radiocarbon dates from the Republic of Serbia in order to reconstruct population dynamics in the Early Neolithic in this part of the Central Balkans. The results indicate that there was a significant population growth after ~6200 calBC, when the Neolithic was introduced into the region, followed by a bust at the end of the Early Neolithic phase (~5400 calBC. These results are broadly consistent with the predictions of the Neolithic Demographic Transition theory and the patterns of population booms and busts detected in other regions of Europe. These results suggest that the cultural process that underlies the patterns observed in Central and Western Europe was also in operation in the Central Balkan Neolithic and that the population increase component of this process can be considered as an important factor for the spread of the Neolithic as envisioned in the demic diffusion hypothesis.

  1. Evolution of the hemiascomycete yeasts: on life styles and the importance of inbreeding.

    Science.gov (United States)

    Knop, Michael

    2006-07-01

    The term 'breeding system' is used to describe the morphological and behavioural aspects of the sexual life cycle of a species. The yeast breeding system provides three alternatives that enable hapoids to return to the diploid state that is necessary for meiosis: mating of unrelated haploids (amphimixis), mating between spores from the same tetrad (intratetrad mating, automixis) and mother daughter mating upon mating type switching (haplo-selfing). The frequency of specific mating events affects the level of heterozygosity present in individuals and the genetic diversity of populations. This review discusses the reproductive strategies of yeasts, in particular S. cerevisiae (Bakers' or budding yeast). Emphasis is put on intratetrad mating, its implication for diversity, and how the particular genome structure could have evolved to ensure the preservation of a high degree of heterozygosity in conjunction with frequent intratetrad matings. I also discuss how the ability of yeast to control the number of spores that are formed accounts for high intratetrad mating rates and for enhanced transmission of genomic variation. I extend the discussion to natural genetic variation and propose that a high level of plasticity is inherent in the yeast breeding system, which may allow variation of the breeding behaviour in accordance with the needs imposed by the environment. (c) 2006 Wiley Periodicals, Inc.

  2. Immunologic proof of DNS irradiation damages and their repair in stationary yeast cells

    International Nuclear Information System (INIS)

    Waller, H.

    1980-08-01

    In rabbits an antiserum was produced by injecting UV-irradiated denaturated calf-thymus DNS; after inhibiting unspecific bindings, a specific serological reaction with UV-induced irradiation damages could be taken as present in this antiserum. By the ammonium sulphate precipitation as immunologic method of detection, after UV-irradiation the genesis of damages at certain sites in the DNS of different yeast lineages and their repair was observed. The elemination of UV-induced DNS damages was observed after an incubation in a nutrien medium, after photo-reactivation and after combining both therapeutic treatments. The following results were obtained: the detected DNS damage (number of induced dimeres/yeast genomes) had the same degree in the four yeast lineages. Apart from the excision-negative mutante 2094 for all yeast lineages a repair efficiency of 60% could be detected. All yeast lineages presented themselves as photographically to be reactivated; however, in all cases a DNS damage of 40 to 50% remained. The examinations for the specificity of antiserum against roentgenologically irradiated DNS led to the conclusion that the antibody population of the serum consisted mainly of immunoglobulines against unchanged DNS areas. A specific immunological reaction of only about 10% could be achieved. (orig./MG) [de

  3. Yeast as a system for modeling mitochondrial disease mechanisms and discovering therapies

    Directory of Open Access Journals (Sweden)

    Jean-Paul Lasserre

    2015-06-01

    Full Text Available Mitochondrial diseases are severe and largely untreatable. Owing to the many essential processes carried out by mitochondria and the complex cellular systems that support these processes, these diseases are diverse, pleiotropic, and challenging to study. Much of our current understanding of mitochondrial function and dysfunction comes from studies in the baker's yeast Saccharomyces cerevisiae. Because of its good fermenting capacity, S. cerevisiae can survive mutations that inactivate oxidative phosphorylation, has the ability to tolerate the complete loss of mitochondrial DNA (a property referred to as ‘petite-positivity’, and is amenable to mitochondrial and nuclear genome manipulation. These attributes make it an excellent model system for studying and resolving the molecular basis of numerous mitochondrial diseases. Here, we review the invaluable insights this model organism has yielded about diseases caused by mitochondrial dysfunction, which ranges from primary defects in oxidative phosphorylation to metabolic disorders, as well as dysfunctions in maintaining the genome or in the dynamics of mitochondria. Owing to the high level of functional conservation between yeast and human mitochondrial genes, several yeast species have been instrumental in revealing the molecular mechanisms of pathogenic human mitochondrial gene mutations. Importantly, such insights have pointed to potential therapeutic targets, as have genetic and chemical screens using yeast.

  4. Immobilization of yeast cells by radiation-induced polymerization

    International Nuclear Information System (INIS)

    Fujimura, T.; Kaetsu, I.

    1982-01-01

    Radiation-induced polymerization method was applied to the immobilization of yeast cells. The effects of irradiation, cooling and monomer, which are neccessary for polymerization, were recovered completely by subsequent aerobical incubation of yeast cells. The ethanol productive in immobilized yeast cells increased with the increase of aerobical incubation period. The growth of yeast cells in immobilized yeast cells was indicated. The maximum ethanol productivity in immobilized yeast cell system was around three times as much as that in free yeast cell system. (orig.)

  5. Evolutionary History of Ascomyceteous Yeasts

    Energy Technology Data Exchange (ETDEWEB)

    Haridas, Sajeet; Riley, Robert; Salamov, Asaf; Goker, Markus; Klenk, Hans-Peter; Kurtzman, Cletus P.; Blackwell, Meredith; Grigoriev, Igor; Jeffries, Thomas W.

    2014-06-06

    Yeasts are important for many industrial and biotechnological processes and show remarkable diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphrinomycotina. A comparison of these with several other previously published yeast genomes have added increased confidence to the phylogenetic positions of previously poorly placed species including Saitoella complicata, Babjeviella inositovora and Metschnikowia bicuspidata. Phylogenetic analysis also showed that yeasts with alternative nuclear codon usage where CUG encodes serine instead of leucine are monophyletic within the Saccharomycotina. Most of the yeasts have compact genomes with a large fraction of single exon genes with Lipomyces starkeyi and the previously published Pneumocystis jirovecii being notable exceptions. Intron analysis suggests that early diverging species have more introns. We also observed a large number of unclassified lineage specific non-simple repeats in these genomes.

  6. Population ecology, nonlinear dynamics, and social evolution. I. Associations among nonrelatives.

    Science.gov (United States)

    Avilés, Leticia; Abbot, Patrick; Cutter, Asher D

    2002-02-01

    Using an individual-based and genetically explicit simulation model, we explore the evolution of sociality within a population-ecology and nonlinear-dynamics framework. Assuming that individual fitness is a unimodal function of group size and that cooperation may carry a relative fitness cost, we consider the evolution of one-generation breeding associations among nonrelatives. We explore how parameters such as the intrinsic rate of growth and group and global carrying capacities may influence social evolution and how social evolution may, in turn, influence and be influenced by emerging group-level and population-wide dynamics. We find that group living and cooperation evolve under a wide range of parameter values, even when cooperation is costly and the interactions can be defined as altruistic. Greater levels of cooperation, however, did evolve when cooperation carried a low or no relative fitness cost. Larger group carrying capacities allowed the evolution of larger groups but also resulted in lower cooperative tendencies. When the intrinsic rate of growth was not too small and control of the global population size was density dependent, the evolution of large cooperative tendencies resulted in dynamically unstable groups and populations. These results are consistent with the existence and typical group sizes of organisms ranging from the pleometrotic ants to the colonial birds and the global population outbreaks and crashes characteristic of organisms such as the migratory locusts and the tree-killing bark beetles.

  7. Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

    Science.gov (United States)

    Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

    2012-01-01

    Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

  8. Climate Effects and Feedback Structure Determining Weed Population Dynamics in a Long-Term Experiment

    Science.gov (United States)

    Lima, Mauricio; Navarrete, Luis; González-Andujar, José Luis

    2012-01-01

    Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years) on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors). Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements. PMID:22272362

  9. Climate effects and feedback structure determining weed population dynamics in a long-term experiment.

    Directory of Open Access Journals (Sweden)

    Mauricio Lima

    Full Text Available Pest control is one of the areas in which population dynamic theory has been successfully applied to solve practical problems. However, the links between population dynamic theory and model construction have been less emphasized in the management and control of weed populations. Most management models of weed population dynamics have emphasized the role of the endogenous process, but the role of exogenous variables such as climate have been ignored in the study of weed populations and their management. Here, we use long-term data (22 years on two annual weed species from a locality in Central Spain to determine the importance of endogenous and exogenous processes (local and large-scale climate factors. Our modeling study determined two different feedback structures and climate effects in the two weed species analyzed. While Descurainia sophia exhibited a second-order feedback and low climate influence, Veronica hederifolia was characterized by a first-order feedback structure and important effects from temperature and rainfall. Our results strongly suggest the importance of theoretical population dynamics in understanding plant population systems. Moreover, the use of this approach, discerning between the effect of exogenous and endogenous factors, can be fundamental to applying weed management practices in agricultural systems and to controlling invasive weedy species. This is a radical change from most approaches currently used to guide weed and invasive weedy species managements.

  10. Yeast Colonies: A Model for Studies of Aging, Environmental Adaptation, and Longevity

    OpenAIRE

    Libuše Váchová; Michal Čáp; Zdena Palková

    2012-01-01

    When growing on solid surfaces, yeast, like other microorganisms, develops organized multicellular populations (colonies and biofilms) that are composed of differentiated cells with specialized functions. Life within these populations is a prevalent form of microbial existence in natural settings that provides the cells with capabilities to effectively defend against environmental attacks as well as efficiently adapt and survive long periods of starvation and other stresses. Under such circum...

  11. Modelling of population dynamics of red king crab using Bayesian approach

    Directory of Open Access Journals (Sweden)

    Bakanev Sergey ...

    2012-10-01

    Modeling population dynamics based on the Bayesian approach enables to successfully resolve the above issues. The integration of the data from various studies into a unified model based on Bayesian parameter estimation method provides a much more detailed description of the processes occurring in the population.

  12. Sexual differentiation in fission yeast

    DEFF Research Database (Denmark)

    Egel, R; Nielsen, O; Weilguny, D

    1990-01-01

    The regulation of sexual reproduction in yeast constitutes the highest level of differentiation observed in these unicellular organisms. The various ramifications of this system involve DNA rearrangement, transcriptional control, post-translational modification (such as protein phosphorylation) a......) and receptor/signal processing. A few basic similarities are common to both fission and budding yeasts. The wiring of the regulatory circuitry, however, varies considerably between these divergent yeast groups....

  13. Elevated nonlinearity as an indicator of shifts in the dynamics of populations under stress.

    Science.gov (United States)

    Dakos, Vasilis; Glaser, Sarah M; Hsieh, Chih-Hao; Sugihara, George

    2017-03-01

    Populations occasionally experience abrupt changes, such as local extinctions, strong declines in abundance or transitions from stable dynamics to strongly irregular fluctuations. Although most of these changes have important ecological and at times economic implications, they remain notoriously difficult to detect in advance. Here, we study changes in the stability of populations under stress across a variety of transitions. Using a Ricker-type model, we simulate shifts from stable point equilibrium dynamics to cyclic and irregular boom-bust oscillations as well as abrupt shifts between alternative attractors. Our aim is to infer the loss of population stability before such shifts based on changes in nonlinearity of population dynamics. We measure nonlinearity by comparing forecast performance between linear and nonlinear models fitted on reconstructed attractors directly from observed time series. We compare nonlinearity to other suggested leading indicators of instability (variance and autocorrelation). We find that nonlinearity and variance increase in a similar way prior to the shifts. By contrast, autocorrelation is strongly affected by oscillations. Finally, we test these theoretical patterns in datasets of fisheries populations. Our results suggest that elevated nonlinearity could be used as an additional indicator to infer changes in the dynamics of populations under stress. © 2017 The Author(s).

  14. Collective dynamics of populations of weakly correlated filaments of incoherent white light

    International Nuclear Information System (INIS)

    Guo, Jinxin; Sheridan, John T; Saravanamuttu, Kalaichelvi

    2013-01-01

    We examined the dynamics of two populations of self-trapped filaments of spatially and temporally incoherent white light. The populations consisted of (i) independent filaments generated through self-trapping of incandescent speckles, and (ii) co-dependent filaments created through modulation instability of a broad incandescent beam. Both filament populations were positionally stable in conditions where individual pairs of self-trapped beams interact strongly. Both also acquired significantly broad intensity distributions, which were independent of their parent optical fields; a small but persistent number of high-intensity filaments was identified in both cases. These studies provide accessible routes to weakly correlated ensembles, insight into their collective behaviour such as self-stabilization and self-selected intensity distributions, and reveal intriguing similarities between the dynamics of two populations of different origins. (paper)

  15. Application of System Dynamics Methodology in Population Analysis

    Directory of Open Access Journals (Sweden)

    August Turina

    2009-09-01

    Full Text Available The goal of this work is to present the application of system dynamics and system thinking, as well as the advantages and possible defects of this analytic approach, in order to improve the analysis of complex systems such as population and, thereby, to monitor more effectively the underlying causes of migrations. This methodology has long been present in interdisciplinary scientific circles, but its scientific contribution has not been sufficiently applied in analysis practice in Croatia. Namely, the major part of system analysis is focused on detailed complexity rather than on dynamic complexity. Generally, the science of complexity deals with emergence, innovation, learning and adaptation. Complexity is viewed according to the number of system components, or through a number of combinations that must be continually analyzed in order to understand and consequently provide adequate decisions. Simulations containing thousands of variables and complex arrays of details distract overall attention from the basic cause patterns and key inter-relations emerging and prevailing within an analyzed population. Systems thinking offers a holistic and integral perspective for observation of the world.

  16. Chaos and order in stateless societies: Intercommunity exchange as a factor impacting the population dynamical patterns

    International Nuclear Information System (INIS)

    Medvinsky, Alexander B.; Rusakov, Alexey V.

    2011-01-01

    Highlights: → We model community dynamics in stateless societies. → Intercommunity barter is shown to be a factor impacting the societies dynamics. → Increase in the human population growth rate can lead to appearance of chaos. → Secular and millennial cycles are found to arise as a result of the barter. - Abstract: The once abstract notions of dynamical chaos now appear naturally in various systems [Kaplan D, Glass L. Understanding nonlinear dynamics. New York: Springer; 1995]. As a result, future trajectories of the systems may be difficult to predict. In this paper, we demonstrate the appearance of chaotic dynamics in model human communities, which consist of producers of agricultural product and producers of agricultural equipment. In the case of a solitary community, the horizon of predictability of the human population dynamics is shown to be dependent on both intrinsic instability of the dynamics and the chaotic attractor sizes. Since a separate community is usually a part of a larger commonality, we study the dynamics of social systems consisting of two interacting communities. We show that intercommunity barter can lead to stabilization of the dynamics in one of the communities, which implies persistence of stable equilibrium under changes of the maximum value of the human population growth rate. However, in the neighboring community, the equilibrium turns into a stable limit cycle as the maximum value of the human population growth rate increases. Following an increase in the maximum value of the human population growth rate leads to period-doubling bifurcations resulting in chaotic dynamics. The horizon of predictability of the chaotic oscillations is found to be limited by 5 years. We demonstrate that the intercommunity interaction can lead to the appearance of long-period harmonics in the chaotic time series. The period of the harmonics is of order 100 and 1000 years. Hence the long-period changes in the population size may be considered as an

  17. Chaos and order in stateless societies: Intercommunity exchange as a factor impacting the population dynamical patterns

    Energy Technology Data Exchange (ETDEWEB)

    Medvinsky, Alexander B., E-mail: medvinsky@iteb.ru [Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Moscow Region (Russian Federation); Rusakov, Alexey V. [Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Moscow Region (Russian Federation)

    2011-06-15

    Highlights: > We model community dynamics in stateless societies. > Intercommunity barter is shown to be a factor impacting the societies dynamics. > Increase in the human population growth rate can lead to appearance of chaos. > Secular and millennial cycles are found to arise as a result of the barter. - Abstract: The once abstract notions of dynamical chaos now appear naturally in various systems [Kaplan D, Glass L. Understanding nonlinear dynamics. New York: Springer; 1995]. As a result, future trajectories of the systems may be difficult to predict. In this paper, we demonstrate the appearance of chaotic dynamics in model human communities, which consist of producers of agricultural product and producers of agricultural equipment. In the case of a solitary community, the horizon of predictability of the human population dynamics is shown to be dependent on both intrinsic instability of the dynamics and the chaotic attractor sizes. Since a separate community is usually a part of a larger commonality, we study the dynamics of social systems consisting of two interacting communities. We show that intercommunity barter can lead to stabilization of the dynamics in one of the communities, which implies persistence of stable equilibrium under changes of the maximum value of the human population growth rate. However, in the neighboring community, the equilibrium turns into a stable limit cycle as the maximum value of the human population growth rate increases. Following an increase in the maximum value of the human population growth rate leads to period-doubling bifurcations resulting in chaotic dynamics. The horizon of predictability of the chaotic oscillations is found to be limited by 5 years. We demonstrate that the intercommunity interaction can lead to the appearance of long-period harmonics in the chaotic time series. The period of the harmonics is of order 100 and 1000 years. Hence the long-period changes in the population size may be considered as an

  18. Biomedical applications of yeast- a patent view, part one: yeasts as workhorses for the production of therapeutics and vaccines.

    Science.gov (United States)

    Roohvand, Farzin; Shokri, Mehdi; Abdollahpour-Alitappeh, Meghdad; Ehsani, Parastoo

    2017-08-01

    Yeasts, as Eukaryotes, offer unique features for ease of growth and genetic manipulation possibilities, making it an exceptional microbial host. Areas covered: This review provides general and patent-oriented insights into production of biopharmaceuticals by yeasts. Patents, wherever possible, were correlated to the original or review articles. The review describes applications of major GRAS (generally regarded as safe) yeasts for the production of therapeutic proteins and subunit vaccines; additionally, immunomodulatory properties of yeast cell wall components were reviewed for use of whole yeast cells as a new vaccine platform. The second part of the review will discuss yeast- humanization strategies and innovative applications. Expert opinion: Biomedical applications of yeasts were initiated by utilization of Saccharomyces cerevisiae, for production of leavened (fermented) products, and advanced to serve to produce biopharmaceuticals. Higher biomass production and expression/secretion yields, more similarity of glycosylation patterns to mammals and possibility of host-improvement strategies through application of synthetic biology might enhance selection of Pichia pastoris (instead of S. cerevisiae) as a host for production of biopharmaceutical in future. Immunomodulatory properties of yeast cell wall β-glucans and possibility of intracellular expression of heterologous pathogen/tumor antigens in yeast cells have expanded their application as a new platform, 'Whole Yeast Vaccines'.

  19. Metastable states and quasicycles in a stochastic Wilson-Cowan model of neuronal population dynamics

    KAUST Repository

    Bressloff, Paul C.

    2010-11-03

    We analyze a stochastic model of neuronal population dynamics with intrinsic noise. In the thermodynamic limit N→∞, where N determines the size of each population, the dynamics is described by deterministic Wilson-Cowan equations. On the other hand, for finite N the dynamics is described by a master equation that determines the probability of spiking activity within each population. We first consider a single excitatory population that exhibits bistability in the deterministic limit. The steady-state probability distribution of the stochastic network has maxima at points corresponding to the stable fixed points of the deterministic network; the relative weighting of the two maxima depends on the system size. For large but finite N, we calculate the exponentially small rate of noise-induced transitions between the resulting metastable states using a Wentzel-Kramers- Brillouin (WKB) approximation and matched asymptotic expansions. We then consider a two-population excitatory or inhibitory network that supports limit cycle oscillations. Using a diffusion approximation, we reduce the dynamics to a neural Langevin equation, and show how the intrinsic noise amplifies subthreshold oscillations (quasicycles). © 2010 The American Physical Society.

  20. Strategy for the extraction of yeast DNA from artisan agave must for quantitative PCR analysis.

    Science.gov (United States)

    Kirchmayr, Manuel Reinhart; Segura-Garcia, Luis Eduardo; Flores-Berrios, Ericka Patricia; Gschaedler, Anne

    2011-11-01

    An efficient method for the direct extraction of yeast genomic DNA from agave must was developed. The optimized protocol, which was based on silica-adsorption of DNA on microcolumns, included an enzymatic cell wall degradation step followed by prolonged lysis with hot detergent. The resulting extracts were suitable templates for subsequent qPCR assays that quantified mixed yeast populations in artisan Mexican mezcal fermentations. Copyright © 2011 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  1. Virgin olive oil yeasts: A review.

    Science.gov (United States)

    Ciafardini, Gino; Zullo, Biagi Angelo

    2018-04-01

    This review summarizes current knowledge on virgin olive oil yeasts. Newly produced olive oil contains solid particles and micro drops of vegetation water in which yeasts reproduce to become the typical microbiota of olive oil. To date, about seventeen yeast species have been isolated from different types of olive oils and their by-products, of which six species have been identified as new species. Certain yeast species contribute greatly to improving the sensorial characteristics of the newly produced olive oil, whereas other species are considered harmful as they can damage the oil quality through the production of unpleasant flavors and triacylglycerol hydrolysis. Studies carried out in certain yeast strains have demonstrated the presence of defects in olive oil treated with Candida adriatica, Nakazawaea wickerhamii and Candida diddensiae specific strains, while other olive oil samples treated with other Candida diddensiae strains were defect-free after four months of storage and categorized as extra virgin. A new acetic acid producing yeast species, namely, Brettanomyces acidodurans sp. nov., which was recently isolated from olive oil, could be implicated in the wine-vinegary defect of the product. Other aspects related to the activity of the lipase-producing yeasts and the survival of the yeast species in the flavored olive oils are also discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Population dynamics in the high Arctic: Climate variations in time and space

    DEFF Research Database (Denmark)

    Hendrichsen, Ditte Katrine

    Climatic factors profoundly influence the population dynamics, species interactions and demography of Arctic species. Analyses of the spatio-temporal dynamics within and across species are therefore necessary to understand and predict the responses of Arctic ecosystems to climatic variability...

  3. Seasonal population dynamics of Brachyiulus jawlowskii (Diplopoda, Julidae in the Dnieper river arena

    Directory of Open Access Journals (Sweden)

    N. G. Gudym

    2016-06-01

    Full Text Available We have researched the population dynamics of Brachyiulus jawlowskii Lohmander, 1928 in the arena of the Dnepr river (within the "Dnieper-Orilsky” Nature Reserve and also present a full picture of the habitat distribution of Julidae within the researched area. The tested models were basic types of arena biogeocenosis: sand steppe, black maple forests, artificial pine plantations, deciduous forest, meadow and swamp. Variation in population density of B. jawlowskii is determined by biotopical features. The swamp and meadow habitats can be characterized by the highest level of population dynamics. B. jawlowskii plays the greatest role in the herpetobiont grouping in swamp and oak forest habitats (6.7% and 4.6% respectively. In other types of habitat this species composes 0.1–3.5% of the total abundance of this group. The highest abundance dynamic was reached by the Julidae cenopopulations which inhabit the swamp, oak forest and meadow habitats. B. jawlowskii occupies a relatively significant share in the herpetobiont communities of these habitats. Thus, the indicators of absolute number of this species and its relative participation in the herpertobiont grouping indicate the preference of this species for marsh, oak forest and meadow habitats. These habitats can be characterized by an excessive or moderate level of edaphotopic humidification. The ecosystem of the steppe zone of Ukraine is subject to significant human impact. In nature reserves, this effect is minimized, which permits research to be conducted on regimes of natural population dynamics. We established that B. jawlowskii inhabits all habitats investigated within the arena zone of the Dnepr river. This indicates that this is an environmentally flexible Julidae species. The population dynamics of B. jawlowskii can be characterized by three distinct periods: spring-summer, summer and autumn. Each of these periods is characterized by a distinct population dynamic, but throughout the

  4. Terroir of yeasts? – Application of FTIR spectroscopy and molecular methods for strain typing of yeasts

    Directory of Open Access Journals (Sweden)

    Gerhards Daniel

    2015-01-01

    Full Text Available The site specific influence on wine (Terroir is an often by wine producers, consumers and scientists discussed topic in the world of wine. A study on grapes and (spontaneous fermentations from six different vineyards was done to investigate the biodiversity of yeasts and to answer the question if there is a terroir of yeast and how it could be influenced. Randomly isolated yeasts were identified by FTIR-spectroscopy and molecular methods on species and strain level. Vineyard specific yeast floras would be observed but they are not such important as expected. Only a few overlapping strain patterns would be identified during both vintages. The yeast flora of the winery had a huge impact on the spontaneous fermentations, but is not really constant and influenced by different factors from outside.

  5. Dynamic analysis of a parasite population model

    Science.gov (United States)

    Sibona, G. J.; Condat, C. A.

    2002-03-01

    We study the dynamics of a model that describes the competitive interaction between an invading species (a parasite) and its antibodies in an living being. This model was recently used to examine the dynamical competition between Tripanosoma cruzi and its antibodies during the acute phase of Chagas' disease. Depending on the antibody properties, the model yields three types of outcomes, corresponding, respectively, to healing, chronic disease, and host death. Here, we study the dynamics of the parasite-antibody interaction with the help of simulations, obtaining phase trajectories and phase diagrams for the system. We show that, under certain conditions, the size of the parasite inoculation can be crucial for the infection outcome and that a retardation in the stimulated production of an antibody species may result in the parasite gaining a definitive advantage. We also find a criterion for the relative sizes of the parameters that are required if parasite-generated decoys are indeed to help the invasion. Decoys may also induce a qualitatively different outcome: a limit cycle for the antibody-parasite population phase trajectories.

  6. 21 CFR 184.1983 - Bakers yeast extract.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Bakers yeast extract. 184.1983 Section 184.1983... Listing of Specific Substances Affirmed as GRAS § 184.1983 Bakers yeast extract. (a) Bakers yeast extract... a selected strain of yeast, Saccharomyces cerevisiae. It may be concentrated or dried. (b) The...

  7. Endoplasmic reticulum involvement in yeast cell death

    International Nuclear Information System (INIS)

    Nicanor Austriaco, O.

    2012-01-01

    Yeast cells undergo programed cell death (PCD) with characteristic markers associated with apoptosis in mammalian cells including chromatin breakage, nuclear fragmentation, reactive oxygen species generation, and metacaspase activation. Though significant research has focused on mitochondrial involvement in this phenomenon, more recent work with both Saccharomyces cerevisiae and Schizosaccharomyces pombe has also implicated the endoplasmic reticulum (ER) in yeast PCD. This minireview provides an overview of ER stress-associated cell death (ER-SAD) in yeast. It begins with a description of ER structure and function in yeast before moving to a discussion of ER-SAD in both mammalian and yeast cells. Three examples of yeast cell death associated with the ER will be highlighted here including inositol starvation, lipid toxicity, and the inhibition of N-glycosylation. It closes by suggesting ways to further examine the involvement of the ER in yeast cell death.

  8. History of genome editing in yeast.

    Science.gov (United States)

    Fraczek, Marcin G; Naseeb, Samina; Delneri, Daniela

    2018-05-01

    For thousands of years humans have used the budding yeast Saccharomyces cerevisiae for the production of bread and alcohol; however, in the last 30-40 years our understanding of the yeast biology has dramatically increased, enabling us to modify its genome. Although S. cerevisiae has been the main focus of many research groups, other non-conventional yeasts have also been studied and exploited for biotechnological purposes. Our experiments and knowledge have evolved from recombination to high-throughput PCR-based transformations to highly accurate CRISPR methods in order to alter yeast traits for either research or industrial purposes. Since the release of the genome sequence of S. cerevisiae in 1996, the precise and targeted genome editing has increased significantly. In this 'Budding topic' we discuss the significant developments of genome editing in yeast, mainly focusing on Cre-loxP mediated recombination, delitto perfetto and CRISPR/Cas. © 2018 The Authors. Yeast published by John Wiley & Sons, Ltd.

  9. 21 CFR 172.898 - Bakers yeast glycan.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Bakers yeast glycan. 172.898 Section 172.898 Food... Multipurpose Additives § 172.898 Bakers yeast glycan. Bakers yeast glycan may be safely used in food in accordance with the following conditions: (a) Bakers yeast glycan is the comminuted, washed, pasteurized, and...

  10. Noise-induced effects in population dynamics

    Science.gov (United States)

    Spagnolo, Bernardo; Cirone, Markus; La Barbera, Antonino; de Pasquale, Ferdinando

    2002-03-01

    We investigate the role of noise in the nonlinear relaxation of two ecosystems described by generalized Lotka-Volterra equations in the presence of multiplicative noise. Specifically we study two cases: (i) an ecosystem with two interacting species in the presence of periodic driving; (ii) an ecosystem with a great number of interacting species with random interaction matrix. We analyse the interplay between noise and periodic modulation for case (i) and the role of the noise in the transient dynamics of the ecosystem in the presence of an absorbing barrier in case (ii). We find that the presence of noise is responsible for the generation of temporal oscillations and for the appearance of spatial patterns in the first case. In the other case we obtain the asymptotic behaviour of the time average of the ith population and discuss the effect of the noise on the probability distributions of the population and of the local field.

  11. The wine and beer yeast Dekkera bruxellensis.

    Science.gov (United States)

    Schifferdecker, Anna Judith; Dashko, Sofia; Ishchuk, Olena P; Piškur, Jure

    2014-09-01

    Recently, the non-conventional yeast Dekkera bruxellensis has been gaining more and more attention in the food industry and academic research. This yeast species is a distant relative of Saccharomyces cerevisiae and is especially known for two important characteristics: on the one hand, it is considered to be one of the main spoilage organisms in the wine and bioethanol industry; on the other hand, it is 'indispensable' as a contributor to the flavour profile of Belgium lambic and gueuze beers. Additionally, it adds to the characteristic aromatic properties of some red wines. Recently this yeast has also become a model for the study of yeast evolution. In this review we focus on the recently developed molecular and genetic tools, such as complete genome sequencing and transformation, to study and manipulate this yeast. We also focus on the areas that are particularly well explored in this yeast, such as the synthesis of off-flavours, yeast detection methods, carbon metabolism and evolutionary history. © 2014 The Authors. Yeast published by John Wiley & Sons, Ltd.

  12. Effects of Peanut-Tobacco Rotations on Population Dynamics of Meloidogyne arenaria in Mixed Race Populations

    OpenAIRE

    Hirunsalee, Anan; Barker, K. R.; Beute, M. K.

    1995-01-01

    A 3-year microplot study was initiated to characterize the population dynamics, reproduction potential, and survivorship of single or mixed populations of Meloidogyne arenaria race 1 (Ma1) and race 2 (Ma2), as affected by crop rotations of peanut 'Florigiant' and M. incognita races 1 and 3-resistant 'McNair 373' and susceptible 'Coker 371-Gold' tobacco. Infection, reproduction, and root damage by Ma2 on peanut and by Ma1 on resistant tobacco were limited in the first year. Infection, reproduc...

  13. Genomic and Phenotypic Characterization of Yeast Biosensor for Deep-space Radiation

    Science.gov (United States)

    Marina, Diana B.; Santa Maria, Sergio; Bhattacharya, Sharmila

    2016-01-01

    The BioSentinel mission was selected to launch as a secondary payload onboard NASA Exploration Mission 1 (EM-1) in 2018. In BioSentinel, the budding yeast Saccharomyces cerevisiae will be used as a biosensor to measure the long-term impact of deep-space radiation to living organisms. In the 4U-payload, desiccated yeast cells from different strains will be stored inside microfluidic cards equipped with 3-color LED optical detection system to monitor cell growth and metabolic activity. At different times throughout the 12-month mission, these cards will be filled with liquid yeast growth media to rehydrate and grow the desiccated cells. The growth and metabolic rates of wild-type and radiation-sensitive strains in deep-space radiation environment will be compared to the rates measured in the ground- and microgravity-control units. These rates will also be correlated with measurements obtained from onboard physical dosimeters. In our preliminary long-term desiccation study, we found that air-drying yeast cells in 10% trehalose is the best method of cell preservation in order to survive the entire 18-month mission duration (6-month pre-launch plus 12-month full-mission periods). However, our study also revealed that desiccated yeast cells have decreasing viability over time when stored in payload-like environment. This suggests that the yeast biosensor will have different population of cells at different time points during the long-term mission. In this study, we are characterizing genomic and phenotypic changes in our yeast biosensor due to long-term storage and desiccation. For each yeast strain that will be part of the biosensor, several clones were reisolated after long-term storage by desiccation. These clones were compared to their respective original isolate in terms of genomic composition, desiccation tolerance and radiation sensitivity. Interestingly, clones from a radiation-sensitive mutant have better desiccation tolerance compared to their original isolate

  14. Biotechnology of non-Saccharomyces yeasts-the basidiomycetes.

    Science.gov (United States)

    Johnson, Eric A

    2013-09-01

    Yeasts are the major producer of biotechnology products worldwide, exceeding production in capacity and economic revenues of other groups of industrial microorganisms. Yeasts have wide-ranging fundamental and industrial importance in scientific, food, medical, and agricultural disciplines (Fig. 1). Saccharomyces is the most important genus of yeast from fundamental and applied perspectives and has been expansively studied. Non-Saccharomyces yeasts (non-conventional yeasts) including members of the Ascomycetes and Basidiomycetes also have substantial current utility and potential applicability in biotechnology. In an earlier mini-review, "Biotechnology of non-Saccharomyces yeasts-the ascomycetes" (Johnson Appl Microb Biotechnol 97: 503-517, 2013), the extensive biotechnological utility and potential of ascomycetous yeasts are described. Ascomycetous yeasts are particularly important in food and ethanol formation, production of single-cell protein, feeds and fodder, heterologous production of proteins and enzymes, and as model and fundamental organisms for the delineation of genes and their function in mammalian and human metabolism and disease processes. In contrast, the roles of basidiomycetous yeasts in biotechnology have mainly been evaluated only in the past few decades and compared to the ascomycetous yeasts and currently have limited industrial utility. From a biotechnology perspective, the basidiomycetous yeasts are known mainly for the production of enzymes used in pharmaceutical and chemical synthesis, for production of certain classes of primary and secondary metabolites such as terpenoids and carotenoids, for aerobic catabolism of complex carbon sources, and for bioremediation of environmental pollutants and xenotoxicants. Notwithstanding, the basidiomycetous yeasts appear to have considerable potential in biotechnology owing to their catabolic utilities, formation of enzymes acting on recalcitrant substrates, and through the production of unique primary

  15. Endogenous Population Dynamics and Economic Growth with Free Trade between Countries

    Directory of Open Access Journals (Sweden)

    Wei-Bin Zhang

    2016-05-01

    Full Text Available This paper builds a model to deal with dynamic interdependence between different countries' birth rates, mortality rates, populations, wealth accumulation, and time distributions between working, leisure and children caring. The model shows the role of human capital, technological and preference changes on national differences in birth rates, mortality rates, time distributions, population change, and wealth accumulation. The economic mechanisms of wealth accumulation, production and trade are based the Solow growth model and the Oniki-Uzawa trade model. We use the utility function proposed by Zhang to describe the behavior of households. We model national and gender differences in human capital, propensity to have children, propensity to use leisure time, and children caring efficiency. We describe the dynamics of global economic growth, trade patterns, national differences in wealth, income, birth rates, mortality rates, and populations with differential equations. We simulate the model to show the motion of the system and identify the existence of equilibrium point. We also examine the effects of changes in the propensity to have children, the propensity to save, woman's propensity to use leisure, woman's human capital, and woman's emotional involvement in children caring on the dynamics of the global and national economies.

  16. Cell wall staining with Trypan blue enables quantitative analysis of morphological changes in yeast cells

    DEFF Research Database (Denmark)

    Liesche, Johannes; Marek, Magdalena; Günther-Pomorski, Thomas

    2015-01-01

    staining with fluorescent dyes is a valuable tool. Furthermore, cell wall staining is used to facilitate sub-cellular localization experiments with fluorescently-labeled proteins and the detection of yeast cells in non-fungal host tissues. Here, we report staining of Saccharomyces cerevisiae cell wall......Yeast cells are protected by a cell wall that plays an important role in the exchange of substances with the environment. The cell wall structure is dynamic and can adapt to different physiological states or environmental conditions. For the investigation of morphological changes, selective...... with Trypan Blue, which emits strong red fluorescence upon binding to chitin and yeast glucan; thereby, it facilitates cell wall analysis by confocal and super-resolution microscopy. The staining pattern of Trypan Blue was similar to that of the widely used UV-excitable, blue fluorescent cell wall stain...

  17. Understanding start-up problems in yeast glycolysis.

    Science.gov (United States)

    Overal, Gosse B; Teusink, Bas; Bruggeman, Frank J; Hulshof, Josephus; Planqué, Robert

    2018-05-01

    Yeast glycolysis has been the focus of research for decades, yet a number of dynamical aspects of yeast glycolysis remain poorly understood at present. If nutrients are scarce, yeast will provide its catabolic and energetic needs with other pathways, but the enzymes catalysing upper glycolytic fluxes are still expressed. We conjecture that this overexpression facilitates the rapid transition to glycolysis in case of a sudden increase in nutrient concentration. However, if starved yeast is presented with abundant glucose, it can enter into an imbalanced state where glycolytic intermediates keep accumulating, leading to arrested growth and cell death. The bistability between regularly functioning and imbalanced phenotypes has been shown to depend on redox balance. We shed new light on these phenomena with a mathematical analysis of an ordinary differential equation model, including NADH to account for the redox balance. In order to gain qualitative insight, most of the analysis is parameter-free, i.e., without assigning a numerical value to any of the parameters. The model has a subtle bifurcation at the switch between an inviable equilibrium state and stable flux through glycolysis. This switch occurs if the ratio between the flux through upper glycolysis and ATP consumption rate of the cell exceeds a fixed threshold. If the enzymes of upper glycolysis would be barely expressed, our model predicts that there will be no glycolytic flux, even if external glucose would be at growth-permissable levels. The existence of the imbalanced state can be found for certain parameter conditions independent of the mentioned bifurcation. The parameter-free analysis proved too complex to directly gain insight into the imbalanced states, but the starting point of a branch of imbalanced states can be shown to exist in detail. Moreover, the analysis offers the key ingredients necessary for successful numerical continuation, which highlight the existence of this bistability and the

  18. Between science and industry-applied yeast research.

    Science.gov (United States)

    Korhola, Matti

    2018-03-01

    I was fortunate to enter yeast research at the Alko Research Laboratories with a strong tradition in yeast biochemistry and physiology studies. At the same time in the 1980s there was a fundamental or paradigm change in molecular biology research with discoveries in DNA sequencing and other analytical and physical techniques for studying macromolecules and cells. Since that time biotechnological research has expanded the traditional fermentation industries to efficient production of industrial and other enzymes and specialty chemicals. Our efforts were directed towards improving the industrial production organisms: minerals enriched yeasts (Se, Cr, Zn) and high glutathione content yeast, baker´s, distiller´s, sour dough and wine yeasts, and the fungal Trichoderma reesei platform for enzyme production. I am grateful for the trust of my colleagues in several leadership positions at the Alko Research Laboratories, Yeast Industry Platform and at the international yeast community.

  19. Border Collision Bifurcations in a Generalized Model of Population Dynamics

    Directory of Open Access Journals (Sweden)

    Lilia M. Ladino

    2016-01-01

    Full Text Available We analyze the dynamics of a generalized discrete time population model of a two-stage species with recruitment and capture. This generalization, which is inspired by other approaches and real data that one can find in literature, consists in considering no restriction for the value of the two key parameters appearing in the model, that is, the natural death rate and the mortality rate due to fishing activity. In the more general case the feasibility of the system has been preserved by posing opportune formulas for the piecewise map defining the model. The resulting two-dimensional nonlinear map is not smooth, though continuous, as its definition changes as any border is crossed in the phase plane. Hence, techniques from the mathematical theory of piecewise smooth dynamical systems must be applied to show that, due to the existence of borders, abrupt changes in the dynamic behavior of population sizes and multistability emerge. The main novelty of the present contribution with respect to the previous ones is that, while using real data, richer dynamics are produced, such as fluctuations and multistability. Such new evidences are of great interest in biology since new strategies to preserve the survival of the species can be suggested.

  20. Molecular dynamics simulations of Hsp40 J-domain mutants identifies disruption of the critical HPD-motif as the key factor for impaired curing in vivo of the yeast prion [URE3].

    Science.gov (United States)

    Xue, You-Lin; Wang, Hao; Riedy, Michael; Roberts, Brittany-Lee; Sun, Yuna; Song, Yong-Bo; Jones, Gary W; Masison, Daniel C; Song, Youtao

    2018-05-01

    Genetic screens using Saccharomyces cerevisiae have identified an array of Hsp40 (Ydj1p) J-domain mutants that are impaired in the ability to cure the yeast [URE3] prion through disrupting functional interactions with Hsp70. However, biochemical analysis of some of these Hsp40 J-domain mutants has so far failed to provide major insight into the specific functional changes in Hsp40-Hsp70 interactions. To explore the detailed structural and dynamic properties of the Hsp40 J-domain, 20 ns molecular dynamic simulations of 4 mutants (D9A, D36A, A30T, and F45S) and wild-type J-domain were performed, followed by Hsp70 docking simulations. Results demonstrated that although the Hsp70 interaction mechanism of the mutants may vary, the major structural change was targeted to the critical HPD motif of the J-domain. Our computational analysis fits well with previous yeast genetics studies regarding highlighting the importance of J-domain function in prion propagation. During the molecular dynamics simulations several important residues were identified and predicted to play an essential role in J-domain structure. Among these residues, Y26 and F45 were confirmed, using both in silico and in vivo methods, as being critical for Ydj1p function.

  1. Dynamic assessments of population exposure to urban greenspace using multi-source big data.

    Science.gov (United States)

    Song, Yimeng; Huang, Bo; Cai, Jixuan; Chen, Bin

    2018-09-01

    A growing body of evidence has proven that urban greenspace is beneficial to improve people's physical and mental health. However, knowledge of population exposure to urban greenspace across different spatiotemporal scales remains unclear. Moreover, the majority of existing environmental assessments are unable to quantify how residents enjoy their ambient greenspace during their daily life. To deal with this challenge, we proposed a dynamic method to assess urban greenspace exposure with the integration of mobile-phone locating-request (MPL) data and high-spatial-resolution remote sensing images. This method was further applied to 30 major cities in China by assessing cities' dynamic greenspace exposure levels based on residents' surrounding areas with different buffer scales (0.5km, 1km, and 1.5km). Results showed that regarding residents' 0.5-km surrounding environment, Wenzhou and Hangzhou were found to be with the greenest exposure experience, whereas Zhengzhou and Tangshan were the least ones. The obvious diurnal and daily variations of population exposure to their surrounding greenspace were also identified to be highly correlated with the distribution pattern of urban greenspace and the dynamics of human mobility. Compared with two common measurements of urban greenspace (green coverage rate and green area per capita), the developed method integrated the dynamics of population distribution and geographic locations of urban greenspace into the exposure assessment, thereby presenting a more reasonable way to assess population exposure to urban greenspace. Additionally, this dynamic framework could hold potential utilities in supporting urban planning studies and environmental health studies and advancing our understanding of the magnitude of population exposure to greenspace at different spatiotemporal scales. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. Changes in Population Dynamics in Mutualistic versus Pathogenic Viruses

    Directory of Open Access Journals (Sweden)

    Marilyn J. Roossinck

    2011-01-01

    Full Text Available Although generally regarded as pathogens, viruses can also be mutualists. A number of examples of extreme mutualism (i.e., symbiogenesis have been well studied. Other examples of mutualism are less common, but this is likely because viruses have rarely been thought of as having any beneficial effects on their hosts. The effect of mutualism on the population dynamics of viruses is a topic that has not been addressed experimentally. However, the potential for understanding mutualism and how a virus might become a mutualist may be elucidated by understanding these dynamics.

  3. Factors affecting population dynamics of maternally transmitted endosymbionts in Bemisia tabaci.

    Directory of Open Access Journals (Sweden)

    Huipeng Pan

    Full Text Available While every individual of Bemisia tabaci (Hemiptera: Aleyrodidae harbors the primary symbiont (P-symbiont Portiera, the infection frequencies of the six secondary symbionts (S-symbionts including Hamiltonella, Arsenophonus, Cardinium, Wolbachia, Rickettsia and Fritschea vary greatly among different populations. To characterize the factors influencing the infection dynamics of the six S-symbionts in B. tabaci, gene-specific PCR were conducted to screen for the presence of the P-symbiont Portiera and the six S-symbionts in 61 (17 B and 44 Q biotypes field populations collected from different plant species and locations in China. All individuals of the 61 populations hosted the P-symbiont Portiera, but none of them harbored Arsenophonus and Fritschea. The presence and infection rates of Hamiltonella, Cardinium, Rickettsia, Wolbachia and their co-infections Rickettsia + Hamiltonella (RH, Rickettsia + Cardinium (RC, Hamiltonella + Cardinium (HC and Rickettsia + Hamiltonella + Cardinium (RHC varied significantly among the 61 field populations; and the observed variations can be explained by biotypes, sexes, host plants and geographical locations of these field populations. Taken together, at least three factors including biotype, host plant and geographical location affect the infection dynamics of S-symbionts in B. tabaci.

  4. Structured population dynamics: continuous size and discontinuous stage structures.

    Science.gov (United States)

    Buffoni, Giuseppe; Pasquali, Sara

    2007-04-01

    A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

  5. The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.

    Directory of Open Access Journals (Sweden)

    David Gresham

    2008-12-01

    Full Text Available The experimental evolution of laboratory populations of microbes provides an opportunity to observe the evolutionary dynamics of adaptation in real time. Until very recently, however, such studies have been limited by our inability to systematically find mutations in evolved organisms. We overcome this limitation by using a variety of DNA microarray-based techniques to characterize genetic changes -- including point mutations, structural changes, and insertion variation -- that resulted from the experimental adaptation of 24 haploid and diploid cultures of Saccharomyces cerevisiae to growth in either glucose, sulfate, or phosphate-limited chemostats for approximately 200 generations. We identified frequent genomic amplifications and rearrangements as well as novel retrotransposition events associated with adaptation. Global nucleotide variation detection in ten clonal isolates identified 32 point mutations. On the basis of mutation frequencies, we infer that these mutations and the subsequent dynamics of adaptation are determined by the batch phase of growth prior to initiation of the continuous phase in the chemostat. We relate these genotypic changes to phenotypic outcomes, namely global patterns of gene expression, and to increases in fitness by 5-50%. We found that the spectrum of available mutations in glucose- or phosphate-limited environments combined with the batch phase population dynamics early in our experiments allowed several distinct genotypic and phenotypic evolutionary pathways in response to these nutrient limitations. By contrast, sulfate-limited populations were much more constrained in both genotypic and phenotypic outcomes. Thus, the reproducibility of evolution varies with specific selective pressures, reflecting the constraints inherent in the system-level organization of metabolic processes in the cell. We were able to relate some of the observed adaptive mutations (e.g., transporter gene amplifications to known features

  6. Yeast-based biosensors: design and applications.

    Science.gov (United States)

    Adeniran, Adebola; Sherer, Michael; Tyo, Keith E J

    2015-02-01

    Yeast-based biosensing (YBB) is an exciting research area, as many studies have demonstrated the use of yeasts to accurately detect specific molecules. Biosensors incorporating various yeasts have been reported to detect an incredibly large range of molecules including but not limited to odorants, metals, intracellular metabolites, carcinogens, lactate, alcohols, and sugars. We review the detection strategies available for different types of analytes, as well as the wide range of output methods that have been incorporated with yeast biosensors. We group biosensors into two categories: those that are dependent upon transcription of a gene to report the detection of a desired molecule and those that are independent of this reporting mechanism. Transcription-dependent biosensors frequently depend on heterologous expression of sensing elements from non-yeast organisms, a strategy that has greatly expanded the range of molecules available for detection by YBBs. Transcription-independent biosensors circumvent the problem of sensing difficult-to-detect analytes by instead relying on yeast metabolism to generate easily detected molecules when the analyte is present. The use of yeast as the sensing element in biosensors has proven to be successful and continues to hold great promise for a variety of applications. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

  7. Life history and population dynamics of an estuarine amphipod, Eriopisa chilkensis Chilton (Gammaridae)

    Digital Repository Service at National Institute of Oceanography (India)

    Aravind, N.P.; Sheeba, P.; Nair, K.K.C.; Achuthankutty, C.T.

    Life history and Population Dynamics of an Estuarine Amphipod –Eriopisa chilkensis Chilton (Gammaridae) Nisha. P. Aravind, P. Sheeba, K.K.C. Nair and C.T.Achuthankutty* National Institute of Oceanography, Regional Centre, Cochin 682018, India... of laboratory data to the field suggests that E. chilkensis in Cochin estuary has a multivoltine life cycle. Key words: - Eriopisa chilkensis, Amphipoda, life cycle, population dynamics, Cochin estuary, India 2 1. Introduction Life-history traits of 214 amphipod...

  8. Effects of Peanut-Tobacco Rotations on Population Dynamics of Meloidogyne arenaria in Mixed Race Populations.

    Science.gov (United States)

    Hirunsalee, A; Barker, K R; Beute, M K

    1995-06-01

    A 3-year microplot study was initiated to characterize the population dynamics, reproduction potential, and survivorship of single or mixed populations of Meloidogyne arenaria race 1 (Ma1) and race 2 (Ma2), as affected by crop rotations of peanut 'Florigiant' and M. incognita races 1 and 3-resistant 'McNair 373' and susceptible 'Coker 371-Gold' tobacco. Infection, reproduction, and root damage by Ma2 on peanut and by Ma1 on resistant tobacco were limited in the first year. Infection, reproduction, and root-damage potentials on susceptible tobacco were similar for Ma1 and Ma2. In the mixed (1:1) population, Ma1 was dominant on peanut and Ma2 was dominant on both tobacco cultivars. Crop rotation affected the population dynamics of different nematode races. For years 2 and 3, the low numbers of Ma1 and Ma2 from a previous-year poor host increased rapidly on suitable hosts. Ma1 had greater reproduction factors ([RF] = population density at harvest/population density at preplandng) than did Ma2 and Ma1 + Ma2 in second-year peanut plots following first-year resistant tobacco, and in third-year peanut plots following second-year tobacco. In mixed infestations, Ma1 predominated over Ma2 in previous-year peanut plots, whereas Ma2 predominated over Ma1 in previous-year tobacco plots. Moderate damage on resistant tobacco was induced by Ma1 in the second year. In the third year, moderate damage on peanut was associated with 'Ma2' from previous-year peanut plots. The resistant tobacco supported sufficient reproduction of Ma1 over 2 years to effect moderate damage and yield suppression to peanut in year 3.

  9. Prevalence of candida and non-candida yeasts isolated from patients with yeast fungal infections in Tehran labs

    Directory of Open Access Journals (Sweden)

    Hashemi SJ

    2011-04-01

    Full Text Available "n 800x600 Normal 0 false false false EN-US X-NONE AR-SA MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman","serif";} Background: Infections caused by opportunistic yeasts such as Candida species, Trichosporon, Rhodotorula and Saccharomyces have increased in immunocompromis-ed patients and their identification is crucial as intrinsic and acquired resistance of some yeast species to antifungal agents are on the rise. The aim of this study was to identify the organisms to the species level in order to suggest accurate and effective antifungal therapies."n"nMethods: In this study that carried out in Tehran, Iran in 2009, 200 patients with yeast infection were medically examined and clinical specimens were prepared for direct examination and culture on Sabouraud dextrose agar. Subsequently, the isolated yeast colonies were identified using various tests including culture on Corn Meal agar with Tween 80, CHROMagar Candida and casein agar. For the definite identification of organisms some biochemical tests were done based on carbohydrate assimilation by RapID Yeast Plus System kit, and, finally, a molecular method, PCR-RFLP, using Hpa II enzyme, was performed for the remaining unknown yeast species."n"nResults: A total of 211 yeast isolates were identified in 200 patients with yeast infections. The most frequent isolated yeasts were Candida albicans, 124 (58.77%, followed by Candida parapsilosis, 36 (17.06%, Candida tropicalis, 17 (8.06%, Candida glabrata, 13 (6.16%, Candida krusei, 8 (3.79%, Candida guilliermondii, 2 (0.96%, Trichosporon, 3 (1.14%, Rhodotorula, 1 (0.47%, Saccaromyces cerevisiae, 1 (0.47% and other

  10. Oral yeast colonization throughout pregnancy.

    Science.gov (United States)

    Rio, R; Simões-Silva, L; Garro, S; Silva, M-J; Azevedo, Á; Sampaio-Maia, B

    2017-03-01

    Recent studies suggest that placenta may harbour a unique microbiome that may have origin in maternal oral microbiome. Although the major physiological and hormonal adjustments observed in pregnant women lead to biochemical and microbiological modifications of the oral environment, very few studies evaluated the changes suffered by the oral microbiota throughout pregnancy. So, the aim of our study was to evaluate oral yeast colonization throughout pregnancy and to compare it with non-pregnant women. The oral yeast colonization was assessed in saliva of 30 pregnant and non-pregnant women longitudinally over a 6-months period. Demographic information was collected, a non-invasive intra-oral examination was performed and saliva flow and pH were determined. Pregnant and non-pregnant groups were similar regarding age and level of education. Saliva flow rate did not differ, but saliva pH was lower in pregnant than in non-pregnant women. Oral yeast prevalence was higher in pregnant than in non-pregnant women, either in the first or in the third trimester, but did not attain statistical significance. In individuals colonized with yeast, the total yeast quantification (Log10CFU/mL) increase from the 1st to the 3rd trimester in pregnant women, but not in non-pregnant women. Pregnancy may favour oral yeast growth that may be associated with an acidic oral environment.

  11. Biotechnological Applications of Dimorphic Yeasts

    Science.gov (United States)

    Doiphode, N.; Joshi, C.; Ghormade, V.; Deshpande, M. V.

    The dimorphic yeasts have the equilibrium between spherical growth (budding) and polarized (hyphal or pseudohyphal tip elongation) which can be triggered by change in the environmental conditions. The reversible growth phenomenon has made dimorphic yeasts as an useful model to understand fungal evolution and fungal differentiation, in general. In nature dimorphism is clearly evident in plant and animal fungal pathogens, which survive and most importantly proliferate in the respective hosts. However, number of organisms with no known pathogenic behaviour also show such a transition, which can be exploited for the technological applications due to their different biochemical make up under different morphologies. For instance, chitin and chitosan production using dimorphic Saccharomyces, Mucor, Rhizopus and Benjaminiella, oil degradation and biotransformation with yeast-form of Yarrowia species, bioremediation of organic pollutants, exopolysac-charide production by yeast-phase of Aureobasidium pullulans, to name a few. Myrothecium verrucaria can be used for seed dressing in its yeast form and it produces a mycolytic enzyme complex in its hyphal-form for the biocontrol of fungal pathogens, while Beauveria bassiana and other entomopathogens kill the insect pest by producing yeast- like cells in the insect body. The form-specific expression of protease, chitinase, lipase, ornithine decarboxylase, glutamate dehydrogenases, etc. make Benjaminiella poitrasii, Basidiobolus sp., and Mucor rouxii strains important in bioremediation, nanobiotechnology, fungal evolution and other areas.

  12. A quantitative characterization of the yeast heterotrimeric G protein cycle

    Science.gov (United States)

    Yi, Tau-Mu; Kitano, Hiroaki; Simon, Melvin I.

    2003-01-01

    The yeast mating response is one of the best understood heterotrimeric G protein signaling pathways. Yet, most descriptions of this system have been qualitative. We have quantitatively characterized the heterotrimeric G protein cycle in yeast based on direct in vivo measurements. We used fluorescence resonance energy transfer to monitor the association state of cyan fluorescent protein (CFP)-Gα and Gβγ-yellow fluorescent protein (YFP), and we found that receptor-mediated G protein activation produced a loss of fluorescence resonance energy transfer. Quantitative time course and dose–response data were obtained for both wild-type and mutant cells possessing an altered pheromone response. These results paint a quantitative portrait of how regulators such as Sst2p and the C-terminal tail of α-factor receptor modulate the kinetics and sensitivity of G protein signaling. We have explored critical features of the dynamics including the rapid rise and subsequent decline of active G proteins during the early response, and the relationship between the G protein activation dose–response curve and the downstream dose–response curves for cell-cycle arrest and transcriptional induction. Fitting the data to a mathematical model produced estimates of the in vivo rates of heterotrimeric G protein activation and deactivation in yeast. PMID:12960402

  13. Electron transport chain in a thermotolerant yeast.

    Science.gov (United States)

    Mejía-Barajas, Jorge A; Martínez-Mora, José A; Salgado-Garciglia, Rafael; Noriega-Cisneros, Ruth; Ortiz-Avila, Omar; Cortés-Rojo, Christian; Saavedra-Molina, Alfredo

    2017-04-01

    Yeasts capable of growing and surviving at high temperatures are regarded as thermotolerant. For appropriate functioning of cellular processes and cell survival, the maintenance of an optimal redox state is critical of reducing and oxidizing species. We studied mitochondrial functions of the thermotolerant Kluyveromyces marxianus SLP1 and the mesophilic OFF1 yeasts, through the evaluation of its mitochondrial membrane potential (ΔΨ m ), ATPase activity, electron transport chain (ETC) activities, alternative oxidase activity, lipid peroxidation. Mitochondrial membrane potential and the cytoplasmic free Ca 2+ ions (Ca 2+ cyt) increased in the SLP1 yeast when exposed to high temperature, compared with the mesophilic yeast OFF1. ATPase activity in the mesophilic yeast diminished 80% when exposed to 40° while the thermotolerant SLP1 showed no change, despite an increase in the mitochondrial lipid peroxidation. The SLP1 thermotolerant yeast exposed to high temperature showed a diminution of 33% of the oxygen consumption in state 4. The uncoupled state 3 of oxygen consumption did not change in the mesophilic yeast when it had an increase of temperature, whereas in the thermotolerant SLP1 yeast resulted in an increase of 2.5 times when yeast were grown at 30 o , while a decrease of 51% was observed when it was exposed to high temperature. The activities of the ETC complexes were diminished in the SLP1 when exposed to high temperature, but also it was distinguished an alternative oxidase activity. Our results suggest that the mitochondria state, particularly ETC state, is an important characteristic of the thermotolerance of the SLP1 yeast strain.

  14. seasonal population dynamics of rodents of mount chilalo, arsi ...

    African Journals Online (AJOL)

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    ABSTRACT: A study on seasonal population dynamics of rodents was carried out on Mount. Chilalo from .... vegetation growth, availability of food and water, and ... vegetation (3,300–4,200 masl) (Alemayehu. Mengistu, 1975; APEDO and ABRDP, 2004). The mountain is one of the Afrotropical biodiversity hotspots areas.

  15. Population Dynamics of Biota on the Roots of Azolla microphylla Kaulfuss

    Directory of Open Access Journals (Sweden)

    NITA ETIKAWATI

    2000-01-01

    Full Text Available Azolla was a special fern that their associations with Anabaena azollae able to fix free nitrogen from air, to produce protein. Although by the ages, biota diversity those habits on the roots of Azolla increased and effected to protein concentration. The research was to find out population dynamics of biota on the roots of Azolla microphylla Kaulfuss and the growth peak. This study used Completely Randomized Design with 10 kinds of biota, i.e. bacteria, Fungi, Actinomycetes, Protozoa, Alga, Crustacean, Rotifers, Coelenterate, Insect and Molluscs, and it was used 3 replications. Research was conducted within 4 weeks and the populations of biota were observed every week. Data were statistically analyzed using Analysis Variant and Duncan’s Multiple Range Test. The population dynamics of biota on the roots of Azolla microphylla Kaulfuss were influenced on its quantity and composition, and the growth peak is done in 2nd week.

  16. Connection between Dynamically Derived Initial Mass Function Normalization and Stellar Population Parameters

    NARCIS (Netherlands)

    McDermid, Richard M.; Cappellari, Michele; Alatalo, Katherine; Bayet, Estelle; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Bureau, Martin; Crocker, Alison F.; Davies, Roger L.; Davis, Timothy A.; de Zeeuw, P. T.; Duc, Pierre-Alain; Emsellem, Eric; Khochfar, Sadegh; Krajnović, Davor; Kuntschner, Harald; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Scott, Nicholas; Serra, Paolo; Weijmans, Anne-Marie; Young, Lisa M.

    We report on empirical trends between the dynamically determined stellar initial mass function (IMF) and stellar population properties for a complete, volume-limited sample of 260 early-type galaxies from the ATLAS3D project. We study trends between our dynamically derived IMF normalization αdyn ≡

  17. Population dynamics of Ascaris suum in trickle-infected pigs.

    Science.gov (United States)

    Nejsum, Peter; Thamsborg, Stig M; Petersen, Heidi H; Kringel, Helene; Fredholm, Merete; Roepstorff, Allan

    2009-10-01

    The population dynamics of Ascaris suum was studied by long-term exposure of pigs to infective eggs. The pigs were experimentally inoculated with 25 A. suum eggs/kg/day, and 7, 8, and 8 pigs were necropsied at weeks 4, 8, and 14 postinoculation (PI), respectively. Despite the fact that the pigs were continuously reinfected, dramatic reductions in numbers of liver lesions (white spots) and migrating lung larvae were observed as a function of time. However, even at the end of the study, a few larvae were able to complete migration, but these larvae seemed unable to mature in the small intestine. Thus, the adult worm population seemed to consist of worms from the first part of the exposure period. The noticeable decrease in number of white spots suggests that the level of exposure is not reflected in the number of white spots in the late phase of a continuous infection. The serum levels of A. suum L3-specific IgG1 and IgA were significantly elevated by week 4 PI, after which the antibody levels declined. The population dynamics and parasite regulating mechanisms are discussed for A. suum in pigs as well as for the closely related species A. lumbricoides in humans.

  18. The Malleable Nature of the Budding Yeast Nuclear Envelope: Flares, Fusion, and Fenestrations.

    Science.gov (United States)

    Meseroll, Rebecca A; Cohen-Fix, Orna

    2016-11-01

    In eukaryotes, the nuclear envelope (NE) physically separates nuclear components and activities from rest of the cell. The NE also provides rigidity to the nucleus and contributes to chromosome organization. At the same time, the NE is highly dynamic; it must change shape and rearrange its components during development and throughout the cell cycle, and its morphology can be altered in response to mutation and disease. Here we focus on the NE of budding yeast, Saccharomyces cerevisiae, which has several unique features: it remains intact throughout the cell cycle, expands symmetrically during interphase, elongates during mitosis and, expands asymmetrically during mitotic delay. Moreover, its NE is safely breached during mating and when large structures, such as nuclear pore complexes and the spindle pole body, are embedded into its double membrane. The budding yeast NE lacks lamins and yet the nucleus is capable of maintaining a spherical shape throughout interphase. Despite these eccentricities, studies of the budding yeast NE have uncovered interesting, and likely conserved, processes that contribute to NE dynamics. In particular, we discuss the processes that drive and enable NE expansion and the dramatic changes in the NE that lead to extensions and fenestrations. J. Cell. Physiol. 231: 2353-2360, 2016. Published 2016. This article is a U.S. Government work and is in the public domain in the USA. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

  19. Yeast mating and image-based quantification of spatial pattern formation.

    Directory of Open Access Journals (Sweden)

    Christian Diener

    2014-06-01

    Full Text Available Communication between cells is a ubiquitous feature of cell populations and is frequently realized by secretion and detection of signaling molecules. Direct visualization of the resulting complex gradients between secreting and receiving cells is often impossible due to the small size of diffusing molecules and because such visualization requires experimental perturbations such as attachment of fluorescent markers, which can change diffusion properties. We designed a method to estimate such extracellular concentration profiles in vivo by using spatiotemporal mathematical models derived from microscopic analysis. This method is applied to populations of thousands of haploid yeast cells during mating in order to quantify the extracellular distributions of the pheromone α-factor and the activity of the aspartyl protease Bar1. We demonstrate that Bar1 limits the range of the extracellular pheromone signal and is critical in establishing α-factor concentration gradients, which is crucial for effective mating. Moreover, haploid populations of wild type yeast cells, but not BAR1 deletion strains, create a pheromone pattern in which cells differentially grow and mate, with low pheromone regions where cells continue to bud and regions with higher pheromone levels and gradients where cells conjugate to form diploids. However, this effect seems to be exclusive to high-density cultures. Our results show a new role of Bar1 protease regulating the pheromone distribution within larger populations and not only locally inside an ascus or among few cells. As a consequence, wild type populations have not only higher mating efficiency, but also higher growth rates than mixed MATa bar1Δ/MATα cultures. We provide an explanation of how a rapidly diffusing molecule can be exploited by cells to provide spatial information that divides the population into different transcriptional programs and phenotypes.

  20. Induction of respiratory deficiency in yeast by manganese, copper, cobalt and nickel

    Energy Technology Data Exchange (ETDEWEB)

    Lindegren, C C; Nagai, S; Nagai, H

    1958-08-16

    Among the chemical agents which induce respiratory deficiency in yeasts, acriflavine, triphenyl tetrazolium chloride, p-nitrophenol, and propamidine isethionate are especially effective in producing the deficiency in a large fraction of the surviving population. The present work is a survey of the efficacy of various metallic salts in inducing respiratory deficiency.

  1. Phase control of light amplification with dynamically irreversible pathways of population transfer in a Λ system

    International Nuclear Information System (INIS)

    Yuan Shi; Wu Jinhui; Gao Jinyue; Pan Chunliu

    2002-01-01

    We use the relative phase of two coherent fields for the control of light amplification with dynamically irreversible pathways of population transfer in a Λ system. The population inversion and gain with dynamically irreversible pathways of population transfer are shown as the relative phase is varied. We support our results by numerical calculation and analytical explanation

  2. Spatial and temporal dynamics of the genetic organization of small mammal populations

    International Nuclear Information System (INIS)

    Smith, M.H.; Manlove, M.N.; Joule, J.

    1978-01-01

    A functional population is a group of organisms and their offspring that contributes to a common gene pool within a certain area and time period. It is also the unit of evolution and should be viewed both in quantitative and qualitative terms. Selection, drift, dispersal, and mutation can alter the composition of populations. Spatial heterogeneity in allele frequencies argues for a conceptual model that has a series of relatively small populations semi-isolated from one another. Because of the relatively high levels of genetic variability characteristic of most mammalian species, significant amounts of gene flow between these spatially subdivided populations must occur when longer time periods are considered. Fluctuations in the genetic structure of populations seem to be important in altering the fitness of the individuals within the populations. The interaction of populations through gene flow is important in changing the levels of intrapopulational genetic variability. Populations can be characterized as existing on a continuum from relatively stable to unstable numbers and by other associated changes in their characteristics. Temporal changes in allele frequency occur in a variety of mammals. Conceptually, a species can be viewed as a series of dynamic populations that vary in numbers and quality in both a spatial and temporal context even over short distances and time periods. Short term changes in the quality of individuals in a population can be important in altering the short term dynamics of a population

  3. Population dynamics of soil microbes and diversity of Bacillus ...

    African Journals Online (AJOL)

    ONOS

    2010-01-25

    Jan 25, 2010 ... Population dynamics of soil microbes and diversity of ... 25.78, 25.78, 86.26, 24.73, 68.0, 26.8 and 26.8 kDa proteins and equivalent to Cyt, Cry5 and Cry2 toxins ..... Molecular weight (kDa) of protein fractions of the BT isolates.

  4. Population dynamics of the invasive fish, Gambusia affinis , in ...

    African Journals Online (AJOL)

    Repeated-measures ANOVA analyses on the catch per unit effort (CPUE) of G. affinis between sampling events and dams revealed significant differences in population dynamics among dams, although an overall trend of rapid increase followed by plateau in summer, with a rapid decline in winter was seen in most dams.

  5. Individual based model of slug population and spatial dynamics

    NARCIS (Netherlands)

    Choi, Y.H.; Bohan, D.A.; Potting, R.P.J.; Semenov, M.A.; Glen, D.M.

    2006-01-01

    The slug, Deroceras reticulatum, is one of the most important pests of agricultural and horticultural crops in UK and Europe. In this paper, a spatially explicit individual based model (IbM) is developed to study the dynamics of a population of D. reticulatum. The IbM establishes a virtual field

  6. Considering transient population dynamics in the conservation of slow life-history species: An application to the sandhill crane

    Science.gov (United States)

    Gerber, Brian D.; Kendall, William L.

    2016-01-01

    The importance of transient dynamics of structured populations is increasingly recognized in ecology, yet these implications are not largely considered in conservation practices. We investigate transient and long-term population dynamics to demonstrate the process and utility of incorporating transient dynamics into conservation research and to better understand the population management of slow life-history species; these species can be theoretically highly sensitive to short- and long-term transient effects. We are specifically interested in the effects of anthropogenic removal of individuals from populations, such as caused by harvest, poaching, translocation, or incidental take. We use the sandhill crane (Grus canadensis) as an exemplar species; it is long-lived, has low reproduction, late maturity, and multiple populations are subject to sport harvest. We found sandhill cranes to have extremely high potential, but low likelihood for transient dynamics, even when the population is being harvested. The typically low population growth rate of slow life-history species appears to buffer against many perturbations causing large transient effects. Transient dynamics will dominate population trajectories of these species when stage structures are highly biased towards the younger and non-reproducing individuals, a situation that may be rare in established populations of long-lived animals. However, short-term transient population growth can be highly sensitive to vital rates that are relatively insensitive under equilibrium, suggesting that stage structure should be known if perturbation analysis is used to identify effective conservation strategies. For populations of slow life-history species that are not prone to large perturbations to their most productive individuals, population growth may be approximated by equilibrium dynamics.

  7. Under pressure: evolutionary engineering of yeast strains for improved performance in fuels and chemicals production.

    Science.gov (United States)

    Mans, Robert; Daran, Jean-Marc G; Pronk, Jack T

    2018-04-01

    Evolutionary engineering, which uses laboratory evolution to select for industrially relevant traits, is a popular strategy in the development of high-performing yeast strains for industrial production of fuels and chemicals. By integrating whole-genome sequencing, bioinformatics, classical genetics and genome-editing techniques, evolutionary engineering has also become a powerful approach for identification and reverse engineering of molecular mechanisms that underlie industrially relevant traits. New techniques enable acceleration of in vivo mutation rates, both across yeast genomes and at specific loci. Recent studies indicate that phenotypic trade-offs, which are often observed after evolution under constant conditions, can be mitigated by using dynamic cultivation regimes. Advances in research on synthetic regulatory circuits offer exciting possibilities to extend the applicability of evolutionary engineering to products of yeasts whose synthesis requires a net input of cellular energy. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  8. Exploiting Fast-Variables to Understand Population Dynamics and Evolution

    Science.gov (United States)

    Constable, George W. A.; McKane, Alan J.

    2017-11-01

    We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are caused by individual events while the dynamics are described in terms of the time-evolution of a probability density function. In general, the application of the diffusion approximation still leaves a description that is quite complex. However, in many biological applications one or more of the processes happen slowly relative to the system's other processes, and the dynamics can be approximated as occurring within a slow low-dimensional subspace. We review these time-scale separation arguments and analyse the more simple stochastic dynamics that result in a number of cases. We stress that it is important to retain the demographic noise derived in this way, and emphasise this point by showing that it can alter the direction of selection compared to the prediction made from an analysis of the corresponding deterministic model.

  9. Genomics and the making of yeast biodiversity.

    Science.gov (United States)

    Hittinger, Chris Todd; Rokas, Antonis; Bai, Feng-Yan; Boekhout, Teun; Gonçalves, Paula; Jeffries, Thomas W; Kominek, Jacek; Lachance, Marc-André; Libkind, Diego; Rosa, Carlos A; Sampaio, José Paulo; Kurtzman, Cletus P

    2015-12-01

    Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has evolved multiple times, most known species belong to the subphylum Saccharomycotina (syn. Hemiascomycota, hereafter yeasts). This diverse group includes the premier eukaryotic model system, Saccharomyces cerevisiae; the common human commensal and opportunistic pathogen, Candida albicans; and over 1000 other known species (with more continuing to be discovered). Yeasts are found in every biome and continent and are more genetically diverse than angiosperms or chordates. Ease of culture, simple life cycles, and small genomes (∼10-20Mbp) have made yeasts exceptional models for molecular genetics, biotechnology, and evolutionary genomics. Here we discuss recent developments in understanding the genomic underpinnings of the making of yeast biodiversity, comparing and contrasting natural and human-associated evolutionary processes. Only a tiny fraction of yeast biodiversity and metabolic capabilities has been tapped by industry and science. Expanding the taxonomic breadth of deep genomic investigations will further illuminate how genome function evolves to encode their diverse metabolisms and ecologies. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Linking individual phenotype to density-dependent population growth: the influence of body size on the population dynamics of malaria vectors

    NARCIS (Netherlands)

    Russell, T.L.; Lwetoijera, D.W.; Knols, B.G.J.; Takken, W.; Killeen, G.F.; Ferguson, H.M.

    2011-01-01

    Understanding the endogenous factors that drive the population dynamics of malaria mosquitoes will facilitate more accurate predictions about vector control effectiveness and our ability to destabilize the growth of either low- or high-density insect populations. We assessed whether variation in

  11. Linking individual phenotype to density-dependent population growth: the influence of body size on the population dynamics of malaria vectors

    NARCIS (Netherlands)

    Russell, T.L.; Lwetoijera, D.W.; Knols, B.G.J.; Takken, W.; Killeen, G.F.; Ferguson, H.M.

    2011-01-01

    Understanding the endogenous factors that drive the population dynamics of malaria mosquitoes will facilitate more accurate predictions about vector control effectiveness and our ability to destabilize the growth of either low-or high-density insect populations. We assessed whether variation in

  12. An obligatory bacterial mutualism in a multi-drug environment exhibits strong oscillatory population dynamics

    Science.gov (United States)

    Conwill, Arolyn; Yurtsev, Eugene; Gore, Jeff

    2014-03-01

    A common mechanism of antibiotic resistance in bacteria involves the production of an enzyme that inactivates the antibiotic. By inactivating the antibiotic, resistant cells can protect other cells in the population that would otherwise be sensitive to the drug. In a multidrug environment, an obligatory mutualism arises because populations of different strains rely on each other to breakdown antibiotics in the environment. Here, we experimentally track the population dynamics of two E. coli strains in the presence of two different antibiotics: ampicillin and chloramphenicol. Together the strains are able to grow in antibiotic concentrations that inhibit growth of either one of the strains alone. Although mutualisms are often thought to stabilize population dynamics, we observe strong oscillatory dynamics even when there is long-term coexistence between the two strains. We expect that our results will provide insight into the evolution of antibiotic resistance and, more generally, the evolutionary origin of phenotypic diversity, cooperation, and ecological stability.

  13. Full Data of Yeast Interacting Proteins Database (Original Version) - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Yeast Interacting Proteins Database Full Data of Yeast Interacting Proteins Database (Origin...al Version) Data detail Data name Full Data of Yeast Interacting Proteins Database (Original Version) DOI 10....18908/lsdba.nbdc00742-004 Description of data contents The entire data in the Yeast Interacting Proteins Database...eir interactions are required. Several sources including YPD (Yeast Proteome Database, Costanzo, M. C., Hoga...ematic name in the SGD (Saccharomyces Genome Database; http://www.yeastgenome.org /). Bait gene name The gen

  14. Yeast Monitoring of Wine Mixed or Sequential Fermentations Made by Native Strains from D.O. “Vinos de Madrid” Using Real-Time Quantitative PCR

    Science.gov (United States)

    García, Margarita; Esteve-Zarzoso, Braulio; Crespo, Julia; Cabellos, Juan M.; Arroyo, Teresa

    2017-01-01

    There is an increasing trend toward understanding the impact of non-Saccharomyces yeasts on the winemaking process. Although Saccharomyces cerevisiae is the predominant species at the end of fermentation, it has been recognized that the presence of non-Saccharomyces species during alcoholic fermentation can produce an improvement in the quality and complexity of the final wines. A previous work was developed for selecting the best combinations between S. cerevisiae and five non-Saccharomyces (Torulaspora delbrueckii, Schizosaccharomyces pombe, Candida stellata, Metschnikowia pulcherrima, and Lachancea thermotolorans) native yeast strains from D.O. “Vinos de Madrid” at the laboratory scale. The best inoculation strategies between S. cerevisiae and non-Saccharomyces strains were chosen to analyze, by real-time quantitative PCR (qPCR) combined with the use of specific primers, the dynamics of inoculated populations throughout the fermentation process at the pilot scale using the Malvar white grape variety. The efficiency of the qPCR system was verified independently of the samples matrix, founding the inoculated yeast species throughout alcoholic fermentation. Finally, we can validate the positive effect of selected co-cultures in the Malvar wine quality, highlighting the sequential cultures of T. delbrueckii CLI 918/S. cerevisiae CLI 889 and C. stellata CLI 920/S. cerevisiae CLI 889 and, mixed and sequential cultures of L. thermotolerans 9-6C combined with S. cerevisiae CLI 889. PMID:29326669

  15. Yeast Monitoring of Wine Mixed or Sequential Fermentations Made by Native Strains from D.O. “Vinos de Madrid” Using Real-Time Quantitative PCR

    Directory of Open Access Journals (Sweden)

    Margarita García

    2017-12-01

    Full Text Available There is an increasing trend toward understanding the impact of non-Saccharomyces yeasts on the winemaking process. Although Saccharomyces cerevisiae is the predominant species at the end of fermentation, it has been recognized that the presence of non-Saccharomyces species during alcoholic fermentation can produce an improvement in the quality and complexity of the final wines. A previous work was developed for selecting the best combinations between S. cerevisiae and five non-Saccharomyces (Torulaspora delbrueckii, Schizosaccharomyces pombe, Candida stellata, Metschnikowia pulcherrima, and Lachancea thermotolorans native yeast strains from D.O. “Vinos de Madrid” at the laboratory scale. The best inoculation strategies between S. cerevisiae and non-Saccharomyces strains were chosen to analyze, by real-time quantitative PCR (qPCR combined with the use of specific primers, the dynamics of inoculated populations throughout the fermentation process at the pilot scale using the Malvar white grape variety. The efficiency of the qPCR system was verified independently of the samples matrix, founding the inoculated yeast species throughout alcoholic fermentation. Finally, we can validate the positive effect of selected co-cultures in the Malvar wine quality, highlighting the sequential cultures of T. delbrueckii CLI 918/S. cerevisiae CLI 889 and C. stellata CLI 920/S. cerevisiae CLI 889 and, mixed and sequential cultures of L. thermotolerans 9-6C combined with S. cerevisiae CLI 889.

  16. Data from: Rapid multiple-level coevolution in experimental populations of yeast killer and non-killer strains

    NARCIS (Netherlands)

    Pieczynska, M.D.; Wloch-Salamon, D.; Korona, R.; Visser, de J.A.G.M.

    2016-01-01

    Coevolution between different biological entities is considered an important evolutionary mechanism at all levels of biological organization. Here we provide evidence for coevolution of a yeast killer strain (K) carrying cytoplasmic dsRNA viruses coding for anti-competitor toxins and an isogenic

  17. Weed populations and crop rotations: exploring dynamics of a structured periodic system

    NARCIS (Netherlands)

    Mertens, S.K.; Bosch, F. van den; Heesterbeek, J.A.P.

    2002-01-01

    The periodic growing of a certain set of crops in a prescribed order, called a crop rotation, is considered to be an important tool for managing weed populations. Nevertheless, the effects of crop rotations on weed population dynamics are not well understood. Explanations for rotation effects on

  18. Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C.

    Science.gov (United States)

    Smukowski Heil, Caiti; Burton, Joshua N; Liachko, Ivan; Friedrich, Anne; Hanson, Noah A; Morris, Cody L; Schacherer, Joseph; Shendure, Jay; Thomas, James H; Dunham, Maitreya J

    2018-01-01

    Interspecific hybridization is a common mechanism enabling genetic diversification and adaptation; however, the detection of hybrid species has been quite difficult. The identification of microbial hybrids is made even more complicated, as most environmental microbes are resistant to culturing and must be studied in their native mixed communities. We have previously adapted the chromosome conformation capture method Hi-C to the assembly of genomes from mixed populations. Here, we show the method's application in assembling genomes directly from an uncultured, mixed population from a spontaneously inoculated beer sample. Our assembly method has enabled us to de-convolute four bacterial and four yeast genomes from this sample, including a putative yeast hybrid. Downstream isolation and analysis of this hybrid confirmed its genome to consist of Pichia membranifaciens and that of another related, but undescribed, yeast. Our work shows that Hi-C-based metagenomic methods can overcome the limitation of traditional sequencing methods in studying complex mixtures of genomes. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  19. Genomics and the making of yeast biodiversity

    NARCIS (Netherlands)

    Hittinger, Chris Todd; Rokas, Antonis; Bai, Feng-Yan; Boekhout, Teun; Gonçalves, Paula; Jeffries, Thomas W; Kominek, Jacek; Lachance, Marc-André; Libkind, Diego; Rosa, Carlos A; Sampaio, José Paulo; Kurtzman, Cletus P

    2015-01-01

    Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has evolved multiple times, most known species belong to the subphylum Saccharomycotina (syn. Hemiascomycota, hereafter yeasts). This diverse group includes the premier eukaryotic model system, Saccharomyces

  20. Relationship between ancient bridges and population dynamics in the lower Yangtze River Basin, China.

    Science.gov (United States)

    Zhao, Yang; Jia, Xin; Lee, Harry F; Zhao, Hongqiang; Cai, Shuliang; Huang, Xianjin

    2017-01-01

    It has been suggested that population growth dynamics may be revealed by the geographic distribution and the physical structure of ancient bridges. Yet, this relationship has not been empirically verified. In this study, we applied the archaeological records for ancient bridges to reveal the population growth dynamics in the lower Yangtze River Basin in late imperial China. We investigated 89 ancient bridges in Yixing that were built during the Ming and Qing dynasties (AD1368-1911). Global Position System information and structure (length, width, and span) of those bridges was measured during our field investigations. Their distribution density was calculated by ArcGIS. The historical socio-economic dynamics of Yixing was inferred from the distribution and structure of ancient bridges. Based on the above information, the population growth dynamics in Yixing was projected. Our results show that 77 bridges were built in Yixing during the Qing dynasty, which is 6.41 times more than the number built during the Ming dynasty. In the Ming dynasty, bridges were built on pivotal routes; in the Qing dynasty, bridges were scattered across various places. Over the period, the density distribution of bridges shifted northwestward, while the average length and width of bridges decreased. The increasing number of bridges corresponded to population growth, largely attributable to massive clan migration from northern China during the Little Ice Age. The shift in the density distribution of bridges corresponded to the formation of settlements of large clans and the blossoming of Yixing Teapot handicrafts. The scattering and the reduction in average length and width of bridges was due to the dispersal of population and the associated formation of small settlements in the latter period. Our approach is innovative and robust, and could be employed to recover long-term historical population growth dynamics in other parts of China.

  1. Relationship between ancient bridges and population dynamics in the lower Yangtze River Basin, China.

    Directory of Open Access Journals (Sweden)

    Yang Zhao

    Full Text Available It has been suggested that population growth dynamics may be revealed by the geographic distribution and the physical structure of ancient bridges. Yet, this relationship has not been empirically verified. In this study, we applied the archaeological records for ancient bridges to reveal the population growth dynamics in the lower Yangtze River Basin in late imperial China. We investigated 89 ancient bridges in Yixing that were built during the Ming and Qing dynasties (AD1368-1911. Global Position System information and structure (length, width, and span of those bridges was measured during our field investigations. Their distribution density was calculated by ArcGIS. The historical socio-economic dynamics of Yixing was inferred from the distribution and structure of ancient bridges. Based on the above information, the population growth dynamics in Yixing was projected. Our results show that 77 bridges were built in Yixing during the Qing dynasty, which is 6.41 times more than the number built during the Ming dynasty. In the Ming dynasty, bridges were built on pivotal routes; in the Qing dynasty, bridges were scattered across various places. Over the period, the density distribution of bridges shifted northwestward, while the average length and width of bridges decreased. The increasing number of bridges corresponded to population growth, largely attributable to massive clan migration from northern China during the Little Ice Age. The shift in the density distribution of bridges corresponded to the formation of settlements of large clans and the blossoming of Yixing Teapot handicrafts. The scattering and the reduction in average length and width of bridges was due to the dispersal of population and the associated formation of small settlements in the latter period. Our approach is innovative and robust, and could be employed to recover long-term historical population growth dynamics in other parts of China.

  2. Yeasts preservation: alternatives for lyophilisation

    OpenAIRE

    Nyanga, Loveness K.; Nout, Martinus J. R.; Smid, Eddy J.; Boekhout, Teun; Zwietering, Marcel H.

    2012-01-01

    The aim of the study was to compare the effect of two low-cost, low technology traditional methods for drying starter cultures with standard lyophilisation. Lyophilised yeast cultures and yeast cultures preserved in dry rice cakes and dry plant fibre strands were examined for viable cell counts during 6 months storage at 4 and 25 °C. None of the yeast cultures showed a significant loss in viable cell count during 6 months of storage at 4 °C upon lyophilisation and preservation in dry rice cak...

  3. Engineered bacterial hydrophobic oligopeptide repeats in a synthetic yeast prion, [REP-PSI+

    Directory of Open Access Journals (Sweden)

    Fátima eGasset-Rosa

    2015-04-01

    Full Text Available The yeast translation termination factor Sup35p, by aggregating as the [PSI+] prion, enables ribosomes to read-through stop codons, thus expanding the diversity of the Saccharomyces cerevisiae proteome. Yeast prions are functional amyloids that replicate by templating their conformation on native protein molecules, then assembling as large aggregates and fibers. Prions propagate epigenetically from mother to daughter cells by fragmentation of such assemblies. In the N-terminal prion-forming domain, Sup35p has glutamine/asparagine-rich oligopeptide repeats (OPRs, which enable propagation through chaperone-elicited shearing. We have engineered chimeras by replacing the polar OPRs in Sup35p by up to five repeats of a hydrophobic amyloidogenic sequence from the synthetic bacterial prionoid RepA-WH1. The resulting hybrid, [REP-PSI+], i was functional in a stop codon read-through assay in S. cerevisiae; ii generates weak phenotypic variants upon both its expression or transformation into [psi-] cells; iii these variants correlated with high molecular weight aggregates resistant to SDS during electrophoresis; and iv according to fluorescence microscopy, the fusion of the prion domains from the engineered chimeras to the reporter protein mCherry generated perivacuolar aggregate foci in yeast cells. All these are signatures of bona fide yeast prions. As assessed through biophysical approaches, the chimeras assembled as oligomers rather than as the fibers characteristic of [PSI+]. These results suggest that it is the balance between polar and hydrophobic residues in OPRs what determines prion conformational dynamics. In addition, our findings illustrate the feasibility of enabling new propagation traits in yeast prions by engineering OPRs with heterologous amyloidogenic sequence repeats.

  4. Synchronization of Budding Yeast by Centrifugal Elutriation.

    Science.gov (United States)

    Rosebrock, Adam P

    2017-01-03

    In yeast, cell size is normally tightly linked to cell cycle progression. Centrifugal elutriation is a method that fractionates cells based on the physical properties of cell size-fluid drag and buoyant density. Using a specially modified centrifuge and rotor system, cells can be physically separated into one or more cohorts of similar size and therefore cell cycle position. Small G 1 daughters are collected first, followed by successively larger cells. Elutriated populations can be analyzed immediately or can be returned to medium and permitted to synchronously progress through the cell cycle. This protocol describes two different elutriation methods. In the first, one or more fractions of synchronized cells are obtained from an asynchronous starting population, reincubated, and followed prospectively across a time series. In the second, an asynchronous starting population is separated into multiple fractions of similarly sized cells, and each cohort of similarly sized cells can be analyzed separately without further growth. © 2017 Cold Spring Harbor Laboratory Press.

  5. Alternating event processes during lifetimes: population dynamics and statistical inference.

    Science.gov (United States)

    Shinohara, Russell T; Sun, Yifei; Wang, Mei-Cheng

    2018-01-01

    In the literature studying recurrent event data, a large amount of work has been focused on univariate recurrent event processes where the occurrence of each event is treated as a single point in time. There are many applications, however, in which univariate recurrent events are insufficient to characterize the feature of the process because patients experience nontrivial durations associated with each event. This results in an alternating event process where the disease status of a patient alternates between exacerbations and remissions. In this paper, we consider the dynamics of a chronic disease and its associated exacerbation-remission process over two time scales: calendar time and time-since-onset. In particular, over calendar time, we explore population dynamics and the relationship between incidence, prevalence and duration for such alternating event processes. We provide nonparametric estimation techniques for characteristic quantities of the process. In some settings, exacerbation processes are observed from an onset time until death; to account for the relationship between the survival and alternating event processes, nonparametric approaches are developed for estimating exacerbation process over lifetime. By understanding the population dynamics and within-process structure, the paper provide a new and general way to study alternating event processes.

  6. Distribution and population dynamics of Rhizobium sp. introduced into soil

    NARCIS (Netherlands)

    Postma, J.

    1989-01-01

    In this thesis the population dynamics of bacteria introduced into soil was studied. In the introduction, the existence of microhabitats favourable for the survival of indigenous bacteria is discussed. Knowledge about the distribution of introduced bacteria over

  7. Cellular-automata model of the dwarf shrubs populations and communities dynamics

    Directory of Open Access Journals (Sweden)

    A. S. Komarov

    2015-06-01

    Full Text Available The probabilistic cellular-automata model of development and long-time dynamics of dwarf shrub populations and communities is developed. It is based on the concept of discrete description of the plant ontogenesis and joint model approaches in terms of probabilistic cellular automata and L-systems by Lindenmayer. Short representation of the basic model allows evaluation of the approach and software implementation. The main variables of the model are a number of partial bushes in clones or area projective cover. The model allows us to investigate the conditions of self-maintenance and sustainability population under different environmental conditions (inaccessibility of the territory for settlement, mosaic moisture conditions of soil and wealth. The model provides a forecast of the total biomass dynamics shrubs and their fractions (stems, leaves, roots, fine roots, fruits on the basis of the data obtained in the discrete description of ontogenesis and further information on the productivity of the plant fractions. The inclusion of the joint dynamics of biomass of shrubs and soil in EFIMOD models cycle of carbon and nitrogen to evaluate the role of shrubs in these circulations, especially at high impact, such as forest fires and clear cutting, allow forecasting of the dynamics of populations and ecosystem functions of shrubs (regulation of biogeochemical cycles maintaining biodiversity, participation in the creation of non-wood products with changing climatic conditions and strong damaging effects (logging, fires; and application of the models developed to investigate the stability and productivity of shrubs and their participation in the cycle of carbon and nitrogen in different climatic and edaphic conditions.

  8. Yeasts Diversity in Fermented Foods and Beverages

    Science.gov (United States)

    Tamang, Jyoti Prakash; Fleet, Graham H.

    People across the world have learnt to culture and use the essential microorganisms for production of fermented foods and alcoholic beverages. A fermented food is produced either spontaneously or by adding mixed/pure starter culture(s). Yeasts are among the essential functional microorganisms encountered in many fermented foods, and are commercially used in production of baker's yeast, breads, wine, beer, cheese, etc. In Asia, moulds are predominant followed by amylolytic and alcohol-producing yeasts in the fermentation processes, whereas in Africa, Europe, Australia and America, fermented products are prepared exclusively using bacteria or bacteria-yeasts mixed cultures. This chapter would focus on the varieties of fermented foods and alcoholic beverages produced by yeasts, their microbiology and role in food fermentation, widely used commercial starters (pilot production, molecular aspects), production technology of some common commercial fermented foods and alcoholic beverages, toxicity and food safety using yeasts cultures and socio-economy

  9. Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis

    DEFF Research Database (Denmark)

    Nosek, J.; Novotna, M.; Hlavatovicova, Z.

    2004-01-01

    The complete sequence of the mitochondrial DNA of the opportunistic yeast pathogen Candida parapsilosis was determined. The mitochondrial genome is represented by linear DNA molecules terminating with tandem repeats of a 738-bp unit. The number of repeats varies, thus generating a population...

  10. Geographic coupling of juvenile and adult habitat shapes spatial population dynamics of a coral reef fish

    NARCIS (Netherlands)

    Huijbers, C.M.; Nagelekerken, I.; Debrot, A.O.; Jongejans, E.

    2013-01-01

    Marine spatial population dynamics are often addressed with a focus on larval dispersal, without taking into account movement behavior of individuals in later life stages. Processes occurring during demersal life stages may also drive spatial population dynamics if habitat quality is perceived

  11. Genetics of Yeasts

    Science.gov (United States)

    Querol, Amparo; Fernández-Espinar, M. Teresa; Belloch, Carmela

    The use of yeasts in biotechnology processes dates back to ancient days. Before 7000 BC, beer was produced in Sumeria. Wine was made in Assyria in 3500 BC, and ancient Rome had over 250 bakeries, which were making leavened bread by 100 BC. And milk has been made into Kefyr and Koumiss in Asia for many centuries (Demain, Phaff, & Kurtzman, 1999). However, the importance of yeast in the food and beverage industries was only realized about 1860, when their role in food manufacturing became evident.

  12. Inheritance of the yeast mitochondrial genome

    DEFF Research Database (Denmark)

    Piskur, Jure

    1994-01-01

    Mitochondrion, extrachromosomal genetics, intergenic sequences, genome size, mitochondrial DNA, petite mutation, yeast......Mitochondrion, extrachromosomal genetics, intergenic sequences, genome size, mitochondrial DNA, petite mutation, yeast...

  13. 21 CFR 172.590 - Yeast-malt sprout extract.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Yeast-malt sprout extract. 172.590 Section 172.590... CONSUMPTION Flavoring Agents and Related Substances § 172.590 Yeast-malt sprout extract. Yeast-malt sprout... prescribed conditions: (a) The additive is produced by partial hydrolysis of yeast extract (derived from...

  14. Yeasts in sustainable bioethanol production: A review.

    Science.gov (United States)

    Mohd Azhar, Siti Hajar; Abdulla, Rahmath; Jambo, Siti Azmah; Marbawi, Hartinie; Gansau, Jualang Azlan; Mohd Faik, Ainol Azifa; Rodrigues, Kenneth Francis

    2017-07-01

    Bioethanol has been identified as the mostly used biofuel worldwide since it significantly contributes to the reduction of crude oil consumption and environmental pollution. It can be produced from various types of feedstocks such as sucrose, starch, lignocellulosic and algal biomass through fermentation process by microorganisms. Compared to other types of microoganisms, yeasts especially Saccharomyces cerevisiae is the common microbes employed in ethanol production due to its high ethanol productivity, high ethanol tolerance and ability of fermenting wide range of sugars. However, there are some challenges in yeast fermentation which inhibit ethanol production such as high temperature, high ethanol concentration and the ability to ferment pentose sugars. Various types of yeast strains have been used in fermentation for ethanol production including hybrid, recombinant and wild-type yeasts. Yeasts can directly ferment simple sugars into ethanol while other type of feedstocks must be converted to fermentable sugars before it can be fermented to ethanol. The common processes involves in ethanol production are pretreatment, hydrolysis and fermentation. Production of bioethanol during fermentation depends on several factors such as temperature, sugar concentration, pH, fermentation time, agitation rate, and inoculum size. The efficiency and productivity of ethanol can be enhanced by immobilizing the yeast cells. This review highlights the different types of yeast strains, fermentation process, factors affecting bioethanol production and immobilization of yeasts for better bioethanol production.

  15. Yeasts in sustainable bioethanol production: A review

    Directory of Open Access Journals (Sweden)

    Siti Hajar Mohd Azhar

    2017-07-01

    Full Text Available Bioethanol has been identified as the mostly used biofuel worldwide since it significantly contributes to the reduction of crude oil consumption and environmental pollution. It can be produced from various types of feedstocks such as sucrose, starch, lignocellulosic and algal biomass through fermentation process by microorganisms. Compared to other types of microoganisms, yeasts especially Saccharomyces cerevisiae is the common microbes employed in ethanol production due to its high ethanol productivity, high ethanol tolerance and ability of fermenting wide range of sugars. However, there are some challenges in yeast fermentation which inhibit ethanol production such as high temperature, high ethanol concentration and the ability to ferment pentose sugars. Various types of yeast strains have been used in fermentation for ethanol production including hybrid, recombinant and wild-type yeasts. Yeasts can directly ferment simple sugars into ethanol while other type of feedstocks must be converted to fermentable sugars before it can be fermented to ethanol. The common processes involves in ethanol production are pretreatment, hydrolysis and fermentation. Production of bioethanol during fermentation depends on several factors such as temperature, sugar concentration, pH, fermentation time, agitation rate, and inoculum size. The efficiency and productivity of ethanol can be enhanced by immobilizing the yeast cells. This review highlights the different types of yeast strains, fermentation process, factors affecting bioethanol production and immobilization of yeasts for better bioethanol production.

  16. Comet assay on tetraploid yeast cells

    DEFF Research Database (Denmark)

    Rank, Jette; Syberg, Kristian; Jensen, Klara

    2009-01-01

    Tetraploid yeast cells (Saccharomyces cerevisiae) were used in the comet assay with the intention of developing a new, fast and easy assay for detecting environmental genotoxic agents without using higher organisms. Two DNA-damaging chemicals, H2O2 and acrylamide, together with wastewater from...... three municipal treatment plants were tested for their effect on the yeast-cell DNA. The main problem with using yeast in the comet assay is the necessity to degrade the cell wall. This was achieved by using Zymolase 100 T twice during the procedure, since Zymolase 20 T did not open the cell wall....... Analytical problems that arose due to the small amount of DNA in the yeast nuclei in haploid and diploid cells, which contain 13 Mbp and 26 Mbp DNA per cell, respectively, were solved by using tetraploid yeast cells (52 Mbp) instead. DNA damage was shown after exposure to H2O2 and acrylamide. The lowest dose...

  17. Growth of non-Saccharomyces yeasts affects nutrient availability for Saccharomyces cerevisiae during wine fermentation.

    Science.gov (United States)

    Medina, Karina; Boido, Eduardo; Dellacassa, Eduardo; Carrau, Francisco

    2012-07-02

    Yeast produces numerous secondary metabolites during fermentation that impact final wine quality. Although it is widely recognized that growth of diverse non-Saccharomyces (NS) yeast can positively affect flavor complexity during Saccharomyces cerevisiae wine fermentation, the inability to control spontaneous or co-fermentation processes by NS yeast has restricted their use in winemaking. We selected two NS yeasts from our Uruguayan native collection to study NS-S. cerevisiae interactions during wine fermentation. The selected strains of Hanseniaspora vineae and Metschnikowia pulcherrima had different yeast assimilable nitrogen consumption profiles and had different effects on S. cerevisiae fermentation and growth kinetics. Studies in which we varied inoculum size and using either simultaneous or sequential inoculation of NS yeast and S. cerevisiae suggested that competition for nutrients had a significant effect on fermentation kinetics. Sluggish fermentations were more pronounced when S. cerevisiae was inoculated 24h after the initial stage of fermentation with a NS strain compared to co-inoculation. Monitoring strain populations using differential WL nutrient agar medium and fermentation kinetics of mixed cultures allowed for a better understanding of strain interactions and nutrient addition effects. Limitation of nutrient availability for S. cerevisiae was shown to result in stuck fermentations as well as to reduce sensory desirability of the resulting wine. Addition of diammonium phosphate (DAP) and a vitamin mix to a defined medium allowed for a comparison of nutrient competition between strains. Addition of DAP and the vitamin mix was most effective in preventing stuck fermentations. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. Yeast diversity during the fermentation of Andean chicha: A comparison of high-throughput sequencing and culture-dependent approaches.

    Science.gov (United States)

    Mendoza, Lucía M; Neef, Alexander; Vignolo, Graciela; Belloch, Carmela

    2017-10-01

    Diversity and dynamics of yeasts associated with the fermentation of Argentinian maize-based beverage chicha was investigated. Samples taken at different stages from two chicha productions were analyzed by culture-dependent and culture-independent methods. Five hundred and ninety six yeasts were isolated by classical microbiological methods and 16 species identified by RFLPs and sequencing of D1/D2 26S rRNA gene. Genetic typing of isolates from the dominant species, Saccharomyces cerevisiae, by PCR of delta elements revealed up to 42 different patterns. High-throughput sequencing (HTS) of D1/D2 26S rRNA gene amplicons from chicha samples detected more than one hundred yeast species and almost fifty filamentous fungi taxa. Analysis of the data revealed that yeasts dominated the fermentation, although, a significant percentage of filamentous fungi appeared in the first step of the process. Statistical analysis of results showed that very few taxa were represented by more than 1% of the reads per sample at any step of the process. S. cerevisiae represented more than 90% of the reads in the fermentative samples. Other yeast species dominated the pre-fermentative steps and abounded in fermented samples when S. cerevisiae was in percentages below 90%. Most yeasts species detected by pyrosequencing were not recovered by cultivation. In contrast, the cultivation-based methodology detected very few yeast taxa, and most of them corresponded with very few reads in the pyrosequencing analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Revaluation of Waste Yeast from Beer Production

    Directory of Open Access Journals (Sweden)

    Nicoleta Suruceanu

    2013-11-01

    Full Text Available Brewing yeast is an important waste product from beer production. The valorification of slurry yeast mainly consists of separation of vitamins and important nitrogen compounds. The hops compounds, one of the most important raw materials in beer technology are removed beforehand valorification. The prenylflavonoids compounds from hops are important bioactive compounds that can be revaluation with proper technology. Revaluation of prenylflavonoids from waste yeast into dietary supplement, identification and quantification of xanthohumol by HPLC method. Waste yeast from brewery pilot plant of USAMV Cluj Napoca it was dried by atomization and the powder was analyzed on xanthohumol content by HPLC method. For quantification a calibration curve it was used. The process of drying by atomisation lead to a powder product. It was used malt dextrin powder for stabilisation. The final product it was encapsulated. The xanthohumol content of powdered yeast it was 1.94 µg/ml. In conclusion the slurry yeast from beer production it is an important source of prenylflavonoids compounds.

  20. Human population and atmospheric carbon dioxide growth dynamics: Diagnostics for the future

    Science.gov (United States)

    Hüsler, A. D.; Sornette, D.

    2014-10-01

    We analyze the growth rates of human population and of atmospheric carbon dioxide by comparing the relative merits of two benchmark models, the exponential law and the finite-time-singular (FTS) power law. The later results from positive feedbacks, either direct or mediated by other dynamical variables, as shown in our presentation of a simple endogenous macroeconomic dynamical growth model describing the growth dynamics of coupled processes involving human population (labor in economic terms), capital and technology (proxies by CO2 emissions). Human population in the context of our energy intensive economies constitutes arguably the most important underlying driving variable of the content of carbon dioxide in the atmosphere. Using some of the best databases available, we perform empirical analyses confirming that the human population on Earth has been growing super-exponentially until the mid-1960s, followed by a decelerated sub-exponential growth, with a tendency to plateau at just an exponential growth in the last decade with an average growth rate of 1.0% per year. In contrast, we find that the content of carbon dioxide in the atmosphere has continued to accelerate super-exponentially until 1990, with a transition to a progressive deceleration since then, with an average growth rate of approximately 2% per year in the last decade. To go back to CO2 atmosphere contents equal to or smaller than the level of 1990 as has been the broadly advertised goals of international treaties since 1990 requires herculean changes: from a dynamical point of view, the approximately exponential growth must not only turn to negative acceleration but also negative velocity to reverse the trend.

  1. Endogenous Population Dynamics and Economic Growth with Free Trade between Countries

    OpenAIRE

    Wei-Bin Zhang

    2016-01-01

    This paper builds a model to deal with dynamic interdependence between different countries' birth rates, mortality rates, populations, wealth accumulation, and time distributions between working, leisure and children caring. The model shows the role of human capital, technological and preference changes on national differences in birth rates, mortality rates, time distributions, population change, and wealth accumulation. The economic mechanisms of wealth accumulation, production and trade ar...

  2. Aboveground Deadwood Deposition Supports Development of Soil Yeasts

    Directory of Open Access Journals (Sweden)

    Thorsten Wehde

    2012-12-01

    Full Text Available Unicellular saprobic fungi (yeasts inhabit soils worldwide. Although yeast species typically occupy defined areas on the biome scale, their distribution patterns within a single type of vegetation, such as forests, are more complex. In order to understand factors that shape soil yeast communities, soils collected underneath decaying wood logs and under forest litter were analyzed. We isolated and identified molecularly a total of 25 yeast species, including three new species. Occurrence and distribution of yeasts isolated from these soils provide new insights into ecology and niche specialization of several soil-borne species. Although abundance of typical soil yeast species varied among experimental plots, the analysis of species abundance and community composition revealed a strong influence of wood log deposition and leakage of organic carbon. Unlike soils underneath logs, yeast communities in adjacent areas harbored a considerable number of transient (phylloplane-related yeasts reaching 30% of the total yeast quantity. We showed that distinguishing autochthonous community members and species transient in soils is essential to estimate appropriate effects of environmental factors on soil fungi. Furthermore, a better understanding of species niches is crucial for analyses of culture-independent data, and may hint to the discovery of unifying patterns of microbial species distribution.

  3. [Distiller Yeasts Producing Antibacterial Peptides].

    Science.gov (United States)

    Klyachko, E V; Morozkina, E V; Zaitchik, B Ts; Benevolensky, S V

    2015-01-01

    A new method of controlling lactic acid bacteria contamination was developed with the use of recombinant Saccharomyces cerevisiae strains producing antibacterial peptides. Genes encoding the antibacterial peptides pediocin and plantaricin with codons preferable for S. cerevisiae were synthesized, and a system was constructed for their secretory expression. Recombinant S. cerevisiae strains producing antibacterial peptides effectively inhibit the growth of Lactobacillus sakei, Pediacoccus pentasaceus, Pediacoccus acidilactici, etc. The application of distiller yeasts producing antibacterial peptides enhances the ethanol yield in cases of bacterial contamination. Recombinant yeasts producing the antibacterial peptides pediocin and plantaricin can successfully substitute the available industrial yeast strains upon ethanol production.

  4. Comparison of New and Traditional Culture-Dependent Media for Enumerating Foodborne Yeasts and Molds.

    Science.gov (United States)

    Beuchat, Larry R; Mann, David A

    2016-01-01

    Fifty-six foods and food ingredients were analyzed for populations of naturally occurring yeasts and molds using Petrifilm rapid yeast and mold (RYM) count plates, Petrifilm yeast and mold (YM) count plates, dichloran rose bengal chloramphenicol (DRBC) agar plates, acidified potato dextrose agar (APDA) plates, and dichloran 18% glycerol (DG18) agar plates. Colonies were counted after incubating plates for 48, 72, and 120 h at 25°C. Of 56 foods in which either yeasts or molds were detected on at least one medium incubated for 120 h, neither yeasts nor molds were detected in 55.4, 73.2, 21.4, 19.6, and 71.4% of foods plated on the five respective media and incubated for 48 h; 10.7, 14.3, 3.6, 1.8, and 19.6% of foods were negative after 72 h, and 3.6, 1.8, 0, 0, and 0% of foods were negative after 120 h. Considering all enumeration media, correlation coefficients were 0.03 to 0.97 at 48 h of incubation; these values increased to 0.75 to 0.99 at 120 h. Coefficients of variation for total yeasts and molds were as high as 30.0, 30.8, and 27.2% at 48, 72, and 120 h, respectively. The general order of performance was DRBC = APDA > RYM Petrifilm > YM Petrifilm ≥ DG18 when plates were incubated for 48 h, DRBC > APDA > RYM Petrifilm > YM Petrifilm ≥ DG18 when plates were incubated for 72 h, and DRBC > APDA > RYM Petrifilm > YM Petrifilm > DG18 when plates were incubated for 120 h. Differences in performance among media are attributed to the diversity of yeasts and molds likely to be present in test foods and differences in nutrient, pH, and water activity requirements for resuscitation of stressed cells and colony development.

  5. Fast stochastic algorithm for simulating evolutionary population dynamics

    Science.gov (United States)

    Tsimring, Lev; Hasty, Jeff; Mather, William

    2012-02-01

    Evolution and co-evolution of ecological communities are stochastic processes often characterized by vastly different rates of reproduction and mutation and a coexistence of very large and very small sub-populations of co-evolving species. This creates serious difficulties for accurate statistical modeling of evolutionary dynamics. In this talk, we introduce a new exact algorithm for fast fully stochastic simulations of birth/death/mutation processes. It produces a significant speedup compared to the direct stochastic simulation algorithm in a typical case when the total population size is large and the mutation rates are much smaller than birth/death rates. We illustrate the performance of the algorithm on several representative examples: evolution on a smooth fitness landscape, NK model, and stochastic predator-prey system.

  6. Optimal growth entails risky localization in population dynamics

    Science.gov (United States)

    Gueudré, Thomas; Martin, David G.

    2018-03-01

    Essential to each other, growth and exploration are jointly observed in alive and inanimate entities, such as animals, cells or goods. But how the environment's structural and temporal properties weights in this balance remains elusive. We analyze a model of stochastic growth with time correlations and diffusive dynamics that sheds light on the way populations grow and spread over general networks. This model suggests natural explanations of empirical facts in econo-physics or ecology, such as the risk-return trade-off and the Zipf law. We conclude that optimal growth leads to a localized population distribution, but such risky position can be mitigated through the space geometry. These results have broad applicability and are subsequently illustrated over an empirical study of financial data.

  7. The growth of solar radiated yeast

    Energy Technology Data Exchange (ETDEWEB)

    Kraft, T.

    1995-09-01

    This researcher plans to determine if solar radiation affects the growth of yeast. The irradiated yeast was obtained from a sample exposed in space during a Space Shuttle flight of September 9-20, 1994. Further, the control groups were held at: (1) Goddard Space Flight Center (GSFC) in Greenbelt, Maryland; and (2) South Dakota School of Mines and Technology. The procedure used was based on the fact that yeast is most often used in consumable baked goods. Therefore, the yeast was incorporated into a basic Betty Crocker bread recipe. Data was collected by placing measured amounts of dough into sample containers with fifteen minute growth in height measurements collected and recorded. This researcher assumed the viability of yeast to be relative to its ability to produce carbon dioxide gas and cause the dough to rise. As all ingredients and surroundings were equal, this researcher assumed the yeast will produce the only significant difference in data collected. This researcher noted the approximate use date on all sample packages to be prior to arrival and experiment date. All dates equal, it was then assumed each would act in a similar manner of response. This assumption will allow for equally correct data collection.

  8. The growth of solar radiated yeast

    Science.gov (United States)

    Kraft, Tyrone

    1995-01-01

    This researcher plans to determine if solar radiation affects the growth of yeast. The irradiated yeast was obtained from a sample exposed in space during a Space Shuttle flight of September 9-20, 1994. Further, the control groups were held at: (1) Goddard Space Flight Center (GSFC) in Greenbelt, Maryland; and (2) South Dakota School of Mines and Technology. The procedure used was based on the fact that yeast is most often used in consumable baked goods. Therefore, the yeast was incorporated into a basic Betty Crocker bread recipe. Data was collected by placing measured amounts of dough into sample containers with fifteen minute growth in height measurements collected and recorded. This researcher assumed the viability of yeast to be relative to its ability to produce carbon dioxide gas and cause the dough to rise. As all ingredients and surroundings were equal, this researcher assumed the yeast will produce the only significant difference in data collected. This researcher noted the approximate use date on all sample packages to be prior to arrival and experiment date. All dates equal, it was then assumed each would act in a similar manner of response. This assumption will allow for equally correct data collection.

  9. Analysis of Population Diversity of Dynamic Probabilistic Particle Swarm Optimization Algorithms

    Directory of Open Access Journals (Sweden)

    Qingjian Ni

    2014-01-01

    Full Text Available In evolutionary algorithm, population diversity is an important factor for solving performance. In this paper, combined with some population diversity analysis methods in other evolutionary algorithms, three indicators are introduced to be measures of population diversity in PSO algorithms, which are standard deviation of population fitness values, population entropy, and Manhattan norm of standard deviation in population positions. The three measures are used to analyze the population diversity in a relatively new PSO variant—Dynamic Probabilistic Particle Swarm Optimization (DPPSO. The results show that the three measure methods can fully reflect the evolution of population diversity in DPPSO algorithms from different angles, and we also discuss the impact of population diversity on the DPPSO variants. The relevant conclusions of the population diversity on DPPSO can be used to analyze, design, and improve the DPPSO algorithms, thus improving optimization performance, which could also be beneficial to understand the working mechanism of DPPSO theoretically.

  10. Dynamic population gratings in rare-earth-doped optical fibres

    Energy Technology Data Exchange (ETDEWEB)

    Stepanov, Serguei [Optics Department, CICESE, km.107 carr. Tijuana-Ensenada, Ensenada, 22860, BC (Mexico)], E-mail: steps@cicese.mx

    2008-11-21

    Dynamic Bragg gratings can be recorded in rare-earth (e.g. Er, Yb) doped optical fibres by two counter-propagating mutually coherent laser waves via local saturation of the fibre optical absorption or gain (in optically pumped fibres). Typical recording cw light power needed for efficient grating formation is of sub-mW-mW scale which results in characteristic recording/erasure times of 10-0.1 ms. This review paper discusses fundamental aspects of the population grating formation, their basic properties, relating wave-mixing processes and also considers different applications of these dynamic gratings in single-frequency fibre lasers, tunable filters, optical fibre sensors and adaptive interferometry.

  11. Dynamic population gratings in rare-earth-doped optical fibres

    International Nuclear Information System (INIS)

    Stepanov, Serguei

    2008-01-01

    Dynamic Bragg gratings can be recorded in rare-earth (e.g. Er, Yb) doped optical fibres by two counter-propagating mutually coherent laser waves via local saturation of the fibre optical absorption or gain (in optically pumped fibres). Typical recording cw light power needed for efficient grating formation is of sub-mW-mW scale which results in characteristic recording/erasure times of 10-0.1 ms. This review paper discusses fundamental aspects of the population grating formation, their basic properties, relating wave-mixing processes and also considers different applications of these dynamic gratings in single-frequency fibre lasers, tunable filters, optical fibre sensors and adaptive interferometry.

  12. Population Dynamics of the Mediterranean Fruit Fly in Montenegro

    Directory of Open Access Journals (Sweden)

    Sanja Radonjić

    2013-01-01

    Full Text Available Population dynamics of the Mediterranean fruit fly was studied along Montenegro seacoast. Tephri traps baited with 3 component female-biased attractants were used in 11 different localities to monitor the fruit fly population in commercial citrus orchards, mixed-fruit orchards, and in backyards. From 2008–2010, the earliest captures were recorded no earlier than July. In 2011, the first adult fly was detected in mid-June. Low captures rates were recorded in July and August (below 0.5 flies per trap per day; FTD and peaked from mid-September to the end of October of each year. Our results indicate fluctuation of fly per trap per day depending on dates of inspection and locality, with significant differences in the adult population density. A maximum population was always reached in the area of Budva-Herceg Novi with an FTD of 66.5, 89.5, 71.63, and 24.64 (from 2008–2011 respectively. Fly activity lasts from mid-June/early-July to end December, with distinct seasonal variation in the population.

  13. Binding properties of SUMO-interacting motifs (SIMs) in yeast.

    Science.gov (United States)

    Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

    2015-03-01

    Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

  14. Sensitivity Analysis for Assessing Effects of Tree Population Dynamics on Soil Bioturbation

    Science.gov (United States)

    Martin, Y. E.; Johnson, E. A.

    2012-12-01

    Bioturbation due to tree root throw is thought to be an important process in soil production and soil mixing. Despite progress in our understanding of root throw processes, the tree population dynamics affecting the occurrence and timing of root throw events remain much less well explained. Unfortunately, research about forest dynamics is not always undertaken from the perspective of those interested in tree death, tree topple and associated root throw. As a result, the necessary field data about tree population dynamics is often unavailable for many locations. The acquisition of such data would allow for improved interpretation of root throw observations and for incorporation within numerical models of tree root throw occurrence. The present study uses our earlier tree population dynamics model calibrated for subalpine forests in the Canadian Rockies to test the sensitivity of forest parameters within the model that determine tree death, tree topple, root throw and soil bioturbation. Crown wildfire disturbance is the primary driver of tree population dynamics, with wind throw being mainly of local importance. The recruitment and mortality of trees during multiple generations of forest determine the number of live trees on the landscape at any given time. Tree death may occur due to competition/thinning of trees between wildfire events or as a result of the wildfire itself. Unless trees die due to sudden wind throw events (as mentioned above, this is only of local significance in our study area), they remain standing for some time period after tree death and before tree topple; these trees are referred to as standing dead trees. The duration of this time window and several other factors influence if a tree breaks at its base or upheaves a relatively intact root plate with attached sediment. Our field research has also suggested that a minimum dbh is required before a root plate is large enough to upheave notable amounts of sediment. Modelling results in this study

  15. Sporulation genes associated with sporulation efficiency in natural isolates of yeast.

    Science.gov (United States)

    Tomar, Parul; Bhatia, Aatish; Ramdas, Shweta; Diao, Liyang; Bhanot, Gyan; Sinha, Himanshu

    2013-01-01

    Yeast sporulation efficiency is a quantitative trait and is known to vary among experimental populations and natural isolates. Some studies have uncovered the genetic basis of this variation and have identified the role of sporulation genes (IME1, RME1) and sporulation-associated genes (FKH2, PMS1, RAS2, RSF1, SWS2), as well as non-sporulation pathway genes (MKT1, TAO3) in maintaining this variation. However, these studies have been done mostly in experimental populations. Sporulation is a response to nutrient deprivation. Unlike laboratory strains, natural isolates have likely undergone multiple selections for quick adaptation to varying nutrient conditions. As a result, sporulation efficiency in natural isolates may have different genetic factors contributing to phenotypic variation. Using Saccharomyces cerevisiae strains in the genetically and environmentally diverse SGRP collection, we have identified genetic loci associated with sporulation efficiency variation in a set of sporulation and sporulation-associated genes. Using two independent methods for association mapping and correcting for population structure biases, our analysis identified two linked clusters containing 4 non-synonymous mutations in genes - HOS4, MCK1, SET3, and SPO74. Five regulatory polymorphisms in five genes such as MLS1 and CDC10 were also identified as putative candidates. Our results provide candidate genes contributing to phenotypic variation in the sporulation efficiency of natural isolates of yeast.

  16. Scaling of the mean and variance of population dynamics under fluctuating regimes.

    Science.gov (United States)

    Pertoldi, Cino; Faurby, S; Reed, D H; Knape, J; Björklund, M; Lundberg, P; Kaitala, V; Loeschcke, V; Bach, L A

    2014-12-01

    Theoretical ecologists have long sought to understand how the persistence of populations depends on the interactions between exogenous (biotic and abiotic) and endogenous (e.g., demographic and genetic) drivers of population dynamics. Recent work focuses on the autocorrelation structure of environmental perturbations and its effects on the persistence of populations. Accurate estimation of extinction times and especially determination of the mechanisms affecting extinction times is important for biodiversity conservation. Here we examine the interaction between environmental fluctuations and the scaling effect of the mean population size with its variance. We investigate how interactions between environmental and demographic stochasticity can affect the mean time to extinction, change optimal patch size dynamics, and how it can alter the often-assumed linear relationship between the census size and the effective population size. The importance of the correlation between environmental and demographic variation depends on the relative importance of the two types of variation. We found the correlation to be important when the two types of variation were approximately equal; however, the importance of the correlation diminishes as one source of variation dominates. The implications of these findings are discussed from a conservation and eco-evolutionary point of view.

  17. [Population dynamics of oligosporous actinomycetes in Chernozem soil].

    Science.gov (United States)

    Zenova, G M; Mikhaĭlova, N V; Zviagintsev, D G

    2000-01-01

    Investigation of the dynamics of an oligosporous actinomycete population in chernozem soil in the course of succession induced by soil wetting allowed us to reveal the time intervals and conditions optimal for the isolation of particular oligosporous actinomycetes. Saccharopolysporas and microbisporas proved to be best isolated in the early and late stages of succession, whereas actinomycetes of the subgroup Actinomadura and saccharomonosporas could be best isolated in the early and intermediate stages of succession.

  18. Scheffersomyces cryptocercus: a new xylose-fermenting yeast associated with the gut of wood roaches and new combinations in the Sugiyamaella yeast clade.

    Science.gov (United States)

    Urbina, Hector; Frank, Robert; Blackwell, Meredith

    2013-01-01

    The gut of wood-feeding insects is a microhabitat for a specialized community of microbes, including bacteria and several groups of eukaryotes such as nematodes, parabasalids and fungi. The characterization of gut yeast communities from a variety of insects has shown that certain yeasts often are associated with the insects. The gut of wood-feeding insects is rich in ascomycete yeasts and in particular xylose-fermenting (X-F) and assimilating yeasts have been consistently present in the gut of lignicolous insects. The objective of this study was the characterization of the yeast flora from the gut of the wood roach Cryptocercus sp. (Blattodea: Cryptocercidae). Five wood roaches were collected along the Appalachian Trail near the border between Tennessee and North Carolina, USA. We isolated 18 yeast strains from the wood roaches identified as Sugiyamaella paludigena and Sugiyamaella lignohabitans, xylose-assimilating yeasts, and Scheffersomyces cryptocercus (NRRL Y-48824(T) = CBS 12658) a new species of X-F yeast. The presence of X-F and certain non X-F yeasts in the gut of the subsocial wood roach Cryptocercus sp. extends the previous findings of associations between certain ascomycete yeasts and lignicolous insects. New combinations were made for 13 asexual members of the Sugiyamaella clade.

  19. Lipidomics in research on yeast membrane lipid homeostasis.

    Science.gov (United States)

    de Kroon, Anton I P M

    2017-08-01

    Mass spectrometry is increasingly used in research on membrane lipid homeostasis, both in analyses of the steady state lipidome at the level of molecular lipid species, and in pulse-chase approaches employing stable isotope-labeled lipid precursors addressing the dynamics of lipid metabolism. Here my experience with, and view on mass spectrometry-based lipid analysis is presented, with emphasis on aspects of quantification of membrane lipid composition of the yeast Saccharomyces cerevisiae. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Dynamic study of yeast species and Saccharomyces cerevisiae strains during the spontaneous fermentations of Muscat blanc in Jingyang, China.

    Science.gov (United States)

    Wang, Chunxiao; Liu, Yanlin

    2013-04-01

    The evolution of yeast species and Saccharomyces cerevisiae genotypes during spontaneous fermentations of Muscat blanc planted in 1957 in Jingyang region of China was followed in this study. Using a combination of colony morphology on Wallerstein Nutrient (WLN) medium, sequence analysis of the 26S rDNA D1/D2 domain and 5.8S-ITS-RFLP analysis, a total of 686 isolates were identified at the species level. The six species identified were S. cerevisiae, Hanseniaspora uvarum, Hanseniaspora opuntiae, Issatchenkia terricola, Pichia kudriavzevii (Issatchenkia orientalis) and Trichosporon coremiiforme. This is the first report of T. coremiiforme as an inhabitant of grape must. Three new colony morphologies on WLN medium and one new 5.8S-ITS-RFLP profile are described. Species of non-Saccharomyces, predominantly H. opuntiae, were found in early stages of fermentation. Subsequently, S. cerevisiae prevailed followed by large numbers of P. kudriavzevii that dominated at the end of fermentations. Six native genotypes of S. cerevisiae were determined by interdelta sequence analysis. Genotypes III and IV were predominant. As a first step in exploring untapped yeast resources of the region, this study is important for monitoring the yeast ecology in native fermentations and screening indigenous yeasts that will produce wines with regional characteristics. Copyright © 2012 Elsevier Ltd. All rights reserved.

  1. Effect of increasing growth temperature on yeast fermentation ...

    African Journals Online (AJOL)

    The effect of increasing growth temperature on yeast fermentation was studied at approximately 5 oC intervals over a range of 18 – 37 oC, using one strain each of ale, lager and wine yeast. The ale and wine yeasts grew at all the temperatures tested, but lager yeast failed to grow at 37 oC. All these strains gave lower ...

  2. Yeasts preservation: alternatives for lyophilisation

    NARCIS (Netherlands)

    Nyanga, L.K.; Nout, M.J.R.; Smid, E.J.; Boekhout, T.; Zwietering, M.H.

    2012-01-01

    The aim of the study was to compare the effect of two low-cost, low technology traditional methods for drying starter cultures with standard lyophilisation. Lyophilised yeast cultures and yeast cultures preserved in dry rice cakes and dry plant fibre strands were examined for viable cell counts

  3. Biotechnology of non-Saccharomyces yeasts--the ascomycetes.

    Science.gov (United States)

    Johnson, Eric A

    2013-01-01

    Saccharomyces cerevisiae and several other yeast species are among the most important groups of biotechnological organisms. S. cerevisiae and closely related ascomycetous yeasts are the major producer of biotechnology products worldwide, exceeding other groups of industrial microorganisms in productivity and economic revenues. Traditional industrial attributes of the S. cerevisiae group include their primary roles in food fermentations such as beers, cider, wines, sake, distilled spirits, bakery products, cheese, sausages, and other fermented foods. Other long-standing industrial processes involving S. cerevisae yeasts are production of fuel ethanol, single-cell protein (SCP), feeds and fodder, industrial enzymes, and small molecular weight metabolites. More recently, non-Saccharomyces yeasts (non-conventional yeasts) have been utilized as industrial organisms for a variety of biotechnological roles. Non-Saccharomyces yeasts are increasingly being used as hosts for expression of proteins, biocatalysts and multi-enzyme pathways for the synthesis of fine chemicals and small molecular weight compounds of medicinal and nutritional importance. Non-Saccharomyces yeasts also have important roles in agriculture as agents of biocontrol, bioremediation, and as indicators of environmental quality. Several of these products and processes have reached commercial utility, while others are in advanced development. The objective of this mini-review is to describe processes currently used by industry and those in developmental stages and close to commercialization primarily from non-Saccharomyces yeasts with an emphasis on new opportunities. The utility of S. cerevisiae in heterologous production of selected products is also described.

  4. Experimental test of an eco-evolutionary dynamic feedback loop between evolution and population density in the green peach aphid.

    Science.gov (United States)

    Turcotte, Martin M; Reznick, David N; Daniel Hare, J

    2013-05-01

    An eco-evolutionary feedback loop is defined as the reciprocal impacts of ecology on evolutionary dynamics and evolution on ecological dynamics on contemporary timescales. We experimentally tested for an eco-evolutionary feedback loop in the green peach aphid, Myzus persicae, by manipulating initial densities and evolution. We found strong evidence that initial aphid density alters the rate and direction of evolution, as measured by changes in genotype frequencies through time. We also found that evolution of aphids within only 16 days, or approximately three generations, alters the rate of population growth and predicts density compared to nonevolving controls. The impact of evolution on population dynamics also depended on density. In one evolution treatment, evolution accelerated population growth by up to 10.3% at high initial density or reduced it by up to 6.4% at low initial density. The impact of evolution on population growth was as strong as or stronger than that caused by a threefold change in intraspecific density. We found that, taken together, ecological condition, here intraspecific density, alters evolutionary dynamics, which in turn alter concurrent population growth rate (ecological dynamics) in an eco-evolutionary feedback loop. Our results suggest that ignoring evolution in studies predicting population dynamics might lead us to over- or underestimate population density and that we cannot predict the evolutionary outcome within aphid populations without considering population size.

  5. Trehalose-6-phosphate synthase and stabilization of yeast glycolysis

    DEFF Research Database (Denmark)

    Fraenkel, Dan; Nielsen, Jens

    2016-01-01

    ‘Lost in transition: Startup of glycolysis yields subpopulations of nongrowing cells…’ (‘LIT’, van Heerden et al. 2014) is a massive paper from groups in Amsterdam and Delft, which deals with broad issues in metabolism and cell heterogeneity, as addressed for the predominant metabolic pathway......, glycolysis, in the context of a long studied but incompletely understood yeast mutant which is impaired in use of glucose without evident direct defects in the pathway. The primary approach is the quite original one of predicting, for the mutant, the dynamics of metabolism upon glucose addition, based...

  6. Taming wild yeast: potential of conventional and nonconventional yeasts in industrial fermentations.

    Science.gov (United States)

    Steensels, Jan; Verstrepen, Kevin J

    2014-01-01

    Yeasts are the main driving force behind several industrial food fermentation processes, including the production of beer, wine, sake, bread, and chocolate. Historically, these processes developed from uncontrolled, spontaneous fermentation reactions that rely on a complex mixture of microbes present in the environment. Because such spontaneous processes are generally inconsistent and inefficient and often lead to the formation of off-flavors, most of today's industrial production utilizes defined starter cultures, often consisting of a specific domesticated strain of Saccharomyces cerevisiae, S. bayanus, or S. pastorianus. Although this practice greatly improved process consistency, efficiency, and overall quality, it also limited the sensorial complexity of the end product. In this review, we discuss how Saccharomyces yeasts were domesticated to become the main workhorse of food fermentations, and we investigate the potential and selection of nonconventional yeasts that are often found in spontaneous fermentations, such as Brettanomyces, Hanseniaspora, and Pichia spp.

  7. Yeast alter micro-oxygenation of wine: oxygen consumption and aldehyde production.

    Science.gov (United States)

    Han, Guomin; Webb, Michael R; Richter, Chandra; Parsons, Jessica; Waterhouse, Andrew L

    2017-08-01

    Micro-oxygenation (MOx) is a common winemaking treatment used to improve red wine color development and diminish vegetal aroma, amongst other effects. It is commonly applied to wine immediately after yeast fermentation (phase 1) or later, during aging (phase 2). Although most winemakers avoid MOx during malolactic (ML) fermentation, it is often not possible to avoid because ML bacteria are often present during phase 1 MOx treatment. We investigated the effect of common yeast and bacteria on the outcome of micro-oxygenation. Compared to sterile filtered wine, Saccharomyces cerevisiae inoculation significantly increased oxygen consumption, keeping dissolved oxygen in wine below 30 µg L -1 during micro-oxygenation, whereas Oenococcus oeni inoculation was not associated with a significant impact on the concentration of dissolved oxygen. The unfiltered baseline wine also had both present, although with much higher populations of bacteria and consumed oxygen. The yeast-treated wine yielded much higher levels of acetaldehyde, rising from 4.3 to 29 mg L -1 during micro-oxygenation, whereas no significant difference was found between the bacteria-treated wine and the filtered control. The unfiltered wine exhibited rapid oxygen consumption but no additional acetaldehyde, as well as reduced pyruvate. Analysis of the acetaldehyde-glycerol acetal levels showed a good correlation with acetaldehyde concentrations. The production of acetaldehyde is a key outcome of MOx and it is dramatically increased in the presence of yeast, although it is possibly counteracted by the metabolism of O. oeni bacteria. Additional controlled experiments are necessary to clarify the interaction of yeast and bacteria during MOx treatments. Analysis of the glycerol acetals may be useful as a proxy for acetaldehyde levels. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  8. About a dynamic model of interaction of insect population with food plant

    Directory of Open Access Journals (Sweden)

    L.V. Nedorezov

    2011-12-01

    Full Text Available In present paper there is the consideration of mathematical model of food plant (resource - consumer (insect population - pathogen system dynamics which is constructed as a system of ordinary differential equations. The dynamic regimes of model are analyzed and, in particular, with the help of numerical methods it is shown that trigger regimes (regimes with two stable attractors can be realized in model under very simple assumptions about ecological and intra-population processes functioning. Within the framework of model it was assumed that the rate of food flow into the system is constant and functioning of intra-population selfregulative mechanisms can be described by Verhulst model. As it was found, trigger regimes are different with respect to their properties: in particular, in model the trigger regimes with one of stable stationary points on the coordinate plane can be realized (it corresponds to the situation when sick individuals in population are absent and their appearance in small volume leads to their asymptotic elimination; also the regimes with several nonzero stationary states and stable periodic fluctuations were found.

  9. CONNECTION BETWEEN DYNAMICALLY DERIVED INITIAL MASS FUNCTION NORMALIZATION AND STELLAR POPULATION PARAMETERS

    International Nuclear Information System (INIS)

    McDermid, Richard M.; Cappellari, Michele; Bayet, Estelle; Bureau, Martin; Davies, Roger L.; Alatalo, Katherine; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Duc, Pierre-Alain; Crocker, Alison F.; Davis, Timothy A.; De Zeeuw, P. T.; Emsellem, Eric; Kuntschner, Harald; Khochfar, Sadegh; Krajnović, Davor; Morganti, Raffaella; Oosterloo, Tom; Naab, Thorsten

    2014-01-01

    We report on empirical trends between the dynamically determined stellar initial mass function (IMF) and stellar population properties for a complete, volume-limited sample of 260 early-type galaxies from the ATLAS 3D project. We study trends between our dynamically derived IMF normalization α dyn ≡ (M/L) stars /(M/L) Salp and absorption line strengths, and interpret these via single stellar population-equivalent ages, abundance ratios (measured as [α/Fe]), and total metallicity, [Z/H]. We find that old and alpha-enhanced galaxies tend to have on average heavier (Salpeter-like) mass normalization of the IMF, but stellar population does not appear to be a good predictor of the IMF, with a large range of α dyn at a given population parameter. As a result, we find weak α dyn -[α/Fe] and α dyn –Age correlations and no significant α dyn –[Z/H] correlation. The observed trends appear significantly weaker than those reported in studies that measure the IMF normalization via the low-mass star demographics inferred through stellar spectral analysis

  10. Connection between Dynamically Derived Initial Mass Function Normalization and Stellar Population Parameters

    Science.gov (United States)

    McDermid, Richard M.; Cappellari, Michele; Alatalo, Katherine; Bayet, Estelle; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Bureau, Martin; Crocker, Alison F.; Davies, Roger L.; Davis, Timothy A.; de Zeeuw, P. T.; Duc, Pierre-Alain; Emsellem, Eric; Khochfar, Sadegh; Krajnović, Davor; Kuntschner, Harald; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Scott, Nicholas; Serra, Paolo; Weijmans, Anne-Marie; Young, Lisa M.

    2014-09-01

    We report on empirical trends between the dynamically determined stellar initial mass function (IMF) and stellar population properties for a complete, volume-limited sample of 260 early-type galaxies from the ATLAS3D project. We study trends between our dynamically derived IMF normalization αdyn ≡ (M/L)stars/(M/L)Salp and absorption line strengths, and interpret these via single stellar population-equivalent ages, abundance ratios (measured as [α/Fe]), and total metallicity, [Z/H]. We find that old and alpha-enhanced galaxies tend to have on average heavier (Salpeter-like) mass normalization of the IMF, but stellar population does not appear to be a good predictor of the IMF, with a large range of αdyn at a given population parameter. As a result, we find weak αdyn-[α/Fe] and αdyn -Age correlations and no significant αdyn -[Z/H] correlation. The observed trends appear significantly weaker than those reported in studies that measure the IMF normalization via the low-mass star demographics inferred through stellar spectral analysis.

  11. Introducing a new breed of wine yeast: interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast and Saccharomyces mikatae.

    Science.gov (United States)

    Bellon, Jennifer R; Schmid, Frank; Capone, Dimitra L; Dunn, Barbara L; Chambers, Paul J

    2013-01-01

    Interspecific hybrids are commonplace in agriculture and horticulture; bread wheat and grapefruit are but two examples. The benefits derived from interspecific hybridisation include the potential of generating advantageous transgressive phenotypes. This paper describes the generation of a new breed of wine yeast by interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast strain and Saccharomyces mikatae, a species hitherto not associated with industrial fermentation environs. While commercially available wine yeast strains provide consistent and reliable fermentations, wines produced using single inocula are thought to lack the sensory complexity and rounded palate structure obtained from spontaneous fermentations. In contrast, interspecific yeast hybrids have the potential to deliver increased complexity to wine sensory properties and alternative wine styles through the formation of novel, and wider ranging, yeast volatile fermentation metabolite profiles, whilst maintaining the robustness of the wine yeast parent. Screening of newly generated hybrids from a cross between a S. cerevisiae wine yeast and S. mikatae (closely-related but ecologically distant members of the Saccharomyces sensu stricto clade), has identified progeny with robust fermentation properties and winemaking potential. Chemical analysis showed that, relative to the S. cerevisiae wine yeast parent, hybrids produced wines with different concentrations of volatile metabolites that are known to contribute to wine flavour and aroma, including flavour compounds associated with non-Saccharomyces species. The new S. cerevisiae x S. mikatae hybrids have the potential to produce complex wines akin to products of spontaneous fermentation while giving winemakers the safeguard of an inoculated ferment.

  12. Phenotypic equilibrium as probabilistic convergence in multi-phenotype cell population dynamics.

    Directory of Open Access Journals (Sweden)

    Da-Quan Jiang

    Full Text Available We consider the cell population dynamics with n different phenotypes. Both the Markovian branching process model (stochastic model and the ordinary differential equation (ODE system model (deterministic model are presented, and exploited to investigate the dynamics of the phenotypic proportions. We will prove that in both models, these proportions will tend to constants regardless of initial population states ("phenotypic equilibrium" under weak conditions, which explains the experimental phenomenon in Gupta et al.'s paper. We also prove that Gupta et al.'s explanation is the ODE model under a special assumption. As an application, we will give sufficient and necessary conditions under which the proportion of one phenotype tends to 0 (die out or 1 (dominate. We also extend our results to non-Markovian cases.

  13. Population dynamics of Greater Scaup breeding on the Yukon-Kuskokwim Delta, Alaska

    Science.gov (United States)

    Flint, Paul L.; Grand, J. Barry; Fondell, Thomas F.; Morse, Julie A.

    2006-01-01

    Populations of greater scaup (Aythya marila) remained relatively stable during a period when populations of lesser scaup (A. affinis) have declined from historic levels. To assist in describing these differences in population trends, from 1991 through 2000, we studied the survival, nesting ecology, and productivity of greater scaup on the Yukon-Kuskokwim Delta (Y-K Delta), Alaska, to develop a model of population dynamics. We located nests, radio-marked females for renesting studies, estimated duckling survival, and leg-banded females to examine nest site fidelity and annual survival.

  14. Integrating count and detection–nondetection data to model population dynamics

    Science.gov (United States)

    Zipkin, Elise F.; Rossman, Sam; Yackulic, Charles B.; Wiens, David; Thorson, James T.; Davis, Raymond J.; Grant, Evan H. Campbell

    2017-01-01

    There is increasing need for methods that integrate multiple data types into a single analytical framework as the spatial and temporal scale of ecological research expands. Current work on this topic primarily focuses on combining capture–recapture data from marked individuals with other data types into integrated population models. Yet, studies of species distributions and trends often rely on data from unmarked individuals across broad scales where local abundance and environmental variables may vary. We present a modeling framework for integrating detection–nondetection and count data into a single analysis to estimate population dynamics, abundance, and individual detection probabilities during sampling. Our dynamic population model assumes that site-specific abundance can change over time according to survival of individuals and gains through reproduction and immigration. The observation process for each data type is modeled by assuming that every individual present at a site has an equal probability of being detected during sampling processes. We examine our modeling approach through a series of simulations illustrating the relative value of count vs. detection–nondetection data under a variety of parameter values and survey configurations. We also provide an empirical example of the model by combining long-term detection–nondetection data (1995–2014) with newly collected count data (2015–2016) from a growing population of Barred Owl (Strix varia) in the Pacific Northwest to examine the factors influencing population abundance over time. Our model provides a foundation for incorporating unmarked data within a single framework, even in cases where sampling processes yield different detection probabilities. This approach will be useful for survey design and to researchers interested in incorporating historical or citizen science data into analyses focused on understanding how demographic rates drive population abundance.

  15. Long-term population dynamics of a managed burrowing owl colony

    Science.gov (United States)

    Barclay, John H.; Korfanta, Nicole M.; Kauffman, Matthew J.

    2011-01-01

    We analyzed the population dynamics of a burrowing owl (Athene cunicularia) colony at Mineta San Jose International Airport in San Jose, California, USA from 1990-2007. This colony was managed by using artificial burrows to reduce the occurrence of nesting owls along runways and within major airport improvement projects during the study period. We estimated annual reproduction in natural and artificial burrows and age-specific survival rates with mark-recapture techniques, and we estimated the relative contribution of these vital rates to population dynamics using a life table response experiment. The breeding colony showed 2 distinct periods of change: high population growth from 7 nesting pairs in 1991 to 40 pairs in 2002 and population decline to 17 pairs in 2007. Reproduction was highly variable: annual nesting success (pairs that raised =1 young) averaged 79% and ranged from 36% to 100%, whereas fecundity averaged 3.36 juveniles/pair and ranged from 1.43 juveniles/pair to 4.54 juveniles/pair. We estimated annual adult survival at 0.710 during the period of colony increase from 1996 to 2001 and 0.465 during decline from 2002 to 2007, but there was no change in annual survival of juveniles between the 2 time periods. Long-term population growth rate (lambda) estimated from average vital rates was lambdaa=1.072 with lambdai=1.288 during colony increase and lambdad=0.921 (DELTA lambda=0.368) during decline. A life table response experiment showed that change in adult survival rate during increasing and declining phases explained more than twice the variation in growth rate than other vital rates. Our findings suggest that management and conservation of declining burrowing owl populations should address factors that influence adult survival.

  16. Yeast Interacting Proteins Database: YFR015C, YFR015C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available yeast homolog; expression induced by glucose limitation, nitrogen starvation, environmental stress, and entr...ression induced by glucose limitation, nitrogen starvation, environmental stress, and entry into stationary ...tion, nitrogen starvation, environmental stress, and entry into stationary phase Rows with this bait as bait..., the more highly expressed yeast homolog; expression induced by glucose limitation, nitrogen starvation, environmental

  17. Dynamics of chemical elements in the fermentation process of ethanol production

    International Nuclear Information System (INIS)

    Nepomuceno, N.; Fernandes, E.A.N.; Bacchi, M.A.

    1997-01-01

    Brazil has become the largest producer of biomass ethanol derived from sugar cane. The industrial production is based on the fermentation of sugar cane juice by yeast, inside of large volume vats, in a fed-batch process that recycles yeast cells. To study the dynamics of chemical elements in each operating cycle, five stages of the fermentation process were considered: must, yeast suspension, wine, non-yeast wine and yeast cream. For this, a mass balance of the terrigenous elements, Ce, Co, Cs, Eu, Fe, Hf, La, Na, Sc, Sm, and Th, and the sugar cane plant elements, Br, K, Rb, and Zn, were established in fermentation vats of an industrial scale unit, with sampling undertaken during different climatic conditions (dry and rainy periods). A similar distribution of the sugar cane characteristics elements was found for the stages analysed, while for the terrigenous elements a trend of accumulation in the yeast cream was observed. Preferential absorption of Br, K, Rb, and Zn by yeast cells was indicated by the smaller concentrations observed in yeast suspension than in yeast cream. (author)

  18. Effect of temperature on the population dynamics of Aedes aegypti

    Science.gov (United States)

    Yusoff, Nuraini; Tokachil, Mohd Najir

    2015-10-01

    Aedes aegypti is one of the main vectors in the transmission of dengue fever. Its abundance may cause the spread of the disease to be more intense. In the study of its biological life cycle, temperature was found to increase the development rate of each stage of this species and thus, accelerate the process of the development from egg to adult. In this paper, a Lefkovitch matrix model will be used to study the stage-structured population dynamics of Aedes aegypti. In constructing the transition matrix, temperature will be taken into account. As a case study, temperature recorded at the Subang Meteorological Station for year 2006 until 2010 will be used. Population dynamics of Aedes aegypti at maximum, average and minimum temperature for each year will be simulated and compared. It is expected that the higher the temperature, the faster the mosquito will breed. The result will be compared to the number of dengue fever incidences to see their relationship.

  19. Emergence of cooperation in phenotypically heterogeneous populations: a replicator dynamics analysis

    International Nuclear Information System (INIS)

    Barreira da Silva Rocha, A; Escobedo, R; Laruelle, A

    2015-01-01

    The emergence of cooperation is analyzed in heterogeneous populations where two kinds of individuals exist according to their phenotypic appearance. Phenotype recognition is assumed for all individuals: individuals are able to identify the type of every other individual, but fail to recognize their own type. Individuals thus behave under partial information conditions. The interactions between individuals are described by the snowdrift game, where individuals can either cooperate or defect. The evolution of such populations is studied in the framework of evolutionary game theory by means of the replicator dynamics. Overlapping generations are considered, so the replicator equations are formulated in discrete-time form. The stability analysis of the dynamical system is carried out and a detailed description of the behavior of trajectories starting from the interior of the state-space is given. We find that the four monomorphic states are unstable and that a polymorphic state exists which is a global attractor for non-degenerate initial states of the population. The result for the discrete-time replicator coincides with the one of the continuous case. (paper)

  20. Radiodiagnosis of yeast alveolits (a clinicoexperimental study)

    International Nuclear Information System (INIS)

    Amosov, I.S.; Smirnov, V.A.

    1984-01-01

    A clinicoroetgenological study was made of 115 workers engaged in the yeast production for different periods of time. Disorders of the respiration biomechanics were revealed depending on the period of service. These data were obtained as a result of the use of roentgenopneumopolygraphy. An experimental study was conducted to establish the nature of lesions in the bronchopulmonary system in allergic alveolitis. The effect of finely divided yeast dust on the bronchopulmonary system was studied on 132 guinea-pigs usinq microbronchography and morphological examination. As a result of the study it has been established that during the inhalation of yeast dust, notnceable dystrophy of the bronchi develops, the sizes of alveoli enlarge and part of them undergo emphysematous distension with the rupture of the interalveolar septa. In the course of the study, it has been shown that yeast dust is little agreessive, yeast alveolitis develops after many years of work. The clinical symptoms are non-specific and insignificant. X-ray and morphological changes are followed by the physical manifestations of yeast alveolitis

  1. Dynamics of a population of oscillatory and excitable elements.

    Science.gov (United States)

    O'Keeffe, Kevin P; Strogatz, Steven H

    2016-06-01

    We analyze a variant of a model proposed by Kuramoto, Shinomoto, and Sakaguchi for a large population of coupled oscillatory and excitable elements. Using the Ott-Antonsen ansatz, we reduce the behavior of the population to a two-dimensional dynamical system with three parameters. We present the stability diagram and calculate several of its bifurcation curves analytically, for both excitatory and inhibitory coupling. Our main result is that when the coupling function is broad, the system can display bistability between steady states of constant high and low activity, whereas when the coupling function is narrow and inhibitory, one of the states in the bistable regime can show persistent pulsations in activity.

  2. Radiation belt seed population and its association with the relativistic electron dynamics: A statistical study: Radiation Belt Seed Population

    International Nuclear Information System (INIS)

    Tang, C. L.; Wang, Y. X.; Ni, B.; Zhang, J.-C.

    2017-01-01

    Using the Van Allen Probes data, we study the radiation belt seed population and it associated with the relativistic electron dynamics during 74 geomagnetic storm events. Based on the flux changes of 1 MeV electrons before and after the storm peak, these storm events are divided into two groups of “non-preconditioned” and “preconditioned”. The statistical study shows that the storm intensity is of significant importance for the distribution of the seed population (336 keV electrons) in the outer radiation belt. However, substorm intensity can also be important to the evolution of the seed population for some geomagnetic storm events. For non-preconditioned storm events, the correlation between the peak fluxes and their L-shell locations of the seed population and relativistic electrons (592 keV, 1.0 MeV, 1.8 MeV, and 2.1 MeV) is consistent with the energy-dependent dynamic processes in the outer radiation belt. For preconditioned storm events, the correlation between the features of the seed population and relativistic electrons is not fully consistent with the energy-dependent processes. It is suggested that the good correlation between the radiation belt seed population and ≤1.0 MeV electrons contributes to the prediction of the evolution of ≤1.0 MeV electrons in the Earth’s outer radiation belt during periods of geomagnetic storms.

  3. Scaling up population dynamic processes in a ladybird–aphid

    Czech Academy of Sciences Publication Activity Database

    Houdková, Kateřina; Kindlmann, Pavel

    2006-01-01

    Roč. 48, - (2006), s. 323-332 ISSN 1438-3896 R&D Projects: GA ČR(CZ) GEDIV/06/E013; GA MŠk(CZ) LC06073; GA AV ČR(CZ) IAA6087301; GA ČR(CZ) GD206/03/H034 Keywords : Aphids * Egg window * Ladybirds * Metapopulation * Model * Population dynamics Subject RIV: EH - Ecology, Behaviour Impact factor: 1.534, year: 2006

  4. Population dynamics of three songbird species in a nestbox population in Central Europe show effects of density, climate and competitive interactions

    NARCIS (Netherlands)

    Smallegange, I.M.; van der Meer, J.; Fiedler, W.

    2011-01-01

    Unravelling the contributions of density-dependent and density-independent factors in determining species population dynamics is a challenge, especially if the two factors interact. One approach is to apply stochastic population models to long-term data, yet few studies have included interactions

  5. Studies on population dynamic of diamondback moth in the field

    International Nuclear Information System (INIS)

    Malakrong, A.; Limohpasmanee, W.; Keawchoung, P.; Kodcharint, P.

    1994-01-01

    The population dynamic of diamondback moth larva in the field was studied at Khao Khor High-land Agricultural Research Station during August-October 1993 and February-April 1994. The distribution patterns of diamondback moth larva was clumped when population was low and would change to be random when population was high. The maximun and minimum number of diamondback moth in the field were 71,203 and 2,732 larva/rai during March and September. Temperature, rainfall and age of cabbage were slightly relative with number of larva (r=-0.2891, p=0.30; r=-0.2816, p=0.31 and r=0.2931, p=0.29 respectively) but relative humidity has no effect on number of larva

  6. MALDI-TOF MS as a tool to identify foodborne yeasts and yeast-like fungi.

    Science.gov (United States)

    Quintilla, Raquel; Kolecka, Anna; Casaregola, Serge; Daniel, Heide M; Houbraken, Jos; Kostrzewa, Markus; Boekhout, Teun; Groenewald, Marizeth

    2018-02-02

    Since food spoilage by yeasts causes high economic losses, fast and accurate identifications of yeasts associated with food and food-related products are important for the food industry. In this study the efficiency of the matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify food related yeasts was evaluated. A CBS in-house MALDI-TOF MS database was created and later challenged with a blinded test set of 146 yeast strains obtained from food and food related products. Ninety eight percent of the strains were correctly identified with log score values>1.7. One strain, Mrakia frigida, gained a correct identification with a score value1.7. Ambiguous identifications were observed due to two incorrect reference mass spectra's found in the commercial database BDAL v.4.0, namely Candida sake DSM 70763 which was re-identified as Candida oleophila, and Candida inconspicua DSM 70631 which was re-identified as Pichia membranifaciens. MALDI-TOF MS can distinguish between most of the species, but for some species complexes, such as the Kazachstania telluris and Mrakia frigida complexes, MALDI-TOF MS showed limited resolution and identification of sibling species was sometimes problematic. Despite this, we showed that the MALDI-TOF MS is applicable for routine identification and validation of foodborne yeasts, but a further update of the commercial reference databases is needed. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Yeasts are essential for cocoa bean fermentation.

    Science.gov (United States)

    Ho, Van Thi Thuy; Zhao, Jian; Fleet, Graham

    2014-03-17

    Cocoa beans (Theobroma cacao) are the major raw material for chocolate production and fermentation of the beans is essential for the development of chocolate flavor precursors. In this study, a novel approach was used to determine the role of yeasts in cocoa fermentation and their contribution to chocolate quality. Cocoa bean fermentations were conducted with the addition of 200ppm Natamycin to inhibit the growth of yeasts, and the resultant microbial ecology and metabolism, bean chemistry and chocolate quality were compared with those of normal (control) fermentations. The yeasts Hanseniaspora guilliermondii, Pichia kudriavzevii and Kluyveromyces marxianus, the lactic acid bacteria Lactobacillus plantarum and Lactobacillus fermentum and the acetic acid bacteria Acetobacter pasteurianus and Gluconobacter frateurii were the major species found in the control fermentation. In fermentations with the presence of Natamycin, the same bacterial species grew but yeast growth was inhibited. Physical and chemical analyses showed that beans fermented without yeasts had increased shell content, lower production of ethanol, higher alcohols and esters throughout fermentation and lesser presence of pyrazines in the roasted product. Quality tests revealed that beans fermented without yeasts were purplish-violet in color and not fully brown, and chocolate prepared from these beans tasted more acid and lacked characteristic chocolate flavor. Beans fermented with yeast growth were fully brown in color and gave chocolate with typical characters which were clearly preferred by sensory panels. Our findings demonstrate that yeast growth and activity were essential for cocoa bean fermentation and the development of chocolate characteristics. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

  8. Linking animal population dynamics to alterations in foraging behaviour

    DEFF Research Database (Denmark)

    Nabe-Nielsen, Jacob; Sibly, Richard; Tougaard, Jakob

    Background/Question/Methods The survival of animal populations is strongly influenced by the individuals’ ability to forage efficiently, yet there are few studies of how populations respond when disturbances cause animals to deviate from their natural foraging behavior. Animals that respond...... that are increasingly exposed to noise from ships, wind turbines, etc. In the present study we investigate how the dynamics of the harbor porpoise population (Phocoena phocoena) in the inner Danish waters is influenced by disturbances using an agent- based simulation model. In the model animal movement, and hence...... the animals’ ability to forage efficiently and to sustain their energy intake, is influenced by noise emitted from wind turbines and ships. The energy levels in turn affect their survival. The fine-scale movements of the simulated animals was governed by a spatial memory, which allowed the model to produce...

  9. Programming strategy for efficient modeling of dynamics in a population of heterogeneous cells.

    Science.gov (United States)

    Hald, Bjørn Olav; Garkier Hendriksen, Morten; Sørensen, Preben Graae

    2013-05-15

    Heterogeneity is a ubiquitous property of biological systems. Even in a genetically identical population of a single cell type, cell-to-cell differences are observed. Although the functional behavior of a given population is generally robust, the consequences of heterogeneity are fairly unpredictable. In heterogeneous populations, synchronization of events becomes a cardinal problem-particularly for phase coherence in oscillating systems. The present article presents a novel strategy for construction of large-scale simulation programs of heterogeneous biological entities. The strategy is designed to be tractable, to handle heterogeneity and to handle computational cost issues simultaneously, primarily by writing a generator of the 'model to be simulated'. We apply the strategy to model glycolytic oscillations among thousands of yeast cells coupled through the extracellular medium. The usefulness is illustrated through (i) benchmarking, showing an almost linear relationship between model size and run time, and (ii) analysis of the resulting simulations, showing that contrary to the experimental situation, synchronous oscillations are surprisingly hard to achieve, underpinning the need for tools to study heterogeneity. Thus, we present an efficient strategy to model the biological heterogeneity, neglected by ordinary mean-field models. This tool is well posed to facilitate the elucidation of the physiologically vital problem of synchronization. The complete python code is available as Supplementary Information. bjornhald@gmail.com or pgs@kiku.dk Supplementary data are available at Bioinformatics online.

  10. Turkey’s Population Dynamics As A Candidate Country For EU Membership

    Directory of Open Access Journals (Sweden)

    Harun Uçak

    2011-01-01

    Full Text Available Literally, it has been accepted that one of the major obstacles to Turkey’s EU membership is in population term. There has not been any enlargement process as large as Turkey’s population as a single state in EU history before. The enlargement in 2004 which includes 10 states involved 74 million people as whole member states while Turkey’s population is 72 million inhabitants in 2007 data which is only lower than Germany’s population in all EU member states. Thus, Turkey's accession would be different from previous enlargements because of the combined impact of high population. This study compares the population dynamics, working conditions, minimum wage rates and main macroeconomic indicators between Turkey and EU member states. Turkey has young generations compared to EU countries. In the comparison of age groups proportion in total population, 0-19 age group %21,9 in EU 27 and %36,5 in Turkey, 20-39 age group is %28 in EU 27 and %34,3 in Turkey, 40-59 age group is %27,9 in EU and %20,9 in Turkey, 60 and above age group is %22,1 in EU and %9,5 in Turkey. Thus, population dynamics of Turkey could make a contribution to offsetting the ageing of EU 27 societies if the membership would occur in the future. However, minimum wage rates in Turkey are lower than many EU member states but generally higher than EU member states located in Central and Eastern Europe. Thus, immigration possibilities from Turkey can be expected to Western European Countries, but not the same direction to Central and Eastern Europe Countries. Furthermore, the process in macroeconomic indicators will be a determinant in immigration expectations while Turkey’s GDP has been grown faster than EU level recently.

  11. Heat exposure in cities: combining the dynamics of temperature and population

    Science.gov (United States)

    Hu, L.; Wilhelmi, O.; Uejio, C. K.

    2017-12-01

    Assessment of human exposure to extreme heat requires the distributions of temperature and population. However, both variables are dynamic, thus presenting many challenges in capturing temperature and population patterns spatially and over time in an urban context. This study aims to improve the understanding of spatiotemporal patterns of urban population exposure to heat, taking Chicago, USA as an example. We estimate the hourly, geographically variable, population distribution considering commute of workers and students in a regular weekday and analyze the diurnal air temperature patterns during different meteorological conditions from satellite observations. The results show a relatively larger temperature increase in less urbanized areas during extreme heat events (EHEs), resulting in a spatially homogeneous temperature distribution over Chicago Metropolitan area. A lake cooling effect is weaker during EHEs. Population dynamics due to daily commute determine higher population density in more urbanized areas during daytime. The city-wide analysis reveals that the exposure is more sensitive to the nighttime temperature increases, and EHEs enhance this sensitivity. The high exposure hotspots are identified at the northwest Chicago, Cicero and Oak Park areas, where the influence from Lake Michigan is weakened, while the spatial extent of high outdoor exposure areas varies diurnally. This study's findings have potential to better inform general heat mitigation strategies during hot summer months and facilitate emergency response during EHEs. Availability of remotely-sensed temperature observations as well as the workers and students commute-adjusted population data allows for the adoption of this study's methodology in other major metropolitan areas. A better understanding of space-time patterns of urban population's exposure to heat will further enable local decision makers to mitigate extreme heat health risks and develop more targeted heat preparedness and

  12. Yeast diversity in rice-cassava fermentations produced by the indigenous Tapirapé people of Brazil

    DEFF Research Database (Denmark)

    Schwan, Rosane F.; Almeida, Euziclei G.; Souza-Dias, Maria Aparecida G.

    2007-01-01

    and peanuts. A fermentation using rice and cassava was conducted, and samples were collected at 4-h intervals for microbial analysis. The yeast population was low at the beginning of the fermentation and reached 6.9 x 10(7) CFU mL(-1) after 48 h. During the fermentation process common yeast species were......The Tapirapé people of the Tapi'itãwa tribe of Brazil produce several fermented foods and beverages, one of which is called 'cauim'. This beverage usually makes up the main staple food for adults and children. Several substrates are used in its production, including cassava, rice, corn, maize...... identified by sequencing of the D1/D2 domain of the large-subunit (26S) rRNA gene. The predominant yeast species found was Candida tropicalis. Candida intermedia, Candida parapsilosis, Pichia guilliermondii, Saccharomyces cerevisiae and Trichosporon asahii were also found in high numbers during...

  13. State-dependent neutral delay equations from population dynamics.

    Science.gov (United States)

    Barbarossa, M V; Hadeler, K P; Kuttler, C

    2014-10-01

    A novel class of state-dependent delay equations is derived from the balance laws of age-structured population dynamics, assuming that birth rates and death rates, as functions of age, are piece-wise constant and that the length of the juvenile phase depends on the total adult population size. The resulting class of equations includes also neutral delay equations. All these equations are very different from the standard delay equations with state-dependent delay since the balance laws require non-linear correction factors. These equations can be written as systems for two variables consisting of an ordinary differential equation (ODE) and a generalized shift, a form suitable for numerical calculations. It is shown that the neutral equation (and the corresponding ODE--shift system) is a limiting case of a system of two standard delay equations.

  14. Survival of commercial yeasts in the winery environment and their prevalence during spontaneous fermentations.

    Science.gov (United States)

    Blanco, P; Orriols, I; Losada, A

    2011-01-01

    Inoculation of active dry yeasts during the wine-making process has become a common practice in most wine-producing regions; this practice may affect the diversity of the indigenous population of Saccharomyces cerevisiae in the winery. The aim of this work was to study the incidence of commercial yeasts in the experimental winery of Estación de Viticultura e Enoloxía de Galicia (EVEGA) and their ability to lead spontaneous fermentations. To do this, 64 spontaneous fermentations were carried out in the experimental cellar of EVEGA over a period of 7 years. Samples were taken from must and at the beginning, vigorous and final stages of fermentation. A representative number of yeast colonies was isolated from each sample. S. cerevisiae strains were characterised by analysis of mitochondrial DNA restriction patterns. The results showed that although more than 40 different strains of S. cerevisiae were identified, only 10 were found as the dominant strain or in codominance with other strains in spontaneous fermentations. The genetic profiles (mtDNA-RFLPs) of eight of these strains were similar to those of different commercial yeasts that had been previously used in the EVEGA cellar. The remaining two strains were autochthonous ones that were able to reach implantation frequencies as high of those of commercial yeasts. These results clearly indicated that commercial wine yeasts were perfectly adapted to survive in EVEGA cellar conditions, and they successfully competed with the indigenous strains of S. cerevisiae, even during spontaneous fermentations. On the other hand, autochthonous dominant strains that presented desirable oenological traits could be of interest to preserve wine typicity.

  15. Seasonal dynamics of snail populations in coastal Kenya: Model calibration and snail control

    Science.gov (United States)

    Gurarie, D.; King, C. H.; Yoon, N.; Wang, X.; Alsallaq, R.

    2017-10-01

    A proper snail population model is important for accurately predicting Schistosoma transmission. Field data shows that the overall snail population and that of shedding snails have a strong pattern of seasonal variation. Because human hosts are infected by the cercariae released from shedding snails, the abundance of the snail population sets ultimate limits on human infection. For developing a predictive dynamic model of schistosome infection and control strategies we need realistic snail population dynamics. Here we propose two such models based on underlying environmental factors and snail population biology. The models consist of two-stage (young-adult) populations with resource-dependent reproduction, survival, maturation. The key input in the system is seasonal rainfall which creates snail habitats and resources (small vegetation). The models were tested, calibrated and validated using dataset collected in Msambweni (coastal Kenya). Seasonal rainfall in Msambweni is highly variable with intermittent wet - dry seasons. Typical snail patterns follow precipitation peaks with 2-4-month time-lag. Our models are able to reproduce such seasonal variability over extended period of time (3-year study). We applied them to explore the optimal seasonal timing for implementing snail control.

  16. The demography of climate-driven and density-regulated population dynamics in a perennial plant

    DEFF Research Database (Denmark)

    Dahlgren, Johan; Bengstsson, Karin; Ehrlén, Johan

    2016-01-01

    Identifying the internal and external drivers of population dynamics is a key objective in ecology, currently accentuated by the need to forecast the effects of climate change on species distributions and abundances. The interplay between environmental and density effects is one particularly...... important aspect of such forecasts. We examined the simultaneous impact of climate and intraspecific density on vital rates of the dwarf shrub Fumana procumbens over 20 yr, using generalized additive mixed models. We then analyzed effects on population dynamics using integral projection models...... to be driven solely by the environment can overestimate extinction risks if there is density dependence. We conclude that density regulation can dampen effects of climate change on Fumana population size, and discuss the need to quantify density dependence in predictions of population responses...

  17. Population Model with a Dynamic Food Supply

    Science.gov (United States)

    Dickman, Ronald; da Silva Nascimento, Jonas

    2009-09-01

    We propose a simple population model including the food supply as a dynamic variable. In the model, survival of an organism depends on a certain minimum rate of food consumption; a higher rate of consumption is required for reproduction. We investigate the stationary behavior under steady food input, and the transient behavior of growth and decay when food is present initially but is not replenished. Under a periodic food supply, the system exhibits period-doubling bifurcations and chaos in certain ranges of the reproduction rate. Bifurcations and chaos are favored by a slow reproduction rate and a long period of food-supply oscillation.

  18. Genomic Evolution of the Ascomycete Yeasts

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Robert; Haridas, Sajeet; Salamov, Asaf; Boundy-Mills, Kyria; Goker, Markus; Hittinger, Chris; Klenk, Hans-Peter; Lopes, Mariana; Meir-Kolthoff, Jan P.; Rokas, Antonis; Rosa, Carlos; Scheuner, Carmen; Soares, Marco; Stielow, Benjamin; Wisecaver, Jennifer H.; Wolfe, Ken; Blackwell, Meredith; Kurtzman, Cletus; Grigoriev, Igor; Jeffries, Thomas

    2015-03-16

    Yeasts are important for industrial and biotechnological processes and show remarkable metabolic and phylogenetic diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphrinomycotina. Phylogenetic analysis of these and previously published yeast genomes helped resolve the placement of species including Saitoella complicata, Babjeviella inositovora, Hyphopichia burtonii, and Metschnikowia bicuspidata. Moreover, we find that alternative nuclear codon usage, where CUG encodes serine instead of leucine, are monophyletic within the Saccharomycotina. Most of the yeasts have compact genomes with a large fraction of single exon genes, and a tendency towards more introns in early-diverging species. Analysis of enzyme phylogeny gives insights into the evolution of metabolic capabilities such as methanol utilization and assimilation of alternative carbon sources.

  19. Specialist nectar-yeasts decline with urbanization in Berlin

    Science.gov (United States)

    Wehner, Jeannine; Mittelbach, Moritz; Rillig, Matthias C.; Verbruggen, Erik

    2017-03-01

    Nectar yeasts are common inhabitants of insect-pollinated flowers but factors determining their distribution are not well understood. We studied the influence of host identity, environmental factors related to pollution/urbanization, and the distance to a target beehive on local distribution of nectar yeasts within Robinia pseudoacacia L. and Tilia tomentosa Moench in Berlin, Germany. Nectar samples of six individuals per species were collected at seven sites in a 2 km radius from each target beehive and plated on YM-Agar to visualise the different morphotypes, which were then identified by sequencing a section of the 26S rDNA gene. Multivariate linear models were used to analyze the effects of all investigated factors on yeast occurrence per tree. Yeast distribution was mainly driven by host identity. The influence of the environmental factors (NO2, height of construction, soil sealing) strongly depended on the radius around the tree, similar to the distance of the sampled beehive. Incidence of specialist nectar-borne yeast species decreased with increasing pollution/urbanization index. Given that specialist yeast species gave way to generalist yeasts that have a reduced dependency on pollinators for between-flower dispersal, our results indicate that increased urbanization may restrict the movement of nectar-specialized yeasts, via limitations of pollinator foraging behavior.

  20. Black yeast-like fungi in skin and nail

    DEFF Research Database (Denmark)

    Saunte, D M; Tarazooie, B; Arendrup, M C

    2011-01-01

    Black yeast-like fungi are rarely reported from superficial infections. We noticed a consistent prevalence of these organisms as single isolations from mycological routine specimens. To investigate the prevalence of black yeast-like fungi in skin, hair and nail specimens and to discuss...... the probability of these species to be involved in disease. Slow-growing black yeast-like fungi in routine specimens were prospectively collected and identified. A questionnaire regarding patient information was sent to physicians regarding black yeast-like fungus positive patients. A total of 20 746...... dermatological specimens were examined by culture. Black yeast-like fungi accounted for 2.2% (n = 108) of the positive cultures. Only 31.0% of the samples, culture positive for black yeast-like fungi were direct microscopy positive when compared with overall 68.8% of the culture positive specimens. The most...

  1. Introducing a new breed of wine yeast: interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast and Saccharomyces mikatae.

    Directory of Open Access Journals (Sweden)

    Jennifer R Bellon

    Full Text Available Interspecific hybrids are commonplace in agriculture and horticulture; bread wheat and grapefruit are but two examples. The benefits derived from interspecific hybridisation include the potential of generating advantageous transgressive phenotypes. This paper describes the generation of a new breed of wine yeast by interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast strain and Saccharomyces mikatae, a species hitherto not associated with industrial fermentation environs. While commercially available wine yeast strains provide consistent and reliable fermentations, wines produced using single inocula are thought to lack the sensory complexity and rounded palate structure obtained from spontaneous fermentations. In contrast, interspecific yeast hybrids have the potential to deliver increased complexity to wine sensory properties and alternative wine styles through the formation of novel, and wider ranging, yeast volatile fermentation metabolite profiles, whilst maintaining the robustness of the wine yeast parent. Screening of newly generated hybrids from a cross between a S. cerevisiae wine yeast and S. mikatae (closely-related but ecologically distant members of the Saccharomyces sensu stricto clade, has identified progeny with robust fermentation properties and winemaking potential. Chemical analysis showed that, relative to the S. cerevisiae wine yeast parent, hybrids produced wines with different concentrations of volatile metabolites that are known to contribute to wine flavour and aroma, including flavour compounds associated with non-Saccharomyces species. The new S. cerevisiae x S. mikatae hybrids have the potential to produce complex wines akin to products of spontaneous fermentation while giving winemakers the safeguard of an inoculated ferment.

  2. Introducing a New Breed of Wine Yeast: Interspecific Hybridisation between a Commercial Saccharomyces cerevisiae Wine Yeast and Saccharomyces mikatae

    Science.gov (United States)

    Bellon, Jennifer R.; Schmid, Frank; Capone, Dimitra L.; Dunn, Barbara L.; Chambers, Paul J.

    2013-01-01

    Interspecific hybrids are commonplace in agriculture and horticulture; bread wheat and grapefruit are but two examples. The benefits derived from interspecific hybridisation include the potential of generating advantageous transgressive phenotypes. This paper describes the generation of a new breed of wine yeast by interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast strain and Saccharomyces mikatae, a species hitherto not associated with industrial fermentation environs. While commercially available wine yeast strains provide consistent and reliable fermentations, wines produced using single inocula are thought to lack the sensory complexity and rounded palate structure obtained from spontaneous fermentations. In contrast, interspecific yeast hybrids have the potential to deliver increased complexity to wine sensory properties and alternative wine styles through the formation of novel, and wider ranging, yeast volatile fermentation metabolite profiles, whilst maintaining the robustness of the wine yeast parent. Screening of newly generated hybrids from a cross between a S. cerevisiae wine yeast and S. mikatae (closely-related but ecologically distant members of the Saccharomyces sensu stricto clade), has identified progeny with robust fermentation properties and winemaking potential. Chemical analysis showed that, relative to the S. cerevisiae wine yeast parent, hybrids produced wines with different concentrations of volatile metabolites that are known to contribute to wine flavour and aroma, including flavour compounds associated with non-Saccharomyces species. The new S. cerevisiae x S. mikatae hybrids have the potential to produce complex wines akin to products of spontaneous fermentation while giving winemakers the safeguard of an inoculated ferment. PMID:23614011

  3. Population dynamics of Trichuris suis in trickle-infected pigs.

    Science.gov (United States)

    Nejsum, P; Thamsborg, S M; Petersen, H H; Kringel, H; Fredholm, M; Roepstorff, A

    2009-05-01

    The population dynamics of Trichuris suis in pigs was studied during long-term experimental infections. Twenty-three 10-week-old pigs were inoculated with 5 T. suis eggs/kg/day. Seven, 8, and 8 pigs were necropsied at weeks 4, 8, and 14 post-start of infection (p.i.), respectively. The median numbers of worms in the colon were 538 (min-max: 277-618), 332 (14-1140) and 0 (0-4) at 4, 8, and 14 weeks p.i. respectively, suggesting an increased aggregation of the worms with time and acquisition of nearly sterile immunity. The serum levels of T. suis specific antibodies (IgG1, IgG2 and IgA) peaked at week 8 p.i. By week 14 p.i. the IgG2 and IgA antibody levels remained significantly elevated above the level of week 0. The population dynamics of T. suis trickle infections in pigs is discussed with focus on interpretation of diagnostic and epidemiological data of pigs, the use of pigs as a model for human Trichuris trichiura infections and the novel approach of using T. suis eggs in the treatment of patients with inflammatory bowel disease.

  4. Acrolein-Induced Oxidative Stress and Cell Death Exhibiting Features of Apoptosis in the Yeast Saccharomyces cerevisiae Deficient in SOD1.

    Science.gov (United States)

    Kwolek-Mirek, Magdalena; Zadrąg-Tęcza, Renata; Bednarska, Sabina; Bartosz, Grzegorz

    2015-04-01

    The yeast Saccharomyces cerevisiae is a useful eukaryotic model to study the toxicity of acrolein, an important environmental toxin and endogenous product of lipid peroxidation. The study was aimed at elucidation of the cytotoxic effect of acrolein on the yeast deficient in SOD1, Cu, Zn-superoxide dismutase which is hypersensitive to aldehydes. Acrolein generated within the cell from its precursor allyl alcohol caused growth arrest and cell death of the yeast cells. The growth inhibition involved an increase in production of reactive oxygen species and high level of protein carbonylation. DNA condensation and fragmentation, exposition of phosphatidylserine at the cell surface as well as decreased dynamic of actin microfilaments and mitochondria disintegration point to the induction of apoptotic-type cell death besides necrotic cell death.

  5. Dynamics of weakly inhomogeneous oscillator populations: perturbation theory on top of Watanabe-Strogatz integrability

    Science.gov (United States)

    Vlasov, Vladimir; Rosenblum, Michael; Pikovsky, Arkady

    2016-08-01

    As has been shown by Watanabe and Strogatz (WS) (1993 Phys. Rev. Lett. 70 2391), a population of identical phase oscillators, sine-coupled to a common field, is a partially integrable system: for any ensemble size its dynamics reduce to equations for three collective variables. Here we develop a perturbation approach for weakly nonidentical ensembles. We calculate corrections to the WS dynamics for two types of perturbations: those due to a distribution of natural frequencies and of forcing terms, and those due to small white noise. We demonstrate that in both cases, the complex mean field for which the dynamical equations are written is close to the Kuramoto order parameter, up to the leading order in the perturbation. This supports the validity of the dynamical reduction suggested by Ott and Antonsen (2008 Chaos 18 037113) for weakly inhomogeneous populations.

  6. Dynamics of weakly inhomogeneous oscillator populations: perturbation theory on top of Watanabe–Strogatz integrability

    International Nuclear Information System (INIS)

    Vlasov, Vladimir; Rosenblum, Michael; Pikovsky, Arkady

    2016-01-01

    As has been shown by Watanabe and Strogatz (WS) (1993 Phys. Rev. Lett. 70 2391), a population of identical phase oscillators, sine-coupled to a common field, is a partially integrable system: for any ensemble size its dynamics reduce to equations for three collective variables. Here we develop a perturbation approach for weakly nonidentical ensembles. We calculate corrections to the WS dynamics for two types of perturbations: those due to a distribution of natural frequencies and of forcing terms, and those due to small white noise. We demonstrate that in both cases, the complex mean field for which the dynamical equations are written is close to the Kuramoto order parameter, up to the leading order in the perturbation. This supports the validity of the dynamical reduction suggested by Ott and Antonsen (2008 Chaos 18 037113) for weakly inhomogeneous populations. (letter)

  7. Chemical signaling and insect attraction is a conserved trait in yeasts.

    Science.gov (United States)

    Becher, Paul G; Hagman, Arne; Verschut, Vasiliki; Chakraborty, Amrita; Rozpędowska, Elżbieta; Lebreton, Sébastien; Bengtsson, Marie; Flick, Gerhard; Witzgall, Peter; Piškur, Jure

    2018-03-01

    Yeast volatiles attract insects, which apparently is of mutual benefit, for both yeasts and insects. However, it is unknown whether biosynthesis of metabolites that attract insects is a basic and general trait, or if it is specific for yeasts that live in close association with insects. Our goal was to study chemical insect attractants produced by yeasts that span more than 250 million years of evolutionary history and vastly differ in their metabolism and lifestyle. We bioassayed attraction of the vinegar fly Drosophila melanogaster to odors of phylogenetically and ecologically distinct yeasts grown under controlled conditions. Baker's yeast Saccharomyces cerevisiae , the insect-associated species Candida californica , Pichia kluyveri and Metschnikowia andauensis , wine yeast Dekkera bruxellensis , milk yeast Kluyveromyces lactis , the vertebrate pathogens Candida albicans and Candida glabrata , and oleophilic Yarrowia lipolytica were screened for fly attraction in a wind tunnel. Yeast headspace was chemically analyzed, and co-occurrence of insect attractants in yeasts and flowering plants was investigated through a database search. In yeasts with known genomes, we investigated the occurrence of genes involved in the synthesis of key aroma compounds. Flies were attracted to all nine yeasts studied. The behavioral response to baker's yeast was independent of its growth stage. In addition to Drosophila , we tested the basal hexapod Folsomia candida (Collembola) in a Y-tube assay to the most ancient yeast, Y. lipolytica, which proved that early yeast signals also function on clades older than neopteran insects. Behavioral and chemical data and a search for selected genes of volatile metabolites underline that biosynthesis of chemical signals is found throughout the yeast clade and has been conserved during the evolution of yeast lifestyles. Literature and database reviews corroborate that yeast signals mediate mutualistic interactions between insects and yeasts

  8. Effect of fungicides on epiphytic yeasts associated with strawberry

    Science.gov (United States)

    Debode, Jane; Van Hemelrijck, Wendy; Creemers, Piet; Maes, Martine

    2013-01-01

    We studied the effect of two commonly used fungicides on the epiphytic yeast community of strawberry. Greenhouse and field experiments were conducted applying Switch (cyprodinil plus fludioxonil) or Signum (boscalid plus pyraclostrobin) to strawberry plants. Yeasts on leaves and fruits were assessed on treated and untreated plants at several time points via plating and denaturing gradient gel electrophoresis (DGGE) analysis. The yeast counts on plates of the treated plants were similar to the control plants. Unripe fruits had 10 times larger yeast concentrations than ripe fruits or leaves. Some dominant yeast types were isolated and in vitro tests showed that they were at least 10 times less sensitive to Switch and Signum as compared with two important fungal strawberry pathogens Botrytis cinerea and Colletotrichum acutatum, which are the targets for the fungicide control. DGGE analysis showed that the applied fungicides had no effect on the composition of the yeast communities, while the growing system, strawberry tissue, and sampling time did affect the yeast communities. The yeast species most commonly identified were Cryptococcus, Rhodotorula, and Sporobolomyces. These results point toward the potential applicability of natural occurring yeast antagonists into an integrated disease control strategy for strawberry diseases.

  9. Lipid droplet organelle distribution in populations of dividing cells studied by simulation

    International Nuclear Information System (INIS)

    Dalhaimer, Paul

    2013-01-01

    One of the key questions in cell biology is how organelles are passed from parent to daughter cells. To help address this question, I used Brownian dynamics to simulate lipid droplets as model organelles in populations of dividing cells. Lipid droplets are dynamic bodies that can form both de novo and by fission, they can also be depleted. The quantitative interplay among these three events is unknown but would seem crucial for controlling droplet distribution in populations of dividing cells. Surprisingly, of the three main events studied: biogenesis, fission, and depletion, the third played the key role in maintaining droplet organelle number—and to a lesser extent volume—in populations of dividing cells where formation events would have seemed paramount. In the case of lipid droplets, this provides computational evidence that they must be sustained, most likely through contacts with the endoplasmic reticulum. The findings also agree with video microscopy experiments over much shorter timescales where droplet depletion in fission yeast cells was not observed. In general, this work shows that organelle maintenance is invaluable and lack thereof cannot necessarily be compensated for by organelle formation. This study provides a time-accurate, physical-based template for long-term cell division studies. (paper)

  10. Lipid droplet organelle distribution in populations of dividing cells studied by simulation

    Science.gov (United States)

    Dalhaimer, Paul

    2013-06-01

    One of the key questions in cell biology is how organelles are passed from parent to daughter cells. To help address this question, I used Brownian dynamics to simulate lipid droplets as model organelles in populations of dividing cells. Lipid droplets are dynamic bodies that can form both de novo and by fission, they can also be depleted. The quantitative interplay among these three events is unknown but would seem crucial for controlling droplet distribution in populations of dividing cells. Surprisingly, of the three main events studied: biogenesis, fission, and depletion, the third played the key role in maintaining droplet organelle number—and to a lesser extent volume—in populations of dividing cells where formation events would have seemed paramount. In the case of lipid droplets, this provides computational evidence that they must be sustained, most likely through contacts with the endoplasmic reticulum. The findings also agree with video microscopy experiments over much shorter timescales where droplet depletion in fission yeast cells was not observed. In general, this work shows that organelle maintenance is invaluable and lack thereof cannot necessarily be compensated for by organelle formation. This study provides a time-accurate, physical-based template for long-term cell division studies.

  11. Dynamics Days US 2013 Conference Held in Denver, Colorado on 3-6 January 2013. Abstracts

    Science.gov (United States)

    2013-12-17

    down before population collapse using replicate laboratory populations of the budding yeast Saccharomyces cerevisiae. We mapped the bifurcation diagram...agreement with the theory. Furthermore, we connected yeast populations spatially to evaluate warning signals based on spatio-temporal fluctuations...Colorado School of Mines $125 ARO 54 Franson, Andrew U Colorado School of Mines $125 ARO 55 Slater, Michael U Colorado School of Mines $125 ARO 56 Brewer

  12. Population dynamics of the epiphytic bromeliad Tillandsia butzii in cloud forest

    Science.gov (United States)

    Toledo-Aceves, Tarin; Hernández-Apolinar, Mariana

    2016-02-01

    Epiphytes are a major component of tropical montane cloud forests. Over-exploitation and forest loss and degradation affect remnant populations. In this study, we analysed the population dynamics of the epiphytic bromeliad Tillandsia butzii over a 2-y period in a tropical montane cloud forest fragment in southern Mexico. Matrix analysis revealed that the T. butzii population is likely to be stable at the study site. On average the λ value did not differ significantly from unity: λ (95% confidence interval) = 0.978 (0.936-1.001). λ was highly influenced by stasis, to a lesser extent by growth and only slightly by fecundity. Overall, adult plant stasis and phalanx growth habit played a fundamental role in population maintenance. T. butzii tolerance to xeric conditions may contribute to population stability in the studied region.

  13. Nonlinearities Lead to Qualitative Differences in Population Dynamics of Predator-Prey Systems

    Czech Academy of Sciences Publication Activity Database

    Ameixa, Olga; Messelink, G. J.; Kindlmann, Pavel

    2013-01-01

    Roč. 8, č. 4 (2013), e62530-e62530 E-ISSN 1932-6203 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0073; GA ČR(CZ) GEVOL/11/E036 Institutional support: RVO:67179843 Keywords : nonlinear system * population density * population dynamics * predator * predator prey interaction * qualitative analysis Subject RIV: EH - Ecology, Behaviour Impact factor: 3.534, year: 2013

  14. Do farming practices influence population dynamics of rodents?

    DEFF Research Database (Denmark)

    Massawe, A W; Rwamugira, W; Leirs, Herwig

    2007-01-01

    A capture-mark-recapture study was conducted in crop fields in Morogoro, Tanzania, to investigate how the population dynamics of multimammate field rats, Mastomys natalensis, was influenced by the commonly practised land preparation methods and cropping systems. Two land preparation methods (trac...... practices. In maize fields in Tanzania, the crop is most susceptible to damage by M. natalensis in the first 2 weeks after planting, and therefore, lower densities of rodents will result into lower crop damage in tractor ploughed fields....

  15. Flor Yeast: New Perspectives Beyond Wine Aging

    Science.gov (United States)

    Legras, Jean-Luc; Moreno-Garcia, Jaime; Zara, Severino; Zara, Giacomo; Garcia-Martinez, Teresa; Mauricio, Juan C.; Mannazzu, Ilaria; Coi, Anna L.; Bou Zeidan, Marc; Dequin, Sylvie; Moreno, Juan; Budroni, Marilena

    2016-01-01

    The most important dogma in white-wine production is the preservation of the wine aroma and the limitation of the oxidative action of oxygen. In contrast, the aging of Sherry and Sherry-like wines is an aerobic process that depends on the oxidative activity of flor strains of Saccharomyces cerevisiae. Under depletion of nitrogen and fermentable carbon sources, these yeast produce aggregates of floating cells and form an air–liquid biofilm on the wine surface, which is also known as velum or flor. This behavior is due to genetic and metabolic peculiarities that differentiate flor yeast from other wine yeast. This review will focus first on the most updated data obtained through the analysis of flor yeast with -omic tools. Comparative genomics, proteomics, and metabolomics of flor and wine yeast strains are shedding new light on several features of these special yeast, and in particular, they have revealed the extent of proteome remodeling imposed by the biofilm life-style. Finally, new insights in terms of promotion and inhibition of biofilm formation through small molecules, amino acids, and di/tri-peptides, and novel possibilities for the exploitation of biofilm immobilization within a fungal hyphae framework, will be discussed. PMID:27148192

  16. On the stochastic approach to marine population dynamics

    Directory of Open Access Journals (Sweden)

    Eduardo Ferrandis

    2007-03-01

    Full Text Available The purpose of this article is to deepen and structure the statistical basis of marine population dynamics. The starting point is the correspondence between the concepts of mortality, survival and lifetime distribution. This is the kernel of the possibilities that survival analysis techniques offer to marine population dynamics. A rigorous definition of survival and mortality based on their properties and their probabilistic versions is briefly presented. Some well established models for lifetime distribution, which generalise the usual simple exponential distribution, might be used with their corresponding survivals and mortalities. A critical review of some published models is also made, including original models proposed in the way opened by Caddy (1991 and Sparholt (1990, which allow for a continuously decreasing natural mortality. Considering these elements, the pure death process dealt with in the literature is used as a theoretical basis for the evolution of a marine cohort. The elaboration of this process is based on Chiang´s study of the probability distribution of the life table (Chiang, 1960 and provides specific structured models for stock evolution as a Markovian process. These models may introduce new ideas in the line of thinking developed by Gudmundsson (1987 and Sampson (1990 in order to model the evolution of a marine cohort by stochastic processes. The suitable approximation of these processes by means of Gaussian processes may allow theoretical and computational multivariate Gaussian analysis to be applied to the probabilistic treatment of fisheries issues. As a consequence, the necessary catch equation appears as a stochastic integral with respect to the mentioned Markovian process of the stock. The solution of this equation is available when the mortalities are proportional, hence the use of the proportional hazards model (Cox, 1959. The assumption of these proportional mortalities leads naturally to the construction of a

  17. Construction of gateway-compatible yeast two-hybrid vectors for ...

    African Journals Online (AJOL)

    Yeast two-hybrid system combined with the gateway technology will greatly facilitate the cloning of interested DNA fragment into yeast two-hybrid vectors and therefore increase the efficiency of yeast two-hybrid analysis. In this study, we constructed a pair of Gateway-compatible yeast two-hybrid vectors pBTM116GW and ...

  18. Successional changes in trophic interactions support a mechanistic model of post-fire population dynamics.

    Science.gov (United States)

    Smith, Annabel L

    2018-01-01

    Models based on functional traits have limited power in predicting how animal populations respond to disturbance because they do not capture the range of demographic and biological factors that drive population dynamics, including variation in trophic interactions. I tested the hypothesis that successional changes in vegetation structure, which affected invertebrate abundance, would influence growth rates and body condition in the early-successional, insectivorous gecko Nephrurus stellatus. I captured geckos at 17 woodland sites spanning a succession gradient from 2 to 48 years post-fire. Body condition and growth rates were analysed as a function of the best-fitting fire-related predictor (invertebrate abundance or time since fire) with different combinations of the co-variates age, sex and location. Body condition in the whole population was positively affected by increasing invertebrate abundance and, in the adult population, this effect was most pronounced for females. There was strong support for a decline in growth rates in weight with time since fire. The results suggest that increased early-successional invertebrate abundance has filtered through to a higher trophic level with physiological benefits for insectivorous geckos. I integrated the new findings about trophic interactions into a general conceptual model of mechanisms underlying post-fire population dynamics based on a long-term research programme. The model highlights how greater food availability during early succession could drive rapid population growth by contributing to previously reported enhanced reproduction and dispersal. This study provides a framework to understand links between ecological and physiological traits underlying post-fire population dynamics.

  19. Antimicrobial activity of yeasts against some pathogenic bacteria

    Directory of Open Access Journals (Sweden)

    Gamal Younis

    2017-08-01

    Full Text Available Aim: This study was designed to isolate and identify yeast species from milk and meat products, and to test their antimicrobial activity against some bacterial species. Materials and Methods: A total of 160 milk and meat products samples were collected from random sellers and super markets in New Damietta city, Damietta, Egypt. Samples were subjected to yeast isolation procedures and tested for its antimicrobial activity against Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. In addition, all yeast species isolates were subjected to polymerase chain reaction (PCR for detection of khs (kievitone hydratase and pelA (pectate degrading enzyme genes. Results: The recovery rate of yeasts from sausage was 20% (2/10 followed by kareish cheese, processed cheese, and butter 10% (1/10 each as well as raw milk 9% (9/100, and fruit yoghurt 30% (6/20. Different yeast species were recovered, namely, Candida kefyr (5 isolates, Saccharomyces cerevisiae (4 isolates, Candida intermedia (3 isolates, Candida tropicalis (2 isolates, Candida lusitaniae (2 isolates, and Candida krusei (1 isolate. khs gene was detected in all S. cerevisiae isolates, however, pelA gene was not detected in all identified yeast species. Antimicrobial activity of recovered yeasts against the selected bacterial species showed high activity with C. intermedia against S. aureus and E. coli, C. kefyr against E. coli, and C. lusitaniae against S. aureus. Moderate activities were obtained with C. tropicalis, C. lusitaniae, and S. cerevisiae against E. coli; meanwhile, all the tested yeasts revealed a very low antimicrobial activity against P. aeruginosa. Conclusion: The obtained results confirmed that some kinds of yeasts have the ability to produce antimicrobial compounds that could inhibit some pathogenic and spoilage bacteria and these antimicrobial activity of yeasts enables them to be one of the novel agents in controlling spoilage of food.

  20. Species Distribution and Susceptibility to Azoles of Vaginal Yeasts Isolated Prostitutes

    Directory of Open Access Journals (Sweden)

    Norma T. Gross

    2007-01-01

    Full Text Available Objective. We investigated the use of miconazole among female prostitutes in Costa Rica as well as the distribution of vaginal yeasts and the susceptibility pattern to azoles of strains obtained from this population. Our intention was to relate a frequent use of miconazole to occurrence of vaginal yeasts resistant to azoles. Methods. Vaginal samples were taken from 277 patients that have previously used azoles. Vaginal swabs were obtained for direct microscopy and culture. Yeast isolates were identified by germ tube test and assimilation pattern. Susceptibility testing was determined using a tablet diffusion method. Results. The number of clinical Candida isolates (one from each patient was 57 (20.6%. C. albicans was the predominant species (70%, followed by C. parapsilosis (12%, C. tropicalis (5.3%, C. glabrata and C. famata (3.5% each, C. krusei, C. inconspicua and C. guilliermondii (1.7% each. The majority of vaginal Candida isolates were susceptible to ketoconazole (91%, fluconazole (96.5%, and itraconazole (98%. A lower susceptibility of some isolates to miconazole (63% was observed as compared to the other azoles tested. Moreover, the strains, nonsusceptible to miconazole, were more often obtained from patients that have used this antifungal at least four times within the last year before taking the samples as compared to those with three or less treatments (P<.01. Conclusion. An indiscriminate use of miconazole, such as that observed among female prostitutes in Costa Rica, results in a reduced susceptibility of vaginal yeasts to miconazole but not to other azoles.