1. Alan T. Bull, Juan A. Asenjo, Michael Goodfellow, and Benito Gómez-Silva. The Atacama Desert: Technical Resources and the Growing Importance of Novel Microbial Diversity. Annual Review of Microbiology, September 2016, Vol. 70:215-234.
    [ Show Abstract ]The Atacama Desert of northern Chile is the oldest and most arid nonpolar environment on Earth. It is a coastal desert covering approximately 180,000 km2, and together with the greater Atacama region it comprises a dramatically wide range of ecological niches. Long known and exploited for its mineral resources, the Atacama Desert harbors a rich microbial diversity that has only recently been discovered; the great majority of it has not yet been recovered in culture or even taxonomically identified. This review traces the progress of microbiology research in the Atacama and dispels the popular view that this region is virtually devoid of life. We examine reasons for such research activity and demonstrate that microbial life is the latest recognized and least explored resource in this inspiring biome.

     

  2. Hamidah Idris, David P. Labeda, Imen Nouioui, Jean Franco Castro, María del Carmen Montero-Calasanz, Alan T. Bull, Juan A. Asenjo, Michael Goodfellow. Streptomyces aridus sp. nov., isolated from a high altitude Atacama Desert soil and emended description of Streptomyces noboritoensis Isono et al. 1957. Journal Antonie van Leeuwenhoek (2017) 110:705–717.
    [ Show Abstract ]A polyphasic study was undertaken to determine the taxonomic status of a Streptomyces strain which had been isolated from a high altitude Atacama Desert soil and shown to have bioactive properties. The strain, isolate H9T, was found to have chemotaxonomic, cultural and morphological properties that place it in the genus Streptomyces. 16S rRNA gene sequence analyses showed that the isolate forms a distinct branch at the periphery of a well-delineated subclade in the Streptomyces 16S rRNA gene tree together with the type strains of Streptomyces crystallinusStreptomyces melanogenes and Streptomyces noboritoensis. Multi-locus sequence analysis (MLSA) based on five house-keeping gene alleles showed that isolate H9T is closely related to the latter two type strains and to Streptomyces polyantibioticus NRRL B-24448T. The isolate was distinguished readily from the type strains of S. melanogenesS. noboritoensis and S. polyantibioticus using a combination of phenotypic properties. Consequently, the isolate is considered to represent a new species of Streptomyces for which the name Streptomyces aridus sp. nov. is proposed; the type strain is H9T (=NCIMB 14965T=NRRL B65268T). In addition, the MLSA and phenotypic data show that the S. melanogenes and S. noboritoensis type strains belong to a single species, it is proposed that S. melanogenes be recognised as a heterotypic synonym of S. noboritoensis for which an emended description is given.

     

  3. Luis Alberto Mejía-Manzano, Gabriela Sandoval, M Elena Lienqueo, Pablo Moisset, Marco Rito-Palomares, Juan A. Asenjo (2017) Simulation of mono-PEGylated lysozyme separation in heparin affinity chromatography using a general rate model. Journal of Chemical Technology and Biotechnology. doi:10.1002/jctb.5309
    [ Show Abstract ]BACKGROUND: The bioavailability of therapeutic proteins is improved through PEGylation. This chemical modification involves the production of isomers with different numbers and sites of attached PEG chains, which are difficult to separate efficiently. Their purification with chromatography requires an understanding of the operation and the evaluation of different operational conditions. The General Rate Model (GRM) was applied for modelling the linear salt gradient elution of mono-PEGylated and native lysozyme in Heparin Affinity Chromatography (HAC) considering mass balance equations for proteins in the bulk-fluid phase, in the particle phase and the kinetic adsorption.
    RESULTS: The model was able to simulate the individual proteins and the separation of these in a PEGylation reaction using as proof-of-concept a mono-PEGylated and native lysozyme mixture under changes of operational parameters such as the gradient length (5, 13, 25 column volumes) and flow (0.8 and 1.2 mL min-1) with a relative error in retention times of less than 6% and correlation coefficients greater than 0.78.
    CONCLUSION: Simulation of the elution curves of PEGylated lysozyme in HAC was performed in this work and the diverse information generated by the model is explained through the physicochemical protein properties. This simulation represents a tool for optimization, prediction and future scale-up of PEGylated proteins purification, which would reduce the investment in time and resources to test several operating conditions.

     

  4. Rafael Soto, Carolina Bonacic, Mauricio Marin, and Veronica Gil-Costa. Simulating Streaming Software Applications Running on Clusters of Processors and Smartphone. Zhang L., Song X., Wu Y. (eds) Theory, Methodology, Tools and Applications for Modeling and Simulation of Complex Systems. AsiaSim 2016, SCS AutumnSim 2016. Communications in Computer and Information Science, vol 646. Springer, Singapore.
    [ Show Abstract ]Social software applications devised to process large and intensive streams of data must be usually run on complex computational infrastructure that ranges from clusters of processors to smartphones. The scalability to thousands or even millions of users is a relevant issue to be considered when designing these applications as they are not expected to collapse when they are mostly needed such as in disaster scenarios. In this context, software tools for performance evaluation of social software applications by means of discrete-event simulation have practical benefits, and yet they have not been fully developed in application domains where performance is critically dependent on massive user dynamics. This paper proposes a simulator to address this problem which combines powerful data centers and the computational power provided by mobile devices. We provide experimental evidence that shows a good agreement between actual and simulation performance measures.

     

  5. Mauricio Marín, Verónica Gil-Costa, Carolina Bonacic and Alonso Inostrosa (2017) Simulating Search EnginesComputing in Science & Engineering (Volume: 19, Issue: 1, Jan.-Feb. 2017)
    [ Show Abstract ]A simulation methodology is proposed to evaluate the performance of large-scale Web search engines hosted by datacenters. The salient features of the methodology are the use of models of parallel computing to overcome the complexities associated with the simulation of hardware and system software details; a circulating tokens approach to represent sequences of operations that compete for search engine resources; benchmark programs to measure the cost of relevant operations; and simulations driven by real user traces to consider the dynamics of user behavior. An experimental evaluation of the methodology, which ranges from clusters of processors to single multi-threaded processors, shows that it can generate respective simulation programs capable of predicting performance in a precise and efficient manner.

     

  6. Joshimar Cordova, Gonzalo Navarro (2016) Simple and efficient fully-functional succinct trees. Theoretical Computer Science Volume 656, Part B, 20 December 2016, Pages 135-145.
    [ Show Abstract ]The fully-functional succinct tree representation of Navarro and Sadakane (2014) supports a large number of operations in constant time using 2n + o(n) bits. However, the full idea is hard to implement. Only a simplified version with O(lgn) operation time has been implemented and shown to be practical and competitive. We describe a new variant of the original idea that is much simpler to implement and has worst-case time O(lg lgn) for the operations. An implementation based on this version is experimentally shown to be superior to existing implementations.

     

  7. Carolina Camus, Paola Ballerino, Rocio Delgado, Álvaro Olivera-Nappa, Carmen Leyton, Alejandro H. Buschmann. (2016) Scaling up bioethanol production from the farmed brown macroalga Macrocystis pyrifera in Chile. Biofuels, Bioproducts and Biorefining, Volume 10, Issue 6, November/December 2016, Pages 673–685.
    [ Show Abstract ]Interest in third-generation biomass such as macroalgae has increased due to their high biomass yield, absence of lignin in their tissues, lower competition for land and fresh water, no fertilization requirements, and efficient CO2 capture in coastal ecosystems. However, several challenges still exist in the development of cost-effective technologies for processing large amounts of macroalgae. Recently, genetically modified microorganisms able to convert brown macroalgae carbohydrates into bioethanol were developed, but still no attempt to scale up production has been proposed. Based on a giant kelp (Macrocystis pyrifera) farming and bioethanol production program carried out in Chile, we were able to test and adapt this technology as a first attempt to scale up this process using a 75 L fermentation of genetically modified Escherichia coli. Laboratory fermentation tests results showed that although biomass growth and yield are not greatly affected by the alginate:mannitol ratio, ethanol yield showed a clear maximum around a 5:8 alginate:mannitol ratio. In M. pyrifera, a much greater proportion of alginate and lower mannitol abundance is found. In order to make the most of the carbohydrates available for fermentation, we developed a four-stage process model for scaling up, including acid leaching, depolymerization, saccharification, and fermentation steps. Using this process we obtained 0.213 Kg ethanol Kg−1 dry macroalgae, equivalent to 9.6 m3 of ethanol hectare−1 year−1, reaching 64% of the maximum theoretical ethanol yield. We propose strategies to increase this yield, including synthetic biology pathway engineering approaches and process optimization targets.

     

  8. Alicia T. Lucero, Sergio A. Mercado, Anamaría C. Sánchez, Carolina A. Contador, Barbara A. Andrews and Juan A. Asenjo. Purification of adenoviral vector serotype 5 for gene therapy against alcoholism using anion exchange chromatography. Journal of Chemical Technology and Biotechnology, 2017. doi:10.1002/jctb.5255
    [ Show Abstract ]BACKGROUND: Gene therapy is a potent alternative for long-lasting inhibition of alcohol consumption. This study compares the purification of a recombinant adenoviral vector serotype 5 (rAdV5) for use in gene therapy against alcoholism using two anion-exchange methods.
    RESULTS: Two anion-exchange chromatography methods using fast protein liquid chromatography were compared using a packed-bed column (Q-SepharoseTM XL) and two monolithic columns (CIMTM QA-1 and CIMTM DEAE-1). An improved and reproducible separation of recombinant adenovirus type 5 from cell lysate contaminants was achieved using the two strong anion-exchange columns in a two-step gradient chromatography. Higher adenovirus yields were achieved using the CIM QA-1 tube monolithic column at sample volumes of both 1 and 10 mL compared with the Q-Sepharose XL column. At higher flow rates, the CIM QA-1 tube monolithic column achieved better separation of the target fraction. Process recovery was improved from 28% using the Q-Sepharose XL column to 34% with the CIM QA-1 tube monolithic column quantified as vector genome. Analysis by SDS-PAGE demonstrated a purity of 70% for purified adenovirus using the CIM QA-1 tube monolithic column.
    CONCLUSION: This study indicated that the use of a CIM QA-1 tube monolithic column is a better alternative than Q-Sepharose XL, and CIM DEAE-1 tube monolithic columns for the primary purification process of rAdV5 carrying the human aldehyde dehydrogenase-2 antisense gene. This purification strategy has been used as a basis to scale-up a GLP process for the production of material at the National Research Council of Canada to be used in preclinical trials of this gene therapy against alcoholism.

     

  9. Carolina Shene, Yusuf Chisti, Daniela Vergara, César Burgos-Díaz, Mónica Rubilar, Mariela Bustamante. (2016) Production of eicosapentaenoic acid by Nannochloropsis oculata: Effects of carbon dioxide and glycerol. Journal of Biotechnology, Volume 239, 10 December 2016, Pages 47-56.
    [ Show Abstract ]The marine microalga Nannochloropsis oculata is a potential source of eicosapentaenoic acid (EPA, C20:5n3) and carotenoids for use in functional foods and nutraceuticals. Mixotrophic culture of N. oculata using glycerol was examined as a possible way of increasing the biomass and metabolite productivity relative to a pure photoautotrophic culture in modified f/2 medium. The effect of CO2 supply was also tested. EPA production in semi-continuous culture with and without glycerol and CO2 was evaluated. The effects of glycerol supplementation and light/dark cycling on the production of the biomass and EPA are reported for cultures conducted at a constant pH controlled using CO2. Consumption of glycerol was small, but its effects were significant. Glycerol enhanced the lipid content of the biomass but reduced the chlorophyll a content. Mixotrophic cultivation favored the production of lipids with a high percentage of saturated fatty acids that are generally desired in oils for making biodiesel. EPA concentration (5.3 ± 0.6 to 27.5 ± 1.6 mg EPA/L) in N. oculata cultures depended strongly on growth conditions. The highest EPA concentration occurred in non-aerated mixotrophic culture with intermittent CO2 supply without pH control. This EPA concentration (= 27.5 ± 1.6 mg/L) was comparable to that obtained in semi-continuous culture without glycerol and pH control, and aerated with CO2 enriched air during the light period (= 23.6 ± 1.1 mg/L).

     

  10. Carolina Camus, Javier Infante and Alejandro H. Buschmann. (2016) Overview of 3 year precommercial seafarming of Macrocystis pyrifera along the Chilean coast. Reviews in Aquaculture (2016) doi:10.1111/raq.12185
    [ Show Abstract ]Chile is one of the main producers of seaweeds in the world; however, most of the production comes from harvesting natural beds and only 2.4% from cultures, dominated by the agarophyte Gracilaria chilensis. One of the most exploited resources is the giant kelp Macrocystis pyrifera, which is sold fresh for abalone feed and dry for alginate extraction. Recently, new possible markets are developing for this species, for example human consumption and biofuel/chemical production that could increase the demand and justify the development of a commercial cultivation system. The objective of this work was to present the recent development of the seafarming of M. pyrifera in Chile, focusing on the fundamental determinants of productivity in cultivated systems and the identification of the binding constraints to productivity. Three experimental plots (up to 21 Ha) were designed and deployed in three study areas (Caldera in northern Chile and Quenac and Ancud in southern Chile) to test different environmental conditions. During a period of 3 years, sporophytes produced in an indoor hatchery were deployed monthly, at different densities, and followed until harvest. Environmental parameters and biomass were monitored on a monthly basis. Our findings demonstrate the feasibility of Macrocystis seafarming on a large scale in Chile. Important differences in yield were observed between the study areas associated with either environmental physical or biological factors, such as the presence of herbivores. Our best production cycle reached 124 WMT Ha−1 month −1 in southern Chile, and the worst, less than 20 WMT Ha−1 month−1 in northern Chile. Finally, some direct and indirect constrains were encountered, including seeding season and depth, and the presence of pests and diseases, that are discussed.

     

  11. Luis Alberto Mejía-Manzano, M. Elena Lienqueo, Edgardo J. Escalante-Vázquez, Marco Rito-Palomares, Juan A. Asenjo. Optimized purification of mono-PEGylated lysozyme by Heparin Affinity Chromatography using Response Surface Methodology. Journal of Chemical Technology and Biotechnology, 2017. doi:10.1002/jctb.5269
    [ Show Abstract ]BACKGROUND: The efficient, controlled and robust purification of conjugates from PEGylation has a growing demand in the biopharmaceuticals market. In general the yield and purity reached through the conventional chromatographic modes are not particularly high nor efficient. Affinity chromatography has so far been scarcely explored. The present work, introduces the purification of mono-PEGylated lysozyme from a PEGylation reaction by heparin affinity chromatography (HAC) for first time in a single step. Response Surface Methodology (RSM), particularly a Box-Behnken design (BBD) was employed to optimize the separation.
    RESULTS: Protein adsorption of PEGylated and native lysozyme on Heparin Sepharose 6 Fast Flow resin was described by Langmuir isotherms, showing a relatively low affinity for the PEGylated proteins. From the experimental design, optimal elution conditions in a linear gradient of sodium chloride (NaCl) for the three response variables (yield, purity and productivity) were: gradient length of 13 column volumes (CVs), flow at 0.8 mL min-1 and protein load of 1 mg mL-1. Based on this optimization, a step gradient procedure was designed that achieved the purification of mono-PEGylated lysozyme with approximately 100% yield and purity in comparison with 92.7% and 99.7% with the linear gradient. Productivity was ca. 0.048 ± 0.001 mg mL-1 min-1 using 0.05 M NaCl for its elution.
    CONCLUSIONS: Mono-PEGylated lysozyme was completely separated from a PEGylation mixture with high yield and purity using HAC for first time. Applying Response Surface Methodology (RSM), adequate conditions for more than one requirements were found as well as optimal conditions for a linear gradient of NaCl. Based on this optimization a step gradient procedure was designed that achieved the purification of mono-PEGylated lysozyme in one step with advantages wih respect to time, resolution, yield and purity compared to other chromatographic modes such as hydrophobic interaction chromatography (HIC) and cation exchange chromatography (CEX).

     

  12. Gabriela Sandoval, Daniel Espinoza, Nicolas Figueroa, Juan A. Asenjo. (2017) Optimization of a Biotechnological Multiproduct Batch Plant Design for the Manufacture of Four Different Products: A Real Case Scenario. Biotechnology and Bioengineering, Vol. 114, No. 6, pp 1252–1263, June 2017.
    [ Show Abstract ]In this work a biotechnological multiproduct batch plant that manufactures four different recombinant proteins for human application is described in some detail. This batch plant design is then optimized with regards to the size of equipment using a mixed-integer linear programming (MILP) formulation recently developed by us in order to find a hypothetical new biotechnological batch plant based on the information of real known processes for the production of the four recombinant protein products. The real plant was divided for practical purposes into two sub-processes or facilities: a fermentation facility and a purification facility. Knowing the specific steps conforming the downstream processing of each product, size, and time factors were computed and used as parameters to solve the aforementioned MILP reformulation. New constraints were included to permit the selection of some equipment—such as centrifuges and membrane filters—in a discrete set of sizes. For equipment that can be built according to customer needs—such as reactors—the original formulation was retained. Computational results show the ability of this optimization methodology to deal with real data giving reliable solutions for a multi-product batch plant composed of 44 unit operations in a relatively small amount of time showing that in the case studied it is possible to save up to a 66% of the capital investment in equipment given the cost data used.

     

  13. Juan Pablo Acevedo, Manfred T. Reetz, Juan Asenjo, Loreto Parra (2017). One-step combined focused epPCR and saturation mutagenesis for thermostability evolution of a new cold-active xylanase. Enzyme and Microbial Technology, Volume 100, May 2017, Pages 60-70.
    [ Show Abstract ]Enzymes active at low temperature are of great interest for industrial bioprocesses due to their high efficiency at a low energy cost. One of the particularities of naturally evolved cold-active enzymes is their increased enzymatic activity at low temperature, however the low thermostability presented in this type of enzymes is still a major drawback for their application in biocatalysis. Directed evolution of cold-adapted enzymes to a more thermostable version, appears as an attractive strategy to fulfill the stability and activity requirements for the industry. This paper describes the recombinant expression and characterization of a new and highly active cold-adapted xylanase from the GH-family 10 (Xyl-L), and the use of a novel one step combined directed evolution technique that comprises saturation mutagenesis and focused epPCR as a feasible semi-rational strategy to improve the thermostability. The Xyl-L enzyme was cloned from a marine-Antarctic bacterium, Psychrobacter sp. strain 2–17, recombinantly expressed in E. coli strain BL21(DE3) and characterized enzymatically. Molecular dynamic simulations using a homology model of the catalytic domain of Xyl-L were performed to detect flexible regions and residues, which are considered to be the possible structural elements that define the thermolability of this enzyme. Mutagenic libraries were designed in order to stabilize the protein introducing mutations in some of the flexible regions and residues identified. Twelve positive mutant clones were found to improve the T5015 value of the enzyme, in some cases without affecting the activity at 25 °C. The best mutant showed a 4.3 °C increase in its T5015. The efficiency of the directed evolution approach can also be expected to work in the protein engineering of stereoselectivity.

     

  14. Patricio Cumsille, Juan A. Asenjo and Carlos Conca (2016) Numerical Solution of a Novel Biofilm Growth Model. Nonlinear Dynamics: Materials, Theory and Experiments pp 207-222.
    [ Show Abstract ]In this work we simulate biofilm structures (“finger-like”, as well as, compact structures) as a result of microbial growth in different environmental conditions. At the same time, the numerical method that we use in order to carry out the computational simulations is new to the biological community, as far as we know. The use of our model sheds light on the biological process of biofilm formation since it simulates some central issues of biofilm growth: the pattern formation of heterogeneous structures, such as finger-like structures, in a substrate-transport-limited regime, and the formation of more compact structures, in a growth-limited-regime.

     

  15. Fernanda S. Valdovinos, Berry J. Brosi, Heather M.Briggs, Pablo Moisset de Espanes, Rodrigo Ramos-Jiliberto and Neo D. Martinez. (2016) Niche partitioning due to adaptive foraging reverses effects of nestedness and connectance on pollination network stability. Ecology Letters, (2016) 19: 1277–1286.
    [ Show Abstract ]Much research debates whether properties of ecological networks such as nestedness and connectance stabilise biological communities while ignoring key behavioural aspects of organisms within these networks. Here, we computationally assess how adaptive foraging (AF) behaviour interacts with network architecture to determine the stability of plant–pollinator networks. We find that AF reverses negative effects of nestedness and positive effects of connectance on the stability of the networks by partitioning the niches among species within guilds. This behaviour enables generalist pollinators to preferentially forage on the most specialised of their plant partners which increases the pollination services to specialist plants and cedes the resources of generalist plants to specialist pollinators. We corroborate these behavioural preferences with intensive field observations of bee foraging. Our results show that incorporating key organismal behaviours with well-known biological mechanisms such as consumer-resource interactions into the analysis of ecological networks may greatly improve our understanding of complex ecosystems.

     

  16. Piergiuseppe Morone, Rodrigo Navia (2016) Editorial: New consumption and production models for a circular economy. Waste Management & Research, Volume 34, Issue 6, June 2016, pp. 489–490.
    [ Show Abstract ]Introduction: Economists have long attempted to understand the dichotomy between the finite quantity of natural resources and the seemingly unlimited human needs and wants. This contrast normally would resolve throughout free market actions and related materials pricing. However, modern societies and their embedded economic systems have proved to be unable to address natural resources scarcity in a satisfactory way. The tension between scarcity and human wants is expected to intensify as we anticipate the significant changes, which are bound to occur in the near future. Most notably, the world population, which in mid-2014 stands at 7.2 billion, is projected to increase by almost one billion people by 2025, and to reach 9.6 billion by 2050, as reported by the Food and Agriculture Organization of the United Nations (FAO) in 2015. At the same time, large and fast-growing economies such as China and India, in spite of the recession declines in recent years, are still growing at high rates of 6.8% and 7.4%, respectively. This will surely lead to increasing wealth. A major effect of these two trends will be a higher demand and consumption of food, manufactured goods and energy sources, adding pressure to the world economic system and the environment. Overarching these issues are the threat of climate change and the mounting concern to manage sustainably the increasing amounts of waste produced worldwide. To continue reading, click here.

     

  17. Héctor Ferrada, Gonzalo Navarro (2017) Improved Range Minimum QueriesJournal of Discrete Algorithms, Volume 43, March 2017, Pages 72-80
    [ Show Abstract ]Fischer and Heun [SICOMP 2011] proposed the first Range Minimum Query (RMQ) data structure on an array A[1,n] that uses 2n + o(n) bits and answers queries in O(1) time without accessing A. Their scheme converts the Cartesian tree of A into a general tree, which is represented using DFUDS. We show that, by using instead the BP representation, the formula becomes simpler since border conditions are eliminated. We also improve the current implementation of the BP representation for this purpose. This leads to the fastest and most compact practical implementation to date.

     

  18. Klaudia L. Hernández, Beatriz Yannicelli, Lasse M. Olsen, Cristina Dorador, Eduardo J. Menschel, Verónica Molina, Francisco Remonsellez, Martha B. Hengst and Wade H. Jeffrey. Microbial Activity Response to Solar Radiation across Contrasting Environmental Conditions in Salar de Huasco, Northern Chilean Altiplano. Frontiers in Microbiology, November 2016, Volume 7, Article 1857.
    [ Show Abstract ]In high altitude environments, extreme levels of solar radiation and important differences of ionic concentrations over narrow spatial scales may modulate microbial activity. In Salar de Huasco, a high-altitude wetland in the Andean mountains, the high diversity of microbial communities has been characterized and associated with strong environmental variability. Communities that differed in light history and environmental conditions, such as nutrient concentrations and salinity from different spatial locations, were assessed for bacterial secondary production (BSP, 3H-leucine incorporation) response from short-term exposures to solar radiation. We sampled during austral spring seven stations categorized as: (a) source stations, with recently emerged groundwater (no-previous solar exposure); (b) stream running water stations; (c) stations connected to source waters but far downstream from source points; and (d) isolated ponds disconnected from ground sources or streams with a longer isolation and solar exposure history. Very high values of 0.25 μE m-2 s-1, 72 W m-2 and 12 W m-2 were measured for PAR, UVA, and UVB incident solar radiation, respectively. The environmental factors measured formed two groups of stations reflected by principal component analyses (near to groundwater sources and isolated systems) where isolated ponds had the highest BSP and microbial abundance (35 microalgae taxa, picoeukaryotes, nanoflagellates, and bacteria) plus higher salinities and PO43- concentrations. BSP short-term response (4 h) to solar radiation was measured by 3H-leucine incorporation under four different solar conditions: full sun, no UVB, PAR, and dark. Microbial communities established in waters with the longest surface exposure (e.g., isolated ponds) had the lowest BSP response to solar radiation treatments, and thus were likely best adapted to solar radiation exposure contrary to ground source waters. These results support our light history (solar exposure) hypothesis where the more isolated the community is from ground water sources, the better adapted it is to solar radiation. We suggest that factors other than solar radiation (e.g., salinity, PO43-, NO3-) are also important in determining microbial productivity in heterogeneous environments such as the Salar de Huasco.

     

  19. Carolina Camus, Alejandro H. Buschmann. Macrocystis pyrifera aquafarming: Production optimization of rope-seeded juvenile sporophytes. Aquaculture, Volume 468, Part 1, 1 February 2017, Pages 107-114.
    [ Show Abstract ]The use of kelp in different human activities has increased over recent decades and this demand is increasing the demand for cost-effective farming technologies. In the case of the giant kelp (Macrocystis pyrifera) there is a large accumulation of knowledge concerning the relevant information required for aquafarming that allowed the installation of a 20 ha pilot culture farm 5 years ago in southern Chile. However, this experience indicated that to achieve a production level above 200 tons per hectare per year it is necessary to optimize all the protocols starting from the hatchery level through to the growing phase in order to be cost effective. In this study we present information on optimizing the hatchery phase of M. pyrifera culture. The results show that it is possible to obtain 4 to 5 mm long M. pyrifera juvenile sporophytes attached to seeded rope in less than 45 days. To obtain this result, temperature should be 12 °C with a photon irradiance of 12 μmol m− 2 s− 1 and a photoperiod of 16:8, L:D. In addition, macro and micronutrient concentrations should be maintained as the traditional Provasoli culture medium indicates, and with aeration of 414 L h− 1 to maintain water movement in the culture system.

     

  20. Hamidah Idris, Imen Nouioui, Juan A. Asenjo, Alan T. Bull, Michael Goodfellow. (2017) Lentzea chajnantorensis sp. nov., an actinobacterium from a very high altitude Cerro Chajnantor gravel soil in northern Chile. Journal Antonie van Leeuwenhoek (2017) 110, Issue 6, pp 795–802.
    [ Show Abstract ]The taxonomic position of a filamentous actinobacterial strain, isolate H45T, recovered from a high altitude Atacama Desert gravel soil, was established using a polyphasic approach. The strain, which is known to produce novel dienes, has chemotaxonomic and morphological properties typical of the genus Lentzea and formed a distinct branch in the Lentzea 16S rRNA gene tree that is closely related to the type strain of Lentzea kentuckyensis. The two strains were distinguished using a combination of phenotypic properties and by a DNA:DNA relatedness value of 37.6 ± 4.0%. On the basis of these genotypic and phenotypic data it is proposed that isolate H45T (=NCIMB 4966T = NRRL B-65282T) be classified in the genus Lentzea as Lentzea chajnantorensis sp. nov.

     

  21. Pablo Aguilar, Eduardo Acosta, Cristina Dorador and Ruben Sommaruga, (2016), Large Differences in Bacterial Community Composition among Three Nearby Extreme Waterbodies of the High Andean Plateau, Frontiers in Microbiology, June 2016, Volume 7, Article 976.
    [ Show Abstract ]The high Andean plateau or Altiplano contains different waterbodies that are subjected to extreme fluctuations in abiotic conditions on a daily and an annual scale. The bacterial diversity and community composition of those shallow waterbodies is largely unexplored, particularly, of the ponds embedded within the peatland landscape (i.e., Bofedales). Here we compare the small-scale spatial variability (<1 m) in bacterial diversity and community composition between two of those ponds with contrasting apparent color, using 454 pyrosequencing of the 16S rRNA gene. Further, we compared the results with the nearest (80 m) main lagoon in the system to elucidate the importance of different environmental factors such as salinity and the importance of these ponds as a source of shared diversity. Bacterial diversity was higher in both ponds than in the lagoon and community composition was largely different among them and characterized by very low operational taxonomic unit sharing. Whereas the “green” pond with relatively low dissolved organic carbon (DOC) concentration (33.5 mg L-1) was dominated by Proteobacteria and Bacteroidetes, the one with extreme DOC concentration (424.1 mg L-1) and red hue was dominated by Cyanobacteria. By contrast, the lagoon was largely dominated by Proteobacteria, particularly by Gammaproteobacteria. A large percentage (47%) of all reads was unclassified suggesting the existence of large undiscovered bacterial diversity. Our results suggest that even at the very small-scale spatial range considered, local environmental factors are important in explaining differences in bacterial community composition in those systems. Further, our study highlights that Altiplano peatland ponds represent a hitherto unknown source of microbial diversity.

     

  22. A. Leyton, R. Pezoa-Conte, P. Mäki-Arvela, J-P Mikkola, M. E Lienqueo (2017), Improvement in carbohydrate and phlorotannin extraction from Macrocystis pyrifera using carbohydrate active enzyme from marine Alternaria sp. as pretreatment, Journal of Applied Phycology (2017). doi:10.1007/s10811-017-1141-3
    [ Show Abstract ]The commercial importance of brown seaweed has been increasing over the past decade, especially due to industries interested in the extraction of phycocolloids and, more recently, of polyphenol compounds such as phlorotannins. The objective of this work was to optimize the extraction conditions of carbohydrates and phlorotannins from Macrocystis pyrifera, evaluated enzymatic pretreatment and different parameters of extraction using design of experiment. The optimal conditions upon extraction of the carbohydrates and phlorotannins were determined by means of a pretreatment protocol taking advantage on a carbohydrate active enzyme, followed by an alkaline hydrolysis with 0.5 N NaOH at 100 °C, 180 min, and S/L ratio of 1/20. In order to extract the carbohydrates, the best conditions found for the pretreatment procedure were 37 °C, pH 7.0 for 24 h, and a S/L ratio of 1/10, giving an extraction yield (EY) of 89.67 ± 12.3 wt.%. In turn, for the extraction of phlorotannins, the best conditions identified in terms of the pretreatment were 25 °C, pH 7.0 for 36 h, and a S/L ratio of 1/20, thus giving a yield (EY) of 2.14 ± 0.25 wt.%. Statistical analysis of both processes revealed a maximum EY of 91.24 wt.% for carbohydrates and 3.31 wt.% EY for phlorotannins.

     

  23. Simon Gog, Gonzalo Navarro, Matthias Petri, (2015), Improved and extended locating functionality on compressed suffix arrays, Journal of Discrete Algorithms 32 (2015) 53-63
    [ Show Abstract ]Compressed Suffix Arrays (CSAs) offer the same functionality as classical suffix arrays (SAs), and more, within space close to that of the compressed text, and in addition they can reproduce any text fragment. Furthermore, their pattern search times are comparable to those of SAs. This combination has made CSAs extremely successful substitutes for SAs in space-demanding applications. Their weakest point is that they are orders of magnitude slower when retrieving the precise positions of pattern occurrences. SAs have other well-known shortcomings, inherited by CSAs, such as not retrieving those positions in a useful order. In this paper we present new techniques that, on the one hand, improve the current space/time tradeoffs for retrieving pattern occurrences in CSAs, and on the other, efficiently support extended pattern locating functionalities, such as retrieving occurrences in text order or limiting the occurrences to within a text window. Our experimental results display considerable savings with respect to the baseline techniques in many cases of interest: in some cases we outperform their time by a factor of two or three.

     

  24. Fernanda Araujo Casares, Sylvain Faugeron (2016), Higher reproductive success for chimeras than solitary individuals in the kelp Lessonia spicata but no benefit for individual genotypes, Evolutionary Ecology, October 2016, Volume 30, Issue 5, pp 953–972.
    [ Show Abstract ]Chimerism is a peculiar, yet widespread, type of group living in which genetically heterogeneous entities are created through fusion between conspecifics. Here we tested whether chimerism provides direct benefits to the kelp Lessonia spicata, by analyzing its consequences on reproductive investment and success, at both the genotype and thallus levels. In addition, we quantified the frequency of chimerism in two natural populations, tested if group members were close kin, and evaluated the effects of relatedness and the number of genotypes per thallus on reproduction. Chimeric thalli were frequent (>60 %) in natural populations of L. spicata. In most cases, average intragroup relatedness was not significantly different from the background population. Reproductive investment was not significantly affected by the type of thallus (chimeric versus non-chimeric), by the number of genotypes per thallus or the average relatedness within thallus. Chimerism did not result in net benefits or costs in terms of genotypic reproductive success or probability of reproducing at the genotypic level. Yet, at the thallus level, chimerism increased reproductive success and the probability of reproducing, since more than one genotype reproduced in chimeric thallus. At the population level, chimerism affects L. spicata reproductive success by allowing the coexistence of a higher density of potential reproducers and mates compared to a scenario with only non-chimeric thallus. Chimerism may then have an important effect on the effective population size and possibly in reducing selfing rates.

     

  25. Kira A. Krumhansl, Daniel K. Okamoto, Andrew Rassweiler, Mark Novak, John J. Bolton, Kyle C. Cavanaugh, Sean D. Connell, Craig R. Johnson, Brenda Konar, Scott D. Ling, Fiorenza Micheli, Kjell M. Norderhaug, Alejandro Pérez-Matus, Isabel Sousa-Pinto, Daniel C. Reed, Anne K. Salomon, Nick T. Shears, Thomas Wernberg, Robert J. Andersond, Nevell S. Barrett, Alejandro H. Buschmanns, Mark H. Carr, Jennifer E. Caselle, Sandrine Derrien-Courtel, Graham J. Edgar, Matt Edwards, James A. Estes, Claire Goodwin, Michael C. Kenner, David J. Kushner, Frithjof E. Moy, Julia Nunn, Robert S. Steneck, Julio Vásquez, Jane Watson, Jon D. Witman, and Jarrett E. K. Byrnes. Global patterns of kelp forest change over the past half-century, (2016), PNAS, November 29, 2016, Vol. 113 No. 48, 13785–13790
    [ Show Abstract ]Kelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change in kelp abundances currently exists. Here, we build and analyze a global database of kelp time series spanning the past half-century to assess regional and global trends in kelp abundances. We detected a high degree of geographic variation in trends, with regional variability in the direction and magnitude of change far exceeding a small global average decline (instantaneous rate of change = −0.018 y−1). Our analysis identified declines in 38% of ecoregions for which there are data (−0.015 to −0.18 y−1), increases in 27% of ecoregions (0.015 to 0.11 y−1), and no detectable change in 35% of ecoregions. These spatially variable trajectories reflected regional differences in the drivers of change, uncertainty in some regions owing to poor spatial and temporal data coverage, and the dynamic nature of kelp populations. We conclude that although global drivers could be affecting kelp forests at multiple scales, local stressors and regional variation in the effects of these drivers dominate kelp dynamics, in contrast to many other marine and terrestrial foundation species.

     

  26. M.E. González, M. Cea, D. Reyes, L. Romero-Hermoso, P. Hidalgo, S. Meier, N. Benito, R. Navia, (2017), Functionalization of biochar derived from lignocellulosic biomass using microwave technology for catalytic application in biodiesel production, 2017, Energy Conversion and Management 137 (2017) 165–173.
    [ Show Abstract ]A study to produce an efficient catalyst to be used for biodiesel production was carried out introducing sulfonic groups in biochar using a microwave reactor. The transesterification reaction of waste cooking oils using the catalyst was also evaluated in a microwave reactor. The results showed that an increase in the temperature up to 140 C during biochar sulfonation enhanced the SO3H content on the catalyst surface. These results were confirmed through FT-IR and XPS analyses. A reduction in the surface area of the biochar was observed during the sulfonation. An increase of SO3H groups on the biochar surface was responsible for a higher FAME yield close to 90%. The catalyst could be re-used for up to six cycles by washing with hexane.

     

  27. Alonso Inostrosa-Psijas, Verónica Gil-Costa, Gabriel Wainer, Mauricio Marín, (2016), Formal Verification of DEVS Simulation: Web Search Engine Model Case Study, Proceeding SCSC 2016, Proceedings of the Summer Computer Simulation Conference, Article No. 18
    [ Show Abstract ]Web search engines (WSE) are complex and highly optimized systems operating over large clusters of processors which manage high and dynamic and unpredictable user query bursts. The modeling, simulation and formal verification of shush systems is a challenge task which includes to manage user behavior and hardware costs. In this paper, we propose a WSE modeled with DEVS to be efficiently deployed on a distributed cluster of computers. The proposed model aims to reduce the communication overhead introduced by the message passage among the different hierarchical components of the DEVS model. This model is formally verified by using an equivalent Timed Automata model.

     

  28. Roberto Solar, Verónica Gil-Costa and Mauricio Marín, (2016), Evaluation of Static/Dynamic Cache for Similarity Search Engines, International Conference on Current Trends in Theory and Practice of Informatics. SOFSEM 2016: Theory and Practice of Computer Science pp 615-627
    [ Show Abstract ]In large scale search systems, where it is important to achieve a high query throughput, cache strategies are a feasible tool to achieve this goal. A number of efficient cache strategies devised for exact query search in different application domains have been proposed so far. In similarity query search on metric spaces it is necessary to consider additional design requirements devised to produce good quality approximate results from the cache content. In this paper, we propose a Static/Dynamic cache strategy for metric spaces which takes advantage of results of static cache miss operations and their associated distance evaluations for increasing the overall performance of the cache. We present an experimental evaluation of the performance obtained with our strategy for different query selection/replacement strategies.

     

  29. Rita F. Patarra, Ana S. Carreiro, Anna A. Lloveras, Maria H. Abreu, Alejandro H. Buschmann, Ana I. Neto, (2017), Effects of light, temperature and stocking density on Halopteris scoparia growth, Journal of Applied Phycology, February 2017, Volume 29, Issue 1, pp 405–411.
    [ Show Abstract ]Halopteris scoparia (Linnaeus) Sauvageau is a cosmopolitan species, common in warm and cold temperate waters around Europe. Several studies have revealed the importance of the genus Halopteris to the nutraceutical and cosmetics industries due to its biological activities. The overexploitation of this natural resource must be prevented, both with sustainable harvesting and cultivation practices. This study investigated the effect of different stocking densities (SD) on the relative growth rate (RGR) and productivity of H. scoparia. A factorial experiment, using the best SD, was then run to test the combined effects of temperature and irradiance on the in vitro vegetative growth of H. scoparia. Overall, obtained results indicate H. scoparia appears to be a potential target species for aquaculture exploitation. It can grow in a wide range of temperatures (14 to 24 °C) providing irradiance is maintained under 150 μmol photons m−2 s−1 in order to restrain the development of epiphytes. Although promising, the methodologies adopted here require demonstration at larger-scale cultivation conditions, before moving to their effective implementation.

     

  30. Mariela Bustamante, B. Dave Oomah, Mónica Rubilar, Carolina Shene, (2017), Effective Lactobacillus plantarum and Bifidobacterium infantis encapsulation with chia seed (Salvia hispanica L.) and flaxseed (Linum usitatissimum L.) mucilage and soluble protein by spray drying, Food Chemistry, Volume 216, 1 February 2017, Pages 97-105.
    [ Show Abstract ]Mucilage (M) and soluble protein (SP) extracted from chia seed and flaxseed were used as encapsulating material for two probiotic bacteria: Bifidobacterium infantis and Lactobacillus plantarum by spray drying. Probiotic survival and viability after spray drying and during storage were evaluated. B. infantis and L. plantarum displayed high survival (⩾98%) after encapsulation with mixtures of maltodextrin (MD) combined with M and SP from flaxseed (MD:FM:FSP – 7.5:0.2:7.5%, w/w/w) and chia seed (MD:CM:CSP – 7.5:0.6:7.5%, w/w/w), respectively. These ternary blends protected the probiotics and enhanced their resistance to simulated gastric juice and bile solution. Probiotics encapsulated with the ternary blends incorporated in instant juice powder exhibited high viability (>9 Log10 CFU/g) after 45 days refrigerated storage. Encapsulation with the ternary blends reduced particle size of the probiotic powders thereby offering additional functional benefits. Our results reveal that chia seed and flaxseed are excellent sources of probiotic encapsulating agents.

     

  31. María Eugenia González, Luis Romero-Hermoso, Aixa González, Pamela Hidalgo, Sebastian Meier, Rodrigo Navia, and Mara Cea, (2017), Effects of Pyrolysis Conditions on Physicochemical Properties of Oat Hull Derived Biochar, BioResources 12(1), 2040-2057, 2017.
    [ Show Abstract ]The effects of the pyrolysis conditions in terms of temperature (400 to 600 °C), residence time (0.5 to 3.5 h), nitrogen flux (0 to 1 L/min), and temperature increase rate (1.5 to 3 °C/min) on the physicochemical properties of biochar were studied. The physicochemical properties evaluated in the biochar were specific surface area, pore volume, average pore size, total carbon content, pH, total acidity, elemental composition, and polycyclic aromatic hydrocarbons (PAHs) content. A higher specific surface area of 108.28 m2/g and a mean pore size diameter of about 2.24 nm were found when the pyrolysis was conducted at 600 °C. In general, the pH and total acidity increased with the increased pyrolysis temperature. The total PAH concentration in all of the combinations studied varied from 0.16 to 8.73 μg/kg, and only phenanthrene, pyrene, and chrysene were detected. The increased temperature seemed to decrease the PAH concentration in the biochar. Nevertheless, there was no correlation found between the PAH content and the combined evaluated parameters.

     

  32. Loredana Bălilescu, Carlos Conca, Tuhin Ghosh, Jorge San Martín and Muthusamy Vanninathan, (2016), Dispersion tensor and its unique minimizer in Hashin-Shtrikman micro-structures, Cornell University arXiv, 2016 | https://arxiv.org/abs/1608.07545
    [ Show Abstract ]In this paper, we introduce the macroscopic quantity, namely the dispersion tensor or the \textit{Burnett coefficient}s in the class of generalized Hashin-Shtrikman micro-structures \cite[page no. 281]{T}. In the case of two-phase materials associated with the periodic Hashin-Shtrikman structures, we settle the issue that the dispersion tensor has an unique minimizer, which is so called Apollonian-Hashin-Shtrikman micro-structure.

     

  33. Jorge L. Alvarado, Andrés Leschot, Álvaro Olivera-Nappa, Ana-María Salgado, Hernán Rioseco, Carolina Lyon, and Pilar Vigil, (2016), Delphinidin-Rich Maqui Berry Extract (Delphinol) (R) Lowers Fasting and Postprandial Glycemia and Insulinemia in Prediabetic Individuals during Oral Glucose Tolerance Tests, BioMed Research International, Volume 2016 (2016), Article ID 9070537, 10 pages
    [ Show Abstract ]Delphinidin anthocyanins have previously been associated with the inhibition of glucose absorption. Blood glucose lowering effects have been ascribed to maqui berry (Aristotelia chilensis) extracts in humans after boiled rice consumption. In this study, we aimed to explore whether a standardized delphinidin-rich extract from maqui berry (Delphinol) affects glucose metabolism in prediabetic humans based on glycemia and insulinemia curves obtained from an oral glucose tolerance test (OGTT) after a challenge with pure glucose. Volunteers underwent four consecutive OGTTs with at least one week washout period, in which different doses of Delphinol were administered one hour before glucose intake. Delphinol significantly and dose-dependently lowered basal glycemia and insulinemia. Lower doses delayed postprandial glycemic and insulinemic peaks, while higher doses reversed this tendency. Glycemia peaks were dose-dependently lowered, while insulinemia peaks were higher for the lowest dose and lower for other doses. The total glucose available in blood was unaffected by treatments, while the total insulin availability was increased by low doses and decreased by the highest dose. Taken together, these open exploratory results suggest that Delphinol could be acting through three possible mechanisms: by inhibition of intestinal glucose transporters, by an incretin-mediated effect, or by improving insulin sensitivity.

     

  34. M. P. Merino, B. A. Andrews, P. Parada, J. A. Asenjo, (2016), Characterization of Ferroplasma acidiphilum Growing in Pure and Mixed Culture with Leptospirillum ferriphilum, American Institute of Chemical Engineers Biotechnol. Progr. 2016 | DOI 10.1002/btpr.2340
    [ Show Abstract ]Biomining is defined as biotechnology for metal recovery from minerals, and is promoted by the concerted effort of a consortium of acidophile prokaryotes, comprised of members of the Bacteria and Archaea domains. Ferroplasma acidiphilum and Leptospirillum ferriphilum are the dominant species in extremely acid environments and have great use in bioleaching applications; however, the role of each species in this consortia is still a subject of research. The hypothesis of this work is that F. acidiphilum uses the organic matter secreted by L. ferriphilum for growth, maintaining low levels of organic compounds in the culture medium, preventing their toxic effects on L. ferriphilum. To test this hypothesis, a characterization of Ferroplasma acidiphilum strain BRL-115 was made with the objective of determining its optimal growth conditions. Subsequently, under the optimal conditions, L. ferriphilum and F. acidiphilum were tested growing in each other’s supernatant, in order to define if there was exchange of metabolites between the species. With these results, a mixed culture in batch cyclic operation was performed to obtain main specific growth rates, which were used to evaluate a mixed metabolic model previously developed by our group. It was observed that F. acidiphilum, strain BRL-115 is a chemomixotrophic organism, and its growth is maximized with yeast extract at a concentration of 0.04% wt/vol. From the experiments of L. ferriphilum growing on F. acidiphilum supernatant and vice versa, it was observed that in both cases cell growth is favorably affected by the presence of the filtered medium of the other microorganism, proving a synergistic interaction between these species. Specific growth rates were obtained in cyclic batch operation of the mixed culture and were used as input data for a Flux Balance Analysis of the mixed metabolic model, obtaining a reasonable behavior of the metabolic fluxes and the system as a whole, therefore consolidating the model previously developed.

     

  35. Verónica Molina, Klaudia Hernández, Cristina Dorador, Yoanna Eissler, Martha Hengst, Vilma Pérez and Chris Harrod, (2016), Bacterial Active Community Cycling in Response to Solar Radiation and Their Influence on Nutrient Changes in a High-Altitude Wetland, Front. Microbiol., 17 November 2016 | https://doi.org/10.3389/fmicb.2016.01823.
    [ Show Abstract ]Microbial communities inhabiting high-altitude spring ecosystems are subjected to extreme changes in solar irradiance and temperature throughout the diel cycle. Here, using 16S rRNA gene tag pyrosequencing (cDNA) we determined the composition of actively transcribing bacteria from spring waters experimentally exposed through the day (morning, noon, and afternoon) to variable levels of solar radiation and light quality, and evaluated their influence on nutrient recycling. Solar irradiance, temperature, and changes in nutrient dynamics were associated with changes in the active bacterial community structure, predominantly by Cyanobacteria, Verrucomicrobia, Proteobacteria, and 35 other Phyla, including the recently described Candidate Phyla Radiation (e.g., Parcubacteria, Gracilibacteria, OP3, TM6, SR1). Diversity increased at noon, when the highest irradiances were measured (3.3–3.9 H′, 1125 W m-2) compared to morning and afternoon (0.6–2.8 H′). This shift was associated with a decrease in the contribution to pyrolibraries by Cyanobacteria and an increase of Proteobacteria and other initially low frequently and rare bacteria phyla (< 0.5%) in the pyrolibraries. A potential increase in the activity of Cyanobacteria and other phototrophic groups, e.g., Rhodobacterales, was observed and associated with UVR, suggesting the presence of photo-activated repair mechanisms to resist high levels of solar radiation. In addition, the percentage contribution of cyanobacterial sequences in the afternoon was similar to those recorded in the morning. The shifts in the contribution by Cyanobacteria also influenced the rate of change in nitrate, nitrite, and phosphate, highlighted by a high level of nitrate accumulation during hours of high radiation and temperature associated with nitrifying bacteria activity. We did not detect ammonia or nitrite oxidizing bacteria in situ, but both functional groups (Nitrosomona and Nitrospira) appeared mainly in pyrolibraries generated from dark incubations. In total, our results reveal that both the structure and the diversity of the active bacteria community was extremely dynamic through the day, and showed marked shifts in composition that influenced nutrient recycling, highlighting how abiotic variation affects potential ecosystem functioning.

     

  36. Verónica Gil-Costa, Emilio Tapia, Mauricio Marín, (2016), Asynchronous Approximate Simulation Algorithm for Stream Processing Platforms (WIP), 2016 International Symposium on Computer Architecture and High Performance Computing Workshops (SBAC-PADW)
    [ Show Abstract ]Simulating streaming software applications running on top of a distributed stream processing platform can be useful to evaluate their performance before putting them into production. However, simulating them in parallel is a complex task as the execution of events across simulation processors is not trivial because causality related events can form different sequences distributed on many processors. In this work, we present a window-based simulation algorithm for approximate parallel discrete-event simulation of streaming software applications. The algorithm is suitable for distributed stream computing platforms containing facilities for supporting fully asynchronous processing elements and downstream event flows. Namely, our simulations can be executed on the same streaming platform where the streaming application is intended to be run. The parallel simulation algorithm is based on two time control barriers. The first one is a time window barrier used to process events with time-stamps within the time window. The second one is an oracle time barrier used to define the values o f the time window barrier in a manner that is based on the intrinsic features of the system being simulated rather than the current value of the time window barrier of the actual parallel simulation. Both barriers are computed asynchronously. For experimentation, on top of the distributed stream computing platform we simulate a Web search engine. The experiments show that our proposal is capable of efficiently scaling up and at the same time achieving good approximate results with respect to the results obtained from sequential simulations of the same Web search engine model.

     

  37. Miguel A. Campodonico, Daniela Vaisman, Jean F. Castro, Valeria Razmilic, Francesca Mercado, Barbara A. Andrews, Adam M. Feist, Juan A. Asenjo, (2016), Acidithiobacillus ferrooxidans’s comprehensive model driven analysisvof the electron transfer metabolism and synthetic strain design for biomining applications, Metabolic Engineering Communications 3 (2016) 84-96
    [ Show Abstract ]Acidithiobacillus ferrooxidans is a gram-negative chemolithoautotrophic γ-proteobacterium. It typically grows at an external pH of 2 using the oxidation of ferrous ions by oxygen, producing ferric ions and water, while fixing carbon dioxide from the environment. A. ferrooxidans is of great interest for biomining and environmental applications, as it can process mineral ores and alleviate the negative environmental consequences derived from the mining processes. In this study, the first genome-scale metabolic re-construction of A. ferrooxidans ATCC 23270 was generated (iMC507). A total of 587 metabolic and transport/exchange reactions, 507 genes and 573 metabolites organized in over 42 subsystems were incorporated into the model. Based on a new genetic algorithm approach, that integrates flux balance analysis, chemiosmotic theory, and physiological data, the proton translocation stoichiometry for a number of enzymes and maintenance parameters under aerobic chemolithoautotrophic conditions using three different electron donors were estimated. Furthermore, a detailed electron transfer and carbon flux distributions during chemolithoautotrophic growth using ferrous ion, tetrathionate and thiosulfate were determined and reported. Finally, 134 growth-coupled designs were calculated that enables Extracellular Polysaccharide production. iMC507 serves as a knowledgebase for summarizing and categorizing the information currently available for A. ferrooxidans and enables the understanding and engineering of Acidithiobacillus and similar species from a comprehensive model-driven perspective for biomining applications.

     

  38. Verónica Gil-Costa, Nicolás Hidalgo, Erika Rosas, Mauricio Marín, (2016), A dynamic load balance algorithm for the S4 Parallel stream processing engine, 2016 International Symposium on Computer Architecture and High Performance Computing Workshops (SBAC-PADW)
    [ Show Abstract ]Large streams of data can be analyzed in real-time by Parallel Stream Processing Engines (PSPEs) which are based on a graph paradigm where vertices represent processing elements (PEs) and edges represent flows of data among PEs. In this work, we propose a new elastic strategy for the S4 PSPE to adjust the overall load of PEs in accordance with the utilization levels and data traffic at each PE. Our approach exploits a producer/consumer model to achieve load balance where new workers pull events from a buffer queue in order to release the amount of traffic in an overloaded PE. Results show that the proposed strategy prevents saturation of PEs and improves the overall throughput of the system by up to 470%.

     

  39. Sevasti Filippidou, Tina Wunderlin, Thomas Junier, Nicole Jeanneret, Cristina Dorador, Veronica Molina, David R. Johnson and Pilar Junier, (2016), A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes, Front. Microbiol. 7:1707 / doi: 10.3389/fmicb.2016.01707
    [ Show Abstract ]Environmental conditions unsuitable for microbial growth are the rule rather than the exception in most habitats. In response to this, microorganisms have developed various strategies to withstand environmental conditions that limit active growth. Endospore-forming Firmicutes (EFF) deploy a myriad of survival strategies in order to resist adverse conditions. Like many bacterial groups, they can form biofilms and detect nutrient scarcity through chemotaxis. Moreover, within this paraphyletic group of Firmicutes, ecophysiological optima are diverse. Nonetheless, a response to adversity that delimits this group is the formation of wet-heat resistant spores. These strategies are energetically demanding and therefore might affect the biological success of EFF. Therefore, we hypothesize that abundance and diversity of EFF should be maximized in those environments in which the benefits of these survival strategies offsets the energetic cost. In order to address this hypothesis, geothermal and mineral springs and drillings were selected because in these environments of steep physicochemical gradients, diversified survival strategies may become a successful strategy. We collected 71 samples from geothermal and mineral environments characterized by none (null), single or multiple limiting environmental factors (temperature, pH, UV radiation, and specific mineral composition). To measure success, we quantified EFF gene copy numbers (GCN; spo0A gene) in relation to total bacterial GCN (16S rRNA gene), as well as the contribution of EFF to community composition. The quantification showed that relative GCN for EFF reached up to 20% at sites characterized by multiple limiting environmental factors, whereas it corresponded to less than 1% at sites with one or no limiting environmental factor. Pyrosequencing of the 16S rRNA gene supports a higher contribution of EFF at sites with multiple limiting factors. Community composition suggested a combination of phylotypes for which active growth could be expected, and phylotypes that are most likely in the state of endospores, in all the sites. In summary, our results suggest that diversified survival strategies, including sporulation and metabolic adaptations, explain the biological success of EFF in geothermal and natural springs, and that multiple extreme environmental factors favor the prevalence of EFF.