1. Castro, J.F., Razmilic, V., Gomez-Escribano, J.P., Andrews, B.A., Asenjo, J.A. and Bibb, M.J. (2015) Identification and Heterologous Expression of the Chaxamycin Biosynthesis Gene Cluster from Streptomyces leeuwenhoekii. Applied Environmental Microbiology, September 2015 vol. 81 no. 17 5820-5831
    [ Show Abstract ] Streptomyces leeuwenhoekii, isolated from the hyperarid Atacama Desert, produces the new ansamycin-like compounds chaxamycins A to D, which possess potent antibacterial activity and moderate antiproliferative activity. We report the development of genetic tools to manipulate S. leeuwenhoekii and the identification and partial characterization of the 80.2-kb chaxamycin bio-synthesis gene cluster, which was achieved by both mutational analysis in the natural producer and heterologous expression in Streptomyces coelicolor A3(2) strain M1152. Restoration of chaxamycin production in a nonproducing ΔcxmK mutant (cxmK encodes 3-amino-5-hydroxybenzoic acid [AHBA] synthase) was achieved by supplementing the growth medium with AHBA, suggesting that mutasynthesis may be a viable approach for the generation of novel chaxamycin derivatives.


  2. Contador, C. A., Shene, C., Olivera, A., Yoshikuni, Y., Buschmann, A., Andrews, B.A, and Asenjo, J.A. (2015), Analyzing redox balance in a synthetic yeast platform to improve utilization of brown macroalgae as feedstock. Metabolic Engineering Communications, Volume 2, December 2015, Pages 76-84, 2, 76-84.
    [ Show Abstract ]Macroalgae have high potential to be an efficient, and sustainable feedstock for the production of biofuels and other more valuable chemicals. Attempts have been made to enable the co-fermentation of alginate and mannitol by Saccharomyces cerevisiae to unlock the full potential of this marine biomass. However, the efficient use of the sugars derived from macroalgae depends on the equilibrium of cofactors derived from the alginate and mannitol catabolic pathways. There are a number of strong metabolic limitations that have to be tackled before this bioconversion can be carried out efficiently by engineered yeast cells.
    An analysis of the redox balance during ethanol fermentation from alginate and mannitol by Saccharomyces cerevisiae using metabolic engineering tools was carried out. To represent the strain designed for conversion of macroalgae carbohydrates to ethanol, a context-specific model was derived from the available yeast genome-scale metabolic reconstructions. Flux balance analysis and dynamic simulations were used to determine the flux distributions. The model indicates that ethanol production is determined by the activity of 4-deoxy-l-erythro-5-hexoseulose uronate (DEHU) reductase (DehR) and its preferences for NADH or NADPH which influences strongly the flow of cellular resources. Different scenarios were explored to determine the equilibrium between NAD(H) and NADP(H) that will lead to increased ethanol yields on mannitol and DEHU under anaerobic conditions. When rates of mannitol dehydrogenase and DehR NADH tend to be close to a ratio in the range 1–1.6, high growth rates and ethanol yields were predicted. The analysis shows a number of metabolic limitations that are not easily identified through experimental procedures such as quantifying the impact of the cofactor preference by DEHU reductase in the system, the low flux into the alginate catabolic pathway, and a detailed analysis of the redox balance. These results show that production of ethanol and other chemicals can be optimized if a redox balance is achieved. A possible methodology to achieve this balance is presented. This paper shows how metabolic engineering tools are essential to comprehend and overcome this limitation. & 2015 Published by Elsevier B.V. on behalf of International Metabolic Engineering Society.


  3. Gomez-Escribano, J.P., Castro,J.F., Razmilic, V., Chandra G., Andrews, B.A., Asenjo, J.A., and Bibb, M.J. (2015), The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contings of the chromosome, circular plasmid pSLE1 and linear plasmid pSLE2. BMC Genomics, 2015, 16, 485. DOI: 10.1186/s12864-015-1652-8
    [ Show Abstract ]Background: Next Generation DNA Sequencing (NGS) and genome mining of actinomycetes and other microorganisms is currently one of the most promising strategies for the discovery of novel bioactive natural products, potentially revealing novel chemistry and enzymology involved in their biosynthesis. This approach also allows rapid insights into the biosynthetic potential of microorganisms isolated from unexploited habitats and ecosystems, which in many cases may prove difficult to culture and manipulate in the laboratory. Streptomyces leeuwenhoekii (formerly Streptomyces sp. strain C34) was isolated from the hyper-arid high-altitude Atacama Desert in Chile and shown to produce novel polyketide antibiotics.
    Results: Here we present the de novo sequencing of the S. leeuwenhoekii linear chromosome (8 Mb) and two extrachromosomal replicons, the circular pSLE1 (86 kb) and the linear pSLE2 (132 kb), all in single contigs, obtained by combining Pacific Biosciences SMRT (PacBio) and Illumina MiSeq technologies. We identified the biosynthetic gene clusters for chaxamycin, chaxalactin, hygromycin A and desferrioxamine E, metabolites all previously shown to be produced by this strain (J Nat Prod, 2011, 74:1965) and an additional 31 putative gene clusters for specialized metabolites. As well as gene clusters for polyketides and non-ribosomal peptides, we also identified three gene clusters encoding novel lasso-peptides.
    Conclusions: The S. leeuwenhoekii genome contains 35 gene clusters apparently encoding the biosynthesis of specialised metabolites, most of them completely novel and uncharacterised. This project has served to evaluate the current state of NGS for efficient and effective genome mining of high GC actinomycetes. The PacBio technology now permits the assembly of actinomycete replicons into single contigs with >99 % accuracy. The assembled Illumina sequence permitted not only the correction of omissions found in GC homopolymers in the PacBio assembly (exacerbated by the high GC content of actinomycete DNA) but it also allowed us to obtain the sequences of the termini of the chromosome and of a linear plasmid that were not assembled by PacBio. We propose an experimental pipeline that uses the Illumina assembled contigs, in addition to just the reads, to complement the current limitations of the PacBio sequencing technology and assembly software.
    Keywords: Second/Third next generation sequencing, Illumina MiSeq, Pacific Biosciences PacBio SMRT, Chaxamycin, Chaxalactin, Lasso peptide, Genome mining


  4. Contador, C., Rodriguez, V., Andrews, B.A., Asenjo, J.A. (2015), Genome-scale reconstruction of Salinispora tropica CNB-440 metabolism to study strain-specific adaptation. Antonie van Leeuwenhoek, November 2015, Volume 108, Issue 5, pp 1075–1090.
    [ Show Abstract ]The first manually curated genome-scale metabolic model for Salinispora tropica strain CNB-440 was constructed. The reconstruction enables characterization of the metabolic capabilities for understanding and modeling the cellular physiology of this actinobacterium. The iCC908 model was based on physiological and biochemical information of primary and specialised metabolism pathways. The reconstructed stoichiometric matrix consists of 1169 biochemical conversions, 204 transport reactions and 1317 metabolites. A total of 908 structural open reading frames (ORFs) were included in the reconstructed network. The number of gene functions included in the reconstructed network corresponds to 20% of all characterized ORFs in the S. tropica genome. The genome-scale metabolic model was used to study strain-specific capabilities in defined minimal media. iCC908 was used to analyze growth capabilities in 41 different minimal growth-supporting environments. These nutrient sources were evaluated experimentally to assess the accuracy of in silico growth simulations. The model predicted no auxotrophies for essential amino acids, which was corroborated experimentally. The strain is able to use 21 different carbon sources, 8 nitrogen sources and 4 sulfur sources from the nutrient sources tested. Experimental observation suggests that the cells may be able to store sulfur. False predictions provided opportunities to gain new insights into the physiology of this species, and to gap fill the missing knowledge. The incorporation of modifications led to increased accuracy in predicting the outcome of growth/no growth experiments from 76 to 93 %. iCC908 can thus be used to define the metabolic capabilities of S. tropica and guide and enhance the production of specialised metabolites. Keywords Salinispora tropica – Metabolic capabilities – Strain adaptation – Genome-scale metabolic reconstruction


  5. Elsayed, S., Trusch, F., Deng, H., Raab, A., Prokes, I., Busarakam, K., Asenjo, J.A., Andrews, B.A., van West, P., Bull, A., Goodfellow, M., Yu, Y., Ebel, R., Jaspars, M. and Rateb, M. (2015), Chaxapeptin, a lasso peptide from the extremotolerant Streptomyces leeuwenhoekii strain C58 from the hyper-arid Atacama Desert. Journal of Organic Chemistry, 2015, 80, 10252-10260.
    [ Show Abstract ]Lasso peptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) that possess a unique “lariat knot” structural motif. Genome mining-targeted discovery of new natural products from microbes obtained from extreme environments has led to the identification of a gene cluster directing the biosynthesis of a new lasso peptide, designated as chaxapeptin 1, in the genome of Streptomyces leeuwenhoekii strain C58 isolated from the Atacama Desert. Subsequently, 1 was isolated and characterized using high-resolution electrospray ionization mass spectrometry and nuclear magnetic resonance methods. The lasso nature of 1 was confirmed by calculating its nuclear Overhauser effect restraint-based solution structure. Chaxapeptin 1 displayed a significant inhibitory activity in a cell invasion assay with human lung cancer cell line A549.


  6. Sandoval, G., Espinoza, D., Figueroa, N. and Asenjo, J.A. (2016), MILP reformulations for the design of biotechnological multi-product batch plants using continuous equipment sizes and discrete host selection. Computers & Chemical Engineering, Volume 84, 4 January 2016, Pages 1-11
    [ Show Abstract ]In this article we present a new approach, relying on mixed-integer linear programming (MILP) formulations, for the design of multi-product batch plants with continuous sizes for processing units and host selection. The main advantage of the proposed approach is its scalability, that allows us to solve, within reasonable precision requirements, realistic instances. Furthermore, we show that many other alternatives are either numerically unstable (for the problem sizes that we are interested in), unable to solve large instances, or much slower than the proposed method. We present extensive computational experiments, which show that we are able to solve almost all tested instances, and, in average, we are ten times faster than alternative approaches. As we use a high level implementation language (AMPL) we should get further time improvements if lower level implementations are used (C, C++). Reproducibility of our results can be tested using our models and data available on-line at BPLIB.1 © 2015 Elsevier Ltd. All rights reserved.


  7. Conca, C., Lecaros, R., Ortega, J., Rosier, L. (2015), Identifiability and Stability of an Inverse Problem Involving a Fredholm Equation. Chinese Annals of Mathematics, 36B, 737-762
    [ Show Abstract ]The authors study a linear inverse problem with a biological interpretation, which is modelled by a Fredholm integral equation of the first kind, where the kernel is represented by step functions. Based on different assumptions, identifiability, stability and reconstruction results are obtained. Keywords Inverse problems, Olfactory system, Kernel determination, Fredholm inte-
    gral equation, Partial differential equations, Numerical reconstruction


  8. Acevedo, P., Amrouche, Ch., Conca, C. (2015), Boussinesq system with non-homogeneous boundary conditions. Applied Mathematics Letters, Volume 53, March 2016, Pages 39-44
    [ Show Abstract ]A classical stationary Boussinesq system with non-homogeneous Dirichlet boundary conditions in a bounded domain Ω ⊂ R3 is considered in this paper; included is the case of a possibly disconnected boundary. We prove existence of a weak, a strong and a very weak solution in Lp-theory. Uniqueness of the very weak solution is proved under a small data assumption.


  9. Caubet, F., Conca, C., Godoy, M. (2016), On the detection of several obstacles in Stokes flow: Topological sensivity and combination with shape derivative. Inverse Problems & Imaging. Pages: 327 – 367, Volume 10, Issue 2, May 2016 doi:10.3934/ipi.2016003
    [ Show Abstract ]We consider the inverse problem of detecting the location and the shape of several obstacles immersed in a fluid flowing in a larger bounded domain Ω from partial boundary measurements in the two dimensional case. The fluid flow is governed by the steady-state Stokes equations. We use a topological sensitivity analysis for the Kohn-Vogelius functional in order to find the number and the qualitative location of the objects. Then we explore the numerical possibilities of this approach and also present a numerical method which combines the topological gradient algorithm with the classical geometric shape gradient algorithm; this blending method allows to find the number of objects, their relative location and their approximate shape. Keywords: Geometric inverse problem, topological sensitivity analysis, topological gradient, shape gradient, Stokes equations, Kohn-Vogelius functional.


  10. Cumsille, P., Coronel, A., Conca, C., Quiñinao, C., Escudero, C. (2015), Proposal of a hybrid approach for tumor progression and tumor-induced angiogenesis. Theoretical Biology and Medical Modelling, 2015, 12:13. DOI: 10.1186/s12976-015-0009-y.
    [ Show Abstract ]One of the main challenges in cancer modelling is to improve the knowledge of tumor progression in areas related to tumor growth, tumor-induced angiogenesis and targeted therapies efficacy. For this purpose, incorporate the expertise from applied mathematicians, biologists and physicians is highly desirable. Despite the existence of a very wide range of models, involving many stages in cancer progression, few models have been proposed to take into account all relevant processes in tumor progression, in particular the effect of systemic treatments and angiogenesis. Composite biological experiments, both in vitro and in vivo, in addition with mathematical modelling can provide a better understanding of theses aspects. In this work we proposed that a rational experimental design associated with mathematical modelling could provide new insights into cancer progression. To accomplish this task, we reviewed mathematical models and cancer biology literature, describing in detail the basic principles of mathematical modelling. We also analyze how experimental data regarding tumor cells proliferation and angiogenesis in vitro may fit with mathematical modelling in order to reconstruct in vivo tumor evolution. Additionally, we explained the mathematical methodology in a comprehensible way in order to facilitate its future use by the scientific community. Keywords: Hybrid approach, Tumor progression, Mathematical modelling, Parameter estimation, Experimental design


  11. Conca, C., Dambrine, M., Quinteros, D., Mahadevan, R. (2016), Minimisation of the ground state of the mixture of two conducting materials in a small contrast regime. Mathematical Methods in the Applied Sciences, Volume 39, Issue 13, 15 September 2016, Pages 3549–3564 doi: 10.1002/mma.3797.
    [ Show Abstract ]We consider the problem of distributing two conducting materials with a prescribed volume ratio in a given domain so as to minimize the first eigenvalue of an elliptic operator with Dirichlet conditions. The gap between the two conductivities is assumed to be small (low contrast regime). For any geometrical configuration of the mixture, we provide a complete asymptotic expansion of the first eigenvalue. We then consider a relaxation approach to minimize the second-order approximation with respect to the mixture. We present numerical simulations in dimensions two and three to illustrate optimal distributions and the advantage of using a second-order method. Copyright © 2016 John Wiley & Sons, Ltd. Keywords: shape optimization; eigenvalue problem; homogenization


  12. Conca C., Donato P., José, E.C. Mishra I.(2016), Asymptotic analysis of optimal controls of a semilinear problem in a perforated domainJournal of the Ramanujan Mathematical Society, Volume 31, Issue 3, September 2016 pp. 265–305.
    [ Show Abstract ]In this paper, we study the L2 and H1 –approximate controllability and homogenization of a semilinear elliptic boundary value problem in a perforated domain. The principal term in the state equation has rapidly oscillating coefficients and the control region is free from perforations (holes). The observable zone is locally distributed in the perforation free region, in the case of H1 –approximate controllability. By using the constructive approach introduced by Lions and which is based on the Fenchel–Rockafeler’s duality theory, we obtain the approximate control of minimal norm. The existence of the control is established by means of a fixed point argument. Another interesting result of this study is that the minimal norm controls of the ε –problem converge to the optimal controls associated with the homogenized problem. The result in the case of rapidly oscillating coefficients in a fixed domain was proved in [Conca, et.al., J. Math.Anal. 285 (2003), 17-36]. The main difficulty relies in passing to the limit in the cost functional (as ε → 0 ) having rapidly oscillating coefficients.


  13. Navarro, G., Ordoñez, A. (2016). Faster Compressed Suffix Trees for Repetitive Collections. ACM Journal of Experimental Algorithmics, 21, Art 1.8
    [ Show Abstract ]Recent compressed suffix trees targeted to highly repetitive text collections reach excellent compression performance, but operation times in the order of milliseconds. We design a new suffix tree representation for this scenario that still achieves very low space usage, only slightly larger than the best previous one, but supports the operations within microseconds. This puts the data structure in the same performance level of compressed suffix trees designed for standard text collections, which on repetitive collections use many times more space than our new structure.


  14. Martínez-Prieto, M.A., Brisaboa, N., Cánovas, R., Claude F., Navarro, G. (2016). Practical compressed string dictionaries. Information Systems, Volume 56, March 2016, Pages 73-108. https://doi.org/10.1016/j.is.2015.08.008
    [ Show Abstract ]The need to store and query a set of strings – a string dictionary – arises in many kinds of applications. While classically these string dictionaries have accounted for a small share of the total space budget (e.g., in Natural Language Processing or when indexing text collections), recent applications in Web engines, Semantic Web (RDF) graphs, Bioinformatics, and many others handle very large string dictionaries, whose size is a significant fraction of the whole data. In these cases, string dictionary management is a scalability issue by itself. This paper focuses on the problem of managing large static string dictionaries in compressed main memory space. We revisit classical solutions for string dictionaries like hashing, tries, and front-coding, and improve them by using compression techniques. We also introduce some novel string dictionary representations built on top of recent advances in succinct data structures and full-text indexes. All these structures are empirically compared on a heterogeneous testbed formed by real-world string dictionaries. We show that the compressed representations may use as little as 5% of the original dictionary size, while supporting lookup operations within a few microseconds. These numbers outperform the state-of-the-art space/time tradeoffs in many cases. Furthermore, we enhance some representations to provide prefix- and substring-based searches, which also perform competitively. The results show that compressed string dictionaries are a useful building block for various data-intensive applications in different domains. & 2015 Elsevier Ltd. All rights reserved.


  15. Navarro, G., Thankachan, S. (2016). Reporting Consecutive Substring Occurrences Under Bounded Gap Constraints. Theoretical Computer Science, Volume 638, 25 July 2016, Pages 108-111, doi:10.1016/j.tcs.2016.02.005
    [ Show Abstract ]We study the problem of indexing a text T[1 …n] such that whenever a pattern P[1 … p] and an interval [α, β] come as a query, we can report all pairs (i, j) of consecutive occurrences of P in T with αjiβ. We present an O(n log n) space data structure with optimal O(p + k) query time, where k is the output size. © 2016 Elsevier B.V. All rights reserved.


  16. Navarro, G., Reyes, N. (2016) New Dynamic Metric Indices for Secondary Memory. Information Systems, Volume 59, July 2016, Pages 48-78. doi:10.1016/j.is.2016.03.009
    [ Show Abstract ]Metric indices support efficient similarity searches in metric spaces. This problem is central to many applications, including multimedia databases and repositories handling complex objects. Most metric indices are designed for main memory, and also most of them are static, that is, do not support insertions and deletions of objects. In this paper we introduce new metric indices for secondary memory that support updates, that is, they are dynamic. First, we show how the dynamic and memory-based Dynamic Spatial Approximation Tree (DSAT) can be extended to operate on secondary memory. Second, we design a dynamic and secondary-memory-based version of the static List of Clusters (LC), which performs well on high-dimensional spaces. The new structure is called Dynamic LC (DLC). Finally, we combine the DLC with the in-memory version of DSAT to create a third structure, Dynamic Set of Clusters (DSC), which improves upon the other two in various cases. We compare the new structures with the state of the art, showing that they are competitive and outstand in several scenarios, especially on spaces of medium and high dimensionality. & 2016 Elsevier Ltd. All rights reserved.


  17. Tomova, A., Ivanova, L., Buschmann, A.H., Rioseco, M., Kalsi, R.K, Godfrey, H.P., Cabello, F.C. (2015), Antimicrobial Resistance genes in marine bacteria and human uropathogenic Escherichia coli from a region of intensive aquaculture. Enviromental Microbiology Reports,Volume 7, Issue 5, October 2015, Pages 803–809.
    [ Show Abstract ]Antimicrobials are heavily used in Chilean salmon aquaculture. We previously found significant differences in antimicrobial-resistant bacteria between sediments from an aquaculture and a non-aquaculture site. We now show that levels of antimicrobial resistance genes (ARG) are significantly higher in antimicrobial-selected marine bacteria than in unselected bacteria from these sites. While ARG in tetracycline- and florfenicol-selected bacteria from aquaculture and non-aquaculture sites were equally frequent, there were significantly more plasmid-mediated quinolone resistance genes per bacterium and significantly higher numbers of qnrB genes in quinolone-selected bacteria from the aquaculture site. Quinolone-resistant urinary Escherichia coli from patients in the Chilean aquacultural region were significantly enriched for qnrB (including a novel qnrB gene), qnrS, qnrA and aac(6′)-1b, compared with isolates from New York City. Sequences of qnrA1qnrB1 and qnrS1 in quinolone-resistant Chilean E. coli and Chilean marine bacteria were identical, suggesting horizontal gene transfer between antimicrobial-resistant marine bacteria and human pathogens.


  18. Barrento, S., Camus, C., Sousa-Pinto, I., Buschmann, A.H. (2016), Germplasm banking of the giant kelp: Our biological insurance in a changing environment. Algal Research, Volume 13, January 2016, Pages 134-140
    [ Show Abstract ]Genetic diversity is being lost at a fast pace — seaweeds are no exception. The giant kelp, Macrocystis pyrifera, forms vast underwater forests in both hemispheres and is a key species for ecosystem functioning. But this species is also a commodity product. M. pyrifera is harvested for its chemical compounds (e.g. alginates) and for feedstock (e.g. abalone). In the past 5 years, some companies tried new farming techniques to boost biomass production for biofuel conversion. But the lack of sustainable management can lead to genetic erosion and degradation of livelihoods. Often, the natural genetic populations are not described, and we may be losing what is yet to be found. Aiming to alert and prevent this situation, we developed a germplasm bank based on the genetic diversity of M. pyrifera from Chile. We preserved female and male gametophytes in separate, from 3 genetic populations in low light, at 10 °C, in Provasoli media but without cryoprotective agents. After 5 years in cold storage, we show for the first time gametophyte viability up to 89% and viability differences between genetic populations. We discuss the benefits of this germplasm bank considering sustainability of seaweed production, food security pressures, and climate change. © 2015 Elsevier B.V. All rights reserved.


  19. Hafting, J.T. , Craigie, J.S. , Stengel, D.B., Loureiro, R.R. , Buschmann, A.H. , Yarish, C., Edwards, M.D., Critchley A.T. (2015), Prospects and challenges for industrial production of seaweed. Journal of Phycology, Volume 51, Issue 5, October 2015, Pages 821–837
    [ Show Abstract ]Large-scale seaweed cultivation has been instrumental in globalizing the seaweed industry since the 1950s. The domestication of seaweed cultivars (begun in the 1940s) ended the reliance on natural cycles of raw material availability for some species, with efforts driven by consumer demands that far exceeded the available supplies. Currently, seaweed cultivation is unrivaled in mariculture with 94% of annual seaweed biomass utilized globally being derived from cultivated sources. In the last decade, research has confirmed seaweeds as rich sources of potentially valuable, health-promoting compounds. Most existing seaweed cultivars and current cultivation techniques have been developed for producing commoditized biomass, and may not necessarily be optimized for the production of valuable bioactive compounds. The future of the seaweed industry will include the development of high value markets for functional foods, cosmeceuticals, nutraceuticals, and pharmaceuticals. Entry into these markets will require a level of standardization, efficacy, and traceability that has not previously been demanded of seaweed products. Both internal concentrations and composition of bioactive compounds can fluctuate seasonally, geographically, bathymetrically, and according to genetic variability even within individual species, especially where life history stages can be important. History shows that successful expansion of seaweed products into new markets requires the cultivation of domesticated seaweed cultivars. Demands of an evolving new industry based upon efficacy and standardization will require the selection of improved cultivars, the domestication of new species, and a refinement of existing cultivation techniques to improve quality control and traceability of products. Key index words: bioactive; cosmeceutical; cultivation; efficacy; fuctional food; nutraceutical; pharmaceutical; seaweed; standardization; traceability; value-added


  20. Leyton, A., Pezoa-Conte, R., Barriga ,A., Buschmann, A. H., Mäki-Arvela, P., Mikkola, J.P., Lienqueo, M.E. (2016), Identification and efficient extraction method of phlorotannins from the brown seaweed Macrocystis pyrifera using an orthogonal experimental design. Algal Research, Volume 16, June 2016, Pages 201-208.
    [ Show Abstract ]The brown seaweed contains a type polyphenol compound characteristic of its species, the phlorotannins, which are produced from the polymerization of phloroglucinol units. They have been extensively studied due to their pharmacological and nutraceutical properties, but there is still a need for an optimized extraction protocol. In this study, the brown seaweed Macrocystis pyrifera was employed to determine the best conditions for extraction of phlorotannins. A set of different variables were evaluated such as the use of pre-treatment, type of solvent, drying temperature, particle size, temperature and extraction time as well as the solid/liquid ratio upon extraction. The optimal conditions for the extractionof phlorotannins were: pre-treatment with hexane, extraction with water, drying temperature 40°C, particle size below 1.4 mm, at 55 °C for 4 h and a solid-to-liquid ratio of 1:15. Under these conditions, the concentration of phlorotannins achieved in the extract was 200.5 ± 5.6 mg gallic acid equivalent (GAE)/100 g dry seaweed (DS) and total antioxidant activity of the extract of 38.4 ± 2.9 mg trolox equivalent (TE)/100 g DS. Further, it was possible to identify two phlorotannins through HPLC-ESI-MS analyses: phloroeckol and a tetrameric phloroglucinol. These phlorotannins have been reported in the literature to have an antidiabetic effect and prevention of Alzheimer’s disease for phloroeckol, and free radical scavenging ability and antiallergic effect for tetrameric phloroglucinol. Therefore, the extract of phlorotannins has potential as medicinal foods or therapeutics for human health applications. © 2016 Elsevier B.V. All rights reserved.


  21. Cabello, F.C., Godfrey, H.P, Buschmann, A.H., Dölz H.J. (2016), Aquaculture as yet another environmental gateway to the development and globalisation of antimicrobial resistance. The Lancet Infectious Diseases, 16, 100-106.
    [ Show Abstract ]Aquaculture uses hundreds of tonnes of antimicrobials annually to prevent and treat bacterial infection. The passage of these antimicrobials into the aquatic environment selects for resistant bacteria and resistance genes and stimulates bacterial mutation, recombination, and horizontal gene transfer. The potential bridging of aquatic and human pathogen resistomes leads to emergence of new antimicrobial-resistant bacteria and global dissemination of them and their antimicrobial resistance genes into animal and human populations. Eff orts to prevent antimicrobial overuse in aquaculture must include education of all stakeholders about its detrimental eff ects on the health of fi sh, human beings, and the aquatic ecosystem (the notion of One Health), and encouragement of environmentally friendly measures of disease prevention, including vaccines, probiotics, and bacteriophages. Adoption of these measures is a crucial supplement to eff orts dealing with antimicrobial resistance by developing new therapeutic agents, if headway is to be made against the increasing problem of antimicrobial resistance in human and veterinary medicine.


  22. Buschmann, A.H, (2016) Seaweed Ecology and Physiology. Journal of Phycology, 52, 315-316.
    [ Show Abstract ]BOOK REVIEW: My research group has heavily utilized the first edition of this book (Lobban and Harrison 1994) for over 20 years, and it has been especially valuable for students preparing dissertation proposals and projects. Upon first reading this new edition by Hurd et al., I was impressed and excited to delve into the text as it contained updated references, illustrations and tables, and chapters. The text goes beyond phycological teaching and includes a detailed analysis of the existing knowledge of seaweed interactions with their physio-chemical and biological environments, providing a dynamic view of how these organisms use and exist in the marine environment. The book also discusses anthropogenic effects on seaweeds, such as pollution, as well as seaweed farming and its applications. The incorporation of new authors added modern and exciting overviews by first-class phycologists on “hot topics” and produced a textbook that will become “the basic guide” during the next decade in our laboratory and surely in many other groups around the world.


  23. Buschmann, A.H., Muñoz, J.L. (2016). Salmonid Farming. Reference Module in Earth Systems and Environmental Sciences (2016).
    [ Show Abstract ]Salmonids have a relatively primitive appearance among the teleost fish corresponding to the Salmonidae family with about 10 genera that are recognized today. All salmonids spawn in freshwater where some species can complete their entire life cycle; however most salmonids are anadromous, i.e. juvenile stages move into the sea for feeding, returning to spawn as large adults after one or more years. Human interest for salmonids can be traced long back in history. Management of wild populations and early farming practices can be recorded back to the 14th century in Europe. In the 19th century spawning, egg management and fertilization techniques were well-established allowing transporting different salmonid species around the world. Today several species can be found in Oceania, America, Africa, Asia and Europe. In several regions some salmonid species have become established, allowing the development of economic activities such as sport fishing in different regions, even as far as the southernmost part of Argentinean and Chilean Patagonia. More relevant is that salmonid farming has become a major global industry with a high demand in United States, Europe and Japan and rapidly emerging markets, such as China, Russia and Brazil. This paper describes the actual status of salmonid aquaculture in the world considering landing statistics, culture technologies and farming operation requirements. We also discuss the most relevant challenges this productive activity is currently facing, several of them have become controversial with an impact on local and regional economies as the global value of this activity has been estimated to be above US$15 billion (value for 2012 after FAO).


  24. Ravanal, M.C., Pezoa-Conte, R., von Schoultz, S., Hemmin,g J., Salazar, O., Anugwom, I., Jogunola, O., Mäki-Arvela, P., Willför, S.,Mikkola J.P., ,Lienqueo, M.E. (2016). Comparison of different types of pretreatment and enzymatic saccharification of Macrocystis pyrifera for the production of biofuel. Algal Research, Volume 13, January 2016, Pages 141-147
    [ Show Abstract ]In this work, the brown algae Macrocystis pyrifera were pretreated with dilute sulfuric acid, water and three different types of ionic liquids (ILs): 1-ethyl-3-methylimidazolium acetate ([EMIM][OAc]), 1,5-diazabicyclo[4.3.0]non-5-ene acetate ([DBNH][OAc]) and 1,8-diazabicyclo-[5.4.0]–undec-7-ene–sulfurdioxide–monoethanolamine (DBU–MEA–SO2–SIL), to disassemble the complex polysaccharide structure. After each pretreatment procedure, enzymatic saccharification was performed to release the monosaccharides. The main building blocks of M. pyrifera were processed by derivatization via acid methanolysis and subjected to gas chromatographic analysis. It was found that the main constituents were alginate (60.6 wt.%) and cellulose (22.6 wt.%) of total carbohydrate content. The degradation of alginate requires the action of alginate lyase and oligoalginate lyase, which hydrolyze the main chain in a synergistic mechanism releasing uronic acid (unsaturated uronate). Upon saccharification of cellulose, cellulases and β-glucosidase were used allowing the release of glucose. It was found that the best pretreatment strategy for M. pyrifera consisted of a pretreatment with 2 vol.% sulfuric acid, followed by saccharification of cellulose with a mixture of cellulases at pH 5.2 for 4 h at 50 °C or by saccharification of alginate with the enzyme lyase/oligoalginate lyase at pH 7.5 for 2 h at 37 °C. The process resulted in a release of 68.4 wt.% of glucose (55.74 ± 0.05 mg glucose/g algae) whereas in the case of alginate 85.8 wt.% of uronic acid (193.7 ± 10.6 mg uronic acid/g algae) was released. To the best of our knowledge this is the first time that saccharification of both cellulose and alginate from brown algae is reported. © 2015 Elsevier B.V. All rights reserved.


  25. Pezoa-Conte, R., Leyton, A. , Anugwom, I., von Schoultz, S. , Paranko, J. , Mäki-Arvela, P., Willför, S., Muszyński, M., Nowicki, J., Lienqueo, M.E, Mikkola J.P. (2016). Deconstruction of the green alga Ulva rigida in ionic liquids: closing the mass balance. Algal Research, Volume 12, November 2015, Pages 262-273.
    [ Show Abstract ]Algae are known to grow at high rates compared to terrestrial plants that contain comparable amounts of carbohydrates by weight. Therefore, this renders them attractive in terms of any biorefinery concept. In this work the green alga Ulva rigida, containing 40 wt.% of carbohydrates was pretreated with a switchable ionic liquid (SIL), distillable ionic liquid (DIL) and low-viscosity ionic liquid (LVIL). The SIL DBU–MEA–SO2 was prepared from a mixture of mono-ethanolamine (MEA) and 1,8-diazabicyclo-[5,4,0]-undec-7-ene (DBU) that was coupled with sulfur dioxide (SO2), whereas the DIL [TMGH+][EtCO−2] (1,1,3,3-tetramethylguanidine propionate) was synthesized by a simple acid–base neutralization reaction. Consequently, the LVIL [HDBU+][5OF−] protonated 1,8-diazabicyclo-[5,4,0]-undec-7-ene- 2,2,3,3,4,4,5,5-octafluoro-1-pentoxide was used as received. The treatments were carried out in the temperature range of 100–160 °C for 6 h. The products obtained after the treatments were analyzed using different techniques like ICP, OES, SEM, TEM, TGA, FTIR and carbohydrate determination by GC. Upon treatment with DIL up to 67 wt.% of carbohydrates could be dissolved. For the first time, processing of U. rigida was carried out in ionic liquids so that the mass balance of the process was obtained. It can be concluded that 1,1,3,3-tetramethylguanidine propionate shows significant potential when aiming at releasing carbohydrates from algal biomass that, consequently, can be applied in the production of platform chemicals and/or biofuels such as bioethanol. © 2015 Elsevier B.V. All rights reserved.


  26. Shene, C., Monsalve, M.T., Vergara, D., Lienqueo, M.E., Rubilar, M. (2015). High pressure homogenization of Nannochloropsis oculata for the extraction of intracellular components: Effect of process conditions and culture age. European Journal of Lipid Science and Technology, June 2015. doi:10.1002/ejlt.201500011
    [ Show Abstract ]Nannochloropsis is a genus of unicellular eukaryotes known primarily from the marine environment whose members are potential sources of lipids and long-chain polyunsaturated fatty acids; for the extraction of these and other valuable cell components, cell disruption is needed. High pressure homogenization (HPH) would be particularly suitable for microalgae with a recalcitrant cell wall such as Nannochloropsis. HPH conditions should be determined based on both the target cell component and properties of the cell suspension that in some cases are dependent on the age of the culture. The yields of soluble protein and total sugars from N. oculata ranged from 22.7 to 50.4mg/g and from 55.0 to 62.5mg/g, respectively, depending on HPH conditions (loading pressure and number of passes). The yield of the lipids extracted with the method of Bligh and Dyer was not affected by HPH conditions whereas lipids extracted with Soxhlet method ranged between 8.2 and 16.2%. Main fatty acids in the lipids extracted with the method of Bligh and Dyer and total lipids were palmitic acid (17.2 0.1–23.0 0.2%), palmitoleic acid (22.9 0.3–19.1 0.9%), and eicosapentaenoic acid (20.6 0.3–29.2 0.3%). HPH of N. oculata cells promoted a different effect on particle size distribution (PSD) depending on the age of the culture. HPH reduced cell aggregation observed in the 10 day cell suspension, whereas it promoted aggregation of the 30 day cell suspension. Practical applications: The feasibility of producing a wide range of products from microalgae is determined by the culture conditions and the conditions of the stages in the downstream processing. Because main microalgae components are intracellular, a scalable cell disruption operation such as HPH is required. Cell disruption degree is determined not only by the equipment design and its operational conditions but also by the cell suspension properties. The results allowed us to conclude that a different combination loading pressure/number of passes in HPH maximizes the recovery of hydrosoluble compounds (proteins and sugars) and lipids in N. oculata. Besides, since the PSD of the microalgae suspension is a function of culture age, this variable could affect process productivity. Keywords: Biodiesel / Cell disruption / Cell size / Lipid extraction / Microalgae / Protein solubility


  27. Lienqueo, M.E., Ravanal, M.C., Pezoa-Conte, R., Cortínez, V., Martínez, L.,Niklitschek, T., Salazar, O., Carmona, R., García, A.,Hyvärinen, S., Mäki-Arvela, P., Mikkola, J.P. (2016). Second generation bioethanol from Eucalyptus globulus Labill and Nothofagus pumilio: ionic liquid pretreatment boosts the yields. Industrial Crops and Products, Volume 80, February 2016, Pages 148-155.
    [ Show Abstract ]The depletion of petroleum reserves and the high level of pollution caused by fossil fuels have led to enhancing renewable energy and fuel production from biomass. Eucalyptus globulus and Nothofagus pumilio residues could constitute an interesting source of biomass for second generation biofuel production. Lenga residues were pretreated with the ionic liquid (IL) 1-N-ethyl-3-methylimidazolium chloride (C2mimCl), followed by subsequent fermentation using both the strategy of Simultaneous Saccharification and Fermentation (SSF) as well as Separate Hydrolysis and Fermentation (SHF). The SHF process yielded 0.134 g ethanol/g glucose (26.3 wt-% of the theoretical yield) compared to the SSF process which yielded 0.173 g ethanol/g glucose (33.9 wt-% of the theoretical yield) within the first 24 h of fermentation. In case of Eucalyptus residues, another IL, 1-N-ethyl-3-methylimidazolium acetate (C2minOAc) was applied. The SSF process was applied for a period of three days. As a result, 3.7 g ethanol/L (corresponding to a yield of 0.19 g of ethanol/g of glucose or 38.0 wt-% of the theoretical maximum) was obtained at 72 h. When fresh Lenga and Eucalyptus residues were fermented without any pretreatment, the SSF process yielded 0.017 and 0.002 g of ethanol/g of glucose, respectively (3.33 wt-% and 0.48 wt-% of the theoretical maximum, respectively). Thus, the pretreatment procedures resulted in a significant increase in ethanol production, therefore justifying the need of pretreatment prior to the co-enzyme hydrolysis and fermentation for this type of biomass. Further, the combination of IL pretreatment and use of SSF process demonstrated the high potential for bioethanol production from Lenga and Eucalyptus residues. Nevertheless, further improvement by optimization of operational conditions is required to maximize the ethanol yield. © 2015 Elsevier B.V. All rights reserved.


  28. Sotomayor-Gerdinga, D., Oomahc D., Acevedo F., Moralesa E., Bustamante M., Shene C., Rubilar M. (2015). High carotenoid bioaccessibility through linseed oil nanoemulsions with enhanced physical and oxidative stability. Food Chemistry, Volume 199, 15 May 2016, Pages 463-470.
    [ Show Abstract ]Carotenoid (astaxanthin or lycopene) emulsions obtained by high pressure homogenization were investigated for their physical, oxidative and storage stability and biological fate on an in vitro digestion model of bioaccessibility. Emulsion stability evaluated at various processing environments (20–50 C, 2–10 pH, 0–500 mM NaCl, and 0–35 days storage at 25 C) depended on carotenoid and homogenization pressures (5, 10, 100 MPa). Trolox increased the oxidative stability of nanoemulsions (100 MPa) and acted synergistically with BHT in increasing the stability of lycopene nanoemulsion. Intestinal digestibility depended on homogenization pressures with the fastest release and lower amount of free fatty acids observed at 100 MPa. Carotenoid nanoemulsions (100 MPa) were partially (66%) digested and highly bioaccessible (>70%). Therefore, nanoemulsions provide an effective and stable system for efficient astaxanthin or lycopene delivery and bioavailability in foods, beverages, nutraceuticals and/or other agriproducts. 2015 Elsevier Ltd. All rights reserved.

  29. Shene, C., Chistic, Y., Bustamante, M., Rubilara, M. (2016). Effect of CO2 in the aeration gas on cultivation of the microalga Nannochloropsis oculata: Experimental study and mathematical modeling of CO2 assimilation. Algal Research, Volume 13, January 2016, Pages 16-29
    [ Show Abstract ]The effects of CO2-supplementation on growth and biomass productivity of the microalga Nannochloropsis oculata are discussed for cultures with and without pH control. In otherwise non-limiting photoautotrophic cultures, the supply of inorganic carbon controls the algal biomass concentration and productivity. Inorganic carbon is nearly always supplied as CO2, but is taken up by the cells mainly as bicarbonate. The culture pH determines the speciation of the dissolved inorganic carbon and its availability for uptake. In air-sparged batch cultures, the pH control at 6.5, 7.0 and 8.0 by injection of CO2 as needed, did not affect the biomass concentration and productivity relative to the control culture (no pH control) sparged with air. In the absence of pH control, the supplementation of air with CO2 at 0.34 to 1.34% v/v levels had no effect on the biomass concentration, but the pH oscillated with the day–night cycle. Compared to the control culture, the range of pH oscillations was reduced if CO2 was added to air at the specified levels. A mathematical model was developed to explain the effect of the culture pH and the CO2 level in the aeration gas, on the rates of photosynthetic CO2 assimilation and CO2 absorption. © 2015 Elsevier B.V. All rights reserved.


  30. Muñoz, E., Vargas, S., Navia, R. (2015). Environmental and economic analysis of residual woody biomass transport for energetic use in Chile. The International Journal of Life Cycle Assessment, July 2015, Volume 20, Issue 7, pp 1033–1043.
    [ Show Abstract ]Purpose. This study compares transport performance of residual biomass using different pre-treatment options. Life cycle inventory data was obtained from forestry companies in southern Chile, databases, scientific and technological literature, as well as equipment operational manuals. Methods: Three different scenarios were evaluated: residual biomass transport without pre-treatment (scenario 1), chipped residual biomass (scenario 2), and compacted residual biomass (scenario 3) transport. The truck’s loading capacity was considered as a function of the residual biomass density. Impact assessment was performed using software SimaPro 7.3.3 using the ReCiPe midpoint methodology. Moreover, an uncertainty analysis was performed using Monte Carlo simulation with a 95 % confidence. Transport costs evaluation variables considered were machine cost, machine residual value, amortization, personnel costs, fuel consumption, machine maintenance, and operational yield. All variables are based on local conditions of La Araucanía Region in Chile. Results and discussion Regarding greenhouse gas (GHG) emissions, optimum transport distance ranges were identified for the different scenarios. For a distance up to 23 km, scenario 1 is the most favorable; for distances between 23 and 206 km, scenario 2 is the most favorable one; and for distances longer than 206 km, compacted residual biomass (scenario 3) presents the lowest GHG emissions balance. When looking the other impact categories, it was established that the benefits are not only related to GHG emission savings but also to other impact categories. Transport impacts are only relevant for large distances, while for short distances biomass pre-treatment and loading stages provoke a higher environmental load. In fact, for scenario 2 where chipped biomass is transported, only for distances longer than 120 km, the transport stage accounts for more than 50 % of the environmental load of all impact categories. For the case of scenario 3 (compacted biomass transport), this situation occurs for a distance of at least 150 km. Conclusions Most probable optimal transport distances were determined for pre-treated and unpretreated biomass. In this sense, for determining the best transport option of residual biomass, transport distance, loading capacity, and pre-treatment processes efficiency, including chipping and compacting, as well as data uncertainty, should be taken into account. From these variables, biomass loading and pre-treatment stages account for a relevant percentage of the environmental impacts generated for transport distances of less than 100 km. In this sense, biomass loading and pre-treatment efficiency coupled with the effective supplies demand should be carefully studied in future research works.


  31. Hidalgo, P., Ciudad, G., Navia, R. (2016). Evaluation of different solvent mixtures in esterifiable lipids extraction from microalgae Botryococcus braunii for biodiesel production. Bioresource Technology, Volume 201, February 2016, Pages 360-364.
    [ Show Abstract ]Non-polar and polar solvents as well as their mixtures were tested for the extraction of microalgae lipids and thus, to evaluate their effect on total and esterifiable lipids extraction yields with potential to be converted to biodiesel. The obtained results show an increase in lipids and esterifiable lipids extraction yields when non-polar and polar solvent mixtures were used. The higher esterifiable lipids extraction yield was responding to a 98.9% wt esterifiable lipids extraction. In addition, esterifiable lipids extraction yield of 18.9% wt (based on dry biomass) was obtained when a petroleum ether–methanol mixture (75% v/v of methanol) was used, corresponding to a 96.9% wt esterifiable lipids extraction. 2015 Elsevier Ltd. All rights reserved.


  32. Urrutia, C., Sangaletti-Gerhard, N., Cea, M., Suazo A., Aliberti, A., Navia, R. (2016). Two step esterification-transesterification process of wet greasy sewage sludge for biodiesel production. Bioresource Technology, Volume 200, January 2016, Pages 1044-1049.
    [ Show Abstract ]Sewage sludge generated in municipal wastewater treatment plants was used as a feedstock for biodiesel production via esterification/transesterification in a two-step process. In the first esterification step, greasy and secondary sludge were tested using acid and enzymatic catalysts. The results indicate that both catalysts performed the esterification of free fatty acids (FFA) simultaneously with the transesterification of triacylglycerols (TAG). Acid catalyst demonstrated better performance in FFA esterification compared to TAG transesterification, while enzymatic catalyst showed the ability to first hydrolyze TAG in FFA, which were esterified to methyl esters. In addition, FAME concentration using greasy sludge were higher (63.9% and 58.7%), compared with those of secondary sludge (11% and 16%), using acid and enzymatic catalysts, respectively. Therefore, only greasy sludge was used in the second step of alkaline transesterification. The alkaline transesterification of the previously esterified greasy sludge reached a maximum FAME concentration of 65.4% when using acid catalyst. 2015 Elsevier Ltd. All rights reserved.


  33. Cea, M., Sangaletti-Gerhard, N., Acuña, P., Fuentes, I., Jorquera, M., Godoy, K., Navia R. (2015). Screening transesterifiable lipid accumulating bacteria from sewage sludge for biodiesel production. Biotechnology Reports, Volume 8, December 2015, Pages 116-123.
    [ Show Abstract ]Sewage sludge was evaluated as high available and low cost microbial oils feedstock for biodiesel production. Samples from four different wastewater treatment plants from La Araucanía Region in Southern Chile presented total lipids content ranging between 7.7 and 12.6%, being Vilcún sewage sludge that with the highest transesterifiable lipids content of about 50% of the total extracted lipids. The most relevant identified bacteria presentin sludge samples were Acinetobacter,Pseudomonas and Bacillus, being Bacillus sp. V10 the strain with the highest transesterfiable lipids content of 7.4%. Bacillus sp. V10 was cultured using urban wastewater supplemented with glucose to achieve nitrogen depleted medium and using milk processing wastewater as a low-cost carbon source. Bacillus sp. V10 lipid profile indicates that low degree unsaturated long chain fatty acids such as C18:1 may account for approximately 50% of the lipids content, indicating its suitability to be used as raw material for biodiesel production. (c) 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).


  34. Navia, R., Muñoz, E. (2015). Biotechnologies for gaseous emissions and by-products management in waste treatment facilities. Waste Management & Research., 33, 593-594.
    [ Show Abstract ]The current status of the design and operation of waste treatment facilities involves the implementation of gaseous emissions management and removal processes to avoid the uncontrolled release to the atmosphere of greenhouse gases, volatile organic compounds (VOCs) and malodorous volatile inorganic compounds (VICs), as well as novel approaches for the valorisation of gaseous by-products. This is particularly true in waste treatment facilities, including incineration, anaerobic digestion, composting, mechanical biological treatment (MBT) and landfilling, where the implementation of these technologies can mitigate gaseous emissions to the atmosphere and promote by-products valorisation, thus contributing to the diminishment of local odour nuisance and to the mitigation of climate change.


  35. Muñoz, E., Navia, R. (2015). Waste management in touristic regions. Waste Management & Research, 33, 593-594.
    [ Show Abstract ]Excerpt: Tourism is one of the most important industries worldwide and a driver for socioeconomic development in many regions, particularly developing countries with unique cultural, historic and natural resources. According to the World Tourism Organization (UNWTO), international tourism revenues reached a record of US$1245 billion in 2014. Moreover, an additional US$221 billion was generated from international passenger transport, bringing total exports from international tourism up to US$1500 billion. However, tourism has been recognised as a high energy and water resources demanding activity, simultaneously generating significant amounts of solid wastes from lodgings and recreational areas. On the global scale, this situation has been already highlighted by the United Nations Environment Programme (UNEP). In fact, during 2011 UNEP estimated a worldwide solid waste generation of 4.8million t just from international tourism, representing about 14% of the total municipal solid wastes generated during this year.


  36. Muñoz E., Navia R., Zaror C. & Alfaro M (2016). Ammonia emissions from livestock production in Chile: inventory and uncertainty analysis. Journal of soil science and plant nutrition, 16(1), 60-75. Epub 18 de enero de 2016. https://dx.doi.org/10.4067/S0718-95162016005000005
    [ Show Abstract ]The objective of this work was to quantify the country’s NH3 calculation was based on the mass flow of total ammoniacal nitrogen (TAN). The analysis was performed for all 15 geographical regions in Chile. The definition of livestock subcategories was based on data from the Chilean Agriculture and Forestry Census as well as technical reports published by the Chilean National Statistics Institute. Significant differences were observed among the sources of livestock emissions in Chile’s regions, and there was high variability depending on the degree of livestock confinement. In 2013, the total calculated emissions were 69.1 kt NH3 /year (± 31.1). The O’Higgins Region had the highest NH3 emissions in Chile, representing 45% of the total. In terms of livestock production, 45% of the emissions were generated by pigs, 22% by poultry, 16% by cattle, 11% by equines and 4% by sheep. Emissions from the TAN that was available during manure and slurry management and the degree of animal confinement were the primary sources of uncertainty. This uncertainty could be greatly reduced by developing regional emission factors and by including the degree of animal confinement in Chile’s national statistics such as the Agriculture, Livestock and Forestry Census. Keywords: Ammonia, livestock, emissions, nitrogen losses, uncertainty


  37. Esparza, A., Gerdtzen, Z., Olivera-Nappa, A., Salgado, Herrera, C., Núñez, M.T. (2015). Iron-induced reactive oxygen species mediate transporter DMT1 endocytosis and iron uptake in intestinal epithelial cells. American Journal of Physiology – Cell Physiology Published 15 October 2015 Vol. 309 no. 8, C558-C567 DOI: 10.1152/ajpcell.00412.2014.
    [ Show Abstract ]Iron-induced reactive oxygen species mediate transporter DMT1 endocytosis and iron uptake in intestinal epithelial cells. Am J Physiol Cell Physiol 309: C558 –C567, 2015. First published August 19, 2015; doi:10.1152/ajpcell.00412.2014.—Recent evidence shows that iron induces the endocytosis of the iron transporter dimetal transporter 1 (DMT1) during intestinal absorption. We, and others, have proposed that iron-induced DMT1 internalization underlies the mucosal block phenomena, a regulatory response that downregulates intestinal iron uptake after a large oral dose of iron. In this work, we investigated the participation of reactive oxygen species (ROS) in the establishment of this response. By means of selective surface protein biotinylation of polarized Caco-2 cells, we determined the kinetics of DMT1 internalization from the apical membrane after an iron challenge. The initial decrease in DMT1 levels in the apical membrane induced by iron was followed at later times by increased levels of DMT1. Addition of Fe2, but not of Cd2, Zn2, Cu2, or Cu1, induced the production of intracellular ROS, as detected by 2=,7=-dichlorofluorescein (DCF) fluorescence. Preincubation with the antioxidant N-acetyl-L-cysteine (NAC) resulted in increased DMT1 at the apical membrane before and after addition of iron. Similarly, preincubation with the hydroxyl radical scavenger dimethyl sulfoxide (DMSO) resulted in the enhanced presence of DMT1 at the apical membrane. The decrease of DMT1 levels at the apical membrane induced by iron was associated with decreased iron uptake rates. A kinetic mathematical model based on operational rate constants of DMT1 endocytosis and exocytosis is proposed. The model qualitatively captures the experimental observations and accurately describes the effect of iron, NAC, and DMSO on the apical distribution of DMT1. Taken together, our data suggest that iron uptake induces the production of ROS, which modify DMT1 endocytic cycling, thus changing the iron transport activity at the apical membrane. DMT1; iron; ROS; mucosal block; mathematical modeling


  38. Wilkens, C., Gerdtzen, Z., (2015). Comparative Metabolic Analysis of CHO Cell Clones Obtained through Cell Engineering, for IgG Productivity, Growth and Cell Longevity. PLoS One, 10, 1-15.
    [ Show Abstract ]Cell engineering has been used to improve animal cells’ central carbon metabolism. Due to the central carbon metabolism’s inefficiency and limiting input of carbons into the TCA cycle, key reactions belonging to these pathways have been targeted to improve cultures’ performance. Previous works have shown the positive effects of overexpressing PYC2, MDH II and fructose transporter. Since each of these modifications was performed in differ-
    ent cell lines and culture conditions, no comparisons between these modifications can be made. In this work we aim at contrasting the effect of each of the modifications by comparing pools of transfected IgG producing CHO cells cultivated in batch cultures. Results of the culture performance of engineered clones indicate that even though all studied clones had a more efficient metabolism, not all of them showed the expected improvement on cell proliferation and/or specific productivity. CHO cells overexpressing PYC2 were able to improve their exponential growth rate but IgG synthesis was decreased, MDH II overexpression lead to a reduction in cell growth and protein production, and cells transfected with the fructose transporter gene were able to increase cell density and reach the same volumetric protein production as parental CHO cells in glucose. We propose that a redox unbalance caused by the new metabolic flux distribution could affect IgG assembly and protein secretion. In addition to reaction dynamics, thermodynamic aspects of metabolism are also discussed to further understand the effect of these modifications over central carbon metabolism.


  39. Gonçalves, V., Cantrell, C.L, Wedge, D., Ferreira, M., Soares, M.A., Jacob, M., Oliveira, F., Galante, D., Rodrigues, F., Alves T.,. Zani, C., Junior, P., Murta, S., Romanha, A., Barbosa, E., Kroon, E., Oliveira, J., Gomez-Silva, B., Galetovic, A., Rosa, C., Rosa, L.H. (2015). Fungi associated with rocks of the Atacama Desert: taxonomy, distribution, diversity, ecology and bioprospection for bioactive compounds. Enviromental Microbiology, 18, 232-245.
    [ Show Abstract ]This study assessed the diversity of cultivable rock-associated fungi from Atacama Desert. A total of 81 fungal isolates obtained were identified as 29 Ascomycota taxa by sequencing different regions of DNA. Cladosporium halotolerans, Penicillium chrysogenum and Penicillium cf. citrinum were the most frequent species, which occur at least in four different altitudes. The diversity and similarity indices ranged in the fungal communities across the latitudinal gradient. The Fisher-α index displayed the higher values for the fungal communities obtained from the siltstone and fine matrix of pyroclastic rocks with finer grain size, which are more degraded. A total of 23 fungal extracts displayed activity against the different targets screened. The extract of P. chrysogenum afforded the compounds α-linolenic acid and ergosterol endoperoxide, which were active against Cryptococcus neoformans and methicillin-resistance Staphylococcus aureus respectively. Our study represents the first report of a new habitat of fungi associated with rocks of the Atacama Desert and indicated the presence of interesting fungal community, including species related with saprobes, parasite/pathogen and mycotoxigenic taxa. The geological characteristics of the rocks, associated with the presence of rich resident/resilient fungal communities suggests that the rocks may provide a favourable microenvironment fungal colonization, survival and dispersal in extreme conditions.


  40. Scott, S., Dorador, C., Oyanedel, J.P, Tobar, I., Hengst, M., Maya, G., Harrod, C., Vila I. (2015). Microbial diversity and trophic components of two high altitude wetlands of the Chilean Altiplano. GAYANA International Journal of Biodiversity, Oceanology and Conservation, Universidad de Concepción, Chile, Vol 79, 45-56.
    [ Show Abstract ]This study examines the limnology and ecology of two high altitude wetlands, Lirima (19°51’24 S; 68°55’02 W; 4000 m asl) and Caya (20°37’21 S; 68°58’28 W; 3700 m asl), located in the Chilean Altiplano. Both wetlands are formed by the evaporitic remnant basins of paleolakes which occupied an extensive area of what today is known as the Altiplano. These systems have a negative hydrological balance, receiving their water from groundwater, snow melt and limited seasonal rains. An ongoing negative water balance and the sediment characteristics in the region have accelerated the salinization process in these systems, as shown by their present physicochemical characteristics. Nutrient values were typical of mesotrophic to eutrophic systems. The ionic content classifi es Lirima as a sodium sulfated wetland and Caya as a calcium chloride one. Conductivity values ranged between 778 μS/cm at Lirima to 2100 μS/cm at Caya, and were refl ected in the differences in biodiversity found in these systems. The Lirima wetland supports a population of the endemic fish Orestias aff. agassii found in several Evolutionary Signifi cant Units (ESU) across the region. Microbial diversity in the water column was characterized by the presence of 5 bacterial phyla and related genera (e.g. Psychrobacter, Bacillus, Eryhtobacter, Halomonas). We present information on several key ecosystem components including macrophytes, plankton, benthos, fish and birds. This descriptive paper highlights the unusual limnological and biological characteristics of high altitude wetlands and highlights the importance of describing their biological communities across levels of organisation (e.g. microbial through to higher vertebrates) as well as their functional role, interactions and sensitivity to changes in water availability. KEYWORDS: Altiplano, biodiversity, endemism, evolutionary signifi cant units, salinity.


  41. Lobos, J., Gil-Costa, V., Reyes, N., Printista, A.M., Marín, M., (2015). Stream processing to solve image search by similarity. Journal of Computer Science & Technology, 15, 93-99.
    [ Show Abstract ]The classic use of Stream Processing platforms enables working with data in real time, which allows you to generate data analysis quickly attending to a decision-making process. However, you can use these platforms for other applications such as indexing and subsequent use of similarity search objects in a database. The images can be displayed on a metric space, which has features that allow rules to discard a not similar image quickly without making costly computations. This paper presents the use of a Stream Processing platform to index images generated by different users. For this, it is necessary to represent these images by vectors containing different MPGE-7 features. This paper shows a Stream Processing platform using its processing elements (PEs) in parallel to speed up the operations involved in the index construction. Keywords: Stream Processing, Metrics Spaces, MPEG-7, Sparse Spatial Selection.


  42. Senger, H., Gil-Costa, V., Arantes, L., Marcondes, C. A. C., Marín, M., Sato, L. M., and da Silva, F. A. B. (2015). BSP cost and scalability analysis for MapReduce operations. Concurrency & Computation: Practice and Experience, Volume 28, Issue 8, 10 June 2016, Pages 2503–2527. doi: 10.1002/cpe.3628
    [ Show Abstract ]Data abundance poses the need for powerful and easy-to-use tools that support processing large amounts of data. MapReduce has been increasingly adopted for over a decade by many companies, and more recently, it has attracted the attention of an increasing number of researchers in several areas. One main advantage is that the complex details of parallel processing, such as complex network programming, task scheduling, data placement, and fault tolerance, are hidden in a conceptually simple framework. MapReduce is supported by mature software technologies for deployment in data centers such as Hadoop. As MapReduce becomes popular for high-performance applications, many questions arise concerning its performance and efficiency. In this paper, we demonstrated formally lower bounds on the isoefficiency function for MapReduce applications, when these applications can be modeled as BSP jobs. We also demonstrate how communication and synchronization costs can be dominant for MapReduce computations and discuss the conditions under which such scalability limits are valid. To our knowledge, this is the first study that demonstrates scalability bounds for MapReduce applications. We also discuss how some MapReduce implementations such as Hadoop can mitigate such costs to approach linear, or near-to-linear speedups. Copyright © 2015 John Wiley & Sons, Ltd.


  43. Hidalgo N., Arantes L., Sens P., Bonnaire X., (2016). ECHO: Efficient Complex Query over DHT Overlays. Journal of Parallel and Distributed Computing, Volume 88, February 2016, Pages 31-45.
    [ Show Abstract ]In this article we propose ECHO, a novel and lightweight solution that efficiently supports range queries over a ring-like Distributed Hash Table (DHT) structure. By implementing a tree-based index structure and an effective query routing strategy, ECHO provides low-latency and low-overhead query searches by exploiting the Tabu Search principle. Load balancing is also improved reducing the traditional bottleneck problems arising in upper level nodes of tree-based index structures such as PHT. Furthermore, ECHO copes with DHT churn problems as its index exploits logical information as opposed to static reference cache approaches or replication techniques. The performance evaluation results obtained using PeerSim simulator show that ECHO achieves efficient performance compared other solutions such as the PHT strategy and its optimized version which includes a query cache.


  44. Borguesan, B., Barbachan e Silva, M., Grisci B., Inostroza-Ponta, M., Dorn M., (2015). APL: An angle probability list to improve knowledge-based metaheuristics for the three-dimensional protein structure prediction. Computational Biology and Chemistry, 59, 142-157
    [ Show Abstract ]Tertiary protein structure prediction is one of the most challenging problems in structural bioinformatics. Despite the advances in algorithm development and computational strategies, predicting the folded structure of a protein only from its amino acid sequence remains as an unsolved problem. We present a new computational approach to predict the native-like three-dimensional structure of proteins. Conformational preferences of amino acid residues and secondary structure information were obtained from protein templates stored in the Protein Data Bank and represented as an Angle Probability List. Two knowledge-based prediction methods based on Genetic Algorithms and Particle Swarm Optimization were developed using this information. The proposed method has been tested with twenty-six case studies selected to validate our approach with different classes of proteins and folding patterns. Stereochemical and structural analysis were performed for each predicted three-dimensional structure. Results achieved suggest that the Angle Probability List can improve the effectiveness of metaheuristics used to predicted the three-dimensional structure of protein molecules by reducing its conformational search space.