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Prof. Spiros N. Agathos
1. Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, Boite L7.05.19, 1348 Louvain-la-Neuve, Belgium</br>2. Escuela de Ciencias Βιοlógicas e Ingeniería/School of Biological Sciences and Engineering, Yachay Tech University, San Miguel de Urcuquí Canton, Ecuador

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0 Microbial Ecology
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Published: 24 July 2020 in Insect Cell Culture Engineering
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Insect cell culture is becoming recognized as an important enabling technology for the production of biologicals, including recombinant proteins and biopesticides, primarily through the use of baculovirus expression vectors. Strategies aimed at outright avoiding of direct sparging or, more generally, of any extended liquid-gas interface, such as attempts to aerate the insect cell culture through semipermeable silicon or teflon tubing are of limited practical use for scale-up. Cell density increases are also possible via immobilization or attachment to inert matrixes. The choice of cell lines will be influenced by the level and type of protein expression, including posttranslational modifications. In addition to the influence of the host cell line, the construction of the baculovirus vector, i.e., the exact location in the viral genome where the recombinant gene is inserted, is clearly of fundamental significance in achieving high levels of protein expression.

ACS Style

Spiros Agathos. The Future of Insect Cell Culture Engineering. Insect Cell Culture Engineering 2020, 221 -240.

AMA Style

Spiros Agathos. The Future of Insect Cell Culture Engineering. Insect Cell Culture Engineering. 2020; ():221-240.

Chicago/Turabian Style

Spiros Agathos. 2020. "The Future of Insect Cell Culture Engineering." Insect Cell Culture Engineering , no. : 221-240.

Primary research
Published: 10 December 2019 in Human Genomics
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Background In South America, the history of human genetics is extensive and its beginnings go back to the onset of the twentieth century. In Ecuador, the historical record of human genetics and genomics research is limited. In this context, our work analyzes the current status and historical panorama of these fields, based on bibliographic searches in Scopus, Google Scholar, PubMed, and Web of Science. Results Our results determined that the oldest paper in human genetics coauthored by an Ecuadorian institution originates from the Central University of Ecuador in 1978. From a historical standpoint, the number of articles has increased since the 1990s. This growth has intensified and it is reflected in 137 manuscripts recorded from 2010 to 2019. Areas such as human population genetics, phylogeography, and forensic sciences are the core of genetics and genomics-associated research in Ecuador. Important advances have been made in the understanding of the bases of cancer, some genetic diseases, and congenital disorders. Fields such as pharmacogenetics and pharmacogenomics have begun to be explored during the last years. Conclusions This work paints a comprehensive picture and provides additional insights into the future panorama of human genetic and genomic research in Ecuador as an example of an emerging, resource-limited country with interesting phylogeographic characteristics and public health implications.

ACS Style

Marlon S. Zambrano-Mila; Spiros N. Agathos; Juergen K. V. Reichardt. Human genetics and genomics research in Ecuador: historical survey, current state, and future directions. Human Genomics 2019, 13, 1 -10.

AMA Style

Marlon S. Zambrano-Mila, Spiros N. Agathos, Juergen K. V. Reichardt. Human genetics and genomics research in Ecuador: historical survey, current state, and future directions. Human Genomics. 2019; 13 (1):1-10.

Chicago/Turabian Style

Marlon S. Zambrano-Mila; Spiros N. Agathos; Juergen K. V. Reichardt. 2019. "Human genetics and genomics research in Ecuador: historical survey, current state, and future directions." Human Genomics 13, no. 1: 1-10.

Encyclopedia
Published: 31 July 2019 in Comprehensive Biotechnology
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Microbial communities that inhabit natural and engineered ecosystems provide essential services for the Earth's life-support system and the human well-being, such as nutrient cycling, protection against diseases or wastewater treatment. The high functional versatility and diversity of microorganisms are the driving forces for upholding ecosystem services and represent a unique resource for novel biotechnological applications. For a stable, secure and sustainable supply of food, feed, energy, materials and chemicals, new microbial community-driven biomanufacturing systems and environmental protection and restoration technologies are developed to achieve a bio-based and environmentally-friendly economy. Microbiome-based therapies also take advantage of emerging strategies to steer microbial ecosystem diversity and functioning. From the agricultural practices to the construction of synthetic microbial factories, the diversity and functionality of microorganisms can be manipulated in natural ecosystems (in situ), in engineered, open ecosystems (ex situ, in vivo) or in confined environments (ex situ, in vitro) for improved applications in medicine, agriculture, bioremediation, and water resource recovery facilities.

ACS Style

Floriana Augelletti; Benoit Stenuit; Spiros Agathos; Alexandre Jousset. Manipulation of Biodiversity to Steer and Optimize Microbial Community Function. Comprehensive Biotechnology 2019, 29 -41.

AMA Style

Floriana Augelletti, Benoit Stenuit, Spiros Agathos, Alexandre Jousset. Manipulation of Biodiversity to Steer and Optimize Microbial Community Function. Comprehensive Biotechnology. 2019; ():29-41.

Chicago/Turabian Style

Floriana Augelletti; Benoit Stenuit; Spiros Agathos; Alexandre Jousset. 2019. "Manipulation of Biodiversity to Steer and Optimize Microbial Community Function." Comprehensive Biotechnology , no. : 29-41.

Encyclopedia
Published: 31 July 2019 in Comprehensive Biotechnology
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Nitro explosives are toxic and persistent anthropogenic compounds. The recent discovery of nitro explosive–degrading biocatalysts (enzymes or redox-active biomolecules) opens new perspectives for the development and design of bioremediation systems. Ordnances contain different explosive formulations with specific mixtures of nitro explosives that are characterized by dissimilar biodegradation and transport patterns in contaminated sites. Because co-contamination is frequently observed in the field, this review presents promising biodegradation pathways for the different classes of nitro explosives and multifaceted approaches to improve and more effectively monitor the performance of a bioremediation process that must integrate multiple biodegradative machineries and biomonitoring circuits.

ACS Style

B.A. Stenuit; S.N. Agathos. Biodegradation and Bioremediation of TNT and Other Nitro Explosives. Comprehensive Biotechnology 2019, 181 -196.

AMA Style

B.A. Stenuit, S.N. Agathos. Biodegradation and Bioremediation of TNT and Other Nitro Explosives. Comprehensive Biotechnology. 2019; ():181-196.

Chicago/Turabian Style

B.A. Stenuit; S.N. Agathos. 2019. "Biodegradation and Bioremediation of TNT and Other Nitro Explosives." Comprehensive Biotechnology , no. : 181-196.

Encyclopedia
Published: 31 July 2019 in Comprehensive Biotechnology
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ACS Style

Spiros Agathos; B.A. Stenuit. Introduction. Comprehensive Biotechnology 2019, 1 -3.

AMA Style

Spiros Agathos, B.A. Stenuit. Introduction. Comprehensive Biotechnology. 2019; ():1-3.

Chicago/Turabian Style

Spiros Agathos; B.A. Stenuit. 2019. "Introduction." Comprehensive Biotechnology , no. : 1-3.

Journal article
Published: 17 June 2019 in BMC Evolutionary Biology
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Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen’s gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common bacterial phytopathogen. We performed a genome-wide scan of Ralstonia solanacearum species complex, an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called ‘bacterial wilt’. Using a sliding window approach, we analyzed 57 genomes from three phylotypes of the R. solanacearum species complex to detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima’s D, θw and Fu & Li’s D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes with known function that map in any of the two main replicons (1.7% of total number of genes). The candidate genes under balancing selection are related to primary metabolism and other basal activities (51.3%) or directly associated to virulence (48.7%), the latter being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process. We identified various genes under balancing selection that play a significant role in basic metabolism as well as in virulence of the R. solanacearum species complex. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses.

ACS Style

José A. Castillo; Spiros N. Agathos. A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum. BMC Evolutionary Biology 2019, 19, 1 -16.

AMA Style

José A. Castillo, Spiros N. Agathos. A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum. BMC Evolutionary Biology. 2019; 19 (1):1-16.

Chicago/Turabian Style

José A. Castillo; Spiros N. Agathos. 2019. "A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum." BMC Evolutionary Biology 19, no. 1: 1-16.

Review
Published: 08 September 2018 in Molecular Biotechnology
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Mesenchymal stem cells and pluripotent stem cells are recognized as promising tools for tissue engineering, cell therapy, and drug screening. Their use in therapy requires the production of a sufficient number of cells committed to functional regenerative phenotypes. Time- and magnitude-controlled application of mechanical and biochemical cues is required to appropriately control the evolution of stem cell phenotype in 3D. The temporal monitoring of the impact of these cues on the diverse fates of individual stem cells is also needed to ensure the reliability of the differentiation processes. However, macro-scale bioreactors are limited in regulating stem environment and display limited capability to monitor heterogeneities at the single cell level. In turn, microfluidics devices are emerging as powerful tools for tightly controlling culture parameters and precisely monitoring stem cell behavior. This work summarizes recent advances in the applications of microfluidics for the dynamic regulation and characterization of stem cells in 3D.

ACS Style

Sébastien Sart; Spiros N. Agathos. Towards Three-Dimensional Dynamic Regulation and In Situ Characterization of Single Stem Cell Phenotype Using Microfluidics. Molecular Biotechnology 2018, 60, 843 -861.

AMA Style

Sébastien Sart, Spiros N. Agathos. Towards Three-Dimensional Dynamic Regulation and In Situ Characterization of Single Stem Cell Phenotype Using Microfluidics. Molecular Biotechnology. 2018; 60 (11):843-861.

Chicago/Turabian Style

Sébastien Sart; Spiros N. Agathos. 2018. "Towards Three-Dimensional Dynamic Regulation and In Situ Characterization of Single Stem Cell Phenotype Using Microfluidics." Molecular Biotechnology 60, no. 11: 843-861.

Other
Published: 09 August 2018
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Plant pathogens are under significant selective pressure by the plant host. Consequently, they are expected to have adapted to this condition or contribute to evading plant defenses. In order to acquire long-term fitness, plant bacterial pathogens are usually forced to maintain advantageous genetic diversity in populations. This strategy ensures that different alleles in the pathogen’s gene pool are maintained in a population at frequencies larger than expected under neutral evolution. This selective process, known as balancing selection, is the subject of this work in the context of a common plant bacterial pathogen. We performed a genome-wide scan ofRalstonia solanacearum,an aggressive plant bacterial pathogen that shows broad host range and causes a devastating disease called ‘bacterial wilt’. Using a sliding window approach, we analyzed 57 genomes from three phylotypes ofR. solanacearumto detect signatures of balancing selection. A total of 161 windows showed extreme values in three summary statistics of population genetics: Tajima’s D, Watterson’s θ and Fu & Li’s D*. We discarded any confounding effects due to demographic events by means of coalescent simulations of genetic data. The prospective windows correspond to 78 genes that map in any of the two main replicons ofR. solanacearum.The candidate genes under balancing selection are related to primary metabolism (51.3%) or directly associated to virulence (48.7%), being involved in key functions targeted to dismantle plant defenses or to participate in critical stages in the pathogenic process. These genes are useful to understand and monitor the evolution of bacterial pathogen populations and emerge as potential candidates for future treatments to induce specific plant immune responses.

ACS Style

José A. Castillo; Spiros N. Agathos. Candidate genes under balancing selection in a plant bacterial pathogen. 2018, 388207 .

AMA Style

José A. Castillo, Spiros N. Agathos. Candidate genes under balancing selection in a plant bacterial pathogen. . 2018; ():388207.

Chicago/Turabian Style

José A. Castillo; Spiros N. Agathos. 2018. "Candidate genes under balancing selection in a plant bacterial pathogen." , no. : 388207.

Journal article
Published: 12 April 2018 in Genome Announcements
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We report here the draft whole-genome sequence of a fluorene-degrading bacterium, Sphingobium sp. strain LB126. The genes involved in the upper biodegradation pathway of fluorene are located on a plasmid, and the lower pathway that generates tricarboxylic acid cycle intermediates is initiated by the meta -cleavage of protocatechuic acid that is chromosomally encoded.

ACS Style

Floriana Augelletti; Julien Tremblay; Spiros Agathos; Ben Stenuit. Draft Whole-Genome Sequence of the Fluorene-Degrading Sphingobium sp. Strain LB126, Isolated from Polycyclic Aromatic Hydrocarbon-Contaminated Soil. Genome Announcements 2018, 6, 1 .

AMA Style

Floriana Augelletti, Julien Tremblay, Spiros Agathos, Ben Stenuit. Draft Whole-Genome Sequence of the Fluorene-Degrading Sphingobium sp. Strain LB126, Isolated from Polycyclic Aromatic Hydrocarbon-Contaminated Soil. Genome Announcements. 2018; 6 (15):1.

Chicago/Turabian Style

Floriana Augelletti; Julien Tremblay; Spiros Agathos; Ben Stenuit. 2018. "Draft Whole-Genome Sequence of the Fluorene-Degrading Sphingobium sp. Strain LB126, Isolated from Polycyclic Aromatic Hydrocarbon-Contaminated Soil." Genome Announcements 6, no. 15: 1.

Review article
Published: 01 November 2017 in OMICS: A Journal of Integrative Biology
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Genomic medicine has greatly matured in terms of its technical capabilities, but the diffusion of genomic innovations worldwide faces significant barriers beyond mere access to technology. New global development strategies are sorely needed for biotechnologies such as genomics and their applications toward precision medicine without borders. Moreover, diffusion of genomic medicine globally cannot adhere to a “one-size-fits-all-countries” development strategy, in the same way that drug treatments should be customized. This begs a timely, difficult but crucial question: How should developing countries, and the resource-limited regions of developed countries, invest in genomic medicine? Although a full-scale investment in infrastructure from discovery to the translational implementation of genomic science is ideal, this may not always be feasible in all countries at all times. A simple “transplantation of genomics” from developed to developing countries is unlikely to be feasible. Nor should developing countries be seen as simple recipients and beneficiaries of genomic medicine developed elsewhere because important advances in genomic medicine have materialized in developing countries as well. There are several noteworthy examples of genomic medicine success stories involving resource-limited settings that are contextualized and described in this global genomic medicine innovation analysis. In addition, we outline here a new long-term development strategy for global genomic medicine in a way that recognizes the individual country's pressing public health priorities and disease burdens. We term this approach the “Fast-Second Winner” model of innovation that supports innovation commencing not only “upstream” of discovery science but also “mid-stream,” building on emerging highly promising biomarker and diagnostic candidates from the global science discovery pipeline, based on the unique needs of each country. A mid-stream entry into innovation can enhance collective learning from other innovators' mistakes upstream in discovery science and boost the probability of success for translation and implementation when resources are limited. This à la carte model of global innovation and development strategy offers multiple entry points into the global genomics innovation ecosystem for developing countries, whether or not extensive and expensive discovery infrastructures are already in place. Ultimately, broadening our thinking beyond the linear model of innovation will help us to enable the vision and practice of genomics without borders in both developed and resource-limited settings.

ACS Style

Konstantinos Mitropoulos; David N. Cooper; Christina Mitropoulou; Spiros Agathos; Juergen Reichardt; Fatma Al-Maskari; Wasun Chantratita; Ambroise Wonkam; Collet Dandara; Theodora Katsila; Catalina Lopez-Correa; Bassam R. Ali; George P. Patrinos. Genomic Medicine Without Borders: Which Strategies Should Developing Countries Employ to Invest in Precision Medicine? A New “Fast-Second Winner” Strategy. OMICS: A Journal of Integrative Biology 2017, 21, 647 -657.

AMA Style

Konstantinos Mitropoulos, David N. Cooper, Christina Mitropoulou, Spiros Agathos, Juergen Reichardt, Fatma Al-Maskari, Wasun Chantratita, Ambroise Wonkam, Collet Dandara, Theodora Katsila, Catalina Lopez-Correa, Bassam R. Ali, George P. Patrinos. Genomic Medicine Without Borders: Which Strategies Should Developing Countries Employ to Invest in Precision Medicine? A New “Fast-Second Winner” Strategy. OMICS: A Journal of Integrative Biology. 2017; 21 (11):647-657.

Chicago/Turabian Style

Konstantinos Mitropoulos; David N. Cooper; Christina Mitropoulou; Spiros Agathos; Juergen Reichardt; Fatma Al-Maskari; Wasun Chantratita; Ambroise Wonkam; Collet Dandara; Theodora Katsila; Catalina Lopez-Correa; Bassam R. Ali; George P. Patrinos. 2017. "Genomic Medicine Without Borders: Which Strategies Should Developing Countries Employ to Invest in Precision Medicine? A New “Fast-Second Winner” Strategy." OMICS: A Journal of Integrative Biology 21, no. 11: 647-657.

Letter
Published: 31 August 2017 in Science
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In his News In Depth story “Turmoil imperils research university in Andes” (28 July, p. [340][1]), E. Rodríguez Mega reported the frustrations of the recently dismissed administrators at Yachay Tech University in Ecuador. These administrators, as well as the rector (author C.C.-C.), all signed

ACS Style

Carlos Castillo-Chavez; Patricio Ponce; Juergen Reichardt; Spiros Agathos; Paul Arellano; Andreas Griewank; Ernesto Medina; Hortencia Rodriguez; Edgar J. Patiño. Yachay's promise. Science 2017, 357, 881.1 -881.

AMA Style

Carlos Castillo-Chavez, Patricio Ponce, Juergen Reichardt, Spiros Agathos, Paul Arellano, Andreas Griewank, Ernesto Medina, Hortencia Rodriguez, Edgar J. Patiño. Yachay's promise. Science. 2017; 357 (6354):881.1-881.

Chicago/Turabian Style

Carlos Castillo-Chavez; Patricio Ponce; Juergen Reichardt; Spiros Agathos; Paul Arellano; Andreas Griewank; Ernesto Medina; Hortencia Rodriguez; Edgar J. Patiño. 2017. "Yachay's promise." Science 357, no. 6354: 881.1-881.

Review
Published: 18 February 2017 in Bioengineering
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Several methodologies have been devised for the design of nanomaterials. The “Holy Grail” for materials scientists is the cost-effective, eco-friendly synthesis of nanomaterials with controlled sizes, shapes and compositions, as these features confer to the as-produced nanocrystals unique properties making them appropriate candidates for valuable bio-applications. The present review summarizes published data regarding the production of nanomaterials with special features via sustainable methodologies based on the utilization of natural bioresources. The richness of the latter, the diversity of the routes adopted and the tuned experimental parameters have led to the fabrication of nanomaterials belonging to different chemical families with appropriate compositions and displaying interesting sizes and shapes. It is expected that these outstanding findings will encourage researchers and attract newcomers to continue and extend the exploration of possibilities offered by nature and the design of innovative and safer methodologies towards the synthesis of unique nanomaterials, possessing desired features and exhibiting valuable properties that can be exploited in a profusion of fields.

ACS Style

Si Amar Dahoumane; Clayton Jeffryes; Mourad Mechouet; Spiros N. Agathos. Biosynthesis of Inorganic Nanoparticles: A Fresh Look at the Control of Shape, Size and Composition. Bioengineering 2017, 4, 14 .

AMA Style

Si Amar Dahoumane, Clayton Jeffryes, Mourad Mechouet, Spiros N. Agathos. Biosynthesis of Inorganic Nanoparticles: A Fresh Look at the Control of Shape, Size and Composition. Bioengineering. 2017; 4 (1):14.

Chicago/Turabian Style

Si Amar Dahoumane; Clayton Jeffryes; Mourad Mechouet; Spiros N. Agathos. 2017. "Biosynthesis of Inorganic Nanoparticles: A Fresh Look at the Control of Shape, Size and Composition." Bioengineering 4, no. 1: 14.

Journal article
Published: 12 December 2016 in Bionatura
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ACS Style

Si Amar Dahoumane; Mourad Mechouet; Francisco J. Alvarez; Spiros N. Agathos; Clayton Jeffryes; Université Mouloud Mammeri Laboratoire De Physique Et Chimie Des Matériaux. Microalgae: An outstanding tool in nanotechnology. Bionatura 2016, 1, 1 .

AMA Style

Si Amar Dahoumane, Mourad Mechouet, Francisco J. Alvarez, Spiros N. Agathos, Clayton Jeffryes, Université Mouloud Mammeri Laboratoire De Physique Et Chimie Des Matériaux. Microalgae: An outstanding tool in nanotechnology. Bionatura. 2016; 1 (4):1.

Chicago/Turabian Style

Si Amar Dahoumane; Mourad Mechouet; Francisco J. Alvarez; Spiros N. Agathos; Clayton Jeffryes; Université Mouloud Mammeri Laboratoire De Physique Et Chimie Des Matériaux. 2016. "Microalgae: An outstanding tool in nanotechnology." Bionatura 1, no. 4: 1.

Review
Published: 01 December 2016 in Biotechnology Advances
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Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.

ACS Style

Emna Bouhajja; Spiros Agathos; Isabelle F. George. Metagenomics: Probing pollutant fate in natural and engineered ecosystems. Biotechnology Advances 2016, 34, 1413 -1426.

AMA Style

Emna Bouhajja, Spiros Agathos, Isabelle F. George. Metagenomics: Probing pollutant fate in natural and engineered ecosystems. Biotechnology Advances. 2016; 34 (8):1413-1426.

Chicago/Turabian Style

Emna Bouhajja; Spiros Agathos; Isabelle F. George. 2016. "Metagenomics: Probing pollutant fate in natural and engineered ecosystems." Biotechnology Advances 34, no. 8: 1413-1426.

Environmental biotechnology
Published: 26 October 2016 in Applied Microbiology and Biotechnology
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The microbial potential for toluene degradation within sediments from a tar oil-contaminated site in Flingern, Germany, was assessed using a metagenomic approach. High molecular weight environmental DNA from contaminated sediments was extracted, purified, and cloned into fosmid and BAC vectors and transformed into Escherichia coli. The fosmid library was screened by hybridization with a PCR amplicon of the α-subunit of the toluene 4-monooxygenase gene to identify genes and pathways encoding toluene degradation. Fourteen clones were recovered from the fosmid library, among which 13 were highly divergent from known tmoA genes and several had the closest relatives among Acinetobacter species. The BAC library was transferred to the heterologous hosts Cupriavidus metallidurans (phylum Proteobacteria) and Edaphobacter aggregans (phylum Acidobacteria). The resulting libraries were screened for expression of toluene degradation in the non-degradative hosts. From expression in C. metallidurans, three novel toluene monooxygenase-encoding operons were identified that were located on IncP1 plasmids. The E. aggregans-hosted BAC library led to the isolation of a cloned genetic locus putatively derived from an Acidobacteria taxon that contained genes involved in aerobic and anaerobic toluene degradation. These data suggest the important role of plasmids in the spread of toluene degradative capacity and indicate putative novel tmoA genes present in this hydrocarbon-polluted environment.

ACS Style

E. Bouhajja; M. McGuire; M. R. Liles; G. Bataille; Spiros Agathos; I. F. George. Identification of novel toluene monooxygenase genes in a hydrocarbon-polluted sediment using sequence- and function-based screening of metagenomic libraries. Applied Microbiology and Biotechnology 2016, 101, 797 -808.

AMA Style

E. Bouhajja, M. McGuire, M. R. Liles, G. Bataille, Spiros Agathos, I. F. George. Identification of novel toluene monooxygenase genes in a hydrocarbon-polluted sediment using sequence- and function-based screening of metagenomic libraries. Applied Microbiology and Biotechnology. 2016; 101 (2):797-808.

Chicago/Turabian Style

E. Bouhajja; M. McGuire; M. R. Liles; G. Bataille; Spiros Agathos; I. F. George. 2016. "Identification of novel toluene monooxygenase genes in a hydrocarbon-polluted sediment using sequence- and function-based screening of metagenomic libraries." Applied Microbiology and Biotechnology 101, no. 2: 797-808.

Journal article
Published: 02 September 2016 in Preparative Biochemistry and Biotechnology
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The production of laccases from Trametes pubescens was investigated along with the role of nutrients and elicitors. Copper proved to be a fundamental inducer, although productivity yields were consistently enhanced only in the presence of additional compounds (textile dyes). Using a central composite design, the optimal culture condition was examined, by taking into consideration the three distinct variables and their combinatorial effect. The 290 U ml(-1) of laccases were produced after setting nitrogen, copper, and reactive blue 19 concentration; in a bioreactor, activity recovery was lower (90 U ml(-1)) and pellet morphology was different. The activity of the laccase crude extract was maximal at 60°C and stable for 14 h at 50°C and for 2 months at pH 6 and room temperature. The biotechnological potential was assessed, confirming the capacity to decolorize single or mixed solutions of textile dyes and to enhance the whitening yield of raw cotton fibers, working in synergism with the conventional H2O2-based method.

ACS Style

Federica Spina; Charles Junghanns; Ilaria Donelli; Rakesh Nair; Philippe Demarche; Alice Romagnolo; Giuliano Freddi; Spiros Agathos; Giovanna Cristina Varese. Stimulation of laccases from Trametes pubescens: Use in dye decolorization and cotton bleaching. Preparative Biochemistry and Biotechnology 2016, 46, 639 -647.

AMA Style

Federica Spina, Charles Junghanns, Ilaria Donelli, Rakesh Nair, Philippe Demarche, Alice Romagnolo, Giuliano Freddi, Spiros Agathos, Giovanna Cristina Varese. Stimulation of laccases from Trametes pubescens: Use in dye decolorization and cotton bleaching. Preparative Biochemistry and Biotechnology. 2016; 46 (7):639-647.

Chicago/Turabian Style

Federica Spina; Charles Junghanns; Ilaria Donelli; Rakesh Nair; Philippe Demarche; Alice Romagnolo; Giuliano Freddi; Spiros Agathos; Giovanna Cristina Varese. 2016. "Stimulation of laccases from Trametes pubescens: Use in dye decolorization and cotton bleaching." Preparative Biochemistry and Biotechnology 46, no. 7: 639-647.

Book chapter
Published: 29 April 2016 in Industrial Biotechnology of Vitamins, Biopigments, and Antioxidants
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Certain strains of microalgae can efficiently and economically produce high-valued carotenoid pigments and anti-oxidants, such as β-carotene, astaxanthin, adonixanthin or canthaxanthin, when exposed to the appropriate bioprocess conditions. This chapter describes the most industrially relevant microalgal genera, such as Chlorella, Dunaliella, Scenedesmus and Haematococcus, the carotenoids they produce and the cultivation conditions under which optimal production is observed. Best practice techniques for downstream processing, i.e. solid-liquid separation, purification, polishing and formulation, of the carotenoid-rich biomass is also summarized, as are the economics and process bottlenecks.

ACS Style

Borhane Samir Grama; Antoine Delhaye; Spiros Agathos; Clayton Jeffryes. β-Carotene and Other Carotenoids and Pigments from Microalgae. Industrial Biotechnology of Vitamins, Biopigments, and Antioxidants 2016, 265 -286.

AMA Style

Borhane Samir Grama, Antoine Delhaye, Spiros Agathos, Clayton Jeffryes. β-Carotene and Other Carotenoids and Pigments from Microalgae. Industrial Biotechnology of Vitamins, Biopigments, and Antioxidants. 2016; ():265-286.

Chicago/Turabian Style

Borhane Samir Grama; Antoine Delhaye; Spiros Agathos; Clayton Jeffryes. 2016. "β-Carotene and Other Carotenoids and Pigments from Microalgae." Industrial Biotechnology of Vitamins, Biopigments, and Antioxidants , no. : 265-286.

Short communication
Published: 09 April 2016 in Sustainability of Water Quality and Ecology
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Today’s water sector is governed by some hot topics, and this is no different in Belgium. As for the International Water Association (IWA), the goal of its Belgian division (B-IWA) is to gather different stakeholders, i.e. academics, policy makers and people from industry active in the (Belgian) water sector and trigger the debate. In May 2015, a first Nocturnal was organised to accomplish just this. Seven hot water topics, proposed by participants at the time of their online registration, were addressed in rotating round table discussions. These topics included resource recovery, micropollutants, water scarcity, hydroinformatics, integrated water management and modeling, technology vs. legislation and Computational Fluid Dynamics in water applications. The lively discussions led to the idea of this short contribution describing the outcomes of these round table discussions, along with some additional research on the topics. Main conclusions include the need for education (both of scholars and young professionals), inter-domain communication and the growing importance of IT in the water sector.

ACS Style

C. De Mulder; S. Van Hoey; S. Van Hulle; S.N. Agathos; P. Cauwenberg; P. Mergen; P. Seuntjens; I. Smets; G. De Gueldre; A. Mouton; D. Schowanek; B. Meesschaert; W. Verstraete; I. Nopens. Pressing topics in the Belgian water sector anno 2015. Sustainability of Water Quality and Ecology 2016, 7, 32 -36.

AMA Style

C. De Mulder, S. Van Hoey, S. Van Hulle, S.N. Agathos, P. Cauwenberg, P. Mergen, P. Seuntjens, I. Smets, G. De Gueldre, A. Mouton, D. Schowanek, B. Meesschaert, W. Verstraete, I. Nopens. Pressing topics in the Belgian water sector anno 2015. Sustainability of Water Quality and Ecology. 2016; 7 ():32-36.

Chicago/Turabian Style

C. De Mulder; S. Van Hoey; S. Van Hulle; S.N. Agathos; P. Cauwenberg; P. Mergen; P. Seuntjens; I. Smets; G. De Gueldre; A. Mouton; D. Schowanek; B. Meesschaert; W. Verstraete; I. Nopens. 2016. "Pressing topics in the Belgian water sector anno 2015." Sustainability of Water Quality and Ecology 7, no. : 32-36.

Journal article
Published: 01 March 2016 in Journal of Biotechnology
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The Acidobacteria phylum is of high ecological interest. Its members are ubiquitous and particularly abundant in soils but many are recalcitrant to cultivation in the laboratory. Thus, the ability of Acidobacteria to capture and maintain plasmids remains largely unexplored. In this work we tested the transfer and the stability of (i) the PromA plasmid pMOL98 and (ii) the IncQ plasmid pKT230 to the acidobacterial strain Edaphobacter aggregans DSM 19364. To this end quantitative conjugation assays were performed and transconjugants were scored for plasmid-borne antibiotic selection markers. The tested plasmids were transferred and maintained in the new host. Plasmid pMOL98 was more stable than pKT230 in Ed. aggregans in the absence of positive selection. Thus, from an ecological point of view, we have extended the host range of PromA and IncQ plasmids for the first time to an acidobacterial strain. Furthermore, we have uncovered the potential of Acidobacteria to capture as-yet-unknown plasmids and to foster the development of new cloning and expression systems for the exploitation of biotechnologically valuable soil resources.

ACS Style

Emna Bouhajja; Theocharis Efthymiopoulos; Isabelle F. George; David Moreels; Rob Van Houdt; Max Mergeay; Spiros N. Agathos. Conjugative transfer of broad host range plasmids to an acidobacterial strain, Edaphobacter aggregans. Journal of Biotechnology 2016, 221, 107 -113.

AMA Style

Emna Bouhajja, Theocharis Efthymiopoulos, Isabelle F. George, David Moreels, Rob Van Houdt, Max Mergeay, Spiros N. Agathos. Conjugative transfer of broad host range plasmids to an acidobacterial strain, Edaphobacter aggregans. Journal of Biotechnology. 2016; 221 ():107-113.

Chicago/Turabian Style

Emna Bouhajja; Theocharis Efthymiopoulos; Isabelle F. George; David Moreels; Rob Van Houdt; Max Mergeay; Spiros N. Agathos. 2016. "Conjugative transfer of broad host range plasmids to an acidobacterial strain, Edaphobacter aggregans." Journal of Biotechnology 221, no. : 107-113.

Opinion article
Published: 10 February 2016 in Frontiers in Microbiology
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Back to the Future of Soil Metagenomics

ACS Style

Joseph Nesme; Wafa Achouak; Spiros Agathos; Mark Bailey; Petr Baldrian; Dominique Brunel; Åsa Frostegård; Thierry Heulin; Janet Jansson; Edouard Jurkevitch; Kristiina L. Kruus; George A. Kowalchuk; Antonio Lagares; Hilary M. Lappin-Scott; Philippe Lemanceau; Denis Le Paslier; Ines Mandic-Mulec; J. Colin Murrell; David Myrold; Renaud Nalin; Paolo Nannipieri; Josh D. Neufeld; Fergal O'Gara; John J. Parnell; Alfred Pühler; Victor Pylro; Juan L. Ramos; Luiz Roesch; Michael Schloter; Christa Schleper; Alexander Sczyrba; Angela Sessitsch; Sara Sjöling; Jan Sørensen; Søren Sørensen; Christoph Tebbe; Ed Topp; George Tsiamis; Jan Dirk Van Elsas; Geertje Van Keulen; Franco Widmer; Michael Wagner; Tong Zhang; Xiaojun Zhang; Liping Zhao; Yong-Guan Zhu; Timothy M. Vogel; Pascal Simonet. Back to the Future of Soil Metagenomics. Frontiers in Microbiology 2016, 7, 73 .

AMA Style

Joseph Nesme, Wafa Achouak, Spiros Agathos, Mark Bailey, Petr Baldrian, Dominique Brunel, Åsa Frostegård, Thierry Heulin, Janet Jansson, Edouard Jurkevitch, Kristiina L. Kruus, George A. Kowalchuk, Antonio Lagares, Hilary M. Lappin-Scott, Philippe Lemanceau, Denis Le Paslier, Ines Mandic-Mulec, J. Colin Murrell, David Myrold, Renaud Nalin, Paolo Nannipieri, Josh D. Neufeld, Fergal O'Gara, John J. Parnell, Alfred Pühler, Victor Pylro, Juan L. Ramos, Luiz Roesch, Michael Schloter, Christa Schleper, Alexander Sczyrba, Angela Sessitsch, Sara Sjöling, Jan Sørensen, Søren Sørensen, Christoph Tebbe, Ed Topp, George Tsiamis, Jan Dirk Van Elsas, Geertje Van Keulen, Franco Widmer, Michael Wagner, Tong Zhang, Xiaojun Zhang, Liping Zhao, Yong-Guan Zhu, Timothy M. Vogel, Pascal Simonet. Back to the Future of Soil Metagenomics. Frontiers in Microbiology. 2016; 7 ():73.

Chicago/Turabian Style

Joseph Nesme; Wafa Achouak; Spiros Agathos; Mark Bailey; Petr Baldrian; Dominique Brunel; Åsa Frostegård; Thierry Heulin; Janet Jansson; Edouard Jurkevitch; Kristiina L. Kruus; George A. Kowalchuk; Antonio Lagares; Hilary M. Lappin-Scott; Philippe Lemanceau; Denis Le Paslier; Ines Mandic-Mulec; J. Colin Murrell; David Myrold; Renaud Nalin; Paolo Nannipieri; Josh D. Neufeld; Fergal O'Gara; John J. Parnell; Alfred Pühler; Victor Pylro; Juan L. Ramos; Luiz Roesch; Michael Schloter; Christa Schleper; Alexander Sczyrba; Angela Sessitsch; Sara Sjöling; Jan Sørensen; Søren Sørensen; Christoph Tebbe; Ed Topp; George Tsiamis; Jan Dirk Van Elsas; Geertje Van Keulen; Franco Widmer; Michael Wagner; Tong Zhang; Xiaojun Zhang; Liping Zhao; Yong-Guan Zhu; Timothy M. Vogel; Pascal Simonet. 2016. "Back to the Future of Soil Metagenomics." Frontiers in Microbiology 7, no. : 73.