Suchergebnisse

Research work of the author is funded by Agencia Estatal de Investigación (AEI), Ministerio de Ciencia e Innovación (grant SETH ref. RTI2018-095584-B-C41-42-43-44 co-financed by ERDF) and the European Union H2020 (BioRobooST project ID 210491758; MIPLACE project ref. PCI2019-111845-2, Programación Conjunta Internacional 2019, AEI). ; Peer reviewed

Synthetic Biology (SB) is a revolutionary discipline with a vast range of practical applications, but is SB research really based on engineering principles? Does it contributing to the artificial synthesis of life or does it utilise approaches sufficiently advanced to fall outside the scope of biotechnology or metabolic engineering? This volume reviews the development of SB and includes the major milestones of the discipline, the 'top-down' and 'bottom-up' approaches towards the construction of an artificial cell and the development of the 'iGEM' competition. We conclude that SB is an emerging field with extraordinary technological potential, but that most research projects actually are an extension of metabolic engineering since the complexity of living organisms, their tight dependence on evolution and our limited knowledge of the interactions between the molecules, actually make life difficult to engineer.

The concept of standard strongly evokes machines, industries, electric or mechanical devices, vehicles, or furniture. Indeed, our technological civilization would not be possible – at least in the terms it is structured today – without universal, reliable components, whose acknowledged use results in competitive costs, robustness and interchangeability. For example, an Ikea screw can be used in a wide set of structurally dissimilar furniture and an app can be run on many different smartphones. The very concept of standardization is linked to the industrial revolution and mass production of goods through assembly lines. The question we will try to answer in the present paper is the extent to which standards and the standardization process can be accomplished in the biological realm. ; The authors' work is funded by the Ministry of Science and Innovation and ERDF (RTI2018-095584-B-C41) and the European Union H2020 (BioRobooST: Fostering synthetic biology standardization through international collaboration, Project ID 210491758). ; Peer reviewed

Synthetic biology is the engineering view on biotechnology that ultimately aims at fulfilling the quest of building an artificial cell. From the very first attempts of synthesizing life, this subject has made an impact on the media through, very often, misleading headlines and news. We review here the historical journalistic approach on synthetic biology and related disciplines, from the early twentieth century to the lastest achievements on designing protocells or genome reduction. However, it would be very naive to consider the research community and the media to be unidirectionally linked, with the latter being mere displayers (and disrupters) of the research "reality". On the contrary, the research community has also received a strong influence from the media, as evidenced by statements from researchers, common metaphors and, even, a trend to unconsciously develop shared techno-social paradigms. We conclude that, beyond overstatements from researchers and journalists' misunderstandings, both communities provide strong feedback to each other and, together, contribute to define the dream that synthetic biologists are aiming for. ; The laboratory work of both authors is supported in part by the Spanish Government (Helios, grant reference: BIO2015–66960-C3–1-R co-financed by FEDER funds and Ministerio de Economía y Competitividad) and by the European Union through the BioRoboost project, H2020-NMBP-TR-IND-2018-2020/BIOTEC-01-2018 (CSA), Project ID 210491758. ; Peer reviewed

The largest survey on the perception of synthetic biology‐related disciplines (Porcar et al., 2019,EMBO Rep 20) recently revealed that the Spanish society does not have a very positive perception of the term synthetic biology. On the other hand, the terms biotechnology and even genetic engineering received relatively higher scores. The issue of nomenclature and perception is a classical one in science perception studies. Synthetic biologists have been debating their neologism (Synthetic Biology, from now on SB) for years. Even in a 2006 blog, Rob Carlson discussed the various labels for the new field, such as intentional biology, constructive biology, natural engineering, synthetic genomics and biological engineering. This diversity of names, along with the above mentioned negative public perception of the term synthetic biology, raises the question on whether the term itself is suitable or whether it could, in an extreme scenario, be replaced by another combining scientific consensus with public acceptance. ; This work was funded by the European Union through the BioRoboost project, H2020‐NMBP‐TR‐IND‐2018‐2020/BIOTEC‐01‐2018 (CSA), Project ID 210491758. ; Peer reviewed

[Background] Determining the factors involved in the likelihood of a gene being under adaptive selection is still a challenging goal in Evolutionary Biology. Here, we perform an evolutionary analysis of the human metabolic genes to explore the associations between network structure and the presence and strength of natural selection in the genes whose products are involved in metabolism. Purifying and positive selection are estimated at interspecific (among mammals) and intraspecific (among human populations) levels, and the connections between enzymatic reactions are differentiated between incoming (in-degree) and outgoing (out-degree) links. ; [Results] We confirm that purifying selection has been stronger in highly connected genes. Long-term positive selection has targeted poorly connected enzymes, whereas short-term positive selection has targeted different enzymes depending on whether the selective sweep has reached fixation in the population: genes under a complete selective sweep are poorly connected, whereas those under an incomplete selective sweep have high out-degree connectivity. The last steps of pathways are more conserved due to stronger purifying selection, with long-term positive selection targeting preferentially enzymes that catalyze the first steps. However, short-term positive selection has targeted enzymes that catalyze the last steps in the metabolic network. Strong signals of positive selection have been found for metabolic processes involved in lipid transport and membrane fluidity and permeability. ; [Conclusions] Our analysis highlights the importance of analyzing the same biological system at different evolutionary timescales to understand the evolution of metabolic genes and of distinguishing between incoming and outgoing links in a metabolic network. Short-term positive selection has targeted enzymes with a different connectivity profile depending on the completeness of the selective sweep, while long-term positive selection has targeted genes with fewer connections that code for enzymes that catalyze the first steps in the network. ; This study has been possible thanks to grant BFU2016–77961-P (AEI/FEDER, UE) awarded by the Agencia Estatal de Investigación (Ministerio de Ciencia, Innovación y Universidades, Spain) and with the support of Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 527 SGR 702) to JB. Part of the "Unidad de Excelencia María de Maeztu" (MDM-2014-0370), funded by the Ministerio de Economía, Industria y Competividad (MINECO, Spain). JP work is supported in part by the Agencia Estatal de Investigación (Ministerio de Ciencia, Innovación y Universidades, Spain) Helios grant reference: BIO2015–66960-C3–1-R (co-financed by FEDER) and by the European Union through the BioRoboost project (H2020-NMBP-TR-IND-2018-2020/BIOTEC-01-2018 (CSA), Project ID 210491758). BD is supported by F.P.U. grant FPU13/06813 from the Ministerio de Educación, Cultura y Deporte (Spain).

Bacterial communities may display metabolic complementation, in which different members of the association partially contribute to the same biosynthetic pathway. In this way, the end product of the pathway is synthesized by the community as a whole. However, the emergence and the benefits of such complementation are poorly understood. Herein, we present a simple model to analyze the metabolic interactions among bacteria, including the host in the case of endosymbiotic bacteria. The model considers two cell populations, with both cell types encoding for the same linear biosynthetic pathway. We have found that, for metabolic complementation to emerge as an optimal strategy, both product inhibition and large permeabilities are needed. In the light of these results, we then consider the patterns found in the case of tryptophan biosynthesis in the endosymbiont consortium hosted by the aphid Cinara cedri. Using in-silico computed physicochemical properties of metabolites of this and other biosynthetic pathways, we verified that the splitting point of the pathway corresponds to the most permeable intermediate. ; Financial support from Spanish Government (grant reference: BFU2012-39816-C02-01 co-financed by FEDER funds and Ministerio de Economía y Competitividad) and Generalitat Valenciana (grant reference: PROMETEOII/2014/065) is grateful acknowledged. ; Peer reviewed

This article belongs to the Section Environmental Microbiology. ; Three novel Gram-positive, aerobic, chemoheterotrophic, motile, non-endospore-forming, orange-pigmented bacteria designated strains T13T, T90T and R8T were isolated from the Tabernas Desert biocrust (Almería, Spain). Cells of the three strains were coccus-shaped and occurred singly, in pairs or clusters. The three strains were oxidase-negative and catalase-positive, and showed a mesophilic, neutrophilic and non-halophilic metabolism. Based on the 16S rRNA gene sequences, the closest neighbours of strains T13T, T90T and R8T were Kineococcus aurantiacus IFO 15268T, Kineococcus gypseus YIM 121300T and Kineococcus radiotolerans SRS 30216T (98.5%, 97.1% and 97.9% gene sequence similarity, respectively). The genomes were sequenced, and have been deposited in the GenBank/EMBL/DDBJ databases under the accession numbers JAAALL000000000, JAAALM000000000 and JAAALN000000000, respectively, for strains T13T, T90T and R8T. The average nucleotide identity (ANIb) and digital DNA-DNA hybridization (dDDH) values confirmed their adscription to three new species within the genus Kineococcus. The genomic G + C content of strains T13T, T90T and R8T ranged from 75.1% to 76.3%. The predominant fatty acid of all three strains was anteiso-C15:0. According to a polyphasic study, strains T13T, T90T and R8T are representatives of three new species in the genus Kineococcus, for which names Kineococcus vitellinus sp. nov. (type strain T13T = CECT 9936T = DSM 110024T), Kineococcus indalonis sp. nov. (type strain T90T = CECT 9938T = DSM 110026T) and Kineococcus siccus sp. nov. (type strain R8T = CECT 9937T = DSM 110025T) are proposed. ; Financial support from Spanish Government (Grant HELIOS with reference: BIO2015-66960-C3-1-R; and grant SETH with reference RTI2018-095584-B-C41-42-43-44 co-financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades) is acknowledged. EMM is a recipient of a Formación del Profesorado Universitario (FPU) grant with reference FPU17/04184, from the Ministerio de Ciencia, Innovación y Universidades (Spain). ; Peer reviewed

Microbial communities from harsh environments hold great promise as sources of biotechnologically relevant strains and compounds. In the present work, we have characterized the microorganisms from the supralittoral and splash zone in three different rocky locations of the Western Mediterranean coast, a tough environment characterized by high levels of irradiation and large temperature and salinity fluctuations. We have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. All three locations displayed very similar taxonomic profiles, with the genus Rubrobacter and the families Xenococcaceae, Flammeovirgaceae, Phyllobacteriaceae, Rhodobacteraceae and Trueperaceae being the most abundant taxa; and Ascomycota and halotolerant archaea as members of the eukaryotic and archaeal community respectively. In parallel, the culture‐dependent approach yielded a 100‐isolates collection, out of which 12 displayed high antioxidant activities, as evidenced by two in vitro (hydrogen peroxide and DPPH) and confirmed in vivo with Caenorhabditis elegans assays, in which two isolates, CR22 and CR24, resulted in extended survival rates of the nematodes. This work is the first complete characterization of the Mediterranean splash‐zone coastal microbiome, and our results indicate that this microbial niche is home of an extremophilic community that holds biotechnological potential. ; Financial support from the Spanish Government (Grant Helios, Reference: BIO2015‐66960‐C3‐1‐R co‐financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades) and from the European CSA on biological standardization BIOROBOOST (EU grant number 820699) is acknowledged. EMM is funded with a Formación de Profesorado Universitario (FPU) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU17/04184. KT is a recipient of a Doctorado Industrial fellowship from the Ministerio de Ciencia, Innovación y Universidades (Spain), with reference DI‐16‐08976. ÀVV is funded with a Formación de Profesorado Universitario (FPU) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU18/02578. ; Peer reviewed

This book collects three outstanding examples of the work of Mexican biologist Alfonso Luis Herrera (1868-1942), a pioneer in experimental origins of life research. Two of the collected works appear here in English for the first time. Herrera's works represent the attempt to deal experimentally with the issue of an autotrophic origin of life, a possibility that was widely accepted prior to Alexander I. Oparin's ideas regarding the possibility of organic synthesis and the origin of life in an early Earth environment. An active promoter of Darwinian ideas in Latin America, Herrera was also among the first 20th century researchers to attempt to "create life in a test tube." This collection shows the remarkable prescience of researchers in Mexico with regards to laboratory approaches to the problem of the origin of life. It also includes a modern commentary by researchers actively engaged in research in prebiotic evolution and the origins of life, and deeply concerned with the historical development of ideas in these fields. The list includes H. James Cleaves, Antonio Lazcano, Ismael Ledesma Mateos, Alicia Negrón-Mendoza, Juli Peretó and Ervin Silva, who discuss in detail the relevance of Herrera's ideas to modern theory and their historical context. The book will expose modern readers and researchers to currents of thinking that have been lost, largely to time and language inaccessibility, of a seminal early theoretical biologist

Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6T and T18T, were isolated from a biocrust (biological soil crust) sample from the vicinity of the Tabernas Desert (Spain). Both strains were catalase-positive and oxidase-negative, and grew under mesophilic, neutrophilic and non-halophilic conditions. According to the 16S rRNA gene sequences, strains T6T and T18T showed similarities with Belnapia rosea CGMCC 1.10758T and Belnapia moabensis CP2CT (98.11 and 98.55% gene sequence similarity, respectively). The DNA G+C content was 69.80 and 68.96% for strains T6T and T18T, respectively; the average nucleotide identity by blast (ANIb) and digital DNA–DNA hybridization (dDDH) values confirmed their adscription to two novel species within the genus Belnapia. The predominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C16 : 0, C18 : 1 2-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). According to he results of the polyphasic study, strains T6T and T18T represent two novel species in the genus Belnapia (which currently includes only three species), for which names Belnapia mucosa sp. nov. (type strain T6T = CECT 30228T=DSM 112073T) and Belnapia arida sp. nov. (type strain T18T=CECT 30229T=DSM 112074T) are proposed, respectively. ; Financial support from Spanish Government (Grant SETH with reference RTI2018-095584-B-C41-42-43-44 co-financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades) is acknowledged. E.M.M. and À.V.V. are recipients of a Formación del Profesorado Universitario (FPU) grant with references FPU17/04184 and FPU18/02578, respectively, from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades, Spain). ; Peer reviewed

Solar panel surfaces can be colonized by microorganisms adapted to desiccation, temperature fluctuations and solar radiation. Although the taxonomic and functional composition of these communities has been studied, the microbial colonization process remains unclear. In the present work, we have monitored this microbial colonization process during 24 months by performing weekly measurements of the photovoltaic efficiency, carrying out 16S rRNA gene high‐throughput sequencing, and studying the effect of antimicrobial compounds on the composition of the microbial biocenosis. This is the first time a long‐term study of the colonization process of solar panels has been performed, and our results reveal that species richness and biodiversity exhibit seasonal fluctuations and that there is a trend towards an increase or decrease of specialist (solar panel‐adapted) and generalist taxa, respectively. On the former, extremophilic bacterial genera Deinococcus, Hymenobacter and Roseomonas and fungal Neocatenulostroma, Symmetrospora and Sporobolomyces tended to dominate the biocenosis; whereas Lactobacillus sp or Stemphyllium exhibited a decreasing trend. This profile was deeply altered by washing the panels with chemical agents (Virkon), but this did not lead to an increase of the solar panels efficiency. Our results show that solar panels are extreme environments that force the selection of a particular microbial community. ; Financial support from the Spanish Government (grant Helios. reference: BIO2015‐66960‐C3‐1‐R co‐financed by FEDER funds and Ministerio de Economía y Competitividad) and from the European CSA on biological standardization BIOROBOOST (EU grant number 820699) are acknowledged. KT is a recipient of a Doctorado Industrial fellowship from the Ministerio de Ciencia, Innovación y Universidades (Spain), with reference DI‐16‐08976. AL is a recipient of a Doctorado Industrial fellowship from the Ministerio de Ciencia, Innovación y Universidades (Spain), with reference DI‐17‐09613. EMM is funded with a Formación de Profesorado Universitario (FPU) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU17/04184. AVV is funded with a Formación de Profesorado Universitario (FPU) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU18/02578. CV is a recipient of a Torres Quevedo fellowship from the Ministerio de Ciencia, Innovación y Universidades (Spain), with reference PTQ‐16‐08227. ; Peer reviewed

Microbial communities that are exposed to sunlight typically share a series of adaptations to deal with the radiation they are exposed to, including efficient DNA repair systems, pigment production and protection against oxidative stress, which makes these environments good candidates for the search of novel antioxidant microorganisms. In this research project, we isolated potential antioxidant pigmented bacteria from a dry and highly-irradiated extreme environment: solar panels. High-throughput in vivo assays using Caenorhabditis elegans as an experimental model demonstrated the high antioxidant and ultraviolet-protection properties of these bacterial isolates that proved to be rich in carotenoids. Our results suggest that solar panels harbor a microbial community that includes strains with potential applications as antioxidants. ; Financial support from the Spanish Government (grant Helios, reference: BIO2015-66960-C3-1-R co-financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades) and from the Regional Government of Valencia (grant MICROBIOSOL, reference: IFIDUA/2015/10 financed by IVACE) are acknowledged. Furthermore, KT is a recipient of a Doctorado Industrial fellowship from the Ministerio de Ciencia, Innovación y Universidades (Spain), with reference DI-16-08976. MR and LZ are members of the CaRed Excellence Network (BIO2017-90877-REDT) and EUROCAROTEN European COST Action (CA15113). ; Peer Reviewed