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Castillo M, Guevara G, Baldanta S, Rodríguez PS, Agudo L, Nogales J, Carrasco AD, Arribas-Aguilar F, Pérez-Pérez J, García JL, Galán B, Navarro Llorens JM. Characterization of Limnospira platensis PCC 9108 R-M and CRISPR-Cas systems. Microbiol Res 2024; 279:127572. [PMID: 38101163 DOI: 10.1016/j.micres.2023.127572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
The filamentous cyanobacterium Limnospira platensis, formerly known as Arthrospira platensis or spirulina, is one of the most commercially important species of microalgae. Due to its high nutritional value, pharmacological and industrial applications it is extensively cultivated on a large commercial scale. Despite its widespread use, its precise manipulation is still under development due to the lack of effective genetic protocols. Genetic transformation of Limnospira has been attempted but the methods reported have not been generally reproducible in other laboratories. Knowledge of the transformation defense mechanisms is essential for understanding its physiology and for broadening their applications. With the aim to understand more about the genetic defenses of L. platensis, in this work we have identified the restriction-modification and CRISPR-Cas systems and we have cloned and characterized thirteen methylases. In parallel, we have also characterized the methylome and orphan methyltransferases using genome-wide analysis of DNA methylation patterns and RNA-seq. The identification and characterization of these enzymes will be a valuable resource to know how this strain avoids being genetically manipulated and for further genomics studies.
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Affiliation(s)
- María Castillo
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Govinda Guevara
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
| | - Sara Baldanta
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
| | - Patricia Suárez Rodríguez
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
| | - Lucía Agudo
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain.
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain.
| | - Asunción Díaz Carrasco
- DNA Sequencing facility, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Fernando Arribas-Aguilar
- SECUGEN SL, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Julián Pérez-Pérez
- SECUGEN SL, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - José Luis García
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Beatriz Galán
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Juana María Navarro Llorens
- Department of Biochemistry and Molecular Biology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Av. Complutense s/n, 28040 Madrid, Spain.
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2
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Kačar D, Cañedo LM, Rodríguez P, Schleissner C, de la Calle F, García JL, Galán B. Tailoring modifications in labrenzin synthesis: a-la-carte production of pathway intermediates. Microb Biotechnol 2024; 17:e14355. [PMID: 37909860 PMCID: PMC10832518 DOI: 10.1111/1751-7915.14355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
Pederin-family polyketides today constitute a group of more than 30 molecules being produced as natural products by different microorganisms across multitude of ecological niches. They are mostly known for their extreme cytotoxic activity and the decades of long exploration as potential antitumor drugs. The difference in their potency and biological activity lies in the tailoring modifications of the core molecule. Despite the isolation of many pederin-like molecules until the date, only marine bacterium Labrenzia sp. PHM005 was reported as a cultivable producer and able to be genetically modified. Here, we study the role of tailoring enzymes from the lab gene cluster responsible for methylation and hydroxylation of labrenzin core molecule. We managed to produce a spectrum of differently tailored labrenzin analogs for the development of future drugs. This work constitutes one-step forward in understanding the biosynthesis of pederin-family polyketides and provides the tools to modify and overproduce these anticancer drugs in a-la-carte manner in Labrenzia sp. PHM005, but also in other producers in the future.
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Affiliation(s)
- Dina Kačar
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita SalasAgencia Estatal Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | | | - Pilar Rodríguez
- Research and Development DepartmentPharmaMar S.A.MadridSpain
| | | | | | - José Luis García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita SalasAgencia Estatal Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita SalasAgencia Estatal Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
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3
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Castilla-Alcantara JC, Posada-Baquero R, Balseiro-Romero M, Fernández-López C, García JL, Fernandez-Vazquez A, Parsons JR, Cantos M, Ortega-Calvo JJ. Risk reductions during pyrene biotransformation and mobilization in a model plant-bacteria-biochar system. Sci Total Environ 2023; 868:161600. [PMID: 36681341 DOI: 10.1016/j.scitotenv.2023.161600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/23/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
The productive application of motile microorganisms for degrading hydrophobic contaminants in soil is one of the most promising processes in modern remediation due to its sustainability and low cost. However, the incomplete biodegradation of the contaminants and the formation of the intermediary metabolites in the process may increase the toxicity in soil during bioremediation, and motile inoculants may mobilize the pollutants through biosorption. Therefore, controlling these factors should be a fundamental part of soil remediation approaches. The aim of this study was to evaluate the sources of risk associated with the cometabolism-based transformation of 14C-labeled pyrene by inoculated Pseudomonas putida G7 and identify ways to minimize risk. Our model scenario examined the increase in bioaccessibility to a distant source of contamination facilitated by sunflower (Helianthus annuus L.) roots. A biochar trap for mobilized pollutant metabolites and bacteria has also been employed. The experimental design consisted of pots filled with a layer of sand with 14C-labeled pyrene (88 mg kg-1) as a contamination focus located several centimeters from the inoculation point. Half of the pots included a biochar layer at the bottom. The pots were incubated in a greenhouse with sunflower plants and P. putida G7 bacteria. Pots with sunflower plants showed a higher biodegradation of pyrene, its mobilization as metabolites through the percolate and the roots, and bacterial mobilization toward the source of contamination, also resulting in increased pyrene transformation. In addition, the biochar layer efficiently reduced the concentrations of pyrene metabolites collected in the leachates. Therefore, the combination of plants, motile bacteria and biochar safely reduced the risk caused by the biological transformation of pyrene.
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Affiliation(s)
| | - Rosa Posada-Baquero
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Seville, Spain
| | - Maria Balseiro-Romero
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Seville, Spain
| | - Carmen Fernández-López
- Centro Universitario de la Defensa, Universidad Politécnica de Cartagena, Santiago de la Ribera, Murcia, Spain
| | - José Luis García
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Seville, Spain
| | | | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Manuel Cantos
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Seville, Spain
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Amaya J, Rubí S, Munar M, García JL, Medina C, Luna B, Sampol C, Peña C. Role of nuclear medicine in the diagnosis of peritoneal leaks in patients in dialysis: Experience of Hospital Universitario Son Espases. Nefrologia 2023; 43:155-157. [PMID: 37012172 DOI: 10.1016/j.nefroe.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/18/2022] [Indexed: 06/12/2023] Open
Affiliation(s)
- Jaime Amaya
- Servicio de Medicina Nuclear, Hospital Universitario Son Espases, Palma de Mallorca, Spain.
| | - Sebastià Rubí
- Servicio de Medicina Nuclear, Hospital Universitario Son Espases, Palma de Mallorca, Spain; Instituto de Investigación Sanitaria Illes Balears (IdISBa), Islas Baleares, Spain
| | - María Munar
- Servicio de Nefrología (Sección Diálisis), Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - José Luis García
- Servicio de Nefrología (Sección Diálisis), Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Celia Medina
- Servicio de Medicina Nuclear, Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Belén Luna
- Servicio de Medicina Nuclear, Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Catalina Sampol
- Servicio de Medicina Nuclear, Hospital Universitario Son Espases, Palma de Mallorca, Spain; Instituto de Investigación Sanitaria Illes Balears (IdISBa), Islas Baleares, Spain
| | - Cristina Peña
- Servicio de Medicina Nuclear, Hospital Universitario Son Espases, Palma de Mallorca, Spain; Instituto de Investigación Sanitaria Illes Balears (IdISBa), Islas Baleares, Spain
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Galán B, Felpeto-Santero C, García JL. Production of 11α-Hydroxysteroid Derivatives by Corynebacterium glutamicum Expressing the Rhizopus oryzae Hydroxylating System. Methods Mol Biol 2023; 2704:277-289. [PMID: 37642851 DOI: 10.1007/978-1-0716-3385-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Hydroxylation of steroids has acquired special relevance for the pharmaceutical industry. Particularly, the 11α-hydroxylation of steroids is a process of biotechnological importance currently carried out at industrial scale for the production of contraceptive drugs and glucocorticoids. This process is performed by several fungal species including Rhizopus nigricans, Aspergillus ochraceus, Aspergillus niger, and Rhizopus oryzae that are used to produce by biotransformation hydroxylated steroids for pharmaceutical purposes (Wang et al., J Steroid Biochem Mol Biol 171:254-261, 2017). However, the development of more efficient biotransformation processes is essential since the steroidal derivatives obtained by the in vivo hydroxylation are often a mixture of hydroxylated compounds in different positions of the steroid molecule. This phenomenon is due to the large number of different CYPs contained in the fungal strains.The genes responsible for the 11α-hydroxylase activity in R. oryzae consisting in the cytochrome CYP509C12 and its redox partner, the reductase RoCPR1, have been chemically synthetized forming a synthetic operon named FUN optimized to be expressed in bacteria. To express this operon, we have selected the strain Corynebacterium glutamicum R31 that is a robust and GRAS bacterial strain widely used for industrial purposes. The synthetic operon has been cloned in the pECXK-99E vector, yielding pXKFUN plasmid, and transformed C. glutamicum R31 to generate C. glutamicum R31 (pXKFUN) strain. This strain is not a steroid degrader and can efficiently transport C19 and C21 steroids across the cytoplasmic membrane (García-Fernandez et al. Catalysts 316:1-12, 2017). C. glutamicum can be used as a clean host for steroid biotransformation, because it does not introduce additional undesired side reactions on the steroids, thus reducing the contamination of the final products (Felpeto-Santero et al., Microbiol Biotechnol 12:856-868, 2019). Here we show a proof of concept that C. glutamicum can be used as a suitable chassis to perform steroid biotransformation expressing eukaryotic cytochromes. The protocol below provides detailed information on steroid 11α-hydroxylations by Corynebacterium recombinant strain.
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Affiliation(s)
- Beatriz Galán
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain.
| | - Carmen Felpeto-Santero
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
| | - José Luis García
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
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6
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Hernández-Fernández G, Galán B, Carmona M, Castro L, García JL. Transcriptional response of the xerotolerant Arthrobacter sp. Helios strain to PEG-induced drought stress. Front Microbiol 2022; 13:1009068. [PMID: 36312951 PMCID: PMC9608346 DOI: 10.3389/fmicb.2022.1009068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
A new bacterial strain has been isolated from the microbiome of solar panels and classified as Arthrobacter sp. Helios according to its 16S rDNA, positioning it in the “Arthrobacter citreus group.” The isolated strain is highly tolerant to desiccation, UV radiation and to the presence of metals and metalloids, while it is motile and capable of growing in a variety of carbon sources. These characteristics, together with observation that Arthrobacter sp. Helios seems to be permanently prepared to handle the desiccation stress, make it very versatile and give it a great potential to use it as a biotechnological chassis. The new strain genome has been sequenced and its analysis revealed that it is extremely well poised to respond to environmental stresses. We have analyzed the transcriptional response of this strain to PEG6000-mediated arid stress to investigate the desiccation resistance mechanism. Most of the induced genes participate in cellular homeostasis such as ion and osmolyte transport and iron scavenging. Moreover, the greatest induction has been found in a gene cluster responsible for biogenic amine catabolism, suggesting their involvement in the desiccation resistance mechanism in this bacterium.
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Affiliation(s)
- Gabriel Hernández-Fernández
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
| | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
| | - Manuel Carmona
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
| | - Laura Castro
- Department of Chemical and Materials Engineering, Complutense University of Madrid, Madrid, Spain
| | - José Luis García
- Department of Microbial and Plant Biotechnology, Margarita Salas Centre for Biological Research-CSIC, Madrid, Spain
- *Correspondence: José Luis García,
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Martínez I, Mohamed MES, García JL, Díaz E. Enhancing biodesulfurization by engineering a synthetic dibenzothiophene mineralization pathway. Front Microbiol 2022; 13:987084. [PMID: 36274708 PMCID: PMC9579287 DOI: 10.3389/fmicb.2022.987084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
A synthetic dibenzothiophene (DBT) mineralization pathway has been engineered in recombinant cells of Pseudomonas azelaica Aramco J strain for its use in biodesulfurization of thiophenic compounds and crude oil. This functional pathway consists of a combination of a recombinant 4S pathway responsible for the conversion of DBT into 2-hydroxybiphenyl (2HBP) and a 2HBP mineralization pathway that is naturally present in the parental P. azelaica Aramco J strain. This novel approach allows overcoming one of the major bottlenecks of the biodesulfurization process, i.e., the feedback inhibitory effect of 2HBP on the 4S pathway enzymes. Resting cells-based biodesulfurization assays using DBT as a sulfur source showed that the 2HBP generated from the 4S pathway is subsequently metabolized by the cell, yielding an increase of 100% in DBT removal with respect to previously optimized Pseudomonas putida biodesulfurizing strains. Moreover, the recombinant P. azelaica Aramco J strain was able to use DBT as a carbon source, representing the best characterized biocatalyst harboring a DBT mineralization pathway and constituting a suitable candidate to develop future bioremediation/bioconversion strategies for oil-contaminated sites.
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Affiliation(s)
- Igor Martínez
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - José Luis García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Eduardo Díaz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- *Correspondence: Eduardo Díaz,
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8
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Kačar D, Schleissner C, Cañedo LM, Rodríguez P, de la Calle F, Cuevas C, Galán B, García JL. In vivo production of pederin by labrenzin pathway expansion. Metab Eng Commun 2022; 14:e00198. [PMID: 35517715 PMCID: PMC9062313 DOI: 10.1016/j.mec.2022.e00198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/01/2022] [Accepted: 04/20/2022] [Indexed: 11/21/2022] Open
Abstract
Pederin is a potent polyketide toxin that causes severe skin lesions in humans after contact with insects of genus Paederus. Due to its potent anticancer activities, pederin family compounds have raised the interest of pharmaceutical industry. Despite the extensive studies on the cluster of biosynthetic genes responsible for the production of pederin, it has not yet been possible to isolate and cultivate its bacterial endosymbiont producer. However, the marine bacterium Labrenzia sp. PHM005 was recently reported to produce labrenzin, the closest pederin analog. By cloning a synthetic pedO gene encoding one of the three O-methyltraferase of the pederin cluster into Labrenzia sp. PHM005 we have been able to produce pederin for the first time by fermentation in the new recombinant strain.
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Affiliation(s)
- Dina Kačar
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | | | - Pilar Rodríguez
- Research and Development Department, PharmaMar S.A, Madrid, Spain
| | | | - Carmen Cuevas
- Research and Development Department, PharmaMar S.A, Madrid, Spain
| | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José Luis García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Santos-Merino M, Gutiérrez-Lanza R, Nogales J, García JL, de la Cruz F. Synechococcus elongatus PCC 7942 as a Platform for Bioproduction of Omega-3 Fatty Acids. Life (Basel) 2022; 12:life12060810. [PMID: 35743841 PMCID: PMC9224711 DOI: 10.3390/life12060810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 12/22/2022] Open
Abstract
Alpha-linolenic acid and stearidonic acid are precursors of omega-3 polyunsaturated fatty acids, essential nutrients in the human diet. The ability of cyanobacteria to directly convert atmospheric carbon dioxide into bio-based compounds makes them promising microbial chassis to sustainably produce omega-3 fatty acids. However, their potential in this area remains unexploited, mainly due to important gaps in our knowledge of fatty acid synthesis pathways. To gain insight into the cyanobacterial fatty acid biosynthesis pathways, we analyzed two enzymes involved in the elongation cycle, FabG and FabZ, in Synechococcus elongatus PCC 7942. Overexpression of these two enzymes led to an increase in C18 fatty acids, key intermediates in omega-3 fatty acid production. Nevertheless, coexpression of these enzymes with desaturases DesA and DesB from Synechococcus sp. PCC 7002 did not improve alpha-linolenic acid production, possibly due to their limited role in fatty acid synthesis. In any case, efficient production of stearidonic acid was not achieved by cloning DesD from Synechocystis sp. PCC 6803 in combination with the aforementioned DesA and DesB, reaching maximum production at 48 h post induction. According to current knowledge, this is the first report demonstrating that S. elongatus PCC 7942 can be used as an autotrophic chassis to produce stearidonic acid.
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Affiliation(s)
- María Santos-Merino
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria—CSIC, 39011 Santander, Spain; (R.G.-L.); (F.d.l.C.)
- Correspondence:
| | - Raquel Gutiérrez-Lanza
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria—CSIC, 39011 Santander, Spain; (R.G.-L.); (F.d.l.C.)
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain;
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), 28040 Madrid, Spain;
| | - José Luis García
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), 28040 Madrid, Spain;
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria—CSIC, 39011 Santander, Spain; (R.G.-L.); (F.d.l.C.)
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Ameri R, García JL, Derenfed AB, Pradel N, Neifar S, Mhiri S, Mezghanni M, Jaouadi NZ, Barriuso J, Bejar S. Genome sequence and Carbohydrate Active Enzymes (CAZymes) repertoire of the thermophilic Caldicoprobacter algeriensis TH7C1 T. Microb Cell Fact 2022; 21:91. [PMID: 35598016 PMCID: PMC9124407 DOI: 10.1186/s12934-022-01818-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/05/2022] [Indexed: 12/31/2022] Open
Abstract
Background Omics approaches are widely applied in the field of biology for the discovery of potential CAZymes including whole genome sequencing. The aim of this study was to identify protein encoding genes including CAZymes in order to understand glycans-degrading machinery in the thermophilic Caldicoprobacter algeriensis TH7C1T strain. Results Caldicoprobacter algeriensis TH7C1T is a thermophilic anaerobic bacterium belonging to the Firmicutes phylum, which grows between the temperatures of 55 °C and 75 °C. Next generation sequencing using Illumina technology was performed on the C. algeriensis strain resulting in 45 contigs with an average GC content of 44.9% and a total length of 2,535,023 bp. Genome annotation reveals 2425 protein-coding genes with 97 ORFs coding CAZymes. Many glycoside hydrolases, carbohydrate esterases and glycosyltransferases genes were found linked to genes encoding oligosaccharide transporters and transcriptional regulators; suggesting that CAZyme encoding genes are organized in clusters involved in polysaccharides degradation and transport. In depth analysis of CAZomes content in C. algeriensis genome unveiled 33 CAZyme gene clusters uncovering new enzyme combinations targeting specific substrates. Conclusions This study is the first targeting CAZymes repertoire of C. algeriensis, it provides insight to the high potential of identified enzymes for plant biomass degradation and their biotechnological applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01818-0.
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Affiliation(s)
- Rihab Ameri
- Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules, Centre of Biotechnology of Sfax (CBS), University of Sfax, Sidi Mansour Road Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
| | - José Luis García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), C/ Ramiro de Maeztu 9, 28040, Madrid, Spain.,IBISBA_ES_CSIC_Cell Factory_MM, Madrid, Spain
| | - Amel Bouanane Derenfed
- Laboratoire de Biologie Cellulaire et Moléculaire (Équipe de Microbiologie), Université des Sciences et de la Technologie Houari Boumédiènne, Bab Ezzouar, Algiers, Algeria
| | - Nathalie Pradel
- Université de Toulon, CNRS, IRD, MIO, Aix Marseille Univ, Marseille, France
| | - Sawssan Neifar
- Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules, Centre of Biotechnology of Sfax (CBS), University of Sfax, Sidi Mansour Road Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Sonia Mhiri
- Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules, Centre of Biotechnology of Sfax (CBS), University of Sfax, Sidi Mansour Road Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Monia Mezghanni
- Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules, Centre of Biotechnology of Sfax (CBS), University of Sfax, Sidi Mansour Road Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Nadia Zaraî Jaouadi
- Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules, Centre of Biotechnology of Sfax (CBS), University of Sfax, Sidi Mansour Road Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Jorge Barriuso
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), C/ Ramiro de Maeztu 9, 28040, Madrid, Spain.,IBISBA_ES_CSIC_Cell Factory_MM, Madrid, Spain
| | - Samir Bejar
- Laboratory of Microbial Biotechnology, Enzymatic and Biomolecules, Centre of Biotechnology of Sfax (CBS), University of Sfax, Sidi Mansour Road Km 6, P.O. Box 1177, 3018, Sfax, Tunisia.
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Felpeto‐Santero C, Galán B, García JL. Production of 11α-hydroxysteroids from sterols in a single fermentation step by Mycolicibacterium smegmatis. Microb Biotechnol 2021; 14:2514-2524. [PMID: 33660943 PMCID: PMC8601193 DOI: 10.1111/1751-7915.13735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
11α-hydroxylated steroid synthons are one of the most important commercially pharmaceutical intermediates used for the production of contraceptive drugs and glucocorticoids. These compounds are currently produced by biotransformation using fungal strains in two sequential fermentation steps. In this work, we have developed by a rational design new recombinant bacteria able to produce 11α-hydroxylated synthons in a single fermentation step using cholesterol (CHO) or phytosterols (PHYTO) as feedstock. We have designed a synthetic operon expressing the 11α-hydroxylating enzymes from the fungus Rhizopus oryzae that was cloned into engineered mutant strains of Mycolicibacterium smegmatis that were previously created to produce 4-androstene-3,17-dione (AD), 1,4-androstadiene-3,17-dione (ADD) from sterols. The introduction of the fungal synthetic operon in these modified bacterial chassis has allowed producing for the first time 11αOH-AD and 11αOH-ADD with high yields directly from sterols in a single fermentation step. Remarkably, the enzymes of sterol catabolic pathway from M. smegmatis recognized the 11α-hydroxylated intermediates as alternative substrates and were able to efficiently funnel sterols to the desired hydroxylated end-products.
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Affiliation(s)
- Carmen Felpeto‐Santero
- Centro de Investigaciones Biológicas Margarita SalasAgencia del Consejo Superior de Investigaciones CientíficasMadridSpain
| | - Beatriz Galán
- Centro de Investigaciones Biológicas Margarita SalasAgencia del Consejo Superior de Investigaciones CientíficasMadridSpain
| | - José Luis García
- Centro de Investigaciones Biológicas Margarita SalasAgencia del Consejo Superior de Investigaciones CientíficasMadridSpain
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12
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Sotelo MJ, Luis García J, Torres-Mattos C, Milián H, Carracedo C, González-Ruiz MÁ, Mielgo-Rubio X, Trujillo-Reyes JC, Couñago F. Recent advances and new insights in the management of early-stage epidermal growth factor receptor-mutated non-small-cell lung cancer. World J Clin Oncol 2021; 12:912-925. [PMID: 34733613 PMCID: PMC8546659 DOI: 10.5306/wjco.v12.i10.912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/29/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
Patients with early-stage non-small-cell lung cancer (NSCLC) are candidates for curative surgery; however, despite multiple advances in lung cancer management, recurrence rates remain high. Adjuvant chemotherapy has been demonstrated to significantly prolong overall survival (OS), but this benefit is modest and there is an urgent need for effective new therapies to provide a cure for more patients. The high efficacy of tyrosine kinase inhibitors (TKIs) against epidermal growth factor receptor-mutated (EGFR) in patients with advanced EGFR-mutated NSCLC has led to the evaluation of these agents in early stages of the disease. Multiple clinical trials have evaluated the safety and efficacy of EGFR TKIs as an adjuvant treatment, in patients with resected EGFR-mutated NSCLC, and shown that they significantly prolong disease-free survival (DFS), but this benefit does not translate to OS. Recently, an interim analysis of the ADAURA trial demonstrated that, surprisingly, osimertinib improved DFS. This led to the study being stopped early, leaving many unanswered questions about its potential effect on OS and its incorporation as a standard adjuvant treatment in this patient subgroup. These targeted agents are also being evaluated in locally-advanced disease, with promising results, although prospective studies with larger sample sizes are needed to confirm these results. In this article, we review the most relevant studies on the role of EGFR TKIs in the management of early-stage EGFR-mutated NSCLC.
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Affiliation(s)
- Miguel J Sotelo
- Department of Medical Oncology, Hospital María Auxiliadora; Department of Medical Oncology, Centro Oncológico Aliada; Oncological Research Unit, Clínica San Gabriel, Lima 15801, Peru
| | - José Luis García
- Department of Thoracic Surgery, Hospital Universitario La Princesa; Department of Thoracic Surgery, MD Anderson Cancer Center; Department of Thoracic Surgery, Hospital HM, Madrid 28006, Spain
| | - Cesar Torres-Mattos
- Department of Medical Oncology, Hospital Nacional Guillermo Almenara; Oncological Research Unit, Clínica San Gabriel, Lima 15033, Peru
| | - Héctor Milián
- Department of Thoracic Surgery, Hospital Universitario La Princesa, Madrid 28006, Spain
| | - Carlos Carracedo
- Department of Medical Oncology, Centro Oncológico Aliada, Lima 15036, Peru
| | | | - Xabier Mielgo-Rubio
- Department of Oncology, Hospital Universitario Fundación Alcorcón, Alcorcón 28922, Madrid, Spain
| | | | - Felipe Couñago
- Department of Radiation Oncology, Hospital Universitario Quirónsalud Madrid; Hospital La Luz; Universidad Europea de Madrid, Madrid 28223, Spain
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13
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Felpeto-Santero C, Galán B, García JL. Engineering the Steroid Hydroxylating System from Cochliobolus lunatus in Mycolicibacterium smegmatis. Microorganisms 2021; 9:microorganisms9071499. [PMID: 34361934 PMCID: PMC8306143 DOI: 10.3390/microorganisms9071499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022] Open
Abstract
14α-hydroxylated steroids are starting materials for the synthesis of contraceptive and anti-inflammatory compounds in the steroid industry. A synthetic bacterial operon containing the cytochrome P450 CYP103168 and the reductase CPR64795 of the fungus Cochlioboluslunatus able to hydroxylate steroids has been engineered into a shuttle plasmid named pMVFAN. This plasmid was used to transform two mutants of Mycolicibacterium smegmatis named MS6039-5941 and MS6039 that accumulate 4-androstene-3,17-dione (AD), and 1,4-androstadiene-3,17-dione (ADD), respectively. The recombinant mutants MS6039-5941 (pMVFAN) and MS6039 (pMVFAN) were able to efficiently express the hydroxylating CYP system of C.lunatus and produced in high yields 14αOH-AD and 14αOH-ADD, respectively, directly from cholesterol and phytosterols in a single fermentation step. These results open a new avenue for producing at industrial scale these and other hydroxylated steroidal synthons by transforming with this synthetic operon other Mycolicibacterium strains currently used for the commercial production of steroidal synthons from phytosterols as feedstock.
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14
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Perdigones A, García I, Porras-Prieto CJ, Gómez-Villarino MT, Baptista F, García JL. Evaluation of the cost-effectiveness of grid-connected photovoltaic solar energy in wineries. Ciência Téc Vitiv 2021. [DOI: 10.1051/ctv/ctv2021360145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The objective of this study was to analyze the cost-effectiveness of photovoltaic (PV) solar energy in wineries. The factors analysed were solar radiation, cost of PV installation, prices in the public electricity grid, size of the winery, power of installed panels, influence of the decreased consumption during weekends, and seasonality in the consumption. The study has been based on the European TESLA project, in which 39 energy audits were carried out in wineries in four European countries. A winery of 30,000 hL/year was characterized as a representative winery. The results showed that seasonality was key in the profitability of the system for self-consumption, related to the optimum power to be installed of PV. It was recommended to install, as an optimal PV power, the stable electrical power that is demanded in the daytime period. Optimizing the installed power of PV panels in the representative winery, the percentage of electrical energy consumption covered by photovoltaic energy varied between 16% and 22%. The percentage of the cost of electric energy covered varied between 18% and 24%, with payback values between 18 years (3.1 peak sun hours of solar radiation -PSH) and 10 years (5.6 peak sun hours of solar radiation - PSH). All the factors involved were analyzed.
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15
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Fernández-López C, Posada-Baquero R, García JL, Castilla-Alcantara JC, Cantos M, Ortega-Calvo JJ. Root-mediated bacterial accessibility and cometabolism of pyrene in soil. Sci Total Environ 2021; 760:143408. [PMID: 33243519 DOI: 10.1016/j.scitotenv.2020.143408] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Partial transformation of pollutants and mobilization of the produced metabolites may contribute significantly to the risks resulting from biological treatment of soils polluted by hydrophobic chemicals such as polycyclic aromatic hydrocarbons (PAHs). Pyrene, a four-ringed PAH, was selected here as a model pollutant to study the effects of sunflower plants on the bacterial accessibility and cometabolism of this pollutant when located at a spatially distant source within soil. We compared the transformation of passively dosed 14C-labeled pyrene in soil slurries and planted pots that were inoculated with the bacterium Pseudomonas putida G7. This bacterium combines flagellar cell motility with the ability to cometabolically transform pyrene. Cometabolism of this PAH occurred immediately in the inoculated and shaken soil slurries, where the bacteria had full access to the passive dosing devices (silicone O-rings). Root exudates did not enhance the survival of P. putida G7 cells in soil slurries, but doubled their transport in column tests. In greenhouse-incubated soil pots with the same pyrene sources instead located centimeters from the soil surface, the inoculated bacteria transformed 14C-labeled pyrene only when the pots were planted with sunflowers. Bacterial inoculation caused mobilization of 14C-labeled pyrene metabolites into the leachates of the planted pots at concentrations of approximately 1 mg L-1, ten times greater than the water solubility of the parent compound. This mobilization resulted in a doubled specific root uptake rate of 14C-labeled pyrene equivalents and a significantly decreased root-to-fruit transfer rate. Our results show that the plants facilitated bacterial access to the distant pollutant source, possibly by increasing bacterial dispersal in the soil; this increased bacterial access was associated with cometabolism, which contributed to the risks of biodegradation.
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Affiliation(s)
- Carmen Fernández-López
- University Centre of Defense at the Spanish Air Force Academy, Santiago de la Ribera, Spain
| | - Rosa Posada-Baquero
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Seville, Spain
| | - José Luis García
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Seville, Spain
| | | | - Manuel Cantos
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Seville, Spain
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16
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Almeida PZD, Oliveira TBD, Lucas RCD, Salgado JCS, Pérez MM, Gálan B, García JL, Polizeli MDLTDM. Heterologous production and biochemical characterization of a new highly glucose tolerant GH1 β-glucosidase from Anoxybacillus thermarum. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Calaf J, Cancelo MJ, Andeyro M, Jiménez JM, Perelló J, Correa M, Parera N, Lete LI, Calvo A, Doval JL, Duarte R, García JL, Colomé C. Development and Psychometric Validation of a Screening Questionnaire to Detect Excessive Menstrual Blood Loss That Interferes in Quality of Life: The SAMANTA Questionnaire. J Womens Health (Larchmt) 2020; 29:1021-1031. [DOI: 10.1089/jwh.2018.7446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
| | | | | | | | | | - Marta Correa
- Hospital Universitario de Canarias, Tenerife, Spain
| | | | | | - Andrés Calvo
- Hospital Quirónsalud Palmaplanas, Mallorca, Spain
| | - José Luis Doval
- Complexo Hospitalario Universitario de Ourense, Orense, Spain
| | | | | | - Clara Colomé
- Clínica de Reproducción Asistida y Fertilidad, IVI, Mallorca, Spain
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18
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Calaf J, Cancelo MJ, Andeyro M, Jiménez JM, Perelló J, Correa M, Parera N, Lete LI, Calvo A, Doval JL, Duarte R, García JL, Colomé C. Development and Psychometric Validation of a Screening Questionnaire to Detect Excessive Menstrual Blood Loss That Interferes in Quality of Life: The SAMANTA Questionnaire. J Womens Health (Larchmt) 2020. [PMID: 32580622 DOI: 10.1089/jwh.2018.744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Background: Heavy menstrual bleeding (HMB) affects up to 35% of women at some point in their lives, and has an important impact on their quality of life (QoL). Current techniques to assess and quantify menstrual blood loss are inconvenient and the correlation between actual and perceived blood loss is poor. This study aimed to develop and validate a screening questionnaire in Spanish to identify HMB in women of reproductive age. Methods: The study consisted of two phases: the conceptual development of a set of items to discriminate between women with and without HMB and the assessment of the sensitivity and specificity of these items. Correlation of the screening tool with women's perception of the intensity of bleeding and the interference in their daily life activities was also assessed. Results: An initial set of 46 items were identified, from which 21 items were selected following the cognitive interviews. For the psychometric validation phase, 389 patients were enrolled, of whom 364 were assessable: 211 cases with Pictorial Blood loss Assessment Chart-confirmed excessive menstrual loss (EML) and 153 controls. Six items met entry criteria in the model and together yielded a sensitivity of 86.7% and specificity of 89.5% to identify cases and controls. These items were weighted according to their contribution to the final model to yield a tool that can be scored from 0 to 10 being 3 the cutoff point to diagnose EML that interferes in QoL. Conclusions: The 6-item SAMANTA questionnaire represents a valid screening tool to easily identify women with EML that interfere with QoL.
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Affiliation(s)
| | | | | | | | | | - Marta Correa
- Hospital Universitario de Canarias, Tenerife, Spain
| | | | | | - Andrés Calvo
- Hospital Quirónsalud Palmaplanas, Mallorca, Spain
| | - José Luis Doval
- Complexo Hospitalario Universitario de Ourense, Orense, Spain
| | | | | | - Clara Colomé
- Clínica de Reproducción Asistida y Fertilidad, IVI, Mallorca, Spain
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19
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Posada-Baquero R, Jiménez-Volkerink SN, García JL, Vila J, Cantos M, Grifoll M, Ortega-Calvo JJ. Rhizosphere-enhanced biosurfactant action on slowly desorbing PAHs in contaminated soil. Sci Total Environ 2020; 720:137608. [PMID: 32143055 DOI: 10.1016/j.scitotenv.2020.137608] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/22/2020] [Accepted: 02/26/2020] [Indexed: 04/15/2023]
Abstract
We studied how sunflower plants affect rhamnolipid biosurfactant mobilization of slowly desorbing fractions of polycyclic aromatic hydrocarbons (PAHs) in soil from a creosote-contaminated site. Desorption kinetics of 13 individual PAHs revealed that the soil contained initially up to 50% slowly desorbing fractions. A rhamnolipid biosurfactant was applied to the soil at the completion of the sunflower cycle (75 days in greenhouse conditions). After this period, the PAHs that remained in the soil were mainly present in a slowly desorbing form as a result of the efficient biodegradation of fast-desorbing PAHs by native microbial populations. The rhamnolipid enhanced the bioavailable fraction of the remaining PAHs by up to 30%, as evidenced by a standardized desorption extraction with Tenax, but the enhancement occurred with only planted soils. The enhanced bioavailability did not decrease residual PAH concentrations under greenhouse conditions, possibly due to ecophysiological limitations in the biodegradation process that were independent of the bioavailability. However, biodegradation was enhanced during slurry treatment of greenhouse planted soils that received the biosurfactant. The addition of rhamnolipids caused a dramatic shift in the soil bacterial community structure, which was magnified in the presence of sunflower plants. The stimulated groups were identified as fast-growing and catabolically versatile bacteria. This new rhizosphere microbial biomass possibly interacted with the biosurfactant to facilitate intra-aggregate diffusion of PAHs, thus enhancing the kinetics of slow desorption. Our results show that the usually limited biosurfactant efficiency with contaminated field soils can be significantly enhanced by integrating the sunflower ontogenetic cycle into the bioremediation design.
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Affiliation(s)
- Rosa Posada-Baquero
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Avenida Reina Mercedes, 10, Seville 41012, Spain
| | - Sara Nienke Jiménez-Volkerink
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | - José Luis García
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Avenida Reina Mercedes, 10, Seville 41012, Spain
| | - Joaquim Vila
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | - Manuel Cantos
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Avenida Reina Mercedes, 10, Seville 41012, Spain
| | - Magdalena Grifoll
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | - Jose Julio Ortega-Calvo
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Avenida Reina Mercedes, 10, Seville 41012, Spain.
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20
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Perea J, García JL, García-Olmo D, Urioste M, González-Sarmiento R. Comment on: Clinicopathological features and oncological outcomes of patients with young-onset rectal cancer. Br J Surg 2020; 107:e277. [PMID: 32424850 DOI: 10.1002/bjs.11678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 11/08/2022]
Affiliation(s)
- J Perea
- Surgery Department, Fundación Jiménez Díaz University Hospital, Madrid, Spain.,Fundación Jiménez Díaz Research Institute, Madrid, Spain
| | - J L García
- Molecular Medicine Unit, Biomedical Research Institute of Salamanca (IBSAL), Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-USAL-CSIC, Salamanca, Spain
| | - D García-Olmo
- Surgery Department, Fundación Jiménez Díaz University Hospital, Madrid, Spain.,Fundación Jiménez Díaz Research Institute, Madrid, Spain
| | - M Urioste
- Familial Cancer Clinical Unit, Spanish National Cancer Centre (CNIO), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain
| | - R González-Sarmiento
- Molecular Medicine Unit, Biomedical Research Institute of Salamanca (IBSAL), Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-USAL-CSIC, Salamanca, Spain
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21
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Kačar D, Schleissner C, Cañedo LM, Rodríguez P, de la Calle F, Galán B, García JL. Genome of Labrenzia sp. PHM005 Reveals a Complete and Active Trans-AT PKS Gene Cluster for the Biosynthesis of Labrenzin. Front Microbiol 2019; 10:2561. [PMID: 31787953 PMCID: PMC6855096 DOI: 10.3389/fmicb.2019.02561] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/23/2019] [Indexed: 11/28/2022] Open
Abstract
The complete genome of the strain Labrenzia sp. PHM005, a free-living producer of a pederin analog 18-O-demethyl pederin, hereinafter labrenzin, has been sequenced. This strain contains two replicons comprising a circular chromosome of 6,167,349 bp and a circular plasmid (named p1BIR) of 19,450 bp. A putative gene cluster responsible for the synthesis of labrenzin (lab cluster) has been identified showing that it encodes a trans-AT mixed type PKS/NRPS biosynthetic pathway that is responsible for the synthesis of pederin and possibly an onnamide analog. The putative boundaries of the lab gene cluster were determined by genetic comparisons with other related strains, suggesting that the cluster consists of a 79-kb region comprising 3 genes encoding multidomain hybrid polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) proteins (PKS4, PKS/NRPS13, and PKS/NRPS15), and 16 auxiliary enzymes. Transcriptomic analyses suggest that all the genes of the cluster are expressed in our culture conditions (i.e., in minimal medium in the absence of any specific inducer) at detectable levels. We have developed genetic tools to facilitate the manipulation of this strain and the functional characterization of the cluster genes. We have created a site-directed mutant unable to produce pederin, demonstrating experimentally for the first time the role of the cluster in the synthesis of pederin. This work paves the way to unravel the clues of the biosynthesis of pederin family compounds and opens the door to modify and overproduce these anticancer drugs for industrial and pharmaceutical purposes.
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Affiliation(s)
- Dina Kačar
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Librada M Cañedo
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | - Pilar Rodríguez
- Research and Development Department, PharmaMar S.A., Madrid, Spain
| | | | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José Luis García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Agencia Estatal Consejo Superior de Investigaciones Científicas, Madrid, Spain
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22
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Abstract
Motivation Synthetic microbial communities begin to be considered as promising multicellular biocatalysts having a large potential to replace engineered single strains in biotechnology applications, in pharmaceutical, chemical and living architecture sectors. In contrast to single strain engineering, the effective and high-throughput analysis and engineering of microbial consortia face the lack of knowledge, tools and well-defined workflows. This manuscript contributes to fill this important gap with a framework, called FLYCOP (FLexible sYnthetic Consortium OPtimization), which contributes to microbial consortia modeling and engineering, while improving the knowledge about how these communities work. FLYCOP selects the best consortium configuration to optimize a given goal, among multiple and diverse configurations, in a flexible way, taking temporal changes in metabolite concentrations into account. Results In contrast to previous systems optimizing microbial consortia, FLYCOP has novel characteristics to face up to new problems, to represent additional features and to analyze events influencing the consortia behavior. In this manuscript, FLYCOP optimizes a Synechococcus elongatus-Pseudomonas putida consortium to produce the maximum amount of bio-plastic (PHA, polyhydroxyalkanoate), and highlights the influence of metabolites exchange dynamics in a four auxotrophic Escherichia coli consortium with parallel growth. FLYCOP can also provide an explanation about biological evolution driving evolutionary engineering endeavors by describing why and how heterogeneous populations emerge from monoclonal ones. Availability and implementation Code reproducing the study cases described in this manuscript are available on-line: https://github.com/beatrizgj/FLYCOP. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Beatriz García-Jiménez
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - José Luis García
- Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas (CIB-CSIC), 28040 Madrid, Spain.,Applied System Biology and Synthetic Biology Department, Institute for Integrative Systems Biology (I2Sysbio-CSIC-UV), 46980 Paterna, Spain
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
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23
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Calvo-Polanco M, Ruiz-Lozano JM, Azcón R, Molina S, Beuzon CR, García JL, Cantos M, Aroca R. Phenotypic and molecular traits determine the tolerance of olive trees to drought stress. Plant Physiol Biochem 2019; 139:521-527. [PMID: 31015091 DOI: 10.1016/j.plaphy.2019.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/28/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Olive trees are known for their capacity to adapt to drought through several phenotypic and molecular variations, although this can vary according to the different provenances of the same olive cultivar. We confronted the same olive cultivar from two different location in Spain: Freila, in the Granada province, with low annual precipitation, and Grazalema, in the Cadiz province, with high annual precipitation, and subjected them to five weeks of severe drought stress. We found distinctive physiological and developmental adaptations among the two provenances. Thus, trees from Freila subjected to drought stress exhibited increasing root dry weights and decreasing leaf numbers and relative stem heights. On the other hand, the treatment with drought in Grazalema trees reduced their leaf chlorophyll contents, but increased their relative stem diameter and their root hydraulic conductivity. The physiological responses of Freila tree roots to drought were linked to different molecular adaptations that involved the regulation of genes related to transcription factors induced by ABA, auxin and ethylene signaling, as well as, the action of a predicted membrane intrinsic protein (MIP). On the other hand, the responses of Grazalema trees were related with different root genes related to oxidation-reduction, ATP synthesis, transduction and posttranslational regulation, with a special mention to the cytokinins signaling through the transcript predicted as a histidine-containing phosphotransfer protein. Our results show that olive trees adapted to dry environments will adjust their growth and water uptake capacity through transcription factors regulation, and this will influence the different physiological responses to drought stress.
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Affiliation(s)
- Mónica Calvo-Polanco
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain.
| | - Juan Manuel Ruiz-Lozano
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain
| | - Rosario Azcón
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain
| | - Sonia Molina
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain
| | - Carmen R Beuzon
- Department of Cellular Biology, Genetics and Physiology, Campus de Teatinos, University of Málaga, 29010, Málaga, Spain
| | - José Luis García
- Department of Cellular Biology, Genetics and Physiology, Campus de Teatinos, University of Málaga, 29010, Málaga, Spain
| | - Manuel Cantos
- Department of Plant Biotechnnology, Instituto de Recursos Naturales y Agrobiología (CSIC), Av. Reina Mercedes, 10 41012, Sevilla, Spain
| | - Ricardo Aroca
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain
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Borrero-Palacios A, Cebrián A, Gómez Del Pulgar MT, García-Carbonero R, Garcia-Alfonso P, Aranda E, Elez E, López-López R, Cervantes A, Valladares M, Nadal C, Viéitez JM, Guillén-Ponce C, Rodríguez J, Hernández I, García JL, Vega-Bravo R, Puime-Otin A, Martínez-Useros J, Del Puerto-Nevado L, Rincón R, Rodríguez-Remírez M, Rojo F, García-Foncillas J. Author Correction: Combination of KIR2DS4 and FcγRIIa polymorphisms predicts the response to cetuximab in KRAS mutant metastatic colorectal cancer. Sci Rep 2019; 9:7706. [PMID: 31097738 PMCID: PMC6522500 DOI: 10.1038/s41598-019-43809-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- A Borrero-Palacios
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - A Cebrián
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain.
| | - M T Gómez Del Pulgar
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | | | - P Garcia-Alfonso
- Medical Oncology Department, Hospital Gral. Univ. Gregorio Marañón, Madrid, Spain
| | - E Aranda
- Medical Oncology Department, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - E Elez
- Medical Oncology Department, Hospital Vall d'Hebrón, Barcelona, Spain
| | - R López-López
- Medical Oncology Department, Complexo Hospitalario Universitario Santiago de Compostela, Galicia, Spain
| | - A Cervantes
- Medical Oncology Department, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - M Valladares
- Medical Oncology Department, Complejo Hospitalario Universitario A Coruña, Galicia, Spain
| | - C Nadal
- Medical Oncology Department, Hospital Clínic i Provincial de Barcelona, Barcelona, Spain
| | - J M Viéitez
- Medical Oncology Department, Hospital Universitario Central de Asturias, Asturias, Spain
| | - C Guillén-Ponce
- Medical Oncology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - J Rodríguez
- Medical Oncology Department, Clínica Universitaria de Navarra, Navarra, Spain
| | - I Hernández
- Medical Oncology Department, Complejo Hospitalario de Navarra, Navarra, Spain
| | - J L García
- Oncology, Medical Unit, Merck S.L, an affiliate of Merck KGaA, Darmstadt, Germany
| | - R Vega-Bravo
- Anatomopathology Department, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - A Puime-Otin
- Anatomopathology Department, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - J Martínez-Useros
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - L Del Puerto-Nevado
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - R Rincón
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - M Rodríguez-Remírez
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - F Rojo
- Anatomopathology Department, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - J García-Foncillas
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain.
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25
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Borrero-Palacios A, Cebrián A, Gómez Del Pulgar MT, García-Carbonero R, Garcia-Alfonso P, Aranda E, Elez E, López-López R, Cervantes A, Valladares M, Nadal C, Viéitez JM, Guillén-Ponce C, Rodríguez J, Hernández I, García JL, Vega-Bravo R, Puime-Otin A, Martínez-Useros J, Del Puerto-Nevado L, Rincón R, Rodríguez-Remírez M, Rojo F, García-Foncillas J. Combination of KIR2DS4 and FcγRIIa polymorphisms predicts the response to cetuximab in KRAS mutant metastatic colorectal cancer. Sci Rep 2019; 9:2589. [PMID: 30796344 PMCID: PMC6385198 DOI: 10.1038/s41598-019-39291-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/13/2018] [Indexed: 12/20/2022] Open
Abstract
Cetuximab is a standard-of-care treatment for RAS wild-type metastatic colorectal cancer (mCRC) but not for those harbor a KRAS mutation since MAPK pathway is constitutively activated. Nevertheless, cetuximab also exerts its effect by its immunomodulatory activity despite the presence of RAS mutation. The aim of this study was to determine the impact of polymorphism FcγRIIIa V158F and killer immunoglobulin-like receptor (KIR) genes on the outcome of mCRC patients with KRAS mutations treated with cetuximab. This multicenter Phase II clinical trial included 70 mCRC patients with KRAS mutated. We found KIR2DS4 gene was significantly associated with OS (HR 2.27; 95% CI, 1.08–4.77; P = 0.03). In non-functional receptor homozygotes the median OS was 2.6 months longer than in carriers of one copy of full receptor. Multivariate analysis confirmed KIR2DS4 as a favorable prognostic marker for OS (HR 6.71) in mCRC patients with KRAS mutation treated with cetuximab. These data support the potential therapeutic of cetuximab in KRAS mutated mCRC carrying non-functional receptor KIR2DS4 since these patients significantly prolong their OS even after heavily treatment. KIR2DS4 typing could be used as predictive marker for identifying RAS mutated patients that could benefit from combination approaches of anti-EGFR monoclonal antibodies and other immunotherapies to overcome the resistance mediated by mutation in RAS.
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Affiliation(s)
- A Borrero-Palacios
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - A Cebrián
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain.
| | - M T Gómez Del Pulgar
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | | | - P Garcia-Alfonso
- Medical Oncology Department, Hospital Gral. Univ. Gregorio Marañón, Madrid, Spain
| | - E Aranda
- Medical Oncology Department, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - E Elez
- Medical Oncology Department, Hospital Vall d'Hebrón, Barcelona, Spain
| | - R López-López
- Medical Oncology Department, Complexo Hospitalario Universitario Santiago de Compostela, Galicia, Spain
| | - A Cervantes
- Medical Oncology Department, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - M Valladares
- Medical Oncology Department, Complejo Hospitalario Universitario A Coruña, Galicia, Spain
| | - C Nadal
- Medical Oncology Department, Hospital Clínic i Provincial de Barcelona, Barcelona, Spain
| | - J M Viéitez
- Medical Oncology Department, Hospital Universitario Central de Asturias, Asturias, Spain
| | - C Guillén-Ponce
- Medical Oncology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - J Rodríguez
- Medical Oncology Department, Clínica Universitaria de Navarra, Navarra, Spain
| | - I Hernández
- Medical Oncology Department, Complejo Hospitalario de Navarra, Navarra, Spain
| | - J L García
- Oncology, Medical Unit, Merck S.L, an affiliate of Merck KGaA, Darmstadt, Germany
| | - R Vega-Bravo
- Anatomopathology Department, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - A Puime-Otin
- Anatomopathology Department, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - J Martínez-Useros
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - L Del Puerto-Nevado
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - R Rincón
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - M Rodríguez-Remírez
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - F Rojo
- Anatomopathology Department, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain
| | - J García-Foncillas
- Translational Oncology Division, Oncohealth Institute, Hospital Universitario "Fundación Jimenez Diaz", Madrid, Spain.
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26
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Martínez I, El-Said Mohamed M, Santos VE, García JL, García-Ochoa F, Díaz E. Metabolic and process engineering for biodesulfurization in Gram-negative bacteria. J Biotechnol 2017; 262:47-55. [PMID: 28947364 DOI: 10.1016/j.jbiotec.2017.09.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/08/2017] [Accepted: 09/09/2017] [Indexed: 11/19/2022]
Abstract
Microbial desulfurization or biodesulfurization (BDS) is an attractive low-cost and environmentally friendly complementary technology to the hydrotreating chemical process based on the potential of certain bacteria to specifically remove sulfur from S-heterocyclic compounds of crude fuels that are recalcitrant to the chemical treatments. The 4S or Dsz sulfur specific pathway for dibenzothiophene (DBT) and alkyl-substituted DBTs, widely used as model S-heterocyclic compounds, has been extensively studied at the physiological, biochemical and genetic levels mainly in Gram-positive bacteria. Nevertheless, several Gram-negative bacteria have been also used in BDS because they are endowed with some properties, e.g., broad metabolic versatility and easy genetic and genomic manipulation, that make them suitable chassis for systems metabolic engineering strategies. A high number of recombinant bacteria, many of which are Pseudomonas strains, have been constructed to overcome the major bottlenecks of the desulfurization process, i.e., expression of the dsz operon, activity of the Dsz enzymes, retro-inhibition of the Dsz pathway, availability of reducing power, uptake-secretion of substrate and intermediates, tolerance to organic solvents and metals, and other host-specific limitations. However, to attain a BDS process with industrial applicability, it is necessary to apply all the knowledge and advances achieved at the genetic and metabolic levels to the process engineering level, i.e., kinetic modelling, scale-up of biphasic systems, enhancing mass transfer rates, biocatalyst separation, etc. The production of high-added value products derived from the organosulfur material present in oil can be regarded also as an economically viable process that has barely begun to be explored.
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Affiliation(s)
- I Martínez
- Environmental Biology Department, Biological Research Center (CIB-CSIC), 28040 Madrid, Spain
| | - M El-Said Mohamed
- Research and Development Center, Saudi Aramco, Dhahran, Saudi Arabia
| | - V E Santos
- Chemical Engineering Department, Complutense University of Madrid, 28040 Madrid Spain
| | - J L García
- Environmental Biology Department, Biological Research Center (CIB-CSIC), 28040 Madrid, Spain; Institute for Integrative Systems Biology (I2SysBio) (University of Valencia-CSIC), 46980 Paterna Valencia, Spain
| | - F García-Ochoa
- Chemical Engineering Department, Complutense University of Madrid, 28040 Madrid Spain
| | - E Díaz
- Environmental Biology Department, Biological Research Center (CIB-CSIC), 28040 Madrid, Spain.
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27
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Vela R, Mazarrón FR, Fuentes-Pila J, Baptista F, Silva LL, García JL. Improved energy efficiency in wineries using data from audits. Ciência Téc Vitiv 2017. [DOI: 10.1051/ctv/20173201062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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28
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Zamarro MT, Barragán MJL, Carmona M, García JL, Díaz E. Engineering a bzd cassette for the anaerobic bioconversion of aromatic compounds. Microb Biotechnol 2017; 10:1418-1425. [PMID: 28736925 PMCID: PMC5658619 DOI: 10.1111/1751-7915.12746] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 01/26/2023] Open
Abstract
Microorganisms able to degrade aromatic contaminants constitute potential valuable biocatalysts to deal with a significant reusable carbon fraction suitable for eco‐efficient valorization processes. Metabolic engineering of anaerobic pathways for degradation and recycling of aromatic compounds is an almost unexplored field. In this work, we present the construction of a functional bzd cassette encoding the benzoyl‐CoA central pathway for the anaerobic degradation of benzoate. The bzd cassette has been used to expand the ability of some denitrifying bacteria to use benzoate as sole carbon source under anaerobic conditions, and it paves the way for future pathway engineering of efficient anaerobic biodegraders of aromatic compounds whose degradation generates benzoyl‐CoA as central intermediate. Moreover, a recombinant Azoarcus sp. CIB strain harbouring the bzd cassette was shown to behave as a valuable biocatalyst for anaerobic toluene valorization towards the synthesis of poly‐3‐hydroxybutyrate (PHB), a biodegradable and biocompatible polyester of increasing biotechnological interest as a sustainable alternative to classical oil‐derived polymers.
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Affiliation(s)
- María Teresa Zamarro
- Centro de Investigaciones Biológicas, CSIC, C/Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - María J L Barragán
- Centro de Investigaciones Biológicas, CSIC, C/Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Manuel Carmona
- Centro de Investigaciones Biológicas, CSIC, C/Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - José Luis García
- Centro de Investigaciones Biológicas, CSIC, C/Ramiro de Maeztu, 9, 28040, Madrid, Spain
| | - Eduardo Díaz
- Centro de Investigaciones Biológicas, CSIC, C/Ramiro de Maeztu, 9, 28040, Madrid, Spain
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29
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Cañueto J, Cardeñoso E, García JL, Santos-Briz Á, Castellanos-Martín A, Fernández-López E, Blanco Gómez A, Pérez-Losada J, Román-Curto C. Epidermal growth factor receptor expression is associated with poor outcome in cutaneous squamous cell carcinoma. Br J Dermatol 2017; 176:1279-1287. [PMID: 27510450 DOI: 10.1111/bjd.14936] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND Cutaneous squamous cell carcinoma (CSCC) is the second most frequent cancer in humans after basal cell carcinoma, and its incidence is dramatically rising. CSCC is rarely problematic, but given its high frequency, the absolute number of complicated cases is also high. It is necessary to identify molecular markers in order to recognize those CSCCs with poor prognosis. There is controversy concerning the role of epidermal growth factor receptor (EGFR) as a marker of prognosis in CSCC. In addition, EGFR-targeted therapies have emerged in recent years and a better understanding of the role of EGFR in CSCC may be of help for some patients in predicting prognosis and guiding curative management. OBJECTIVES To evaluate the role of EGFR as a prognostic factor in CSCC. METHODS We evaluated clinical and histopathological features, including events of poor clinical evolution, in a series of 94 cases of CSCC. We also analysed EGFR expression by immunohistochemistry, fluorescent in situ hybridization and quantitative polymerase chain reaction. RESULTS We detected EGFR in 85 cases (90%), with overexpression in 33 cases (35%), and aberrant EGFR expression in the cytoplasm in 50 cases (53%). EGFR overexpression in the primary tumours was associated with lymph node progression, tumour-nodes-metastasis stage progression and proliferation (Ki-67 staining) in CSCC. EGFR overexpression and poor grade of differentiation were the strongest independent variables defining lymph node metastasis and progression in CSCC in a logistic regression model. CONCLUSIONS We demonstrate that EGFR overexpression has prognostic implications associated with lymph node metastasis and progression in CSCC.
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Affiliation(s)
- J Cañueto
- Departamento de Dermatología, Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
| | - E Cardeñoso
- Departamento de Dermatología, Hospital Virgen de la Concha, Avenida de Requejo, Zamora, Spain
| | - J L García
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca/CSIC, Campus Miguel de Unamuno, s/n. 37007, Salamanca, Spain
| | - Á Santos-Briz
- Departamento de Dermatología, Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
| | - A Castellanos-Martín
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca/CSIC, Campus Miguel de Unamuno, s/n. 37007, Salamanca, Spain
| | - E Fernández-López
- Departamento de Dermatología, Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
| | - A Blanco Gómez
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca/CSIC, Campus Miguel de Unamuno, s/n. 37007, Salamanca, Spain
| | - J Pérez-Losada
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca/CSIC, Campus Miguel de Unamuno, s/n. 37007, Salamanca, Spain
| | - C Román-Curto
- Departamento de Dermatología, Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
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30
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Cantos M, Arroyo-García R, García JL, Lara M, Morales R, López MÁ, Gallardo A, Ocete CA, Rodríguez Á, Valle JM, Vaca R, González-Maestro M, Bánáti H, Ocete R. Current distribution and characterization of the wild grapevine populations in Andalusia (Spain). C R Biol 2017; 340:164-177. [PMID: 28256414 DOI: 10.1016/j.crvi.2017.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 10/20/2022]
Abstract
For decades, human activities have gradually destroyed the natural habitats of wild grapevine, Vitis vinifera L. subsp. sylvestris (Gmelin) Hegi, and nowadays this species is endangered in southern Europe. In this paper, 94 populations of this species have been localized and characterized in the Andalusian region in the Iberian Peninsula between 1989 and 2013. Location, ecological aspects, and sanitary characteristics are described. Must properties and in vitro tolerance to calcareous conditions were also checked. The paper also contains a global description of female and male individuals. Two hundred individuals from six river basin populations have been sampled, and their genetic structure analyzed by using 25 nuclear microsatellites loci to investigate the gene diversity of wild grape populations in Andalusia at two levels: total individuals and at river basin populations. Also, the genetic relationship of wild and cultivated accessions has been tested. Wild grapevine is considered the ancestor of the cultivated varieties and should be preserved as this material could be used to start breeding programs of cultivated varieties and also to restore riverbank forests, which constitute one of the worst preserved ecosystems in the area.
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Affiliation(s)
- Manuel Cantos
- Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC), avenue Reina Mercedes 10, 41012 Sevilla, Spain.
| | - Rosa Arroyo-García
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - José Luis García
- Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC), avenue Reina Mercedes 10, 41012 Sevilla, Spain
| | - Miguel Lara
- IFAPA Rancho de la Merced, Ctra. de Trebujena km. 3.2, 11431 Jerez de la Frontera, Cádiz, Spain
| | - Ramón Morales
- Real Jardín Botánico (CSIC), Plaza de Murillo 2, 28014 Madrid, Spain
| | - María Ángeles López
- Laboratorio Entomología Aplicada, Universidad de Sevilla, avenue Reina Mercedes 6, 41012 Sevilla, Spain
| | - Antonio Gallardo
- Laboratorio Entomología Aplicada, Universidad de Sevilla, avenue Reina Mercedes 6, 41012 Sevilla, Spain
| | - Carlos Alvar Ocete
- Laboratorio Entomología Aplicada, Universidad de Sevilla, avenue Reina Mercedes 6, 41012 Sevilla, Spain
| | - Álvaro Rodríguez
- Escuela Universitaria de Ingeniería, Universidad del País Vasco, Vitoria-Gasteiz, Spain
| | - José Manuel Valle
- Escuela Universitaria de Ingeniería, Universidad del País Vasco, Vitoria-Gasteiz, Spain
| | - Ramón Vaca
- Macià Batle Wineries, 07320 Santa María del Camí, Illes Balears, Spain
| | - Magdalena González-Maestro
- Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC), avenue Reina Mercedes 10, 41012 Sevilla, Spain
| | - Hajnalka Bánáti
- Department of Ecotoxicology, Central Environmental and Food Science Research Institute, Herman Ottó út 15, 1022 Budapest, Hungary
| | - Rafael Ocete
- Laboratorio Entomología Aplicada, Universidad de Sevilla, avenue Reina Mercedes 6, 41012 Sevilla, Spain
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31
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Wallach JC, García JL, Cardinali PS, Seijo AP, Benchetrit AG, Echazarreta SE, Garro SL, Deodato B, Baldi PC. High Incidence of Respiratory Involvement in a Cluster of Brucella suis-Infected Workers from a Pork Processing Plant in Argentina. Zoonoses Public Health 2016; 64:550-553. [PMID: 28032696 DOI: 10.1111/zph.12339] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 11/27/2022]
Abstract
Epidemiological and clinical aspects of Brucella suis infection in 17 workers from a pork processing plant in Argentina occurring between January 2014 and July 2015 are presented. All patients reported working 9 h daily without adequate personal protection garment. Blood cultures were positive for Brucella spp. in 14 of the 17 patients (82.3%). All isolates were identified as B. suis biovar 1. Although fever, sweats, asthenia, myalgia and hepatic involvement were the most frequent clinical manifestations, an unusually high incidence of respiratory involvement was found. From 13 patients in which chest radiography was performed, four (30%) had radiological abnormalities, including lobar pneumonia in two cases (one with pleural effusion) and interstitial involvement in other two. The high frequency of respiratory involvement in our series makes necessary to consider brucellosis in the differential diagnosis of respiratory diseases in pork processing plant employees.
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Affiliation(s)
- J C Wallach
- 'Francisco J. Muñiz' Hospital, Buenos Aires, Argentina
| | - J L García
- 'Francisco J. Muñiz' Hospital, Buenos Aires, Argentina
| | - P S Cardinali
- 'Francisco J. Muñiz' Hospital, Buenos Aires, Argentina
| | - A P Seijo
- 'Francisco J. Muñiz' Hospital, Buenos Aires, Argentina
| | | | | | - S L Garro
- 'Francisco J. Muñiz' Hospital, Buenos Aires, Argentina
| | - B Deodato
- 'Francisco J. Muñiz' Hospital, Buenos Aires, Argentina
| | - P C Baldi
- Instituto de Estudios de la Inmunidad Humoral (IDEHU, CONICET-UBA), Buenos Aires, Argentina
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32
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Calvo-Polanco M, Sánchez-Castro I, Cantos M, García JL, Azcón R, Ruiz-Lozano JM, Beuzón CR, Aroca R. Effects of different arbuscular mycorrhizal fungal backgrounds and soils on olive plants growth and water relation properties under well-watered and drought conditions. Plant Cell Environ 2016; 39:2498-2514. [PMID: 27448529 DOI: 10.1111/pce.12807] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 05/21/2023]
Abstract
The adaptation capacity of olive trees to different environments is well recognized. However, the presence of microorganisms in the soil is also a key factor in the response of these trees to drought. The objective of the present study was to elucidate the effects of different arbuscular mycorrhizal (AM) fungi coming from diverse soils on olive plant growth and water relations. Olive plants were inoculated with native AM fungal populations from two contrasting environments, that is, semi-arid - Freila (FL) and humid - Grazalema (GZ) regions, and subjected to drought stress. Results showed that plants grew better on GZ soil inoculated with GZ fungi, indicating a preference of AM fungi for their corresponding soil. Furthermore, under these conditions, the highest AM fungal diversity was found. However, the highest root hydraulic conductivity (Lpr ) value was achieved by plants inoculated with GZ fungi and growing in FL soil under drought conditions. So, this AM inoculum also functioned in soils from different origins. Nine novel aquaporin genes were also cloned from olive roots. Diverse correlation and association values were found among different aquaporin expressions and abundances and Lpr , indicating how the interaction of different aquaporins may render diverse Lpr values.
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Affiliation(s)
- Monica Calvo-Polanco
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda, Granada, 18008, Spain
- Biochimie et Physiologie Moléculaire des Plantes, SupAgro/INRA UMR 5004. 2, Place Viala, Montpellier, Cedex 2 34060, France
| | - Iván Sánchez-Castro
- Department of Microbiology, University of Granada, Av. Fuentenueva s/n, Granada, 18071, Spain
| | - Manuel Cantos
- Department of Plant Biotechnology, Instituto de Recursos Naturales y Agrobiología (CSIC), Av. Reina Mercedes, 10, Sevilla, 41012, Spain
| | - José Luis García
- Department of Plant Biotechnology, Instituto de Recursos Naturales y Agrobiología (CSIC), Av. Reina Mercedes, 10, Sevilla, 41012, Spain
| | - Rosario Azcón
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda, Granada, 18008, Spain
| | - Juan Manuel Ruiz-Lozano
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda, Granada, 18008, Spain
| | - Carmen R Beuzón
- Department of Cellular Biology, Genetics and Physiology, Campus de Teatinos, University of Málaga, Málaga, 29010, Spain
| | - Ricardo Aroca
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda, Granada, 18008, Spain.
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Fernández-Cabezón L, García-Fernández E, Galán B, García JL. Identification of a new gene cluster for steroid degradation in Mycobacterium smegmatis. N Biotechnol 2016. [DOI: 10.1016/j.nbt.2016.06.1175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Figueras A, Robledo D, Corvelo A, Hermida M, Pereiro P, Rubiolo JA, Gómez-Garrido J, Carreté L, Bello X, Gut M, Gut IG, Marcet-Houben M, Forn-Cuní G, Galán B, García JL, Abal-Fabeiro JL, Pardo BG, Taboada X, Fernández C, Vlasova A, Hermoso-Pulido A, Guigó R, Álvarez-Dios JA, Gómez-Tato A, Viñas A, Maside X, Gabaldón T, Novoa B, Bouza C, Alioto T, Martínez P. Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life. DNA Res 2016; 23:181-92. [PMID: 26951068 PMCID: PMC4909306 DOI: 10.1093/dnares/dsw007] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/03/2016] [Indexed: 01/25/2023] Open
Abstract
The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish. We compare the turbot genome with model fish genomes to investigate teleost chromosome evolution. We observe a conserved macrosyntenic pattern within Percomorpha and identify large syntenic blocks within the turbot genome related to the teleost genome duplication. We identify gene family expansions and positive selection of genes associated with vision and metabolism of membrane lipids, which suggests adaptation to demersal lifestyle and to cold temperatures, respectively. Our data indicate a quick evolution and diversification of flatfish to adapt to benthic life and provide clues for understanding their controversial origin. Moreover, we investigate the genomic architecture of growth, sex determination and disease resistance, key traits for understanding local adaptation and boosting turbot production, by mapping candidate genes and previously reported quantitative trait loci. The genomic architecture of these productive traits has allowed the identification of candidate genes and enriched pathways that may represent useful information for future marker-assisted selection in turbot.
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Affiliation(s)
- Antonio Figueras
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Diego Robledo
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - André Corvelo
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, USA
| | - Miguel Hermida
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Patricia Pereiro
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Juan A Rubiolo
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Jèssica Gómez-Garrido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Laia Carreté
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Xabier Bello
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain Xenómica Comparada de Parasitos Humanos, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela 15706, Spain
| | - Marta Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Ivo Glynne Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Marina Marcet-Houben
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Gabriel Forn-Cuní
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Beatriz Galán
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - José Luis García
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - José Luis Abal-Fabeiro
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain Xenómica Comparada de Parasitos Humanos, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela 15706, Spain
| | - Belen G Pardo
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Xoana Taboada
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Carlos Fernández
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Anna Vlasova
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Antonio Hermoso-Pulido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Roderic Guigó
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - José Antonio Álvarez-Dios
- Departamento de Matemática Aplicada, Facultade de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Antonio Gómez-Tato
- Departamento de Xeometría e Topoloxía, Facultade de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ana Viñas
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Xulio Maside
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain Xenómica Comparada de Parasitos Humanos, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela 15706, Spain
| | - Toni Gabaldón
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Carmen Bouza
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Tyler Alioto
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Paulino Martínez
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
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Martínez I, Mohamed MES, Rozas D, García JL, Díaz E. Engineering synthetic bacterial consortia for enhanced desulfurization and revalorization of oil sulfur compounds. Metab Eng 2016; 35:46-54. [PMID: 26802977 DOI: 10.1016/j.ymben.2016.01.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/27/2015] [Accepted: 01/11/2016] [Indexed: 01/04/2023]
Abstract
The 4S pathway is the most studied bioprocess for the removal of the recalcitrant sulfur of aromatic heterocycles present in fuels. It consists of three sequential functional units, encoded by the dszABCD genes, through which the model compound dibenzothiophene (DBT) is transformed into the sulfur-free 2-hydroxybiphenyl (2HBP) molecule. In this work, a set of synthetic dsz cassettes were implanted in Pseudomonas putida KT2440, a model bacterial "chassis" for metabolic engineering studies. The complete dszB1A1C1-D1 cassette behaved as an attractive alternative - to the previously constructed recombinant dsz cassettes - for the conversion of DBT into 2HBP. Refactoring the 4S pathway by the use of synthetic dsz modules encoding individual 4S pathway reactions revealed unanticipated traits, e.g., the 4S intermediate 2HBP-sulfinate (HBPS) behaves as an inhibitor of the Dsz monooxygenases, and once secreted from the cells it cannot be further taken up. That issue should be addressed for the rational design of more efficient biocatalysts for DBT bioconversions. In this sense, the construction of synthetic bacterial consortia to compartmentalize the 4S pathway into different cell factories for individual optimization was shown to enhance the conversion of DBT into 2HBP, overcome the inhibition of the Dsz enzymes by the 4S intermediates, and enable efficient production of unattainable high added value intermediates, e.g., HBPS, that are difficult to obtain using the current monocultures.
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Affiliation(s)
- Igor Martínez
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | | | - Daniel Rozas
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - José Luis García
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain.
| | - Eduardo Díaz
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain.
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Revelles O, Tarazona N, García JL, Prieto MA. Carbon roadmap from syngas to polyhydroxyalkanoates in Rhodospirillum rubrum. Environ Microbiol 2015; 18:708-20. [PMID: 26472698 DOI: 10.1111/1462-2920.13087] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/11/2015] [Indexed: 11/30/2022]
Abstract
The gasification of organic waste materials to synthesis gas (syngas), followed by microbial fermentation, provides a significant resource for generating bioproducts such as polyhydroxyalkanoates (PHA). The anaerobic photosynthetic bacterium, Rhodospirillum rubrum, is an organism particularly attractive for the bioconversion of syngas into PHAs. In this study, a quantitative physiological analysis of R. rubrum was carried out by implementing GC-MS and HPLC techniques to unravel the metabolic pathway operating during syngas fermentation that leads to PHA production. Further, detailed investigations of the central carbon metabolites using (13) C-labelled substrate showed significant CO2 assimilation (of 40%) into cell material and PHA from syngas carbon fraction. By a combination of quantitative gene expression and enzyme activity analyses, the main role of carboxylases from the central carbon metabolism in CO2 assimilation was shown, where the Calvin-Benson-Bassham cycle (CBB) played a minor role. This knowledge sheds light about the biochemical pathways that contribute to synthesis of PHA during syngas fermentation being valuable information to further optimize the fermentation process.
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Affiliation(s)
- O Revelles
- Department of Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040, Madrid, Spain
| | - N Tarazona
- Department of Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040, Madrid, Spain
| | - J L García
- Department of Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040, Madrid, Spain
| | - M A Prieto
- Department of Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040, Madrid, Spain
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Martín-Moldes Z, Zamarro MT, del Cerro C, Valencia A, Gómez MJ, Arcas A, Udaondo Z, García JL, Nogales J, Carmona M, Díaz E. Whole-genome analysis of Azoarcus sp. strain CIB provides genetic insights to its different lifestyles and predicts novel metabolic features. Syst Appl Microbiol 2015; 38:462-71. [DOI: 10.1016/j.syapm.2015.07.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/29/2015] [Accepted: 07/06/2015] [Indexed: 11/25/2022]
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Lallana E, Mañes M, Rubio B, Vázquez MJ, García JL, Segura M. PS-065 Analysis of medicines errors made in a general hospital. Eur J Hosp Pharm 2015. [DOI: 10.1136/ejhpharm-2015-000639.390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Cambrollé J, García JL, Figueroa ME, Cantos M. Evaluating wild grapevine tolerance to copper toxicity. Chemosphere 2015; 120:171-178. [PMID: 25025740 DOI: 10.1016/j.chemosphere.2014.06.044] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/14/2014] [Indexed: 06/03/2023]
Abstract
We evaluate copper tolerance and accumulation in Vitis vinifera ssp. sylvestris in populations from a copper contaminated site and an uncontaminated site, and in the grapevine rootstock "41B", investigating the effects of copper (0-23 mM) on growth, photosynthetic performance and mineral nutrient content. The highest Cu treatment induced nutrient imbalances and inhibited photosynthetic function, causing a drastic reduction in growth in the three study plants. Effective concentration was higher than 23 mM Cu in the wild grapevines and around 9 mM in the "41B" plants. The wild grapevine accessions studied controlled root Cu concentration more efficiently than is the case with the "41B" rootstock and must be considered Cu-tolerant. Wild grapevines from the Cu-contaminated site present certain physiological characteristics that make them relatively more suitable for exploitation in the genetic improvement of vines against conditions of excess Cu, compared to wild grapevine populations from uncontaminated sites.
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Affiliation(s)
- J Cambrollé
- Facultad de Biología, Universidad de Sevilla, P.O. Box 1095, 41080 Sevilla, Spain.
| | - J L García
- Instituto de Recursos Naturales y Agrobiología de Sevilla (C.S.I.C.), P.O. Box 1052, 41080 Sevilla, Spain
| | - M E Figueroa
- Facultad de Biología, Universidad de Sevilla, P.O. Box 1095, 41080 Sevilla, Spain
| | - M Cantos
- Instituto de Recursos Naturales y Agrobiología de Sevilla (C.S.I.C.), P.O. Box 1052, 41080 Sevilla, Spain
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40
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Singh V, Perdigones A, García JL, Cañas-Guerrero I, Mazarrón FR. Analysis of worldwide research in the field of cybernetics during 1997-2011. Biol Cybern 2014; 108:757-776. [PMID: 25008075 DOI: 10.1007/s00422-014-0617-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 06/17/2014] [Indexed: 06/03/2023]
Abstract
The study provides an overview of the research activity carried out in the field of cybernetics. To do so, all research papers from 1997 to 2011 (16,445 research papers) under the category of "Computer Science, Cybernetics" of Web of Science have been processed using our in-house software which is developed specifically for this purpose. Among its multiple capabilities, this software analyses individual and compound keywords, quantifies productivity taking into account the work distribution, estimates the impact of each article and determines the collaborations established at different scales. Keywords analysis identifies the evolution of the most important research topics in the field of cybernetics and their specificity in biological aspects, as well as the research topics with lesser interest. The analysis of productivity, impact and collaborations provides a framework to assess research activity in a specific and realistic context. The geographical and institutional distribution of publications reveals the leading countries and research centres, analysing their relation to main research journals. Moreover, collaborations analysis reveals great differences in terms of internationalization and complexity of research networks. The results of this study may be very useful for the characterization and the decisions made by research in the field of cybernetics.
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García-Fernández E, Medrano FJ, Galán B, García JL. Deciphering the transcriptional regulation of cholesterol catabolic pathway in mycobacteria: identification of the inducer of KstR repressor. J Biol Chem 2014; 289:17576-88. [PMID: 24802756 PMCID: PMC4067193 DOI: 10.1074/jbc.m113.545715] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 05/02/2014] [Indexed: 11/06/2022] Open
Abstract
Cholesterol degradation plays a prominent role in Mycobacterium tuberculosis infection; therefore, to develop new tools to combat this disease, we need to decipher the components comprising and regulating the corresponding pathway. A TetR-like repressor (KstR) regulates the upper part of this complex catabolic pathway, but the induction mechanism remains unknown. Using a biophysical approach, we have discovered that the inducer molecule of KstR in M. smegmatis mc(2)155 is not cholesterol but 3-oxo-4-cholestenoic acid, one of the first metabolic intermediates. Binding this compound induces dramatic conformational changes in KstR that promote the KstR-DNA interaction to be released from the operator, retaining its dimeric state. Our findings suggest a regulatory model common to all cholesterol degrading bacteria in which the first steps of the pathway are critical to its mineralization and explain the high redundancy of the enzymes involved in these initial steps.
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Affiliation(s)
| | - Francisco Javier Medrano
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
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Fernández C, Díaz E, García JL. Insights on the regulation of the phenylacetate degradation pathway from Escherichia coli. Environ Microbiol Rep 2014; 6:239-250. [PMID: 24983528 DOI: 10.1111/1758-2229.12117] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 10/16/2013] [Indexed: 06/03/2023]
Abstract
The paa genes for phenylacetic acid (PA) catabolism encode the best characterized aerobic hybrid route involved in the bacterial degradation of aromatic compounds. Here, we demonstrate that the divergent paaZ and paaA-K catabolic operons of Escherichia coli are regulated by two genes, paaXY, that form a distinct transcriptional unit driven by the Px promoter. In vivo and in vitro approaches using purified PaaX regulatory protein revealed that this regulator is able to bind and inhibit the activity of Px in a phenylacetyl-coenzyme A (PA-CoA) dependent manner. The autoregulation of paaXY is due to the competition between PaaX and RNA polymerase for binding to the regulatory Px promoter. Whereas a similar mechanism of repression mediated by PaaX was shown to occur at the catabolic Pz promoter; the catabolic Pa promoter is inhibited by PaaX by a mechanism that does not involves competition with RNA polymerase. We have shown for the first time that the paaY gene product is essential for an efficient growth in PA. Purified PaaY was shown to be a trimer in solution with a broad thioesterase activity stimulated by some metals. This thioesterase activity will allow the detoxification of some CoA-intermediates that block the aerobic catabolism of PA, as previously suggested, but also will avoid the accumulation of some CoA derivatives that could behave as antagonists of the inducer effect caused by PA-CoA on the PaaX repressor for an efficient expression of the paa genes. This regulatory function mediated by PaaY constitutes an additional regulatory checkpoint that makes the circuit that controls the transcription of the paa genes more complex than previously thought, and it could represent a general strategy present in most bacterial paa gene clusters that also harbour the paaY gene.
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Affiliation(s)
- Cristina Fernández
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
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Alvarez RM, Rodríguez B, Romano JM, Díaz AO, Gómez E, Miró D, Navarro L, Saura G, García JL. Lipid accumulation inRhodotorula glutinis on sugar cane molasses in single-stage continuous culture. World J Microbiol Biotechnol 2014; 8:214-5. [PMID: 24425415 DOI: 10.1007/bf01195853] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/1991] [Accepted: 08/24/1991] [Indexed: 11/24/2022]
Abstract
Microbial lipids produced byRhodotorula glutinis grown in continuous culture with molasses under nitrogen-limiting conditions were evaluated and the effects of growth rate on fatty acid composition were studied. As the growth rate decreased, cell biomass, lipid content and lipid yield gradually increased. The maximum lipid content recorded was 39% (w/w) of dry cell biomass at a dilution rate of 0.04 h(-1). The growth rate also affected fatty acid composition: oleic acid decreased with decreasing growth rate while stearic acid increased.
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Affiliation(s)
- R M Alvarez
- Instituto Cubano de Investigaciones de los Derivados de la Caña de Azúcar, Apartado 4026, CUBA-10, C. Habana, Cuba
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Cambrollé J, García JL, Ocete R, Figueroa ME, Cantos M. Growth and photosynthetic responses to copper in wild grapevine. Chemosphere 2013; 93:294-301. [PMID: 23746388 DOI: 10.1016/j.chemosphere.2013.04.080] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/20/2013] [Accepted: 04/27/2013] [Indexed: 06/02/2023]
Abstract
The present study evaluates the tolerance and accumulation potential of Vitis vinifera ssp. sylvestris under moderate and high external Cu levels. A greenhouse experiment was conducted in order to investigate the effects of a range of external Cu concentrations (0-23mmolL(-1)) on growth and photosynthetic performance by measuring gas exchange, chlorophyll fluorescence parameters and photosynthetic pigments. We also measured the total copper, nitrogen, phosphorus, sulphur, calcium, magnesium, iron, potassium and sodium concentrations in the plant tissues. All the experimental plants survived even with external Cu concentrations as high as 23mmolL(-1) (1500mg Cu L(-1)), although the excess of metal resulted in a biomass reduction of 35%. The effects of Cu on growth were linked to a reduction in net photosynthesis, which may be related to the effect of the high concentration of the metal on photosynthetic electron transport. V. vinifera ssp. sylvestris survived with leaf Cu concentrations as high as 80mgkg(-1) DW and growth parameters were unaffected by leaf tissue concentrations of 35mg Cu kg(-1) DW. The results of our study indicate that plants of V. vinifera ssp. sylvestris from the studied population are more tolerant to Cu than the commercial varieties of grapevine that have been studied in the literature, and could constitute a basis for the genetic improvement of Cu tolerance in grapevine.
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Affiliation(s)
- J Cambrollé
- Instituto de Recursos Naturales y Agrobiología de Sevilla (C.S.I.C.), P.O. Box 1052, 41080 Sevilla, Spain.
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Cimbollek S, Plaza V, Quirce S, Costa R, Urrutia I, Ojeda P, García JL, Sabadell C, Blanco M, Rosado A, Roura P. Knowledge, attitude and adherence of Spanish healthcare professionals to asthma management recommendations during pregnancy. Allergol Immunopathol (Madr) 2013; 41:114-20. [PMID: 22340959 DOI: 10.1016/j.aller.2011.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 09/22/2011] [Indexed: 11/17/2022]
Abstract
BACKGROUND The aim of the present study was to evaluate the knowledge, attitude and adherence to asthma management recommendations during pregnancy of Spanish health care professionals. METHODS A multiple choice survey with 14 questions was designed. Items assessed opinion about asthma guidelines and attitudes towards treatment, spirometry, specific immunotherapy and labour in pregnant asthmatic patients. Test completion was voluntary, individual, and anonymous. RESULTS A total of 1000 questionnaires were fulfilled: respiratory medicine specialists (19.8%); allergy specialists (17.2%); primary care physicians (46.1%); and gynaecologists/obstetricians (16.9%). Guidelines were considered useful by 96.5% although 64% admitted that they followed them seldom or never. Most physicians (55.9%) answered that they would maintain asthma therapy in clinically stable patients. Almost 30% of physicians would not perform spirometry in pregnant asthma patients. 19% declared they would interrupt specific immunotherapy which had proven safe and effective. Univariate analysis revealed low adherence to be associated with the following variables: age, primary care or gynaecology/obstetrician specialisation, number of asthmatics attended per month, and declared use of guidelines for pregnant asthmatic patients. Multivariate analysis showed that being a primary care physician and a gynaecologist/obstetrician, attending a low number of asthma patients per month, and poor use of spirometry during pregnancy are associated to low adherence to asthma guidelines. CONCLUSION Even though the majority of Spanish physicians surveyed seem to consider guidelines useful, their adherence to those is very low if translated to managing pregnant asthmatic patients. Educational strategies seem unavoidable and should be targetted mainly to primary care and gynaecology/obstetrician physicians.
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Monzó C, Urbaneja A, Ximénez-Embún M, García-Fernández J, García JL, Castañera P. Selection of Ceratitis capitata (Diptera: Tephritidae) specific recombinant monoclonal phage display antibodies for prey detection analysis. PLoS One 2012; 7:e51440. [PMID: 23272105 PMCID: PMC3522712 DOI: 10.1371/journal.pone.0051440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 11/01/2012] [Indexed: 11/23/2022] Open
Abstract
Several recombinant antibodies against the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), one of the most important pests in agriculture worldwide, were selected for the first time from a commercial phage display library of human scFv antibodies. The specificity and sensitivity of the selected recombinant antibodies were compared with that of a rabbit polyclonal serum raised in parallel using a wide range of arthropod species as controls. The selected recombinant monoclonal antibodies had a similar or greater specificity when compared with classical monoclonal antibodies. The selected recombinant antibodies were successfully used to detect the target antigen in the gut of predators and the scFv antibodies were sequenced and compared. These results demonstrate the potential for recombinant scFv antibodies to be used as an alternative to the classical monoclonal antibodies or even molecular probes in the post-mortem analysis studies of generalist predators.
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Affiliation(s)
- César Monzó
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Alberto Urbaneja
- Unidad Asociada de Entomología IVIA-CIB, CSIC, Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
| | - Miguel Ximénez-Embún
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Julia García-Fernández
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - José Luis García
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Pedro Castañera
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
- Unidad Asociada de Entomología IVIA-CIB, CSIC, Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
- * E-mail:
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Martínez V, Jurkevitch E, García JL, Prieto MA. Reward forBdellovibrio bacteriovorusfor preying on a polyhydroxyalkanoate producer. Environ Microbiol 2012; 15:1204-15. [DOI: 10.1111/1462-2920.12047] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/29/2012] [Accepted: 11/03/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Virginia Martínez
- Environmental Biology Department; Centro de Investigaciones Biológicas; CSIC, C/ Ramiro de Maeztu, 9; 28040; Madrid; Spain
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology; Faculty of Agricultural, Food and Environmental Quality Sciences; the Hebrew University of Jerusalem; Rehovot; 76100; Israel
| | - José Luis García
- Environmental Biology Department; Centro de Investigaciones Biológicas; CSIC, C/ Ramiro de Maeztu, 9; 28040; Madrid; Spain
| | - María Auxiliadora Prieto
- Environmental Biology Department; Centro de Investigaciones Biológicas; CSIC, C/ Ramiro de Maeztu, 9; 28040; Madrid; Spain
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del Rey M, O'Hagan K, Dellett M, Aibar S, Colyer HAA, Alonso ME, Díez-Campelo M, Armstrong RN, Sharpe DJ, Gutiérrez NC, García JL, De Las Rivas J, Mills KI, Hernández-Rivas JM. Genome-wide profiling of methylation identifies novel targets with aberrant hypermethylation and reduced expression in low-risk myelodysplastic syndromes. Leukemia 2012; 27:610-8. [PMID: 22936014 DOI: 10.1038/leu.2012.253] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gene expression profiling signatures may be used to classify the subtypes of Myelodysplastic syndrome (MDS) patients. However, there are few reports on the global methylation status in MDS. The integration of genome-wide epigenetic regulatory marks with gene expression levels would provide additional information regarding the biological differences between MDS and healthy controls. Gene expression and methylation status were measured using high-density microarrays. A total of 552 differentially methylated CpG loci were identified as being present in low-risk MDS; hypermethylated genes were more frequent than hypomethylated genes. In addition, mRNA expression profiling identified 1005 genes that significantly differed between low-risk MDS and the control group. Integrative analysis of the epigenetic and expression profiles revealed that 66.7% of the hypermethylated genes were underexpressed in low-risk MDS cases. Gene network analysis revealed molecular mechanisms associated with the low-risk MDS group, including altered apoptosis pathways. The two key apoptotic genes BCL2 and ETS1 were identified as silenced genes. In addition, the immune response and micro RNA biogenesis were affected by the hypermethylation and underexpression of IL27RA and DICER1. Our integrative analysis revealed that aberrant epigenetic regulation is a hallmark of low-risk MDS patients and could have a central role in these diseases.
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Affiliation(s)
- M del Rey
- Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca, Spain
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Rodríguez AE, Robledo C, García JL, González M, Gutiérrez NC, Hernández JA, Sandoval V, García de Coca A, Recio I, Risueño A, Martín-Núñez G, García E, Fisac R, Conde J, de Las Rivas J, Hernández JM. Identification of a novel recurrent gain on 20q13 in chronic lymphocytic leukemia by array CGH and gene expression profiling. Ann Oncol 2012; 23:2138-2146. [PMID: 22228453 DOI: 10.1093/annonc/mdr579] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND The presence of genetic changes is a hallmark of chronic lymphocytic leukemia (CLL). The most common cytogenetic abnormalities with independent prognostic significance in CLL are 13q14, ATM and TP53 deletions and trisomy 12. However, CLL displays a great genetic and biological heterogeneity. The aim of this study was to analyze the genomic imbalances in CLL cytogenetic subsets from both genomic and gene expression perspectives to identify new recurrent alterations. PATIENTS AND METHODS The genomic imbalances and expression levels of 67 patients were analyzed. The novel recurrent abnormalities detected with bacterial artificial chromosome array were confirmed by FISH and oligonucleotide microarrays. In all cases, gene expression profiling was assessed. RESULTS Copy number alterations were identified in 75% of cases. Overall, the results confirmed FISH studies for the regions frequently involved in CLL and also defined a new recurrent gain on chromosome 20q13.12, in 19% (13/67) of the CLL patients. Oligonucleotide expression correlated with the regions of loss or gain of genomic material, suggesting that the changes in gene expression are related to alterations in copy number. CONCLUSION Our study demonstrates the presence of a recurrent gain in 20q13.12 associated with overexpression of the genes located in this region, in CLL cytogenetic subgroups.
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Affiliation(s)
- A E Rodríguez
- IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - C Robledo
- IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - J L García
- Instituto de Estudios de Ciencias de la Salud de Castilla y León (IECSCYL)-HUSAL, Castill y León
| | - M González
- Department of Hematology, Hospital Clínico Universitario de Salamanca, Salamanca
| | - N C Gutiérrez
- Department of Hematology, Hospital Clínico Universitario de Salamanca, Salamanca
| | - J A Hernández
- Department of Hematology, Hospital Infanta Leonor, Madrid
| | - V Sandoval
- Department of Hematology, Hospital Virgen Blanca, León
| | - A García de Coca
- Department of Hematology, Hospital Clínico Universitario, Valladolid
| | - I Recio
- Department of Hematology, Hospital Nuestra Señora de Sonsoles, Ávila
| | - A Risueño
- Bioinformatics and Functional Genomics, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - G Martín-Núñez
- Department of Hematology, Hospital Virgen del Puerto, Plasencia
| | - E García
- Genomics and Proteomics Unit, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - R Fisac
- Department of Hematology, Hospital General de Segovia, Segovia
| | - J Conde
- Department of Hematology, Hospital del Río Hortega, Valladolid, Spain
| | - J de Las Rivas
- Bioinformatics and Functional Genomics, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - J M Hernández
- IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca; Department of Hematology, Hospital Clínico Universitario de Salamanca, Salamanca.
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Cañueto J, Girós M, Ciria S, Pi-Castán G, Artigas M, García-Dorado J, García-Patos V, Virós A, Vendrell T, Torrelo A, Hernández-Martín A, Martín-Hernández E, Garcia-Silva MT, Fernández-Burriel M, Rosell J, Tejedor M, Martínez F, Valero J, García JL, Sánchez-Tapia EM, Unamuno P, González-Sarmiento R. Clinical, molecular and biochemical characterization of nine Spanish families with Conradi-Hünermann-Happle syndrome: new insights into X-linked dominant chondrodysplasia punctata with a comprehensive review of the literature. Br J Dermatol 2012; 166:830-8. [PMID: 22121851 DOI: 10.1111/j.1365-2133.2011.10756.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Conradi-Hünermann-Happle syndrome (CDPX2, OMIM 302960) is an inherited X-linked dominant variant of chondrodysplasia punctata which primarily affects the skin, bones and eyes. CDPX2 results from mutations in EBP (emopamil binding protein), and presents with increased levels of sterol precursors 8(9)-cholesterol and 8-dehydrocholesterol. OBJECTIVES To expand the understanding of CDPX2, clinically, biochemically and genetically. METHODS We present one of the largest series reported to date, including 13 female patients belonging to nine Spanish families. Patients were studied biochemically using gas chromatography-mass spectrometry, genetically using polymerase chain reaction and in their methylation status using the HUMARA assay. RESULTS In our cases, there was a clear relationship between abnormal sterol profile and the EBP gene mutation. We describe three novel mutations in the EBP gene. EBP mutations were inherited in three out of nine families and were sporadic in the remaining cases. CONCLUSIONS No clear genotype-phenotype correlation was found. Patients' biochemical profiles did not reveal a relationship between sterol profiles and severity of disease. A skewed X-chromosome inactivation may explain the clinical phenotype in CDPX2 in some familial cases.
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Affiliation(s)
- J Cañueto
- Department of Dermatology, University Hospital of Salamanca, Salamanca, Spain.
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