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361 results on '"Caldana, Camila"'

52. A Reductionist Approach Using Primary and Metastatic Cell–Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis

Author

Busso-Lopes, Ariane Fidelis, primary, Carnielli, Carolina Moretto, additional, Winck, Flavia Vischi, additional, Patroni, Fábio Malta de Sá, additional, Oliveira, Ana Karina, additional, Granato, Daniela Campos, additional, e Costa, Rute Alves Pereira, additional, Domingues, Romênia Ramos, additional, Pauletti, Bianca Alves, additional, Riaño-Pachón, Diego Mauricio, additional, Aricetti, Juliana, additional, Caldana, Camila, additional, Graner, Edgard, additional, Coletta, Ricardo Della, additional, Dryden, Kelly, additional, Fox, Jay William, additional, and Paes Leme, Adriana Franco, additional

Published
2021
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53. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence

Author

Thieme, Frank, Koebnik, Ralf, Bekel, Thomas, Berger, Carolin, Boch, Jens, Buttner, Daniela, Caldana, Camila, Gaigalat, Lars, Goesmann, Alexander, Kay, Sabine, Kirchner, Oliver, Lanz, Christa, Linke, Burkhard, McHardy, Alice C., Meyer, Folker, Mittenhuber, Gerhard, Nies, Dietrich H., Niesbach-Klosgen, Ulla, Patschkowski, Thomas, Ruckert, Christian, Rupp, Oliver, Schneiker, Susanne, Schuster, Stephan C., Vorholter, Frank-Jorg, Weber, Ernst, Puhler, Alfred, Bonas, Ulla, Bartels, Daniela, and Kaiser, Olaf

Subjects
Nucleotide sequence -- Research, Microbial polysaccharides -- Research, Bacterial proteins -- Research, Genetic research, Biological sciences
Abstract

The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses. This pathosystem has become a well-established model for studying bacterial infection strategies. Here, we present the whole-genome sequence of the pepper-pathogenic Xanthomonas campestris pv. vesicatoria strain 85-10, which comprises a 5.17-Mb circular chromosome and four plasmids. The genome has a high G+C content (64.75%) and signatures of extensive genome plasticity. Whole-genome comparisons revealed a gene order similar to both Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris and a structure completely different from Xanthomonas oryzae pv. oryzae. A total of 548 coding sequences (12.2%) are unique to X. campestris pv. vesicatoria. In addition to a type III secretion system, which is essential for pathogenicity., the genome of strain 85-10 encodes all other types of protein secretion systems described so far in gram-negative bacteria. Remarkably, one of the putative type IV secretion systems encoded on the largest plasmid is similar to the Icm/Dot systems of the human pathogens Legionella pneumophila and Coxiella burnetii. Comparisons with other completely sequenced plant pathogens predicted six novel type III effector proteins and several other virulence factors, including adhesins, cell wall-degrading enzymes, and extracellular polysaccharides.

Published
2005

56. Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development

Author

Rohrmann, Johannes, Tohge, Takayuki, Alba, Rob, Osorio, Sonia, Caldana, Camila, McQuinn, Ryan, Arvidsson, Samuel, van der Merwe, Margaretha J., Riaño-Pachón, Diego Mauricio, Mueller-Roeber, Bernd, Fei, Zhangjun, Nesi, Adriano Nunes, Giovannoni, James J., and Fernie, Alisdair R.

Published
2011
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59. Physiological and metabolic bases of increased growth in the tomato ethylene-insensitive mutant Never ripe: extending ethylene signaling functions

Author

Nascimento, Vitor L., primary, Pereira, Auderlan M., additional, Pereira, Aurelio S., additional, Silva, Victor F., additional, Costa, Lucas C., additional, Bastos, Carla E. A., additional, Ribeiro, Dimas M., additional, Caldana, Camila, additional, Sulpice, Ronan, additional, Nunes-Nesi, Adriano, additional, Zsögön, Agustin, additional, and Araújo, Wagner L., additional

Published
2020
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63. Clinical Metabolomics Identifies Blood Serum Branched Chain Amino Acids as Potential Predictive Biomarkers for Chronic Graft vs. Host Disease

Author

Alborghetti, Marcos Rodrigo, primary, Correa, Maria Elvira Pizzigatti, additional, Whangbo, Jennifer, additional, Shi, Xu, additional, Aricetti, Juliana Aparecida, additional, Silva, Andreia Aparecida da, additional, Miranda, Eliana Cristina Martins, additional, Sforca, Mauricio Luis, additional, Caldana, Camila, additional, Gerszten, Robert E., additional, Ritz, Jerome, additional, and Zeri, Ana Carolina de Mattos, additional

Published
2019
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65. TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data

Author

Lisec Jan, Kusano Miyako, Redestig Henning, Caldana Camila, Cuadros-Inostroza Álvaro, Peña-Cortés Hugo, Willmitzer Lothar, and Hannah Matthew A

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Metabolite profiling, the simultaneous quantification of multiple metabolites in an experiment, is becoming increasingly popular, particularly with the rise of systems-level biology. The workhorse in this field is gas-chromatography hyphenated with mass spectrometry (GC-MS). The high-throughput of this technology coupled with a demand for large experiments has led to data pre-processing, i.e. the quantification of metabolites across samples, becoming a major bottleneck. Existing software has several limitations, including restricted maximum sample size, systematic errors and low flexibility. However, the biggest limitation is that the resulting data usually require extensive hand-curation, which is subjective and can typically take several days to weeks. Results We introduce the TargetSearch package, an open source tool which is a flexible and accurate method for pre-processing even very large numbers of GC-MS samples within hours. We developed a novel strategy to iteratively correct and update retention time indices for searching and identifying metabolites. The package is written in the R programming language with computationally intensive functions written in C for speed and performance. The package includes a graphical user interface to allow easy use by those unfamiliar with R. Conclusions TargetSearch allows fast and accurate data pre-processing for GC-MS experiments and overcomes the sample number limitations and manual curation requirements of existing software. We validate our method by carrying out an analysis against both a set of known chemical standard mixtures and of a biological experiment. In addition we demonstrate its capabilities and speed by comparing it with other GC-MS pre-processing tools. We believe this package will greatly ease current bottlenecks and facilitate the analysis of metabolic profiling data.

Published
2009
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66. Shedding Light on the Dynamic Role of the "Target of Rapamycin" Kinase in the Fast-Growing C4 Species Setaria viridis , a Suitable Model for Biomass Crops.

Author

da Silva, Viviane Cristina Heinzen, Martins, Marina C. M., Calderan-Rodrigues, Maria Juliana, Artins, Anthony, Monte Bello, Carolina Cassano, Gupta, Saurabh, Sobreira, Tiago J. P., Riaño-Pachón, Diego Mauricio, Mafra, Valéria, and Caldana, Camila

Subjects
ENERGY crops, RAPAMYCIN, METABOLISM, SETARIA, RESPONSE inhibition, ARABIDOPSIS thaliana
Abstract

The Target of Rapamycin (TOR) kinase pathway integrates energy and nutrient availability into metabolism promoting growth in eukaryotes. The overall higher efficiency on nutrient use translated into faster growth rates in C4 grass plants led to the investigation of differential transcriptional and metabolic responses to short-term chemical TOR complex (TORC) suppression in the model Setaria viridis. In addition to previously described responses to TORC inhibition (i.e., general growth arrest, translational repression, and primary metabolism reprogramming) in Arabidopsis thaliana (C3), the magnitude of changes was smaller in S. viridis , particularly regarding nutrient use efficiency and C allocation and partitioning that promote biosynthetic growth. Besides photosynthetic differences, S. viridis and A. thaliana present several specificities that classify them into distinct lineages, which also contribute to the observed alterations mediated by TOR. Indeed, cell wall metabolism seems to be distinctly regulated according to each cell wall type, as synthesis of non-pectic polysaccharides were affected in S. viridis , whilst assembly and structure in A. thaliana. Our results indicate that the metabolic network needed to achieve faster growth seems to be less stringently controlled by TORC in S. viridis. [ABSTRACT FROM AUTHOR]

Published
2021
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67. A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors

Author

Mueller-Roeber Bernd, Scheible Wolf-Rüdiger, Caldana Camila, and Ruzicic Slobodan

Subjects
Plant culture, SB1-1110, Biology (General), QH301-705.5
Abstract

Abstract Background Quantitative reverse transcription – polymerase chain reaction (qRT-PCR) has been demonstrated to be particularly suitable for the analysis of weakly expressed genes, such as those encoding transcription factors. Rice (Oryza sativa L.) is an important crop and the most advanced model for monocotyledonous species; its nuclear genome has been sequenced and molecular tools are being developed for functional analyses. However, high-throughput methods for rice research are still limited and a large-scale qRT-PCR platform for gene expression analyses has not been reported. Results We established a qRT-PCR platform enabling the multi-parallel determination of the expression levels of more than 2500 rice transcription factor genes. Additionally, using different rice cultivars, tissues and physiological conditions, we evaluated the expression stability of seven reference genes. We demonstrate this resource allows specific and reliable detection of the expression of transcription factor genes in rice. Conclusion Multi-parallel qRT-PCR allows the versatile and sensitive transcriptome profiling of large numbers of rice transcription factor genes. The new platform complements existing microarray-based expression profiling techniques, by allowing the analysis of lowly expressed transcription factor genes to determine their involvement in developmental or physiological processes. We expect that this resource will be of broad utility to the scientific community in the further development of rice as an important model for plant science.

Published
2007
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68. The Aspergillus nidulans pyruvate dehydrogenase kinases are essential to integrate carbon source metabolism

Author

Ries, Laure Nocolas Annick, de Assis, Leandro José, Rodrigues, Fernando José Santos, Caldana, Camila, Rocha, Maria Campos, Malavazi, Iran, Bayram, Ozgur, Goldman, Gustavo H., Ries, Laure Nocolas Annick, de Assis, Leandro José, Rodrigues, Fernando José Santos, Caldana, Camila, Rocha, Maria Campos, Malavazi, Iran, Bayram, Ozgur, and Goldman, Gustavo H.

Abstract

The pyruvate dehydrogenase complex (PDH), that converts pyruvate to acetyl-coA, is regulated by pyruvate dehydrogenase kinases (PDHK) and phosphatases (PDHP) that have been shown to be important for morphology, pathogenicity and carbon source utilization in different fungal species. The aim of this study was to investigate the role played by the three PDHKs PkpA, PkpB and PkpC in carbon source utilization in the reference filamentous fungus Aspergillus nidulans, in order to unravel regulatory mechanisms which could prove useful for fungal biotechnological and biomedical applications. PkpA and PkpB were shown to be mitochondrial whereas PkpC localized to the mitochondria in a carbon sourcedependent manner. Only PkpA was shown to regulate PDH activity. In the presence of glucose, deletion of pkpA and pkpC resulted in reduced glucose utilization, which affected carbon catabolite repression (CCR) and hydrolytic enzyme secretion, due to de-regulated glycolysis and TCA cycle enzyme activities. Furthermore, PkpC was shown to be required for the correct metabolic utilization of cellulose and acetate. PkpC negatively regulated the activity of the glyoxylate cycle enzyme isocitrate lyase (ICL), required for acetate metabolism. In summary, this study identified PDHKs important for the regulation of central carbon metabolism in the presence of different carbon sources, with effects on the secretion of biotechnologically important enzymes and carbon source-related growth. This work demonstrates how central carbon metabolism can affect a variety of fungal traits and lays a basis for further investigation into these characteristics with potential interest for different applications.

Published
2018

69. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald P. de, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Akemi Uchima, Cristiane, Anderluh, Gregor, Asaollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Diallinas, George, Flipphi, Michel, Freyburg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio F., MacCabe, Andrew, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Ngan, Chew Yee, Orejas, Margarita, Ouedraogo, Jean Paul, Overkamp, Karin M., Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J., Ram, Arthur F.J., Ramon, Ana, Rauscher, Stefan, Record, Eric, Robert, Vincent, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sanguinetti, Manuel, Sep?i?, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio M., Sun, Hui, Susca, Antonia, Todd, Richard B., Tsang, Adrian, Unkles, Shiela E., Wiele, Nathalie van de, Rossen-Uffink, Diana van, Velasco de Castro Oliveira, Juliana, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, Andersen, Mikael R., Archer, David B., Baker, Scott E., Benoit, Isabelle, Brakhage, Axel A., Braus, Gerhard H., Fischer, Reinhard, Frisvad, Jens C., Goldman, Gustavo H., Houbraken, Jos, Oakley, Berl, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A., Wortman, Jennifer, Dyer, Paul S., and Grigoriev, Igor V.

Subjects
Genome sequencing, Comparative genomics, Fungal biology
Abstract

Background: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. Results: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. Conclusions: Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.

Published
2017

70. Additional file 8: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Subjects
body regions, inorganic chemicals, nervous system, fungi
Abstract

Effect of SHAM and KCN on fungal growth and sporulation. (PDF 252 kb)

Published
2017
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71. Additional file 27: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Abstract

Maximum likelihood rooted phylogeny of the FCY-like transporters of the aspergilli and some penicillia. (PDF 324 kb)

Published
2017
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72. Additional file 7: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Abstract

Comparative growth profiling of the aspergilli and selected other fungi. (PDF 8.65 kb)

Published
2017
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73. Additional file 6: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Subjects
body regions, animal structures, nervous system, fungi
Abstract

Overview of number of putative orthologs/paralogs in the compared fungal species related to primary carbon metabolism. (PDF 237 kb)

Published
2017
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74. Additional file 5: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Subjects
body regions, nervous system, fungi, behavior and behavior mechanisms, reproductive and urinary physiology
Abstract

Expression of mating and pheromone-signalling pathway genes in representative asexual aspergilli. (PDF 488 kb)

Published
2017
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75. Additional file 15: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Abstract

Extended analysis of stress tolerance of the aspergilli. (PDF 706 kb)

Published
2017
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76. Additional file 35: of Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Vries, Ronald De, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Sotiris Amillis, Cristiane Uchima, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Özgür, Benocci, Tiziano, Braus-Stromeyer, Susanna, Caldana, Camila, Cánovas, David, Cerqueira, Gustavo, Fusheng Chen, Wanping Chen, Choi, Cindy, Clum, Alicia, Santos, Renato Dos, Damásio, André, Diallinas, George, Emri, Tamás, Fekete, Erzsébet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, María, Henrissat, Bernard, Hildén, Kristiina, Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karányi, Zsolt, Kraševec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen, Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio, MacCabe, Andrew, Mäkelä, Miia, Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Márton, Molnár, Ákos, Mulé, Giuseppina, Chew Ngan, Orejas, Margarita, Orosz, Erzsébet, Ouedraogo, Jean, Overkamp, Karin, Park, Hee-Soo, Perrone, Giancarlo, Francois Piumi, Punt, Peter, Ram, Arthur, Ramón, Ana, Rauscher, Stefan, Record, Eric, Riaño-Pachón, Diego, Robert, Vincent, Röhrig, Julian, Ruller, Roberto, Salamov, Asaf, Nadhira Salih, Samson, Rob, Sándor, Erzsébet, Sanguinetti, Manuel, Schütze, Tabea, Sepčić, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio, Sun, Hui, Susca, Antonia, Todd, Richard, Tsang, Adrian, Unkles, Shiela, Wiele, Nathalie Van De, Rossen-Uffink, Diana Van, Oliveira, Juliana, Vesth, Tammi, Visser, Jaap, Jae-Hyuk Yu, Miaomiao Zhou, Andersen, Mikael, Archer, David, Baker, Scott, Benoit, Isabelle, Brakhage, Axel, Braus, Gerhard, Fischer, Reinhard, Frisvad, Jens, Goldman, Gustavo, Houbraken, Jos, Berl Oakley, Pócsi, István, Scazzocchio, Claudio, Seiboth, Bernhard, VanKuyk, Patricia, Wortman, Jennifer, Dyer, Paul, and Grigoriev, Igor

Abstract

Maximal likelihood phylogeny of MASC1/RID1 orthologs. (PDF 115 kb)

Published
2017
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79. Abstract 5649: Multi-omics data indicate that primary and lymph node oral cancer cells-derived extracellular vesicles carry cargo molecules with a specific aggressive pattern

Author

Busso-Lopes, Ariane F., primary, Carnielli, Carolina M., additional, Winck, Flávia, additional, Riaño-Pachón, Diego M., additional, Oliveira, Ana K., additional, Costa, Rute A., additional, Rivera, César, additional, Caldana, Camila, additional, Fox, Jay W., additional, and Leme, Adriana F. Paes, additional

Published
2018
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81. Metabolite Profiles of Sugarcane Culm Reveal the Relationship Among Metabolism and Axillary Bud Outgrowth in Genetically Related Sugarcane Commercial Cultivars

Author

Ferreira, Danilo A., primary, Martins, Marina C. M., additional, Cheavegatti-Gianotto, Adriana, additional, Carneiro, Monalisa S., additional, Amadeu, Rodrigo R., additional, Aricetti, Juliana A., additional, Wolf, Lucia D., additional, Hoffmann, Hermann P., additional, de Abreu, Luis G. F., additional, and Caldana, Camila, additional

Published
2018
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84. Exploring the metabolic and physiological diversity of native microalgal strains (Chlorophyta) isolated from tropical freshwater reservoirs

Author

Rocha, Renan Paulo, primary, Machado, Mariana, additional, Vaz, Marcelo Gomes Marçal Vieira, additional, Vinson, Christina C., additional, Leite, Maurício, additional, Richard, Rafael, additional, Mendes, Leonardo Brantes Bacellar, additional, Araujo, Wagner L., additional, Caldana, Camila, additional, Martins, Marcio Arêdes, additional, Williams, Thomas C.R., additional, and Nunes-Nesi, Adriano, additional

Published
2017
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85. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

de Vries, Ronald P., Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Uchima, Cristiane Akemi, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie W, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Canovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Correa dos Santos, Renato Augusto, de Lima Damasio, Andre Ricardo, Diallinas, George, Emri, Tamas, Fekete, Erzsebet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Laura Harispe, Maria, Henrissat, Bernard, Hilden, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt M, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika A, Lipzen, Anna M, Logrieco, Antonio F., Maccabe, Andrew, Makela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Marton, Molnar, Akos P., Mule, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsebet, Ouedraogo, Jean Paul, Overkamp, Karin M, Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J, Ram, Arthur F J, Ramon, Ana, Rauscher, Stefan, Record, Eric, Riano-Pachon, Diego Mauricio, Robert, Vincent, Roehrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sandor, Erzsebet, Sanguinetti, Manuel, Schutze, Tabea, Sepcic, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, FabioM., Sun, Hui, Susca, Antonia, Todd, Richard B, Tsang, Adrian, Unkles, Shiela E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, de Castro Oliveira, Juliana Velasco, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, Andersen, Mikael R, Archer, David B., Baker, Scott E, Benoit, Isabelle, Brakhage, Axel A, Braus, Gerhard H., Fischer, Reinhard, Frisvad, Jens C., Goldman, Gustavo H., Houbraken, Jos, Oakley, Berl R, Pocsi, Istvan, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A, Wortman, Jennifer Russo, Dyer, Paul S, Grigoriev, Igor V, de Vries, Ronald P., Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Uchima, Cristiane Akemi, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie W, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Canovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Correa dos Santos, Renato Augusto, de Lima Damasio, Andre Ricardo, Diallinas, George, Emri, Tamas, Fekete, Erzsebet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Laura Harispe, Maria, Henrissat, Bernard, Hilden, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt M, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika A, Lipzen, Anna M, Logrieco, Antonio F., Maccabe, Andrew, Makela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Marton, Molnar, Akos P., Mule, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsebet, Ouedraogo, Jean Paul, Overkamp, Karin M, Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J, Ram, Arthur F J, Ramon, Ana, Rauscher, Stefan, Record, Eric, Riano-Pachon, Diego Mauricio, Robert, Vincent, Roehrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sandor, Erzsebet, Sanguinetti, Manuel, Schutze, Tabea, Sepcic, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, FabioM., Sun, Hui, Susca, Antonia, Todd, Richard B, Tsang, Adrian, Unkles, Shiela E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, de Castro Oliveira, Juliana Velasco, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miaomiao, Andersen, Mikael R, Archer, David B., Baker, Scott E, Benoit, Isabelle, Brakhage, Axel A, Braus, Gerhard H., Fischer, Reinhard, Frisvad, Jens C., Goldman, Gustavo H., Houbraken, Jos, Oakley, Berl R, Pocsi, Istvan, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A, Wortman, Jennifer Russo, Dyer, Paul S, and Grigoriev, Igor V

Published
2017

86. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

de Vries, Ronald, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Akemi Uchima, Cristiane, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Canovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Correa dos Santos, Renato Augusto, de Lima Damasio, Andre Ricardo, Diallinas, George, Emri, Tamas, Fekete, Erzsebet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hilden, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio F., MacCabe, Andrew, Makela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Marton, Molnar, Akos P., Mule, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsebet, Ouedraogo, Jean Paul, Overkamp, Karin M., Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J., Ram, Arthur F.J., Ramon, Ana, Rauscher, Stefan, Record, Eric, Riano-Pachon, Diego Mauricio, Robert, Vincent, Rohrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sandor, Erzsebet, Sanguinetti, Manuel, Schutze, Tabea, Sepcic, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio M., Sun, Hui, Susca, Antonia, Todd, Richard B., Tsang, Adrian, Unkles, Sheila E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, Velasco de Castro Oliveria, Juliana, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miamiao, Andersen, Mikael R., Archer, David B., Baker, Scott E., Benoit, Isabelle, Brakhage, Axel A., Braus, Gerhard H., Fischer, Reinhard, Frisvad, Jens C., Goldman, Gustavo H., Houbraken, Jos, Oakley, Berl, Pocsi, Istvan, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A., Wortman, Jennifer, Dyer, Paul S., Grigoriev, Igor V., de Vries, Ronald, Riley, Robert, Wiebenga, Ad, Aguilar-Osorio, Guillermo, Amillis, Sotiris, Akemi Uchima, Cristiane, Anderluh, Gregor, Asadollahi, Mojtaba, Askin, Marion, Barry, Kerrie, Battaglia, Evy, Bayram, Ozgur, Benocci, Tiziano, Braus-Stromeyer, Susanna A., Caldana, Camila, Canovas, David, Cerqueira, Gustavo C., Chen, Fusheng, Chen, Wanping, Choi, Cindy, Clum, Alicia, Correa dos Santos, Renato Augusto, de Lima Damasio, Andre Ricardo, Diallinas, George, Emri, Tamas, Fekete, Erzsebet, Flipphi, Michel, Freyberg, Susanne, Gallo, Antonia, Gournas, Christos, Habgood, Rob, Hainaut, Matthieu, Harispe, Maria Laura, Henrissat, Bernard, Hilden, Kristiina S., Hope, Ryan, Hossain, Abeer, Karabika, Eugenia, Karaffa, Levente, Karanyi, Zsolt, Krasevec, Nada, Kuo, Alan, Kusch, Harald, LaButti, Kurt, Lagendijk, Ellen L., Lapidus, Alla, Levasseur, Anthony, Lindquist, Erika, Lipzen, Anna, Logrieco, Antonio F., MacCabe, Andrew, Makela, Miia R., Malavazi, Iran, Melin, Petter, Meyer, Vera, Mielnichuk, Natalia, Miskei, Marton, Molnar, Akos P., Mule, Giuseppina, Ngan, Chew Yee, Orejas, Margarita, Orosz, Erzsebet, Ouedraogo, Jean Paul, Overkamp, Karin M., Park, Hee-Soo, Perrone, Giancarlo, Piumi, Francois, Punt, Peter J., Ram, Arthur F.J., Ramon, Ana, Rauscher, Stefan, Record, Eric, Riano-Pachon, Diego Mauricio, Robert, Vincent, Rohrig, Julian, Ruller, Roberto, Salamov, Asaf, Salih, Nadhira S., Samson, Rob A., Sandor, Erzsebet, Sanguinetti, Manuel, Schutze, Tabea, Sepcic, Kristina, Shelest, Ekaterina, Sherlock, Gavin, Sophianopoulou, Vicky, Squina, Fabio M., Sun, Hui, Susca, Antonia, Todd, Richard B., Tsang, Adrian, Unkles, Sheila E., van de Wiele, Nathalie, van Rossen-Uffink, Diana, Velasco de Castro Oliveria, Juliana, Vesth, Tammi C., Visser, Jaap, Yu, Jae-Hyuk, Zhou, Miamiao, Andersen, Mikael R., Archer, David B., Baker, Scott E., Benoit, Isabelle, Brakhage, Axel A., Braus, Gerhard H., Fischer, Reinhard, Frisvad, Jens C., Goldman, Gustavo H., Houbraken, Jos, Oakley, Berl, Pocsi, Istvan, Scazzocchio, Claudio, Seiboth, Bernhard, vanKuyk, Patricia A., Wortman, Jennifer, Dyer, Paul S., and Grigoriev, Igor V.

Abstract

Background The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. Results We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. Conclusions Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.

Published
2017

87. TOR Signaling and Nutrient Sensing

Author

Dobrenel, Thomas, Caldana, Camila, Hanson, Johannes, Robaglia, Christophe, Vincentz, Michel, Veit, Bruce, Meyer, Christian, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Umeå University, Brazilian Bioethanol Science and Technology Laboratory, Partenaires INRAE, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Universidade Estadual de Campinas (UNICAMP), and Massey University

Subjects
sugars, [SDV]Life Sciences [q-bio], [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, TOR kinase, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, SnRK1 kinase, nutrient signaling, nitrogen
Abstract

International audience; All living organisms rely on nutrients to sustain cell metabolism and energy production, which in turn need to be adjusted based on available resources. The evolutionarily conserved target of rapamycin (TOR) protein kinase is a central regulatory hub that connects environmental information about the quantity and quality of nutrients to developmental and metabolic processes in order to maintain cellular homeostasis. TOR is activated by both nitrogen and carbon metabolites and promotes energy-consuming processes such as cell division, mRNA translation, and anabolism in times of abundance while repressing nutrient remobilization through autophagy. In animals and yeasts, TOR acts antagonistically to the starvation-induced AMP-activated kinase (AMPK)/sucrose nonfermenting 1 (Snf1) kinase, called Snf1-related kinase 1 (SnRK1) in plants. This review summarizes the immense knowledge on the relationship betweenTORsignaling and nutrients in nonphotosynthetic organisms and presents recent findings in plants that illuminate the crucial role of this pathway in conveying nutrient-derived signals and regulating many aspects of metabolism and growth.

Published
2016

88. Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress

Author

Jorge, Tiago F., Rodrigues, João A., Caldana, Camila, Schmidt, Romy, van Dongen, Joost T., Thomas-Oates, Jane, and António, Carla

Subjects
Metabolome, Metabolomics, Amino Acids, Plants, Mass Spectrometry
Abstract

Metabolomics is one omics approach that can be used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include analysis of a wide range of chemical species with diverse physical properties, from ionic inorganic compounds to biochemically derived hydrophilic carbohydrates, organic and amino acids, and a range of hydrophobic lipid-related compounds. This complexitiy brings huge challenges to the analytical technologies employed in current plant metabolomics programs, and powerful analytical tools are required for the separation and characterization of this extremely high compound diversity present in biological sample matrices. The use of mass spectrometry (MS)-based analytical platforms to profile stress-responsive metabolites that allow some plants to adapt to adverse environmental conditions is fundamental in current plant biotechnology research programs for the understanding and development of stress-tolerant plants. In this review, we describe recent applications of metabolomics and emphasize its increasing application to study plant responses to environmental (stress-) factors, including drought, salt, low oxygen caused by waterlogging or flooding of the soil, temperature, light and oxidative stress (or a combination of them). Advances in understanding the global changes occurring in plant metabolism under specific abiotic stress conditions are fundamental to enhance plant fitness and increase stress tolerance. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:620-649, 2016.

Published
2016
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92. Root extracts of Bracchiaria humidicola and Saccharum spontaneum to increase N use by sugarcane

Author

Kölln, Oriel Tiago, Franco, Henrique Coutinho Junqueira, Ferreira, Danilo Alves, Vargas, Vitor Paulo, Castro, Saulo Augusto de Quassi, Cantarella, Heitor, Caldana, Camila, Trivelin, Paulo Cesar Ocheuze, Kölln, Oriel Tiago, Franco, Henrique Coutinho Junqueira, Ferreira, Danilo Alves, Vargas, Vitor Paulo, Castro, Saulo Augusto de Quassi, Cantarella, Heitor, Caldana, Camila, and Trivelin, Paulo Cesar Ocheuze

Abstract

Retaining the mineral N in the form of NH4+ in the soil for a lengthy period is desirable for reducing losses. Furthermore, there is evidence that sugarcane prefers NH4+-N in place of NO3−-N. This study aimed firstly, to evaluate the potential of root extracts of Bracchiaria humidicola andSaccharum spontaneum, in contrast with the DCD (Dicyandiamide) inhibitor, to increase absorption of N by plants fertilized with ammonium sulfate, and secondly, to quantify the emission of N2O fluxes with the use of this inhibitor. The experiment was developed in a glasshouse in an entirely randomized design where four treatments were applied: AS) ammonium sulfate (control); AS+DCD) ammonium sulfate associated with dicyandiamide; AS+BCH) ammonium sulfate associated with root extracts ofBrachiaria humidicola; and AS+SCS) ammonium sulfate associated with root extracts of Saccharum spontaneum. Differences were observed in biomass production in plants 45 and 60 days after fertilization (DAF) and 15 and 60 days in biomass accumulation of roots. The application of AS associated with DCD synthetic inhibitor kept NO3−-N values low throughout the evaluation period, while in other treatments the concentration increased right up to the second evaluation 15 DAF. Sugarcane plants did not benefit from the increased presence of ammoniacal N promoted by DCD. The use of DCD reduced the average flux of N2O during the evaluation period compared to plants receiving AS treatments only, which was not observed when root extracts of B. humidicola and S. spontaneum were used.

Published
2016

93. The Aspergillus fumigatus SchASCH9 kinase modulates SakAHOG1 MAP kinase activity and it is essential for virulence

Author

Alves de Castro, Patrícia, primary, dos Reis, Thaila Fernanda, additional, Dolan, Stephen K., additional, Oliveira Manfiolli, Adriana, additional, Brown, Neil Andrew, additional, Jones, Gary W., additional, Doyle, Sean, additional, Riaño‐Pachón, Diego M., additional, Squina, Fábio Márcio, additional, Caldana, Camila, additional, Singh, Ashutosh, additional, Del Poeta, Maurizio, additional, Hagiwara, Daisuke, additional, Silva‐Rocha, Rafael, additional, and Goldman, Gustavo H., additional

Published
2016
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94. TOR Signaling and Nutrient Sensing

Author

Dobrenel, Thomas, primary, Caldana, Camila, additional, Hanson, Johannes, additional, Robaglia, Christophe, additional, Vincentz, Michel, additional, Veit, Bruce, additional, and Meyer, Christian, additional

Published
2016
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97. Development of a Chlamydomonas reinhardtii metabolic network dynamic model to describe distinct phenotypes occurring at different CO2 levels.

Author

Salguero, Daniela Alejandra Mora, Fernández-Niño, Miguel, Serrano-Bermúdez, Luis Miguel, Melo, David O. Páez, Winck, Flavia V., Caldana, Camila, and Barrios, Andrés Fernando González

Subjects
CHLAMYDOMONAS reinhardtii, CHLAMYDOMONAS, DYNAMIC models, BIOMASS production, ENVIRONMENTAL remediation, METABOLIC models
Abstract

The increase in atmospheric CO2 due to anthropogenic activities is generating climate change, which has resulted in a subsequent rise in global temperatures with severe environmental impacts. Biological mitigation has been considered as an alternative for environmental remediation and reduction of greenhouse gases in the atmosphere. In fact, the use of easily adapted photosynthetic organisms able to fix CO2 with lowcost operation is revealing its high potential for industry. Among those organism, the algae Chlamydomonas reinhardtii have gain special attention as a model organism for studying CO2 fixation, biomass accumulation and bioenergy production upon exposure to several environmental conditions. In the present study, we studied the Chlamydomonas response to different CO2 levels by comparing metabolomics and transcriptomics data with the predicted results from our new-improved genomic-scale metabolic model. For this, we used in silico methods at steady dynamic state varying the levels of CO2. Our main goal was to improve our capacity for predicting metabolic routes involved in biomass accumulation. The improved genomic-scale metabolic model presented in this study was shown to be phenotypically accurate, predictive, and a significant improvement over previously reported models. Our model consists of 3726 reactions and 2436 metabolites, and lacks any thermodynamically infeasible cycles. It was shown to be highly sensitive to environmental changes under both steady-state and dynamic conditions. As additional constraints, our dynamic model involved kinetic parameters associated with substrate consumption at different growth conditions (i.e., low CO2-heterotrophic and high CO2-mixotrophic). Our results suggest that cells growing at high CO2 (i.e., photoautotrophic and mixotrophic conditions) have an increased capability for biomass production. In addition, we have observed that ATP production also seems to be an important limiting factor for growth under the conditions tested. Our experimental data (metabolomics and transcriptomics) and the results predicted by our model clearly suggest a differential behavior between low CO2-heterotrophic and high CO2-mixotrophic growth conditions. The data presented in the current study contributes to better dissect the biological response of C. reinhardtii, as a dynamic entity, to environmental and genetic changes. These findings are of great interest given the biotechnological potential of this microalga for CO2 fixation, biomass accumulation, and bioenergy production. [ABSTRACT FROM AUTHOR]

Published
2018
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98. The target of rapamycin kinase affects biomass accumulation and cell cycle progression by altering carbon/nitrogen balance in synchronized Chlamydomonas reinhardtii cells.

Author

Jüppner, Jessica, Mubeen, Umarah, Leisse, Andrea, Caldana, Camila, Wiszniewski, Andrew, Steinhauser, Dirk, and Giavalisco, Patrick

Subjects
RAPAMYCIN, PLANT cells & tissues, CHLAMYDOMONAS reinhardtii, BIOACCUMULATION in plants, PLANT biomass, EUKARYOTES
Abstract

Several metabolic processes tightly regulate growth and biomass accumulation. A highly conserved protein complex containing the target of rapamycin ( TOR) kinase is known to integrate intra- and extracellular stimuli controlling nutrient allocation and hence cellular growth. Although several functions of TOR have been described in various heterotrophic eukaryotes, our understanding lags far behind in photosynthetic organisms. In the present investigation, we used the model alga Chlamydomonas reinhardtii to conduct a time-resolved analysis of molecular and physiological features throughout the diurnal cycle after TOR inhibition. Detailed examination of the cell cycle phases revealed that growth is not only repressed by 50%, but also that significant, non-linear delays in the progression can be observed. By using metabolomics analysis, we elucidated that the growth repression was mainly driven by differential carbon partitioning between anabolic and catabolic processes. Accordingly, the time-resolved analysis illustrated that metabolic processes including amino acid-, starch- and triacylglycerol synthesis, as well RNA degradation, were redirected within minutes of TOR inhibition. Here especially the high accumulation of nitrogen-containing compounds indicated that an active TOR kinase controls the carbon to nitrogen balance of the cell, which is responsible for biomass accumulation, growth and cell cycle progression. [ABSTRACT FROM AUTHOR]

Published
2018
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99. Unraveling retrograde signaling pathways: finding candidate signaling molecules via metabolomics and systems biology driven approaches

Author

Caldana, Camila, Fernie, Alisdair R., Willmitzer, Lothar, and Steinhauser, Dirk

Subjects
retrograde signaling, metabolic signals, Perspective, systems biology, Plant Science, metabolomics, sub-cellular metabolomics
Abstract

A tight coordination of biological processes between cellular compartments and organelles is crucial for the survival of any eukaryotic organism. According to cellular requirements, signals can be generated within organelles, such as chloroplasts and mitochondria, modulating the nuclear gene expression in a process called retrograde signaling. Whilst many research efforts have been focused on dissecting retrograde signaling pathways using biochemical and genetics approaches, metabolomics and systems biology driven studies have illustrated their great potential for hypotheses generation and for dissecting signaling networks in a rather unbiased or untargeted fashion. Recently, integrative genomics approaches, in which correlation analysis has been applied on transcript and metabolite profiling data of Arabidopsis thaliana, revealed the identification of metabolites which are putatively acting as mediators of nuclear gene expression. Complimentary, the continuous technological developments in the field of metabolomics per se has further demonstrated its potential as a very suitable readout to unravel metabolite-mediated signaling processes. As foundation for these studies here we outline and discuss recent advances in elucidating retrograde signaling molecules and pathways with an emphasis on metabolomics and systems biology driven approaches.

Published
2012
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100. Compromise of multiple time-resolved transcriptomics experiments identifies tightly regulated functions

Author

Klie, Sebastian, Caldana, Camila, and Nikoloski, Zoran

Subjects
transcriptomics time-series data, multi-way data analysis, Arabidopsis, lcsh:SB1-1110, Plant Science, time-series data, lcsh:Plant culture, Transcriptomics, Original Research, compromise of data tables
Abstract

With the advent of high-throughput technologies for data acquisition from different components (i.e., genes, proteins, and metabolites) of a given biological system, generation of hypotheses, and biological interpretations based on multivariate data sets become increasingly important. These technologies allow for simultaneous gathering of data from the same biological components under different perturbations, including genotypic variation and/or changes in conditions, resulting in so-called multiple data tables. Moreover, these data tables are obtained over a well-chosen time domain to capture the dynamics of the response of the biological system to the perturbation. The computational problem we address in this study is twofold: (1) derive a single data table, referred to as a compromise, which captures information common to the investigated set of multiple tables and (2) identify biological components which contribute most to the determined compromise. Here we argue that recent extensions to principle component analysis called STATIS and dual-STATIS can be used to determine the compromise on which classical techniques for data analysis, such as clustering and term over-enrichment, can be subsequently applied. In addition, we illustrate that STATIS and dual-STATIS facilitate interpretations of a publically available transcriptomics data set capturing the time-resolved response of Arabidopsis thaliana to changing light and/or temperature conditions. We demonstrate that STATIS and dual-STATIS can be used not only to identify the components of a biological system whose behavior is similarly affected due to the perturbation (e.g., in time or condition), but also to specify the extent to which each dimension of the data tables reflect the perturbation. These findings ultimately provide insights in the components and pathways which could be under tight control in plant systems.

Published
2012

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