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dmrpPublications.bib

@article{Arvidsson2008,
  title = {QuantPrime--a flexible tool for reliable high-throughput primer design for quantitative PCR.},
  author = {Arvidsson, Samuel and Kwasniewski, Miroslaw and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Mueller-Roeber, Bernd},
  journal = {BMC Bioinformatics},
  year = {2008},
  pages = {465},
  volume = {9},
  abstract = {Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays.Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/ or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96\%.QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays.},
  doi = {10.1186/1471-2105-9-465},
  institution = {Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. arvid@uni-potsdam.de},
  keywords = {Base Sequence; DNA Primers; Databases, Genetic; Internet; Molecular Sequence Data; Nucleic Acid Probes; Polymerase Chain Reaction, methods; Sensitivity and Specificity; Sequence Analysis, DNA, methods; Software; User-Computer Interface},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {1471-2105-9-465},
  pmid = {18976492},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1186/1471-2105-9-465}
}
@article{Balazadeh2008,
  title = {Transcription factors regulating leaf senescence in Arabidopsis thaliana.},
  author = {Balazadeh, S. and Ria{\~{n}}o-Pach{\'{o}}n, D. M. and Mueller-Roeber, B.},
  journal = {Plant Biol (Stuttg)},
  year = {2008},
  month = {Sep},
  pages = {63--75},
  volume = {10 Suppl 1},
  abstract = {Senescence is a highly regulated process, eventually leading to cell and tissue disintegration: a physiological process associated with nutrient (e.g. nitrogen) redistribution from leaves to reproductive organs. Senescence is not observed in young leaves, indicating that repressors efficiently act to suppress cell degradation during early leaf development and/or that senescence activators are switched on when a leaf ages. Thus, massive regulatory network re-wiring likely constitutes an important component of the pre-senescence process. Transcription factors (TFs) have been shown to be central elements of such regulatory networks. Here, we used quantitative real-time polymerase chain reaction (qRT-PCR) analysis to study the expression of 1880 TF genes during pre-senescence and early-senescence stages of leaf development, using Arabidopsis thaliana as a model. We show that the expression of 185 TF genes changes when leaves develop from half to fully expanded leaves and finally enter partial senescence. Our analysis identified 41 TF genes that were gradually up-regulated as leaves progressed through these developmental stages. We also identified 144 TF genes that were down-regulated during senescence. A considerable number of the senescence-regulated TF genes were found to respond to abiotic stress, and salt stress appeared to be the major factor controlling their expression. Our data indicate a peculiar fine-tuning of developmental shifts during late-leaf development that is controlled by TFs.},
  doi = {10.1111/j.1438-8677.2008.00088.x},
  institution = {Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, Germany.},
  keywords = {Arabidopsis Proteins, genetics/physiology; Arabidopsis, genetics/growth /&/ development/physiology; Cell Aging, genetics; Gene Expression Profiling; Gene Expression Regulation, Plant; Oligonucleotide Array Sequence Analysis; Plant Leaves, genetics/growth /&/ development/physiology; Reverse Transcriptase Polymerase Chain Reaction; Seeds, genetics/growth /&/ development/physiology; Sodium Chloride, metabolism; Transcription Factors, genetics/physiology; Water, metabolism},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pii = {PLB088},
  pmid = {18721312},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1111/j.1438-8677.2008.00088.x}
}
@article{Banks2011,
  title = {The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.},
  author = {Banks, Jo Ann and Nishiyama, Tomoaki and Hasebe, Mitsuyasu and Bowman, John L. and Gribskov, Michael and dePamphilis, Claude and Albert, Victor A. and Aono, Naoki and Aoyama, Tsuyoshi and Ambrose, Barbara A. and Ashton, Neil W. and Axtell, Michael J. and Barker, Elizabeth and Barker, Michael S. and Bennetzen, Jeffrey L. and Bonawitz, Nicholas D. and Chapple, Clint and Cheng, Chaoyang and Correa, Luiz Gustavo Guedes and Dacre, Michael and DeBarry, Jeremy and Dreyer, Ingo and Elias, Marek and Engstrom, Eric M. and Estelle, Mark and Feng, Liang and Finet, C{\'{e}}dric and Floyd, Sandra K. and Frommer, Wolf B. and Fujita, Tomomichi and Gramzow, Lydia and Gutensohn, Michael and Harholt, Jesper and Hattori, Mitsuru and Heyl, Alexander and Hirai, Tadayoshi and Hiwatashi, Yuji and Ishikawa, Masaki and Iwata, Mineko and Karol, Kenneth G. and Koehler, Barbara and Kolukisaoglu, Uener and Kubo, Minoru and Kurata, Tetsuya and Lalonde, Sylvie and Li, Kejie and Li, Ying and Litt, Amy and Lyons, Eric and Manning, Gerard and Maruyama, Takeshi and Michael, Todd P. and Mikami, Koji and Miyazaki, Saori and Morinaga, Shin-ichi and Murata, Takashi and Mueller-Roeber, Bernd and Nelson, David R. and Obara, Mari and Oguri, Yasuko and Olmstead, Richard G. and Onodera, Naoko and Petersen, Bent Larsen and Pils, Birgit and Prigge, Michael and Rensing, Stefan A. and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Roberts, Alison W. and Sato, Yoshikatsu and Scheller, Henrik Vibe and Schulz, Burkhard and Schulz, Christian and Shakirov, Eugene V. and Shibagaki, Nakako and Shinohara, Naoki and Shippen, Dorothy E. and S{\o}rensen, Iben and Sotooka, Ryo and Sugimoto, Nagisa and Sugita, Mamoru and Sumikawa, Naomi and Tanurdzic, Milos and Theissen, G{\"{u}}nter and Ulvskov, Peter and Wakazuki, Sachiko and Weng, Jing-Ke and Willats, William W G T. and Wipf, Daniel and Wolf, Paul G. and Yang, Lixing and Zimmer, Andreas D. and Zhu, Qihui and Mitros, Therese and Hellsten, Uffe and Loqu{\'{e}}, Dominique and Otillar, Robert and Salamov, Asaf and Schmutz, Jeremy and Shapiro, Harris and Lindquist, Erika and Lucas, Susan and Rokhsar, Daniel and Grigoriev, Igor V.},
  journal = {Science},
  year = {2011},
  month = {May},
  number = {6032},
  pages = {960--963},
  volume = {332},
  abstract = {Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.},
  doi = {10.1126/science.1203810},
  institution = {Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA. banksj@purdue.edu},
  keywords = {Angiosperms, chemistry/genetics; Biological Evolution; Bryopsida, genetics; Chlamydomonas, chemistry/genetics; DNA Transposable Elements; Evolution, Molecular; Gene Expression Regulation, Plant; Genes, Plant; Genome, Plant; MicroRNAs, genetics; Molecular Sequence Data; Phylogeny; Plant Proteins, genetics/metabolism; Proteome, analysis; RNA Editing; RNA, Plant, genetics; Repetitive Sequences, Nucleic Acid; Selaginellaceae, genetics/growth /&/ development/metabolism; Sequence Analysis, DNA},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pii = {science.1203810},
  pmid = {21551031},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1126/science.1203810}
}
@article{Brown2016,
  title = {RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose.},
  author = {Brown, Neil Andrew and Ries, Laure N A. and Reis, Thaila F. and Rajendran, Ranjith and {Corr{\^{e}}a Dos Santos}, Renato Augusto and Ramage, Gordon and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Goldman, Gustavo H.},
  journal = {Biotechnol Biofuels},
  year = {2016},
  pages = {145},
  volume = {9},
  abstract = {Sugarcane is one of the world's most profitable crops. Waste steam-exploded sugarcane bagasse (SEB) is a cheap, abundant, and renewable lignocellulosic feedstock for the next-generation biofuels. In nature, fungi seldom exist as planktonic cells, similar to those found in the nutrient-rich environment created within an industrial fermenter. Instead, fungi predominantly form biofilms that allow them to thrive in hostile environments.In turn, we adopted an RNA-sequencing approach to interrogate how the model fungus, Aspergillus nidulans, adapts to SEB, revealing the induction of carbon starvation responses and the lignocellulolytic machinery, in addition to morphological adaptations. Genetic analyses showed the importance of hydrophobins for growth on SEB. The major hydrophobin, RodA, was retained within the fungal biofilm on SEB fibres. The StuA transcription factor that regulates fungal morphology was up-regulated during growth on SEB and controlled hydrophobin gene induction. The absence of the RodA or DewC hydrophobins reduced biofilm formation. The loss of a RodA or a functional StuA reduced the retention of the hydrolytic enzymes within the vicinity of the fungus. Hence, hydrophobins promote biofilm formation on SEB, and may enhance lignocellulose utilisation via promoting a compact substrate-enzyme-fungus structure.This novel study highlights the importance of hydrophobins to the formation of biofilms and the efficient deconstruction of lignocellulose.},
  doi = {10.1186/s13068-016-0558-2},
  institution = {Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil.},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {558},
  pmid = {27437031},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1186/s13068-016-0558-2}
}
@article{Buitrago-Florez2014,
  title = {Identification of transcription factor genes and their correlation with the high diversity of stramenopiles.},
  author = {Buitrago-Fl{\'{o}}rez, Francisco Javier and Restrepo, Silvia and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio},
  journal = {PLoS One},
  year = {2014},
  number = {11},
  pages = {e111841},
  volume = {9},
  abstract = {The biological diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they embrace many ecologically important autothrophic (e.g., diatoms, brown algae), and heterotrophic (e.g., oomycetes) groups. Transcription factors (TFs) and other transcription regulators (TRs) regulate spatial and temporal gene expression. A plethora of transcriptional regulatory proteins have been identified and classified into families on the basis of sequence similarity. The purpose of this work is to identify the TF and TR complement in diverse species belonging to Stramenopiles in order to understand how these regulators may contribute to their observed diversity. We identified and classified 63 TF and TR families in 11 species of Stramenopiles. In some species we found gene families with high relative importance. Taking into account the 63 TF and TR families identified, 28 TF and TR families were established to be positively correlated with specific traits like number of predicted proteins, number of flagella and number of cell types during the life cycle. Additionally, we found gains and losses in TF and TR families specific to some species and clades, as well as, two families with high abundance specific to the autotrophic species and three families with high abundance specific to the heterotropic species. For the first time, there is a systematic search of TF and TR families in Stramenopiles. The attempts to uncover relationships between these families and the complexity of this group may be of great impact, considering that there are several important pathogens of plants and animals, as well as, important species involved in carbon cycling. Specific TF and TR families identified in this work appear to be correlated with particular traits in the Stramenopiles group and may be correlated with the high complexity and diversity in Stramenopiles.},
  doi = {10.1371/journal.pone.0111841},
  institution = {Laboratório Nacional de Ciência e Tecnología do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brasil.},
  keywords = {Animals; Biodiversity; Evolution, Molecular; Gene Expression Regulation; Genome; Multigene Family; Phylogeny; Stramenopiles, classification/genetics; Transcription Factors, genetics},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {PONE-D-14-20048},
  pmid = {25375671},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1371/journal.pone.0111841}
}
@article{Correa2008,
  title = {The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes.},
  author = {Corr{\^{e}}a, Luiz Gustavo Guedes and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Schrago, Carlos Guerra and {dos Santos}, Renato Vicentini and Mueller-Roeber, Bernd and Vincentz, Michel},
  journal = {PLoS One},
  year = {2008},
  number = {8},
  pages = {e2944},
  volume = {3},
  abstract = {Transcription factors of the basic leucine zipper (bZIP) family control important processes in all eukaryotes. In plants, bZIPs are regulators of many central developmental and physiological processes including photomorphogenesis, leaf and seed formation, energy homeostasis, and abiotic and biotic stress responses. Here we performed a comprehensive phylogenetic analysis of bZIP genes from algae, mosses, ferns, gymnosperms and angiosperms.We identified 13 groups of bZIP homologues in angiosperms, three more than known before, that represent 34 Possible Groups of Orthologues (PoGOs). The 34 PoGOs may correspond to the complete set of ancestral angiosperm bZIP genes that participated in the diversification of flowering plants. Homologous genes dedicated to seed-related processes and ABA-mediated stress responses originated in the common ancestor of seed plants, and three groups of homologues emerged in the angiosperm lineage, of which one group plays a role in optimizing the use of energy.Our data suggest that the ancestor of green plants possessed four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments.},
  doi = {10.1371/journal.pone.0002944},
  institution = {Centro de Biologia Molecular e Engenharia Genética, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil.},
  keywords = {Angiosperms, genetics; Basic-Leucine Zipper Transcription Factors, genetics/physiology; Evolution, Molecular; Founder Effect; Gene Pool; Genes, Plant; Genetic Variation; Heterozygote Detection; Phylogeny; Plant Proteins, genetics/physiology; Plants, classification/genetics},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pmid = {18698409},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1371/journal.pone.0002944}
}
@article{Cristancho2014,
  title = {Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales.},
  author = {Cristancho, Marco A. and Botero-Rozo, David Octavio and Giraldo, William and Tabima, Javier and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Escobar, Carolina and Rozo, Yomara and Rivera, Luis F. and Dur{\'{a}}n, Andr{\'{e}}s and Restrepo, Silvia and Eilam, Tamar and Anikster, Yehoshua and Gait{\'{a}}n, Alvaro L.},
  journal = {Front Plant Sci},
  year = {2014},
  pages = {594},
  volume = {5},
  abstract = {Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4\% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94\% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8\%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.},
  doi = {10.3389/fpls.2014.00594},
  institution = {Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pmid = {25400655},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.3389/fpls.2014.00594}
}
@article{deCastro2016,
  title = {The Aspergillus fumigatus SchA(SCH9) kinase modulates SakA(HOG1) MAP kinase activity and it is essential for virulence.},
  author = {{de Castro}, Patr{\'{\i}}cia Alves and {Dos Reis}, Thaila Fernanda and Dolan, Stephen K. and Manfiolli, Adriana Oliveira and Brown, Neil Andrew and Jones, Gary W. and Doyle, Sean and Ria{\~{n}}o-Pach{\'{o}}n, Diego M. and Squina, F{\'{a}}bio M{\'{a}}rcio and Caldana, Camila and Singh, Ashutosh and {Del Poeta}, Maurizio and Hagiwara, Daisuke and Silva-Rocha, Rafael and Goldman, Gustavo H.},
  journal = {Mol Microbiol},
  year = {2016},
  month = {Aug},
  abstract = {The serine-threonine kinase TOR, the Target of Rapamycin, is an important regulator of nutrient, energy, and stress signaling in eukaryotes. Sch9, a Ser/Thr kinase of AGC family (the cAMP-dependent PKA, cGMP- dependent protein kinase G and phospholipid-dependent protein kinase C family), is a substrate of TOR. Here, we characterized the fungal opportunistic pathogen Aspergillus fumigatus Sch9 homologue (SchA). The schA null mutant was sensitive to rapamycin, high concentrations of calcium, hyperosmotic stress, and SchA was involved in iron metabolism. The ΔschA null mutant showed increased phosphorylation of SakA, the A. fumigatus Hog1 homologue. The schA null mutant has increased and decreased trehalose and glycerol accumulation, respectively, suggesting SchA performs different roles for glycerol and trehalose accumulation during osmotic stress. The schA was transcriptionally regulated by osmotic stress and this response was dependent on SakA and MpkC. The double ΔschA ΔsakA and ΔschA ΔmpkC mutants were more sensitive to osmotic stress than the corresponding parental strains. Transcriptomics and proteomics identified direct and indirect targets of SchA post-exposure to hyperosmotic stress. Finally, ΔschA was avirulent in a low dose murine infection model. Our results suggest there is a complex network of interactions amongst the A. fumigatus TOR, SakA and SchA pathways. This article is protected by copyright. All rights reserved.},
  doi = {10.1111/mmi.13484},
  institution = {Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.},
  language = {eng},
  medline-pst = {aheadofprint},
  owner = {diriano},
  pmid = {27538790},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1111/mmi.13484}
}
@article{DosSantos2015,
  title = {Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea.},
  author = {{Dos Santos}, Renato Augusto Corr{\^{e}}a and Berretta, Andresa Aparecida and Barud, Hernane da Silva and Ribeiro, Sidney Jos{\'{e}} Lima and Gonz{\'{a}}lez-Garc{\'{\i}}a, Laura Natalia and Zucchi, Tiago Domingues and Goldman, Gustavo H. and Ria{\~{n}}o-Pach{\'{o}}n, Diego M.},
  journal = {Genome Announc},
  year = {2015},
  number = {6},
  volume = {3},
  abstract = {Here, we present the draft genome sequence of Komagataeibacter intermedius strain AF2, which was isolated from Kombucha tea and is capable of producing cellulose, although at lower levels compared to another bacterium from the same environment, K. rhaeticus strain AF1.},
  doi = {10.1128/genomeA.01404-15},
  institution = {Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brazil diego.riano@bioetanol.org.br ggoldman@usp.br.},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {3/6/e01404-15},
  pmid = {26634755},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1128/genomeA.01404-15}
}
@article{DosSantos2014,
  title = {Draft Genome Sequence of Komagataeibacter rhaeticus Strain AF1, a High Producer of Cellulose, Isolated from Kombucha Tea.},
  author = {{Dos Santos}, Renato Augusto Corr{\^{e}}a and Berretta, Andresa A. and Barud, Hernane da Silva and Ribeiro, Sidney Jos{\'{e}} Lima and Gonz{\'{a}}lez-Garc{\'{\i}}a, Laura Natalia and Zucchi, Tiago Domingues and Goldman, Gustavo H. and Ria{\~{n}}o-Pach{\'{o}}n, Diego M.},
  journal = {Genome Announc},
  year = {2014},
  number = {4},
  volume = {2},
  abstract = {Here, we present the draft genome sequence of Komagatabaeicter rhaeticus strain AF1, which was isolated from Kombucha tea and is capable of producing high levels of cellulose.},
  doi = {10.1128/genomeA.00731-14},
  institution = {Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Campinas, SP, Brazil diego.riano@bioetanol.org.br ggoldman@usp.br.},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {2/4/e00731-14},
  pmid = {25059874},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1128/genomeA.00731-14}
}
@article{Dreyer2012,
  title = {Molecular Evolution of Slow and Quick Anion Channels (SLACs and QUACs/ALMTs).},
  author = {Dreyer, Ingo and Gomez-Porras, Judith Lucia and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Hedrich, Rainer and Geiger, Dietmar},
  journal = {Front Plant Sci},
  year = {2012},
  pages = {263},
  volume = {3},
  abstract = {Electrophysiological analyses conducted about 25 years ago detected two types of anion channels in the plasma membrane of guard cells. One type of channel responds slowly to changes in membrane voltage while the other responds quickly. Consequently, they were named SLAC, for SLow Anion Channel, and QUAC, for QUick Anion Channel. Recently, genes SLAC1 and QUAC1/ALMT12, underlying the two different anion current components, could be identified in the model plant Arabidopsis thaliana. Expression of the gene products in Xenopus oocytes confirmed the quick and slow current kinetics. In this study we provide an overview on our current knowledge on slow and quick anion channels in plants and analyze the molecular evolution of ALMT/QUAC-like and SLAC-like channels. We discovered fingerprints that allow screening databases for these channel types and were able to identify 192 (177 non-redundant) SLAC-like and 422 (402 non-redundant) ALMT/QUAC-like proteins in the fully sequenced genomes of 32 plant species. Phylogenetic analyses provided new insights into the molecular evolution of these channel types. We also combined sequence alignment and clustering with predictions of protein features, leading to the identification of known conserved phosphorylation sites in SLAC1-like channels along with potential sites that have not been yet experimentally confirmed. Using a similar strategy to analyze the hydropathicity of ALMT/QUAC-like channels, we propose a modified topology with additional transmembrane regions that integrates structure and function of these membrane proteins. Our results suggest that cross-referencing phylogenetic analyses with position-specific protein properties and functional data could be a very powerful tool for genome research approaches in general.},
  doi = {10.3389/fpls.2012.00263},
  institution = {Plant Biophysics, Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid Madrid, Spain.},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pmid = {23226151},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.3389/fpls.2012.00263}
}
@article{Gomez-Porras2007,
  title = {Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice.},
  author = {G{\'{o}}mez-Porras, Judith L. and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Dreyer, Ingo and Mayer, Jorge E. and Mueller-Roeber, Bernd},
  journal = {BMC Genomics},
  year = {2007},
  pages = {260},
  volume = {8},
  abstract = {In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa).Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters.Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks.},
  doi = {10.1186/1471-2164-8-260},
  institution = {University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str, 24-25, Haus 20, D-14476 Potsdam-Golm, Germany. judith.gomez@uni-bielefeld.de},
  keywords = {Abscisic Acid, pharmacology; Arabidopsis, genetics; Base Sequence; Chromosome Mapping, methods; Computational Biology; Gene Dosage; Gene Expression Regulation, Plant, drug effects; Gene Order; Genes, Plant; Genome, Plant; Molecular Sequence Data; Oryza, genetics; Response Elements, drug effects},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {1471-2164-8-260},
  pmid = {17672917},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1186/1471-2164-8-260}
}
@article{Gomez-Porras2012,
  title = {Phylogenetic analysis of k(+) transporters in bryophytes, lycophytes, and flowering plants indicates a specialization of vascular plants.},
  author = {Gomez-Porras, Judith Lucia and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Benito, Bego{\~{n}}a and Haro, Rosario and Sklodowski, Kamil and Rodr{\'{\i}}guez-Navarro, Alonso and Dreyer, Ingo},
  journal = {Front Plant Sci},
  year = {2012},
  pages = {167},
  volume = {3},
  abstract = {As heritage from early evolution, potassium (K(+)) is absolutely necessary for all living cells. It plays significant roles as stabilizer in metabolism and is important for enzyme activation, stabilization of protein synthesis, and neutralization of negative charges on cellular molecules as proteins and nucleic acids. Land plants even enlarged this spectrum of K(+) utilization after having gone ashore, despite the fact that K(+) is far less available in their new oligotrophic habitats than in sea water. Inevitably, plant cells had to improve and to develop unique transport systems for K(+) accumulation and distribution. In the past two decades a manifold of K(+) transporters from flowering plants has been identified at the molecular level. The recently published genome of the fern ally Selaginella moellendorffii now helps in providing a better understanding on the molecular changes involved in the colonization of land and the development of the vasculature and the seeds. In this article we present an inventory of K(+) transporters of this lycophyte and pigeonhole them together with their relatives from the moss Physcomitrella patens, the monocotyledon Oryza sativa, and two dicotyledonous species, the herbaceous plant Arabidopsis thaliana, and the tree Populus trichocarpa. Interestingly, the transition of green plants from an aqueous to a dry environment coincides with a dramatic reduction in the diversity of voltage-gated potassium channels followed by a diversification on the basis of one surviving K(+) channel class. The first appearance of K(+) release (K(out)) channels in S. moellendorffii that were shown in Arabidopsis to be involved in xylem loading and guard cell closure coincides with the specialization of vascular plants and may indicate an important adaptive step.},
  doi = {10.3389/fpls.2012.00167},
  institution = {Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid Madrid, Spain.},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pmid = {22876252},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.3389/fpls.2012.00167}
}
@article{Lopez-Kleine2013,
  title = {Chromosome 10 in the tomato plant carries clusters of genes responsible for field resistance/defence to Phytophthora infestans.},
  author = {L{\'{o}}pez-Kleine, Liliana and Pinz{\'{o}}n, Andr{\'{e}}s and Chaves, Diego and Restrepo, Silvia and Ria{\~{n}}o-Pach{\'{o}}n, Diego M.},
  journal = {Genomics},
  year = {2013},
  month = {Apr},
  number = {4},
  pages = {249--255},
  volume = {101},
  abstract = {The main objective of the present study was to reanalyse tomato expression data that was previously submitted to the Tomato Expression Database to dissect the resistance/defence genomic and metabolic responses of tomato to Phytophthora infestans under field conditions. Overrepresented gene sets belonging to chromosome 10 were identified using the Gene Set Enrichment Analysis, and we found that these genes tend to be located towards the end of the chromosome 10. An analysis of syntenic regions between Arabidopsis thaliana chromosomes and the tomato chromosome 10 allowed us to identify conserved regions in the two genomes. In addition to allowing for the identification of tomato candidate genes participating in resistance/defence in the field, this approach allowed us to investigate the relationships of the candidate genes with chromosomal position and participation in metabolic functions, thus offering more insight into the phenomena occurring during the infection process.},
  doi = {10.1016/j.ygeno.2013.02.001},
  institution = {Departamento de Estadística, Universidad Nacional de Colombia, Bogotá D.C., Colombia. llopezk@unal.edu.co},
  keywords = {Arabidopsis, genetics; Chromosomes, Plant, genetics; Conserved Sequence; Databases, Genetic; Disease Resistance, genetics; Genes, Plant; Lycopersicon esculentum, genetics/metabolism/microbiology; Multigene Family; Phytophthora infestans; Synteny},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pii = {S0888-7543(13)00017-7},
  pmid = {23402767},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1016/j.ygeno.2013.02.001}
}
@article{Lang2010,
  title = {Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity.},
  author = {Lang, Daniel and Weiche, Benjamin and Timmerhaus, Gerrit and Richardt, Sandra and Ria{\~{n}}o-Pach{\'{o}}n, Diego M. and Corr{\^{e}}a, Luiz G G. and Reski, Ralf and Mueller-Roeber, Bernd and Rensing, Stefan A.},
  journal = {Genome Biol Evol},
  year = {2010},
  pages = {488--503},
  volume = {2},
  abstract = {Evolutionary retention of duplicated genes encoding transcription-associated proteins (TAPs, comprising transcription factors and other transcriptional regulators) has been hypothesized to be positively correlated with increasing morphological complexity and paleopolyploidizations, especially within the plant kingdom. Here, we present the most comprehensive set of classification rules for TAPs and its application for genome-wide analyses of plants and algae. Using a dated species tree and phylogenetic comparative (PC) analyses, we define the timeline of TAP loss, gain, and expansion among Viridiplantae and find that two major bursts of gain/expansion occurred, coinciding with the water-to-land transition and the radiation of flowering plants. For the first time, we provide PC proof for the long-standing hypothesis that TAPs are major driving forces behind the evolution of morphological complexity, the latter in Plantae being shaped significantly by polyploidization and subsequent biased paleolog retention. Principal component analysis incorporating the number of TAPs per genome provides an alternate and significant proxy for complexity, ideally suited for PC genomics. Our work lays the ground for further interrogation of the shaping of gene regulatory networks underlying the evolution of organism complexity.},
  doi = {10.1093/gbe/evq032},
  institution = {Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Germany.},
  keywords = {Evolution, Molecular; Gene Duplication; Gene Expression Regulation, Plant; Genome, Plant; Genome-Wide Association Study; Markov Chains; MicroRNAs, genetics; Phylogeny; Plant Proteins, classification/genetics/metabolism; Plants, genetics/metabolism; RNA, Plant, genetics; Time Factors; Transcription Factors, classification/genetics/metabolism; Transcription, Genetic},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {evq032},
  pmid = {20644220},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1093/gbe/evq032}
}
@article{Mandelli2015,
  title = {Draft Genome Sequence of the Thermophile Thermus filiformis ATCC 43280, Producer of Carotenoid-(Di)glucoside-Branched Fatty Acid (Di)esters and Source of Hyperthermostable Enzymes of Biotechnological Interest.},
  author = {Mandelli, Fernanda and {Oliveira Ramires}, Brenda and Couger, Matthew Brian and Paix{\~{a}}o, Douglas A A. and Camilo, Cesar M. and Polikarpov, Igor and Prade, Rolf and Ria{\~{n}}o-Pach{\'{o}}n, Diego M. and Squina, Fabio M.},
  journal = {Genome Announc},
  year = {2015},
  number = {3},
  volume = {3},
  abstract = {Here, we present the draft genome sequence of Thermus filiformis strain ATCC 43280, a thermophile bacterium capable of producing glycosylated carotenoids acylated with branched fatty acids and enzymes of biotechnological potential.},
  doi = {10.1128/genomeA.00475-15},
  institution = {Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil diego.riano@bioetanol.org.br fabio.squina@bioetanol.org.br.},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {3/3/e00475-15},
  pmid = {25977443},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1128/genomeA.00475-15}
}
@article{Marine2015,
  title = {On and Under the Skin: Emerging Basidiomycetous Yeast Infections Caused by Trichosporon Species.},
  author = {Marin{\'{e}}, Mar{\c{c}}al and Brown, Neil Andrew and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Goldman, Gustavo Henrique},
  journal = {PLoS Pathog},
  year = {2015},
  month = {Jul},
  number = {7},
  pages = {e1004982},
  volume = {11},
  doi = {10.1371/journal.ppat.1004982},
  institution = {Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil; Laboratório Nacional de Ciência e Tecnologia do Bioetanol-CTBE, Campinas, São Paulo, Brazil.},
  keywords = {Animals; DNA, Ribosomal, genetics; Humans; Mycological Typing Techniques, methods; Piedra, diagnosis/microbiology/therapy; Skin, microbiology; Trichosporon, classification/pathogenicity; Trichosporonosis, diagnosis/microbiology/therapy; Yeasts},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {PPATHOGENS-D-15-00581},
  pmid = {26226483},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1371/journal.ppat.1004982}
}
@article{Mattiello2015,
  title = {Physiological and transcriptional analyses of developmental stages along sugarcane leaf.},
  author = {Mattiello, Lucia and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Martins, Marina Camara Mattos and {da Cruz}, Larissa Prado and Bassi, Denis and Marchiori, Paulo Eduardo Ribeiro and Ribeiro, Rafael Vasconcelos and Labate, M{\^{o}}nica T Veneziano and Labate, Carlos Alberto and Menossi, Marcelo},
  journal = {BMC Plant Biol},
  year = {2015},
  pages = {300},
  volume = {15},
  abstract = {Sugarcane is one of the major crops worldwide. It is cultivated in over 100 countries on 22 million ha. The complex genetic architecture and the lack of a complete genomic sequence in sugarcane hamper the adoption of molecular approaches to study its physiology and to develop new varieties. Investments on the development of new sugarcane varieties have been made to maximize sucrose yield, a trait dependent on photosynthetic capacity. However, detailed studies on sugarcane leaves are scarce. In this work, we report the first molecular and physiological characterization of events taking place along a leaf developmental gradient in sugarcane.Photosynthetic response to CO2 indicated divergence in photosynthetic capacity based on PEPcase activity, corroborated by activity quantification (both in vivo and in vitro) and distinct levels of carbon discrimination on different segments along leaf length. Additionally, leaf segments had contrasting amount of chlorophyll, nitrogen and sugars. RNA-Seq data indicated a plethora of biochemical pathways differentially expressed along the leaf. Some transcription factors families were enriched on each segment and their putative functions corroborate with the distinct developmental stages. Several genes with higher expression in the middle segment, the one with the highest photosynthetic rates, were identified and their role in sugarcane productivity is discussed. Interestingly, sugarcane leaf segments had a different transcriptional behavior compared to previously published data from maize.This is the first report of leaf developmental analysis in sugarcane. Our data on sugarcane is another source of information for further studies aiming to understand and/or improve C4 photosynthesis. The segments used in this work were distinct in their physiological status allowing deeper molecular analysis. Although limited in some aspects, the comparison to maize indicates that all data acquired on one C4 species cannot always be easily extrapolated to other species. However, our data indicates that some transcriptional factors were segment-specific and the sugarcane leaf undergoes through the process of suberizarion, photosynthesis establishment and senescence.},
  doi = {10.1186/s12870-015-0694-z},
  institution = {Laboratório de Genoma Funcional, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Caixa Postal 6109, Campinas, 13083-862, SP, Brazil. menossi@unicamp.br.},
  keywords = {Gene Expression Regulation, Plant; Molecular Sequence Data; Plant Leaves, genetics/growth /&/ development; Plant Proteins, genetics/metabolism; Saccharum, genetics/growth /&/ development; Sequence Analysis, DNA},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {10.1186/s12870-015-0694-z},
  pmid = {26714767},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1186/s12870-015-0694-z}
}
@article{Merchant2007,
  title = {The Chlamydomonas genome reveals the evolution of key animal and plant functions.},
  author = {Merchant, Sabeeha S. and Prochnik, Simon E. and Vallon, Olivier and Harris, Elizabeth H. and Karpowicz, Steven J. and Witman, George B. and Terry, Astrid and Salamov, Asaf and Fritz-Laylin, Lillian K. and Mar{\'{e}}chal-Drouard, Laurence and Marshall, Wallace F. and Qu, Liang-Hu and Nelson, David R. and Sanderfoot, Anton A. and Spalding, Martin H. and Kapitonov, Vladimir V. and Ren, Qinghu and Ferris, Patrick and Lindquist, Erika and Shapiro, Harris and Lucas, Susan M. and Grimwood, Jane and Schmutz, Jeremy and Cardol, Pierre and Cerutti, Heriberto and Chanfreau, Guillaume and Chen, Chun-Long and Cognat, Val{\'{e}}rie and Croft, Martin T. and Dent, Rachel and Dutcher, Susan and Fern{\'{a}}ndez, Emilio and Fukuzawa, Hideya and Gonz{\'{a}}lez-Ballester, David and Gonz{\'{a}}lez-Halphen, Diego and Hallmann, Armin and Hanikenne, Marc and Hippler, Michael and Inwood, William and Jabbari, Kamel and Kalanon, Ming and Kuras, Richard and Lefebvre, Paul A. and Lemaire, St{\'{e}}phane D. and Lobanov, Alexey V. and Lohr, Martin and Manuell, Andrea and Meier, Iris and Mets, Laurens and Mittag, Maria and Mittelmeier, Telsa and Moroney, James V. and Moseley, Jeffrey and Napoli, Carolyn and Nedelcu, Aurora M. and Niyogi, Krishna and Novoselov, Sergey V. and Paulsen, Ian T. and Pazour, Greg and Purton, Saul and Ral, Jean-Philippe and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Riekhof, Wayne and Rymarquis, Linda and Schroda, Michael and Stern, David and Umen, James and Willows, Robert and Wilson, Nedra and Zimmer, Sara Lana and Allmer, Jens and Balk, Janneke and Bisova, Katerina and Chen, Chong-Jian and Elias, Marek and Gendler, Karla and Hauser, Charles and Lamb, Mary Rose and Ledford, Heidi and Long, Joanne C. and Minagawa, Jun and Page, M Dudley and Pan, Junmin and Pootakham, Wirulda and Roje, Sanja and Rose, Annkatrin and Stahlberg, Eric and Terauchi, Aimee M. and Yang, Pinfen and Ball, Steven and Bowler, Chris and Dieckmann, Carol L. and Gladyshev, Vadim N. and Green, Pamela and Jorgensen, Richard and Mayfield, Stephen and Mueller-Roeber, Bernd and Rajamani, Sathish and Sayre, Richard T. and Brokstein, Peter and Dubchak, Inna and Goodstein, David and Hornick, Leila and Huang, Y Wayne and Jhaveri, Jinal and Luo, Yigong and Mart{\'{\i}}nez, Diego and Ngau, Wing Chi Abby and Otillar, Bobby and Poliakov, Alexander and Porter, Aaron and Szajkowski, Lukasz and Werner, Gregory and Zhou, Kemin and Grigoriev, Igor V. and Rokhsar, Daniel S. and Grossman, Arthur R.},
  journal = {Science},
  year = {2007},
  month = {Oct},
  number = {5848},
  pages = {245--250},
  volume = {318},
  abstract = {Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.},
  doi = {10.1126/science.1143609},
  institution = {Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.},
  keywords = {Algal Proteins, genetics/physiology; Animals; Biological Evolution; Chlamydomonas reinhardtii, genetics/physiology; Chloroplasts, metabolism; Computational Biology; DNA, Algal, genetics; Flagella, metabolism; Genes; Genome; Genomics; Membrane Transport Proteins, genetics/physiology; Molecular Sequence Data; Multigene Family; Photosynthesis, genetics; Phylogeny; Plants, genetics; Proteome; Sequence Analysis, DNA},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pii = {318/5848/245},
  pmid = {17932292},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1126/science.1143609}
}
@article{Oliveira2014,
  title = {Pseudozyma brasiliensis sp. nov., a xylanolytic, ustilaginomycetous yeast species isolated from an insect pest of sugarcane roots.},
  author = {Oliveira, Juliana Velasco de Castro and Borges, Thuanny A. and {Corr{\^{e}}a dos Santos}, Renato Augusto and Freitas, Larissa F D. and Rosa, Carlos Augusto and Goldman, Gustavo Henrique and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio},
  journal = {Int J Syst Evol Microbiol},
  year = {2014},
  month = {Jun},
  number = {Pt 6},
  pages = {2159--2168},
  volume = {64},
  abstract = {A novel ustilaginomycetous yeast isolated from the intestinal tract of an insect pest of sugarcane roots in Ribeirão Preto, São Paulo State, Brazil, represents a novel species of the genus Pseudozyma based on molecular analyses of the D1/D2 rDNA large subunit and the internal transcribed spacer (ITS1+ITS2) regions. The name Pseudozyma brasiliensis sp. nov. is proposed for this species, with GHG001(T) ( = CBS 13268(T) = UFMG-CM-Y307(T)) as the type strain. P. brasiliensis sp. nov. is a sister species of Pseudozyma vetiver, originally isolated from leaves of vetiver grass and sugarcane in Thailand. P. brasiliensis sp. nov. is able to grow well with xylan as the sole carbon source and produces high levels of an endo-1,4-xylanase that has a higher specific activity in comparison with other eukaryotic xylanases. This enzyme has a variety of industrial applications, indicating the great biotechnological potential of P. brasiliensis.},
  doi = {10.1099/ijs.0.060103-0},
  institution = {Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6170, 13083-970 Campinas, São Paulo, Brazil ggoldman@usp.br diego.riano@bioetanol.org.br.},
  keywords = {Animals; Brazil; DNA, Fungal, genetics; DNA, Ribosomal Spacer, genetics; Endo-1,4-beta Xylanases, metabolism; Insects, microbiology; Intestines, microbiology; Molecular Sequence Data; Mycological Typing Techniques; Phylogeny; Plant Roots; Saccharum; Sequence Analysis, DNA; Ustilaginales, classification/genetics/isolation /&/ purification},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pii = {ijs.0.060103-0},
  pmid = {24682702},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1099/ijs.0.060103-0}
}
@article{Oliveira2013,
  title = {Draft Genome Sequence of Pseudozyma brasiliensis sp. nov. Strain GHG001, a High Producer of Endo-1,4-Xylanase Isolated from an Insect Pest of Sugarcane.},
  author = {Oliveira, Juliana Velasco de Castro and {Dos Santos}, Renato Augusto Corr{\^{e}}a and Borges, Thuanny A. and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Goldman, Gustavo Henrique},
  journal = {Genome Announc},
  year = {2013},
  number = {6},
  volume = {1},
  abstract = {Here, we present the nuclear and mitochondrial genome sequences of Pseudozyma brasiliensis sp. nov. strain GHG001. P. brasiliensis sp. nov. is the closest relative of Pseudozyma vetiver. P. brasiliensis sp. nov. is capable of growing on xylose or xylan as a sole carbon source and has great biotechnological potential.},
  doi = {10.1128/genomeA.00920-13},
  institution = {a e Materiais (CNPEM), Campinas, São Paulo, Brazil.},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {1/6/e00920-13},
  pmid = {24356824},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1128/genomeA.00920-13}
}
@article{Omidbakhshfard2014,
  title = {A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana.},
  author = {Omidbakhshfard, Mohammad Amin and Winck, Flavia Vischi and Arvidsson, Samuel and Ria{\~{n}}o-Pach{\'{o}}n, Diego M. and Mueller-Roeber, Bernd},
  journal = {J Integr Plant Biol},
  year = {2014},
  month = {Jun},
  number = {6},
  pages = {527--538},
  volume = {56},
  abstract = {The control of gene expression by transcriptional regulators and other types of functionally relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in all organisms. DNA transactions require the controlled interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions (NDRs) of the chromatin. Formaldehyde-assisted isolation of regulatory elements (FAIRE) has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successfully employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol will be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species.},
  doi = {10.1111/jipb.12151},
  institution = {University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, 14476, Germany; Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany.},
  keywords = {Arabidopsis, drug effects/genetics; Chromosomes, Plant, genetics; DNA, Plant, genetics/isolation /&/ purification; Formaldehyde, pharmacology; Genes, Essential; Genome, Plant, genetics; High-Throughput Nucleotide Sequencing; Molecular Biology, methods; Polymerase Chain Reaction; Regulatory Sequences, Nucleic Acid, genetics; Sonication},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pmid = {24373132},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1111/jipb.12151}
}
@article{Perez-Rodriguez2010,
  title = {PlnTFDB: updated content and new features of the plant transcription factor database.},
  author = {P{\'{e}}rez-Rodr{\'{\i}}guez, Paulino and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Corr{\^{e}}a, Luiz Gustavo Guedes and Rensing, Stefan A. and Kersten, Birgit and Mueller-Roeber, Bernd},
  journal = {Nucleic Acids Res},
  year = {2010},
  month = {Jan},
  number = {Database issue},
  pages = {D822--D827},
  volume = {38},
  abstract = {The Plant Transcription Factor Database (PlnTFDB; http://plntfdb.bio.uni-potsdam.de/v3.0/) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species (sensu lato) whose genomes have been completely sequenced and annotated. The complete sets of 84 families of TFs and TRs from 19 species ranging from unicellular red and green algae to angiosperms are included in PlnTFDB, representing >1.6 billion years of evolution of gene regulatory networks. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.},
  doi = {10.1093/nar/gkp805},
  institution = {Department of Molecular Biology, Institute of Biochemistry and Biology, GoFORSYS, University of Potsdam, Karl-Liebknecht-Str 24-25, Haus 20, 14476 Potsdam-Golm, Germany.},
  keywords = {Computational Biology, methods/trends; Databases, Genetic; Databases, Protein; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes, Plant; Genome, Plant; Information Storage and Retrieval, methods; Internet; Plant Diseases, genetics; Plant Proteins, metabolism; Plants, metabolism; Protein Structure, Tertiary; Software; Transcription Factors, metabolism},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pii = {gkp805},
  pmid = {19858103},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1093/nar/gkp805}
}
@article{Read2013,
  title = {Pan genome of the phytoplankton Emiliania underpins its global distribution.},
  author = {Read, Betsy A. and Kegel, Jessica and Klute, Mary J. and Kuo, Alan and Lefebvre, Stephane C. and Maumus, Florian and Mayer, Christoph and Miller, John and Monier, Adam and Salamov, Asaf and Young, Jeremy and Aguilar, Maria and Claverie, Jean-Michel and Frickenhaus, Stephan and Gonzalez, Karina and Herman, Emily K. and Lin, Yao-Cheng and Napier, Johnathan and Ogata, Hiroyuki and Sarno, Analissa F. and Shmutz, Jeremy and Schroeder, Declan and {de Vargas}, Colomban and Verret, Frederic and {von Dassow}, Peter and Valentin, Klaus and {Van de Peer}, Yves and Wheeler, Glen and , Emiliania huxleyi Annotation Consortium and Dacks, Joel B. and Delwiche, Charles F. and Dyhrman, Sonya T. and Gl{\"{o}}ckner, Gernot and John, Uwe and Richards, Thomas and Worden, Alexandra Z. and Zhang, Xiaoyu and Grigoriev, Igor V.},
  journal = {Nature},
  year = {2013},
  month = {Jul},
  number = {7457},
  pages = {209--213},
  volume = {499},
  abstract = {Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.},
  doi = {10.1038/nature12221},
  institution = {Department of Biological Sciences, California State University San Marcos, San Marcos, California 92096, USA.},
  keywords = {Calcification, Physiologic; Calcium, metabolism; Carbonic Anhydrases, genetics/metabolism; Ecosystem; Genome, genetics; Haptophyta, classification/genetics/isolation /&/ purification/metabolism; Oceans and Seas; Phylogeny; Phytoplankton, genetics; Proteome, genetics; Seawater},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pii = {nature12221},
  pmid = {23760476},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1038/nature12221}
}
@article{Riano-Pachon2008,
  title = {Green transcription factors: a chlamydomonas overview.},
  author = {Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Corr{\^{e}}a, Luiz Gustavo Guedes and Trejos-Espinosa, Ra{\'{u}}l and Mueller-Roeber, Bernd},
  journal = {Genetics},
  year = {2008},
  month = {May},
  number = {1},
  pages = {31--39},
  volume = {179},
  abstract = {Transcription factors (TFs) control gene expression by interacting with cis-elements in target gene promoters. Transcription regulators (TRs) assist in controlling gene expression through interaction with TFs, chromatin remodeling, or other mechanisms. Both types of proteins thus constitute master controllers of dynamic transcriptional networks. To uncover such control elements in the photosynthetic green alga Chlamydomonas reinhardtii, we performed a comprehensive analysis of its genome sequence. In total, we identified 234 genes encoding 147 TFs and 87 TRs of approximately 40 families. The set of putative TFs and TRs, including their transcript and protein sequences, domain architectures, and supporting information about putative orthologs, is available at http://plntfdb.bio.uni-potsdam.de/v2.0/. Twelve of 34 plant-specific TF families were found in at least one algal species, indicating their early evolutionary origin. Twenty-two plant-specific TF families and one plant-specific TR family were not observed in algae, suggesting their specific association with developmental or physiological processes characteristic to multicellular plants. We also analyzed the occurrence of proteins that constitute the light-regulated transcriptional network in angiosperms and found putative algal orthologs for most of them. Our analysis provides a solid ground for future experimental studies aiming at deciphering the transcriptional regulatory networks in green algae.},
  doi = {10.1534/genetics.107.086090},
  institution = {Department of Molecular Biology, University of Potsdam, 14476 Potsdam-Golm, Germany.},
  keywords = {Angiosperms, genetics; Animals; Chlamydomonas reinhardtii, genetics; Computational Biology; Genes, Protozoan, genetics; Genomics; Phylogeny; Species Specificity; Transcription Factors, genetics},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pii = {179/1/31},
  pmid = {18493038},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1534/genetics.107.086090}
}
@article{Riano-Pachon2005,
  author = {Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Dreyer, Ingo and Mueller-Roeber, Bernd},
  title = {Orphan transcripts in Arabidopsis thaliana: identification of several hundred previously unrecognized genes.},
  journal = {Plant J},
  year = {2005},
  volume = {43},
  number = {2},
  pages = {205--212},
  month = {Jul},
  abstract = {Expressed sequence tags (ESTs) represent a huge resource for the discovery of previously unknown genetic information and functional genome assignment. In this study we screened a collection of 178 292 ESTs from Arabidopsis thaliana by testing them against previously annotated genes of the Arabidopsis genome. We identified several hundreds of new transcripts that match the Arabidopsis genome at so far unassigned loci. The transcriptional activity of these loci was independently confirmed by comparison with the Salk Whole Genome Array Data. To a large extent, the newly identified transcriptionally active genomic regions do not encode 'classic' proteins, but instead generate non-coding RNAs and/or small peptide-coding RNAs of presently unknown biological function. More than 560 transcripts identified in this study are not represented by the Affymetrix GeneChip arrays currently widely used for expression profiling in A. thaliana. Our data strongly support the hypothesis that numerous previously unknown genes exist in the Arabidopsis genome.},
  doi = {10.1111/j.1365-313X.2005.02438.x},
  institution = {Department of Molecular Biology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 25, Haus 20, D-14476 Golm/Potsdam, Germany.},
  keywords = {Arabidopsis Proteins, genetics; Arabidopsis, genetics; Expressed Sequence Tags; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes, Plant; RNA, Messenger; RNA, Plant; Transcription, Genetic},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pii = {TPJ2438},
  pmid = {15998307},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1111/j.1365-313X.2005.02438.x}
}
@article{Riano-Pachon2010,
  title = {Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana.},
  author = {Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Kleessen, Sabrina and Neigenfind, Jost and Durek, Pawel and Weber, Elke and Engelsberger, Wolfgang R. and Walther, Dirk and Selbig, Joachim and Schulze, Waltraud X. and Kersten, Birgit},
  journal = {BMC Genomics},
  year = {2010},
  pages = {411},
  volume = {11},
  abstract = {Protein phosphorylation is an important post-translational modification influencing many aspects of dynamic cellular behavior. Site-specific phosphorylation of amino acid residues serine, threonine, and tyrosine can have profound effects on protein structure, activity, stability, and interaction with other biomolecules. Phosphorylation sites can be affected in diverse ways in members of any species, one such way is through single nucleotide polymorphisms (SNPs). The availability of large numbers of experimentally identified phosphorylation sites, and of natural variation datasets in Arabidopsis thaliana prompted us to analyze the effect of non-synonymous SNPs (nsSNPs) onto phosphorylation sites.From the analyses of 7,178 experimentally identified phosphorylation sites we found that: (i) Proteins with multiple phosphorylation sites occur more often than expected by chance. (ii) Phosphorylation hotspots show a preference to be located outside conserved domains. (iii) nsSNPs affected experimental phosphorylation sites as much as the corresponding non-phosphorylated amino acid residues. (iv) Losses of experimental phosphorylation sites by nsSNPs were identified in 86 A. thaliana proteins, among them receptor proteins were overrepresented.These results were confirmed by similar analyses of predicted phosphorylation sites in A. thaliana. In addition, predicted threonine phosphorylation sites showed a significant enrichment of nsSNPs towards asparagines and a significant depletion of the synonymous substitution. Proteins in which predicted phosphorylation sites were affected by nsSNPs (loss and gain), were determined to be mainly receptor proteins, stress response proteins and proteins involved in nucleotide and protein binding. Proteins involved in metabolism, catalytic activity and biosynthesis were less affected.We analyzed more than 7,100 experimentally identified phosphorylation sites in almost 4,300 protein-coding loci in silico, thus constituting the largest phosphoproteomics dataset for A. thaliana available to date. Our findings suggest a relatively high variability in the presence or absence of phosphorylation sites between different natural accessions in receptor and other proteins involved in signal transduction. Elucidating the effect of phosphorylation sites affected by nsSNPs on adaptive responses represents an exciting research goal for the future.},
  doi = {10.1186/1471-2164-11-411},
  institution = {Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.},
  keywords = {Amino Acid Sequence; Arabidopsis, cytology/genetics/metabolism; Binding Sites; Cell Nucleus, genetics; DNA, Plant, genetics; Humans; Molecular Sequence Data; Phosphorylation; Plant Proteins, chemistry/genetics/metabolism; Polymorphism, Single Nucleotide; Proteome, chemistry/genetics/metabolism},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {1471-2164-11-411},
  pmid = {20594336},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1186/1471-2164-11-411}
}
@article{Riano-Pachon2009,
  title = {GabiPD: the GABI primary database--a plant integrative 'omics' database.},
  author = {Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Nagel, Axel and Neigenfind, Jost and Wagner, Robert and Basekow, Rico and Weber, Elke and Mueller-Roeber, Bernd and Diehl, Svenja and Kersten, Birgit},
  journal = {Nucleic Acids Res},
  year = {2009},
  month = {Jan},
  number = {Database issue},
  pages = {D954--D959},
  volume = {37},
  abstract = {The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different 'omics' fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text-based retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.},
  doi = {10.1093/nar/gkn611},
  institution = {GabiPD team, Bioinformatics group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Berlin, Germany.},
  keywords = {Databases, Genetic; Gene Expression Profiling; Genes, Plant; Genome, Plant; Metabolomics; Plant Proteins, chemistry/genetics/metabolism; Plants, metabolism; Proteomics; Software; Systems Integration},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pii = {gkn611},
  pmid = {18812395},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1093/nar/gkn611}
}
@article{Riano-Pachon2007,
  author = {Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Ruzicic, Slobodan and Dreyer, Ingo and Mueller-Roeber, Bernd},
  title = {PlnTFDB: an integrative plant transcription factor database.},
  journal = {BMC Bioinformatics},
  year = {2007},
  volume = {8},
  pages = {42},
  abstract = {Transcription factors (TFs) are key regulatory proteins that enhance or repress the transcriptional rate of their target genes by binding to specific promoter regions (i.e. cis-acting elements) upon activation or de-activation of upstream signaling cascades. TFs thus constitute master control elements of dynamic transcriptional networks. TFs have fundamental roles in almost all biological processes (development, growth and response to environmental factors) and it is assumed that they play immensely important functions in the evolution of species. In plants, TFs have been employed to manipulate various types of metabolic, developmental and stress response pathways. Cross-species comparison and identification of regulatory modules and hence TFs is thought to become increasingly important for the rational design of new plant biomass. Up to now, however, no computational repository is available that provides access to the largely complete sets of transcription factors of sequenced plant genomes.PlnTFDB is an integrative plant transcription factor database that provides a web interface to access large (close to complete) sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. It also provides an access point to its daughter databases of a species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags (ESTs), domain architecture and scientific literature is provided for each family.We have created lists of putatively complete sets of transcription factors and other transcriptional regulators for five plant genomes. They are publicly available through http://plntfdb.bio.uni-potsdam.de. Further data will be included in the future when the sequences of other plant genomes become available.},
  doi = {10.1186/1471-2105-8-42},
  institution = {Department of Molecular Biology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str, 25 Haus 20, D-14476, Golm, Germany. diriano@uni-potsdam.de},
  keywords = {Databases, Protein; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genome, Plant; Plants, genetics; Promoter Regions, Genetic; Sequence Alignment, methods; Transcription Factors, genetics; User-Computer Interface},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {1471-2105-8-42},
  pmid = {17286856},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1186/1471-2105-8-42}
}
@article{Rohrmann2011,
  title = {Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development.},
  author = {Rohrmann, Johannes and Tohge, Takayuki and Alba, Rob and Osorio, Sonia and Caldana, Camila and McQuinn, Ryan and Arvidsson, Samuel and {van der Merwe}, Margaretha J. and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Mueller-Roeber, Bernd and Fei, Zhangjun and Nesi, Adriano Nunes and Giovannoni, James J. and Fernie, Alisdair R.},
  journal = {Plant J},
  year = {2011},
  month = {Dec},
  number = {6},
  pages = {999--1013},
  volume = {68},
  abstract = {Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real-time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC-MS and LC-MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild-type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes.},
  doi = {10.1111/j.1365-313X.2011.04750.x},
  institution = {Max-Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam, Germany.},
  keywords = {Fruit, growth /&/ development; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes, Plant; Lycopersicon esculentum, genetics/growth /&/ development/metabolism; Oligonucleotide Array Sequence Analysis; Real-Time Polymerase Chain Reaction; Transcription Factors, genetics/metabolism},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pmid = {21851430},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1111/j.1365-313X.2011.04750.x}
}
@article{Rosas-Morales2015,
  title = {Draft genome sequences of clostridium strains native to Colombia with the potential to produce solvents.},
  author = {Rosas-Morales, Juan Pablo and Perez-Mancilla, Ximena and L{\'{o}}pez-Kleine, Liliana and {Montoya Casta{\~{n}}o}, Dolly and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio},
  journal = {Genome Announc},
  year = {2015},
  number = {3},
  volume = {3},
  abstract = {Genomes from four Clostridium sp. strains considered to be mesophilic anaerobic bacteria, isolated from crop soil in Colombia, with a strong potential to produce alcohols like 1,3-propanediol, were analyzed. We present the draft genome of these strains, which will be useful for developing genetic engineering strategies.},
  doi = {10.1128/genomeA.00486-15},
  institution = {Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials, Campinas, Brazil dmontoyac@unal.edu.co diego.riano@bioetanol.org.br.},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {3/3/e00486-15},
  pmid = {25999575},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1128/genomeA.00486-15}
}
@article{Winck2016,
  title = {Analysis of Sensitive CO2 Pathways and Genes Related to Carbon Uptake and Accumulation in Chlamydomonas reinhardtii through Genomic Scale Modeling and Experimental Validation.},
  author = {Winck, Flavia V. and Melo, David O P{\'{a}}ez and Ria{\~{n}}o-Pach{\'{o}}n, Diego M. and Martins, Marina C M. and Caldana, Camila and Barrios, Andr{\'{e}}s F Gonz{\'{a}}lez},
  journal = {Front Plant Sci},
  year = {2016},
  pages = {43},
  volume = {7},
  abstract = {The development of microalgae sustainable applications needs better understanding of microalgae biology. Moreover, how cells coordinate their metabolism toward biomass accumulation is not fully understood. In this present study, flux balance analysis (FBA) was performed to identify sensitive metabolic pathways of Chlamydomonas reinhardtii under varied CO2 inputs. The metabolic network model of Chlamydomonas was updated based on the genome annotation data and sensitivity analysis revealed CO2 sensitive reactions. Biological experiments were performed with cells cultivated at 0.04\% (air), 2.5, 5, 8, and 10\% CO2 concentration under controlled conditions and cell growth profiles and biomass content were measured. Pigments, lipids, proteins, and starch were further quantified for the reference low (0.04\%) and high (10\%) CO2 conditions. The expression level of candidate genes of sensitive reactions was measured and validated by quantitative real time PCR. The sensitive analysis revealed mitochondrial compartment as the major affected by changes on the CO2 concentrations and glycolysis/gluconeogenesis, glyoxylate, and dicarboxylate metabolism among the affected metabolic pathways. Genes coding for glycerate kinase (GLYK), glycine cleavage system, H-protein (GCSH), NAD-dependent malate dehydrogenase (MDH3), low-CO2 inducible protein A (LCIA), carbonic anhydrase 5 (CAH5), E1 component, alpha subunit (PDC3), dual function alcohol dehydrogenase/acetaldehyde dehydrogenase (ADH1), and phosphoglucomutase (GPM2), were defined, among other genes, as sensitive nodes in the metabolic network simulations. These genes were experimentally responsive to the changes in the carbon fluxes in the system. We performed metabolomics analysis using mass spectrometry validating the modulation of carbon dioxide responsive pathways and metabolites. The changes on CO2 levels mostly affected the metabolism of amino acids found in the photorespiration pathway. Our updated metabolic network was compared to previous model and it showed more consistent results once considering the experimental data. Possible roles of the sensitive pathways in the biomass metabolism are discussed.},
  doi = {10.3389/fpls.2016.00043},
  institution = {Grupo de Diseño de Productos y Procesos, Department of Chemical Engineering, Universidad de los Andes Bogotá, Colombia.},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pmid = {26904035},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.3389/fpls.2016.00043}
}
@article{Winck2015,
  title = {Insights into immune responses in oral cancer through proteomic analysis of saliva and salivary extracellular vesicles.},
  author = {Winck, Flavia V. and {Prado Ribeiro}, Ana Carolina and {Ramos Domingues}, Rom{\^{e}}nia and Ling, Liu Yi and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Rivera, C{\'{e}}sar and Brand{\~{a}}o, Tha{\'{\i}}s Bianca and Gouvea, Adriele Ferreira and Santos-Silva, Alan Roger and Coletta, Ricardo D. and {Paes Leme}, Adriana F.},
  journal = {Sci Rep},
  year = {2015},
  pages = {16305},
  volume = {5},
  abstract = {The development and progression of oral cavity squamous cell carcinoma (OSCC) involves complex cellular mechanisms that contribute to the low five-year survival rate of approximately 20\% among diagnosed patients. However, the biological processes essential to tumor progression are not completely understood. Therefore, detecting alterations in the salivary proteome may assist in elucidating the cellular mechanisms modulated in OSCC and improve the clinical prognosis of the disease. The proteome of whole saliva and salivary extracellular vesicles (EVs) from patients with OSCC and healthy individuals were analyzed by LC-MS/MS and label-free protein quantification. Proteome data analysis was performed using statistical, machine learning and feature selection methods with additional functional annotation. Biological processes related to immune responses, peptidase inhibitor activity, iron coordination and protease binding were overrepresented in the group of differentially expressed proteins. Proteins related to the inflammatory system, transport of metals and cellular growth and proliferation were identified in the proteome of salivary EVs. The proteomics data were robust and could classify OSCC with 90\% accuracy. The saliva proteome analysis revealed that immune processes are related to the presence of OSCC and indicate that proteomics data can contribute to determining OSCC prognosis.},
  doi = {10.1038/srep16305},
  institution = {Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, SP, Brazil.},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {srep16305},
  pmid = {26538482},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1038/srep16305}
}
@article{Winck2012,
  title = {The nuclear proteome of the green alga Chlamydomonas reinhardtii.},
  author = {Winck, Flavia V. and Ria{\~{n}}o-Pach{\'{o}}n, Diego M. and Sommer, Frederik and Rupprecht, Jens and Mueller-Roeber, Bernd},
  journal = {Proteomics},
  year = {2012},
  month = {Jan},
  number = {1},
  pages = {95--100},
  volume = {12},
  abstract = {Nuclear proteins play a central role in regulating gene expression. Their identification is important for understanding how the nuclear repertoire changes over time under different conditions. Nuclear proteins are often underrepresented in proteomic studies due to the frequently low abundance of proteins involved in regulatory processes. So far, only few studies describing the nuclear proteome of plant species have been published. Recently, the genome sequence of the unicellular green alga Chlamydomonas reinhardtii has been obtained and annotated, allowing the development of further detailed studies for this organism. However, a detailed description of its nuclear proteome has not been reported so far. Here, we present an analysis of the nuclear proteome of the sequenced Chlamydomonas strain cc503. Using LC-MS/MS, we identified 672 proteins from nuclei isolates with a maximum 1\% peptide spectrum false discovery rate. Besides well-known proteins (e.g. histones), transcription factors and other transcriptional regulators (e.g. tubby and HMG) were identified. The presence of protein motifs in nuclear proteins was investigated by computational tools, and specific over-represented protein motifs were identified. This study provides new insights into the complexity of the nuclear environment and reveals novel putative protein targets for further studies of nuclear mechanisms.},
  doi = {10.1002/pmic.201000782},
  institution = {GoFORSYS Research Unit for Systems Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany.},
  keywords = {Amino Acid Motifs; Amino Acid Sequence; Cell Nucleus, metabolism; Chlamydomonas reinhardtii, metabolism; Molecular Sequence Data; Peptide Fragments, chemistry; Plant Proteins, chemistry/metabolism; Proteome, chemistry/metabolism; Tandem Mass Spectrometry},
  language = {eng},
  medline-pst = {ppublish},
  owner = {diriano},
  pmid = {22065562},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1002/pmic.201000782}
}
@article{Winck2013,
  title = {Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation.},
  author = {Winck, Flavia Vischi and {Vischi Winck}, Flavia and Arvidsson, Samuel and Ria{\~{n}}o-Pach{\'{o}}n, Diego Mauricio and Hempel, Sabrina and Koseska, Aneta and Nikoloski, Zoran and {Urbina Gomez}, David Alejandro and Rupprecht, Jens and Mueller-Roeber, Bernd},
  journal = {PLoS One},
  year = {2013},
  number = {11},
  pages = {e79909},
  volume = {8},
  abstract = {The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO 2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.},
  doi = {10.1371/journal.pone.0079909},
  institution = {GoFORSYS Research Unit for Systems Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany ; GoFORSYS Research Unit for Systems Biology, Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.},
  keywords = {Carbon, deficiency/metabolism; Carbonic Anhydrases, genetics/metabolism; Chlamydomonas reinhardtii, genetics/metabolism; Gene Regulatory Networks, genetics/physiology; Transcription Factors, genetics/metabolism},
  language = {eng},
  medline-pst = {epublish},
  owner = {diriano},
  pii = {PONE-D-12-35326},
  pmid = {24224019},
  timestamp = {2016.09.10},
  url = {http://dx.doi.org/10.1371/journal.pone.0079909}
}
@article{Winck2016a,
  author = {Winck, Flavia V and Riaño-Pachón, Diego M and Franco, Telma T},
  title = {Editorial: Advances in Microalgae Biology and Sustainable Applications.},
  journal = {Frontiers in plant science},
  year = {2016},
  volume = {7},
  pages = {1385},
  country = {Switzerland},
  created = {2016-10-06},
  doi = {10.3389/fpls.2016.01385},
  issn-linking = {1664-462X},
  keywords = {bioenergy; biofuels; biomass; biotechnology; carbon dioxide; hydrogen; lipids; nutrients},
  nlm-id = {101568200},
  owner = {NLM},
  pmc = {PMC5030231},
  pmid = {27708651},
  pubmodel = {Electronic-eCollection},
  pubstatus = {epublish},
  revised = {2016-11-02}
}
@article{Santos2016,
  author = {Santos, Renato Augusto Correa and Goldman, Gustavo H. and Ria\~no\-Pach\'on, Diego Mauricio},
  title = {ploidyNGS: Visually exploring ploidy with Next Generation Sequencing data},
  journal = {BioRxiv},
  year = {2016},
  month = nov,
  abstract = {Summary: ploidyNGS is a model-free, open source tool to visualize and explore ploidy levels in a newly sequenced genome, exploiting short read data. We tested ploidyNGS using both simulated and real NGS data of the model yeast Saccharomyces cerevisiae. ploidyNGS allows the identification of the ploidy level of a newly sequenced genome in a visual way. Availability and implementation: ploidyNGS is available under the GNU General Public License (GPL) at https://github.com/diriano/ploidyNGS. ploidyNGS is implemented in Python and R.},
  doi = {10.1101/086488},
  keywords = {ploidy, python, R},
  timestamp = {2017-02-01},
  url = {http://biorxiv.org/content/early/2016/11/08/086488}
}
@article{DosSantos2017,
  author = {Dos Santos, Renato Augusto Corrêa and Goldman, Gustavo Henrique and Riaño-Pachón, Diego Mauricio},
  title = {ploidyNGS: Visually exploring ploidy with Next Generation Sequencing data.},
  journal = {Bioinformatics (Oxford, England)},
  year = {2017},
  month = apr,
  issn = {1367-4811},
  abstract = {ploidyNGS is a model-free, open source tool to visualize and explore ploidy levels in a newly sequenced genome, exploiting short read data. We tested ploidyNGS using both simulated and real NGS data of the model yeast Saccharomyces cerevisiae. ploidyNGS allows the identification of the ploidy level of a newly sequenced genome in a visual way. ploidyNGS is available under the GNU General Public License (GPL) at https://github.com/diriano/ploidyNGS . ploidyNGS is implemented in Python and R. diriano@gmail.com.},
  country = {England},
  created = {2017-04-06},
  doi = {10.1093/bioinformatics/btx204},
  issn-linking = {1367-4803},
  nlm-id = {9808944},
  owner = {NLM},
  pii = {3104472},
  pmid = {28383704},
  pubmodel = {Print-Electronic},
  pubstatus = {aheadofprint},
  revised = {2017-04-06}
}
@article{DosReis2017,
  author = {Dos Reis, Thaila Fernanda and Nitsche, Benjamin M and de Lima, Pollyne Borborema Almeida and de Assis, Leandro José and Mellado, Laura and Harris, Steven D and Meyer, Vera and Dos Santos, Renato A Corrêa and Riaño-Pachón, Diego M and Ries, Laure Nicolas Annick and Goldman, Gustavo H},
  title = {The low affinity glucose transporter HxtB is also involved in glucose signalling and metabolism in Aspergillus nidulans.},
  journal = {Scientific reports},
  year = {2017},
  volume = {7},
  pages = {45073},
  month = mar,
  issn = {2045-2322},
  abstract = {One of the drawbacks during second-generation biofuel production from plant lignocellulosic biomass is the accumulation of glucose, the preferred carbon source of microorganisms, which causes the repression of hydrolytic enzyme secretion by industrially relevant filamentous fungi. Glucose sensing, subsequent transport and cellular signalling pathways have been barely elucidated in these organisms. This study therefore characterized the transcriptional response of the filamentous fungus Aspergillus nidulans to the presence of high and low glucose concentrations under continuous chemostat cultivation with the aim to identify novel factors involved in glucose sensing and signalling. Several transcription factor- and transporter-encoding genes were identified as being differentially regulated, including the previously characterized glucose and xylose transporter HxtB. HxtB was confirmed to be a low affinity glucose transporter, localizing to the plasma membrane under low- and high-glucose conditions. Furthermore, HxtB was shown to be involved in conidiation-related processes and may play a role in downstream glucose signalling. A gene predicted to encode the protein kinase PskA was also identified as being important for glucose metabolism. This study identified several proteins with predicted roles in glucose metabolic processes and provides a foundation for further investigation into the response of biotechnologically important filamentous fungi to glucose.},
  country = {England},
  created = {2017-03-31},
  doi = {10.1038/srep45073},
  issn-linking = {2045-2322},
  nlm-id = {101563288},
  owner = {NLM},
  pii = {srep45073},
  pmc = {PMC5374493},
  pmid = {28361917},
  pubmodel = {Electronic},
  pubstatus = {epublish},
  revised = {2017-04-04}
}
@article{Coutoune2017,
  author = {Coutouné, Natalia and Mulato, Aline Tieppo Nogueira and Riaño-Pachón, Diego Mauricio and Oliveira, Juliana Velasco de Castro},
  title = {Draft Genome Sequence of Saccharomyces cerevisiae Barra Grande (BG-1), a Brazilian Industrial Bioethanol-Producing Strain.},
  journal = {Genome announcements},
  year = {2017},
  volume = {5},
  month = mar,
  abstract = {Here, we present the draft genome sequence of Saccharomyces cerevisiae BG-1, a Brazilian industrial strain widely used for bioethanol production from sugarcane. The 11.7-Mb genome sequence consists of 216 scaffolds and harbors 5,607 predicted protein-coding genes.},
  country = {United States},
  created = {2017-03-31},
  doi = {10.1128/genomeA.00111-17},
  issue = {13},
  nlm-id = {101595808},
  owner = {NLM},
  pii = {e00111-17},
  pmid = {28360170},
  pubmodel = {Electronic},
  pubstatus = {epublish},
  revised = {2017-03-31}
}
@article{Vries2017,
  author = {de Vries, Ronald P and Riley, Robert and Wiebenga, Ad and Aguilar-Osorio, Guillermo and Amillis, Sotiris and Uchima, Cristiane Akemi and Anderluh, Gregor and Asadollahi, Mojtaba and Askin, Marion and Barry, Kerrie and Battaglia, Evy and Bayram, Özgür and Benocci, Tiziano and Braus-Stromeyer, Susanna A and Caldana, Camila and Cánovas, David and Cerqueira, Gustavo C and Chen, Fusheng and Chen, Wanping and Choi, Cindy and Clum, Alicia and Dos Santos, Renato Augusto Corrêa and Damásio, André Ricardo de Lima and Diallinas, George and Emri, Tamás and Fekete, Erzsébet and Flipphi, Michel and Freyberg, Susanne and Gallo, Antonia and Gournas, Christos and Habgood, Rob and Hainaut, Matthieu and Harispe, María Laura and Henrissat, Bernard and Hildén, Kristiina S and Hope, Ryan and Hossain, Abeer and Karabika, Eugenia and Karaffa, Levente and Karányi, Zsolt and Kraševec, Nada and Kuo, Alan and Kusch, Harald and LaButti, Kurt and Lagendijk, Ellen L and Lapidus, Alla and Levasseur, Anthony and Lindquist, Erika and Lipzen, Anna and Logrieco, Antonio F and MacCabe, Andrew and Mäkelä, Miia R and Malavazi, Iran and Melin, Petter and Meyer, Vera and Mielnichuk, Natalia and Miskei, Márton and Molnár, Ákos P and Mulé, Giuseppina and Ngan, Chew Yee and Orejas, Margarita and Orosz, Erzsébet and Ouedraogo, Jean Paul and Overkamp, Karin M and Park, Hee-Soo and Perrone, Giancarlo and Piumi, Francois and Punt, Peter J and Ram, Arthur F J and Ramón, Ana and Rauscher, Stefan and Record, Eric and Riaño-Pachón, Diego Mauricio and Robert, Vincent and Röhrig, Julian and Ruller, Roberto and Salamov, Asaf and Salih, Nadhira S and Samson, Rob A and Sándor, Erzsébet and Sanguinetti, Manuel and Schütze, Tabea and Sepčić, Kristina and Shelest, Ekaterina and Sherlock, Gavin and Sophianopoulou, Vicky and Squina, Fabio M and Sun, Hui and Susca, Antonia and Todd, Richard B and Tsang, Adrian and Unkles, Shiela E and van de Wiele, Nathalie and van Rossen-Uffink, Diana and Oliveira, Juliana Velasco de Castro and Vesth, Tammi C and Visser, Jaap and Yu, Jae-Hyuk and Zhou, Miaomiao and Andersen, Mikael R and Archer, David B and Baker, Scott E and Benoit, Isabelle and Brakhage, Axel A and Braus, Gerhard H and Fischer, Reinhard and Frisvad, Jens C and Goldman, Gustavo H and Houbraken, Jos and Oakley, Berl and Pócsi, István and Scazzocchio, Claudio and Seiboth, Bernhard and vanKuyk, Patricia A and Wortman, Jennifer and Dyer, Paul S and Grigoriev, Igor V},
  title = {Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.},
  journal = {Genome biology},
  year = {2017},
  volume = {18},
  pages = {28},
  month = feb,
  issn = {1474-760X},
  abstract = {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. 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. 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.},
  country = {England},
  created = {2017-02-15},
  doi = {10.1186/s13059-017-1151-0},
  issn-linking = {1474-7596},
  issue = {1},
  keywords = {Aspergillus; Comparative genomics; Fungal biology; Genome sequencing},
  nlm-id = {100960660},
  owner = {NLM},
  pii = {10.1186/s13059-017-1151-0},
  pmc = {PMC5307856},
  pmid = {28196534},
  pubmodel = {Electronic},
  pubstatus = {epublish},
  revised = {2017-03-14}
}
@article{PereiraSilva2017,
  author = {Pereira Silva, Lilian and Alves de Castro, Patrícia and Dos Reis, Thaila Fernanda and Paziani, Mario Henrique and Von Zeska Kress, Márcia Regina and Riaño-Pachón, Diego M and Hagiwara, Daisuke and Ries, Laure N A and Brown, Neil Andrew and Goldman, Gustavo H},
  title = {Genome-wide transcriptome analysis of Aspergillus fumigatus exposed to osmotic stress reveals regulators of osmotic and cell wall stresses that are SakA(HOG1) and MpkC dependent.},
  journal = {Cellular microbiology},
  year = {2017},
  volume = {19},
  month = apr,
  issn = {1462-5822},
  abstract = {Invasive aspergillosis is predominantly caused by Aspergillus fumigatus, and adaptations to stresses experienced within the human host are a prerequisite for the survival and virulence strategies of the pathogen. The central signal transduction pathway operating during hyperosmotic stress is the high osmolarity glycerol mitogen-activated protein kinase cascade. A. fumigatus MpkC and SakA, orthologues of the Saccharomyces cerevisiae Hog1p, constitute the primary regulator of the hyperosmotic stress response. We compared A. fumigatus wild-type transcriptional response to osmotic stress with the ΔmpkC, ΔsakA, and ΔmpkC ΔsakA strains. Our results strongly indicate that MpkC and SakA have independent and collaborative functions during the transcriptional response to transient osmotic stress. We have identified and characterized null mutants for four A. fumigatus basic leucine zipper proteins transcription factors. The atfA and atfB have comparable expression levels with the wild-type in ΔmpkC but are repressed in ΔsakA and ΔmpkC ΔsakA post-osmotic stress. The atfC and atfD have reduced expression levels in all mutants post-osmotic stress. The atfA-D null mutants displayed several phenotypes related to osmotic, oxidative, and cell wall stresses. The ΔatfA and ΔatfB were shown to be avirulent and to have attenuated virulence, respectively, in both Galleria mellonella and a neutropenic murine model of invasive pulmonary aspergillosis.},
  country = {England},
  created = {2016-10-05},
  doi = {10.1111/cmi.12681},
  issn-linking = {1462-5814},
  issue = {4},
  nlm-id = {100883691},
  owner = {NLM},
  pmid = {27706915},
  pubmodel = {Print-Electronic},
  pubstatus = {ppublish},
  revised = {2017-03-08}
}
@article{Borin2017,
  author = {Borin, Gustavo Pagotto and Sanchez, Camila Cristina and de Santana, Eliane Silva and Zanini, Guilherme Keppe and Dos Santos, Renato Augusto Corrêa and de Oliveira Pontes, Angélica and de Souza, Aline Tieppo and Dal'Mas, Roberta Maria Menegaldo Tavares Soares and Riaño-Pachón, Diego Mauricio and Goldman, Gustavo Henrique and Oliveira, Juliana Velasco de Castro},
  title = {Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei.},
  journal = {BMC genomics},
  year = {2017},
  volume = {18},
  pages = {501},
  month = jun,
  issn = {1471-2164},
  abstract = {Second generation (2G) ethanol is produced by breaking down lignocellulosic biomass into fermentable sugars. In Brazil, sugarcane bagasse has been proposed as the lignocellulosic residue for this biofuel production. The enzymatic cocktails for the degradation of biomass-derived polysaccharides are mostly produced by fungi, such as Aspergillus niger and Trichoderma reesei. However, it is not yet fully understood how these microorganisms degrade plant biomass. In order to identify transcriptomic changes during steam-exploded bagasse (SEB) breakdown, we conducted a RNA-seq comparative transcriptome profiling of both fungi growing on SEB as carbon source. Particular attention was focused on CAZymes, sugar transporters, transcription factors (TFs) and other proteins related to lignocellulose degradation. Although genes coding for the main enzymes involved in biomass deconstruction were expressed by both fungal strains since the beginning of the growth in SEB, significant differences were found in their expression profiles. The expression of these enzymes is mainly regulated at the transcription level, and A. niger and T. reesei also showed differences in TFs content and in their expression. Several sugar transporters that were induced in both fungal strains could be new players on biomass degradation besides their role in sugar uptake. Interestingly, our findings revealed that in both strains several genes that code for proteins of unknown function and pro-oxidant, antioxidant, and detoxification enzymes were induced during growth in SEB as carbon source, but their specific roles on lignocellulose degradation remain to be elucidated. This is the first report of a time-course experiment monitoring the degradation of pretreated bagasse by two important fungi using the RNA-seq technology. It was possible to identify a set of genes that might be applied in several biotechnology fields. The data suggest that these two microorganisms employ different strategies for biomass breakdown. This knowledge can be exploited for the rational design of enzymatic cocktails and 2G ethanol production improvement.},
  country = {England},
  created = {2017-07-01},
  doi = {10.1186/s12864-017-3857-5},
  issn-linking = {1471-2164},
  issue = {1},
  keywords = {Aspergillus niger; CAZymes; RNA-seq; Sugarcane bagasse; Transcription factors; Transporters; Trichoderma reesei},
  nlm-id = {100965258},
  owner = {NLM},
  pii = {10.1186/s12864-017-3857-5},
  pmc = {PMC5493111},
  pmid = {28666414},
  pubmodel = {Electronic},
  pubstatus = {epublish},
  revised = {2017-07-06}
}
@article{Mandelli2017,
  author = {Mandelli, F and Couger, M B and Paixão, D A A and Machado, C B and Carnielli, C M and Aricetti, J A and Polikarpov, I and Prade, R and Caldana, C and Paes Leme, A F and Mercadante, A Z and Riaño-Pachón, D M and Squina, Fabio Marcio},
  title = {Thermal adaptation strategies of the extremophile bacterium Thermus filiformis based on multi-omics analysis.},
  journal = {Extremophiles : life under extreme conditions},
  year = {2017},
  volume = {21},
  pages = {775--788},
  month = jul,
  issn = {1433-4909},
  abstract = {Thermus filiformis is an aerobic thermophilic bacterium isolated from a hot spring in New Zealand. The experimental study of the mechanisms of thermal adaptation is important to unveil response strategies of the microorganism to stress. In this study, the main pathways involved on T. filiformis thermoadaptation, as well as, thermozymes with potential biotechnological applications were revealed based on omics approaches. The strategy adopted in this study disclosed that pathways related to the carbohydrate metabolism were affected in response to thermoadaptation. High temperatures triggered oxidative stress, leading to repression of genes involved in glycolysis and the tricarboxylic acid cycle. During heat stress, the glucose metabolism occurred predominantly via the pentose phosphate pathway instead of the glycolysis pathway. Other processes, such as protein degradation, stringent response, and duplication of aminoacyl-tRNA synthetases, were also related to T. filiformis thermoadaptation. The heat-shock response influenced the carotenoid profile of T. filiformis, favoring the synthesis of thermozeaxanthins and thermobiszeaxanthins, which are related to membrane stabilization at high temperatures. Furthermore, antioxidant enzymes correlated with free radical scavenging, including superoxide dismutase, catalase and peroxidase, and metabolites, such as oxaloacetate and α-ketoglutarate, were accumulated at 77 °C.},
  country = {Germany},
  created = {2017-05-13},
  doi = {10.1007/s00792-017-0942-2},
  issn-linking = {1431-0651},
  issue = {4},
  keywords = {Metabolomics; Peroxyl radical scavenging activity; Proteomics; Thermozeaxanthins; Transcriptomics},
  nlm-id = {9706854},
  owner = {NLM},
  pii = {10.1007/s00792-017-0942-2},
  pmid = {28500387},
  pubmodel = {Print-Electronic},
  pubstatus = {ppublish},
  revised = {2017-06-21}
}
@article{Riano-Pachon2017,
  author = {Ria\~no-Pach\'on, DM and Mattiello, L},
  title = {Draft genome sequencing of the sugarcane hybrid SP80-3280 [version 2; referees: 2 approved]},
  journal = {F1000Research},
  year = {2017},
  volume = {6},
  number = {861},
  doi = {10.12688/f1000research.11859.2},
  pmid = {28713559}
}
@article{Nobile2017,
  author = {Nobile, Paula Macedo and Bottcher, Alexandra and Mayer, Juliana L S and Brito, Michael S and Dos Anjos, Ivan A and Landell, Marcos Guimarães de Andrade and Vicentini, Renato and Creste, Silvana and Riaño-Pachón, Diego Mauricio and Mazzafera, Paulo},
  title = {Identification, classification and transcriptional profiles of dirigent domain-containing proteins in sugarcane.},
  journal = {Molecular genetics and genomics : MGG},
  year = {2017},
  month = jul,
  issn = {1617-4623},
  abstract = {Dirigent (DIR) proteins, encoded by DIR genes, are referred to as "dirigent" because they direct the outcome of the coupling of the monolignol coniferyl alcohol into (+) or (-) pinoresinol, the first intermediates in the enantiocomplementary pathways for lignan biosynthesis. DIR domain-containing or DIR-like proteins are, thus, termed for not having a clear characterization. A transcriptome- and genome-wide survey of DIR domain-containing proteins in sugarcane was carried out, in addition to phylogenetic, physicochemical and transcriptional analyses. A total of 120 non-redundant sequences containing the DIR domain were identified and classified into 64 groups according to phylogenetic and sequence alignment analyses. In silico analysis of transcript abundance showed that these sequences are expressed at low levels in leaves and genes in the same phylogenetic clade have similar expression patterns. Expression analysis of ShDIR1-like transcripts in the culm internodes of sugarcane demonstrates their abundance in mature internodes, their induction by nitrogen fertilization and their predominant expression in cells that have a lignified secondary cell wall, such as vascular bundles of young internodes and parenchymal cells of the pith of mature internodes. Due to the lack of information about the functional role of DIR in plants, a possible relationship is discussed between the ShDIR1-like transcriptional profile and cell wall development in parenchyma cells of sugarcane culm, which typically accumulates large amounts of sucrose. The number of genes encoding the DIR domain-containing proteins in sugarcane is intriguing and is an indication per se that these proteins may have an important metabolic role and thus deserve to be better studied.},
  country = {Germany},
  created = {2017-07-12},
  doi = {10.1007/s00438-017-1349-6},
  issn-linking = {1617-4623},
  keywords = {Lignan; Phylogeny; Protein homology modeling; Saccharum spp.; Transcriptome- and genome-wide survey},
  nlm-id = {101093320},
  owner = {NLM},
  pii = {10.1007/s00438-017-1349-6},
  pmid = {28699001},
  pubmodel = {Print-Electronic},
  pubstatus = {aheadofprint},
  revised = {2017-07-12}
}
@article{Mello2017,
  author = {Mello, Bruno L and Alessi, Anna M and Riaño-Pachón, Diego M and deAzevedo, Eduardo R and Guimarães, Francisco E G and Espirito Santo, Melissa C and McQueen-Mason, Simon and Bruce, Neil C and Polikarpov, Igor},
  title = {Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity.},
  journal = {Biotechnology for biofuels},
  year = {2017},
  volume = {10},
  pages = {254},
  issn = {1754-6834},
  abstract = {Using globally abundant crop residues as a carbon source for energy generation and renewable chemicals production stand out as a promising solution to reduce current dependency on fossil fuels. In nature, such as in compost habitats, microbial communities efficiently degrade the available plant biomass using a diverse set of synergistic enzymes. However, deconstruction of lignocellulose remains a challenge for industry due to recalcitrant nature of the substrate and the inefficiency of the enzyme systems available, making the economic production of lignocellulosic biofuels difficult. Metatranscriptomic studies of microbial communities can unveil the metabolic functions employed by lignocellulolytic consortia and identify novel biocatalysts that could improve industrial lignocellulose conversion. In this study, a microbial community from compost was grown in minimal medium with sugarcane bagasse sugarcane bagasse as the sole carbon source. Solid-state nuclear magnetic resonance was used to monitor lignocellulose degradation; analysis of metatranscriptomic data led to the selection and functional characterization of several target genes, revealing the first glycoside hydrolase from Carbohydrate Active Enzyme family 11 with exo-1,4-β-xylanase activity. The xylanase crystal structure was resolved at 1.76 Å revealing the structural basis of exo-xylanase activity. Supplementation of a commercial cellulolytic enzyme cocktail with the xylanase showed improvement in Avicel hydrolysis in the presence of inhibitory xylooligomers. This study demonstrated that composting microbiomes continue to be an excellent source of biotechnologically important enzymes by unveiling the diversity of enzymes involved in in situ lignocellulose degradation.},
  country = {England},
  created = {2017-11-09},
  doi = {10.1186/s13068-017-0944-4},
  issn-linking = {1754-6834},
  keywords = {Bioethanol; Compost; Lignocellulose; Metatranscriptomics; Microbial community; Xylanase},
  nlm-id = {101316935},
  owner = {NLM},
  pii = {944},
  pmc = {PMC5667448},
  pmid = {29118851},
  pubmodel = {Electronic-eCollection},
  pubstatus = {epublish},
  revised = {2017-11-12}
}
@article{Contesini2017,
  author = {Contesini, Fabiano Jares and Liberato, Marcelo Vizoná and Rubio, Marcelo Ventura and Calzado, Felipe and Zubieta, Mariane Paludetti and Riaño-Pachón, Diego Mauricio and Squina, Fabio Marcio and Bracht, Fabricio and Skaf, Munir S and Damasio, André Ricardo},
  title = {Structural and functional characterization of a highly secreted α-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse.},
  journal = {Biochimica et biophysica acta},
  year = {2017},
  volume = {1865},
  pages = {1758--1769},
  month = dec,
  issn = {0006-3002},
  abstract = {Carbohydrate-Active Enzymes are key enzymes for biomass-to-bioproducts conversion. α-l-Arabinofuranosidases that belong to the Glycoside Hydrolase family 62 (GH62) have important applications in biofuel production from plant biomass by hydrolyzing arabinoxylans, found in both the primary and secondary cell walls of plants. In this work, we identified a GH62 α-l-arabinofuranosidase (AnAbf62Awt) that was highly secreted when Aspergillus nidulans was cultivated on sugarcane bagasse. The gene AN7908 was cloned and transformed in A. nidulans for homologous production of AnAbf62Awt, and we confirmed that the enzyme is N-glycosylated at asparagine 83 by mass spectrometry analysis. The enzyme was also expressed in Escherichia coli and the studies of circular dichroism showed that the melting temperature and structural profile of AnAbf62Awt and the non-glycosylated enzyme from E. coli (AnAbf62Adeglyc) were highly similar. In addition, the designed glycomutant AnAbf62AN83Q presented similar patterns of secretion and activity to the AnAbf62Awt, indicating that the N-glycan does not influence the properties of this enzyme. The crystallographic structure of AnAbf62Adeglyc was obtained and the 1.7Å resolution model showed a five-bladed β-propeller fold, which is conserved in family GH62. Mutants AnAbf62AY312F and AnAbf62AY312S showed that Y312 was an important substrate-binding residue. Molecular dynamics simulations indicated that the loop containing Y312 could access different conformations separated by moderately low energy barriers. One of these conformations, comprising a local minimum, is responsible for placing Y312 in the vicinity of the arabinose glycosidic bond, and thus, may be important for catalytic efficiency.},
  country = {Netherlands},
  created = {2017-09-11},
  doi = {10.1016/j.bbapap.2017.09.001},
  issn-linking = {0006-3002},
  issue = {12},
  keywords = {Arabinoxylan; Aspergillus nidulans; GH62; N-glycosylation; α-l-Arabinofuranosidase},
  nlm-id = {0217513},
  owner = {NLM},
  pii = {S1570-9639(17)30209-1},
  pmid = {28890404},
  pubmodel = {Print-Electronic},
  pubstatus = {ppublish},
  revised = {2017-10-20}
}
@article{Manfiolli2017,
  author = {Manfiolli, Adriana Oliveira and de Castro, Patrícia Alves and Dos Reis, Thaila Fernanda and Dolan, Stephen and Doyle, Sean and Jones, Gary and Riaño Pachón, Diego M and Ulaa, Mevl{\"{u}}t and Noble, Luke M and Mattern, Derek J and Brakhage, Axel A and Valiante, Vito and Silva-Rocha, Rafael and Bayram, Ozgur and Goldman, Gustavo H},
  title = {Aspergillus fumigatus protein phosphatase PpzA is involved in iron assimilation, secondary metabolite production, and virulence.},
  journal = {Cellular microbiology},
  year = {2017},
  volume = {19},
  month = dec,
  issn = {1462-5822},
  __markedentry = {[diriano:]},
  abstract = {Metal restriction imposed by mammalian hosts during an infection is a common mechanism of defence to reduce or avoid the pathogen infection. Metals are essential for organism survival due to its involvement in several biological processes. Aspergillus fumigatus causes invasive aspergillosis, a disease that typically manifests in immunocompromised patients. A. fumigatus PpzA, the catalytic subunit of protein phosphatase Z (PPZ), has been recently identified as associated with iron assimilation. A. fumigatus has 2 high-affinity mechanisms of iron acquisition during infection: reductive iron assimilation and siderophore-mediated iron uptake. It has been shown that siderophore production is important for A. fumigatus virulence, differently to the reductive iron uptake system. Transcriptomic and proteomic comparisons between ∆ppzA and wild-type strains under iron starvation showed that PpzA has a broad influence on genes involved in secondary metabolism. Liquid chromatography-mass spectrometry under standard and iron starvation conditions confirmed that the ΔppzA mutant had reduced production of pyripyropene A, fumagillin, fumiquinazoline A, triacetyl-fusarinine C, and helvolic acid. The ΔppzA was shown to be avirulent in a neutropenic murine model of invasive pulmonary aspergillosis. PpzA plays an important role at the interface between iron starvation, regulation of SM production, and pathogenicity in A. fumigatus.},
  country = {England},
  created = {2017-07-28},
  doi = {10.1111/cmi.12770},
  issn-linking = {1462-5814},
  issue = {12},
  nlm-id = {100883691},
  owner = {NLM},
  pmid = {28753224},
  pubmodel = {Print-Electronic},
  pubstatus = {ppublish},
  revised = {2017-11-09}
}
@article{Gouvea2018,
  author = {de Gouvêa, Paula Fagundes and Bernardi, Aline Vianna and Gerolamo, Luis Eduardo and de Souza Santos, Emerson and Riaño-Pachón, Diego Mauricio and Uyemura, Sergio Akira and Dinamarco, Taisa Magnani},
  title = {Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse.},
  journal = {BMC genomics},
  year = {2018},
  volume = {19},
  pages = {232},
  month = apr,
  issn = {1471-2164},
  __markedentry = {[diriano:6]},
  abstract = {Sugarcane bagasse has been proposed as a lignocellulosic residue for second-generation ethanol (2G) produced by breaking down biomass into fermentable sugars. The enzymatic cocktails for biomass degradation are mostly produced by fungi, but low cost and high efficiency can consolidate 2G technologies. A. fumigatus plays an important role in plant biomass degradation capabilities and recycling. To gain more insight into the divergence in gene expression during steam-exploded bagasse (SEB) breakdown, this study profiled the transcriptome of A. fumigatus by RNA sequencing to compare transcriptional profiles of A. fumigatus grown on media containing SEB or fructose as the sole carbon source. Secretome analysis was also performed using SDS-PAGE and LC-MS/MS. The maximum activities of cellulases (0.032 U mL-1), endo-1,4-β--xylanase (10.82 U mL-1) and endo-1,3-β glucanases (0.77 U mL-1) showed that functional CAZymes (carbohydrate-active enzymes) were secreted in the SEB culture conditions. Correlations between transcriptome and secretome data identified several CAZymes in A. fumigatus. Particular attention was given to CAZymes related to lignocellulose degradation and sugar transporters. Genes encoding glycoside hydrolase classes commonly expressed during the breakdown of cellulose, such as GH-5, 6, 7, 43, 45, and hemicellulose, such as GH-2, 10, 11, 30, 43, were found to be highly expressed in SEB conditions. Lytic polysaccharide monooxygenases (LPMO) classified as auxiliary activity families AA9 (GH61), CE (1, 4, 8, 15, 16), PL (1, 3, 4, 20) and GT (1, 2, 4, 8, 20, 35, 48) were also differentially expressed in this condition. Similarly, the most important enzymes related to biomass degradation, including endoxylanases, xyloglucanases, β-xylosidases, LPMOs, α-arabinofuranosidases, cellobiohydrolases, endoglucanases and β-glucosidases, were also identified in the secretome. This is the first report of a transcriptome and secretome experiment of Aspergillus fumigatus in the degradation of pretreated sugarcane bagasse. The results suggest that this strain employs important strategies for this complex degradation process. It was possible to identify a set of genes and proteins that might be applied in several biotechnology fields. This knowledge can be exploited for the improvement of 2G ethanol production by the rational design of enzymatic cocktails.},
  country = {England},
  doi = {10.1186/s12864-018-4627-8},
  issn-linking = {1471-2164},
  issue = {1},
  keywords = {Aspergillus fumigatus; CAZymes; Lignocellulose breakdown; RNA-Seq; Secretome; Sugarcane bagasse},
  nlm-id = {100965258},
  owner = {NLM},
  pii = {10.1186/s12864-018-4627-8},
  pmc = {PMC5883313},
  pmid = {29614953},
  pubmodel = {Electronic},
  pubstatus = {epublish},
  revised = {2018-04-11}
}
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