Papers by Marie Anne van Sluys
De 1985 ao fim da década Criação da União dos Produtores de Bioenergia (UDOP) A União dos Produto... more De 1985 ao fim da década Criação da União dos Produtores de Bioenergia (UDOP) A União dos Produtores de Bioenergia (UDOP), fundada em 1985 pelos diretores das destilarias autônomas criadas com o Proálcool, tinha como objetivo propiciar a troca de informações entre seus diretores, além de capacitar profissionais para as unidades e proporcionar a troca de conhecimentos e informações por meio das reuniões dos comitês técnicos instituídos. Segundo Antonio César Salibe, a formação de capital humano era considerada chave para a boa operação das usinas, de modo que um programa de capacitação foi criado. Nos últimos trinta anos, a UDOP formou mais de 100 mil pessoas, ainda de acordo com Salibe 1. 1985-1986: uma vitória na guerra comercial do etanol Em 1985, o Brasil foi acusado na International Trade Commission (ITC), em Washington, de exportar etanol aos EUA aproveitando-se de subsídios governamentais e praticando dumping de preço. Para coordenar a defesa contra as duas ações (direitos compensatórios e anti-dumping), os produtores brasileiros organizaram o Comitê Especial de Exportação dos Produtores Brasileiros de Álcool, com a seguinte composição: Lamartine Navarro Júnior, André Francisco de Andrade Arantes, 1 Para mais informações, ver <www.udop.com.br/>. 3. 62 | Universidades e empresas: 40 anos de ciência e tecnologia para o etanol brasileiro
Sequence logos and PlotCon of U3 and U5 vl-att putative sites of 9 LTR-retrotransposon lineages d... more Sequence logos and PlotCon of U3 and U5 vl-att putative sites of 9 LTR-retrotransposon lineages divided by genome and plant group. Sequence logos of the first and last 40 bases of the LTR from 9 LTR-RT lineages divided by genome or plant group (eudicot - monocot species). Sequence logo is a graphical representation of nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each nucleic acid at that position. Behind each logo it is the PlotCon analysis, where the X-axis for all plots refers to the relative residue position in each alignment and the Y-axis to their similarity, indicated as the pairwise scores that are taken from the specified similarity matrix. The PlotCon graphics are based on an algorithm that shows, along the alignment, the region...
Background: Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a ma... more Background: Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of strain PXO99 A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another. Results: The PXO99 A genome is a single circular chromosome of 5,240,075 bp, considerably longer than the genomes of the other strains (4,941,439 bp and 4,940,217 bp, respectively), and it contains 5083 protein-coding genes, including 87 not found in KACC10331 or MAFF311018. PXO99 A contains a greater number of virulence-associated transcription activator-like effector genes and has at least ten major chromosomal rearrangements relative to KACC10331 and MAFF311018. PXO99 A contains numerous copies of diverse insertion sequence elements, members of which are associated with 7 out of 10 of the major rearrangements. A rapidly-evolving CRISPR (clustered regularly interspersed short palindromic repeats) region contains evidence of dozens of phage infections unique to the PXO99 A lineage. PXO99 A also contains a unique, nearperfect tandem repeat of 212 kilobases close to the replication terminus. Conclusion: Our results provide striking evidence of genome plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The comparisons point to sources of genomic variation and candidates for strain-specific adaptations of this pathogen that help to explain the extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and races that have been isolated from around the world.
Proálcool - Universidades e Empresas: 40 Anos de Ciência e Tecnologia para o Etanol Brasileiro, 2016
O século XXI 2003: a introdução dos carros modelo FFV (flex-fuel vehicle) Com o aumento do preço ... more O século XXI 2003: a introdução dos carros modelo FFV (flex-fuel vehicle) Com o aumento do preço do petróleo na primeira década do século XXI, o etanol de cana-de-açúcar ganhou um novo impulso. Após diversas tentativas pelos sistemistas de introduzir no país uma variante da tecnologia flex que já vinha sendo aplicada nos Estados Unidos, e após a realização pelo IPT do seminário mencionado no Capítulo 3 de disseminação e conscientização sobre o potencial da tecnologia, a indústria automobilística percebeu que o consumidor demandava um veículo com motor flexível, que funcionasse com qualquer proporção de etanol na mistura combustível. A introdução da tecnologia flex-fuel representou um verdadeiro marco para o uso de biocombustíveis no Brasil. Nesse sentido, pode-se dizer que houve uma história antes e outra depois da introdução dessa tecnologia, segundo comunicação de Eduardo Carvalho, ex-presidente da Unica 1. O consumidor queria um carro a álcool que pudesse funcionar com gasolina para não ficar à mercê das oscilações de preço, comuns ainda hoje na entressafra da cana, e também não queria ficar refém de um combustível que poderia faltar e consequentemente desvalorizar seu patrimônio. Recorde-se aqui a experiência da crise de 1989, já comentada neste texto. Os modelos FFV (flex-fuel vehicle) já existiam nos EUA e operavam com misturas de gasolina e etanol anidro. Nesse contexto, em 2002, a Ford apresentou o Ford Fiesta no Brasil. Todavia, o primeiro veículo FFV no mercado brasileiro foi o Gol (Figura 75), lançado pela Volkswagen em 2003 e que operava com 1 Mais sobre a história da introdução da tecnologia flex-fuel pode ser encontrado em Teixeira (2005) e Nascimento (2009).
Gene, 2020
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Este livro representa um projeto desafiador: o estudo de sequencias geneticas repetidas que sao c... more Este livro representa um projeto desafiador: o estudo de sequencias geneticas repetidas que sao capazes de se mover, tornando os genomas dinâmicos e flexiveis. Os elementos de transposicao (TEs) tem a capacidade de se multiplicar e mudar de lugar no genoma, levar consigo genes, promover rearranjos cromossomicos e alterar a expressao de genes vizinhos. Trata-se de um dos topicos mais instigantes na area da genetica, que durante decadas nao recebeu o devido reconhecimento. O livro surgiu de uma reuniao de integrantes do grupo de pesquisa Elementos de Transposicao como Agentes de Diversidade, do CNPq, que consideram indispensavel disponibilizar a pesquisadores e estudantes informacoes que permitam compreender a dinâmica e a plasticidade dos genomas em decorrencia da presenca dos TEs. O livro nao esgota as inumeras informacoes e implicacoes decorrentes da interacao genoma-TE mas propicia aos leitores o contato atualizado e a compreensao dos principais temas relacionados a estrutura e funcionamento dessas sequencias geneticas moveis e sua relacao com a evolucao dos organismos, afirmam as organizadoras...
American Journal of Botany, 2019
Best known for its exotic flowers, the Passifloraceae (Malpighiales) is also an interesting group... more Best known for its exotic flowers, the Passifloraceae (Malpighiales) is also an interesting group for comparative developmental studies of inflorescence architecture due to diverse degrees of inflorescence reduction (Krosnick and Freudenstein, 2005). Some genera such as Adenia Forssk. and Mitostemma Mast. have inflorescences with elongated peduncles that may show higher-order branching. In the subgenus Passiflora L., on the other hand, peduncles are virtually absent in the majority of species, and inflorescence ramification can be reduced to one flower, although some subgroups may have elongated peduncles, e.g., the subgenera Deidamioides and Tetrapathaea (Krosnick and Freudenstein, 2005; Krosnick et al., 2009). Passiflora is the most diverse genus of Passifloraceae, comprising more than 525 species among five subgenera: Astrophea (DC.) Mast., Deidamioides (Harms) Killip, Decaloba (DC.
The EMBO Journal, 1987
We have co-transformed carrot (Daucus carota) and Arabidopsis thaliana with an Agrobacterium tume... more We have co-transformed carrot (Daucus carota) and Arabidopsis thaliana with an Agrobacterium tumefaciens nontumorigenic T-DNA carrying the maize transposable element Activator (Ac) and an Agrobacterium rhizogenes Ri T-DNA. We present evidence that the Ac element transposes in transformed root or root-derived callus cultures of both species. We show that fertile plants can be regenerated from transformed, root-derived callus cultures of Arabidopsis, demonstrating the utility of the Ri plasmid for introducing the maize Ac element into plants. We also present evidence that Ac elements that excise from the transforming T-DNA early after transformation continue to be mobile in carrot root cultures.
PloS one, 2016
Sugarcane smut disease is caused by the biotrophic fungus Sporisorium scitamineum. The disease is... more Sugarcane smut disease is caused by the biotrophic fungus Sporisorium scitamineum. The disease is characterized by the development of a whip-like structure from the primary meristems, where billions of teliospores are produced. Sugarcane smut also causes tillering and low sucrose and high fiber contents, reducing cane productivity. We investigated the biological events contributing to disease symptoms in a smut intermediate-resistant sugarcane genotype by examining the transcriptional profiles (RNAseq) shortly after inoculating the plants and immediately after whip emission. The overall picture of disease progression suggests that premature transcriptional reprogramming of the shoot meristem functions continues until the emergence of the whip. The guidance of this altered pattern is potentially primarily related to auxin mobilization in addition to the involvement of other hormonal imbalances. The consequences associated with whip emission are the modulation of typical meristematic ...
Nascimento AL, Verjovski-Almeida S, Van Sluys MA, Monteiro-Vitorello CB, Camargo LE, Digiampietri LA, Harstkeerl RA, Ho PL, Marques MV, Oliveira MC, Setubal JC, Haake DA, Martins EA Brazilian Journal of Medical and Biological Research
Systematic Botany
The chloroplast trnL-F region was sequenced for 20 species of Velloziaceae sensu stricto plus Aca... more The chloroplast trnL-F region was sequenced for 20 species of Velloziaceae sensu stricto plus Acanthochlamys and representative species of Cyclanthus (Cyclanthaceae) and Pandanus (Pandanaceae) as outgroups. Phylogenetic analysis of the trnL intron and trnL-F intergenic spacer placed the Asian Acanthochlamys as a distant but well-supported sister-group to a monophyletic Velloziaceae sensu stricto. Within the Velloziaceae, the subfamily Barbacenioideae sensu Menezes is well supported as monophyletic, in agreement with chromosomal and morphological data, while the subfamily Vellozioideae may be paraphyletic. At least two of the currently recognized genera within the Barbacenioideae (Aylthonia and Barbacenia) appear to be paraphyletic or polyphyletic as currently delimited, while the genus Burlemarxia appears to have arisen recently within a subgroup of Barbacenia. These results appear most consistent with the inclusion of all or almost all of the taxa of the Barbacenioideae within a br...
International Journal of Plant Genomics, 2008
Sugarcane is a highly productive crop used for centuries as the main source of sugar and recently... more Sugarcane is a highly productive crop used for centuries as the main source of sugar and recently to produce ethanol, a renewable bio-fuel energy source. There is increased interest in this crop due to the impending need to decrease fossil fuel usage. Sugarcane has a highly polyploid genome. Expressed sequence tag (EST) sequencing has significantly contributed to gene discovery and expression studies used to associate function with sugarcane genes. A significant amount of data exists on regulatory events controlling responses to herbivory, drought, and phosphate deficiency, which cause important constraints on yield and on endophytic bacteria, which are highly beneficial. The means to reduce drought, phosphate deficiency, and herbivory by the sugarcane borer have a negative impact on the environment. Improved tolerance for these constraints is being sought. Sugarcane's ability to accumulate sucrose up to 16% of its culm dry weight is a challenge for genetic manipulation. Genome-...
Sugarcane bioethanol — R&D for Productivity and Sustainability, 2014
ABSTRACT Sugarcane is an important model for studies of source-sink relations due to its ability ... more ABSTRACT Sugarcane is an important model for studies of source-sink relations due to its ability to store high concentrations of sucrose in the culms. The main objective of this study is to understand the behaviour of physiological processes, such as photosynthesis and yield, in high brix genotypes. Through the evaluation of the transcriptome associated to sucrose content we have defined signal transduction components that might have a role in the process. We identified regulatory pathways associated with the activation or deactivation of photosynthesis and sucrose accumulation that were targeted in the generation of transgenic plants and in search for molecular markers useful for the selection processes. Also, we are obtaining data on sugarcane promoters by sequencing the sugarcane genome and ChIP-Seq samples. Data from different sources are being integrated (http://sucest-fun.org) to exploit the sugarcane genome and functional data to allow for a Systems Biology approach in this crop. Supported by Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP and CNPq.
Annual Review of Phytopathology, Vol 51, 2013
A diverse set of phage lineages is associated with the bacterial plant-pathogen genomes sequenced... more A diverse set of phage lineages is associated with the bacterial plant-pathogen genomes sequenced to date. Analysis of 37 genomes revealed 5,169 potential genes (approximately 4.3 Mbp) of phage origin, and at least 50% had no function assigned or are nonessential to phage biology. Some phytopathogens have transcriptionally active prophage genes under conditions that mimic plant infection, suggesting an association between plant disease and prophage transcriptional modulation. The role of prophages within genomes for cell biology varies. For pathogens such as Pectobacterium, Pseudomonas, Ralstonia, and Streptomyces, involvement of prophage in disease symptoms has been demonstrated. In Xylella and Xanthomonas, prophage activity is associated with genome rearrangements and strain differentiation. For other pathogens, prophage roles are yet to be established. This review integrates available information in a unique interface ( http://propnav.esalq.usp.br ) that may be assessed to improve research in prophage biology and its association with genome evolution and pathogenicity.
BMC Genomics, 2014
Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is bec... more Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an ongoing initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome. Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences. Conclusion: This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery.
Tropical Plant Biology, 2012
Sugarcane is the most important crop for sugar industry and raw material for bioethanol. Here we ... more Sugarcane is the most important crop for sugar industry and raw material for bioethanol. Here we present a quantitative analysis of the gene content from publicly available sugarcane ESTs. The current sugarcane EST collection sampled orthologs for~58 % of the closely-related sorghum proteome, suggesting that more than 10,000 sugarcane coding-genes remain undiscovered. Moreover the existence of more than 2,000 ncRNAs conserved between sugarcane and sorghum was revealed, among which over 500 are also detected in rice, supporting the existence of hundreds of conserved ncRNAs in grasses. New efforts towards sugarcane transcriptome sequencing were needed to sample the missing coding-genes as well as to expand the catalog of ncRNAs.
Plant Physiology, 2004
Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expresse... more Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the ...
Nature Reviews Microbiology, 2011
Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant ho... more Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant hosts, including many economically important crops. Pathogenic species and pathovars within species show a high degree of host plant specificity and many exhibit tissue specificity, invading either the vascular system or the mesophyll tissue of the host. In this Review, we discuss the insights that functional and comparative genomic studies are providing into the adaptation of this group of bacteria to exploit the extraordinary diversity of plant hosts and different host tissues.
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Papers by Marie Anne van Sluys