Gabriela Gomes | Universidade de São Paulo (original) (raw)
Papers by Gabriela Gomes
Plant Physiology, 2008
In flowering plants, the two sperm cells are embedded within the cytoplasm of the growing pollen ... more In flowering plants, the two sperm cells are embedded within the cytoplasm of the growing pollen tube and as such are passively transported to the embryo sac, wherein double fertilization occurs upon their release. Understanding the mechanisms and conditions by which male gametes mature and take part in fertilization are crucial goals in the study of plant reproduction. Studies of gene expression in male gametes of maize (Zea mays) and Plumbago and in lily (Lilium longiflorum) generative cells already showed that the previously held view of transcriptionally inert male gametes was not true, but genome-wide studies were lacking. Analyses in the model plant Arabidopsis (Arabidopsis thaliana) were hindered, because no method to isolate sperm cells was available. Here, we used fluorescence-activated cell sorting to isolate sperm cells from Arabidopsis, allowing GeneChip analysis of their transcriptome at a genome-wide level. Comparative analysis of the sperm cell transcriptome with those of representative sporophytic tissues and of pollen showed that sperm has a distinct and diverse transcriptional profile. Functional classifications of genes with enriched expression in sperm cells showed that DNA repair, ubiquitin-mediated proteolysis, and cell cycle progression are overrepresented Gene Ontology categories. Moreover, analysis of the small RNA and DNA methylation pathways suggests that distinct mechanisms might be involved in regulating the epigenetic state of the paternal genome. We identified numerous candidate genes whose involvement in sperm cell development and fertilization can now be directly tested in Arabidopsis. These results provide a roadmap to decipher the role of sperm-expressed proteins.
Journal of Biological Dynamics, 2010
Recently, the notion of a reinfection threshold in epidemiological models of only partial immunit... more Recently, the notion of a reinfection threshold in epidemiological models of only partial immunity has been debated in the literature. We present a rigorous analysis of a model of reinfection which shows a clear threshold behaviour at the parameter point where the reinfection threshold was originally described. Furthermore, we demonstrate that this threshold is the mean field version of a transition in corresponding spatial models of immunization. The reinfection threshold corresponds to the transition between annular growth of an epidemics spreading into a susceptible area leaving recovered behind and compact growth of a susceptible-infected-susceptible region growing into a susceptible area. This transition between annular growth and compact growth was described in the physics literature long before the reinfection threshold debate broke out in the theoretical biology literature.
Separation and Purification Technology, 2009
Polymer/salt aqueous two phase systems (ATPS) based on polyethylene glycol (PEG) 600, sodium citr... more Polymer/salt aqueous two phase systems (ATPS) based on polyethylene glycol (PEG) 600, sodium citrate and ammonium sulfate were used to partially purify plasmid DNA (pDNA) from Escherichia coli alkaline lysates. The effect of pH and lysate load on the binodal curve was analyzed and tie-lines were determined in order to establish the optimal conditions for ATPS formation. A series of extraction experiments were performed at pH 6.9 using a 20% (w/w) lysate load and systems with 16.5% (w/w) salt, 19.0% (w/w) PEG 600, and a tie-line length of 37.1% (w/w). Under these conditions, plasmid DNA was recovered in the salt-rich bottom phase. However, whereas with sodium citrate-based systems recovery yields closer to 100% were obtained, the use of ammonium sulfate enabled higher purification although with lower recoveries. Thus, the performance of ATPS prepared by combining sodium citrate and ammonium sulfate was also evaluated. A mixture of 25% (w/w) ammonium sulfate and 75% (w/w) sodium citrate offered a good compromise between plasmid recovery (91.1%) and purity (17.2%). Multi-step extraction procedures were evaluated in order to improve the process performance. Although the majority of the impurities were removed in the first step, incremental increases in the purity were obtained with the inclusion of extra steps. The top to bottom phase volume ratio was increased in order to increase plasmid concentration in the bottom phase. Although this was achieved using a phase ratio of 4, it was not possible to concentrate plasmid relatively to the starting lysate. Overall, the results show that ammonium sulfate, a salt which has a high environmental impact, can be partially replaced in ATPS by sodium citrate, without significant decrease in the performance of plasmid purification.
Para autor de 'A Ralé Brasileira', rolezinhos são vistos como tão ameaçadores porque rompem a dem... more Para autor de 'A Ralé Brasileira', rolezinhos são vistos como tão ameaçadores porque rompem a demarcação do apartheid social
Plant Physiology, 2008
In flowering plants, the two sperm cells are embedded within the cytoplasm of the growing pollen ... more In flowering plants, the two sperm cells are embedded within the cytoplasm of the growing pollen tube and as such are passively transported to the embryo sac, wherein double fertilization occurs upon their release. Understanding the mechanisms and conditions by which male gametes mature and take part in fertilization are crucial goals in the study of plant reproduction. Studies of gene expression in male gametes of maize (Zea mays) and Plumbago and in lily (Lilium longiflorum) generative cells already showed that the previously held view of transcriptionally inert male gametes was not true, but genome-wide studies were lacking. Analyses in the model plant Arabidopsis (Arabidopsis thaliana) were hindered, because no method to isolate sperm cells was available. Here, we used fluorescence-activated cell sorting to isolate sperm cells from Arabidopsis, allowing GeneChip analysis of their transcriptome at a genome-wide level. Comparative analysis of the sperm cell transcriptome with those of representative sporophytic tissues and of pollen showed that sperm has a distinct and diverse transcriptional profile. Functional classifications of genes with enriched expression in sperm cells showed that DNA repair, ubiquitin-mediated proteolysis, and cell cycle progression are overrepresented Gene Ontology categories. Moreover, analysis of the small RNA and DNA methylation pathways suggests that distinct mechanisms might be involved in regulating the epigenetic state of the paternal genome. We identified numerous candidate genes whose involvement in sperm cell development and fertilization can now be directly tested in Arabidopsis. These results provide a roadmap to decipher the role of sperm-expressed proteins.
Journal of Biological Dynamics, 2010
Recently, the notion of a reinfection threshold in epidemiological models of only partial immunit... more Recently, the notion of a reinfection threshold in epidemiological models of only partial immunity has been debated in the literature. We present a rigorous analysis of a model of reinfection which shows a clear threshold behaviour at the parameter point where the reinfection threshold was originally described. Furthermore, we demonstrate that this threshold is the mean field version of a transition in corresponding spatial models of immunization. The reinfection threshold corresponds to the transition between annular growth of an epidemics spreading into a susceptible area leaving recovered behind and compact growth of a susceptible-infected-susceptible region growing into a susceptible area. This transition between annular growth and compact growth was described in the physics literature long before the reinfection threshold debate broke out in the theoretical biology literature.
Separation and Purification Technology, 2009
Polymer/salt aqueous two phase systems (ATPS) based on polyethylene glycol (PEG) 600, sodium citr... more Polymer/salt aqueous two phase systems (ATPS) based on polyethylene glycol (PEG) 600, sodium citrate and ammonium sulfate were used to partially purify plasmid DNA (pDNA) from Escherichia coli alkaline lysates. The effect of pH and lysate load on the binodal curve was analyzed and tie-lines were determined in order to establish the optimal conditions for ATPS formation. A series of extraction experiments were performed at pH 6.9 using a 20% (w/w) lysate load and systems with 16.5% (w/w) salt, 19.0% (w/w) PEG 600, and a tie-line length of 37.1% (w/w). Under these conditions, plasmid DNA was recovered in the salt-rich bottom phase. However, whereas with sodium citrate-based systems recovery yields closer to 100% were obtained, the use of ammonium sulfate enabled higher purification although with lower recoveries. Thus, the performance of ATPS prepared by combining sodium citrate and ammonium sulfate was also evaluated. A mixture of 25% (w/w) ammonium sulfate and 75% (w/w) sodium citrate offered a good compromise between plasmid recovery (91.1%) and purity (17.2%). Multi-step extraction procedures were evaluated in order to improve the process performance. Although the majority of the impurities were removed in the first step, incremental increases in the purity were obtained with the inclusion of extra steps. The top to bottom phase volume ratio was increased in order to increase plasmid concentration in the bottom phase. Although this was achieved using a phase ratio of 4, it was not possible to concentrate plasmid relatively to the starting lysate. Overall, the results show that ammonium sulfate, a salt which has a high environmental impact, can be partially replaced in ATPS by sodium citrate, without significant decrease in the performance of plasmid purification.
Para autor de 'A Ralé Brasileira', rolezinhos são vistos como tão ameaçadores porque rompem a dem... more Para autor de 'A Ralé Brasileira', rolezinhos são vistos como tão ameaçadores porque rompem a demarcação do apartheid social