Papers by Marcelo Carazzolle
The bioethanol production system used in Brazil is based on the alcoholic fermentation of sucrose... more The bioethanol production system used in Brazil is based on the alcoholic fermentation of sucrose derived from sugarcane feedstock by highly adapted strains of the yeast Saccharomyces cerevisiae. PE-2 and CAT-1 are the most productive and widely adopted S. cerevisiae strains used by distilleries in Brazil. Due to no sterile condition at industrial scale, the process carries a variety of bacterial contaminants that are regularly related to yeast-bacteria co-aggregation phenotype, decreasing bioethanol yield. In this study we investigate the molecular physiology of the main S. cerevisiae commercial strain (PE-2) used on Brazilian bioethanol process under two distinct conditions: typical fermentation and flocculated (co-aggregated) fermentation. We collected samples on 13 time-points (6 time-points of typical fermentation and 7 time-points of flocculated fermentation) on sugarcane mills. Transcriptional machinery of PE-2 was assessed by high throughput sequencing-based methods (RNA-seq...
Surface Science, 2008
We propose a modified zirconium silicide model for the structure of HfSi 2 islands on Si(1 0 0). ... more We propose a modified zirconium silicide model for the structure of HfSi 2 islands on Si(1 0 0). We studied this system in a combined investigation by means of photoelectron diffraction (XPD), photoelectron spectroscopy and atomic force microscopy. Synchrotron radiation was used for enhanced energy resolution and surface sensitivity. Calculated XPD patterns of model clusters reflecting the structure as well as the morphology of the islands exhibit an excellent agreement with the experimental results. From LEED and AFM measurements a preferential nano structure growth along the [0 1 1] and ½0 1 1 direction was observed. Complementary XPD results clearly show that the HfSi 2 structures are silicon terminated.
Brazilian Journal of Infectious Diseases, 2011
Escherichia coli has been isolated frequently, showing flagellar antigens that are not recognized... more Escherichia coli has been isolated frequently, showing flagellar antigens that are not recognized by any of the 53 antisera, provided by the most important reference center of E. coli, The International Escherichia and Klebsiella Center (WHO) of the Statens Serum Institute, Copenhagen, Denmark. The objective of this study was to characterize flagellar antigens of E. coli that express non-typeable H antigens. The methods used were serology, PCR-RFLP and DNA sequencing. This characterization was performed by gene amplification of the fliC (flagellin protein) by polymerase chain reaction in all 53 standards E.coli strains for the H antigens and 20 E. coli strains for which the H antigen was untypeable. The amplicons were digested by restriction enzymes, and different restriction enzyme profiles were observed. Anti-sera were produced in rabbits, for the non-typeable strains, and agglutination tests were carried out. In conclusion,the results showed that although non-typeable and typable H antigens strains had similar flagellar antigens, the two types of strains were distinct in terms of nucleotide sequence, and did not phenotypically react with the standard antiserum, as expected. Thirteen strains had been characterized as likely putative new H antigen using PCR-RFLP techniques, DNA sequencing and/or serology.
Microbial Cell Factories, 2015
Background: The bioethanol production system used in Brazil is based on the fermentation of sucro... more Background: The bioethanol production system used in Brazil is based on the fermentation of sucrose from sugarcane feedstock by highly adapted strains of the yeast Saccharomyces cerevisiae. Bacterial contaminants present in the distillery environment often produce yeast-bacteria cellular co-aggregation particles that resemble yeast-yeast cell adhesion (flocculation). The formation of such particles is undesirable because it slows the fermentation kinetics and reduces the overall bioethanol yield. Results: In this study, we investigated the molecular physiology of one of the main S. cerevisiae strains used in Brazilian bioethanol production, PE-2, under two contrasting conditions: typical fermentation, when most yeast cells are in suspension, and co-aggregated fermentation. The transcriptional profile of PE-2 was assessed by RNA-seq during industrial scale fed-batch fermentation. Comparative analysis between the two conditions revealed transcriptional profiles that were differentiated primarily by a deep gene repression in the co-aggregated samples. The data also indicated that Lactobacillus fermentum was likely the main bacterial species responsible for cellular co-aggregation and for the high levels of organic acids detected in the samples.
PloS one, 2014
High-throughput screening of physical, genetic and chemical-genetic interactions brings important... more High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled...
Genetics and Molecular Biology, 2014
The phytopathogenic fungus Moniliophthora perniciosa (Stahel) Aime & Philips-Mora, causal agent o... more The phytopathogenic fungus Moniliophthora perniciosa (Stahel) Aime & Philips-Mora, causal agent of witches' broom disease of cocoa, causes countless damage to cocoa production in Brazil. Molecular studies have attempted to identify genes that play important roles in fungal survival and virulence. In this study, sequences deposited in the M. perniciosa Genome Sequencing Project database were analyzed to identify potential biological targets. For the first time, the ergosterol biosynthetic pathway in M. perniciosa was studied and the lanosterol 14a-demethylase gene (ERG11) that encodes the main enzyme of this pathway and is a target for fungicides was cloned, characterized molecularly and its phylogeny analyzed. ERG11 genomic DNA and cDNA were characterized and sequence analysis of the ERG11 protein identified highly conserved domains typical of this enzyme, such as SRS1, SRS4, EXXR and the heme-binding region (HBR). Comparison of the protein sequences and phylogenetic analysis revealed that the M. perniciosa enzyme was most closely related to that of Coprinopsis cinerea.
PLoS ONE, 2014
Understanding the molecular mechanisms of oral carcinogenesis will yield important advances in di... more Understanding the molecular mechanisms of oral carcinogenesis will yield important advances in diagnostics, prognostics, effective treatment, and outcome of oral cancer. Hence, in this study we have investigated the proteomic and peptidomic profiles by combining an orthotopic murine model of oral squamous cell carcinoma (OSCC), mass spectrometry-based proteomics and biological network analysis. Our results indicated the up-regulation of proteins involved in actin cytoskeleton organization and cell-cell junction assembly events and their expression was validated in human OSCC tissues. In addition, the functional relevance of talin-1 in OSCC adhesion, migration and invasion was demonstrated. Taken together, this study identified specific processes deregulated in oral cancer and provided novel refined OSCC-targeting molecules.
Topics in Catalysis, 2011
We present X-ray photoelectron spectroscopy (XPS) and X-ray photoelectron diffraction (XPD) inves... more We present X-ray photoelectron spectroscopy (XPS) and X-ray photoelectron diffraction (XPD) investigations of ordered chromium oxide ultrathin films prepared on a Pd(111) single-crystal surface. The films where grown by thermal evaporation of Cr under an oxygen atmosphere and sample temperature of 600 K. The ordered films produced are strongly dependent on the film thickness and annealing treatment. Films with thickness below 5 Å , produced at low coverages, display a p(2 9 2) structure relative to Pd(111). Thicker films (thickness [ 10 Å ) always have a ffiffi ffi 3 p  ffiffi ffi 3 p À Á R30 structure. The photoemission measurements were done using conventional X-ray sources as well as synchrotron radiation taken at the Laboratório Nacional de Luz Síncrotron. The XPD data were interpreted through the use of a multiple scattering calculation approach combined with a genetic algorithm for surface structure optimization. Combining the information from XPS, low energy electron diffraction and XPD measurements we have determined the surface structure of the ffiffi ffi 3 p  ffiffi ffi 3 p À Á R30 phase. Elsewhere, we report on the structure of the p(2 9 2) phase.
Topics in Catalysis, 2011
Ultra-thin films (1 and 3 monolayers) of Pd were deposited on the Au(111) surface and then charac... more Ultra-thin films (1 and 3 monolayers) of Pd were deposited on the Au(111) surface and then characterized by X-ray photoelectron spectroscopy (XPS), X-ray excited Auger spectroscopy (XAES), low-energy electron diffraction (LEED), and X-ray photoelectron diffraction (XPD). For the 1 ML Pd film annealed at 450°C, XPS and XAES results indicated that Pd had diffused into the Au substrate. For the 3 ML Pd film deposited at room temperature, the comparison between experimental and theoretical XPD results indicated approximately 30% of the surface was formed by 2 ML Au layers, and 70% of the surface, by 1 ML Au layers.
Surface Science, 2006
Ultra-thin palladium films deposited on the Ni(1 1 1) surface were characterized by X-ray photoel... more Ultra-thin palladium films deposited on the Ni(1 1 1) surface were characterized by X-ray photoelectron spectroscopy (XPS), lowenergy electron diffraction (LEED) and X-ray photoelectron diffraction (XPD). For low coverage, LEED shows a (1 · 1) pattern similar to that of the substrate. For intermediate coverage, the LEED pattern displays extra spots around the main (1 · 1) spots, resembling a Moiré coincidence pattern, probably associated with the formation of Pd bi-dimensional islands oriented in different directions on the Ni(1 1 1) surface. The results obtained by XPS and XPD corroborate this finding. The LEED pattern displays this structure up to 500°C. Annealing at 650°C brings back the (1 · 1) pattern, which is associated with a Pd island coalescence and alloy formation by Pd diffusion in the first atomic layers of the Ni(1 1 1). In this paper we present a detailed study of this surface structure via a comparison between XPD experiment and theory.
Polymer Reviews, 2009
There is a common concept in life: large and complex molecules result from the synthesis of units... more There is a common concept in life: large and complex molecules result from the synthesis of units that are later joined together. Mankind learned this principle and employed it to develop language, culture, and technology. This same principle is applied in the petrochemical industry by fractionating the fossilized carbon chains into small molecules and then polymerizing them in order to
Molecular Plant-Microbe Interactions, 2008
Marked dimorphism characterizes this fungus, showing a monokaryotic or biotrophic phase that caus... more Marked dimorphism characterizes this fungus, showing a monokaryotic or biotrophic phase that causes disease symptoms and a later dikaryotic or saprotrophic phase. A combined strategy of DNA microarray, expressed sequence tag, and real-time reverse-transcriptase polymerase chain reaction analyses was employed to analyze differences between these two fungal stages in vitro. In all, 1,131 putative genes were hybridized with cDNA from different phases, resulting in 189 differentially expressed genes, and 4,595 reads were clusterized, producing 1,534 unigenes. The analysis of these genes, which represent approximately 21% of the total genes, indicates that the biotrophic-like phase undergoes carbon and nitrogen catabolite repression that correlates to the expression of phytopathogenicity genes. Moreover, downregulation of mitochondrial oxidative phosphorylation and the presence of a putative ngr1 of Saccharomyces cerevisiae could help explain its lower growth rate. In contrast, the saprotrophic mycelium expresses genes related to the metabolism of hexoses, ammonia, and oxidative phosphorylation, which could explain its faster growth. Antifungal toxins were upregulated and could prevent the colonization by competing fungi. This work significantly contributes to our understanding of the molecular mechanisms of WBD and, to our knowledge, is the first to analyze differential gene expression of the different phases of a hemibiotrophic fungus.
Molecular Breeding, 2012
The large-fruited cranberry (Vaccinium macrocarpon Ait.) is a native North American fruit that is... more The large-fruited cranberry (Vaccinium macrocarpon Ait.) is a native North American fruit that is a rich source of dietary phytochemicals with demonstrated and potential benefits for human health. Cranberry is a perennial, self-fertile 2n = 2x = 24 diploid, with a haploid genome size of about 570 Mbp. Present commercial cultivars are only a few breeding and selection cycles removed from their wild progenitors. With an irreducible minimum of 2 years per generation, and significant space and time requirements for phenotypic selection of traits of horticultural interest, genetic enhancement of cranberry could be facilitated by marker-assisted selection (MAS); however, the necessary resources, such as transcript or genomic sequences, molecular genetic markers, and genetic linkage maps, are not yet available. We have begun to generate these resources, starting with nextgeneration [sequencing by oligonucleotide ligation and detection (SOLiD) mate-paired] sequencing of an inbred cranberry clone, assembling the reads, and developing microsatellite markers from the assembled sequence. Evaluation of the resulting cranberry genomic microsatellite primers has provided a test of the accuracy of the sequence assembly and supplied much-needed molecular markers for a genetic linkage map of cranberry. Mapping these markers will permit sequence scaffolds to be anchored on the genetic map.
Micron, 2011
Heterochromatin bodies in single-and multichromocentered interphase cell nuclei of Triatoma infes... more Heterochromatin bodies in single-and multichromocentered interphase cell nuclei of Triatoma infestans, a vector of Chagas disease, have been suggested to contain AT-rich DNA, based on their positive response to Q-banding and Hoechst 33248 treatment. No information exists on whether GC-rich DNA is also present in these nuclei and whether it plays a role on chromatin condensation. Considering that methodologies more precise than those previously used to determine DNA base composition in situ are currently available, and that the spatial distribution of chromatin areas differing in composition in interphase cell nuclei of different species is a matter of interest, the localization of AT-and GC-rich DNA in T. infestans nuclei is revisited here. The methodologies used included DAPI/AMD and CMA 3 /Distamycin differential staining, Feulgen-DNA image analysis following Msp I and Hpa II enzymatic digestion, 5-methylcytidine immunodetection, AgNOR response, confocal microscopy, and the 5-aza-2 -deoxycytidine (5-AZA) demethylation assay. The results identified the presence of AT-rich/GC-poor DNA in chromocenters and evenly distributed AT and GC sequences in euchromatin. A GC-rich DNA zone encircling the chromocenters was also found but it could not be associated with NOR regions. To corroborate the DNA AT-richness in T. infestans nuclei, bioinformatic analyses were also performed. Methylated cytosine was evident at some points of the chromocenters' edge in single-and multichromocentered nuclei and at the euchromatin of multichromocentered nuclei and could be transiently affected by the 5-AZA treatment. The present results suggest that in the particular case of chromocenters of the hemipteran T. infestans, cytosine methylation is not a relevant factor involved in chromatin condensation.
Materials Science in Semiconductor Processing, 2006
Continuous down-scaling of silicon based transistors results in device lengths of less than 100 n... more Continuous down-scaling of silicon based transistors results in device lengths of less than 100 nm. This requires a reduction of the gate dielectric thickness to less than 15Å which is not possible for SiO 2 due to an increasing leakage current. One of the most promising candidates for a replacement material for the gate dielectric is HfO 2 [Wilk GD, Wallace RM, Anthony JM. J Appl Phys 2001; 89:5243].
Materials Science in Semiconductor Processing, 2006
Due to the ongoing miniaturization of semiconductor devices new gate dielectrics are required for... more Due to the ongoing miniaturization of semiconductor devices new gate dielectrics are required for future applications. In this work we investigated hafnium silicide as a pre-system for hafnium oxide, one of the most promising candidates. One of the major problems of HfO 2 -films on silicon is the formation of hafnium silicide at the HfO 2 =Si interface. Therefore, ultrathin films of the system HfSi on Sið1 0 0Þ with a systematic varied thickness from 3 to 30 Å were prepared. Measurements were conducted by means of X-ray photoelectron spectroscopy and low energy electron diffraction (LEED). Also full 2p X-ray photoelectron diffraction (XPD) patterns with high spectral resolution were recorded. Against other reports related to thicker films, several heating cycles showed no phase transitions of the ultrathin films. However, above temperatures of 630 C an island formation is strongly indicated. The experimental XPD patterns are compared to simulated patterns of model structures. For the first time we present a modification of the C49 structure a possible structure for ultrathin HfSi 2 -films on bulk Si. As an outlook possibilities for preparing the system HfO 2 =Sið1 0 0Þ are introduced. r
Journal of Molecular Evolution, 2010
Journal of Molecular Catalysis A: Chemical, 2008
Photoemission spectra collected over a large solid angle give information about the form and ener... more Photoemission spectra collected over a large solid angle give information about the form and energies of spectral features, which are related to the underlying electronic structure of the sample. Spectra measured as a function of exit angle reflect the phenomenon of photoelectron diffraction, which is related to the underlying crystallographic structure of the sample. We report applications of these techniques by our group to the study of a number of systems involving ultra-thin metallic layers on surfaces, which can be true surface alloys, whose properties are often very different from those in the bulk. The surface systems we chose manifest surfactant behavior, catalytic activity and intercomponent effects. Our electronic structure results were derived from photoemission and X-ray excited Auger spectroscopies: interpretation of these data requires inclusion of the phenomena of relaxation and screening. Our crystallographic results were derived from photoelectron diffraction in combination with LEED: derivation of the results requires comparison with multiple scattering theoretical simulations and involves considerable computational effort. We have studied 1)-we present representative results of these studies.
Journal of Electron Spectroscopy and Related Phenomena, 2007
A well-known final state effect in photoemission is that of the "shake-up" satellite in core leve... more A well-known final state effect in photoemission is that of the "shake-up" satellite in core level and valence band spectra from Pd in the bulk metals. The satellite is explained in terms of the existence of two Pd final state configurations, 4d 9 5s 1 and 4d 10 5s 2 . The present paper is a preliminary report of studies of the suppression of the shake-up satellite in surface alloys of Pd with the "sp metals", In and Sb, on Pd(1 1 1), whose surface structure was determined as being ( √ 3 × √ 3)R30 • from LEED and X-ray photoelectron diffraction (XPD). Although satellite suppression has been reported for bulk alloys, no such report has been made for a metallic surface alloy system. From the satellite suppression and the related spectra asymmetry reduction, as well as the small binding energy shifts, we are able to interpret the results in terms of valence band splitting.
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Papers by Marcelo Carazzolle