A5075298953- Biofuel production and bioconversion
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Sugarcane Cultivation and Processing
- Gut microbiota and health
- Microbial Metabolic Engineering and Bioproduction
- Chromosomal and Genetic Variations
- Plant pathogens and resistance mechanisms
- Genetic and phenotypic traits in livestock
- Diet and metabolism studies
- Genetics and Plant Breeding
- Bioinformatics and Genomic Networks
- Plant-Microbe Interactions and Immunity
- Legume Nitrogen Fixing Symbiosis
- Genetic Mapping and Diversity in Plants and Animals
- Natural Products and Biological Research
- Ubiquitin and proteasome pathways
- Tryptophan and brain disorders
- Enzyme Production and Characterization
- Thyroid Cancer Diagnosis and Treatment
- Plant Pathogenic Bacteria Studies
- Data Management and Algorithms
- Polyamine Metabolism and Applications
- Scientific Computing and Data Management
- Gene expression and cancer classification
Institute of Science and Technology
2024
Universidade Federal de São Paulo
2013-2024
Federal Institute of São Paulo
2013-2018
Universidade Federal de São Carlos
2014
Universidade de São Paulo
2012-2014
The University of Tokyo
2009-2010
Japan Science and Technology Agency
2009
Abstract Poaceae, among the most abundant plant families, includes many economically important polyploid species, such as forage grasses and sugarcane ( Saccharum spp.). These species have elevated genomic complexities limited genetic resources, hindering application of marker-assisted selection strategies. Currently, promising approach for increasing gains in breeding is selection. However, due to polyploidy nature these more accurate models incorporating into schemes are needed. This study...
Profiling the transcriptome that underlies biomass degradation by fungus Trichoderma harzianum allows identification of gene sequences with potential application in enzymatic hydrolysis processing. In present study, T. IOC-3844 was analyzed using RNA-seq technology. The sequencing generated 14.7 Gbp for downstream analyses. De novo assembly resulted 32,396 contigs, which were submitted and classified according to their identities. This analysis allowed us define a principal set genes are...
Abstract Sugarcane is an economically important crop, but its genomic complexity has hindered advances in molecular approaches for genetic breeding. New cultivars are released based on the identification of interesting traits, and sugarcane, brown rust resistance a desirable characteristic due to large economic impact disease. Although marker-assisted selection been successful, genes involved still unknown, associated regions vary among cultivars, thus restricting methodological...
Trichoderma harzianum IOC-3844 secretes high levels of cellulolytic-active enzymes and is therefore a promising strain for use in biotechnological applications second-generation bioethanol production. However, the T. biomass degradation mechanism has not been well explored at genetic level. The present work investigates six genomic regions (~150 kbp each) this fungus that are enriched with genes related to conversion. A BAC library consisting 5,760 clones was constructed, an average insert...
Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses reveal the biological functions of coded proteins. However, previous approaches sequencing were expensive or time-consuming, therefore, a fast efficient approach was demanded.We developed program, MuSICA 2, that assembles millions short (36-nucleotide) reads collected from single flow cell lane Illumina Genome Analyzer...
The advent of high-throughput DNA sequencers has increased the pace collecting enormous amounts genomic information, yielding billions nucleotides on a weekly basis. This advance represents an improvement two orders magnitude over traditional Sanger in terms number per unit time, allowing even small groups researchers to obtain huge volumes data fairly short period. Consequently, pressing need exists for development personalized genome browsers analyzing these immense locally stored data....
Fundamental questions such as what are the genes that really necessary for survival of cells have motivated many studies to investigate essentiality in different species. Initial efforts attempted address this problem through exhaustive knockout experiments simple bacteria. Recently, results obtained these also been applied emerging field synthetic biology with possible implications other fields health and energy. Motivated by evolution DNA sequencing technology high-throughput biological...
This study aimed to investigate the efficacy of chitosan-whey protein complex coacervation (Coa), galactooligosaccharide (GOS), and their combination (COAG) in mitigating obesity-induced alterations caused by a high-fat (HF) diet. Male C57BL/6 mice were fed for 16 weeks with the: N - 2 normolipid diet, HF treatments.The gut microbiota composition treated HFCOAG more closely resembled group, displaying greater dissimilarity health-associated bacteria, such as Lachnospiraceae, Porphyromonas,...
Abstract Sugarcane ( Saccharum spp.) holds significant economic importance in sugar and biofuel production. Despite extensive research, understanding highly quantitative traits, such as sucrose content, remains challenging due to the complex genomic landscape of crop. In this study, we conducted a multiomic investigation elucidate genetic architecture molecular mechanisms governing accumulation sugarcane. Using biparental cross (IACSP95-3018 × IACSP93-3046) genetically diverse collection...
ABSTRACT Sugarcane is an economically important crop, but its genomic complexity has hindered advances in molecular approaches for genetic breeding. New cultivars are released based on the identification of interesting traits, and sugarcane, brown rust resistance a desirable characteristic due to large economic impact disease. Although marker-assisted selection been successful, genes involved still unknown, associated regions vary among cultivars, thus restricting methodological...
Abstract The protein kinase (PK) superfamily is one of the largest superfamilies in plants and core regulator cellular signaling. Even considering this substantial importance, kinome common bean ( Phaseolus vulgaris ) has not been profiled yet. Here, we identified characterised complete set kinases bean, performing an in-depth investigation with phylogenetic analyses measurements gene distribution, structural organization, properties, expression patterns over a large RNA-Sequencing data....
One common parameter of many clustering algorithms is the number k clusters required to partition data. This case k-means, one most popular from Machine Learning literature, and its variants. Indeed, when a dataset, right use often not obvious, choosing automatically hard algorithmic problem. In this context, procedure used estimate present in dataset run algorithm multiple times varying solutions obtained chosen based on given internal validation measure (e.g., silhouette coefficient)....
Gut microbiota (GM) modulation has been considered a nutritional approach to manage obesity. Reduced Firmicutes/Bacteroidetes ratio (F/B) is associated with reduced energy harvesting capacity from the diet, ameliorates endotoxemia and inflammation, restores gut hormone signaling related hypothalamic control of homeostasis. As anti-obesogenic anti-inflammatory properties have attributed Ginkgo biloba extract (GbE), present study investigated whether GbE supplementation for two weeks modulates...
Simultaneously sequencing multiple clones using second-generation sequencers can speed up many essential clone-based methods. However, in applications such as fosmid clone and full-length cDNA sequencing, it is important to create pools of that do not overlap on the genome for identification structural variations alternatively spliced transcripts, respectively. We define nonoverlapping pooling problem provide practical solutions based optimal graph coloring bin-packing algorithms with...
Simultaneously sequencing multiple clones using second generation sequencers can speed up many essential clone-based methods. However, in applications such as fosmid clone and full-length cDNA it is important to create pools of that do not overlap on the genome for identification structural variations alternatively spliced transcripts, respectively. We define non-overlapping pooling problem provide practical solutions based optimal graph coloring bin-packing algorithms with constant absolute...
ABSTRACT Poaceae, among the most abundant plant families, includes many economically important polyploid species, such as forage grasses and sugarcane ( Saccharum spp.). These species have elevated genomic complexities limited genetic resources, hindering application of marker-assisted selection strategies. Currently, promising approach for increasing gains in breeding is selection. However, due to polyploidy nature these more accurate models incorporating into schemes are needed. This study...