Publications by authors named "Daniel Guariz Pinheiro"

17 Publications

  • Page 1 of 1

Bacterial communities associated with sugarcane under different agricultural management exhibit a diversity of plant growth-promoting traits and evidence of synergistic effect.

Microbiol Res 2021 Jun 18;247:126729. Epub 2021 Feb 18.

Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Câmpus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, 14884- 900, SP, Brazil. Electronic address:

Plant-associated microbiomes have been a target of interest for the prospection of microorganisms, which may be acting as effectors to increase agricultural productivity. For years, the search for beneficial microorganisms has been carried out from the characterization of functional traits of growth-promotion using tests with a few isolates. However, eventually, the expectations with positive results may not be realized when the evaluation is performed in association with plants. In our study, we accessed the cultivable sugarcane microbiome under two conditions of agronomic management: organic and conventional. From the use of a new customized culture medium, we recovered 944 endophytic and epiphytic bacterial communities derived from plant roots, stalks, leaves, and rhizospheric soil. This could be accomplished by using a large-scale approach, initially performing an in planta (Cynodon dactylon) screening process of inoculation to avoid early incompatibility. The inoculation was performed using the bacterial communities, considering that in this way, they could act synergistically. This process resulted in 38 candidate communities, 17 of which had higher Indole-3-acetic acid (IAA) production and phosphate solubilization activity and, were submitted to a new in planta test using Brachiaria ruziziensis and quantification of functional traits for growth-promotion and physiological tests. Enrichment analysis of selected communities has shown that they derived mainly from epiphytic populations of sugarcane stalks under conventional management. The sequencing of the V3-V4 region of the 16S rRNA gene revealed 34 genera and 24 species distributed among the phylum Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. We also observed a network of genera in these communities where the genus Chryseobacterium stands out with a greater degree of interaction, indicating a possible direct or indirect role as a keystone taxon in communities with plant-growth promotion capacities. From the results achieved, we can conclude that the approach is useful in the recovery of a set of sugarcane bacterial communities and that there is, evidence of synergistic action providing benefits to plants, and that they are compatible with plants of the same family (Poaceae). Thus, we are reporting the beneficial bacterial communities identified as suitable candidates with rated potential to be exploited as bioinoculants for crops.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.micres.2021.126729DOI Listing
June 2021

In vivo biocompatibility and biodegradability of poly(lactic acid)/poly(ε-caprolactone) blend compatibilized with poly(ε-caprolactone--tetrahydrofuran) in Wistar rats.

Biomed Phys Eng Express 2021 Mar 2. Epub 2021 Mar 2.

Animal Morphology and Physiology, UNESP Jaboticabal, Via de Acesso Prof.Paulo Donato Castellane s/n - Jaboticabal/SP, Jaboticabal, 14884-900, BRAZIL.

Poly(lactic acid) (PLA) and poly(ɛ-caprolactone) (PCL) are two important aliphatic esters known for their biodegradability and bioresorbability properties; the former is stiffer and brittle while the smaller modulus of the latter allows a suitable elongation. The new biomaterials being developed from the blend of these two polymers (PLA and PCL) is opportune due to the reducing interfacial tension between their immiscible phases. In a previous study, PLA/PCL immiscible blend when compatibilized with poly(ε-caprolactone-b-tetrahydrofuran) resulted in enhanced ductility and toughness no cytotoxic effect in vitro tests. There is little published data on the effect of poly(ε-caprolactone-b-tetrahydrofuran) on PLA and PCL biocompatibility and biodegradability in vivo tests. This study focuses on evaluating the behavioral response and polymer-tissue interaction of compatibilized PLA/PCL blend compared to neat PLA implanted via intraperitoneal (IP) and subcutaneous (SC) in male Wistar rats, distributed in four experimental groups: neat PLA, PLA/PCL blend, sham, and control at 2-, 8- and 24-weeks post-implantation (WPI). Open-field test was performed to appraise emotionality and spontaneous locomotor activity. Histopathological investigation using hematoxylin-eosin (H&E) and picrosirius-hematoxylin (PSH) was used to assess polymer-tissue interaction. Modifications in PLA and the PLA / PCL blend's surface morphology were determined by scanning electron microscopy (SEM). PLA group defecated more often than PLA/PCL rats 2 and 8 WPI. Conjunctive capsule development around implants, cell adhesion, angiogenesis, and giant cells of a foreign body to the biomaterial was observed in light microscopy. Both groups displayed a fibrous reaction along with collagen deposition around the biomaterials. In the SEM, the images showed a higher degradation rate for the PLA/PCL blend in both implantation routes. The polymers implanted via IP exhibited a higher degradation rate compared to SC. These findings emphasize the biocompatibility of the PLA/PCL blend compatibilized with poly(ε-caprolactone-b-tetrahydrofuran), making this biopolymer an acceptable alternative in a variety of biomedical applicatio.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1088/2057-1976/abeb5aDOI Listing
March 2021

Late Embryogenesis Abundant Protein-Client Protein Interactions.

Plants (Basel) 2020 Jun 29;9(7). Epub 2020 Jun 29.

Department of Horticulture, University of Kentucky Seed Biology Program, Plant Science Building, 1405 Veterans Drive, University of Kentucky, Lexington, KY 40546-0312, USA.

The intrinsically disordered proteins belonging to the LATE EMBRYOGENESIS ABUNDANT protein (LEAP) family have been ascribed a protective function over an array of intracellular components. We focus on how LEAPs may protect a stress-susceptible proteome. These examples include instances of LEAPs providing a shield molecule function, possibly by instigating liquid-liquid phase separations. Some LEAPs bind directly to their client proteins, exerting a holdase-type chaperonin function. Finally, instances of LEAP-client protein interactions have been documented, where the LEAP modulates (interferes with) the function of the client protein, acting as a surreptitious rheostat of cellular homeostasis. From the examples identified to date, it is apparent that client protein modulation also serves to mitigate stress. While some LEAPs can physically bind and protect client proteins, some apparently bind to assist the degradation of the client proteins with which they associate. Documented instances of LEAP-client protein binding, even in the absence of stress, brings to the fore the necessity of identifying how the LEAPs are degraded post-stress to render them innocuous, a first step in understanding how the cell regulates their abundance.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/plants9070814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7412488PMC
June 2020

Transcriptome Profiling of Pacu () Challenged With Pathogenic : Inference on Immune Gene Response.

Front Genet 2020 9;11:604. Epub 2020 Jun 9.

Aquaculture Center, São Paulo State University (Unesp), Jaboticabal, Brazil.

Pacu () is a Neotropical fish of major importance for South American aquaculture. Septicemia caused by bacteria is currently considered a substantial threat for pacu aquaculture that have provoked infectious disease outbreaks with high economic losses. The understanding of molecular aspects on progress of infection and pacu immune response is scarce, which have limited the development of genomic selection for resistance to this infection. The present study aimed to generate information on transcriptome of pacu in face of infection, and compare the transcriptomic responses between two groups of time-series belonging to a disease resistance challenge, peak mortality (HM) and mortality plateau (PM) groups of individuals. Nine RNA sequencing (RNA-Seq) libraries were prepared from liver tissue of challenged individuals, generating ∼160 million 150 bp pair-end reads. After quality trimming/cleanup, these reads were assembled generating 211,259 contigs. When the expression of genes from individuals of HM group were compared to individuals from control group, a total of 4,413 differentially expressed transcripts were found (2,000 upregulated and 2,413 downregulated candidate genes). Additionally, 433 transcripts were differentially expressed when individuals from MP group were compared with those in the control group (155 upregulated and 278 downregulated candidate genes). The resulting differentially expressed transcripts were clustered into the following functional categories: cytokines and signaling, epithelial protection, antigen processing and presentation, apoptosis, phagocytosis, complement system cascades and pattern recognition receptors. The proposed results revealing relevant differential gene expression on HM and PM groups which will contribute to a better understanding of the molecular defense mechanisms during infection.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2020.00604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295981PMC
June 2020

Characterization and comprehensive analysis of the ecological interaction networks of bacterial communities in Paullinia cupana var. sorbilis by 16S rRNA gene metabarcoding.

World J Microbiol Biotechnol 2019 Nov 14;35(12):182. Epub 2019 Nov 14.

Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.

Endophytes improve the host performance in areas of high plant endemicity. Paullinia cupana is an Amazonia plant species of economic and social importance due to the high caffeine concentration in its seeds. An interesting strategy to identify endophytic microorganisms with potential biotechnological application is to understand the factors that influence the endophytic community to rationalize the host management programs. We used the next-generation sequencing for bacterial 16S rRNA gene to examine how the P. cupana organ, genotype, and geographic location influenced its endophytic bacterial community. We obtained 1520 operational taxonomic units (OTUs) distributed in 19 phyla, 32 classes, 79 orders, 114 families and 174 genera. The P. cupana roots and leaves were specifically colonized by the bacterial genera Acidothermus and Porphyromonas, respectively, with high relative frequency. The plant organ type influenced the endophytic community's richness, diversity, OTUs composition, relative abundance of phyla and genera, and genera interaction network. However, the host plant genotype and geographic location influenced the composition and interaction among genera in the network analysis. Prevotella is a super-generalist genus in the interaction network of endophytic bacteria of P. cupana. This study revealed endophytic bacterial groups of importance to P. cupana and stressed that the host plant organ modulates the structure and interactions within this community. Our results indicated that the microbial community adapted to colonize P. cupana by adjusting to its composition and interaction network. The isolation of abundant and super-generalist bacterial genera shall help to examine their functionality to the composition and fitness of the endophytic community of P. cupana.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11274-019-2758-yDOI Listing
November 2019

Transcriptome profiling of muscle in Nelore cattle phenotypically divergent for the ribeye muscle area.

Genomics 2020 03 24;112(2):1257-1263. Epub 2019 Jul 24.

School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil; National Council for Scientific and Technological Development (CNPq), Brasilia, DF, Brazil. Electronic address:

This study aimed to use RNA-Seq to identify differentially expressed genes (DEGs) in muscle of uncastrated Nelore males phenotypically divergent for ribeye muscle area (REA). A total of 80 animals were phenotyped for REA, and 15 animals each with the highest REA and the lowest REA were selected for analyses. DEGs found (N = 288) belonging to families related to muscle cell growth, development, motility and proteolysis, such as actin, myosin, collagen, integrin, solute carrier, ubiquitin and kelch-like. Functional analysis showed that many of the significantly enriched gene ontology terms were closely associated with muscle development, growth, and degradation. Through co-expression network analysis, we predicted three hub genes (PPP3R1, FAM129B and UBE2G1), these genes are involved in muscle growth, proteolysis and immune system. The genes expression levels and its biological process found this study may result in differences in muscle deposition, and therefore, Nelore animals with different REA proportions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ygeno.2019.07.012DOI Listing
March 2020

Prediction of hub genes associated with intramuscular fat content in Nelore cattle.

BMC Genomics 2019 Jun 25;20(1):520. Epub 2019 Jun 25.

School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.

Background: The aim of this study was to use transcriptome RNA-Seq data from longissimus thoracis muscle of uncastrated Nelore males to identify hub genes based on co-expression network obtained from differentially expressed genes (DEGs) associated with intramuscular fat content.

Results: A total of 30 transcriptomics datasets (RNA-Seq) obtained from longissimus thoracis muscle were selected based on the phenotypic value of divergent intramuscular fat content: 15 with the highest intramuscular fat content (HIF) and 15 with the lowest intramuscular fat content (LIF). The transcriptomics datasets were aligned with a reference genome and 65 differentially expressed genes (DEGs) were identified, including 21 upregulated and 44 downregulated genes in HIF animals. The normalized count data from DEGs was then used for co-expression network construction. From the co-expression network, four modules were identified. The topological properties of the network were analyzed; those genes engaging in the most interactions (maximal clique centrality method) with other DEGs were predicted to be hub genes (PDE4D, KLHL30 and IL1RAP), which consequently may play a role in cellular and/or systemic lipid biology in Nelore cattle. Top modules screened from the gene co-expression network were identify. The two candidate modules had clear associated biological pathways related to fat development, cell adhesion, and muscle differentiation, immune system, among others. The hub genes belonged in top modules and were downregulated in HIF animals. PDE4D and IL1RAP have known effects on lipid metabolism and the immune system through the regulation of cAMP signaling. Given that cAMP is known to play a role in lipid systems, PDE4D and IL1RAP downregulation may contribute to increased levels of intracellular cAMP and thus may have effects on IF content differences in Nelore cattle. KLHL30 may have effects on muscle metabolism. Klhl protein families play a role in protein degradation. However, the downregulation of this gene and its role in lipid metabolism has not yet been clarified.

Conclusions: The results reported in this study indicate candidate genes and molecular mechanisms involved in IF content difference in Nelore cattle.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-5904-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591902PMC
June 2019

Post-transcriptional markers associated with clinical complications in Type 1 and Type 2 diabetes mellitus.

Mol Cell Endocrinol 2019 06 26;490:1-14. Epub 2019 Mar 26.

Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, 14048-900, Ribeirão Preto, SP, Brazil. Electronic address:

The delayed diagnosis and the inadequate treatment of diabetes increase the risk of chronic complications. The study of regulatory molecules such as miRNAs can provide expression profiles of diabetes and diabetes complications. We evaluated the mononuclear cell miRNA profiles of 63 Type 1 and Type 2 diabetes patients presenting or not microvascular complications, and 40 healthy controls, using massive parallel sequencing. Gene targets, enriched pathways, dendograms and miRNA-mRNA networks were performed for the differentially expressed miRNAs. Six more relevant miRNAs were validated by RT-qPCR and data mining analysis. MiRNAs associated with specific complications included: i) neuropathy (miR-873-5p, miR-125a-5p, miR-145-3p and miR-99b-5p); ii) nephropathy (miR-1249-3p, miR-193a-5p, miR-409-5p, miR-1271-5p, miR-501-3p, miR-148b-3p and miR-9-5p); and iii) retinopathy (miR-143-3p, miR-1271-5p, miR-409-5p and miR-199a-5p). These miRNAs mainly targeted gene families and specific genes associated with advanced glycation end products and their receptors. Sets of miRNAs were also defined as potential targets for diabetes/diabetes complication pathogenesis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mce.2019.03.008DOI Listing
June 2019

Intestinal Dysbiosis in Autoimmune Diabetes Is Correlated With Poor Glycemic Control and Increased Interleukin-6: A Pilot Study.

Front Immunol 2018 25;9:1689. Epub 2018 Jul 25.

Microbiome Study Group, School of Health Sciences Dr. Paulo Prata (FACISB), Barretos, Brazil.

Intestinal dysbiosis associated with immunological deregulation, leaky gut, bacterial translocation, and systemic inflammation has been associated with autoimmune diseases, such as type 1 diabetes (T1D). The aim of this study was to investigate the intestinal dysbiosis in T1D patients and correlate these results with clinical parameters and cytokines. The present study was approved by the Barretos Cancer Hospital (Process number 903/2014), and all participants have signed the informed consent in accordance with the Declaration of Helsinki, and answered a questionnaire about dietary habits. Stool samples were used for bacterial 16S sequencing by MiSeq Illumina platform. IL-2, IL-4, IL-6, IL-10, IL-17A, TNF, and IFN-γ plasma concentrations were determined by cytometric bead arrays. The Pearson's chi-square, Mann-Whitney and Spearman correlation were used for statistical analyses. Alpha and beta diversities were conducted by using an annotated observed taxonomic units table. This study included 20 patients and 28 controls, and we found significant differences ( < 0.05) among consumption of vegetables, proteins, milk and derivatives, spicy food, and canned food when we compare patients and controls. We detected intestinal dysbiosis in T1D patients when we performed the beta diversity analysis ( = 0.01). The prevalent species found in patients' stool were the Gram-negatives , and . The inflammatory interleukin-6 was significantly increased ( = 0.017) in patients' plasma. Furthermore, we showed correlation among patients with poor glycemic control, represented by high levels of HbA1 percentages and Bacteroidetes, Lactobacillales, and relative abundances. We concluded that there are different gut microbiota profiles between T1D patients and healthy controls. The prevalent Gram-negative species in T1D patients could be involved in the leaky gut, bacterial translocation, and poor glycemic control. However, additional studies, with larger cohorts, are required to determine a "signature" of the intestinal microbiota in T1D patients in the Brazilian population.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fimmu.2018.01689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6068285PMC
July 2018

Highly expressed placental miRNAs control key biological processes in human cancer cell lines.

Oncotarget 2018 May 4;9(34):23554-23563. Epub 2018 May 4.

Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.

Despite being a healthy tissue, the constituent cells of the placenta, share similar characteristics with tumor cells, such as increased cell growth, migration, and invasion. However, while these processes are stochastic and uncontrolled in cancer cells, in placenta they are precisely controlled. Since miRNAs have been reported to regulate genes that control the molecular mechanisms necessary for the development of both human placenta and cancer, we addressed for miRNAs highly expressed in the placenta that could be involved in tumorigenesis. Here, we assessed the miRNA profile in placenta samples using microarray analysis. The results showed that miR-451 and miR-720, highly expressed placental miRNAs, presented very low or undetectable expression in cancer cell lines compared to the normal placenta and healthy tissues. Additionally, transfection of miR-451 or miR-720 mimics in choriocarcinoma cell line (JEG3) and colorectal adenocarcinoma cell line (HT-29) resulted in impaired cell proliferation, decreased cell migration and invasion and reduced ability of colony formation. These findings provide evidence that placenta may work as an alternative model to identify novel miRNAs involved in pathways controlling tumorigenesis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.18632/oncotarget.25264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5955126PMC
May 2018

Detection of Increased Plasma Interleukin-6 Levels and Prevalence of and in the Feces of Type 2 Diabetes Patients.

Front Immunol 2017 15;8:1107. Epub 2017 Sep 15.

Microbiome Study Group, School of Health Sciences Dr. Paulo Prata (FACISB), Barretos, Brazil.

Intestinal dysbiosis and metabolic endotoxemia have been associated with metabolic disorders, such as obesity, insulin resistance, and type 2 diabetes (T2D). The main goal of the present study was to evaluate the intestinal dysbiosis in Brazilian T2D patients and correlate these data with inflammatory cytokines and lipopolysaccharides (LPS) plasma concentrations. This study was approved by the Ethics Committees from Barretos Cancer Hospital and all individuals signed the informed consent form. Stool samples were required for DNA extraction, and the V3/V4 regions of bacterial 16S were sequenced using an Illumina platform. Peripheral blood was used to quantify inflammatory cytokines and plasma LPS concentrations, by CBA flex and ELISA, respectively. Statistical analyses were performed using Mann-Whitney and Spearman's tests. Analysis of variance, diversity indexes, and analysis of alpha- and beta-diversity were conducted using an annotated Operational Taxonomic Unit table. This study included 20 patients and 22 controls. We observed significant differences ( < 0.01) in the microbiota composition (beta-diversity) between patients and controls, suggesting intestinal dysbiosis in Brazilian T2D patients. The prevalent species found in patients' feces were the Gram-negatives , and . The proinflammatory interleukin-6 (IL-6) was significantly increased ( < 0.05) in patients' plasma and LPS levels were decreased. We find correlations between the proinflammatory interferon-gamma with Gram-negatives and species, and a positive correlation between the LPS levels and reads. The and species were associated with insulin resistance in previous studies. In this study, we suggested that the prevalence of Gram-negative species in the gut and the increased plasma IL-6 in patients could be linked to low-grade inflammation and insulin resistance. In conclusion, the and species could represent an intestinal microbiota signature, associated with T2D development. Furthermore, the identification of these Gram-negative bacteria, and the detection of inflammatory markers, such as increased IL-6, could be used as diabetes predictive markers in overweight, obese and in genetically predisposed individuals to develop T2D.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fimmu.2017.01107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5605568PMC
September 2017

HOX genes: potential candidates for the progression of laryngeal squamous cell carcinoma.

Tumour Biol 2016 Nov 22;37(11):15087-15096. Epub 2016 Sep 22.

Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, SP, CEP: 14049-900, Brazil.

Laryngeal squamous cell carcinoma (LSCC) is a very aggressive cancer, considered to be a subtype of the head and neck squamous cell carcinoma (HNSCC). Despite significant advances in the understanding and treatment of cancer, prognosis of patients with LSCC has not improved recently. In the present study, we sought to understand better the genetic mechanisms underlying LSCC development. Thirty-two tumor samples were collected from patients undergoing surgical resection of LSCC. The samples were submitted to whole-genome cDNA microarray analysis aiming to identify genetic targets in LSCC. We also employed bioinformatic approaches to expand our findings using the TCGA database and further performed functional assays, using human HNSCC cell lines, to evaluate viability, cell proliferation, and cell migration after silencing of selected genes. Eight members of the homeobox gene family (HOX) were identified to be overexpressed in LSCC samples when compared to normal larynx tissue. Quantitative RT-PCR analysis validated the overexpression of HOX gene family members in LSCC. Receiver operating characteristic (ROC) statistical method curve showed that the expression level of seven members of HOX gene family can distinguish tumor from nontumor tissue. Correlation analysis of clinical and gene expression data revealed that HOXC8 and HOXD11 genes were associated with the differentiation degree of tumors and regional lymph node metastases, respectively. Additionally, siRNA assays confirmed that HOXC8, HOXD10, and HOXD11 genes might be critical for cell colony proliferation and cell migration. According to our findings, several members of the HOX genes were overexpressed in LSCC samples and seem to be required in biological processes involved in tumor development. This suggests that HOX genes might play a critical role in the physiopathology of LSCC tumors.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s13277-016-5356-8DOI Listing
November 2016

Gene expression analysis of laryngeal squamous cell carcinoma.

Genom Data 2015 Sep 8;5:9-12. Epub 2015 May 8.

Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, SP CEP 14049-900, Brazil ; National Institute of Science and Technology in Stem Cell and Cell Therapy and Center For Cell-Based Therapy, Rua Tenente Catão Roxo, 2501, Monte Alegre, Ribeirão Preto, SP CEP 14051-140, Brazil ; Center for Integrative Systems Biology, CISBi, NAP/USP, Rua Catão Roxo, 2501, Monte Alegre, Ribeirão Preto, SP CEP 14051-140, Brazil.

Laryngeal squamous cell carcinoma (LSCC) is one of the most common malignancies of the head and neck tumors Zhang et al., 2013 [1]). Previous studies have associated its occurrence with social activities, such as tobacco and alcohol consumption (Hashibe et al., 2007a [2]; Hashibe et al., 2007b [3]; Shangina et al., 2006 [4]). Here, we performed a genome-wide gene expression profiling in thirty-one patients positively diagnosed for LSCC, in order to investigate new targets involved in tumorigenesis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.gdata.2015.04.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583618PMC
September 2015

Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.

Science 2015 Jun 14;348(6239):1139-43. Epub 2015 May 14.

China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aaa4788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5471836PMC
June 2015

De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers.

BMC Genomics 2014 Mar 26;15:236. Epub 2014 Mar 26.

Departamento de Genética/FMRP/USP, Laboratório de Genética Molecular e Bioinformática, Rua Tenente Catão Roxo, 2501, CEP 14,051- 140 Ribeirão Preto, São Paulo, Brazil.

Background: The rubber tree, Hevea brasiliensis, is a species native to the Brazilian Amazon region and it supplies almost all the world's natural rubber, a strategic raw material for a variety of products. One of the major challenges for developing rubber tree plantations is adapting the plant to biotic and abiotic stress. Transcriptome analysis is one of the main approaches for identifying the complete set of active genes in a cell or tissue for a specific developmental stage or physiological condition.

Results: Here, we report on the sequencing, assembling, annotation and screening for molecular markers from a pool of H. brasiliensis tissues. A total of 17,166 contigs were successfully annotated. Then, 2,191 Single Nucleotide Variation (SNV) and 1.397 Simple Sequence Repeat (SSR) loci were discriminated from the sequences. From 306 putative, mainly non-synonymous SNVs located in CDS sequences, 191 were checked for their ability to characterize 23 Hevea genotypes by an allele-specific amplification technology. For 172 (90%), the nucleotide variation at the predicted genomic location was confirmed, thus validating the different steps from sequencing to the in silico detection of the SNVs.

Conclusions: This is the first study of the H. brasiliensis transcriptome, covering a wide range of tissues and organs, leading to the production of the first developed SNP markers. This process could be amplified to a larger set of in silico detected SNVs in expressed genes in order to increase the marker density in available and future genetic maps. The results obtained in this study will contribute to the H. brasiliensis genetic breeding program focused on improving of disease resistance and latex yield.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-15-236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4051172PMC
March 2014

Genes related to antiviral activity, cell migration, and lysis are differentially expressed in CD4(+) T cells in human t cell leukemia virus type 1-associated myelopathy/tropical spastic paraparesis patients.

AIDS Res Hum Retroviruses 2014 Jun 16;30(6):610-22. Epub 2013 Oct 16.

1 National Institute of Science and Technology in Stem Cell and Cell Therapy , Center for Cell-Based Therapy and Regional Blood Center of Ribeirão Preto, Ribeirão Preto, Brazil .

Human T cell leukemia virus type 1 (HTLV-1) preferentially infects CD4(+) T cells and these cells play a central role in HTLV-1 infection. In this study, we investigated the global gene expression profile of circulating CD4(+) T cells from the distinct clinical status of HTLV-1-infected individuals in regard to TAX expression levels. CD4(+) T cells were isolated from asymptomatic HTLV-1 carrier (HAC) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) patients in order to identify genes involved in HAM/TSP development using a microarray technique. Hierarchical clustering analysis showed that healthy control (CT) and HTLV-1-infected samples clustered separately. We also observed that the HAC and HAM/TSP groups clustered separately regardless of TAX expression. The gene expression profile of CD4(+) T cells was compared among the CT, HAC, and HAM/TSP groups. The paxillin (Pxn), chemokine (C-X-C motif ) receptor 4 (Cxcr4), interleukin 27 (IL27), and granzyme A (Gzma) genes were differentially expressed between the HAC and HAM/TSP groups, regardless of TAX expression. The perforin 1 (Prf1) and forkhead box P3 (Foxp3) genes were increased in the HAM/TSP group and presented a positive correlation to the expression of TAX and the proviral load (PVL). The frequency of CD4(+)FOXP3(+) regulatory T cells (Treg) was higher in HTLV-1-infected individuals. Foxp3 gene expression was positively correlated with cell lysis-related genes (Gzma, Gzmb, and Prf1). These findings suggest that CD4(+) T cell activity is distinct between the HAC and HAM/TSP groups.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1089/aid.2013.0109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046198PMC
June 2014

Computational framework to support integration of biomolecular and clinical data within a translational approach.

BMC Bioinformatics 2013 Jun 6;14:180. Epub 2013 Jun 6.

Department of Computing and Mathematics, Faculty of Philosophy, Sciences and Languages of Ribeirão Preto, University of São Paulo, São Paulo, Brazil.

Background: The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information.

Results: We have implemented an extension of Chado - the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications.

Conclusions: Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different "omics" technologies with patient's clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-14-180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3688149PMC
June 2013