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Search Results: 1 - 10 of 32210 matches for " Ana CQ Simoes "
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New insights about host response to smallpox using microarray data
Gustavo H Esteves, Ana CQ Simoes, Estevao Souza, Rodrigo A Dias, Raydonal Ospina, Thiago M Venancio
BMC Systems Biology , 2007, DOI: 10.1186/1752-0509-1-38
Abstract: We used KEGG pathways annotations to define groups of genes (or modules), and subsequently compared them to macaque survival times. This technique provided additional insights about the host response to this disease, such as increased expression of the cytokines and ECM receptors in the individuals with higher survival times. These results could indicate that these gene groups could influence an effective response from the host to smallpox.Macaques with higher survival times clearly express some specific pathways previously unidentified using regular gene-by-gene approaches. Our work also shows how third party analysis of public datasets can be important to support new hypotheses to relevant biological problems.Large scale gene expression analysis with microarray technology is expanding and generating a large amount of high quality, publicly available data. In the present work we analyzed a dataset derived from monkeys infected by smallpox, published by Rubins et al [1]. Smallpox is a lethal disease that was endemic in many parts of the world until eradicated by a massive immunization program developed by the World Health Organization. Its fatality rate was estimated to be 30%, and the survivors often had disfiguring scars [2].There are serious concerns about the use of smallpox as a bioweapon [3,4]. Recently, some health care workers were vaccinated by the UK government for the analysis of antibody responses [5]. Pox viruses display unique abilities to interfere with the host immune system, producing immune modulators [6] and there are at least 16 viral genes involved in combating the host immune response [7]. The original study's goal was to analyze the evolution of the gene expression of the peripheral blood cells of variola-infected monkeys, so as to clarify the biological processes associated with host-pathogen interactions [1].Among the important results was the absence of a TNF-α/NF-κB-activated transcriptional mechanism during systemic infection, which could
Functional microarray analysis suggests repressed cell-cell signaling and cell survival-related modules inhibit progression of head and neck squamous cell carcinoma
Anna EL Coló, Ana CQ Simoes, André L Carvalho, Camila M Melo, Lucas Fahham, Luiz P Kowalski, Fernando A Soares, Eduardo J Neves, Luiz FL Reis, Alex F Carvalho
BMC Medical Genomics , 2011, DOI: 10.1186/1755-8794-4-33
Abstract: Tumor samples were obtained from untreated HNSCC patients undergoing surgery. Patients were classified according to pathologic lymph node status (positive or negative) or tumor recurrence (recurrent or non-recurrent tumor) after treatment (surgery with neck dissection followed by radiotherapy). Using microarray gene expression, we screened tumor samples according to modules comprised by genes in the same pathway or functional category.The most frequent alterations were the repression of modules in negative lymph node (N0) and in non-recurrent tumors rather than induction of modules in N+ or in recurrent tumors. N0 tumors showed repression of modules that contain cell survival genes and in non-recurrent tumors cell-cell signaling and extracellular region modules were repressed.The repression of modules that contain cell survival genes in N0 tumors reinforces the important role that apoptosis plays in the regulation of metastasis. In addition, because tumor samples used here were not microdissected, tumor gene expression data are represented together with the stroma, which may reveal signaling between the microenvironment and tumor cells. For instance, in non-recurrent tumors, extracellular region module was repressed, indicating that the stroma and tumor cells may have fewer interactions, which disable metastasis development. Finally, the genes highlighted in our analysis can be implicated in more than one pathway or characteristic, suggesting that therapeutic approaches to prevent tumor progression should target more than one gene or pathway, specially apoptosis and interactions between tumor cells and the stroma.Head and neck squamous cell carcinomas (HNSCC) are the seventh most common solid malignancy in the United States, accounting for more than 47,000 new cancer cases per year [1]. Surgery of patients clinically diagnosed with lymph node metastasis (N+) usually involves neck dissection, which can cause disfigurement, functional impairment, and pain. However, af
Epidemiology of attention deficit disorder in Brazil: Implications for the Brazilian legal system  [PDF]
Sergio L. Schmidt, Eunice Do Nascimento Simoes, Guilherme J. Schmidt, Marcela J. Schmidt, Ana Lucia Novais Carvalho
Open Journal of Epidemiology (OJEpi) , 2013, DOI: 10.4236/ojepi.2013.34034
Abstract: In spite of the fact that the legal system adopted in Brazil is codified on the Roman tradition, there is no specific protection in law for people suffering from Attention Deficit Disorder (ADD). In contrast, the law of the United States is largely derived from the common law system and there are two federal laws that guarantee a free appropriate public education and provide services to eligible students with disabilities. They are: Section 504 and Individuals with Disabilities Education Act2. The American Legal System reflects the social demand based on epidemiological studies. In the present investigation, we studied the prevalence of attention disorders in Brazil. The sample included 239 students, rated regarding attention problems with a checklist filled by 45 different teachers. As left-handers show greater problems in the impulsive-hyperactivity domain, we investigated the influence of gender on attention problems using handedness as a covariate. Hand preference was assessed by direct observation. A student was classified into the ADD group if he (she) was rated maximum score in at least six questions concerning impulsivity, hyperactivity, and inattention. Sixty-eight students (28% of the total sample) were included in the ADD group. The percentage of males was found to be greater in ADD group as compared to the percentage of males in the normal-control group. The gender effect was not explained by handedness. Our data is similar with other studies. For instance, the rate of ADD symptoms among indigenous students from the Brazilian Amazon was found to be 24.5%. In Brazilian juvenile offenders, the percentage was 33%. The differences with other studies are discussed considering sampling procedures. In accordance with the tradition of the Roman system, we urgently need Federal specific laws to deal with this public health problem. We must convert into specific laws, the Convention on the Rights of Persons with Disabilities (United Nations) that was recently ratified in Brazil.
Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection
Guimar?es Patricia M,Brasileiro Ana CM,Morgante Carolina V,Martins Andressa CQ
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-387
Abstract: Background Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, being valued for its high protein and unsaturated oil contents. Worldwide, the major constraints to peanut production are drought and fungal diseases. Wild Arachis species, which are exclusively South American in origin, have high genetic diversity and have been selected during evolution in a range of environments and biotic stresses, constituting a rich source of allele diversity. Arachis stenosperma harbors resistances to a number of pests, including fungal diseases, whilst A. duranensis has shown improved tolerance to water limited stress. In this study, these species were used for the creation of an extensive databank of wild Arachis transcripts under stress which will constitute a rich source for gene discovery and molecular markers development. Results Transcriptome analysis of cDNA collections from A. stenosperma challenged with Cercosporidium personatum (Berk. and M.A. Curtis) Deighton, and A. duranensis submitted to gradual water limited stress was conducted using 454 GS FLX Titanium generating a total of 7.4 x 105 raw sequence reads covering 211 Mbp of both genomes. High quality reads were assembled to 7,723 contigs for A. stenosperma and 12,792 for A. duranensis and functional annotation indicated that 95% of the contigs in both species could be appointed to GO annotation categories. A number of transcription factors families and defense related genes were identified in both species. Additionally, the expression of five A. stenosperma Resistance Gene Analogs (RGAs) and four retrotransposon (FIDEL-related) sequences were analyzed by qRT-PCR. This data set was used to design a total of 2,325 EST-SSRs, of which a subset of 584 amplified in both species and 214 were shown to be polymorphic using ePCR. Conclusions This study comprises one of the largest unigene dataset for wild Arachis species and will help to elucidate genes involved in responses to biological processes such as fungal diseases and water limited stress. Moreover, it will also facilitate basic and applied research on the genetics of peanut through the development of new molecular markers and the study of adaptive variation across the genus.
Hox Gene Expression Leads to Differential Hind Leg Development between Honeybee Castes
Ana Durvalina Bomtorin, Angel Roberto Barchuk, Livia Maria Moda, Zila Luz Paulino Simoes
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0040111
Abstract: Beyond the physiological and behavioural, differences in appendage morphology between the workers and queens of Apis mellifera are pre-eminent. The hind legs of workers, which are highly specialized pollinators, deserve special attention. The hind tibia of worker has an expanded bristle-free region used for carrying pollen and propolis, the corbicula. In queens this structure is absent. Although the morphological differences are well characterized, the genetic inputs driving the development of this alternative morphology remain unknown. Leg phenotype determination takes place between the fourth and fifth larval instar and herein we show that the morphogenesis is completed at brown-eyed pupa. Using results from the hybridization of whole genome-based oligonucleotide arrays with RNA samples from hind leg imaginal discs of pre-pupal honeybees of both castes we present a list of 200 differentially expressed genes. Notably, there are castes preferentially expressed cuticular protein genes and members of the P450 family. We also provide results of qPCR analyses determining the developmental transcription profiles of eight selected genes, including abdominal-A, distal-less and ultrabithorax (Ubx), whose roles in leg development have been previously demonstrated in other insect models. Ubx expression in workers hind leg is approximately 25 times higher than in queens. Finally, immunohistochemistry assays show that Ubx localization during hind leg development resembles the bristles localization in the tibia/basitarsus of the adult legs in both castes. Our data strongly indicate that the development of the hind legs diphenism characteristic of this corbiculate species is driven by a set of caste-preferentially expressed genes, such as those encoding cuticular protein genes, P450 and Hox proteins, in response to the naturally different diets offered to honeybees during the larval period.
The sugarcane signal transduction (SUCAST) catalogue: prospecting signal transduction in sugarcane
Souza Glaucia Mendes,Simoes Ana Carolina Quirino,Oliveira Katia Cristina,Garay Humberto Miguel
Genetics and Molecular Biology , 2001,
Abstract: EST sequencing has enabled the discovery of many new genes in a vast array of organisms, and the utility of this approach to the scientific community is greatly increased by the establishment of fully annotated databases. The present study aimed to identify sugarcane ESTs sequenced in the sugarcane expressed sequence tag (SUCEST) project (http://sucest.lad.ic.unicamp.br) that corresponded to signal transduction components. We also produced a sugarcane signal transduction (SUCAST) catalogue (http://sucest.lad.ic.unicamp.br/private/mining-reports/QG/QG-mining.htm) that covered the main categories and pathways. Expressed sequence tags (ESTs) encoding enzymes for hormone (gibberellins, ethylene, auxins, abscisic acid and jasmonic acid) biosynthetic pathways were found and tissue specificity was inferred from their relative frequency of occurrence in the different libraries. Whenever possible, transducers of hormones and plant peptide signaling were catalogued to the respective pathway. Over 100 receptors were found in sugarcane, which contains a large family of Ser/Thr kinase receptors and also photoreceptors, histidine kinase receptors and their response regulators. G-protein and small GTPases were analyzed and compared to known members of these families found in mammalian and plant systems. Major kinase and phosphatase pathways were mapped, with special attention being given to the MAP kinase and the inositol pathway, both of which are well known in plants.
Key Modulatory Role of Presynaptic Adenosine A2A Receptors in Cortical Neurotransmission to the Striatal Direct Pathway
César Quiroz,Rafael Luján,Motokazu Uchigashima,Ana Patrícia Simoes
The Scientific World Journal , 2009, DOI: 10.1100/tsw.2009.143
ThermInfo: Collecting, Retrieving, and Estimating Reliable Thermochemical Data
Ana L. Teixeira,Rui C. Santos,Joao P. Leal,Jose A. Martinho Simoes,Andre O. Falcao
Computer Science , 2013,
Abstract: Standard enthalpies of formation are used for assessing the efficiency and safety of chemical processes in the chemical industry. However, the number of compounds for which the enthalpies of formation are available is many orders of magnitude smaller than the number of known compounds. Thermochemical data prediction methods are therefore clearly needed. Several commercial and free chemical databases are currently available, the NIST WebBook being the most used free source. To overcome this problem a cheminformatics system was designed and built with two main objectives in mind: collecting and retrieving critically evaluated thermochemical values, and estimating new data. In its present version, by using cheminformatics techniques, ThermInfo allows the retrieval of the value of a thermochemical property, such as a gas-phase standard enthalpy of formation, by inputting, for example, the molecular structure or the name of a compound. The same inputs can also be used to estimate data (presently restricted to non-polycyclic hydrocarbons) by using the Extended Laidler Bond Additivity (ELBA) method. The information system is publicly available at http://www.therminfo.com or http://therminfo.lasige.di.fc.ul.pt. ThermInfo's strength lies in the data quality, availability (free access), search capabilities, and, in particular, prediction ability, based on a user-friendly interface that accepts inputs in several formats.
Altered States of Consciousness and Psychotherapy: A Cross-Cultural Perspective
Mario Simoes
International Journal of Transpersonal Studies , 2002,
Reference genes for quantitative reverse transcription-polymerase chain reaction expression studies in wild and cultivated peanut
Carolina V Morgante, Patricia M Guimar?es, Andressa CQ Martins, Ana CG Araújo, Soraya CM Leal-Bertioli, David J Bertioli, Ana CM Brasileiro
BMC Research Notes , 2011, DOI: 10.1186/1756-0500-4-339
Abstract: A set of ten reference genes were analyzed in four Arachis species (A. magna; A. duranensis; A. stenosperma and A. hypogaea) subjected to biotic (root-knot nematode and leaf spot fungus) and abiotic (drought) stresses, in two distinct plant organs (roots and leaves). By the use of three programs (GeNorm, NormFinder and BestKeeper) and taking into account the entire dataset, five of these ten genes, ACT1 (actin depolymerizing factor-like protein), UBI1 (polyubiquitin), GAPDH (glyceraldehyde-3-phosphate dehydrogenase), 60S (60S ribosomal protein L10) and UBI2 (ubiquitin/ribosomal protein S27a) emerged as top reference genes, with their stability varying in eight subsets. The former three genes were the most stable across all species, organs and treatments studied.This first in-depth study of reference genes validation in wild Arachis species will allow the use of specific combinations of secure and stable reference genes in qRT-PCR assays. The use of these appropriate references characterized here should improve the accuracy and reliability of gene expression analysis in both wild and cultivated Arachis and contribute for the better understanding of gene expression in, for instance, stress tolerance/resistance mechanisms in plants.Cultivated peanut (Arachis hypogaea) is one of the most widely grown grain legumes in the world, thanks to its high protein and unsaturated oil contents [1]. It is grown extensively in Asia, Africa, United States and Latin America, but is subject to attacks from various pests and diseases, necessitating substantial pesticide use. By contrast, wild Arachis species, which are exclusively South American in origin, are a rich source of new alleles for peanut improvement, with sufficient polymorphism for their genetic characterization [2-4]. Basic resources for gene discovery, interpretation of genomic sequences and marker development have been developed for a number of wild Arachis species [5-7], and constitute important tools for the analysis o
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