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TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets
Renato Vicentini, Marcelo Menossi
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-160
Abstract: An efficient web-based tool entitled TISs-ST (Translation Initiation Sites and Secretory Targets) evaluates putative translation initiation sites and indicates the prediction of a signal peptide of the protein encoded from this site. The TISs-ST web server is freely available to both academic and commercial users and can be accessed at http://ipe.cbmeg.unicamp.br/pub/TISs-ST webcite.The program can be used to evaluate alternative translation initiation site consensus with user-specified sequences, based on their composition or on many position weight matrix models. TISs-ST provides analytical and visualization tools for evaluating the periodic frequency, the consensus pattern and the total information content of a sequence data set. A search option allows for the identification of signal peptides from predicted proteins using the PrediSi software.Translation by cytosolic ribosomes generally occurs at the first AUG in the transcript. However, in eukaryotic mRNAs, efficient recognition of an AUG codon as a translation initiation site (TIS) depends on several factors, such as the nucleotide sequence that flanks the site [1-3]. There is evidence that the context surrounding the initiation codon contributes to the control of translational initiation [4]. The sequence context of the first AUG codon, in particular that part located in the untranslated region, may modulate the efficiency with which it is recognized as a translation initiation codon [5]. If the first initiation codon lies in a suitable context, protein synthesis will be started. When the context is less than favorable, most of the protein synthesis will start at the next downstream AUG codon [6]. Moreover, other structural features of the mRNA are considered important for the efficiency of the translation initiation at a specific AUG codon, such as: the proximity of AUG to the 5' end, the secondary structure upstream and downstream from the AUG codon, the leader sequence length and the multiple upstream AUG
Pipeline for macro- and microarray analyses
Vicentini, R.;Menossi, M.;
Brazilian Journal of Medical and Biological Research , 2007, DOI: 10.1590/S0100-879X2006005000089
Abstract: the pipeline for macro- and microarray analyses (pmma) is a set of scripts with a web interface developed to analyze dna array data generated by array image quantification software. pmma is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps). it can also be used as a plugin in the bioarray software environment, an open-source database for array analysis, or used in a local version of the web service. all scripts in pmma were developed in the perl programming language and statistical analysis functions were implemented in the r statistical language. consequently, our package is a platform-independent software. our algorithms can correctly select almost 90% of the differentially expressed genes, showing a superior performance compared to other methods of analysis. the pipeline software has been applied to 1536 expressed sequence tags macroarray public data of sugarcane exposed to cold for 3 to 48 h. pmma identified thirty cold-responsive genes previously unidentified in this public dataset. fourteen genes were up-regulated, two had a variable expression and the other fourteen were down-regulated in the treatments. these new findings certainly were a consequence of using a superior statistical analysis approach, since the original study did not take into account the dependence of data variability on the average signal intensity of each gene. the web interface, supplementary information, and the package source code are available, free, to non-commercial users at http://ipe.cbmeg.unicamp.br/pub/pmma.
Repercuss es do ruído na unidade de terapia intensiva neonatal
Gabriela Menossi GRECCO
Acta Paulista de Enfermagem , 2013,
Análise do discurso e derris o: um caminho a percorrer
Lígia Mara Boin Menossi de ARAUJO
Entrepalavras : Revista de Linguística do Departamento de Letras Vernáculas da UFC , 2012,
Abstract: Com base no aparato teórico-metodológico da Análise do Discurso de linha francesa, derivada de Michel Pêcheux (1997), temos como principais objetivos tentar pensar o funcionamento e a constitui o do discurso derrisório, assim como tentar situar a derris o no processo de desenvolvimento da Análise do Discurso. Para isso, mobilizamos alguns teóricos como Maldidier (2003), Bonnafous (2001), Mercier (2001), Bergson (2004) e iremos construir uma breve análise discursiva derrisória em vídeomontagens do YouTube intituladas Lula o analfabeto, Lula Bebum e Novas Pérolas de Sabedoria de Lula da Silva em que o alvo da derris o é o ent o candidato à presidência Luis Inácio Lula da Silva.
A dor da crian?a e do adolescente com cancer: dimens?es de seu cuidar
Menossi, Maria José;Lima, Regina Aparecida Garcia de;
Revista Brasileira de Enfermagem , 2004, DOI: 10.1590/S0034-71672004000200009
Abstract: focusing on the pain of a child/adolescent with cancer as a complex phenomenon, this study aims at describing the experiences of health professionals involved in caring for these patients in hospitalisations and analysing them, looking for a foundation in edgar morin's complexity ideas. empirical data were collected in interviews, allowing for the visualisation of possibilities, such as a formation of fixed and integrated teams and the family's involvement in the care. evidently, it is necessary to distinguish the professionals' multiple focuses and compose a care unit in which these focuses are articulated by means of a common project, to provide caring for the multiple dimensions of these patients' care.
A problemática do sofrimento: percep?ao do adolescente com cancer
Menossi, Maria José;Lima, Regina Aparecida Garcia de;
Revista da Escola de Enfermagem da USP , 2000, DOI: 10.1590/S0080-62342000000100006
Abstract: adolescents with cancer undergo suffering resulting from diagnosis, therapy and changes in their routine and family life. the objective of this study was to identify the chief causes of their suffering, identified in interviews with those patients themselves. the study population were 12 adolescents admitted to the paediatric clinic of the ribeir?o preto medical school clinical hospital, university of s?o paulo, from the 13th. november, 1997 to 16th. december, 1997. data were analysed by means of qualitative approach. the chief causes of suffering reported by the studied adolescents were: hospitalization, restrictions in routine activities, aggressive therapy, modification of self-image and fear of dying. the adolescents not only talked about their suffering but also offered some suggestions to lessen it, as for instance, use of central venous catheter, liberation of visiting time, reducing number of hospitalization events, efficient communication and good rapport with the attending team.
Cancer in children: the diagnostic itinerary
Cavicchioli, Aline Cristiane;Menossi, Maria José;Lima, Regina Aparecida Garcia de;
Revista Latino-Americana de Enfermagem , 2007, DOI: 10.1590/S0104-11692007000500022
Abstract: this study aims to describe the trajectory children and adolescents experience from the beginning of cancer signs and symptoms until the confirmation of the diagnosis, based on their parents' report. a total of eight mothers and two fathers participated in the study. data were collected through semi structured interviews, and data were subject to qualitative analysis. we found that this period is significant for parents, who are capable of recognizing that something wrong started to happen to their children, expressed through signs and symptoms. they precisely reported the chronological time of this trajectory. the challenges they mentioned refer to the different diagnostic hypotheses, the difficulty to performing specific diagnostic exams and to be referred to specialized care services. this search for health service care revealed to be a difficult journey, which permits to identify that the brazilian basic health system's principles of accessibility and problem-solving capacity are jeopardized.
Transcriptional profile of maize roots under acid soil growth
Lucia Mattiello, Matias Kirst, Felipe R da Silva, Renato A Jorge, Marcelo Menossi
BMC Plant Biology , 2010, DOI: 10.1186/1471-2229-10-196
Abstract: When grown in acid soil containing toxic levels of Al, the Al-sensitive genotype (S1587-17) showed greater root growth inhibition, more Al accumulation and more callose deposition in root tips than did the tolerant genotype (Cat100-6). Transcriptome profiling showed a higher number of genes differentially expressed in S1587-17 grown in acid soil, probably due to secondary effects of Al toxicity. Genes involved in the biosynthesis of organic acids, which are frequently associated with an Al tolerance response, were not differentially regulated in both genotypes after acid soil exposure. However, genes related to the biosynthesis of auxin, ethylene and lignin were up-regulated in the Al-sensitive genotype, indicating that these pathways might be associated with root growth inhibition. By comparing the two maize lines, we were able to discover genes up-regulated only in the Al-tolerant line that also presented higher absolute levels than those observed in the Al-sensitive line. These genes encoded a lipase hydrolase, a retinol dehydrogenase, a glycine-rich protein, a member of the WRKY transcriptional family and two unknown proteins.This work provides the first characterization of the physiological and transcriptional responses of maize roots when grown in acid soil containing toxic levels of Al. The transcriptome profiles highlighted several pathways that are related to Al toxicity and tolerance during growth in acid soil. We found several genes that were not found in previous studies using hydroponic experiments, increasing our understanding of plant responses to acid soil. The use of two germplasms with markedly different Al tolerances allowed the identification of genes that are a valuable tool for assessing the mechanisms of Al tolerance in maize in acid soil.Acid soils are the most important cause of low yield for many crops [1]. About 30% of the world's soils are acidic, and 60% of them are in tropical and subtropical areas associated with long periods of hot an
In silico evaluation of the Eucalyptus transcriptome
Vicentini, Renato;Sassaki, Flávio T.;Gimenes, Marcos A.;Maia, Ivan G.;Menossi, Marcelo;
Genetics and Molecular Biology , 2005, DOI: 10.1590/S1415-47572005000400002
Abstract: the expressed sequence tags (ests) produced in the forests project provide an invaluable opportunity to assess the eucalyptus transcriptome. besides providing information on the different proteins produced by this plant, it is possible to infer gene expression profiles because non-normalized cdna libraries were used. the est frequency from any gene is correlated to the transcript levels in the tissues from which the cdna libraries were constructed. the goal of this work was to identify eucalyptus genes that showed either differential expression pattern or were ubiquitously expressed in the tissues sampled in the forests project. six robust statistical tests and very restrictive rules were applied to gain confidence in the in silico data aiming to avoid false positives. several genes with interesting expression profiles were identified and some of them were validated by rt-pcr.
Metabolism and root exudation of organic acid anions under aluminium stress
Mariano, Eduardo D.;Jorge, Renato A.;Keltjens, Willem G.;Menossi, Marcelo;
Brazilian Journal of Plant Physiology , 2005, DOI: 10.1590/S1677-04202005000100013
Abstract: numerous plant species can release organic acid anions (oa) from their roots in response to toxic aluminium (al) ions present in the rooting medium. hypothetically oa complex al in the root apoplast and/or rhizosphere and thus avoid its interaction with root cellular components and its entry in the root symplast. two temporal patterns of root oa exudation are observed. in pattern i, oa release is rapidly activated after the contact of the root with al ions while in pattern ii there is a lag phase between the addition of al and the beginning of oa release. compounds other than oa have been detected in root exudates and are also correlated with al resistance in plants. plant species like buckwheat and tea show mechanisms of al tolerance, which confer them the capacity to inactivate and store al internally in the leaves. disturbances in metabolic pathways induced by al are still obscure and their relation to the altered oa concentration observed in roots under al stress is not yet established. high concentrations of oa in roots do not always lead to high rates of oa release even when the spatial distribution of these two characteristics along the root axis is taken into account. al induces high permeability to oa in young root cells and anion channels located in the cell membrane have been proposed to mediate the transport of oa to outside the cell. genetically modified plants that overexpress genes involved in the biosynthesis and transport of oa as well as in al toxicity events at the cell level have been generated. in most cases the transformations resulted in an improved ability of the plant to cope with al stress. these promising findings reinforce the possibility of engineering plants with superior resistance to al-toxic acid soils. the environmental impact of the large amounts of root exudates possibly conferred by these genetically modified plants is discussed, with special emphasis on soil microbiota.
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