Identification of sense and antisense transcripts regulated by drought in sugarcane

Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relationship with carbon partition would greatly help to define routes to increase yield. In this work we studied sugarcane responses to drought using a custom designed oligonucleotide array with 21,901 different probes. The oligoarrays were designed to contain probes that detect transcription in both sense and antisense orientation. We validated the results obtained using quantitative real-time PCR (qPCR). A total of 987 genes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h. Among them, 928 were sense transcripts and 59 were antisense transcripts. Genes related to Carbohydrate Metabolism, RNA Metabolism and Signal Transduction were selected for gene expression validation by qPCR that indicated a validation percentage of 90 %. From the probes presented on the array, 75 % of the sense probes and 11.9 % of the antisense probes have signal above background and can be classified as expressed sequences. Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs). The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.

The production of critical-reflexive narratives and their effect on nursing students' portfolios

The objective of this study is to analyze the process of producing reflexive narratives on nursing students' portfolios. This qualitative study performed an analysis of the portfolios of the class discipline Health Promotion in Primary Education, taught in the fourth semester of the Nursing Licensure Course. Results showed an initial predominance of descriptive records, with the incipient approach of theoretical aspects associated with the aspects regarding their experience. Further, in the group and experience discussions, there were narratives containing more critical and reflexive elements, with justifications for the described actions and the relationships with the theoretical-practical aspects studied in the class and in the course. In conclusion, there is a process of producing critical-reflexive narratives in portfolios that could include a summarized description, using common sense and idealization which allows for including the differences and the theoretical review.

Performance of an electronic tongue during monitoring 2-rnethylisoborneol and geosmin in water samples

2-Methylisoborneol (MIB) and geosmin (GSM) are sub products from algae decomposition and, depending on their concentration, can be toxic: otherwise, they give unpleasant taste and odor to water. For water treatment companies it is important to constantly monitor their presence in the distributed water and avoid further costumer complaints. Lower-cost and easy-to-read instrumentation would be very promising in this regard. In this study, we evaluate the potentiality of an electronic tongue (ET) system based on non-specific polymeric sensors and impedance measurements in monitoring MIB and GSM in water samples. Principal component analysis (PCA) applied to the generated data matrix indicated that this ET was capable to perform with remarkable reproducibility the discrimination of these two contaminants in either distilled or tap water, in concentrations as low as 25 ng L-1. Nonetheless, this analysis methodology was rather qualitative and laborious, and the outputs it provided were greatly subjective. Also, data analysis based on PCA severely restricts automation of the measuring system or its use by non-specialized operators. To circumvent these drawbacks, a fuzzy controller was designed to quantitatively perform sample classification while providing outputs in simpler data charts. For instance, the ET along with the referred fuzzy controller performed with a 100% hit rate the quantification of MIB and GSM samples in distilled and tap water. The hit rate could be read directly from the plot. The lower cost of these polymeric sensors allied to the especial features of the fuzzy controller (easiness on programming and numerical outputs) provided initial requirements for developing an automated ET system to monitor odorant species in water production and distribution. (C) 2012 Elsevier B.V. All rights reserved.

Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription

Abstract Background RNAs transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression. However, the complement of human genes in which introns are transcribed, and the number of intronic transcriptional units and their tissue expression patterns are not known. Results A survey of mRNA and EST public databases revealed more than 55,000 totally intronic noncoding (TIN) RNAs transcribed from the introns of 74% of all unique RefSeq genes. Guided by this information, we designed an oligoarray platform containing sense and antisense probes for each of 7,135 randomly selected TIN transcripts plus the corresponding protein-coding genes. We identified exonic and intronic tissue-specific expression signatures for human liver, prostate and kidney. The most highly expressed antisense TIN RNAs were transcribed from introns of protein-coding genes significantly enriched (p = 0.002 to 0.022) in the 'Regulation of transcription' Gene Ontology category. RNA polymerase II inhibition resulted in increased expression of a fraction of intronic RNAs in cell cultures, suggesting that other RNA polymerases may be involved in their biosynthesis. Members of a subset of intronic and protein-coding signatures transcribed from the same genomic loci have correlated expression patterns, suggesting that intronic RNAs regulate the abundance or the pattern of exon usage in protein-coding messages. Conclusion We have identified diverse intronic RNA expression patterns, pointing to distinct regulatory roles. This gene-oriented approach, using a combined intron-exon oligoarray, should permit further comparative analysis of intronic transcription under various physiological and pathological conditions, thus advancing current knowledge about the biological functions of these noncoding RNAs.

Bakhtin e o grupo: incongruências de uma linguística ortodoxa

For these Russian authors, a sign has to be faithful to reality but what is, in fact, «to be faithful», what is «reality»? They suggest that thought structures itself only by means of signs – as Peirce, who denies the reality of dreams saying that the act to feel hunger is an ideological expression and the shouts of a new-born are already appreciative manifestations of this new human being. The authors had inspired the structuralism, saying that a «semiodiscourse» structures men. Although this instance, word remains neutral, assertion strange to their Hegelian and Marxist roots; their paradigm in contrast, can be Heideggerian, according to which, only the «marked» being exists: looking at one determined thing, I place it, I fit it in its context. To place something is to attribute sense and that is more Stoic than, in fact, Marxist.

Persistent luminescence mechanisms: human imagination at work

The present status and future progress of the mechanisms of persistent luminescence are critically treated with the present knowledge. The advantages to be achieved by a further need as well as the pitfalls of the excessive use of imagination are shown. As usual, in the beginning of the present era of persistent luminescence since the mid 1990s, the imagination played a more important role than the sparse solid experimental data and the chemical common sense and knowledge was largely ignored. Since some five years, the mechanistic studies seem to have reached the maturity and - perhaps deceivingly - it seems that there are only details to be solved. However, the development of red emitting nanocrystalline materials poses a challenge also to the more fundamental studies and interpretation. The questions still luring in the darkness include the problems how the increased surface area affects the defect structure and how the "persistent energy transfer" really works. There is still some light to be thrown onto these matters starting with agreeing on the terminology: the term phosphorescence should be abandoned altogether. The long lifetime of persistent luminescence is due to trapping of excitation energy, not to the forbidden nature of the luminescent transition. However, the technically well-suited term "afterglow" should be retained for harmful, short persistent luminescence. (C) 2012 Optical Society of America

Using the National Institute of Health Stroke Scale to Predict Dysphagia in Acute Ischemic Stroke

Background and Purpose: Oropharyngeal dysphagia is a common manifestation in acute stroke. Aspiration resulting from difficulties in swallowing is a symptom that should be considered due to the frequent occurrence of aspiration pneumonia that could influence the patient's recovery as it causes clinical complications and could even lead to the patient's death. The early clinical evaluation of swallowing disorders can help define approaches and avoid oral feeding, which may be detrimental to the patient. This study aimed to create an algorithm to identify patients at risk of developing dysphagia following acute ischemic stroke in order to be able to decide on the safest way of feeding and minimize the complications of stroke using the National Institutes of Health Stroke Scale (NHISS). Methods: Clinical assessment of swallowing was performed in 50 patients admitted to the emergency unit of the University Hospital, Faculty of Medicine of Ribeirao Preto, Sao Paulo, Brazil, with a diagnosis of ischemic stroke, within 48 h after the beginning of symptoms. Patients, 25 females and 25 males with a mean age of 64.90 years (range 26-91 years), were evaluated consecutively. An anamnesis was taken before the patient's participation in the study in order to exclude a prior history of deglutition difficulties. For the functional assessment of swallowing, three food consistencies were used, i.e. pasty, liquid and solid. After clinical evaluation, we concluded whether there was dysphagia. For statistical analysis we used the Fisher exact test, verifying the association between the variables. To assess whether the NIHSS score characterizes a risk factor for dysphagia, a receiver operational characteristics curve was constructed to obtain characteristics for sensitivity and specificity. Results: Dysphagia was present in 32% of the patients. The clinical evaluation is a reliable method of detection of swallowing difficulties. However, the predictors of risk for the swallowing function must be balanced, and the level of consciousness and the presence of preexisting comorbidities should be considered. Gender, age and cerebral hemisphere involved were not significantly associated with the presence of dysphagia. NIHSS, Glasgow Coma Scale, and speech and language changes had a statistically significant predictive value for the presence of dysphagia. Conclusions: The NIHSS is highly sensitive (88%) and specific (85%) in detecting dysphagia; a score of 12 may be considered as the cutoff value. The creation of an algorithm to detect dysphagia in acute ischemic stroke appears to be useful in selecting the optimal feeding route while awaiting a specialized evaluation. Copyright (C) 2012 S. Karger AG, Basel

Xylella fastidiosa: An in vivo system to study possible survival strategies within citrus xylem vessels based on global gene expression analysis

Xylella fastidiosa inhabits the plant xylem, a nutrient-poor environment, so that mechanisms to sense and respond to adverse environmental conditions are extremely important for bacterial survival in the plant host. Although the complete genome sequences of different Xylella strains have been determined, little is known about stress responses and gene regulation in these organisms. In this work, a DNA microarray was constructed containing 2,600 ORFs identified in the genome sequencing project of Xylella fastidiosa 9a5c strain, and used to check global gene expression differences in the bacteria when it is infecting a symptomatic and a tolerant citrus tree. Different patterns of expression were found in each variety, suggesting that bacteria are responding differentially according to each plant xylem environment. The global gene expression profile was determined and several genes related to bacterial survival in stressed conditions were found to be differentially expressed between varieties, suggesting the involvement of different strategies for adaptation to the environment. The expression pattern of some genes related to the heat shock response, toxin and detoxification processes, adaptation to atypical conditions, repair systems as well as some regulatory genes are discussed in this paper. DNA microarray proved to be a powerful technique for global transcriptome analyses. This is one of the first studies of Xylella fastidiosa gene expression in vivo which helped to increase insight into stress responses and possible bacterial survival mechanisms in the nutrient-poor environment of xylem vessels.

Influence of HAART on Alternative Reading Frame Immune Responses over the Course of HIV-1 Infection

Background: Translational errors can result in bypassing of the main viral protein reading frames and the production of alternate reading frame (ARF) or cryptic peptides. Within HIV, there are many such ARFs in both sense and the antisense directions of transcription. These ARFs have the potential to generate immunogenic peptides called cryptic epitopes (CE). Both antiretroviral drug therapy and the immune system exert a mutational pressure on HIV-1. Immune pressure exerted by ARF CD8(+) T cells on the virus has already been observed in vitro. HAART has also been described to select HIV-1 variants for drug escape mutations. Since the mutational pressure exerted on one location of the HIV-1 genome can potentially affect the 3 reading frames, we hypothesized that ARF responses would be affected by this drug pressure in vivo. Methodology/Principal findings: In this study we identified new ARFs derived from sense and antisense transcription of HIV-1. Many of these ARFs are detectable in circulating viral proteins. They are predominantly found in the HIV-1 env nucleotide region. We measured T cell responses to 199 HIV-1 CE encoded within 13 sense and 34 antisense HIV-1 ARFs. We were able to observe that these ARF responses are more frequent and of greater magnitude in chronically infected individuals compared to acutely infected patients, and in patients on HAART, the breadth of ARF responses increased. Conclusions/Significance: These results have implications for vaccine design and unveil the existence of potential new epitopes that could be included as vaccine targets.

Aesthetic analysis of an implant-supported denture at the cleft area

Objective: To evaluate the aesthetics of an implant-supported denture at the cleft area, comparing the peri-implant tissues and prosthetic crown with the contralateral tooth. Settings: Hospital for Rehabilitation of Craniofacial Anomalies, Bauru, São Paolo, Brazil. Patients: A total of 39 individuals of both genders, with complete unilateral cleft lip and palate, who received secondary alveolar bone graft and were rehabilitated with single implant-supported dentures at the area of the missing maxillary lateral incisor after completion of orthodontic treatment. Interventions: The following parameters were analyzed in follow-up sessions: length and width of prosthetic crown and contralateral tooth, characteristics of implants, filling of interproximal space by the papilla, and smile height of the patients. Results: The implant-supported prosthetic crowns were longer than the contralateral tooth (p < .001). Among the 78 papillae analyzed, 29 (37.17%) received a score of 3; 32 (41.02%) papillae had a score of 2; and 17 (21.79%) received a score of 1. Concerning the smile height, among the 39 patients analyzed, 23 (56.41%) had a medium smile, 15 (38.46%) had a high smile, and two (5.12%) presented a low smile. Conclusion: The use of dental implants to rehabilitate the edentulous cleft area is an excellent option. However, adequate evaluation of the bone quantity and quality, positioning and shape of adjacent teeth, smile height, and patient expectations should be considered to achieve success and avoid aesthetic deformities such as elongated teeth and absence of gingival papillae.

Análise do conforto térmico na obra de João Filgueiras Lima, Lelé: Hospitais Sarah de Salvador e do Rio de Janeiro

Estratégias passivas de projeto reduzem significativamente o uso de ar condicionado e melhoram o conforto térmico dos usuários. Isto pode ser ilustrado através dos hospitais da Rede Sarah Kubitschek projetados pelo arquiteto João Filgueiras Lima, Lelé, cujas soluções além de propiciarem ambientes mais agradáveis e salubres, evitam o uso de sistemas mecânicos de resfriamento, reduzindo o consumo de energia elétrica. Deste modo, o presente artigo tem como objetivo avaliar o conforto térmico dos hospitais Sarah de Salvador e do Rio de Janeiro, através de medições in loco da temperatura do ar, umidade relativa do ar e velocidade do ar. A análise dos resultados foi baseada em leituras de projeto, na norma ASHRAE Standard 55/2004 e em parâmetros adquiridos na literatura especializada. Os resultados demonstram a preocupação de Lelé na incorporação de aspectos bioclimáticos nos projetos. No Sarah - Salvador, alguns ambientes permaneceram fora da zona de conforto no período do meio dia, devido ao ganho de calor pela cobertura. No entanto, o uso da ventilação natural auxilia no efeito de resfriamento, melhorando o conforto térmico nos espaços internos. Já no Sarah - Rio, todos os ambientes permanecem dentro da zona de conforto proposta pela ASHRAE 55.

Constraint-based analysis of gene interactions using restricted boolean networks and time-series data

Abstract Background A popular model for gene regulatory networks is the Boolean network model. In this paper, we propose an algorithm to perform an analysis of gene regulatory interactions using the Boolean network model and time-series data. Actually, the Boolean network is restricted in the sense that only a subset of all possible Boolean functions are considered. We explore some mathematical properties of the restricted Boolean networks in order to avoid the full search approach. The problem is modeled as a Constraint Satisfaction Problem (CSP) and CSP techniques are used to solve it. Results We applied the proposed algorithm in two data sets. First, we used an artificial dataset obtained from a model for the budding yeast cell cycle. The second data set is derived from experiments performed using HeLa cells. The results show that some interactions can be fully or, at least, partially determined under the Boolean model considered. Conclusions The algorithm proposed can be used as a first step for detection of gene/protein interactions. It is able to infer gene relationships from time-series data of gene expression, and this inference process can be aided by a priori knowledge available.