Validation of reference genes for RT-qPCR normalization in common bean during biotic and abiotic stresses

Selection of reference genes is an essential consideration to increase the precision and quality of relative expression analysis by the quantitative RT-PCR method. The stability of eight expressed sequence tags was evaluated to define potential reference genes to study the differential expression of common bean target genes under biotic (incompatible interaction between common bean and fungus Colletotrichum lindemuthianum) and abiotic (drought; salinity; cold temperature) stresses. The efficiency of amplification curves and quantification cycle (C (q)) were determined using LinRegPCR software. The stability of the candidate reference genes was obtained using geNorm and NormFinder software, whereas the normalization of differential expression of target genes [beta-1,3-glucanase 1 (BG1) gene for biotic stress and dehydration responsive element binding (DREB) gene for abiotic stress] was defined by REST software. High stability was obtained for insulin degrading enzyme (IDE), actin-11 (Act11), unknown 1 (Ukn1) and unknown 2 (Ukn2) genes during biotic stress, and for SKP1/ASK-interacting protein 16 (Skip16), Act11, Tubulin beta-8 (beta-Tub8) and Unk1 genes under abiotic stresses. However, IDE and Act11 were indicated as the best combination of reference genes for biotic stress analysis, whereas the Skip16 and Act11 genes were the best combination to study abiotic stress. These genes should be useful in the normalization of gene expression by RT-PCR analysis in common bean, the most important edible legume.

Evaluating different methods of microarray data normalization

Abstract Background With the development of DNA hybridization microarray technologies, nowadays it is possible to simultaneously assess the expression levels of thousands to tens of thousands of genes. Quantitative comparison of microarrays uncovers distinct patterns of gene expression, which define different cellular phenotypes or cellular responses to drugs. Due to technical biases, normalization of the intensity levels is a pre-requisite to performing further statistical analyses. Therefore, choosing a suitable approach for normalization can be critical, deserving judicious consideration. Results Here, we considered three commonly used normalization approaches, namely: Loess, Splines and Wavelets, and two non-parametric regression methods, which have yet to be used for normalization, namely, the Kernel smoothing and Support Vector Regression. The results obtained were compared using artificial microarray data and benchmark studies. The results indicate that the Support Vector Regression is the most robust to outliers and that Kernel is the worst normalization technique, while no practical differences were observed between Loess, Splines and Wavelets. Conclusion In face of our results, the Support Vector Regression is favored for microarray normalization due to its superiority when compared to the other methods for its robustness in estimating the normalization curve.

Comparative analysis of rating curve and ADP estimates of instantaneous water discharge through estuaries in two contrasting Brazilian rivers

This work quantifies, using ADP and rating curve techniques, the instantaneous outflows at estuarine interfaces: higher to middle estuary and middle to lower estuary, in two medium-sized watersheds (72 000 and 66 000 km(2) of area, respectively), the Jaguaribe and Contas Rivers located in the northeastern (semi-arid) and eastern (tropical humid) Brazilian coasts, respectively. Results from ADP showed that the net water balances show the Contas River as a net water exporter, whereas the Jaguaribe River Estuary is a net water importer. At the Jaguaribe Estuary, water retention during flood tide contributes to 58% of the total volume transferred during the ebb tide from the middle to lower estuary. However, 42% of the total water volume (452 m(3) s(-1)) that entered during flood tide is retained in the middle estuary. In the Contas River, 90% of the total water is retained during the flood tide contributing to the volume transported in the ebb tide from the middle to the lower estuary. Outflows obtained with the rating curve method for the Contas and Jaguaribe Rivers were uniform through time due to river flow normalization by dams in both basins. Estimated outflows with this method are about 65% (Contas) and 95% (Jaguaribe) lower compared to outflows obtained with ADP. This suggests that the outflows obtained with the rating curve method underestimate the net water balance in both systems, particularly in the Jaguaribe River under a semi-arid climate. This underestimation is somewhat decreased due to wetter conditions in the Contas River basin. Copyright. (C) 2011 John Wiley & Sons, Ltd.

Co-occurrence of microcystin and microginin congeners in Brazilian strains of Microcystis sp.

Species of Microcystis are the most common bloom-forming cyanobacteria in several countries. Despite extensive studies regarding the production of bioactive cyanopeptides in this genus, there are limited data on isolated strains from Brazil. Three Microcystis sp. strains were isolated from the Salto Grande Reservoir (LTPNA01, 08 and 09) and investigated for the presence of mcy genes, microcystins and other cyanopeptides. Microcystin and microginin production was confirmed in two isolates using high-resolution tandem mass spectrometry after electrospray ionization (ESI-Q-TOF), and the structures of two new microginin congeners were proposed (MG756 Ahda-Val-Leu-Hty-Tyr and MG770 MeAhda-Val-Leu-Hty-Tyr). The biosynthesis profile of the identified cyanopeptides was evaluated at different growth phases via a newly developed HPLC-UV method. Results demonstrated no substantial differences in the production of microcystins and microginins after data normalization to cell quota, suggesting a constitutive biosynthesis. This study represents the first confirmed co-production of microginins and microcystins in Brazilian strains of Microcystis sp. and highlights the potential of Brazilian cyanobacteria as a source of natural compounds with pharmaceutical interest.

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.

Necessidades de saúde, políticas públicas e gênero: a perspectiva das práticas profissionais

Examina-se a relação entre políticas públicas e práticas dos profissionais, relativamente às necessidades de saúde. Em abordagem teórico-conceitual, as práticas são definidas como desempenhos permeados por determinantes técnico-cien­tíficos e sócio-históricos para a produção social de um trabalho, analisando-se suas possibilidades de mudanças culturais, éticas e políticas, para um agir crítico das desigualdades de gênero. Tomando-se a atenção integral à saúde dos homens, examina-se a relevância da distinção entre necessidades masculinas e femininas, enquanto realidades parciais não necessariamente convergentes na (re)produção daquelas desigualdades. Igualmente se examinam as práticas profissionais, como realidade parcial e distinta das políticas, estabelecendo relações não imediatas. Desenvolve-se que são obstáculos simbólicos e práticos para mudanças: a normalização biomédica redutora das necessidades, a cultura do trabalho autônomo e da abordagem individualizante das necessidades, a cultura tradicional de gênero conservando práticas desiguais para homens e mulheres e a ausência de inscrição dos direitos como parte do agir profissio­nal. Isto exige propostas específicas às práticas de saúde e às necessidades masculinas para maior convergência com as reformas das políticas.

Fish Oil Supplementation Reduces Cachexia and Tumor Growth While Improving Renal Function in Tumor-Bearing Rats

The objective of the present work was to study the renal function of healthy and tumor-bearing rats chronically supplemented with fish oil (FO), a source of n-3 polyunsaturated fatty acids. Weanling male rats were divided in two groups, one control (C) and another orally supplemented for 70 days with FO (1 g/kg body weight). After this time, half the animals of each group were injected in the right flank with a suspension of Walker 256 tumor cells (W and WFO). The W group had less proteinemia reflecting cachectic proteolysis, FO reversed this fact. Tumor weight gain was also reduced in WFO. Glomerular filtration rate (GFR) was not different in FO or W compared to C, but was higher in WFO. Renal plasma flow (RPF) was higher in the FO supplemented groups. The W group had lower plasma osmolality than the C group, but FO supplementation resulted in normalization of this parameter. Fractional sodium excretion (FENa+) of FO rats was similar to C. Proximal Na+ reabsorption, evaluated by lithium clearance, was similar among the groups. Urinary thromboxane B-2 (TXB2) excretion was lower in the supplemented groups. The number of macrophages in renal tissue was higher in W compared to C rats, but was lower in WFO rats compared to W rats. In conclusion, FO supplementation resulted in less tumor growth and cachexia, and appeared to be renoprotective, as suggested by higher RPF and GFR.

rpb2 is a reliable reference gene for quantitative gene expression analysis in the dermatophyte Trichophyton rubrum

The selection of reference genes used for data normalization to quantify gene expression by real-time PCR amplifications (qRT-PCR) is crucial for the accuracy of this technique. In spite of this, little information regarding such genes for qRT-PCR is available for gene expression analyses in pathogenic fungi. Thus, we investigated the suitability of eight candidate reference genes in isolates of the human dermatophyte Trichophyton rubrum subjected to several environmental challenges, such as drug exposure, interaction with human nail and skin, and heat stress. The stability of these genes was determined by geNorm, NormFinder and Best-Keeper programs. The gene with the most stable expression in the majority of the conditions tested was rpb2 (DNA-dependent RNA polymerase II), which was validated in three T. rubrum strains. Moreover, the combination of rpb2 and chs1 (chitin synthase) genes provided for the most reliable qRT-PCR data normalization in T. rubrum under a broad range of biological conditions. To the best of our knowledge this is the first report on the selection of reference genes for qRT-PCR data normalization in dermatophytes and the results of these studies should permit further analysis of gene expression under several experimental conditions, with improved accuracy and reliability.

FINDING FOSSIL GROUPS: OPTICAL IDENTIFICATION AND X-RAY CONFIRMATION

We report the discovery of 12 new fossil groups (FGs) of galaxies, systems dominated by a single giant elliptical galaxy and cluster-scale gravitational potential, but lacking the population of bright galaxies typically seen in galaxy clusters. These FGs, selected from the maxBCG optical cluster catalog, were detected in snapshot observations with the Chandra X-ray Observatory. We detail the highly successful selection method, with an 80% success rate in identifying 12 FGs from our target sample of 15 candidates. For 11 of the systems, we determine the X-ray luminosity, temperature, and hydrostatic mass, which do not deviate significantly from expectations for normal systems, spanning a range typical of rich groups and poor clusters of galaxies. A small number of detected FGs are morphologically irregular, possibly due to past mergers, interaction of the intra-group medium with a central active galactic nucleus (AGN), or superposition of multiple massive halos. Two-thirds of the X-ray-detected FGs exhibit X-ray emission associated with the central brightest cluster galaxy (BCG), although we are unable to distinguish between AGN and extended thermal galaxy emission using the current data. This sample representing a large increase in the number of known FGs, will be invaluable for future planned observations to determine FG temperature, gas density, metal abundance, and mass distributions, and to compare to normal (non-fossil) systems. Finally, the presence of a population of galaxy-poor systems may bias mass function determinations that measure richness from galaxy counts. When used to constrain power spectrum normalization and Omega(m), these biased mass functions may in turn bias these results.

Multi-criteria analysis in the strategic environmental assessment of the sugar and alcohol sector

The Strategic Environmental Assessment (SEA) of the sugar and alcohol sector guides a territorial and sectoral planning that benefits most of the local society and supports this economic activity in all its stages. In this way, the present work aims to determine an index of aggregation of the indicators generated in the baseline of the SEA process, called Index of Sustainability of Expansion of the Sugar and Alcohol Sector (IScana). For this, it was used the normalization of the indicators of each city by the fuzzy logic and attribution of weights by the Analytic Hierarchy Process (AHP). Then, the IScana values had been spatialized in the region of 'Grande Dourados'-Mato Grosso do Sul State. The northern portion concentrated the highest values of IScana, 0.48 and 0.55, referring to the cities of Nova Alvorada do Sul and Rio Brilhante, while, in the central portion, the city of Dourados presented the lowest value, 0.10. The selection of the set of indicators forming the IScana, and their relative importance, was satisfactory for the application of fuzzy logic and AHP techniques. The IScana index supplies objective information regarding the diagnosis of the region for the application of SEA.

Influence of adenotonsillectomy on hard palate dimensions

Objective: To evaluate hard palate width and height in mouth-breathing children pre- and post-adenotonsillectomy. Methods: We evaluated 44 children in the 3-6 year age bracket, using dental study casts in order to determine palatal height, intercanine width, and intermolar width. The children were divided into two groups: nasal breathing (n = 15) and mouth breathing (n = 29). The children in the latter group underwent adenotonsillectomy. The study casts were obtained prior to adenotonsillectomy, designated time point 1(11), at 13 months after adenotonsillectomy (T2), and at 28 months after adenotonsillectomy (13). Similar periods of observation were obtained for nasal breathing children. Results: At T1, there was a significantly lower intercanine width in mouth breathing children; intermolar width and palate height were similar between groups. After surgery, there was a significant increase in all the analyzed parameters in both groups, probably due to facial growth. Instead, the increase in intercanine width was substantially more prominent in mouth breathing children than in nasal breathing children, and the former difference failed in significance after the procedure. Conclusions: There were no significant differences between the nasal-breathing and mouth-breathing children in terms of intermolar width and palatal height prior to or after tonsillectomy. Although intercanine width was initially narrower in the mouth-breathing children, it showed normalization after the surgical procedure. These results confirm that the restoration of nasal breathing is central to proper occlusal development. (C) 2012 Elsevier Ireland Ltd. All rights reserved.

Parathyroid adenoma apoplexy as a temporary solution of primary hyperparathyroidism: a case report

Abstract Introduction The natural history of patients with spontaneous parathyroid necrosis is unknown. In this case report we describe the clinical course, laboratory, radiographic, bone densitometry tests, parathyroid ultrasonography and scintigraphy examinations of a patient performed over a period of eight years after she first presented with a sudden episode of spontaneous resolution of primary hyperparathyroidism (PHPT). Case presentation A 24-year-old woman with a clinical history and laboratory and radiographic tests compatible with PHPT suffered a sudden episode of cervical pain and presented with clinical evidence of hypocalcemia. Biopsy of a cervical nodule revealed necrotic material compatible with ischemia of the parathyroid. The follow-up of the patient presented four distinct phases: the first, which lasted two years, was compatible with a period of bone hunger during which it was necessary to introduce calcitriol and calcium carbonate. During this period, the patient showed bone mass gain. The second phase was characterized by normalization of calcium and parathyroid hormone levels and its end was difficult to define. During the third phase there was a recurrence of hypercalcemia associated with elevated parathyroid hormone (PTH) levels and loss of bone mass. The last phase corresponded to the interval after parathyroidectomy, which was characterized by normalization of serum levels of calcium and PTH, as well as bone mass gain. Conclusion This case report indicates that spontaneous resolution of PHPT by adenoma necrosis is potentially temporary. Thus, in cases in which a conservative approach is chosen, clinical and laboratory follow-up is indispensable. Bone mass measurement is a useful tool in the follow-up of these cases. However, this option exposes the patient to a potential roller-coaster ride of bone mass gain and loss, whose long term consequences are still unknown.

ENDNOTE: A EXPERIÊNCIA DA FMVZ/USP NA CAPACITAÇÃO E NORMALIZAÇÃO DE TRABALHOS

O presente trabalho relata a experiência da Biblioteca Virginie Buff D’Ápice da FMVZ/USP na capacitação do uso do software EndNote e sua aplicabilidade por seus usuários; objetiva ainda demonstrar o potencial de uso dessa ferramenta na normalização de trabalhos científicos e acadêmicos. Com dados preliminares obtidos entre os anos de 2009 e 2010, além da experiência vivenciada nesse período, foi possível constatar que o uso do EndNote pelos estudantes que participaram da capacitação oferecida pela biblioteca promoveu um índice de acerto na normalização de seus trabalhos muito acima daqueles que não foram capacitados e/ou não o utilizaram o programa. Dessa forma, pode-se considerar que uma capacitação efetiva e o uso adequado do EndNote facilitam o trabalho do pesquisador que, ao utilizá-lo, pode focar mais seus esforços na escrita do trabalho, bem como o da biblioteca responsável pela normalização de trabalhos científicos/acadêmicos

Pituitary tumors in patients with MEN1 syndrome

We briefly review the characteristics of pituitary tumors associated with multiple endocrine neoplasia type 1. Multiple endocrine neoplasia type 1 is an autosomal-dominant disorder most commonly characterized by tumors of the pituitary, parathyroid, endocrine-gastrointestinal tract, and pancreas. A MEDLINE search for all available publications regarding multiple endocrine neoplasia type 1 and pituitary adenomas was undertaken. The prevalence of pituitary tumors in multiple endocrine neoplasia type 1 may vary from 10% to 60% depending on the studied series, and such tumors may occur as the first clinical manifestation of multiple endocrine neoplasia type 1 in 25% of sporadic and 10% of familial cases. Patients were younger and the time between initial and subsequent multiple endocrine neoplasia type 1 endocrine lesions was significantly longer when pituitary disease was the initial manifestation of multiple endocrine neoplasia type 1. Tumors were larger and more invasive and clinical manifestations related to the size of the pituitary adenoma were significantly more frequent in patients with multiple endocrine neoplasia type 1 than in subjects with non-multiple endocrine neoplasia type 1. Normalization of pituitary hypersecretion was much less frequent in patients with multiple endocrine neoplasia type 1 than in subjects with non-multiple endocrine neoplasia type 1. Pituitary tumors in patients with multiple endocrine neoplasia type 1 syndrome tend to be larger, invasive and more symptomatic, and they tend to occur in younger patients when they are the initial presentation of multiple endocrine neoplasia type 1.