Selection and validation of reference genes for gene expression studies by reverse transcription quantitative PCR in Xanthomonas citri subsp citri during infection of Citrus sinensis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Prospective study of soft tissue contour changes following chin bone graft harvesting

This study sought to evaluate changes in the soft tissue contour after chin bone graft harvesting. Thirty selected patients underwent chin bone graft harvesting and evaluations were made using lateral cephalograms preoperatively and postoperatively at 30 and 180 days. Fixed points and lines were established on cephalometric tracings and used to measure the selected vertical and sagittal parameters. Results showed statistically significant alterations to the vertical position values of the vermilion (V-VPV) which increased from 9.70 to 11.01 and the exposure of lower incisors (V-ELI) which increased from 1.85 to 3.5, showing an increase in their distance from the plane of reference and a lowering of their position, the clinical equivalent of a labial ptosis condition. None of the sagittal parameters analysed showed any statistically significant variation in the final evaluation. The study concluded that the alterations to patients' soft tissue contours resulted mainly from failure to ensure precise reattachment of the mentalis muscles and identified the need for further investigation of that aspect.

Identification of reference genes for expression analysis by real-time quantitative PCR in drought-stressed soybean

O objetivo deste trabalho foi validar, pela técnica de PCR quantitativo em tempo real (RT-qPCR) genes para serem utilizados como referência em estudos de expressão gênica em soja, em ensaios de estresse hídrico. Foram avaliados quatro genes comumente utilizados em soja: Gmβ-actin, GmGAPDH, GmLectin e GmRNAr18S. O RNA total foi extraído de seis amostras: três amostras de raízes em sistema de hidroponia com diferentes intensidades de déficit hídrico (0, 25, 50, 75 e 100 minutos de estresse hídrico), e três amostras de folhas de plantas cultivadas em areia com diferentes umidades do solo (15, 5 e 2,5% de umidade gravimétrica). Os dados brutos do intervalo cycle threshold (Ct) foram analisados, e a eficiência de cada iniciador foi calculada para uma analise da Ct entre as diferentes amostras. A aplicação do programa GeNorm foi utilizada para a avaliação dos melhores genes de referência, de acordo com a estabilidade. O GmGAPDH foi o gene menos estável, com o maior valor médio de estabilidade de expressão (M), e os genes mais estáveis, com menor valor de M, foram o Gmβ-actin e GmRNAr18S, tanto nas amostras de raízes como nas de folhas. Estes genes podem ser usados em RT-qPCR como gens de referência para análises de expressão gênica.

Estimation methods of reference evapotranspiration (ETo) for Uberlândia -MG

One approach to verify the adequacy of estimation methods of reference evapotranspiration is the comparison with the Penman-Monteith method, recommended by the United Nations of Food and Agriculture Organization - FAO, as the standard method for estimating ET0. This study aimed to compare methods for estimating ET0, Makkink (MK), Hargreaves (HG) and Solar Radiation (RS), with Penman-Monteith (PM). For this purpose, we used daily data of global solar radiation, air temperature, relative humidity and wind speed for the year 2010, obtained through the automatic meteorological station, with latitude 18° 91' 66 S, longitude 48° 25' 05 W and altitude of 869m, at the National Institute of Meteorology situated in the Campus of Federal University of Uberlandia - MG, Brazil. Analysis of results for the period were carried out in daily basis, using regression analysis and considering the linear model y = ax, where the dependent variable was the method of Penman-Monteith and the independent, the estimation of ET0 by evaluated methods. Methodology was used to check the influence of standard deviation of daily ET0 in comparison of methods. The evaluation indicated that methods of Solar Radiation and Penman-Monteith cannot be compared, yet the method of Hargreaves indicates the most efficient adjustment to estimate ETo.

Comment on Effect of spin-orbit interaction on the plasma excitations in a quantum wire

We comment on the recent results [Phys. Rev. B 70, 235314 (2004)] showing the dispersion relations of single-particle and collective excitations in quantum wires in the presence of the Rashba spin-orbit interaction (SOI). We claim that those calculations performed in the absence of SOI, and used as a strong reference to the interacting case, are unlikely to be correct. We show the correct omega-q plane of the system in the absence of Rashba SOI.

Morphology of flux avalanches in patterned superconducting films

It is well known that under certain circumstances, magnetic fields applied perpendicularly to the plane of superconducting films can trigger flux avalanches. In such cases, the penetration has a tree-like profile. However, in samples where a regular array of antidots, ADs, is present, the avalanches follow the rows of ADs as if they were guiding lines for the abrupt penetration. In this work, we used the magnetooptical imaging technique to study the morphology of flux avalanches in two Nb films with a square lattice of square ADs, each one with a different lateral size, and a plain film for reference. We show that the morphology of the flux avalanches is greatly influenced by the size of the interstitial region. © 2012 Springer Science+Business Media, LLC.

Reference Gene Selection for Gene Expression Analysis of Oocytes Collected from Dairy Cattle and Buffaloes during Winter and Summer

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Thermal treatment of superconductor thin film of the BSCCO system using domestic microwave oven

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The HUman MicroNucleus project on eXfoLiated buccal cells (HUMNXL): The role of life-style, host factors, occupational exposures, health status, and assay protocol

The human buccal micronucleus cytome assay (BMCyt) is one of the most widely used techniques to measure genetic damage in human population studies. Reducing protocol variability, assessing the role of confounders, and estimating a range of reference values are research priorities that will be addressed by the HUMNXL, collaborative study. The HUMNXL, project evaluates the impact of host factors, occupation, life-style, disease status, and protocol features on the occurrence of MN in exfoliated buccal cells. In addition, the study will provide a range of reference values for all cytome endpoints. A database of 5424 subjects with buccal MN values obtained from 30 laboratories worldwide was compiled and analyzed to investigate the influence of several conditions affecting MN frequency. Random effects models were mostly used to investigate MN predictors. The estimated spontaneous MN frequency was 0.74 parts per thousand (95% CI 0.52-1.05). Only staining among technical features influenced MN frequency, with an abnormal increase for non-DNA-specific stains. No effect of gender was evident, while the trend for age was highly significant (p < 0.001). Most occupational exposures and a diagnosis of cancer significantly increased MN and other endpoints frequencies. MN frequency increased in heavy smoking (>= 40 cig/day. FR = 1.37:95% CI 1.03-.82) and decreased with daily fruit consumption (FR = 0.68; 95% CI 0.50-0.91). The results of the HUMNXL, project identified priorities for validation studies, increased the basic knowledge of the assay, and contributed to the creation of a laboratory network which in perspective may allow the evaluation of disease risk associated with MN frequency. (C) 2011 Elsevier B.V. All rights reserved.

Amino acid availability and protein digestibility of several protein sources for Nile tilapia, Oreochromis niloticus

Apparent amino acid availability coefficients and protein digestibility of four animal products [fish meal (FM), meat and bone meal (MBM), poultry by-product and feather meal] and four plant protein-rich products [soybean meal (SBM), cottonseed meal-28, cottonseed meal-38 and corn gluten meal (CGM)] were determined for Nile tilapia, Oreochromis niloticus. Ingredients were incorporated to a practical reference diet at a 7 : 3 ratio (70% of reference diet and 30% of test ingredient). Chromic oxide was used as external digestibility marker. Among animal products poultry by-product meal (PBM; 89.7%) and FM (88.6%) presented the highest apparent protein digestibility (APD) while MBM (78.4%) and feather meal (78.5%) presented the lowest APD. Among plant protein-rich products CGM (91.4%) and SBM (92.4%) presented the highest APD values while cottonseed meal-28 presented the lowest APD (78.6%). Average apparent amino acid availability of feed ingredients was similar to protein digestibility with 92.3%, 89.6%, 73.4%, 80.7%, 88.9%, 84.4%, 91.2% and 79.7% values for SBM, CGM, cottonseed meal-28 and 38, FM, MBM, PBM and feather meal respectively. These results indicate that O. niloticus is able to utilize efficiently different feedstuffs.

Evaluation of cytologic and biochemical variables in blood, plasma, and peritoneal fluid from calves before and after umbilical herniorrhaphy

Objective-To establish reference intervals for cytologic and biochemical variables in peritoneal fluid, whole blood, and plasma in calves with congenital umbilical hernias (CUHs) before and after herniorrhaphy and to assess whether those variables in calves with CUHs were altered, compared with findings in clinically normal calves.Animals-20 Holstein calves with or without a CUH.Procedures-10 calves with CUHs underwent herniorrhaphy. Blood and peritoneal fluid samples from all 20 calves were collected for cytologic and biochemical analyses on days 0 (before surgery), 1, 3, 5, 7, and 15. Data from the 2 groups were compared.Results-Reference intervals for the variables of interest were established for each group, Before surgery, calves with CUHs had significantly greater plasma total protein concentration and creatine kinase (CK) and aspartate aminotransferase activities and peritoneal fluid specific gravity values, compared with values for calves without CUHs. At various time points after surgery, peritoneal fluid total protein concentration; fibrinogen concentration; nucleated cell, polymorphonuclear cell, and lymphocyte counts; specific gravity; and lactate dehydrogenase, aspartate aminotransferase, and CK activities in calves with CUHs were significantly different from values in calves without CUHs. Some plasma and blood variables leg, total protein concentration, neutrophil count, and CK activity were significantly different between the 2 groups.Conclusions and Clinical Relevance-Values of certain cytologic and biochemical variables in peritoneal fluid, blood, and plasma were different between calves with and without CUHs. Thus, determination of reference intervals for these variables is important for interpreting diagnostic test results in calves with CUHs. (Am J Vet Res 2009;70:423-432)

Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions

Background: Quantitative data from gene expression experiments are often normalized by transcription levels of reference or housekeeping genes. An inherent assumption for their use is that the expression of these genes is highly uniform in living organisms during various phases of development, in different cell types and under diverse environmental conditions. To date, the validation of reference genes in plants has received very little attention and suitable reference genes have not been defined for a great number of crop species including Coffea arabica. The aim of the research reported herein was to compare the relative expression of a set of potential reference genes across different types of tissue/organ samples of coffee. We also validated the expression profiles of the selected reference genes at various stages of development and under a specific biotic stress.Results: The expression levels of five frequently used housekeeping genes (reference genes), namely alcohol dehydrogenase (adh), 14-3-3, polyubiquitin (poly), beta-actin (actin) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) was assessed by quantitative real-time RT-PCR over a set of five tissue/organ samples (root, stem, leaf, flower, and fruits) of Coffea arabica plants. In addition to these commonly used internal controls, three other genes encoding a cysteine proteinase (cys), a caffeine synthase (ccs) and the 60S ribosomal protein L7 (rpl7) were also tested. Their stability and suitability as reference genes were validated by geNorm, NormFinder and BestKeeper programs. The obtained results revealed significantly variable expression levels of all reference genes analyzed, with the exception of gapdh, which showed no significant changes in expression among the investigated experimental conditions.Conclusion: Our data suggests that the expression of housekeeping genes is not completely stable in coffee. Based on our results, gapdh, followed by 14-3-3 and rpl7 were found to be homogeneously expressed and are therefore adequate for normalization purposes, showing equivalent transcript levels in different tissue/ organ samples. Gapdh is therefore the recommended reference gene for measuring gene expression in Coffea arabica. Its use will enable more accurate and reliable normalization of tissue/organ-specific gene expression studies in this important cherry crop plant.

Spermatozoal ultrastructure in three species of the genus Uca Leach, 1814 (Crustacea, Brachyura, Ocypodidae)

Morphological aspects of spermatozoa in marine animals have been used in recent decades as phylogenetic criteria (spermiotaxonomy). This paper presents ultrastructural descriptions of the spermatozoa from Uca maracoani, U. thayeri, and U. vocator. A small portion of the vas deferens of each species was examined under the transmission and scanning electron microscopy. The ultrastructural analysis showed that each spermatophore consists of a varying number of spermatozoa embedded in a dense fibrillar matrix surrounded by a membrane. The spermatozoa of U. maracoani, U. thayeri, and U. vocator are typical of brachyurans. The Voluminous acrosome is characterized by three different layers. The postero-lateral surface of the acrosome is cupped by the reduced cytoplasm, and the anterior surface is covered by the operculum. The perforatorium consists of coiled, helicoidal membranous tubules and is continuous with the cytoplasm. The nucleus is composed by uncondensed chromatin and presents several lateral arms distributed over the entire equatorial plane of the cell. The presence of the apical button is a well defined character among all species of the genus Uca, but in U. thayeri it was not observed. The accessory opercular ring can be found in the three studied species, but in distinct development degree-Two centrioles were detected in U. thayeri and U. vocator, but only one was found in U. maracoani. The presence of centrioles in the mature spermatozoa is the first account for the genus Uca upto-date. Considering the ultrastructure of the spermatozoa of U. maracoani, U. thayeri, and U. vocator, we suggest that these three species partially follow the morphological patterns previously described in other Thoracotremata brachyurans. The absence of the apical button in U. thayeri spermatozoa may represent an evolutionary novelty in the genus Uca. (C) 2007 Elsevier Ltd. All rights reserved.

Fish community structure along a conservation gradient in Bodoquena Plateau streams, central West of Brazil.

Aim: To investigate whether composition and structure of stream ichthyofauna vary along the conservation gradient in the Bodoquena Plateau; Methods: Standardized sampling was performed in nine stream stretches (three references, three in the pasture, and three in urban areas), each 80 m long, in April, May and June/08; Results: A quantity of 8,102 individuals representing 36 species was collected. There were no significant differences with respect to absolute species richness among stretches. Urban stretches were more similar to each other than the other two groups, both regarding species composition and abundance. A set of six species was considered an indicator of reference stretches, whereas two were of pasture stretches and four of urban stretches. Poecilia reticulata and Corydoras aeneus, occurring only in urban stretches, were unique in showing the maximum values in the indicator species analysis; Conclusions: Results indicate changes in the ichthyofauna with urbanized surrounding water courses. The presence and abundance of Poecilia reticulata and Corydoras aeneus may indicate the quality loss of these environments.

Measurement of W gamma and Z gamma production in pp collisions at root s=7 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)