Amplification of 16S rRNA gene sequences to differentiate two highly related bradyrhizobia species

A 16S rRNA gene PCR-based assay was developed aiming at a fast molecular diagnostic method to differentiate the two phylogenetically closely related species Bradyrhizobium japonicum and B. elkanii, isolated from soybean nodules, in order to identify those more competitive and comprising greater nitrogen fixation ability for use in the formulation of commercial inoculants. The assay used was able to discriminate ten reference strains belonging to these two Bradyrhizobium species, as well as to efficiently identify 37 strains isolated from fields cultivated with soybean.

Fruitone CPA para retardar la maduración en piña Ananas comosus (L.) Merr., cv. Cayena Lisa, cosechada en primavera

El objetivo fue determinar el efecto de dosis y número de aplicaciones de Fruitone CPA (ácido 2-3 clorofenoxi-propiónico) en el retraso de la maduración, rendimiento y calidad del fruto de piña en el periodo de primavera. El experimento se llevó al cabo en el Campo Experimental Papaloapan, del INIFAP, en Veracruz, México. Se estableció con el cv. Cayena Lisa de México, en un diseño de bloques al azar con cuatro repeticiones; los tratamientos fueron nueve, incluido el testigo sin aplicación, 300, 600, 900 y 1200 mL por hectárea en una aplicación y 600, 900, 1500 y 2100 mL por hectárea divididas en dos aplicaciones iguales, espaciadas ocho días, de Fruitone CPA; los tratamientos se establecieron a los 135 días después de la inducción floral, a 65 días antes de la cosecha del testigo. Los resultados muestran un alto y significativo efecto del Fruitone en el peso de la fruta, aunque no hubo diferencias entre el número de aplicaciones; el contenido de ácido cítrico y los sólidos solubles totales se incrementaron con la aplicación del Fruitone. No se presentaron frutos agrietados ni con Mancha Café interna en ningún tratamiento. El retraso de la cosecha con respecto al testigo varió desde los seis hasta los 21 días, en función de la dosis. Se concluye que el mejor tratamiento fue el de 900 mL de Fruitone CPA por hectárea, en una sola aplicación, el cual incrementó el peso del fruto en un 14% y retrasó la cosecha 19 días.

PCR amplification and sequence analyses of reverse transcriptase-like genes in Crinipellis perniciosa isolates

Reverse transcriptase (RT) sequence analysis is an important technique used to detect the presence of transposable elements in a genome. Putative RT sequences were analyzed in the genome of the pathogenic fungus C. perniciosa, the causal agent of witches' broom disease of cocoa. A 394 bp fragment was amplified from genomic DNA of different isolates of C. perniciosa belonging to C-, L-, and S-biotypes and collected from various geographical areas. The cleavage of PCR products with restriction enzymes and the sequencing of various RT fragments indicated the presence of several sequences showing transition events (G:C to A:T). Southern blot analysis revealed high copy numbers of RT signals, forming different patterns among C-, S-, and L-biotype isolates. Sequence comparisons of the predicted RT peptide indicate a close relationship with the RT protein from thegypsy family of LTR-retrotransposons. The possible role of these retrotransposons in generating genetic variability in the homothallic C. perniciosa is discussed.

Bartlett-Lewis of rectangular pulse modified model: estimate of parameters for simulation of precipitation in sub-hourly duration

The Bartlett-Lewis Rectangular Pulse Modified (BLPRM) model simulates the precipitous slide in the hourly and sub-hourly and has six parameters for each of the twelve months of the year. This study aimed to evaluate the behavior of precipitation series in the duration of 15 min, obtained by simulation using the model BLPRM in situations: (a) where the parameters are estimated from a combination of statistics, creating five different sets; (b) suitability of the model to generate rain. To adjust the parameters were used rain gauge records of Pelotas/RS/Brazil, which statistics were estimated - mean, variance, covariance, autocorrelation coefficient of lag 1, the proportion of dry days in the period considered. The results showed that the parameters related to the time of onset of precipitation (λ) and intensities (μx) were the most stable and the most unstable were ν parameter, related to rain duration. The BLPRM model adequately represented the mean, variance, and proportion of the dry period of the series of precipitation lasting 15 min and, the time dependence of the heights of rain, represented autocorrelation coefficient of the first retardation was statistically less simulated series suitability for the duration of 15 min.

Detection of Pneumocystis in lungs of bats from Brazil by PCR amplification

Pneumocystis has been isolated from a wide range of unrelated mammalian hosts, including humans, domestic and wild animals. It has been demonstrated that the genome of Pneumocystis of one host differs markedly from that of other hosts. Also, variation in the chromosome and DNA sequence of Pneumocystis within a single host species has been observed. Since information about the occurrence and nature of infections in wild animals is still limited, the objective of this work was to detect the presence of Pneumocystis sp. in lungs of bats from two states from Brazil by Nested-PCR amplification. The bats, captured in caves and in urban areas, were obtained from the Program of Rabies Control of two States in Brazil, Mato Grosso and Rio Grande do Sul, located in the Mid-Western and Southern regions of the country, respectively. DNAs were extracted from 102 lung tissues and screened for Pneumocystis by nested PCR at the mtLSU rRNA gene and small subunit of mitochondrial ribosomal RNA (mtSSU rRNA). Gene amplification was performed using the mtLSU rRNA, the primer set pAZ102H - pAZ102E and pAZ102X - pAZY, and the mtSSU rRNA primer set pAZ102 10FRI - pAZ102 10R-RI and pAZ102 13RI - pAZ102 14RI. The most frequent bats were Tadarida brasiliensis (25), Desmodus rotundus (20), and Nyctinomops laticaudatus (19). Pneumocystis was more prevalent in the species Nyctinomops laticaudatus (26.3% = 5/19), Tadarida brasiliensis (24% = 6/25), and Desmodus rotundus (20% = 4/20). Besides these species, Pneumocystis also was detected in lungs from Molossus molossus (1/11, 9.1%), Artibeus fimbriatus (1/1, 100%), Sturnira lilium (1/3, 33.3%), Myotis levis (2/3, 66.7%)and Diphylla ecaudata (1/2, 50%). PCR products which could indicate the presence of Pneumocystis (21.56%) were identified in DNA samples obtained from 8 out of 16 classified species from both states (5 bats were not identified). This is the first report of detection of Pneumocystis in bats from Brazil.

Development and evaluation of a loop-mediated isothermal amplification (LAMP) assay for rapid detection of Actinobacillus pleuropneumoniae based the dsbE-like gene

This paper reports on the development and validation of a loop-mediated isothermal amplification assay (LAMP) for the rapid and specific detection of Actinobacillus pleuropneumoniae (A. pleuropneumoniae). A set of six primers were designed derived from the dsbE-like gene of A.pleuropneumoniae and validate the assay using 9 A. pleuropneumoniae reference/field strains, 132 clinical isolates and 9 other pathogens. The results indicated that positive reactions were confirmed for all A. pleuropneumoniae strains and specimens by LAMP at 63ºC for 60 min and no cross-reactivity were observed from other non-A.pleuropneumoniae including Haemophilus parasuis, Escherichia coli, Pasteurella multocida, Bordetella bronchiseptica, Streptococcus suis, Salmonella enterica, Staphylococcus, porcine reproductive and respiratory syndrome virus (PRRSV), and Pseudorabies virus. The detection limit of the conventional PCR was 10² CFU per PCR test tube, while that of the LAMP was 5 copies per tube. Therefore, the sensitivity of LAMP was higher than that of PCR. Moreover, the LAMP assay provided a rapid yet simple test of A. pleuropneumoniae suitable for laboratory diagnosis and pen-side detection due to ease of operation and the requirement of only a regular water bath or heat block for the reaction.

Rapid and sensitive detection of Bordetella bronchiseptica by loop-mediated isothermal amplification (LAMP)

Bordetella bronchiseptica causes acute and chronic respiratory infections in diverse animal species and occasionally in humans. In this study, we described the establishment of a simple, sensitive and cost-efficient loop-mediated isothermal amplification (LAMP) assay for the detection of B. bronchiseptica. A set of primers towards a 235 bp region within the flagellum gene of B. bronchiseptica was designed with online software.. The specificity of the LAMP assay was examined by using 6 porcine pathogens and 100 nasal swabs collected from healthy pigs and suspect infected pigs. The results indicated that positive reactions were confirmed for all B. bronchiseptica and no cross-reactivity was observed from other non-B. bronchiseptica. In sensitivity evaluations, the technique successfully detected a serial dilutions of extracted B. bronchiseptica DNA with a detection limit of 9 copies, which was 10 times more sensitive than that of PCR. Compared with conventional PCR, the higher sensitivity of LAMP method and no need for the complex instrumentation make this LAMP assay a promising alternative for the diagnosis of B. bronchiseptica in rural areas and developing countries where there lacks of complex laboratory services.

Pulse response based control for positive definite systems

Pulse Response Based Control (PRBC) is a recently developed minimum time control method for flexible structures. The flexible behavior of the structure is represented through a set of discrete time sequences, which are the responses of the structure due to rectangular force pulses. The rectangular force pulses are given by the actuators that control the structure. The set of pulse responses, desired outputs, and force bounds form a numerical optimization problem. The solution of the optimization problem is a minimum time piecewise constant control sequence for driving the system to a desired final state. The method was developed for driving positive semi-definite systems. In case the system is positive definite, some final states of the system may not be reachable. Necessary conditions for reachability of the final states are derived for systems with a finite number of degrees of freedom. Numerical results are presented that confirm the derived analytical conditions. Numerical simulations of maneuvers of distributed parameter systems have shown a relationship between the error in the estimated minimum control time and sampling interval

Simulation of Active Control Using Fuzzy Logic Applied to a Pulse Combustor

This work analyzes an active fuzzy logic control system in a Rijke type pulse combustor. During the system development, a study of the existing types of control for pulse combustion was carried out and a simulation model was implemented to be used with the package Matlab and Simulink. Blocks which were not available in the simulator library were developed. A fuzzy controller was developed and its membership functions and inference rules were established. The obtained simulation showed that fuzzy logic is viable in the control of combustion instabilities. The obtained results indicated that the control system responded to pulses in an efficient and desirable way. It was verified that the system needed approximately 0.2 s to increase the tube internal pressure from 30 to 90 mbar, with an assumed total delay of 2 ms. The effects of delay variation were studied. Convergence was always obtained and general performance was not affected by the delay. The controller sends a pressure signal in phase with the Rijke tube internal pressure signal, through the speakers, when an increase the oscillations pressure amplitude is desired. On the other hand, when a decrease of the tube internal pressure amplitude is desired, the controller sends a signal 180º out of phase.

Efeitos do ácido 2-(3-clorofenoxi) propionico (3-CPA) sobre frutos de abacaxi 'cayenne'

Estudaram-se os efeitos do ácido 2-(3-clorofenoxi) propiônico (3-CPA) nas doses de 37,5, 75,0, 112,5 ppm e 75,0 ppm + 2% de uréia, sobre frutos de abacaxi 'Cayenne'. As aplicações do 3-CPA foram efetuadas quando as flores apicais do fruto apresentavam-se no estádio final de deiscéncia. Verificou-se que todos os tratamentos com 3-CPA, isoladamente ou em mistura com uréia, aumentaram significativamente o peso do fruto e reduziram o peso da coroa. O peso do fruto aumentou de 20 a 34% em relação ao controle (plantas não tratadas com 3-CPA). A presença de uréia não alterou o efeito do 3-CPA sobre o tamanho do fruto, entretanto, a eficiência desse regulador de crescimento em reduzir o tamanho da coroa tendeu a ser menor em presença de uréia. O 3-CPA uniformizou e retardou a maturação do fruto em cerca de 30 dias. Nas doses empregadas não se observou efeito fitotóxico do 3-CPA sobre a coroa do fruto.

Amplification of 9q34 in childhood adrenocortical tumors: a specific feature unrelated to ethnic origin or living conditions

Adrenocortical tumors (ACT) in children under 15 years of age exhibit some clinical and biological features distinct from ACT in adults. Cell proliferation, hypertrophy and cell death in adrenal cortex during the last months of gestation and the immediate postnatal period seem to be critical for the origin of ACT in children. Studies with large numbers of patients with childhood ACT have indicated a median age at diagnosis of about 4 years. In our institution, the median age was 3 years and 5 months, while the median age for first signs and symptoms was 2 years and 5 months (N = 72). Using the comparative genomic hybridization technique, we have reported a high frequency of 9q34 amplification in adenomas and carcinomas. This finding has been confirmed more recently by investigators in England. The lower socioeconomic status, the distinctive ethnic groups and all the regional differences in Southern Brazil in relation to patients in England indicate that these differences are not important to determine 9q34 amplification. Candidate amplified genes mapped to this locus are currently being investigated and Southern blot results obtained so far have discarded amplification of the abl oncogene. Amplification of 9q34 has not been found to be related to tumor size, staging, or malignant histopathological features, nor does it seem to be responsible for the higher incidence of ACT observed in Southern Brazil, but could be related to an ACT from embryonic origin.

Fingerprinting of cell lines by directed amplification of minisatellite-region DNA (DAMD)

The development of in vitro propagation of cells has been an extraordinary technical advance for several biological studies. The correct identification of the cell line used, however, is crucial, as a mistaken identity or the presence of another contaminating cell may lead to invalid and/or erroneous conclusions. We report here the application of a DNA fingerprinting procedure (directed amplification of minisatellite-region DNA), developed by Heath et al. [Nucleic Acids Research (1993) 21: 5782-5785], to the characterization of cell lines. Genomic DNA of cells in culture was extracted and amplified by PCR in the presence of VNTR core sequences, and the amplicons were separated by agarose gel electrophoresis. After image capture with a digital camera, the banding profiles obtained were analyzed using a software (AnaGel) specially developed for the storage and analysis of electrophoretic fingerprints. The fingerprints are useful for construction of a data base for identification of cell lines by comparison to reference profiles as well as comparison of similar lines from different sources and periodic follow-up of cells in culture.

Random amplification of polymorphic DNA reveals clonal relationships among enteropathogenic Escherichia coli isolated from non-human primates and humans

Enteropathogenic Escherichia coli (EPEC) strains are important agents of infantile diarrhea all over the world, gaining even greater importance in developing countries. EPEC have also been isolated from various animal species, but most isolates belong to serotypes that differ from those recovered from humans. However, it has been demonstrated that several isolates from non-human primates belong to the serogroups and/or serotypes related to those implicated in human disease. The objective of this study was to evaluate the genetic differences between thirteen strains isolated from non-human primates and the same number of strains isolated from human infections. Human isolates belonged to the same serogroup/serotype as the monkey strains and the evaluation was done by analysis of random amplified polymorphic DNA. Dendrogram analysis showed that there was no clustering between human and monkey strains. Human and non-human isolates of the EPEC serotypes O127:H40 and O128:H2 shared 90 and 87% of their bands, respectively, indicating strong genomic similarity between the strains, leading to the speculation that they may have arisen from the same pathogenic clone. To our knowledge, this study is the first one comparing genomic similarity between human and non-human primate strains and the results provide further evidence that monkey EPEC strains correlate with human EPEC, as suggested in a previous investigation.

Correlations between pulse oximetry and peak expiratory flow in acute asthma

Few studies are available concerning correlations between pulse oximetry and peak expiratory flow in children and adolescents with acute asthma. Although the Global Initiative for Asthma states that measurements of lung function and oximetry are critical for the assessment of patients, it is not clear if both methods should necessarily be included in their evaluation. Since there is a significant difference in cost between pulse oximetry equipment and peak expiratory flow devices, we determined whether clinical findings and peak expiratory flow measurements are sufficient to determine the severity of acute asthma. The present prospective observational study was carried out to determine if there is correlation between pulse oximetry and peak expiratory flow determination in 196 patients with acute asthma aged 4 to 15 years diagnosed according to the Global Initiative for Asthma criteria. Patients experiencing their first or second wheezing episode, with fever, related acute or chronic diseases, and unable to perform the peak expiratory flow maneuver were excluded. Measurements of peak expiratory flow and pulse oximetry were performed at admission and after 15 min of each inhaled salbutamol cycle. Correlations obtained by linear regression using the Pearson correlation coefficients (r) were 0.41 (P < 0.0001), 0.53 (P < 0.0001), 0.51 (P < 0.0001), and 0.61 (P < 0.0001) at admission and after the first, second and third cycles of salbutamol, respectively. These correlations showed that one measure cannot substitute the other (Pearson's coefficient <0.7), probably because they evaluate different aspects in the airways, suggesting that peak expiratory flow should not be used alone in the assessment of acute asthma in children and adolescents.

Immediate effects of submaximal effort on pulse wave velocity in patients with Marfan syndrome

Marfan syndrome (MS) is a dominant autosomal disease caused by mutations in chromosome 15, the locus controlling fibrillin 1 synthesis, and may exhibit skeletal, ocular, cardiovascular, and other manifestations. Pulse wave velocity (PWV) is used to measure arterial elasticity and stiffness and is related to the elastic properties of the vascular wall. Since the practice of exercise is limited in MS patients, it was of interest to analyze the acute effect of submaximal exercise on aortic distensibility using PWV and other hemodynamic variables in patients with MS with either mild or no aortic dilatation. PWV and physiological variables were evaluated before and after submaximal exercise in 33 patients with MS and 18 controls. PWV was 8.51 ± 0.58 at rest and 9.10 ± 0.63 m/s at the end of exercise (P = 0.002) in the group with MS and 8.07 ± 0.35 and 8.98 ± 0.56 m/s in the control group, respectively (P = 0.004). Comparative group analysis regarding PWV at rest and at the end of exercise revealed no statistically significant differences. The same was true for the group that used β-blockers and the one that did not. The final heart rate was 10% higher in the control group than in the MS group (P = 0.01). Final systolic arterial pressure was higher in the control group (P = 0.02). PWV in MS patients with mild or no aortic dilatation did not differ from the control group after submaximal effort.