Development of a novel DNA microarray to detect bacterial pathogens in patients with chronic obstructive pulmonary disease (COPD)

A novel microarray was constructed with DNA PCR product probes targeting species specific functional genes of nine clinically significant respiratory pathogens, including the Gram-positive organisms (Streptococcus pneumoniae, Streptococcus pyogenes), the Gram-negative organisms (Chlamydia pneumoniae, Coxiella burnetii Haemophilus spp., Legionella pneumophila, Moraxella catarrhalis, and Pseudomonas aeruginosa), as well as the atypical bacterium, Mycoplasma pneumoniae. In a "proof-of-concept" evaluation of the developed microarray, the microarray was compared with real-time PCR from 14 sputum specimens from COPD patients. All of the samples positive for bacterial species in real-time PCR were also positive for the same bacterial species using the microarray. This study shows that a microarray using PCR probes is a potentially useful method to monitor the populations of bacteria in respiratory specimens and can be tailored to specific clinical needs such as respiratory infections of particular patient populations, including patients with cystic fibrosis and bronchiectasis. (C) 2010 Elsevier B.V. All rights reserved.

Development of a genotyping microarray for Usher syndrome

Usher syndrome, a combination of retinitis pigmentosa (RP) and sensorineural hearing loss with or without vestibular dysfunction, displays a high degree of clinical and genetic heterogeneity. Three clinical subtypes can be distinguished, based on the age of onset and severity of the hearing impairment, and the presence or absence of vestibular abnormalities. Thus far, eight genes have been implicated in the syndrome, together comprising 347 protein-coding exons.

Development of a planar waveguide microarray for the monitoring and early detection of five harmful algal toxins in water and cultures

A novel multiplex microarray has been developed for the detection of five groups of harmful algal and cyanobacterial toxins found in marine, brackish, and freshwater environments including domoic acid (DA), okadaic acid (OA, and analogues), saxitoxin (STX, and analogues), cylindrospermopsin (CYN) and microcystins (MC, and analogues). The sensitivity and specificity were determined and feasibility to be used as a screening tool investigated. Results for algal/cyanobacterial cultures (n = 12) and seawater samples (n = 33) were compared to conventional analytical methods, such as high performance liquid chromatography (HPLC) and liquid chromatography tandem mass spectrometry (LC-MS/MS). Detection limits for the 15 min assay were 0.37, 0.44, 0.05, 0.08, and 0.40 ng/mL for DA, OA, STX, CYN, and MC, respectively. The correlation of data obtained from the microarray compared to conventional analysis for the 12 cultures was r(2) = 0.83. Analysis of seawater samples showed that 82, 82, 70, 82, and 12% of samples were positive (>IC20) compared to 67, 55, 36, 0, and 0% for DA, OA, STX, CYN, and MC, respectively, for conventional analytical methods. The discrepancies in results can be attributed to the enhanced sensitivity and cross-reactivity profiles of the antibodies in the MBio microarray. The feasibility of the microarray as a rapid, easy to use, and highly sensitive screening tool has been illustrated for the five-plex detection of biotoxins. The research demonstrates an early warning screening assay to support national monitoring agencies by providing a faster and more accurate means of identifying and quantifying harmful toxins in water samples.

Development of polyaniline microarray electrodes for cadmium analysis

Disposable screen-printed electrodes (SPCE) were modified using a cosmetic product to partially block the electrode surface in order to obtain a microelectrode array. The microarrays formed were electropolymerized with aniline. Scanning electron microscopy was used to evaluate the modified and polymerized electrode surface. Electrochemical characteristics of the constructed sensor for cadmium analysis were evaluated by cyclic and square-wave voltammetry. Optimized stripping procedure in which the preconcentration of cadmium was achieved by depositing at –1.20 V (vs. Ag/AgCl) resulted in a well defined anodic peak at approximately –0.7 V at pH 4.6. The achieved limit of detection was 4 × 10−9 mol dm−3. Spray modified and polymerized microarray electrodes were successfully applied to quantify cadmium in fish sample digests.

Bud development, flowering and fruit set of Moringa oleifera Lam. (Horseradish Tree) as affected by various irrigation levels

Moringa oleifera is becoming increasingly popular as an industrial crop due to its multitude of useful attributes as water purifier, nutritional supplement and biofuel feedstock. Given its tolerance to sub-optimal growing conditions, most of the current and anticipated cultivation areas are in medium to low rainfall areas. This study aimed to assess the effect of various irrigation levels on floral initiation, flowering and fruit set. Three treatments namely, a 900 mm (900IT), 600 mm (600IT) and 300 mm (300IT) per annum irrigation treatment were administered through drip irrigation, simulating three total annual rainfall amounts. Individual inflorescences from each treatment were tagged during floral initiation and monitored throughout until fruit set. Flower bud initiation was highest at the 300IT and lowest at the 900IT for two consecutive growing seasons. Fruit set on the other hand, decreased with the decrease in irrigation treatment. Floral abortion, reduced pollen viability as well as moisture stress in the style were contributing factors to the reduction in fruiting/yield observed at the 300IT. Moderate water stress prior to floral initiation could stimulate flower initiation, however, this should be followed by sufficient irrigation to ensure good pollination, fruit set and yield.

Development of a miniaturised microarray-based assay for the rapid identification of antimicrobial resistance genes in Gram-negative bacteria

We describe the development of a miniaturised microarray for the detection of antimicrobial resistance genes in Gram-negative bacteria. Included on the array are genes encoding resistance to aminoglycosides, trimethoprim, sulphonamides, tetracyclines and beta-lactams, including extended-spectrum beta-lactamases. Validation of the array with control strains demonstrated a 99% correlation between polymerase chain reaction and array results. There was also good correlation between phenotypic and genotypic results for a large panel of Escherichia coli and Salmonella isolates. Some differences were also seen in the number and type of resistance genes harboured by E. coli and Salmonella strains. The array provides an effective, fast and simple method for detection of resistance genes in clinical isolates suitable for use in diagnostic laboratories, which in future will help to understand the epidemiology of isolates and to detect gene linkage in bacterial populations. (C) 2008 Published by Elsevier B.V. and the International Society of Chemotherapy.

Evaluation and development of passion fruit (Passiflora alata Dryander) propagated by cutting and seet in conditions of commercial orchard

The present work was conducted in a fruit tree propagation area of the Plant Production Department of the Faculdade de Ciencias Agrarias e Veterinarias, Universidade Estadual Paulista (FCAV/UNESP) in Jaboticabal, SP, and also in a commercial orchard in Araguari, MG, with the objective to verify the potential of vegetative growth (stem diameter, height of plants and leaf number) of plants of passion fruit (Passiflora alata Dryander), gotten by cutting and seed, comparing the initial development of plants in the field. This experiment was carried out from January 2002 to February 2003. The experiment using seeds was conducted at a shadow house, and the one that used cuttings in an intermitent mist. The cuttings and seeds were collected from adult plants which came from Passifloraceae Active Germoplasm Bank (BAG) of the Plant Production Department of FCAC/UNESP. For the cuttings, it was used the intermediate part of the branches in stadium of vegetative growth. The seeds, in order to obtain the seedlings, had been sown in plastic trays. Cuttings and seedlings were transplanted to plastic bags with substrate in shadow house and with daily irrigation. They were acclimatized and planted on field, after 60 days. on field, the stem diameter, plant height and number of leaves were better for cuttings than for seedlings in Jaboticabal, SP. In Araguari, MG, stem diameter was larger in the seedlings, which plant heights and number of leaves were larger on cuttings.

Soil-liming effects on the development and nutritional status of the carambola tree and its fruit-yielding capacity

Soil acidity is one of the most important factors limiting agricultural production in the tropics. For this reason, the objective of this research work was to evaluate the effects of soil liming on the performance of carambola (Averrhoa carambola) trees. The experiment took place at the Citrus Experimental Station in Bebedouro, state of São Paulo, Brazil. The soil was a Typic Haplustox (V = 26% at the 0- to 20-cm layer) between August 1999 and July 2003. The following doses of limestone were employed: 0, 1.85, 3.71, 5.56, and 7.41 t ha(-1). During 40 months after the experiment was set up, soil chemical attributes were periodically examined. For a period of 2 years, the trees had their leaves analyzed for micro-and macronutrients; their trunk diameter, height, and crown volume measured; and the production of fruits determined. Liming improved in evaluated chemical attributes of the soil: pH, calcium (Ca), magnesium (Mg), BS, V, and hydrogen and aluminium (H + At) from the upper 60 cm of soil when the samples were taken from both the line and between the lines of plants. In the leaves, the levels of Ca and Mg also increased. The highest fruit yields were observed when soil base saturations reached 45% on the lines and 50% between the lines, as well as when foliar levels of 8.0 g of Ca and 4.7 a of Mg per kilogram of leaves were attained.

Identification of oligomers in polyethyleneterephthalate bottles for mineral water and fruit juice - Development and validation of a high-performance liquid chromatographic method for the determination of first series cyclic trimer

Cyclic oligomers were identified in PET bottles used for mineral water and fruit juice using MS and H-1 and C-13 NMR: a first series cyclic trimer, a first series cyclic tetramer, a first series cyclic dimmer and a second series cyclic trimer. An analytical method to determine first series cyclic trimer in these bottles was developed and validated, using HPLC. The first series cyclic trimer levels were 316-462 mg/100 g of PET bottle. (c) 2005 Elsevier B.V. All rights reserved.

Development of a supercritical fluid extraction method for simultaneous determination of organophosphorus, organohalogen, organonitrogen and pyretroids pesticides in fruit and vegetables and its comparison with a conventional method by GC-ECD and GC-MS

The aim of this paper was to apply a multiresidue method using Supercritical Fluid Extraction (SFE) and capillary gas chromatography with electron capture and mass spectrometry detections in the analysis of the levels of pesticide residues in fruits and vegetables. Single laboratory validation of both solid-liquid and supercritical fluid extraction methods was carried out for 32 compounds selected from four pesticide classes (organochlorine, organonitrogen, organophosphorus and pyretroid) in blank and fortified samples of fresh lettuce, potato, apple and tomato. Recoveries for the majority of pesticides from fortified samples at fortification level of 0.04-0.10 mg kg -1 ranged 74-96% for both methods and confirmation of pesticide identity was performed by gas-chromatography-mass spectrometry in a selected-ion monitoring mode. Both methods showed good limits of detection (less 0.01 mg kg-1, depending on the pesticide and matrix) and the SFE method minimized environmental concerns, time, and laboratory work. ©2005 Sociedade Brasileira de Química.

Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

Background. From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings. The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions. Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas. © 2010 Moreira et al; licensee BioMed Central Ltd.

Pulp fruit added to culture medium for in vitro orchid development

As an additive in in vitro culture media, fruits have a great potential for facilitating economical orchid production because of lower technology requirements and the ease of obtaining raw materials to formulate culture media. We studied the in vitro growth of Cattleya bicolor Lindl. grown in a simplified culture medium supplemented with different kinds of fruit pulp. The experimental design was completely randomised, with eight seedlings per replication and ten replications per treatment, for a total of 80 seedlings per treatment. The culture medium was made using 150 g L -1 of pulp (without peel or seed) from the following fruits: ripe Santa Cruz tomatoes (Solanum lycopersicum L.), dwarf bananas (Musa cavendishii L.) of intermediate ripeness, light green chayote (Sechium edule (Jacq.) Sw), ripe papaya (Carica papaya L.) or green coconut (Cocos nucifera L.).The treatment control was MS 50 %. The treatments and the control were kept in a growth chamber for seven months before evaluating seedling survival percentage, shoot height, number of leaves, rooting percentage, root number, root length and dry masses of shoot and roots. The highest percentages of seedling survival were obtained using MS 50 %, banana and coconut medium. The seedling survival and rooting percentages illustrate that it is possible to emphasise the culture medium MS 50% and the culture medium supplemented with coconut on the most traditional culture medium with banana or tomato pulp. For the in vitro development of Cattleya bicolor Lindl., a simplified culture medium supplemented with coconut pulp is the most suitable for use as an alternative to MS 50%. A simplified culture medium supplemented with papaya pulp is not recommended for the in vitro development of Cattleya bicolor Lindl.

Ovule, fruit and seed development in Abolboda (Xyridaceae, Poales): implications for taxonomy and phylogeny

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