High-throughput bioinformatics with the Cyrille2 pipeline system

Background  

Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases. The analyses are often interdependent and chained together to form complex workflows or pipelines. Given the volume of the data used and the multitude of computational resources available, specialized pipeline software is required to make high-throughput analysis of large-scale omics datasets feasible.     

Effects of zinc sulfate on limbic motor epilepsy induced by kainic acid

In the present study the Authors have investigated the effects of chronic pretreatment with injections of Zn++ sulphate solution on kainic acid induced epilepsy, to verify wether or not Zn++ is able to change the epileptiform pattern induced by kainic acid infection. Results obtained show that Zn++ do not produce any significant change in the experimental parameters by us study.     

Toxic effects of mechlorethamine on mammalian respiratory mucociliary epithelium in primary culture

Mechlorethamine (HN2) is an alkylating agent usually used in cancer chemotherapy. Nevertheless, HN2 is extremely toxic and its use is accompanied by severe side-effects that may cause lung complications. Many studies report the morphological and biochemical modifications induced by sulfur mustard (SM) but no report has been published concerning the toxic effects of HN2 on the ultrastructural and functional activity of surface respiratory epithelial cells. This study was performed on rabbit tracheal epithelium (RTE) cells in primary culture. The functional activity of the culture was evaluated by measuring the ciliary beating frequency (CBF) of the ciliated cells using a videomicroscopic method, and the culture growth was determined by an image analysis system. The morphological aspects of the cells were analyzed by light, scanning electron, and transmission electron microscopy. An important inhibition of cell growth was observed associated with a detachment of the outgrowth cells. Morphological changes were expressed by vacuolization, increases in the intercellular spaces, and by disorganization of the cytoskeleton associated with a specific attack of the ciliated cells that show ciliary blebbing. The sudden CBF inhibition is more likely due to the detachment and the death of the ciliated cells than to a specific ciliotoxic effect of HN2. All these observations demonstrated the high sensitivity of respiratory epithelial cells to HN2 and showed that HN2-induced injuries were irreversible, and time- and dose-dependent.Abbreviations CBF ciliary beating frequency - HN2 nitrogen mustard, or mechlorethamine - RTE rabbit tracheal epithelium - SEM scanning electron microscopy - SM sulfur mustard - TEM transmission electron microscopy     

Bivalent binding of an anti-CD3 antibody to Jurkat cells induces association of the T cell receptor complex with the cytoskeleton

Ligand binding and cross-linking of TCR/CD3 complex leads to T cell stimulation in immunologic responses. As a prelude to investigating the dynamic interactions of these receptors, we have characterized binding of the mAb OKT3 specific for CD3 on Jurkat cells. The association of both OKT3 and its Fab' fragment is rapid at 4 degrees C, and dissociation of Fab' is also rapid, but dissociation of OKT3 is slow, indicating bivalent binding in this case. Dissociation of OKT3 is substantially accelerated at 37 degrees C if internalization is prevented. From the concentration dependence, the binding of OKT3 at 4 degrees C appears to be very tight whereas binding of the Fab' fragment is weaker and biphasic. Scatchard analysis of the Fab' equilibrium binding data indicates two binding sites with KD values of 5.1 x 10(-9) M and 2.7 x 10(-8) M. The very tight binding of the bivalent antibody may be caused by inter- or intramolecular cross-linking between these sites. If Jurkat cells are warmed to 37 degrees C, there is an energy-dependent increase by about one-third of sites bound by OKT3 or its Fab' fragment over that seen at 4 degrees C. This increase may be related to a receptor recycling process because internalization of a similar number of the bound ligands occurs at similar rates. Other experiments have revealed that OKT3, but not its Fab' fragment, causes the receptor complex to become associated with the detergent-insoluble cytoskeleton, and there are also insoluble intracellular OKT3-binding sites. These cross-linking-induced receptor-cytoskeletal interactions are sensitive to moderate changes in salt concentration that should allow their molecular basis to be investigated.     

Extracellular matrix-dependent differentiation of rabbit tracheal epithelial cells in primary culture

Summary The differentiation of tracheal epithelial cells in primary culture was investigated according to the nature of the extracellular matrix used. Cultures obtained by the explant technique were realized on a type I collagen substratum either as a thin, dried coating or as a thick, hydrated gel supplemented with culture medium and serum. These two types of substratum induced distinct cell morphology and cytokeratin expression in the explant derived cells. Where cells are less proliferating (from Day 7 to 10 of culture), differentiation was evaluated by morphologic ultrastructural observations, immunocytochemical detection of cytokeratins, and determination of cytokeratin pattern by biochemical analysis. The epithelium obtained on gel was multilayered, with small, round basal cells under large, flattened upper cells. The determination of the keratin pattern expressed by cells grown on gel revealed an expression of keratin 13, already considered as a specific marker of squamous metaplasia, that diminished with retinoic acid treatment. Present results demonstrated by confocal microscopy that K13-positive cells were large upper cells with a dense keratin network, whereas lower cells were positively stained with a specific monoclonal antibody to basal cells (KB37). Moreover, keratin neosynthesis analysis pointed out a higher expression of K6, a marker of hyperproliferation, on gel than on coating. All these data suggest a differentiation of rabbit tracheal epithelial cells grown on gel toward squamous metaplasia. By contrast, the epithelium observed on coating is nearly a monolayer of very large and spread out cells. No K13-positive cells were observed, but an increase in the synthesis of simple epithelium marker (K18) was detected. These two substrata, similar in composition and different in structure, induce separate differentiation and appear as good tools to explore the mechanisms of differentiation of epithelial tracheal cells.     

Rapid and sensitive detection of Citrus Bacterial Canker by loop-mediated isothermal amplification combined with simple visual evaluation methods

Background  

Citrus Bacterial Canker (CBC) is a major, highly contagious disease of citrus plants present in many countries in Asia, Africa and America, but not in the Mediterranean area. There are three types of Citrus Bacterial Canker, named A, B, and C that have different genotypes and posses variation in host range within citrus species. The causative agent for type A CBC is Xanthomonas citri subsp. citri, while Xanthomonas fuscans subsp. aurantifolii, strain B causes type B CBC and Xanthomonas fuscans subsp. aurantifolii strain C causes CBC type C. The early and accurate identification of those bacteria is essential for the protection of the citrus industry. Detection methods based on bacterial isolation, antibodies or polymerase chain reaction (PCR) have been developed previously; however, these approaches may be time consuming, laborious and, in the case of PCR, it requires expensive laboratory equipment. Loop-mediated isothermal amplification (LAMP), which is a novel isothermal DNA amplification technique, is sensitive, specific, fast and requires no specialized laboratory equipment.     

Technique of stereotactic biopsy of two cranial target employing spherical coordinates to define a single trajectory

A 'spherical coordinate system' has been developed to allow either stereotactic biopsy of two intracranial lesions using a single predetermined trajectory or biopsy of a single lesion through an existing burr hole. By means of the Gildenberg technique, the CT coordinates of the targets (or target and burr hole) are obtained. These are employed in three simple trigonometric equations to give three coordinates-two angles for the probe carrier (theta and alpha) and the radius (T) of a sphere, defined by one target as the center and the other target on the surface. These can be utilized in the Todd-Wells stereotactic frame. This system was evaluated using hollow skulls and crossed 30-gauge wire for phantom targets. The system was tried on ten different target combinations, and eight successful trajectories were obtained to within 3 mm. Two target combinations were inaccessible because of technical limitations of the Todd-Wells frame. This 'spherical coordinate system' can decrease the time to localize multiple targets as well as minimize the number of passes.