A new avenue for classification and prediction of olive cultivars using supervised and unsupervised algorithms

Various methods have been used to identify cultivares of olive trees; herein we used different bioinformatics algorithms to propose new tools to classify 10 cultivares of olive based on RAPD and ISSR genetic markers datasets generated from PCR reactions. Five RAPD markers (OPA0a21, OPD16a, OP01a1, OPD16a1 and OPA0a8) and five ISSR markers (UBC841a4, UBC868a7, UBC841a14, U12BC807a and UBC810a13) selected as the most important markers by all attribute weighting models. K-Medoids unsupervised clustering run on SVM dataset was fully able to cluster each olive cultivar to the right classes. All trees (176) induced by decision tree models generated meaningful trees and UBC841a4 attribute clearly distinguished between foreign and domestic olive cultivars with 100% accuracy. Predictive machine learning algorithms (SVM and Naïve Bayes) were also able to predict the right class of olive cultivares with 100% accuracy. For the first time, our results showed data mining techniques can be effectively used to distinguish between plant cultivares and proposed machine learning based systems in this study can predict new olive cultivars with the best possible accuracy.     

Analysis of shear wave propagation in skin; application to an experimental procedure

An analysis of an experimental procedure used to determine age-related changes in the skin was performed. The experiment is based on the propagation of a shear wave through the skin. The analysis of the experiment was used to determine the effects of parameters such as properties of the skin and subcutaneous fat, skin thickness and experimental conditions on the propagation. Computer simulations showed that at lower frequencies (less than 1000 Hz), measured results depended strongly on skin thickness, while at higher frequencies (2000 Hz) the results were relatively insensitive to both skin thickness and the properties of the subcutaneous fat. Results also depended upon the distance between the applied shear disturbance and the measurement point. The analysis suggests that higher frequency (2000 Hz) experimental results are more indicative of mechanical properties of skin than lower frequency (less than 1000 Hz) results.     

Neuroinflammatory reactions in sickness behavior induced by bacterial infection: Protective effect of minocycline

The neurological changes elicited by bacterial infection are called sickness behavior. Minocycline (MIN) is neuroprotective with a remarkable brain tissue penetration. MIN was orally administered at a dose 90 mg/kg for 3 days, whereas Escherichia coli was given as a single intraperitoneal injection (0.2 mL of 24 h growth) on the third day. After 24 h of bacterial infection, behavioral tests namely open field and forced swimming were carried out, then animals were decapitated. Rats infected with E. coli displayed reduced struggling time in forced swimming test, as well as, exploration and locomotion in open field test with reduction in neurotransmitters (norepinephrine, dopamine, and serotonin) versus elevation in the inflammatory (tumor necrosis factor‐alpha, interferon‐gamma) and oxidative stress (thiobarbituric acid reactive substance, reduced glutathione) biomarkers. Inflammatory infiltrates of nuclear cells were observed in brains of infected rats. MIN administration prevented the deleterious effects of E. coli infection, thus protects against sickness behavior possibly via defending from neuroinflammation.     

A mosquito predator survey in Townsville, Australia, and an assessment of Diplonychus sp. and Anisops sp. predatorial capacity against Culex annulirostris mosquito immatures.

A twelve-month survey for mosquito predators was conducted in Townsville, Queensland, Australia, which is located in the arid tropics. The survey revealed the presence of five predaceous insects but only Anisops sp. (backswimmers) and Diplonychus sp. were common. Predatorial capacity and factors influencing this capacity were then assessed for adult Anisops sp. and adult and nymph stages of Diplonychus sp. against Culex annulirostris mosquito immatures under laboratory conditions. Predatorial capacity bioassays showed that adult Diplonychus sp. preyed upon both larval and pupal stages of Cx. annulirostris quite successfully. Nymphs of Diplonychus sp. proved to be more successful with smaller prey immatures, and Anisops sp adults did not prey successfully on any prey pupae. Increasing the foraging area and introducing aquatic vegetation significantly reduced the predatorial capacity of Diplonychus sp. nymphs, while only vegetation and not foraging area had a significant effect on adult Diplonychus sp. predation capacity. Overall, adult Diplonychus sp. proved to be a more efficient predator than Anisops sp., and field trials are now recommended to further assess the potential of Diplonychus sp. as a biocontrol agent.     

In Vitro Scolicidal Effects of Salvadora persica Root Extract against Protoscolices of Echinococcus granulosus

It has been known that Arak, Salvadora persica, has a number of medicinal properties. We tried to investigate in vitro scolicidal effect of root extracts of this plant against protoscolices from hydatid cysts of Echinococcus granulosus. Protoscolices were aseptically collected from sheep livers containing hydatid cysts. S. persica root extract was used in 10, 30, and 50 mg/ml concentration for 10, 20, and 30 min. The viability of protoscolices was ascertained by 0.1% eosin staining. Scolicidal activity of S. persica extract at a concentration of 10 mg/ml was 36.3%, 50.3%, and 70.8% after 10, 20, and 30 min of exposure, respectively. The scolicidal effect of this extract at a concentration of 30 mg/ml was 52.9%, 86.7%, and 100% after 10, 20, and 30 min of exposure, respectively. S. persica extract at a concentration of 50 mg/ml, meanwhile, killed 81.4%, 100%, and 100% of protoscolices after 10, 20, and 30 min, respectively. Also, the cytotoxic potential of S. persica was assessed on human liver cells (HepG2) using trypan blue exclusion test. No cytotoxic effect was observed on HepG2 cell line. The present study confirmed for the first time that the ethanolic extract of S. persica has high scolicidal power in vitro. However, in vivo effect of this material remains to be studied for treatment of echinococcosis in humans and herbivorous animals.     

The spiders of a citrus grove in israel and their role as biocontrol agents ofCeroplastes floridensis [Homoptera: Coccidae]

A 12 month survey was carried out of the spider population in a commercial citrus grove at Kibbutz Afeq in Northern Israel. The spiders collected from grapefruit foliage and ground cover were identified; young stages were reared to maturity and then identified.Chiracanthium mildei L. Koch represented 52% of all spiders captured during the year andTheridion sp. accounted for 34%. In the undercover,Gnaphosidae spiders represented 43% of the total spiders captured in pitfall traps andLycosidae 35%. A field experiment was carried out to evaluate the effectivness of spiders in biological control of the scaleCeroplastes floridensis Mask. in the citrus ecosystem. Wherever spiders were undisturbed on tree branches, populations ofC. floridensis were not able to develop to a level sufficient to cause economic damage. The increase in the number of scales was minimal: from 47 initially to 56. There was no damage to leaves nor was honeydew or sooty mold observed. During the same time period, on the 3 branches from which spiders had been eliminated, the number of scales increased seven-fold from 44 to 309. Leaves were heavily infested with sooty mold fungi that developed on the honeydew produced by the scales. Contribution from the Agricultural Research Organization, Neve Ya'ar, Regional Experiment Station. P.O. Haifa 31999, Israel. No. 1314-E 1984, series.     

Preventing and curing citrulline-induced autoimmune arthritis in a humanized mouse model using a Th2-polarizing iNKT cell agonist

Invariant natural killer T (iNKT) cells are innate lymphocytes with unique reactivity to glycolipid antigens bound to non-polymorphic CD1d molecules. They are capable of rapidly releasing pro- and/or anti-inflammatory cytokines and constitute attractive targets for immunotherapy of a wide range of diseases including autoimmune disorders. In this study, we have explored the beneficial effects of OCH, a Th2-polarizing glycolipid agonist of iNKT cells, in a humanized mouse model of rheumatoid arthritis (RA) in which citrullinated human proteins are targeted by autoaggressive immune responses in mice expressing an RA susceptibility human leukocyte antigen (HLA) DR4 molecule. We found for the first time that treatment with OCH both prevents and cures citrulline-induced autoimmune arthritis as evidenced by resolved ankle swelling and reversed histopathological changes associated with arthritis. Also importantly, OCH treatment blocked the arthritogenic capacity of citrullinated antigen-experienced splenocytes without compromising their global responsiveness or altering the proportion of splenic naturally occurring CD4(+)CD25(+)FoxP3(+) regulatory T cells. Interestingly, administering the Th1-promoting iNKT cell glycolipid ligand α-C-galactosylceramide into HLA-DR4 transgenic mice increased the incidence of arthritis in these animals and exacerbated their clinical symptoms, strongly suggesting a role for Th1 responses in the pathogenesis of citrulline-induced arthritis. Therefore, our findings indicate a role for Th1-mediated immunopathology in citrulline-induced arthritis and provide the first evidence that iNKT cell manipulation by Th2-skewing glycolipids may be of therapeutic value in this clinically relevant model, a finding that is potentially translatable to human RA.     

Nasal gene expression differentiates COPD from controls and overlaps bronchial gene expression

Background

Nasal gene expression profiling is a promising method to characterize COPD non-invasively. We aimed to identify a nasal gene expression profile to distinguish COPD patients from healthy controls. We investigated whether this COPD-associated gene expression profile in nasal epithelium is comparable with the profile observed in bronchial epithelium.

Methods

Genome wide gene expression analysis was performed on nasal epithelial brushes of 31 severe COPD patients and 22 controls, all current smokers, using Affymetrix Human Gene 1.0 ST Arrays. We repeated the gene expression analysis on bronchial epithelial brushes in 2 independent cohorts of mild-to-moderate COPD patients and controls.

Results

In nasal epithelium, 135 genes were significantly differentially expressed between severe COPD patients and controls, 21 being up- and 114 downregulated in COPD (false discovery rate?<?0.01). Gene Set Enrichment Analysis (GSEA) showed significant concordant enrichment of COPD-associated nasal and bronchial gene expression in both independent cohorts (FDR_GSEA <?0.001).

Conclusion

We identified a nasal gene expression profile that differentiates severe COPD patients from controls. Of interest, part of the nasal gene expression changes in COPD mimics differentially expressed genes in the bronchus. These findings indicate that nasal gene expression profiling is potentially useful as a non-invasive biomarker in COPD.

Trial registration

ClinicalTrials.gov registration number NCT01351792 (registration date May 10, 2011), ClinicalTrials.gov registration number NCT00848406 (registration date February 19, 2009), ClinicalTrials.gov registration number NCT00807469 (registration date December 11, 2008).