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1.  Phenotyping date palm varieties via leaflet cross-sectional imaging and artificial neural network application 
BMC Bioinformatics  2014;15:55.
Background
True date palms (Phoenix dactylifera L.) are impressive trees and have served as an indispensable source of food for mankind in tropical and subtropical countries for centuries. The aim of this study is to differentiate date palm tree varieties by analysing leaflet cross sections with technical/optical methods and artificial neural networks (ANN).
Results
Fluorescence microscopy images of leaflet cross sections have been taken from a set of five date palm tree cultivars (Hewlat al Jouf, Khlas, Nabot Soltan, Shishi, Um Raheem). After features extraction from images, the obtained data have been fed in a multilayer perceptron ANN with backpropagation learning algorithm.
Conclusions
Overall, an accurate result in prediction and differentiation of date palm tree cultivars was achieved with average prediction in tenfold cross-validation is 89.1% and reached 100% in one of the best ANN.
doi:10.1186/1471-2105-15-55
PMCID: PMC3941935  PMID: 24564551
Artificial neural network; Backpropagation algorithm; Fluorescence microscopy; Cultivars; Date palm leaf; Vascular bundles; Phenotyping
2.  Effects of spermine NONOate and ATP on protein aggregation: light scattering evidences 
BMC Biophysics  2013;6:1.
Background and objective
Regulating protein function in the cell by small molecules, provide a rapid, reversible and tunable tool of metabolic control. However, due to its complexity the issue is poorly studied so far. The effects of small solutes on protein behavior can be studied by examining changes of protein secondary structure, in its hydrodynamic radius as well as its thermal aggregation. The study aim was to investigate effects of adenosine-5’-triphosphate (ATP), spermine NONOate (NO donor) as well as sodium/potassium ions on thermal aggregation of albumin and hemoglobin. To follow aggregation of the proteins, their diffusion coefficients were measured by quasi-elastic light scattering (QELS) at constant pH (7.4) in the presence of solutes over a temperature range from 25°C to 80°C.
Results and discussion
1) Spermine NONOate persistently decreased the hemoglobin aggregation temperature Tairrespectively of the Na+/K+ environment, 2) ATP alone had no effect on the protein’s thermal stability but it facilitated protein’s destabilization in the presence of spermine NONOate and 3) mutual effects of ATP and NO were strongly influenced by particular buffer ionic compositions.
Conclusion
The ATP effect on protein aggregation was ambiguous: ATP alone had no effect on the protein’s thermal stability but it facilitated protein’s destabilization in the presence of nitric oxide. The magnitude and direction of the observed effects strongly depended on concentrations of K+ and Na+ in the solution.
doi:10.1186/2046-1682-6-1
PMCID: PMC3561150  PMID: 23289636
3.  Effects of spermine NONOate and ATP on the thermal stability of hemoglobin 
BMC Biophysics  2012;5:16.
Background
Minor changes in protein structure induced by small organic and inorganic molecules can result in significant metabolic effects. The effects can be even more profound if the molecular players are chemically active and present in the cell in considerable amounts. The aim of our study was to investigate effects of a nitric oxide donor (spermine NONOate), ATP and sodium/potassium environment on the dynamics of thermal unfolding of human hemoglobin (Hb). The effect of these molecules was examined by means of circular dichroism spectrometry (CD) in the temperature range between 25°C and 70°C. The alpha-helical content of buffered hemoglobin samples (0.1 mg/ml) was estimated via ellipticity change measurements at a heating rate of 1°C/min.
Results
Major results were: 1) spermine NONOate persistently decreased the hemoglobin unfolding temperature Tuirrespectively of the Na + /K + environment, 2) ATP instead increased the unfolding temperature by 3°C in both sodium-based and potassium-based buffers and 3) mutual effects of ATP and NO were strongly influenced by particular buffer ionic compositions. Moreover, the presence of potassium facilitated a partial unfolding of alpha-helical structures even at room temperature.
Conclusion
The obtained data might shed more light on molecular mechanisms and biophysics involved in the regulation of protein activity by small solutes in the cell.
doi:10.1186/2046-1682-5-16
PMCID: PMC3443461  PMID: 22929146
4.  Fluid Shear Attenuates Endothelial Pseudopodia Formation into the Capillary Lumen 
Objective
Endothelial cells have the ability to undergo morphological shape changes, including projection of cytoplasmic pseudopodia into the capillary lumen. These cytoplasmic projections significantly influence the hemodynamic resistance to blood flow. To examine mechanotransduction mechanisms, we investigated in vivo the hemodynamic conditions in capillaries that control endothelial pseudopod formation.
Materials and Methods
Capillaries in rat skeletal muscle were fixed under carefully controlled perfusion conditions. The formation of endothelial pseudopodia were observed in cross-sections with electron microscopy and quantified with differential interference contrast microscopy under physiological, stasis, and reperfusion flow conditions.
Results
Application of physiological levels of fluid flow prevents capillary endothelium to project pseudopodia into the capillary lumen. Reduction of fluid flow to near zero promotes the incidence of pseudopod projection from 5% to 55% of capillaries. After capillary pseudopodia have formed under static conditions, about one-half retract upon restoration of fluid flow. The presence of red blood cells in the capillary lumen prevents pseudopod formation.
Conclusions
The results suggest that there is a mechanism that serves to control cytoplasmic projections in capillary endothelium that is under the control of hemodynamic fluid stress. Investigation of pseudopodia growth on endothelial cells may be significant in understanding capillary obstruction in cardiovascular diseases.
doi:10.1080/10739680801904174
PMCID: PMC2671553  PMID: 19086262
skeletal muscle; gracilis muscle; microcirculation; actin polymerization; rat; endothelium; pseudopod formation; cytoskeleton

Results 1-4 (4)