Effect of Iranian strains of Pseudomonas spp. on the control of root-knot nematodes on Pistachios

The role of some Iranian strains of Pseudomonas spp. as biocontrol agents against Meloidogyne incognita and their ability to colonise pistachio roots was investigated. The results of in vitro experiments indicated that all tested bacteria produced significant suppression of M. incognita and showed that all strains were able to kill M. incognita juveniles with strain VUPf428 achieving about 99% mortality at 72 h. The results of in vivo treatments indicated that the best strains that could build high populations in soil infested with nematodes were VUPf5, VUPf52 and VUPf205. These isolates also caused highest reduction in galling and nematode multiplication in a greenhouse test although all strains native to Iran could colonise pistachio roots in pots. Some strains could produce secondary metabolites such as siderophores, proteases and volatile metabolites at high population levels.     

Endothelium Expression of Bcl-2 Is Essential for Normal and Pathological Ocular Vascularization

Bcl–2 is an anti-apoptotic protein with important roles in vascular homeostasis and angiogenesis. Mice globally lacking Bcl–2 (Bcl–2 -/-) are small in stature and succumb to renal failure shortly after weaning as a result of renal hypoplasia/cystic dysplasia. We have shown that Bcl–2 -/- mice displayed attenuated retinal vascular development and neovascularization. In vitro studies indicated that in addition to modulating apoptosis, Bcl–2 expression also impacts endothelial and epithelial cell adhesion, migration and extracellular matrix production. However, studies delineating the cell autonomous role Bcl–2 expression plays in the endothelium during vascular development, pruning and remodeling, and neovascularization are lacking. Here we generated mice carrying a conditional Bcl–2 allele (Bcl-2^Flox/Flox) and VE-cadherin-cre (Bcl-2^EC mice). Bcl-2^EC mice were of normal stature and lifespan and displayed some but not all of the retinal vascular defects previously observed in global Bcl–2 deficient mice. Bcl-2^EC mice had decreased numbers of endothelial cells, decreased retinal arteries and premature primary branching of the retinal vasculature, but unlike the global knockout mice, spreading of the retinal superficial vascular layer proceeded normally. Choroidal neovascularization was attenuated in Bcl-2^EC mice, although retinal neovascularization accompanying oxygen-induced ischemic retinopathy was not. Thus, Bcl–2 expression in the endothelium plays a significant role during postnatal retinal vascularization, and pathological choroidal but not retinal neovascularization, suggesting vascular bed specific Bcl–2 function in the endothelium.     

Selective high throughput protein quantification based on UV absorption spectra

The application of high throughput experimentation (HTE) in protein purification process development has created an analytical bottleneck. Recently, a new label‐free and non‐invasive methodology for analyzing multicomponent protein mixtures by means of spectral measurements was presented. Analytics based on the methodology was shown to increase analytical throughput for selective protein quantification significantly, however this was only demonstrated for one particular protein combination. In this work, the possibilities and limitations of the analytical method are investigated further. Principal component analysis (PCA) was performed on a broad range of absorption spectra to investigate their common characteristics and differences. The PCA was used both for cluster analysis and to define a measure for spectral similarity. For binary protein combinations, the calibration precision was shown to decrease exponentially with the defined spectral similarity factor. Knowledge of this correlation can be used to determine a priori whether a calibration will be successful or not. Calibration robustness was investigated by applying the analytics to liquid chromatography performed in HTE mode. Further it was shown, that a spectral difference of 0.6% was sufficient to sucessfully preform a spectral based calibration of two IgG1 monoclonals. Biotechnol. Bioeng. 2013; 110: 448–460. © 2012 Wiley Periodicals, Inc.     

Kinetics of anti-CD4-induced T helper cell depletion and inhibition of function. Activation of T cells by the CD3 pathway inhibits anti-CD4-mediated T cell elimination and down-regulation of cell surface CD4.

In vivo treatment with anti-CD4 antibody profoundly suppresses a number of T cell-dependent responses and is clinically useful in the treatment of certain mouse models of autoimmune disease. Treatment with anti-CD4 antibody will inactivate and can deplete CD4 T cells, but the mechanisms responsible for these effects are incompletely understood. When mouse spleen cells were exposed in vitro to both SRBC and monoclonal anti-CD4, there was 55% reduction of the anti-SRBC response. If cultures were preincubated with anti-CD4 for 48 h before in vitro challenge, the reduction was greater than 80%. When unfractionated spleen cells were cultured with anti-CD4 for 96 h, there was actual elimination of CD4 cells in these cultures since virtually all CD3+ cells were CD8+. Activation of T cells by exposure to anti-CD3 rendered them resistant to antibody-mediated CD4 depletion. This resistance to CD4 depletion was seen even in cultures that were pretreated with anti-CD4 for as long as 24 h before anti-CD3 exposure. In cultures of purified T cells, anti-CD4 did not eliminate CD4 T cells. However, culture of T cells with macrophage-rich adherent cells and anti-CD4 resulted in elimination of CD4 T cells. Thus, it appears that macrophages play a role in anti-CD4-induced T cell elimination. While anti-CD4 did not eliminate CD4 cells from a population of purified T cells, there was profound down-regulation of cell surface CD4. Activating T cells with immobilized anti-CD3 before addition of anti-CD4 prevented down-regulation of CD4. These experiments demonstrate that T cell activation by anti-CD3 renders the activated cells resistant to antibody-induced CD4 down-regulation and to antibody-induced CD4 T cell depletion. These findings may have relevance to the application of anti-CD4 therapy in human diseases that are mediated by activated Th cells.     

The Combined Effect of Hydrophobic Mismatch and Bilayer Local Bending on the Regulation of Mechanosensitive Ion Channels

The hydrophobic mismatch between the lipid bilayer and integral membrane proteins has well-defined effect on mechanosensitive (MS) ion channels. Also, membrane local bending is suggested to modulate MS channel activity. Although a number of studies have already shown the significance of each individual factor, the combined effect of these physical factors on MS channel activity have not been investigated. Here using finite element simulation, we study the combined effect of hydrophobic mismatch and local bending on the archetypal mechanosensitive channel MscL. First we show how the local curvature direction impacts on MS channel modulation. In the case of MscL, we show inward (cytoplasmic) bending can more effectively gate the channel compared to outward bending. Then we indicate that in response to a specific local curvature, MscL inserted in a bilayer with the same hydrophobic length is more expanded in the constriction pore region compared to when there is a protein-lipid hydrophobic mismatch. Interestingly in the presence of a negative mismatch (thicker lipids), MscL constriction pore is more expanded than in the presence of positive mismatch (thinner lipids) in response to an identical membrane curvature. These results were confirmed by a parametric energetic calculation provided for MscL gating. These findings have several biophysical consequences for understanding the function of MS channels in response to two major physical stimuli in mechanobiology, namely hydrophobic mismatch and local membrane curvature.     

Association of Environmental Toxic Elements in Biological Samples of Myocardial Infarction Patients at Different Stages

The exposure of toxic elements may directly or indirectly associate with different pathogenesis of heart diseases. In the present study, the association of arsenic (As), cadmium (Cd), cobalt (Co), lead (Pb), and nickel (Ni) in biological samples (whole blood and urine) and mortality from myocardial infarction (MI) patients at first, second, and third heart attacks was carried out. Both biological samples of 130 MI patients (77 male and 53 female), with ages ranging from 45 to 60?years, and 61 healthy persons (33 male and 28 female) of the same age group were collected. The elements in biological samples were assessed by electrothermal atomic absorption spectrophotometer, prior to microwave-assisted acid digestion. The validity of methodology was checked by the biological certified reference materials. During this study, 78% of 32 patients aged above 50?years, registered after third MI attack, died. In these subjects, the levels of As, Cd, Co, Ni, and Pb in blood samples were higher in MI patients as compared with referents (p?<?0.05), while increased by 11.7%, 12.2%, 5.55%, and 7.2%, respectively, in the blood samples of those patients who tolerated the third MI attack (p?=?0.12). The high level of understudied toxic elements may play a role in the mortality of MI patients.     

Status of Toxic Metals in Biological Samples of Diabetic Mothers and Their Neonates

The mechanism of transport of trace elements from the mother to the newborn is still not well known. The aim of present study was to compare the status of trace toxic elements, arsenic (As), cadmium (Cd), and lead (Pb) in biological samples (whole blood, urine and scalp hair) of insulin-dependent diabetic mothers (age ranged 30-40) and their newly born infants (n = 76). An age and socioeconomics matched 68 nondiabetic mothers and their infants, residing in the same locality, who were selected as referents. The elemental concentrations in all three biological samples were determined by an electrothermal atomic absorption spectrometer, prior to microwave-assisted acid digestion. The mean values of As, Cd, and Pb in all biological samples of diabetic mothers and their infants were significantly higher as compared to the referent mother-infant pair samples (p < 0.01). The high levels of As, Cd, and Pb in biological samples of diabetic women may play a role in the pathogenesis of diabetes mellitus and impacts on their neonates.     

Accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion

Diffusion plays a key role in many biochemical reaction systems seen in nature. Scenarios where diffusion behavior is critical can be seen in the cell and subcellular compartments where molecular crowding limits the interaction between particles. We investigate the application of a computational method for modeling the diffusion of molecules and macromolecules in three-dimensional solutions using agent based modeling. This method allows for realistic modeling of a system of particles with different properties such as size, diffusion coefficients, and affinity as well as the environment properties such as viscosity and geometry. Simulations using these movement probabilities yield behavior that mimics natural diffusion. Using this modeling framework, we simulate the effects of molecular crowding on effective diffusion and have validated the results of our model using Langevin dynamics simulations and note that they are in good agreement with previous experimental data. Furthermore, we investigate an extension of this framework where single discrete cells can contain multiple particles of varying size in an effort to highlight errors that can arise from discretization that lead to the unnatural behavior of particles undergoing diffusion. Subsequently, we explore various algorithms that differ in how they handle the movement of multiple particles per cell and suggest an algorithm that properly accommodates multiple particles of various sizes per cell that can replicate the natural behavior of these particles diffusing. Finally, we use the present modeling framework to investigate the effect of structural geometry on the directionality of diffusion in the cell cytoskeleton with the observation that parallel orientation in the structural geometry of actin filaments of filopodia and the branched structure of lamellipodia can give directionality to diffusion at the filopodia-lamellipodia interface.