Hydrolysis by phospholipase D of phospholipids in solution state or adsorbed on a silica matrix

Phospholipases D (PLD) catalyse hydrolysis and transphosphatidylation reactions in phospholipids. In the present study, the hydrolytic activity for cabbage PLD was investigated with five different substrates (dipalmitoylphosphatidylethanolamine (DPPE), dipalmitoylphosphatidylcholine (DPPC), didecanoylphosphatidylcholine (DDPC), 1-alkyl-2-acetyl-sn-glycero-3-phosphocholine and lyso-phosphatidylcholine (lyso-PC)) in solution or adsorbed on a silica matrix. In the specific buffer solutions, where the substrates were proved to form large multilamellar polydisperse aggregates, PLD showed preference for DPPC > DPPE > DDPC > 1-alkyl-2-acetyl-sn-glycero-3-phosphocholine > lyso-PC. When the substrates were adsorbed on the silica matrix, PLD hydrolysed 1-alkyl-2-acetyl-sn-glycero-3-phosphocholine and lyso-PC, DDPC, but not DPPC or DPPE. Theoretical studies of the simplest possible adducts between the phospholipids and the silica matrix were performed. Examination of local geometries of DPPC showed a significant blocking of the P-O-X bond-prone to hydrolysis, which could possibly block the access of PLD. Immobilization of phospholipids could be applied for improving the yield of reactions catalysed by PLD as well as for performing a targeted production of short-chain length phosphatidic acid analogs.     

The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase

Trypanosomatids contain an unusual DNA base J (beta-d-glucosylhydroxymethyluracil), which replaces a fraction of thymine in telomeric and other DNA repeats. To determine the function of base J, we have searched for enzymes that catalyze J biosynthesis. We present evidence that a protein that binds to J in DNA, the J-binding protein 1 (JBP1), may also catalyze the first step in J biosynthesis, the conversion of thymine in DNA into hydroxymethyluracil. We show that JBP1 belongs to the family of Fe(2+) and 2-oxoglutarate-dependent dioxygenases and that replacement of conserved residues putatively involved in Fe(2+) and 2-oxoglutarate-binding inactivates the ability of JBP1 to contribute to J synthesis without affecting its ability to bind to J-DNA. We propose that JBP1 is a thymidine hydroxylase responsible for the local amplification of J inserted by JBP2, another putative thymidine hydroxylase.     

Tyrosine protein kinase activity of the EGF receptor is required to induce activation of receptor-operated calcium channels

We have investigated the effects of epidermal growth factor (EGF) on calcium ion channels in A431 epidermoid carcinoma cells. We have found that: -1- EGF stimulates Ca2+ channels. -2- EGF stimulated Ca2+ channels are voltage independent, exhibit a low conductance (8 pS) and a bursting multichannels activity (BMC). -3- Activation of the tyrosine-kinase function of the EGF receptor is required to generate Ca2+ current. -4- Inositol (1,4,5) triphosphate (Ins (1,4,5) P3) and EGF have similar effect on the channel activation. These results suggest that: stimulation of tyrosine-kinase activity of the EGF receptor, production of Ins (1,4,5)P3 and calcium entry via voltage independent channels are important connected steps in mediating the mitogenic effect of this growth factor.     

Protein loop modeling by using fragment assembly and analytical loop closure

Protein loops are often involved in important biological functions such as molecular recognition, signal transduction, or enzymatic action. The three dimensional structures of loops can provide essential information for understanding molecular mechanisms behind protein functions. In this article, we develop a novel method for protein loop modeling, where the loop conformations are generated by fragment assembly and analytical loop closure. The fragment assembly method reduces the conformational space drastically, and the analytical loop closure method finds the geometrically consistent loop conformations efficiently. We also derive an analytic formula for the gradient of any analytical function of dihedral angles in the space of closed loops. The gradient can be used to optimize various restraints derived from experiments or databases, for example restraints for preferential interactions between specific residues or for preferred backbone angles. We demonstrate that the current loop modeling method outperforms previous methods that employ residue‐based torsion angle maps or different loop closure strategies when tested on two sets of loop targets of lengths ranging from 4 to 12. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Acetic Acid, Ethanol and Steam Effects on the Growth of Botrytis cinerea in vitro and Combination of Steam and Modified Atmosphere Packaging to Control Decay in Kiwifruit

The effects of acetic acid fumigation, ethanol fumigation, and steam heat treatment on growth of Botrytis cinerea in vitro were investigated. The effect of steam heat treatments in combination with modified atmosphere packaging (MAP) on Botrytis decay development on 'Hayward' kiwifruit was also studied. The fungus was grown in Petri dishes on potato dextrose agar. Ethanol fumigation with 100  μ l/l for 3 or 6 min, or 200  μ l/l for 6 min enhanced the growth of B. cinerea . The effect of acetic acid on growth of B. cinerea was time and dosage-dependent. Fumigation with 1  μ l/l for 6 min, 2  μ l/l for 3 min, and 4  μ l/l for 3 min promoted radial growth of the fungus when compared to the growth of the untreated control. Fumigation with 2  μ l/l for 6 min delayed the growth of the fungus for the first 6 days, while fumigation with 6  μ l/l for 3 min delayed the growth of the fungus after the sixth day. Fumigation with 4 or 6  μ l/l acetic acid for 6 min, and 8  μ l/l acetic acid for 3 or 6 min resulted in complete inhibition of fungal growth. Steam heat treatment at 45°C for 6 min, and at 48, 51, and 54°C for 3 or 6 min completely inhibited fungal growth in vitro . Furthermore, steam treatments at 47, 50, and 53°C for 3 or 6 min completely inhibited decay at the stem end of kiwifruit kept at 10°C in MAP for 12 days. However, none of the steam treatments inhibited decay in wounds on the surface of the fruit kept in MAP.     

Digoxin Suppresses Pyruvate Kinase M2-Promoted HIF-1α Transactivation in Steatohepatitis

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Proteomics reveals that redox regulation is disrupted in patients with ethylmalonic encephalopathy

Deficiency of the sulfide metabolizing protein ETHE1 is the cause of ethylmalonic encephalopathy (EE), an inherited and severe metabolic disorder. To study the molecular effects of EE, we performed a proteomics study on mitochondria from cultured patient fibroblast cells. Samples from six patients were analyzed and revealed seven differentially regulated proteins compared with healthy controls. Two proteins involved in pathways of detoxification and oxidative/reductive stress were underrepresented in EE patient samples: mitochondrial superoxide dismutase (SOD2) and aldehyde dehydrogenase X (ALDH1B). Sulfide:quinone oxidoreductase (SQRDL), which takes part in the same sulfide pathway as ETHE1, was also underrepresented in EE patients. The other differentially regulated proteins were apoptosis inducing factor (AIFM1), lactate dehydrogenase (LDHB), chloride intracellular channel (CLIC4) and dimethylarginine dimethylaminohydrolase 1 (DDAH1). These proteins have been reported to be involved in encephalopathy, energy metabolism, ion transport, and nitric oxide regulation, respectively. Interestingly, oxidoreductase activity was overrepresented among the regulated proteins indicating that redox perturbation plays an important role in the molecular mechanism of EE. This observation may explain the wide range of symptoms associated with the disease, and highlights the potency of the novel gaseous mediator sulfide.     

N-6 polyunsaturated fatty acids confer hemodynamic stability in an experimental model of multiple trauma

Immunonutrition with diets enriched in polyunsaturated fatty acids (PUFAs) are becoming mandatory for multiple trauma patients. Solutions containing single n-6 PUFAs were administered intravenously in an experimental model of trauma. Thirty-five rabbits were studied; 13 controls; 10 administered gamma-linolenic acid (GLA) 30 min after fracture of the right femor; and 12 arachidonic acid (AA). Systolic, diastolic and mean arterial pressures and heart rate were recorded; serum levels of tumor necrosis factor-alpha (TNFalpha), malondialdehyde (MDA) and nitrate were estimated before and after therapy. Mean survival of controls, of animals treated with GLA and of animals treated with AA was 0.80, 1.41 and 3.60 days, respectively. Administration of PUFAs induced higher levels of blood pressure; that of AA decreased serum TNFalpha and tissue bacterial load compared to controls. Intravenous administration of n-6 PUFAs conferred hemodynamic stability and increased survival in a model of trauma rendering further research mandatory.     

In situ cooling in a lung hilar clamping model of ischemia-reperfusion injury

Experimental models for studying transplantation have up to now been unable to isolate reperfusion injury with minimal surgical manipulation and without the interference of graft rejection. Six pigs were subjected to left hilum preparation only (control group), and eight pigs were subjected to left hilum preparation plus in situ cooling ischemia and reperfusion of the lung (experimental group). The hilum was dissected free from other tissues in both groups. Lung preservation was achieved by antegrade flush perfusion via the left pulmonary artery. Pulmonary veins were clamped at the left atrium and a vent was created. The left main bronchus was clamped. Lung temperature was maintained at 4 degrees -8 degrees C, while core temperature was kept at 38 degrees C. After 3 hrs of cold ischemia the clamps were removed and the lung was reperfused. Elevated pulmonary vascular resistance and local and systemic aspects of ischemia-reperfusion syndrome were consistently reproduced. This large-animal model of in situ unilateral lung cold ischemia with warm reperfusion proved to be very reliable in reproducing all aspects of ischemia-reperfusion injury. It excludes the interference of rejection and extensive surgical manipulation. We therefore propose its use in experimental studies investigating pharmaceutical or cooling modifications affecting lung ischemia-reperfusion outcomes.