Mesophyll versus epidermal anthocyanins as potential in vivo antioxidants: evidence linking the putative antioxidant role to the proximity of oxy-radical source

The hypothesis that anthocyanins in red leaves may be potential in vivo antioxidants whose efficiency is linked to their proximity with the oxy-radical source was tested. Advantage was taken of intra-individual and intra-species variations in the anthocyanic trait and green and red leaves on the same individuals or leaves of green and red phenotypes were compared for the extent of PSII damage by reactive oxygen species generated by methyl viologen treatment in the light. Two species possessing anthocyanins in the mesophyll (Cistus creticus and Photinia x fraseri) and two in the epidermis (Rosa sp. and Ricinus communis) were used, while red actinic light (which is not absorbed by anthocyanins) allowed discrimination between an indirect sunscreen and a direct antioxidant function. Red leaves whose anthocyanins were located in the mesophyll were more resistant to methyl viologen treatment than their green counterparts. In one of these species (Cistus creticus), where anthocyanins are induced in some individuals within the natural population after bright cool days in winter, both green and future-red morphs displayed the same sensitivity to methyl viologen before anthocyanin induction. Immediately after reddening, however, resistance to methyl viologen was considerably increased in the red morphs. By contrast, red leaves whose anthocyanins were restricted to epidermal cells were more sensitive to the herbicide. Total leaf phenolic levels in green/red pairs were similar. The results indicate that vacuolar anthocyanins may be an effective in vivo target for oxy-radicals, provided that the oxy-radical source and the anthocyanic detoxifying sink are in close vicinity.     

Crystal structure, spectroscopic, and biological study of the copper(II) complex with third-generation quinolone antibiotic sparfloxacin

The neutral mononuclear copper(II) complex with the quinolone antibacterial drug sparfloxacin has been prepared and characterized with IR, UV-vis, and EPR spectroscopies and X-ray crystallography. The interaction of the complex with calf-thymus DNA has also been investigated and the antimicrobial activity has been evaluated against three different microorganisms.     

Bioactivity of glycogen phosphorylase inhibitors that bind to the purine nucleoside site

The bioactivity in hepatocytes of glycogen phosphorylase inhibitors that bind to the active site, the allosteric activator site and the indole carboxamide site has been described. However, the pharmacological potential of the purine nucleoside inhibitor site has remained unexplored. We report the chemical synthesis and bioactivity in hepatocytes of four new olefin derivatives of flavopiridol (1-4) that bind to the purine site. Flavopiridol and 1-4 counteracted the activation of phosphorylase in hepatocytes caused by AICAR (5-aminoimidazole-4-carboxamide 1-beta-D-ribofuranoside), which is metabolised to an AMP analogue. Unlike an indole carboxamide inhibitor, the analogues 1 and 4 suppressed the basal rate of glycogenolysis in hepatocytes by allosteric inhibition rather than by inactivation of phosphorylase, and accordingly caused negligible stimulation of glycogen synthesis. However, they counteracted the stimulation of glycogenolysis by dibutyryl cAMP by both allosteric inhibition and inactivation of phosphorylase. Cumulatively, the results show key differences between purine site and indole carboxamide site inhibitors in terms of (i) relative roles of dephosphorylation of phosphorylase-a as compared with allosteric inhibition, (ii) counteraction of the efficacy of the inhibitors on glycogenolysis by dibutyryl-cAMP and (iii) stimulation of glycogen synthesis.     

Gene regulatory networks from multifactorial perturbations using Graphical Lasso: application to the DREAM4 challenge

A major challenge in the field of systems biology consists of predicting gene regulatory networks based on different training data. Within the DREAM4 initiative, we took part in the multifactorial sub-challenge that aimed to predict gene regulatory networks of size 100 from training data consisting of steady-state levels obtained after applying multifactorial perturbations to the original in silico network. Due to the static character of the challenge data, we tackled the problem via a sparse Gaussian Markov Random Field, which relates network topology with the covariance inverse generated by the gene measurements. As for the computations, we used the Graphical Lasso algorithm which provided a large range of candidate network topologies. The main task was to select the optimal network topology and for that, different model selection criteria were explored. The selected networks were compared with the golden standards and the results ranked using the scoring metrics applied in the challenge, giving a better insight in our submission and the way to improve it.Our approach provides an easy statistical and computational framework to infer gene regulatory networks that is suitable for large networks, even if the number of the observations (perturbations) is greater than the number of variables (genes).     

Calcium diffusion coefficient in rod photoreceptor outer segments.

Calcium (Ca(2+)) modulates several of the enzymatic pathways that mediate phototransduction in the outer segments of vertebrate rod photoreceptors. Ca(2+) enters the rod outer segment through cationic channels kept open by cyclic GMP (cGMP) and is pumped out by a Na(+)/Ca(2+),K(+) exchanger. Light initiates a biochemical cascade, which leads to closure of the cGMP-gated channels, and a concomitant decline in the concentration of Ca(2+). This decline mediates the recovery from stimulation by light and underlies the adaptation of the cell to background light. The speed with which the decline in the Ca(2+) concentration propagates through the rod outer segment depends on the Ca(2+) diffusion coefficient. We have used the fluorescent Ca(2+) indicator fluo-3 and confocal microscopy to measure the profile of the Ca(2+) concentration after stimulation of the rod photoreceptor by light. From these measurements, we have obtained a value of 15 +/- 1 microm(2)s(-1) for the radial Ca(2+) diffusion coefficient. This value is consistent with the effect of a low-affinity, immobile buffer reported to be present in the rod outer segment (L.Lagnado, L. Cervetto, and P.A. McNaughton, 1992, J. Physiol. 455:111-142) and with a buffering capacity of approximately 20 for rods in darkness(S. Nikonov, N. Engheta, and E.N. Pugh, Jr., 1998, J. Gen. Physiol. 111:7-37). This value suggests that diffusion provides a significant delay for the radial propagation of the decline in the concentration of Ca(2+). Also, because of baffling by the disks, the longitudinal Ca(2+) diffusion coefficient will be in the order of 2 microm(2)s(-1), which is much smaller than the longitudinal cGMP diffusion coefficient (30-60 microm(2)s(-1); ). Therefore, the longitudinal decline of Ca(2+) lags behind the longitudinal spread of excitation by cGMP.     

Efforts to Explain and Control the Prolonged Thermophilic Period in Two-phase Olive Oil Mill Sludge Composting

The aim of this paper was to evaluate the use of different bulking agents in different ratios as a means to control, optimise and eventually reduce the duration of the thermophilic period in two-phase olive oil mill sludge (OOMS) composting. The bulking agents used were: (i) olive tree leaves (OTL), (ii) olive tree shredded branches (OTB) and (iii) woodchips (WDC). The selection of these materials was based on their abundance and availability on the island of Crete, the southernmost point of Greece. The ratios studied were: Pile 1, OOMS:OTL in 1:1 v/v; Pile 2, OOMS:WDC in 1:1.5 v/v; Pile 3, OOMS:OTL in 1:2 v/v; Pile 4, OOMS:OTL:OTB in 1:1:1 v/v; and Pile 5, OOMS:OTL:OTB in 1:1:2 v/v. The composting system used was that of windrows with the volume of each pile approximately 20–25 m³. The experiments took place over two consecutive years. A composting turner was used and turnings were performed at one and two week intervals. In each pile a variety of physiochemical parameters were monitored. Temperature remained high in all five trials. Piles 1, 2, 3, 4 and 5 temperatures recorded values of above 50 °C for 106, 158, 160, 175 and 183 days, respectively. Volumes were reduced by approximately 67%, 62%, 63%, 80% and 84%, respectively. Temperature remained high, mainly due to the presence in large amounts of oily substances which during their complete oxidation release important amounts of energy and aid the cometabolism of more stable molecules such as lignin. This process is better described as the slow “burning” of a “fuel” mixture in an “engine” than composting. This approach is based on the extensive similarities of this process to that of crude oil sludge or similar waste composting.     

Evidence of increased muscle atrophy and impaired quality of life parameters in patients with uremic restless legs syndrome

Background

Restless Legs Syndrome is a very common disorder in hemodialysis patients. Restless Legs Syndrome negatively affects quality of life; however it is not clear whether this is due to mental or physical parameters and whether an association exists between the syndrome and parameters affecting survival.

Methodοlogy/Principal Findings

Using the Restless Legs Syndrome criteria and the presence of Periodic Limb Movements in Sleep (PLMS/h >15), 70 clinically stable hemodialysis patients were assessed and divided into the RLS (n = 30) and non-RLS (n = 40) groups. Physical performance was evaluated by a battery of tests: body composition by dual energy X ray absorptiometry, muscle size and composition by computer tomography, while depression symptoms, perception of sleep quality and quality of life were assessed through validated questionnaires. In this cross sectional analysis, the RLS group showed evidence of thigh muscle atrophy compared to the non-RLS group. Sleep quality and depression score were found to be significantly impaired in the RLS group. The mental component of the quality of life questionnaire appeared significantly diminished in the RLS group, reducing thus the overall quality of life score. In contrast, there were no significant differences between groups in any of the physical performance tests, body and muscle composition.

Conclusions

The low level of quality of life reported by the HD patients with Restless Legs Syndrome seems to be due mainly to mental health and sleep related aspects. Increased evidence of muscle atrophy is also observed in the RLS group and possibly can be attributed to the lack of restorative sleep.     

Stochastic simulations of the tetracycline operon

Background  

The tetracycline operon is a self-regulated system. It is found naturally in bacteria where it confers resistance to antibiotic tetracycline. Because of the performance of the molecular elements of the tetracycline operon, these elements are widely used as parts of synthetic gene networks where the protein production can be efficiently turned on and off in response to the presence or the absence of tetracycline. In this paper, we investigate the dynamics of the tetracycline operon. To this end, we develop a mathematical model guided by experimental findings. Our model consists of biochemical reactions that capture the biomolecular interactions of this intriguing system. Having in mind that small biological systems are subjects to stochasticity, we use a stochastic algorithm to simulate the tetracycline operon behavior. A sensitivity analysis of two critical parameters embodied this system is also performed providing a useful understanding of the function of this system.     

Molecular dynamics investigation of the influence of anionic and zwitterionic interfaces on antimicrobial peptides' structure: implications for peptide toxicity and activity

Molecular dynamics simulations of three related helical antimicrobial peptides have been carried out in zwitterionic diphosphocholine (DPC) micelles and anionic sodiumdodecylsulfate (SDS) micelles. These systems can be considered as model mammalian and bacterial membrane interfaces, respectively. The goal of this study is to dissect the differences in peptide composition which make the mutant peptides (novispirin-G10 and novispirin-T7) less toxic than the parent peptide ovispirin (OVIS), although all three peptides have highly antibacterial properties. Compared to G10 and T7, OVIS inserts deepest into the DPC micelle. This correlates well with the lesser toxicity of G10 and T7. There is strong evidence which suggests that synergistic binding of hydrophobic residues drives binding of OVIS to the micelle. The helical content of G10 and T7 is reduced in the presence of DPC, and this leads to less amphipathic peptide structures, which bind weakly to the micelle. Simulations in SDS were carried out to compare the influence of membrane electrostatics on peptide structure. All three peptides bound strongly to SDS, and retained helical form. This corresponds well with their equally potent antibacterial properties. Based on the simulations, we argue that secondary structure stability often leads to toxic properties. We also propose that G10 and T7 operate by the carpet mechanism of cell lysis. Toxicity of peptides operating by the carpet mechanism can be attenuated by reducing the peptide helical content. The simulations successfully capture experimental binding states, and the different depths of binding of the three peptides to the two micelles correlate with their antibacterial and toxic properties.