Dasty3, a WEB framework for DAS

MOTIVATION: Dasty3 is a highly interactive and extensible Web-based framework. It provides a rich Application Programming Interface upon which it is possible to develop specialized clients capable of retrieving information from DAS sources as well as from data providers not using the DAS protocol. Dasty3 provides significant improvements on previous Web-based frameworks and is implemented using the 1.6 DAS specification. AVAILABILITY: Dasty3 is an open-source tool freely available at http://www.ebi.ac.uk/dasty/ under the terms of the GNU General public license. Source and documentation can be found at http://code.google.com/p/dasty/. CONTACT: hhe@ebi.ac.uk.     

Ochratoxin A and aflatoxins in dried vine fruits from the Iranian market

Forty samples of dried vine fruit (raisin, n?=?22; currant, n?=?18) were collected in 2009?C2011 from the Iranian market. Aflatoxins (AFs) and ochratoxin A (OTA) were determined in these samples after immunoaffinity column clean-up by high performance liquid chromatography (HPLC) with fluorescence detection. The limit of quantification (LOQ) for AFs B₁. B₂, G₁, G₂, and OTA were 0.62, 0.50, 0.70, 0.40, and 0.42?ng/g, respectively. AFB₁ was found in one sample of raisin (0.64?ng/g) and in two samples of currant (0.20 and 0.63?ng/g). AFB₂ (0.33?ng/g) and AFG₂ (0.49?ng/g) were found in 2 samples of currant. OTA was detected in 3 of the 22 samples of raisin (mean 2.21?ng/g) and in one sample of currant (2.99?ng/g). The results show that in AFs and OTA levels are well below the regulatory limits both of the European Union and of Iran.     

Biochemical and Functional Analysis of Two Plasmodium falciparum Blood-Stage 6-Cys Proteins: P12 and P41

The genomes of Plasmodium parasites that cause malaria in humans, other primates, birds, and rodents all encode multiple 6-cys proteins. Distinct 6-cys protein family members reside on the surface at each extracellular life cycle stage and those on the surface of liver infective and sexual stages have been shown to play important roles in hepatocyte growth and fertilization respectively. However, 6-cys proteins associated with the blood-stage forms of the parasite have no known function. Here we investigate the biochemical nature and function of two blood-stage 6-cys proteins in Plasmodium falciparum, the most pathogenic species to afflict humans. We show that native P12 and P41 form a stable heterodimer on the infective merozoite surface and are secreted following invasion, but could find no evidence that this complex mediates erythrocyte-receptor binding. That P12 and P41 do not appear to have a major role as adhesins to erythrocyte receptors was supported by the observation that antisera to these proteins did not substantially inhibit erythrocyte invasion. To investigate other functional roles for these proteins their genes were successfully disrupted in P. falciparum, however P12 and P41 knockout parasites grew at normal rates in vitro and displayed no other obvious phenotypic changes. It now appears likely that these blood-stage 6-cys proteins operate as a pair and play redundant roles either in erythrocyte invasion or in host-immune interactions.     

Optical protein sensor for detecting cancer markers in saliva

A surface immobilized optical protein sensor has been utilized to detect Interleukin-8 (IL-8) protein, an oral cancer marker, and can reach limit of detection (LOD) at 1.1pM in buffer without using enzymatic amplification. Only after applying enzymatic amplification to increase the signal level by a few orders of magnitude, ELISA can reach the LOD of 1pM level. We then develop the confocal optics based sensor for further reducing the optical noise and can extend the LOD of the surface immobilized optical protein sensor two orders in magnitude. These improvements have allowed us to detect IL-8 protein at 4.0fM in buffer. In addition, these sensitive LODs were achieved without the use of enzymatic signal amplification, such that the simplified protocol can further facilitate the development of point-of-care devices. The ultra sensitive optical protein sensor presented in this paper has a wide number of applications in disease diagnoses. Measurements for detecting biomarkers in clinical sample are much more challenging than the measurements in buffer, due to high background noise contributed by large collections of non-target molecules. We used clinical saliva samples to validate the functionality of the optical protein sensor. Clinical detection of disease-specific biomarkers in saliva offers a non-invasive, alternative approach to using blood or urine. Currently, the main challenge of using saliva as a diagnostic fluid is its inherently low concentration of biomarkers. We compare the measurements of 40 saliva samples; half from oral cancer patients and half from a control group. The data measured by the optical protein sensor is compared with the traditional Enzyme-Linked Immunosorbant Assay (ELISA) values to validate the accuracy of our system. These positive results enable us to proceed to using confocal optical protein sensor to detect other biomarkers, which have much lower concentrations.     

Substrate binding and formation of an occluded state in the leucine transporter

Translocation through the extracellular vestibule and binding of leucine in the leucine transporter (LeuT) have been studied with molecular dynamics simulations. More than 0.1 μs of all-atom molecular dynamics simulations have been performed on different combinations of LeuT, bound substrate, and bound structural Na⁺ ions to describe molecular events involved in substrate binding and in the formation of the occluded state and to investigate the dynamics of this state. Three structural features are found to be directly involved in the initial steps of leucine transport: a Na⁺ ion directly coordinated to leucine (Na-1), two aromatic residues closing the binding site toward the extracellular vestibule (Tyr-108 and Phe-253), and a salt bridge in the extracellular vestibule (Arg-30 and Asp-404). These features account for observed differences between simulations of LeuT with and without bound substrate and for a possible pathway for leucine binding and thereby formation of the occluded LeuT binding site.     

Cortisol and hypothalamic–pituitary–gonadal axis hormones in follicular-phase women with fibromyalgia and chronic fatigue syndrome and effect of depressive symptoms on these hormones

We investigated abnormalities of the hypothalamic–pituitary–gonadal axis and cortisol concentrations in women with fibromyalgia and chronic fatigue syndrome (CFS) who were in the follicular phase of their menstrual cycle, and whether their scores for depressive symptoms were related to levels of these hormones. A total of 176 subjects participated – 46 healthy volunteers, 68 patients with fibromyalgia, and 62 patients with CFS. We examined concentrations of follicle-stimulating hormone, luteinizing hormone (LH), estradiol, progesterone, prolactin, and cortisol. Depressive symptoms were assessed using the Beck Depression Inventory (BDI). Cortisol levels were significantly lower in patients with fibromyalgia or CFS than in healthy controls (P < 0.05); there were no significant differences in other hormone levels between the three groups.     

Determination of ochratoxin A in fruit juice by high-performance liquid chromatography after vortex-assisted emulsification microextraction based on solidification of floating organic drop

A rapid, simple, and green vortex-assisted emulsification microextraction method based on solidification of floating organic drop was developed for the extraction and determination of ochratoxin A (OTA) with high-performance liquid chromatography. Some factors influencing the extraction efficiency of OTA such as the type and volume of extraction solvent, sample pH, salt concentration, vortex time, and sample volume were optimized. Under optimized conditions, the calibration curve exhibited linearity in the range of 50.0–500 ng L^?1 with a coefficient of determination higher than 0.999. The limit of detection was 15.0 ng L^?1. The inter- and intra-assays relative standard deviations were in a range of 4.7–8.7%. The accuracy of the developed method was investigated through recovery experiments, and it was successfully used for the quantification of OTA in 40 samples of fruit juice.     

Association of mitochondrial dysfunction and lipid metabolism with type 2 diabetes mellitus: A review of literature

Background

Diabetes mellitus (DM) is one of the most prevalent chronic diseases, and its prevalence continues to increase globally. The impact of mitochondrial dysfunction and lipid metabolism on diabetes mellitus and insulin resistance (IR) has been implicated in several previous reports; however, the results of studies are confusing despite four decades of study.

Methods/Results

This review has evaluated updated understanding of the role of mitochondrial dysfunction and lipid metabolism on type 2 diabetes, and found that mitochondrial dysfunction and lipid metabolism disorder induce the dysregulation of liver and pancreatic beta cells, insulin resistance, and type 2 diabetes.

Conclusion

Mitochondrial dysfunction and lipid metabolism induce metabolic dysregulation and finally increasing the possibility of diabetes.

     

Mixture of fibroblast, epithelial and endothelial cells conditioned media induce monocyte-derived dendritic cell maturation

Fully matured DCs with large amount cytoplasm and copious dendritic projections were visible at the end of culturing period in the presence of MCM, TNF-α and poly (I:C), with or without FEECM. Thus, DCs generated with these maturation factors are nonadherent and have typical satellite morphology. Flow cytometric analysis using anti-CD14, -CD80, -CD86, -HLA-DR and -CD83 revealed that expression of CD14 is decreased in particular in FEECM treated DCs, on day 5 and expression of CD80, CD86 and HLA-DR was the higher when FEECM are added to maturation factor. Functionally, when DCs matured in the presence of FEECM elicited stronger MLR, reduced phagocytic activity. These results support the use of the FEECM with MCM, TNF-α and poly (I–C) as maturation factor in DC generation that could result in functionally mature monocyte-derived DCs in comparison to either alone.     

A model-based parametric study of impact force during running

This paper deals with the impact force during foot-ground impact activities such as the running. A previously developed model is used for this study. The model is a lumped-parameter one consisting of four masses connected to each other via linear springs and viscous dampers. A shoe-specific nonlinear function is used for representation of the ground reaction force. The authors have previously showed that the previous version of the model as well as its simulation is incorrect. This paper slightly modifies the previous model so as it is able to produce results in agreement with the experiments. Then, the modified model is simulated for two typical shoe types. A parametric study is also conducted. The parametric study concerns with the effects of masses, mass ratios, stiffness constants, and damping coefficients on the dynamics of the impact. It is shown that the impact forces increase as the rigid and wobbling masses increase. However, the increase in the impact forces is not the same for all the masses. It is found that the impact force increases as the touchdown velocities increase. Simulations imply that the variations of the damping coefficients result in larger variations of the impact force compared to the stiffness. The effect of the variation of gravity on the simulated impact force is also explored. It is concluded that both the first and the second peaks of the impact force are increased with gravity. An in-depth discussion is included to compare results of the current paper with results of other investigators.