Effect of Amphipathic HIV Fusion Inhibitor Peptides on POPC and POPC/Cholesterol Membrane Properties: A Molecular Simulation Study

T-20 and T-1249 fusion inhibitor peptides were shown to interact with 1-palmitoyl-2-oleyl-phosphatidylcholine (POPC) (liquid disordered, ld) and POPC/cholesterol (1:1) (POPC/Chol) (liquid ordered, lo) bilayers, and they do so to different extents. Although they both possess a tryptophan-rich domain (TRD), T-20 lacks a pocket binding domain (PBD), which is present in T-1249. It has been postulated that the PBD domain enhances FI interaction with HIV gp41 protein and with model membranes. Interaction of these fusion inhibitor peptides with both the cell membrane and the viral envelope membrane is important for function, i.e., inhibition of the fusion process. We address this problem with a molecular dynamics approach focusing on lipid properties, trying to ascertain the consequences and the differences in the interaction of T-20 and T-1249 with ld and lo model membranes. T-20 and T-1249 interactions with model membranes are shown to have measurable and different effects on bilayer structural and dynamical parameters. T-1249’s adsorption to the membrane surface has generally a stronger influence in the measured parameters. The presence of both binding domains in T-1249 appears to be paramount to its stronger interaction, and is shown to have a definite importance in membrane properties upon peptide adsorption.     

Functionalization of wool fabric with phase‐change materials microcapsules after plasma surface modification

The use of microcapsules has increased in several different areas, namely, textile applications. They have been used as a possible means of introducing new properties, namely, in medical care by antibiotics, skin moisturizers, and other drugs and for thermal comfort. In this study, we examined the influence of dielectric barrier discharge (DBD) plasma treatment on the adhesion of phase‐change material (PCM) microcapsules on wool fabric. Several experimental techniques were used to evaluate the wool surface modification after plasma treatment and the influence of the microcapsules' resistance to washing conditions, namely, the determination of the static and dynamic contact angles, surface energy, and adhesion work; X‐ray photoelectron spectroscopy; Fourier transform infrared spectroscopy; differential scanning calorimetry; and scanning electron microscopy. Chemical and physical characterization of the wool fiber in the fabric confirmed significant surface modification. The plasma treatment greatly increased the hydrophilicity, surface energy, and adhesion work of the wool fabric; this proved that more microcapsules were adsorbed on the fabric and more microcapsules remained on the fabric surface after the washing procedures. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013     

Authenticity Control of Roasted Coffee Brands Using Near-Infrared Spectroscopy

In this work, a methodology based on near-infrared spectroscopy (NIRS) was exploited in order to discriminate between commercial coffee brands. The main advantages of this approach compared to other strategies (e.g., wet chemistry methods) are its lower cost, less labor, and lower time per analysis. Two commercial brands were discriminated among several others present in the Portuguese market. The chemometric method used to estimate discriminant models was partial least squares discriminant analysis (PLSDA). Results show that it is possible to discriminate coffee brands using this strategy with a correct classification of 100 %. The spectral region, more favorable to discrimination of roasted coffee brands, can be related with differences in the concentrations of compounds, such as, chlorogenic acid and sucrose, and also due to differences on lipid fraction. This methodology is adequate for field implementation, namely, adopting handheld NIRS instruments.     

Berry Phenolics of Grapevine under Challenging Environments

Plant phenolics have been for many years a theme of major scientific and applied interest. Grape berry phenolics contribute to organoleptic properties, color and protection against environmental challenges. Climate change has already caused significant warming in most grape-growing areas of the world, and the climatic conditions determine, to a large degree, the grape varieties that can be cultivated as well as wine quality. In particular, heat, drought and light/UV intensity severely affect phenolic metabolism and, thus, grape composition and development. In the variety Chardonnay, water stress increases the content of flavonols and decreases the expression of genes involved in biosynthesis of stilbene precursors. Also, polyphenolic profile is greatly dependent on genotype and environmental interactions. This review deals with the diversity and biosynthesis of phenolic compounds in the grape berry, from a general overview to a more detailed level, where the influence of environmental challenges on key phenolic metabolism pathways is approached. The full understanding of how and when specific phenolic compounds accumulate in the berry, and how the varietal grape berry metabolism responds to the environment is of utmost importance to adjust agricultural practices and thus, modify wine profile.     

A proposed multigeneration protocol for Japanese medaka (Oryzias latipes) to evaluate effects of endocrine disruptors.

Definitive data on reproductive impairment of chronically exposed populations may be required to assess the appropriateness of the existing test methods for hazard identification and prioritization of endocrine modulators. Multigeneration toxicity testing protocols for wildlife receptors are lacking. To help address this gap we describe a multigeneration fish assay using the freshwater fish, Japanese medake (Oryzias latipes). This test species has been used for the evaluation of carcinogenic, teratogenic and reproductive effects and is sensitive to estrogen exposure producing ovo-testis, altered biochemical parameters and phenotypic characteristics. Due to the short life cycle, a multigeneration test with medaka can be conducted in 1 year. Endpoints evaluated include: survival, growth, sex ratio, fecundity, embryonic lesion occurrence, embryonic stage development, gonadal and hepatic somatic indices, histopathology and biochemical parameters. As new endpoints are developed they can be incorporated into the protocol. Results of a positive control (17 beta-estradiol) study are presented to give an indication of the baseline associated with various test endpoints and to highlight the importance of nutrition in the experimental design. 17 beta-Estradiol treatment induced vitellogenin production in male and female medaka, feminized males, and disrupted egg production. The proposed protocol provides researchers with an effective multigeneration fish test that can be used to examine potential effects of stressors at the population, individual, cellular and subcellular level.     

Diversity of free-living and attached bacteria in offshore Western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA

In a previous study (S. G. Acinas, F. Rodríguez-Valera, and C. Pedrós-Alió, FEMS Microbiol. Ecol. 24:27-40, 1997), community fingerprinting by 16S rDNA restriction analysis applied to Mediterranean offshore waters showed that the free-living pelagic bacterial community was very different from the bacterial cells aggregated or attached to particles of more than about 8 micrometer. Here we have studied both assemblages at three depths (5, 50, and 400 m) by cloning and sequencing the 16S rDNA obtained from the same samples, and we have also studied the samples by scanning electron microscopy to detect morphology patterns. As expected, the sequences retrieved from the assemblages were very different. The subsample of attached bacteria contained very little diversity, with close relatives of a well-known species of marine bacteria, Alteromonas macleodii, representing the vast majority of the clones at every depth. On the other hand, the free-living assemblage was highly diverse and varied with depth. At 400 m, close relatives of cultivated gamma Proteobacteria predominated, but as shown by other authors, near the surface most clones were related to phylotypes described only by sequence, in which the alpha Proteobacteria of the SAR11 cluster predominated. The new technique of rDNA internal spacer analysis has been utilized, confirming these results. Clones representative of the A. macleodii cluster have been completely sequenced, producing a picture that fits well with the idea that they could represent a genus with at least two species and with a characteristic depth distribution.     

The ParTriCluster Algorithm for Gene Expression Analysis

Analyzing gene expression patterns is becoming a highly relevant task in the Bioinformatics area. This analysis makes it possible to determine the behavior patterns of genes under various conditions, a fundamental information for treating diseases, among other applications. A recent advance in this area is the Tricluster algorithm, which is the first algorithm capable of determining 3D clusters (genes × samples × timestamps), that is, groups of genes that behave similarly across samples and timestamps. However, even though biological experiments collect an increasing amount of data to be analyzed and correlated, the triclustering problem remains a bottleneck due to its NP-Completeness, so its parallelization seems to be an essential step towards obtaining feasible solutions. In this work we propose and evaluate the implementation of a parallel version of the Tricluster algorithm using the filter-labeled-stream paradigm supported by the Anthill parallel programming environment. The results show that our parallelization scales well with the data size, being able to handle severe load imbalances that are inherent to the problem. Further more, the parallelization strategy is applicable to any depth-first searches.