Protein folding in hydrophobic-polar lattice model: a flexible ant colony optimization approach

This paper proposes a flexible ant colony (FAC) algorithm for solving protein folding problems based on the hydrophobic-polar square lattice model. Collaborations of novel pheromone and heuristic strategies in the proposed algorithm make it more effective in predicting structures of proteins compared with other state-of-the-art algorithms

Unraveling the Early Events of Amyloid-β Protein (Aβ) Aggregation: Techniques for the Determination of Aβ Aggregate Size

The aggregation of proteins into insoluble amyloid fibrils coincides with the onset of numerous diseases. An array of techniques is available to study the different stages of the amyloid aggregation process. Recently, emphasis has been placed upon the analysis of oligomeric amyloid species, which have been hypothesized to play a key role in disease progression. This paper reviews techniques utilized to study aggregation of the amyloid-β protein (Aβ) associated with Alzheimer’s disease. In particular, the review focuses on techniques that provide information about the size or quantity of oligomeric Aβ species formed during the early stages of aggregation, including native-PAGE, SDS-PAGE, Western blotting, capillary electrophoresis, mass spectrometry, fluorescence correlation spectroscopy, light scattering, size exclusion chromatography, centrifugation, enzyme-linked immunosorbent assay, and dot blotting

Technologies and Techniques for Detection of Nitrate in potable water: A Review

In agricultural and industrial production nitrate is widely used. Nitrate is appearing in water, environment, biology and food. Nitrate is a toxic inorganic contaminant, that’s why it is perilous to the health living organisms and humans. In recent years, a variety of techniques has been developed for monitoring of nitrate. This paper aggregated as a general survey of the techniques proposed for nitrate monitoring and important monitoring parameters (such as detection limit, working pH, detection range and materials) were classified. This paper is composed of the sort of signal got from techniques, including optical and electrical signals.Electrochemical techniques get an electric signal from dissolved nitrate, with impedimetric, potentiometric and voltammetric techniques are included. Raman Spectrometry, fluorescence and absorption techniques receive an optical signal. In recent years, Biosensors are proposed for monitoring the nitrate in water. The limitations and disadvantages/advantages of the techniques are discussed in this paper. At last, techniques employed to perform nitrate, monitoring is summarized, and their future scope and development are discussed

Absolute quantification of cohesin, CTCF and their regulators in human cells.

The organisation of mammalian genomes into loops and topologically associating domains (TADs) contributes to chromatin structure, gene expression and recombination. TADs and many loops are formed by cohesin and positioned by CTCF. In proliferating cells, cohesin also mediates sister chromatid cohesion, which is essential for chromosome segregation. Current models of chromatin folding and cohesion are based on assumptions of how many cohesin and CTCF molecules organise the genome. Here we have measured absolute copy numbers and dynamics of cohesin, CTCF, NIPBL, WAPL and sororin by mass spectrometry, fluorescence-correlation spectroscopy and fluorescence recovery after photobleaching in HeLa cells. In G1-phase, there are similar to 250,000 nuclear cohesin complexes, of which similar to 160,000 are chromatin-bound. Comparison with chromatin immunoprecipitation-sequencing data implies that some genomic cohesin and CTCF enrichment sites are unoccupied in single cells at any one time. We discuss the implications of these findings for how cohesin can contribute to genome organisation and cohesion

Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle.

Chaperones TAPBPR and tapasin associate with class I major histocompatibility complexes (MHC-I) to promote optimization (editing) of peptide cargo. Here, we use solution NMR to investigate the mechanism of peptide exchange. We identify TAPBPR-induced conformational changes on conserved MHC-I molecular surfaces, consistent with our independently determined X-ray structure of the complex. Dynamics present in the empty MHC-I are stabilized by TAPBPR and become progressively dampened with increasing peptide occupancy. Incoming peptides are recognized according to the global stability of the final pMHC-I product and anneal in a native-like conformation to be edited by TAPBPR. Our results demonstrate an inverse relationship between MHC-I peptide occupancy and TAPBPR binding affinity, wherein the lifetime and structural features of transiently bound peptides control the regulation of a conformational switch located near the TAPBPR binding site, which triggers TAPBPR release. These results suggest a similar mechanism for the function of tapasin in the peptide-loading complex

Development of Nanoemulsion-based Delivery Systems for Evaluation of Triglycerides Bioactivity in Caernohabditis Elegans

Digestion and absorption of bioactive free fatty acids have been studied using the nematode Caernohabditis elegans (C. elegans). However, fatty acids mostly occur in foods in the form of triglycerides, which are highly hydrophobic molecules with low water-solubility, thereby making it difficult to study the fate of ingested fatty acids in C. elegans. The purpose of this research was to develop a method to deliver hydrophobic bioactives, including triglycerides, into C. elegans. Nanoemulsions containing triglyceride nanoparticles were prepared by sonication, and nanoparticle ingestion was confirmed by optical and confocal microscopy, and quantified by spectrometry. Changes in fatty acid composition were measured to confirm the absorption of triglycerides delivered as nanoparticles. Nanoparticles with a wide range of particle diameters (40 to 500 nm) were ingested by C. elegans. The ingested triglyceride amount was dependent on the size and concentration of the nanoparticles, but the fatty acid composition of C. elegans was not significantly changed by dietary triglycerides. Nanoemulsion based-delivery systems enable C. elegans to be used for evaluation of hydrophobic bioactives and may provide a useful tool for testing their biological activities

Discovery of Inhibitors by Combinatorial-Chemistry Approaches

This thesis describes our efforts to develop inhibitors using combinatorial-chemistry approaches. These approaches can potentially speed-up the drug discovery trajectory and the discovered molecules could be used as starting points for future drug development projects targeting 15-LOX-1, MIF and/or MDM2. The aforementioned targets are all proteins that play an important role in common diseases