Understanding complex systems often requires a bottom-up analysis towards biology approach. The need to investigate system, not only as individual components but whole, emerges. This can be done by examining the elementary constituents individually and then how these are connected. myriad of system their interactions best characterized networks they mainly represented graphs where thousands nodes connected with vertices. In this article we demonstrate approaches, models methods from graph...

This study aimed to identify candidate new diagnosis and prognosis markers medicinal targets of prostate cancer (PCa), using state the art proteomics. A total 20 tissue specimens from 10 patients with benign prostatic hyperplasia (BPH) PCa (Tumour Node Metastasis [TNM] stage T1−T3) were analyzed by isobaric stable isotope labeling (iTRAQ) two-dimensional liquid chromatography−tandem mass spectrometry (2DLC−MS/MS) approaches a hybrid quadrupole time-of-flight system (QqTOF). The resulted in...

Representative animal models for diabetes-associated vascular complications are extremely relevant in assessing potential therapeutic drugs. While several rodent type 2 diabetes (T2D) available, their relevance recapitulating renal and cardiovascular features of man is not entirely clear. Here we evaluate at the molecular level similarity between Zucker diabetic fatty (ZDF) rats, as a model T2D-associated complications, human disease by urinary proteome analysis. Urine analysis ZDF rats...

The protein components of urine are useful indicators renal function and human health in general. Urine samples easily attainable making them ideal substrates for biomarker research. Analysis the proteome however, has been hindered by great variability specimens, presence various proteins low abundance or modified forms. To alleviate some these problems from five different individuals were pooled, concentrated characterized a combination preparative electrophoresis 2-DE, followed PMF. A...

Abstract Background microRNAs (miRNAs) are single-stranded RNA molecules of about 20–23 nucleotides length found in a wide variety organisms. miRNAs regulate gene expression, by interacting with target mRNAs at specific sites order to induce cleavage the message or inhibit translation. Predicting verifying mRNA targets is difficult process great importance. Results GOmir novel stand-alone application consisting two separate tools: JTarget and TAGGO. integrates miRNA prediction functional...

Secreted proteins play a key role in cell signaling, communication, and migration. We recently described the development of an aggressive variant (T24M) bladder cancer line T24. Using this model, objective our work was identification secreted involved acquisition phenotype. vitro assays, we demonstrate that conditioned media T24M cells promote motility parental less T24 cells. Proteomic analysis culture by use 2-dimensional gel electrophoresis coupled to MALDI TOF MS LC-MS approaches...

The quest for small drug-like compounds that selectively inhibit the function of biological targets has always been a major focus in pharmaceutical industry and academia as well. High-throughput screening compound libraries requires time, cost resources. Therefore, use alternative methods is necessary facilitating lead discovery. Computational techniques dock molecules into macromolecular predict affinity activity molecule are widely used drug design discovery, have become an integral part...

Bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse often extreme habitats. Apart from oxygenic photosynthesis oxidative phosphorylation, well-studied processes chloroplasts mitochondria of plants animals, prokaryotes utilize various chemo- or lithotrophic modes, such as anoxygenic photosynthesis, iron oxidation reduction, sulfate methanogenesis. Most bioenergetic pathways have a similar general structure, with electron transport...

Abstract Background Natural mutations in the human glucocorticoid receptor ( hGR , NR 3C1 ) gene cause Chrousos syndrome, a rare condition characterized by generalized, partial, target‐tissue insensitivity to glucocorticoids. Objective To present new case of syndrome caused novel mutation gene, and elucidate molecular mechanisms through which natural mutant affects signal transduction. Design Results The index presented with hirsutism, acne, alopecia, anxiety, fatigue irregular menstrual...

Abstract Summary: Drugster is a fully interactive pipeline designed to break the command line barrier and introduce new user-friendly environment perform drug design, lead structure optimization experiments through an efficient combination of PDB2PQR, Ligbuilder, Gromacs Dock suites. Our platform features novel workflow that guides user each logical step iterative 3D structural setup design process, by providing seamless interface all incorporated packages. Availability: can be freely...

A library of Tau class GSTs (glutathione transferases) was constructed by DNA shuffling using the encoding Glycine max GmGSTU2-2, GmGSTU4-4 and GmGSTU10-10. The parental are >88% identical at sequence level; however, their specificity varies towards different substrates. contained chimaeric structures alternated segments sequences point mutations. Chimaeric GST were expressed in Escherichia coli enzymatic activities CDNB (1-chloro-2,4-dinitrobenzene) herbicide fluorodifen (4-nitrophenyl...

The Greek Goat Encephalitis virus (GGE) belongs to the Flaviviridae family of genus Flavivirus. GGE constitutes an important pathogen livestock that infects goat’s central nervous system. viral enzymes GGE, helicase and RNA-dependent RNA polymerase (RdRP), are ideal targets for inhibitor design, since those crucial virus’ survival, proliferation transmission. In effort understand molecular structure underlying functions enzymes, three dimensional structures NS3 NS5 RdRP have been modelled....

Viral RNA helicases are involved in duplex unwinding during the replication of virus. It is suggested that these represent very promising antiviral targets. Viruses flaviviridae family causative agents many common and devastating diseases, including hepatitis, yellow fever dengue fever. As there currently no available anti-Flaviviridae therapy, urgent need for development efficient anti-viral pharmaceutical strategies. Herein, we report complete phylogenetic analysis across alongside a more...

The Classical Swine Fever virus (CSFV) is a major pathogen of livestock and belongs to the flaviviridae viral family. Even though there aren't any verified zoonosis cases yet, outcomes CSFV epidemics have been devastating local communities. In an effort shed light molecular mechanisms underlying structural drug design potential helicase, three dimensional structure helicase has modeled using conventional homology modeling techniques crystal Hepatitis C (HCV) as template. established in...

During the past few years, pharmacophore modeling has become one of key components in computer-aided drug design and modern discovery. DrugOn is a fully interactive pipeline designed to exploit advantages programming overcome command line barrier with two friendly environments for user (either novice or experienced field Computer Aided Drug Design) perform through an efficient combination PharmACOphore, Gromacs, Ligbuilder PDB2PQR suites. Our platform features novel workflow that guides each...

Understanding the structure and function of intermediate filaments (IFs) is necessary in order to explain why more than 70 related IF genes have evolved vertebrates while maintaining such dramatically tissue-specific expression. Desmin a member large multigene family proteins specifically expressed myocytes. In an effort elucidate its muscle-specific behavior, we used yeast two-hybrid system identify desmin's head binding partners. We described mitochondrial lysosomal protein, NADH...

Notch is a highly conserved family of transmembrane receptors and transcription factors that are key players in several developmental processes. In this study, we identified novel sequences from various species covering worm to human conducted comprehensive phylogenetic analysis order confirm extend the evolutionary history Notch. Our findings an independent duplication event Caenorhabditis elegans resulting two genes show vertebrate resulted events, both which occurred before divergence...