Gastric cancer biomarkers; A systems biology approach

Gastric cancer is one of the most fatal cancers in the world. Many efforts in recent years have attempted to find effective proteins in gastric cancer. By using a comprehensive list of proteins involved in gastric cancer, scientists were able to retrieve interaction information. The study of protein-protein interaction networks through systems biology based analysis provides appropriate strategies to discover candidate proteins and key biological pathways.In this study, we investigated dominant functional themes and centrality parameters including betweenness as well as the degree of each topological clusters and expressionally active sub-networks in the resulted network. The results of functional analysis on gene sets showed that neurotrophin signaling pathway, cell cycle and nucleotide excision possess the strongest enrichment signals. According to the computed centrality parameters, HNF4A, TAF1 and TP53 manifested as the most significant nodes in the interaction network of the engaged proteins in gastric cancer. This study also demonstrates pathways and proteins that are applicable as diagnostic markers and therapeutic targets for future attempts to overcome gastric cancer.     

Mechanosensitivity of an epithelial Na+ channel in planar lipid bilayers: release from Ca2+ block.

A family of novel epithelial Na+ channels (ENaCs) have recently been cloned from several different tissues. Three homologous subunits (alpha, beta, gamma-ENaCs) from the core conductive unit of Na(+)-selective, amiloride-sensitive channels that are found in epithelia. We here report the results of a study assessing the regulation of alpha,beta,gamma-rENaC by Ca2+ in planar lipid bilayers. Buffering of the bilayer bathing solutions to [Ca2+] < 1 nM increased single-channel open probability by fivefold. Further investigation of this phenomenon revealed that Ca2+ ions produced a voltage-dependent block, affecting open probability but not the unitary conductance of ENaC. Imposing a hydrostatic pressure gradient across bilayers containing alpha,beta,gamma-rENaC markedly reduced the sensitivity of these channels to inhibition by [Ca2+]. Conversely, in the nominal absence of Ca2+, the channels lost their sensitivity to mechanical stimulation. These results suggest that the previously observed mechanical activation of ENaCs reflects a release of the channels from block by Ca2+.     

Point mutations in alpha bENaC regulate channel gating, ion selectivity, and sensitivity to amiloride.

We have generated two site-directed mutants, K504E and K515E, in the alpha subunit of an amiloride-sensitive bovine epithelial Na+ channel, alpha bENaC. The region in which these mutations lie is in the large extracellular loop immediately before the second membrane-spanning domain (M2) of the protein. We have found that when membrane vesicles prepared from Xenopus oocytes expressing either K504E or K515E alpha bENaC are incorporated into planar lipid bilayers, the gating pattern, cation selectivity, and amiloride sensitivity of the resultant channel are all altered as compared to the wild-type protein. The mutated channels exhibit either a reduction or a complete lack of its characteristic burst-type behavior, significantly reduced Na+:K+ selectivity, and an approximately 10-fold decrease in the apparent inhibitory equilibrium dissociation constant (Ki) for amiloride. Single-channel conductance for Na+ was not affected by either mutation. On the other hand, both K504E and K515E alpha bENaC mutants were significantly more permeable to K+, as compared to wild type. These observations identify a lysine-rich region between amino acid residues 495 and 516 of alpha bENaC as being important to the regulation of fundamental channel properties.     

ZFP57 recognizes multiple and closely spaced sequence motif variants to maintain repressive epigenetic marks in mouse embryonic stem cells

Imprinting Control Regions (ICRs) need to maintain their parental allele-specific DNA methylation during early embryogenesis despite genome-wide demethylation and subsequent de novo methylation. ZFP57 and KAP1 are both required for maintaining the repressive DNA methylation and H3-lysine-9-trimethylation (H3K9me3) at ICRs. In vitro, ZFP57 binds a specific hexanucleotide motif that is enriched at its genomic binding sites. We now demonstrate in mouse embryonic stem cells (ESCs) that SNPs disrupting closely-spaced hexanucleotide motifs are associated with lack of ZFP57 binding and H3K9me3 enrichment. Through a transgenic approach in mouse ESCs, we further demonstrate that an ICR fragment containing three ZFP57 motif sequences recapitulates the original methylated or unmethylated status when integrated into the genome at an ectopic position. Mutation of Zfp57 or the hexanucleotide motifs led to loss of ZFP57 binding and DNA methylation of the transgene. Finally, we identified a sequence variant of the hexanucleotide motif that interacts with ZFP57 both in vivo and in vitro. The presence of multiple and closely located copies of ZFP57 motif variants emerges as a distinct characteristic that is required for the faithful maintenance of repressive epigenetic marks at ICRs and other ZFP57 binding sites.     

Effect of polymer/nanosilver composite packaging on long-term microbiological status of Iranian saffron (Crocus sativus L.)

Crocus sativus L. (saffron) is a valuable plant which is native to Iran. Saffron is the dried stigmata of the flowering part of the plant that is usually contaminated with different bacteria and fungi through production process. Antimicrobial properties of silver nanoparticles are well recognized. To survey the effects of nanosilver packaging on microbiological status of spiked, saffron samples over a six month period were chosen. Saffron samples from five regions of Khorasan province were purchased and de novo frequencies of microbial contaminants were determined using standard procedures. Totally 35 g of saffron was spiked with known numbers of four bacterial and two fungal species and packaged into one gram packets. The packaging materials consisted of polyethylene polymers containing 0, 400, 800, 1200 or 4000 ppm nanosilver (as Ag). Total and differential numbers of spiked microorganisms in the packaged saffrons were enumerated at initial and at six time points of seven, 14, 28, 64, 90 and 180 days. Baird-Parker agar (BP agar), Kenner Fecal (KF), Salmonella–Shigella agar (SS agar), Violet Red Bile Glucose Agar (VRBGA), and Sabouraud Dextrose agar (SD agar) media were used for enumeration of the six spiked microorganisms including Staphylococcus aureus, Enterococcus faecalis, Salmonella Enteritidis, Enterobacter species and Escherichia coli, Fusarium oxysporum and Aspergillus flavus, respectively. Direct antibacterial activity of the composites was also determined. De novo frequencies of microorganisms in five saffron samples were at acceptable levels with dominance of fungi species. Nanosilver embedded packages accelerated the reduction in live microbial numbers in saffron samples and the efficacy was the best in packages containing 4000 ppm nanosilver particles. Nanosilver packaging can significantly reduce microbial burden of saffron.     

Radiodiagnosis of echinococcosis of the lungs]

The paper is devoted to analysis of radio-diagnostic findings of 79 patients with parietal round pulmonary formations. All the patients were investigated by x-ray and ultrasound, perfusion scintigraphy of the lungs with a postural test was performed in 43 of them. Diagnostic x-ray and echographic methods were compared and evaluated in terms of defining the origin of pulmonary formations. The origin of pulmonary formations was established by x-ray in 50 of 79 patients (63.3 per cent) whereas ultrasound findings proved correct in 74 of 79 patients (93.6 per cent). Perfusion scintigraphy can be recommended to patients with pulmonary echinococcosis only for limited indications when a necessity arises to assess the lesser circulatory state in terms of patients' functional operability.     

Mechanosensitivity of gramicidin A channels in bulged bilayer membranes at constant tension

Mechanoelectrical transduction in gramicidin A channels was studied in macroscopic planar lipid bilayer membranes bulged at constant tension. We found a supralinear increase in the single channel activity that was proportional to the square of membrane radius, but could not be accounted for by the increase in membrane surface area, or by recruitment of new channels. Extrapolated to biological membranes, these observations may suggest that the permeability of ion channels can be influenced simply by changing shape of the membrane, with or without stretching. Published in Russian in Biofizika, 2006, Vol. 51, No. 6, pp. 1014–1018. The text was submitted by the authors in English.     

A method for determining the CO2 released by resting cells of microorganisms during the oxidation of hydrocarbons

A method is proposed for determining the oxidation of hydrocarbon substrates by microorganisms. The method is based on measuring the evolution of CO2 into the medium when the substrate is oxidized by washed microbial cells adsorbed on a spongy surface and incubated in a closed space into which CO2-free air is passed.