A data-mining approach to biomarker identification from protein profiles using discrete stationary wavelet transform

Objective： To develop a new bioinformatic tool based on a data-mining approach for extraction of the most informative proteins that could be used to find the potential biomarkers for the detection of cancer. Methods： Two independent datasets from serum samples of 253 ovarian cancer and 167 breast cancer patients were used. The samples were examined by surfaceenhanced laser desorption/ionization time-of-flight mass spectrometry （SELDI-TOF MS）. The datasets were used to extract the informative proteins using a data-mining method in the discrete stationary wavelet transform domain. As a dimensionality reduction procedure, the hard thresholding method was applied to reduce the number of wavelet coefficients. Also, a distance measure was used to select the most discriminative coefficients. To find the potential biomarkers using the selected wavelet coefficients, we applied the inverse discrete stationary wavelet transform combined with a two-sided t-test. Results： From the ovarian cancer dataset, a set of five proteins were detected as potential biomarkers that could be used to identify the cancer patients from the healthy cases with accuracy, sensitivity, and specificity of 100%. Also, from the breast cancer dataset, a set of eight proteins were found as the potential biomarkers that could separate the healthy cases from the cancer patients with accuracy of 98.26%, sensitivity of 100%, and specificity of 95.6%. Conclusion： The results have shown that the new bioinformatic tool can be used in combination with the high-throughput proteomic data such as SELDI-TOF MS to find the potential biomarkers with high discriminative power.     

Satellite phage TLCφ enables toxigenic conversion by CTX phage through dif site alteration

Bacterial chromosomes often carry integrated genetic elements (for example plasmids, transposons, prophages and islands) whose precise function and contribution to the evolutionary fitness of the host bacterium are unknown. The CTXφ prophage, which encodes cholera toxin in Vibrio cholerae, is known to be adjacent to a chromosomally integrated element of unknown function termed the toxin-linked cryptic (TLC). Here we report the characterization of a TLC-related element that corresponds to the genome of a satellite filamentous phage (TLC-Knφ1), which uses the morphogenesis genes of another filamentous phage (fs2φ) to form infectious TLC-Knφ1 phage particles. The TLC-Knφ1 phage genome carries a sequence similar to the dif recombination sequence, which functions in chromosome dimer resolution using XerC and XerD recombinases. The dif sequence is also exploited by lysogenic filamentous phages (for example CTXφ) for chromosomal integration of their genomes. Bacterial cells defective in the dimer resolution often show an aberrant filamentous cell morphology. We found that acquisition and chromosomal integration of the TLC-Knφ1 genome restored a perfect dif site and normal morphology to V.?cholerae wild-type and mutant strains with dif(-) filamentation phenotypes. Furthermore, lysogeny of a dif(-) non-toxigenic V.?cholerae with TLC-Knφ1 promoted its subsequent toxigenic conversion through integration of CTXφ into the restored dif site. These results reveal a remarkable level of cooperative interactions between multiple filamentous phages in the emergence of the bacterial pathogen that causes cholera.     

Positional cloning uncovers mutations in PLCE1 responsible for a nephrotic syndrome variant that may be reversible

Nephrotic syndrome, a malfunction of the kidney glomerular filter, leads to proteinuria, edema and, in steroid-resistant nephrotic syndrome, end-stage kidney disease. Using positional cloning, we identified mutations in the phospholipase C epsilon gene (PLCE1) as causing early-onset nephrotic syndrome with end-stage kidney disease. Kidney histology of affected individuals showed diffuse mesangial sclerosis (DMS). Using immunofluorescence, we found PLCepsilon1 expression in developing and mature glomerular podocytes and showed that DMS represents an arrest of normal glomerular development. We identified IQ motif-containing GTPase-activating protein 1 as a new interaction partner of PLCepsilon1. Two siblings with a missense mutation in an exon encoding the PLCepsilon1 catalytic domain showed histology characteristic of focal segmental glomerulosclerosis. Notably, two other affected individuals responded to therapy, making this the first report of a molecular cause of nephrotic syndrome that may resolve after therapy. These findings, together with the zebrafish model of human nephrotic syndrome generated by plce1 knockdown, open new inroads into pathophysiology and treatment mechanisms of nephrotic syndrome.     

Diffusion mechanism in molten salt baths during the production of carbide coatings via thermal reactive diffusion

The diffusion mechanism of carbide-forming elements from a molten salt bath to a substrate surface was studied in this research, with particular focus on the processes occurring in the molten bath at the time of coating. Metal, oxide, and metal-oxide baths were investigated, and the coating process was performed on H13 steel substrates. Scanning electron microscopy and electron-probe microanalysis were used to study the coated samples and the quenched salt bath. The thickness of the carbide coating layer was 6.5 ±0.5, 5.2 ±0.5, or 5.7 ±0.5 μm depending on whether it was deposited in a metal, oxide, or metal-oxide bath, respectively. The phase distribution of vanadium-rich regions was 63%, 57%, and 74% of the total coating deposited in metal, oxide, and metal-oxide baths, respectively. The results obtained using the metal bath indicated that undissolved suspended metal particles deposited onto the substrate surface. Then, carbon subsequently diffused to the substrate surface and reacted with the metal particles to form the carbides. In the oxide bath, oxide powders dissolved in the bath with or without binding to the oxidative structure (Na₂O) of borax; they were then reduced by aluminum and converted into metal particles. We concluded that, in the metal and oxide baths, the deposition of metal particles onto the sample surface is an important step in the formation of the coating.     

Culture of a new medicinal leech: growth,survival and reproduction of Hirudo orientalis Utevsky and Trontelj, 2005 under laboratory conditions

The increasing demands for medicinal leeches around the world has increased the need for new sources of leeches. To assess the feasibility of culturing a new medicinal leech species, growth, survival and reproduction of Hirudo orientalis was investigated under laboratory conditions (28°C; 9.5D:14.5L light regime; monthly feeding by sheep blood) from hatching until sexual maturity. Several interesting results emerged from this study. (1) The first copulation was observed in 5.5-month-old leeches and cocoon deposition started by six months. (2) Cocoon length and diameter did not differ significantly between six- and nine-month-old leeches, but the percentage of leeches depositing cocoons was significantly higher in the nine-month old group. (3) The growth curve was saltatory, similar to other sanguivorous species. The mean (±SE) wet weight of 6-month-old individuals was 4.70 (±0.86) g. (4) Weight gain rate decreased with increasing age. (5) Mortality only occurred in the one-, seven- and eight-month age groups at the rate of 5.7%, 23.1% and 14.3%, respectively.     

Optimization of Cutting Parameters for Face Milling Titanium Alloy Using MQL

When using MQL as a cooling technique, many parameters have to be adjusted. The Taguchi method was used in this study to investigate the cutting characteristics of face milling of titanium alloys using PVD-coated inserts. To find the optimal volume removed and surface roughness, an orthogonal array, the signal-to-noise （S/N） ratio and the analysis of variance （ANOVA） were employed. The optimum cutting parameters was obtained. Throughout this study, it was found that the feed rate is the most influencing cutting parameter in the face milling of titanium alloys.     

伊朗Lorestan省粉虱物种多样性研究（半翅目：粉虱科）

粉虱（半翅目：粉虱科）是一类通过吸食植物体汁和传播病毒危害农作物的害虫。本文研究了伊朗西部Lorestan省的这一类具重要经济意义的粉虱类群物种多样性，调查了16属27种粉虱，进行了种类鉴定研究，包括种的异名和分布。     

Physicochemical characteristics of various milk samples available in Pakistan

We report physicochemical characteristics of various kinds of liquid milk commercially available in Pakistan in comparison with those of fresh natural milk from animals. Milk samples were collected from local markets at Peshawar, Pakistan, and analyzed for their physical features, including moisture, total solids, specific gravity, conductivity, viscosity and titratable acidity （lactic acid equivalent）, and chemical components and macro-minerals, including total protein, casein, lactose, ash and minerals （Na, K and Mg）. These items were compared with the physicochemical characteristics of the fresh natural milk samples from buffalo, cow and goat. The results were also compared with reported nutritional quality of milk from various countries and World Health Organization （WHO） standards. We found that all the physical features and chemical components of commercially available milk in Pakistan markets meet WHO＇s requirements, except for Na, K, Ca and Mg, which are below the standards.     

Antibacterial and antifungal activities of different parts of Tribulus terrestris L. growing in Iraq

Antimicrobial activity of organic and aqueous extracts from fruits, leaves and roots of Tribulus terrestris L., an Iraqi medicinal plant used as urinary anti-infective in folk medicine, was examined against I l species of pathogenic and non-pathogenic microorganisms： Staphylococcus aureus, Bacillus subtilis, Bacillus cereus, Corynebacterium diphtheriae, Escherichia coli, Proteus vulgaris, Serratia marcescens, Salmonella typhimurium, Klebsiella pneumoniae, Pseudomonas aeruginosa and Candida albicans using microdilution method in 96 multiwell microtiter plates. All the extracts from the different parts of the plant showed antimicrobial activity against most tested microorganisms. The most active extract against both Gram-negative and Gram-positive bacteria was ethanol extract from the fruits with a minimal inhibitory concentration （MIC） value of 0.15 mg/ml against B. subtilis, B. cereus, P. vulgaris and C. diphtheriae. In addition, the same extract from the same plant part demonstrated the strongest antifungal activity against C. albicans with an MIC value of 0.15 mg/ml.     

S-glutathionylation uncouples eNOS and regulates its cellular and vascular function

Endothelial nitric oxide synthase (eNOS) is critical in the regulation of vascular function, and can generate both nitric oxide (NO) and superoxide (O(2)(?-)), which are key mediators of cellular signalling. In the presence of Ca(2+)/calmodulin, eNOS produces NO, endothelial-derived relaxing factor, from l-arginine (l-Arg) by means of electron transfer from NADPH through a flavin containing reductase domain to oxygen bound at the haem of an oxygenase domain, which also contains binding sites for tetrahydrobiopterin (BH(4)) and l-Arg. In the absence of BH(4), NO synthesis is abrogated and instead O(2)(?-) is generated. While NOS dysfunction occurs in diseases with redox stress, BH(4) repletion only partly restores NOS activity and NOS-dependent vasodilation. This suggests that there is an as yet unidentified redox-regulated mechanism controlling NOS function. Protein thiols can undergo S-glutathionylation, a reversible protein modification involved in cellular signalling and adaptation. Under oxidative stress, S-glutathionylation occurs through thiol-disulphide exchange with oxidized glutathione or reaction of oxidant-induced protein thiyl radicals with reduced glutathione. Cysteine residues are critical for the maintenance of eNOS function; we therefore speculated that oxidative stress could alter eNOS activity through S-glutathionylation. Here we show that S-glutathionylation of eNOS reversibly decreases NOS activity with an increase in O(2)(?-) generation primarily from the reductase, in which two highly conserved cysteine residues are identified as sites of S-glutathionylation and found to be critical for redox-regulation of eNOS function. We show that eNOS S-glutathionylation in endothelial cells, with loss of NO and gain of O(2)(?-) generation, is associated with impaired endothelium-dependent vasodilation. In hypertensive vessels, eNOS S-glutathionylation is increased with impaired endothelium-dependent vasodilation that is restored by thiol-specific reducing agents, which reverse this S-glutathionylation. Thus, S-glutathionylation of eNOS is a pivotal switch providing redox regulation of cellular signalling, endothelial function and vascular tone.