In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip(® )technology

BACKGROUND: Genomic approaches in large animal models (canine, ovine etc) are challenging due to insufficient genomic information for these species and the lack of availability of corresponding microarray platforms. To address this problem, we speculated that conserved interspecies genetic sequences can be experimentally detected by cross-species hybridization. The Affymetrix platform probe redundancy offers flexibility in selecting individual probes with high sequence similarities between related species for gene expression analysis. RESULTS: Gene expression profiles of 40 canine samples were generated using the human HG-U133A GeneChip (U133A). Due to interspecies genetic differences, only 14 ± 2% of canine transcripts were detected by U133A probe sets whereas profiling of 40 human samples detected 49 ± 6% of human transcripts. However, when these probe sets were deconstructed into individual probes and examined performance of each probe, we found that 47% of human probes were able to find their targets in canine tissues and generate a detectable hybridization signal. Therefore, we restricted gene expression analysis to these probes and observed the 60% increase in the number of identified canine transcripts. These results were validated by comparison of transcripts identified by our restricted analysis of cross-species hybridization with transcripts identified by hybridization of total lung canine mRNA to new Affymetrix Canine GeneChip(®). CONCLUSION: The experimental identification and restriction of gene expression analysis to probes with detectable hybridization signal drastically increases transcript detection of canine-human hybridization suggesting the possibility of broad utilization of cross-hybridizations of related species using GeneChip technology

Chromatography-mass spectrometry studies on the metabolism of synthetic cannabinoids JWH-018 and JWH-073, psychoactive components of smoking mixtures

The lack or low content of their native compounds in urine requires detailed identification of their metabolites, which are excreted with urine and are present in blood. Using gas and liquid chromatography-mass spectrometry, we identified a series of metabolites in urine samples from humans and ratsyesBelgorod State Universit

Calculation of thermal parameters of SiGe microbolometers

The thermal parameters of a SiGe microbolometer were calculated using numerical modeling. The calculated thermal conduction and thermal response time are in good agreement with the values found experimentally and range between 2x10$^-7$ and 7x10$^-8$ W/K and 1.5 and 4.5 ms, respectively. High sensitivity of microbolometer is achieved due to optimization of the thermal response time and thermal conduction by fitting the geometry of supporting heat-removing legs or by selection of a suitable material providing boundary thermal resistance higher than 8x10$^-3$ cm$^2$K/W at the SiGe interface.Comment: 11 pages, 6 figure

Enzymatic Synthesis of Nucleoside Triphosphates. Does It Involve An Ion-Radical Path ?

Accumulation and release of energy in the nucleoside triphosphate enzymatic synthesis and hydrolysis does not limited to a routine energy consuming nucleophilic mechanism. These processes require an overcoming the large energy barrier exceeding a total value of accumulated or released energy level by at least 3 – 4 times (~10 kcal/mol). This energy is supposed to be taken from the mechanical compression of the catalytic site and used to form P–O chemical bond by a direct nucleophilic addition of phosphate to nucleoside diphosphate (ADP as an example). A new, energetically “cheapâ€, ion-radical mechanism of the ATP biosynthesis has been proposed due to the observation of magnetic isotope and magnetic field effects on the ATP synthesis. This mechanism is about to generate  a compression energy to “spend†on a partial dehydratation of magnesium ion inside the nucleotidyl transferase catalyric site (energy cost of this process is 3-5 kcal/mol, i.e. by 2-3 times less than a total accumulated or released energy). Dehydration of this ion is to increase its electron affinity and hence to stimulate an electron transfer from ADP3- to Mg2+. This reaction is a starting point of the ion-radical mechanism considering the molecular mechanics of enzymatic machines and its quantum chemistry background as well. To the contrast of a hardly controllable nucleophilic path, the ion-radical mechanism might be turned on/off  by a targeted delivery of  paramagnetic magnesium ions, 25Mg2+, towards the phosphate transferring enzyme catalytic site. The magnesium isotope substitution is easily reachable by the endo-osmotic pressure techniques, which makes it attractive for further biotechnological and/or pharmacological application(s)

Group analysis and renormgroup symmetries

An original regular approach to constructing special type symmetries for boundary value problems, namely renormgroup symmetries, is presented. Different methods of calculating these symmetries, based on modern group analysis are described. Application of the approach to boundary value problems is demonstrated with the help of a simple mathematical model.Comment: 17 pages, RevTeX LATeX file, to appear in Journal of Mathematical Physic

Therapeutic distant organ effects of regional hypothermia during mesenteric ischemia-reperfusion injury

IntroductionMesenteric ischemia-reperfusion injury (IRI) leads to systemic inflammation and multiple organ failure in clinical and laboratory settings. We investigated the lung structural, functional, and genomic response to mesenteric IRI with and without regional intraischemic hypothermia (RIH) in rodents and hypothesized that RIH would protect the lung and preferentially modulate the distant organ transcriptome under these conditions.MethodsSprague-Dawley rats underwent sham laparotomy or superior mesenteric artery occlusion (SMAO) for 60 minutes with or without RIH. Gut temperature was maintained at 15°-20°C during SMAO, and systemic normothermia (37°C) was maintained throughout the study period. At 6 or 24 hours, lung tissue was collected for (1) histology, (2) myeloperoxidase activity, (3) bronchoalveolar lavage (BAL) fluid protein concentrations, (4) lung wet/dry ratios, and (5) total RNA isolation and hybridization to Illumina's Sentrix BeadChips (>22,000 probes) for gene expression profiling. Significantly affected genes (false discovery rate <5% and fold change ≥1.5) were linked to gene ontology (GO) terms using MAPPFinder, and hypothermia-suppressed genes were further analyzed with Pubmatrix.ResultsMesenteric IRI-induced lung injury, as evidenced by leukocyte trafficking, alveolar hemorrhage, and increased BAL protein and wet/dry ratios, and activated a proinflammatory lung transcriptome compared with sham. In contrast, rats treated with RIH exhibited lung histology, BAL protein, and wet/dry ratios similar to sham. At 6 hours, GO analysis identified 232 hypothermia-suppressed genes related to inflammation, innate immune response, and cell adhesion, and 33 hypothermia-activated genes related to lipid and amine metabolism and defense response. Quantitative real-time polymerase chain reaction validated select array changes in top hypothermia-suppressed genes lipocalin-2 (lcn-2) and chemokine ligand 1 (CXCL-1), prominent genes associated with neutrophil activation and trafficking.ConclusionsTherapeutic hypothermia during SMAO provides distant organ protection and preferentially modulates the IRI-activated transcriptome in the rat lung. This study identifies potential novel diagnostic and therapeutic targets of mesenteric IRI and provides a platform for further mechanistic study of hypothermic protection at the cellular and subcellular level.Clinical RelevanceVisceral organ ischemia-reperfusion injury (IRI) is a common clinical problem in the settings of shock, sepsis, vascular surgery, and organ transplantation and is a particularly vexing problem in the repair of complex aortic aneurysms. IRI is associated with considerable patient morbidity and mortality, for which there are virtually no therapeutic options. It systematically causes local organ injury and dysfunction, systemic inflammation, and multiple organ failure. Clinical trials investigating the efficacy of pharmacologic blockade of individual downstream inflammatory mediators in critically ill patients have been largely unsuccessful, and such studies highlight the need for novel top-down approaches, such as gene expression profiling for biologic discovery, as well as application of broader therapeutic interventions, such as targeted hypothermia. In this study, we demonstrate the potential application of visceral cooling for distant organ protection during mesenteric IRI, identify broad changes in lung gene expression under these conditions, and have elucidated potential novel diagnostic and therapeutic targets for disease targeting