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

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)

RNA-seq analysis of synovial fibroblasts brings new insights into rheumatoid arthritis

BACKGROUND: Rheumatoid arthritis (RA) is a chronic autoimmune-disease of unknown origin that primarily affects the joints and ultimately leads to their destruction. Growing evidence suggests that synvovial fibroblasts play important roles in the initiation and the perpetuation of RA but underlying molecular mechanisms are not understood fully. In the present study, Illumina RNA sequencing was used to profile two human normal control and two rheumatoid arthritis synvovial fibroblasts (RASFs) transcriptomes to gain insights into the roles of synvovial fibroblasts in RA. RESULTS: We found that besides known inflammatory and immune responses, other novel dysregulated networks and pathways such as Cell Morphology, Cell-To-Cell Signaling and Interaction, Cellular Movement, Cellular Growth and Proliferation, and Cellular Development, may all contribute to the pathogenesis of RA. Our study identified several new genes and isoforms not previously associated with rheumatoid arthritis. 122 genes were up-regulated and 155 genes were down-regulated by at least two-fold in RASFs compared to controls. Of note, 343 known isoforms and 561 novel isoforms were up-regulated and 262 known isoforms and 520 novel isoforms were down-regulated by at least two-fold. The magnitude of difference and the number of differentially expressed known and novel gene isoforms were not detected previously by DNA microarray. CONCLUSIONS: Since the activation and proliferation of RASFs has been implicated in the pathogenesis of rheumatoid arthritis, further in-depth follow-up analysis of the transcriptional regulation reported in this study may shed light on molecular pathogenic mechanisms underlying synovial fibroblasts in arthritis and provide new leads of potential therapeutic targets

Coherent spin dynamics of electrons and holes in CsPbBr3_3 perovskite crystals

The lead halide perovskites demonstrate huge potential for optoelectronic applications, high energy radiation detectors, light emitting devices and solar energy harvesting. Those materials exhibit strong spin-orbit coupling enabling efficient optical orientation of carrier spins in perovskite-based devices with performance controlled by a magnetic field. Perovskites are promising for spintronics due to substantial bulk and structure inversion asymmetry, however, their spin properties are not studied in detail. Here we show that elaborated time-resolved spectroscopy involving strong magnetic fields can be successfully used for perovskites. We perform a comprehensive study of high-quality CsPbBr$_3$ crystals by measuring the exciton and charge carrier $g$-factors, spin relaxation times and hyperfine interaction of carrier and nuclear spins by means of coherent spin dynamics. Owing to their "inverted" band structure, perovskites represent appealing model systems for semiconductor spintronics exploiting the valence band hole spins, while in conventional semiconductors the conduction band electrons are considered for spin functionality.Comment: 8 pages, 3 figures + supplementary informatio

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

Combined meta-analysis of systemic effects of allogeneic stem cell transplantation and systemic sclerosis

Abstract Background Chronic graft-versus-host disease (cGVHD) is a major factor of morbidity and mortality for allogeneic stem cell transplantation (aSCT). The skin and internal organ involvement is the most common systemic complication of cGVHD and closely resembles systemic sclerosis (SSc). Circulating lymphocytes characterize the autoimmune nature of both conditions. Therefore we hypothesized that the common clinical manifestation (systemic organ and skin injury) and the common underlying players (lymphocytes) justify the combined meta-analysis of these diseases. Results The aSCT and SSc datasets were uploaded from Gene Expression Omnibus (GEO), a public functional genomics data repository. The available microarray studies of peripheral blood mononuclear cells (PBMCs) and isolated lymphocytes were limited to well established microarray platforms (Affymetrix, Agilent, Canvac, and Illumina) and experimental settings with &#8805;10 patients per group. The resulting pools of data were merged by unique gene identifier and analyzed by the expression genome-wide association studies (eGWAS) coupled with the subtraction of the cGVHD+ and cGVHD&#8722; molecular signatures. The eGWAS was applied to 47 and 50 lymphocyte profiles from aSCT and SSc patients, respectively. The identified 35 candidates were represented by 8 known cGVHD genes (including CXCR4, LTBR and PML) and 28 new candidate genes (including SEPX1 and DNJGB1). The further mutual subtraction of cGVHD+ and cGVHD&#8722; candidates and pathway analysis identified a list of 25 genes. Seven of these genes belong to the fibroblast development and function pathway, consisting of the well known cGVHD genes CCND1, JUN, and FOS, and the new molecular targets MMP2, FOSB, TNFAIP8, and DUSP1. These genes become primary candidates for a potential link of systemic effects of cGVHD and SSc. Conclusions We designed a new approach for meta-analysis by combining data from different diseases using common clinical manifestation as a linker. This allowed us to power up the insufficient standalone meta-analysis of aSCT microarray studies, by adding SSc samples to the data pool. This new method has successfully identified novel molecular targets for systemic effects of both aSCT and SSc. We believe that this approach is generalizable and can be applied to an array of diseases with common clinical manifestations.Peer Reviewe

Meta-analysis of molecular response of kidney to ischemia reperfusion injury for the identification of new candidate genes

Abstract Background Accumulated to-date microarray data on ischemia reperfusion injury (IRI) of kidney represent a powerful source for identifying new targets and mechanisms of kidney IRI. In this study, we conducted a meta-analysis of gene expression profiles of kidney IRI in human, pig, rat, and mouse models, using a new scoring method to correct for the bias of overrepresented species. The gene expression profiles were obtained from the public repositories for 24 different models. After filtering against inclusion criteria 21 experimental settings were selected for meta-analysis and were represented by 11 rat models, 6 mouse models, and 2 models each for pig and human, with a total of 150 samples. Meta-analysis was conducted using expression-based genome-wide association study (eGWAS). The eGWAS results were corrected for a rodent species bias using a new weighted scoring algorithm, which favors genes with unidirectional change in expression in all tested species. Results Our meta-analysis corrected for a species bias, identified 46 upregulated and 1 downregulated genes, of which 26 (55%) were known to be associated with kidney IRI or kidney transplantation, including LCN2, CCL2, CXCL1, HMOX1, ICAM1, ANXA1, and TIMP1, which justified our approach. Pathway analysis of our candidates identified &#8220;Acute renal failure panel&#8221; as the most implicated pathway, which further validates our new method. Among new IRI candidates were 10 novel (&lt;5 published reports related to kidney IRI) and 11 new candidates (0 reports related to kidney IRI) including the most prominent candidates ANXA2, CLDN4, and TYROBP. The cross-species expression pattern of these genes allowed us to generate three workable hypotheses of kidney IRI, one of which was confirmed by an additional study. Conclusions Our first in the field kidney IRI meta-analysis of 150 microarray samples, corrected for a species bias, identified 10 novel and 11 new candidate genes. Moreover, our new meta-analysis correction method improved gene candidate selection by identifying genes that are model and species independent, as a result, function of these genes can be directly extrapolated to the disease state in human and facilitate translation of potential diagnostic or therapeutic properties of these candidates to the bedside.Peer Reviewe