Gene expression profiles in the rat streptococcal cell wall-induced arthritis model identified using microarray analysis

Experimental arthritis models are considered valuable tools for delineating mechanisms of inflammation and autoimmune phenomena. Use of microarray-based methods represents a new and challenging approach that allows molecular dissection of complex autoimmune diseases such as arthritis. In order to characterize the temporal gene expression profile in joints from the reactivation model of streptococcal cell wall (SCW)-induced arthritis in Lewis (LEW/N) rats, total RNA was extracted from ankle joints from naïve, SCW injected, or phosphate buffered saline injected animals (time course study) and gene expression was analyzed using Affymetrix oligonucleotide microarray technology (RAE230A). After normalization and statistical analysis of data, 631 differentially expressed genes were sorted into clusters based on their levels and kinetics of expression using Spotfire(® )profile search and K-mean cluster analysis. Microarray-based data for a subset of genes were validated using real-time PCR TaqMan(® )analysis. Analysis of the microarray data identified 631 genes (441 upregulated and 190 downregulated) that were differentially expressed (Delta > 1.8, P < 0.01), showing specific levels and patterns of gene expression. The genes exhibiting the highest fold increase in expression on days -13.8, -13, or 3 were involved in chemotaxis, inflammatory response, cell adhesion and extracellular matrix remodelling. Transcriptome analysis identified 10 upregulated genes (Delta > 5), which have not previously been associated with arthritis pathology and are located in genomic regions associated with autoimmune disease. The majority of the downregulated genes were associated with metabolism, transport and regulation of muscle development. In conclusion, the present study describes the temporal expression of multiple disease-associated genes with potential pathophysiological roles in the reactivation model of SCW-induced arthritis in Lewis (LEW/N) rat. These findings improve our understanding of the molecular events that underlie the pathology in this animal model, which is potentially a valuable comparator to human rheumatoid arthritis (RA)

Between modernization and conflict: the business role, municipal management and the demand for a state drinking water service for Iquique (1830-1924)

Resumen: El abastecer de agua potable a Iquique desde su habilitación como puerto a inicios del siglo XIX, fue una verdadera odisea a razón de ubicarse en una zona costera del desierto de Atacama que no tenía fuentes naturales cercanas de donde extraerla. En estos términos, el rol de los empresarios del agua fue clave para que los iquiqueños se pudieran proveer de este vital recurso, más aún con la ausencia de iniciativas estatales. Sin embargo, la hegemonía empresarial terminó por provocar una serie de incovenientes al primar los intereses comerciales por sobre los sociales que, hacia fines del periodo decimonónico, terminó por afianzar una opinión pública demandante de un servicio estatal de agua potable. Este artículo aborda las distintas iniciativas privadas, las característas del negocio del agua y el conflicto entre el municipio y algunos empresarios por la exigencia de un servicio más equitativo y de mejor calidad.Supplying drinking water to Iquique since its authorization as a port at the beginning of the 19th century was a real odyssey because it was located in a coastal area of the Atacama Desert that had no natural water sources nearby. Thus, the role of water entrepreneurs was essential to provide the Iquique inhabitants with this vital resource, especially as there were no state initiatives to that effect. However, business hegemony ended up causing a series of inconveniences as commercial interests prevailed over social ones. Therefore, at the end of the 19th century, a public opinion demanding a state drinking water service was established. The objective of this article is to analyze the different private initiatives, the characteristics of the water business, the conflict between the municipality and some businessmen around the demand for a service of higher quality and, finally, to demonstrate – based on the analysis of judicial and legislative sources, as well as of the local press – that the commercialization of the service was a greater obsta

Hemodynamic and cardiorespiratory predictors of sport rock climbing performance

Rock-climbing performance is largely dependent on the endurance of the forearm flexors. Recently, it was reported that forearm flexor endurance in elite climbers is independent of the ability to regulate conduit artery (brachial) blood flow, suggesting that endurance is not primarily dependent on the ability of the brachial artery to deliver oxygen, but rather the ability of the muscle to perfuse and use oxygen, i.e. skeletal muscle oxidative capacity. Purpose: The aim of the study was to determine whether an index of oxidative capacity in the flexor digitorum profundus (FDP) predicts the best sport climbing red-point grade within the last 6 months. Participants consisted of 46 sport climbers with a range of abilities. Methods: Using near infrared spectroscopy, the oxidative capacity index of the FDP was assessed by calculating the half-time for tissue oxygen re-saturation (O2HTR) following 3-5 min of ischemia. Results: Linear regression, adjusted for age, sex, BMI and training experience, revealed a 1s decrease in O2HTR was associated with an increase in red-point grade by 0.65 (95% CI: 0.35-0.94, AdjR2 = 0.53). Conclusions: Considering a grade of 0.4 separated the top 4 competitors in the 2015 International Federation Sport Climbing World Cup, these findings suggest that forearm flexor oxidative capacity index is an important determinant of rock climbing performance.N/

Differences in oxygenation kinetics between the dominant and non-dominant flexor digitorum profundus in rock climbers

Purpose. This study examined differences in oxygenation kinetics in the non-dominant and dominant flexor digitorum profundus (FDP) of rock climbers. Methods. Participants consisted of 28 sport climbers with a range of on-sight abilities (6a+ to 8a French Sport). Using near infrared spectroscopy, oxygenation kinetics of the FDP was assessed by calculating the time to half recovery (t½ recovery) of the tissue saturation index (TSI) following 3-5 min of ischemia. Results. A 2-way mixed model ANOVA found a non-significant interaction (p =0.112) for TSI x sex. However, there was a significant the main effect (p =0.027) handedness (dominant vs. non-dominant FDP). The dominant forearm recovered 13.6% quicker (t½ recovery mean difference = 1.12 sec, 95% CI 0.13 to 2.10 sec) compared to the non-dominant FDP. This was not affected by 6-month on-sight climbing ability or sex (p =0.839, p =0.683). Conclusions. Significant intra-individual differences in oxygenation kinetics of the FDP were found. Improvements in oxygenation kinetics within the FDP are likely due to the abilities of the muscle to deliver, perfuse and consume oxygen. These enhancements may be due to structural adaptations in the microvasculature such as an increase in capillary density and an enhanced improvement in capillary filtration

Xanthinuria: a rare cause of urolithiasis in the cat

Xanthinuria is a very rare disease in cats. Its etiology may have a genetic origin or may be due to an iatrogenic xan- thine-dehydrogenase inhibition that nally results in urolithiasis. The present work reports two cases of xanthine uro- lithiasis in European Shorthair unrelated male and female cats. Both uroliths were analyzed by stereoscopic microsco- py, infrared spectroscopy and scanning electron microscopy. Besides the report of these two clinical cases, a detailed pathophysiologic review and some updated recommendations for diagnosis and treatment for this condition were done.La xantinuria es una patología que se presenta raramente en los gatos. Su etiología puede tener origen genético o de- berse a una inhibición yatrogénica de la enzima xantina deshidrogenasa, que generalmente se mani esta con urolitiasis. En este trabajo se informa el hallazgo de dos urolitos de xantina en dos gatos, un macho y una hembra, de raza Euro- pea de pelo corto, no emparentados. Los urolitos fueron analizados mediante microscopía estereoscópica, espectrosco- pía infrarroja y microscopía electrónica de barrido. Además de informar sobre estos casos clínicos, se hace una revisión detallada de la siopatología y de las recomendaciones actuales para el diagnóstico y manejo médico de esta patología.Se agradece al Consejo Nacional de Ciencia y Tecnolo- gía de México (CONACyT) y al Programa de Mejora- miento del Profesorado de la Secretaria de Educación Pública de México 2011 (PROMEP-SEP), el apoyo complementario para la realización de este trabajo

Characterisation of microRNA expression in post-natal mouse mammary gland development.

BACKGROUND: The differential expression pattern of microRNAs (miRNAs) during mammary gland development might provide insights into their role in regulating the homeostasis of the mammary epithelium. Our aim was to analyse these regulatory functions by deriving a comprehensive tissue-specific combined miRNA and mRNA expression profile of post-natal mouse mammary gland development.We measured the expression of 318 individual murine miRNAs by bead-based flow-cytometric profiling of whole mouse mammary glands throughout a 16-point developmental time course, including juvenile, puberty, mature virgin, gestation, lactation, and involution stages. In parallel whole-genome mRNA expression data were obtained. RESULTS: One third (n = 102) of all murine miRNAs analysed were detected during mammary gland development. MicroRNAs were represented in seven temporally co-expressed clusters, which were enriched for both miRNAs belonging to the same family and breast cancer-associated miRNAs. Global miRNA and mRNA expression was significantly reduced during lactation and the early stages of involution after weaning. For most detected miRNA families we did not observe systematic changes in the expression of predicted targets. For miRNA families whose targets did show changes, we observed inverse patterns of miRNA and target expression. The data sets are made publicly available and the combined expression profiles represent an important community resource for mammary gland biology research. CONCLUSION: MicroRNAs were expressed in likely co-regulated clusters during mammary gland development. Breast cancer-associated miRNAs were significantly enriched in these clusters. The mechanism and functional consequences of this miRNA co-regulation provide new avenues for research into mammary gland biology and generate candidates for functional validation.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

The pitfalls of platform comparison: DNA copy number array technologies assessed

<p>Abstract</p> <p>Background</p> <p>The accurate and high resolution mapping of DNA copy number aberrations has become an important tool by which to gain insight into the mechanisms of tumourigenesis. There are various commercially available platforms for such studies, but there remains no general consensus as to the optimal platform. There have been several previous platform comparison studies, but they have either described older technologies, used less-complex samples, or have not addressed the issue of the inherent biases in such comparisons. Here we describe a systematic comparison of data from four leading microarray technologies (the Affymetrix Genome-wide SNP 5.0 array, Agilent High-Density CGH Human 244A array, Illumina HumanCNV370-Duo DNA Analysis BeadChip, and the Nimblegen 385 K oligonucleotide array). We compare samples derived from primary breast tumours and their corresponding matched normals, well-established cancer cell lines, and HapMap individuals. By careful consideration and avoidance of potential sources of bias, we aim to provide a fair assessment of platform performance.</p> <p>Results</p> <p>By performing a theoretical assessment of the reproducibility, noise, and sensitivity of each platform, notable differences were revealed. Nimblegen exhibited between-replicate array variances an order of magnitude greater than the other three platforms, with Agilent slightly outperforming the others, and a comparison of self-self hybridizations revealed similar patterns. An assessment of the single probe power revealed that Agilent exhibits the highest sensitivity. Additionally, we performed an in-depth visual assessment of the ability of each platform to detect aberrations of varying sizes. As expected, all platforms were able to identify large aberrations in a robust manner. However, some focal amplifications and deletions were only detected in a subset of the platforms.</p> <p>Conclusion</p> <p>Although there are substantial differences in the design, density, and number of replicate probes, the comparison indicates a generally high level of concordance between platforms, despite differences in the reproducibility, noise, and sensitivity. In general, Agilent tended to be the best aCGH platform and Affymetrix, the superior SNP-CGH platform, but for specific decisions the results described herein provide a guide for platform selection and study design, and the dataset a resource for more tailored comparisons.</p

Epigenetic regulation of gene expression in response to a changing environment in CHO cell batch culture

Chinese Hamster Ovary (CHO) cells have been the workhorse for industrial production of recombinant therapeutic proteins since 1987. Variations in cellular environment and phenotypes that occur throughout the bioprocess can bring about significant changes in productivity and quality of recombinant proteins. This can potentially lead to rejection of the production lot. Hence, there is interest in an in-depth understanding of cell-line behavior and control to achieve more predictable and reliable process performance. Biological systems undergo dynamic changes over time, where individual genes are turned “on”, “off” or “paused” as and when required. So far, there is very little information available for CHO cell lines, that elucidates the effect of dynamic epigenetic regulation on temporal expression of genes in response to altered substrate availability and culture conditions. While DNA methylation levels around TSS induce either expression or silencing of genes, transcriptional regulation is primarily considered to be an interplay of transcription factors and chromatin modifiers. On top of these, there is a rapid increase in indications that connects phase-specific long non-coding RNAs (lncRNAs) in transcriptional and post-transcriptional gene regulation. Unfortunately, the mechanism of interaction of these lncRNAs with coding genes have not been studied extensively. In this study, the gene transcription dynamics throughout a batch culture of CHO cells was examined by analyzing expression profiles and histone modifications in regular 12-24 hour intervals. Chromatin states and differential methylation profiles were used to understand the role of epigenetic modifiers in the regulation of gene expression. A good correlation between expression level and absence of DNA-methylation in the promoter regions was observed. Genes having all essential active chromatin marks - specific for promoter activity, genic enhancer and active transcription, also showed significantly high positive correlation between the changes in expression levels and histone marks. Both transcription and chromatin modifications during different growth phases were found to be highly dynamic. Clusters of genes showing similar trends of expression depict gradual and continuous adaptation to the changing substrate concentrations. Less narrowly spaced temporal analyses would have prevented detection of critical regulators involved in transient changes during the batch culture. Here, we also report a plausible mode of interaction of lncRNAs with the coding genes mediated by RNA-DNA-DNA triplex formations. Based on the identified interactions, we could predict possible gene targets and the target sites for the expressed lncRNAs and show high level of correlation of expression levels between interacting pairs. To the best of our knowledge this is the first and most comprehensive report of genome wide transcriptional regulation by epigenetic modifiers for CHO. Please click Additional Files below to see the full abstract

The Notch intracellular domain represses CRE-dependent transcription

AbstractMembers of the cyclic-AMP response-element binding protein (CREB) transcription factor family regulate the expression of genes needed for long-term memory formation. Loss of Notch impairs long-term, but not short-term, memory in flies and mammals. We investigated if the Notch-1 (N1) exerts an effect on CREB-dependent gene transcription. We observed that N1 inhibits CREB mediated activation of cyclic-AMP response element (CRE) containing promoters in a γ-secretase-dependent manner. We went on to find that the γ-cleaved N1 intracellular domain (N1ICD) sequesters nuclear CREB1α, inhibits cAMP/PKA-mediated neurite outgrowth and represses the expression of specific CREB regulated genes associated with learning and memory in primary cortical neurons. Similar transcriptional effects were observed with the N2ICD, N3ICD and N4ICDs. Together, these observations indicate that the effects of Notch on learning and memory are, at least in part, via an effect on CREB-regulated gene expression