Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton

<p>Abstract</p> <p>Background</p> <p>The actin cytoskeleton plays a crucial role in supporting and regulating numerous cellular processes. Mutations or alterations in the expression levels affecting the actin cytoskeleton system or related regulatory mechanisms are often associated with complex diseases such as cancer. Understanding how qualitative or quantitative changes in expression of the set of actin cytoskeleton genes are integrated to control actin dynamics and organisation is currently a challenge and should provide insights in identifying potential targets for drug discovery. Here we report the development of a dedicated microarray, the Actichip, containing 60-mer oligonucleotide probes for 327 genes selected for transcriptome analysis of the human actin cytoskeleton.</p> <p>Results</p> <p>Genomic data and sequence analysis features were retrieved from GenBank and stored in an integrative database called Actinome. From these data, probes were designed using a home-made program (CADO4MI) allowing sequence refinement and improved probe specificity by combining the complementary information recovered from the UniGene and RefSeq databases. Actichip performance was analysed by hybridisation with RNAs extracted from epithelial MCF-7 cells and human skeletal muscle. Using thoroughly standardised procedures, we obtained microarray images with excellent quality resulting in high data reproducibility. Actichip displayed a large dynamic range extending over three logs with a limit of sensitivity between one and ten copies of transcript per cell. The array allowed accurate detection of small changes in gene expression and reliable classification of samples based on the expression profiles of tissue-specific genes. When compared to two other oligonucleotide microarray platforms, Actichip showed similar sensitivity and concordant expression ratios. Moreover, Actichip was able to discriminate the highly similar actin isoforms whereas the two other platforms did not.</p> <p>Conclusion</p> <p>Our data demonstrate that Actichip is a powerful alternative to commercial high density microarrays for cytoskeleton gene profiling in normal or pathological samples. Actichip is available upon request.</p

Use of intranasal mupirocin to prevent methicillin-resistant Staphylococcus aureus infection in intensive care units

INTRODUCTION: Methicillin-resistant Staphylococcus aureus (MRSA) causes severe morbidity and mortality in intensive care units (ICUs) worldwide. The purpose of this study was to determine whether intranasal mupirocin prophylaxis is useful to prevent ICU-acquired infections with MRSA. MATERIALS AND METHODS: We conducted a 4-year observational retrospective study in a 15-bed adult medical ICU. During the first 2-year period mupirocin ointment was included in the MRSA control programme; during the second, mupirocin was not used. The main endpoint was the number of endogenous ICU-acquired infections with MRSA. RESULTS: The number of endogenous acquired infections was significantly higher during the second period than during the first (11 versus 1; P = 0.02), although there was no significant difference in the total number of patients infected with MRSA between the two periods. We also observed that nasal MRSA decolonisation was significantly higher in the mupirocin period than in mupirocin-free period (P = 0.002). CONCLUSION: Our findings suggest that intranasal mupirocin can prevent endogenous acquired MRSA infection in an ICU. Further double-blind, randomised, placebo-controlled studies are needed to demonstrate its cost-effectiveness and its impact on resistance

Advanced spot quality analysis in two-colour microarray experiments

Background: Image analysis of microarrays and, in particular, spot quantification and spot quality control, is one of the most important steps in statistical analysis of microarray data. Recent methods of spot quality control are still in early age of development, often leading to underestimation of true positive microarray features and, consequently, to loss of important biological information. Therefore, improving and standardizing the statistical approaches of spot quality control are essential to facilitate the overall analysis of microarray data and subsequent extraction of biological information. Findings: We evaluated the performance of two image analysis packages MAIA and GenePix (GP) using two complementary experimental approaches with a focus on the statistical analysis of spot quality factors. First, we developed control microarrays with a priori known fluorescence ratios to verify the accuracy and precision of the ratio estimation of signal intensities. Next, we developed advanced semi-automatic protocols of spot quality evaluation in MAIA and GP and compared their performance with available facilities of spot quantitative filtering in GP. We evaluated these algorithms for standardised spot quality analysis in a whole-genome microarray experiment assessing well-characterised transcriptional modifications induced by the transcription regulator SNAI1. Using a set of RT-PCR or qRT-PCR validated microarray data, we found that the semi-automatic protocol of spot quality control we developed with MAIA allowed recovering approximately 13% more spots and 38% more differentially expressed genes (at FDR = 5%) than GP with default spot filtering conditions. Conclusion: Careful control of spot quality characteristics with advanced spot quality evaluation can significantly increase the amount of confident and accurate data resulting in more meaningful biological conclusions. © 2008 Friederich et al; licensee BioMed Central Ltd

Chlorine-bearing molecules in molecular absorbers at intermediate redshifts

We use observations of chlorine-bearing species in molecular absorbers at intermediate redshifts to investigate chemical properties and Cl-35/Cl-37 isotopic ratios in the absorbing sightlines. Chloronium (H2Cl+) is detected along three independent lines of sight in the z = 0.89 and z = 0.68 molecular absorbers located in front of the lensed quasars PKS 1830-211 and B 0218+357, respectively. Hydrogen chloride (HCl) was observed only toward PKS 1830-211, and is found to behave differently from H2Cl+. It is detected in one line of sight with an abundance ratio [H2Cl+]/[HCl] similar to 1, but remains undetected in the other, more diffuse, line of sight, with a ratio [H2Cl+] / [HCl] &gt; 17. The absorption profiles of these two chlorine-bearing species are compared to other species and discussed in terms of the physical properties of the absorbing gas. Our findings are consistent with the picture emerging from chemical models where different species trace gas with different molecular hydrogen fraction. The Cl-35/Cl-37 isotopic ratios are measured in the different lines of sight and are discussed in terms of stellar nucleosynthesis

Radiative and mechanical feedback into the molecular gas in the Large Magellanic Cloud. I. N159W

We present Herschel SPIRE Fourier Transform Spectrometer (FTS) observations of N159W, an active star-forming region in the Large Magellanic Cloud (LMC). In our observations, a number of far-infrared cooling lines including CO(4-3) to CO(12-11), [CI] 609 and 370 micron, and [NII] 205 micron are clearly detected. With an aim of investigating the physical conditions and excitation processes of molecular gas, we first construct CO spectral line energy distributions (SLEDs) on 10 pc scales by combining the FTS CO transitions with ground-based low-J CO data and analyze the observed CO SLEDs using non-LTE radiative transfer models. We find that the CO-traced molecular gas in N159W is warm (kinetic temperature of 153-754 K) and moderately dense (H2 number density of (1.1-4.5)e3 cm-3). To assess the impact of the energetic processes in the interstellar medium on the physical conditions of the CO-emitting gas, we then compare the observed CO line intensities with the models of photodissociation regions (PDRs) and shocks. We first constrain the properties of PDRs by modelling Herschel observations of [OI] 145, [CII] 158, and [CI] 370 micron fine-structure lines and find that the constrained PDR components emit very weak CO emission. X-rays and cosmic-rays are also found to provide a negligible contribution to the CO emission, essentially ruling out ionizing sources (ultraviolet photons, X-rays, and cosmic-rays) as the dominant heating source for CO in N159W. On the other hand, mechanical heating by low-velocity C-type shocks with ~10 km/s appears sufficient enough to reproduce the observed warm CO.Comment: accepted for publication in A&

Methicillin-resistant Staphylococcus aureus carriage in a long-term care facility: hypothesis about selection and transmission

Background: many studies have identified long-term care facilities (LTCFs) as reservoirs of patients carrying methicillin-resistant Staphylococcus aureus (MRSA). However, few data about the mechanisms of MRSA diffusion in these settings are available.Objectives: the purpose of our study was to suggest hypothesis on the possible ways of MRSA transmission to residents in or outside a LTCF. Methods: data concerning patients on the day of the survey and within the preceding year were collected. Multivariate analysis was performed by logistic regression to identify characteristics associated with MRSA carriage. MRSA strains were analysed by pulsed-field gel electrophoresis (PFGE) and the relatedness between DNA patterns was studied with Gel Compar software. Results: the prevalence of MRSA carriage was 37.6%. Treatment with fluoroquinolones or third-generation cephalosporins [odds ratio (OR) = 12.07; 95% confidence interval (CI) = 5.90–24.7], treatment with other antimicrobial agents (OR = 4.40; 95% CI = 2.43–7.97), at least one medical imaging session (OR = 5.08; 95% CI = 2.66–9.69) within the 12 preceding months, and the presence of a subcutaneous catheter on the day of the survey (OR = 3.09; 95% CI = 1.87–5.10) were independently associated with MRSA carriage. Twenty-eight of the 38 strains tested were clustered in two major groups. In each of these groups, strains had at least a 90% relatedness. These strains were isolated in patients hospitalised in different areas of the LTCF. Conclusion: we identified that both molecular and epidemiological arguments support the hypothesis of the possibility of MRSA cross-transmission inside the LTCF. Further studies are needed to confirm and explain the association identified between MRSA carriage and medical imaging

Transfusion Related Acute Lung Injury (TRALI) Caused by Red Blood Cell Transfusion Involving Residual Plasma Anti-HLA Antibodies: A report on two Cases and General Considerations

TRALI is considered a serious hazard among immune complications of blood transfusion and its occurrence is admitted to be globally underestimated. Each type of blood product is likely to cause TRALI. We report here on two consecutive observations of TRALI caused by red blood cell concentrates, in which anti-HLA class I and class II antibodies resulting from post-gravitational allo-immunization were evidenced in donors. HLA class I and II antigenic community between recipients and donors' husbands were found and strong reacting IgG antibodies directed at several of those common antigens were detected in the donors' serum. Both donors had more than 3 pregnancies, raising the issue of blood donor selection or of plasma reduction for cellular products

A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments

Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments—including ground and surface waters—from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the β-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth

High-resolution HLA-A, HLA-B, and HLA-DRB1 haplotype frequencies from the French Bone Marrow Donor Registry

We have estimated human leukocyte antigen (HLA) haplotype frequencies using the maximum likelihood mode, which accommodates typing ambiguities. The results of the frequency distribution of the 7015 haplotypes obtained are presented here. These include a total of 114 HLA-A, 185 HLA-B, and 76 HLA-DRB1 unique alleles at each locus. Across all populations, although the most common individual HLA alleles were HLA-A*02:01 (29.0%), HLA-B*07:02 (11.4%), and HLA-DRB1*07:01 (15.9%), the most frequent haplotype was found to be HLA-A*01:01~B*08:01~DRB1*03:01