Impact of the spotted microarray preprocessing method on fold-change compression and variance stability

<p>Abstract</p> <p>Background</p> <p>The standard approach for preprocessing spotted microarray data is to subtract the local background intensity from the spot foreground intensity, to perform a log2 transformation and to normalize the data with a global median or a lowess normalization. Although well motivated, standard approaches for background correction and for transformation have been widely criticized because they produce high variance at low intensities. Whereas various alternatives to the standard background correction methods and to log2 transformation were proposed, impacts of both successive preprocessing steps were not compared in an objective way.</p> <p>Results</p> <p>In this study, we assessed the impact of eight preprocessing methods combining four background correction methods and two transformations (the log2 and the glog), by using data from the MAQC study. The current results indicate that most preprocessing methods produce fold-change compression at low intensities. Fold-change compression was minimized using the Standard and the Edwards background correction methods coupled with a log2 transformation. The drawback of both methods is a high variance at low intensities which consequently produced poor estimations of the p-values. On the other hand, effective stabilization of the variance as well as better estimations of the p-values were observed after the glog transformation.</p> <p>Conclusion</p> <p>As both fold-change magnitudes and p-values are important in the context of microarray class comparison studies, we therefore recommend to combine the Edwards correction with a hybrid transformation method that uses the log2 transformation to estimate fold-change magnitudes and the glog transformation to estimate p-values.</p

A Modified Protocol for Bisulfite Genomic Sequencing of Difficult Samples

The bisulfite genomic sequencing protocol is a widely used method for analyzing DNA methylation. It relies on the deamination of unmethylated cytosine residues to uracil; however, its high rates of DNA degradation and incomplete cytosine to uracil conversion often lead to failed experiments, uninformative results, and false positives. Here, we report the addition of a single-step multiple restriction enzyme digestion (MRED) designed to differentially digest polymerase chain reaction products amplified from unconverted DNA while leaving those of converted DNA intact. We show that for our model system, RARB2 P2 promoter, use of MRED increased informative sequencings ninefold, and MRED did not alter the clonal representation in one fully methylated cell line, H-596, treated or not with 5-azadeoxycytidine, a methylation inhibitor. We believe that this method may easily be adapted for analyzing other genes and provide guidelines for selecting the most appropriate MRED restriction enzymes

Altered neuron excitability and synaptic plasticity in the cerebellar granular layer of juvenile prion protein knock-out mice with impaired motor control.

Although the role of abnormal prion protein (PrP) conformation in generating infectious brain diseases (transmissible spongiform encephalopathy) has been recognized, the function of PrP in the normal brain remains mostly unknown. In this investigation, we considered the effect of PrP gene knock-out (PrP(0/0)) on cerebellar neural circuits and in particular on granule cells, which show intense PrP expression during development and selective affinity for PrP. At the third postnatal week, when PrP expression would normally attain mature levels, PrP(0/0) mice showed low performance in the accelerating rotarod and runway tests and the functioning of 40% of granule cells was abnormal. Spikes were slow, nonovershooting, and nonrepetitive in relation with a reduction in transient inward and outward membrane currents, and also the EPSPs and EPSCs had slow kinetics. Overall, these alterations closely resembled an immature phenotype. Moreover, in slow-spiking PrP(0/0) granule cells, theta-burst stimulation was unable to induce any long-term potentiation. This profound impairment in synaptic excitation and plasticity was associated with a protracted proliferation of granule cells and disappeared at P40-P50 along with the recovery of normal motor behavior (Büeler et al. 1992). These results suggest that PrP plays an important role in granule cell development eventually regulating cerebellar network formation and motor control.Journal ArticleResearch Support, Non-U.S. Gov'tinfo:eu-repo/semantics/publishe

Whole-genome sequences of multidrug-resistant Escherichia coli in South-Kivu Province, Democratic Republic of Congo: characterization of phylogenomic changes, virulence and resistance genes.

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are responsible for severe infections worldwide. Whereas their genotypic and pathogenic characteristics are not documented in Democratic Republic of Congo (DRC), recent studies conducted at the Bukavu General Hospital in the South Kivu province highlighted their high prevalence in extra-intestinal infections. Here we provide data on molecular characterization of ESBL producing-Escherichia coli isolates from patients with extra-intestinal infections at this provincial hospital. Whole-genome sequencing was carried out on 21 of these ESBL-producing Extra-intestinal Pathogenic Escherichia coli (ExPEC) for analysis of phylogenomic evolution, virulence factor and antimicrobial resistance (AMR) genes. Data were compared to phylogenetically close genomes using Multi-Locus Sequence Typing and Single Nucleotide Polymorphism-based phylogenetic approaches. The distribution of E. coli sequence types (ST) was as follows: ST 131 (n = 7), ST405 (n = 4), ST410 (n = 2), and other STs (ST10, ST58, ST95, ST393, ST443, S617, ST648, and ST2450). All ST131 belonged to the O25b-ST131 pandemic clone. Unexpectedly, they harbored more virulence genes than their GenBank counterparts. IncF plasmid replicons included novel FIB 69, FII 105 and FII 107 alleles. ESBL-genes included the plasmid-mediated CTX-M-15 in all isolates, and the SHV-12 allele. Other AMR genes included blaOXA-1, blaTEM-1, as well as genes encoding resistance against aminoglycosides, quinolones, chloramphenicol, rifampicin, tetracyclines, sulfonamides and trimethoprim. Current data confirm the clonal spread of ESBL-producing ST131 and ST405 clones in patients from South Kivu, and the acquisition of resistance and virulence genes. A closer survey of AMR and virulence should therefore be prompted in this high-risk area

Altered neuronal excitability in cerebellar granule cells of mice lacking calretinin

Calcium-binding proteins such as calretinin are abundantly expressed in distinctive patterns in the CNS, but their physiological function remains poorly understood. Calretinin is expressed in cerebellar granule cells, which provide the major excitatory input to Purkinje cells through parallel fibers. Calretinin-deficient mice exhibit dramatic alterations in motor coordination and Purkinje cell firing recorded in vivo through unknown mechanisms. In the present study, we used patch-clamp recording techniques in acute slice preparation to investigate the effect of a null mutation of the calretinin gene on the intrinsic electroresponsiveness of cerebellar granule cells at a mature developmental stage. Calretinin-deficient granule cells exhibit faster action potentials and generate repetitive spike discharge showing an enhanced frequency increase with injected currents. These alterations disappear when 0.15 mm of the exogenous fast-calcium buffer BAPTA is infused in the cytosol to restore the calcium-buffering capacity. A proposed mathematical model demonstrates that the observed alterations of granule cell excitability can be explained by a decreased cytosolic calcium-buffering capacity resulting from the absence of calretinin. This result suggests that calcium-binding proteins modulate intrinsic neuronal excitability and may therefore play a role in information processing in the CN

Reactive cholangiocytes differentiate into proliferative hepatocytes with efficient DNA repair in mice with chronic liver injury.

Chronic liver diseases are characterized by expansion of the small immature cholangiocytes - a mechanism named ductular reaction (DR) - which have the capacity to differentiate into hepatocytes. We investigated the kinetics of this differentiation, as well as analyzing several important features of the newly formed hepatocytes, such as functional maturity, clonal expansion and resistance to stress in mice with long-term liver damage. We tracked cholangiocytes using osteopontin-iCreER &lt;sup&gt;T2&lt;/sup&gt; and hepatocytes with AAV8-TBG-Cre. Mice received carbon tetrachloride (CCl &lt;sub&gt;4&lt;/sub&gt; ) for &gt;24 weeks to induce chronic liver injury. Livers were collected for the analysis of reporter proteins, cell proliferation and death, DNA damage, and nuclear ploidy; hepatocytes were also isolated for RNA sequencing. During liver injury we observed a transient DR and the differentiation of DR cells into hepatocytes as clones that expanded to occupy 12% of the liver parenchyma by week 8. By lineage tracing, we confirmed that these new hepatocytes derived from cholangiocytes but not from native hepatocytes. They had all the features of mature functional hepatocytes. In contrast to the exhausted native hepatocytes, these newly formed hepatocytes had higher proliferative capability, less apoptosis, a lower proportion of highly polyploid nuclei and were better at eliminating DNA damage. In chronic liver injury, DR cells differentiate into stress-resistant hepatocytes that repopulate the liver. The process might account for the observed parenchymal reconstitution in livers of patients with advanced-stage hepatitis and could be a target for regenerative purposes. During chronic liver disease, while native hepatocytes are exhausted and genetically unstable, a subset of cholangiocytes clonally expand to differentiate into young, functional and robust hepatocytes. This cholangiocyte cell population is a promising target for regenerative therapies in patients with chronic liver insufficiency

Purkinje cell dysfunction and alteration of long-term synaptic plasticity in fetal alcohol syndrome

In cerebellum and other brain regions, neuronal cell death because of ethanol consumption by the mother is thought to be the leading cause of neurological deficits in the offspring. However, little is known about how surviving cells function. We studied cerebellar Purkinje cells in vivo and in vitro to determine whether function of these cells was altered after prenatal ethanol exposure. We observed that Purkinje cells that were prenatally exposed to ethanol presented decreased voltage-gated calcium currents because of a decreased expression of the γ-isoform of protein kinase C. Long-term depression at the parallel fiber–Purkinje cell synapse in the cerebellum was converted into long-term potentiation. This likely explains the dramatic increase in Purkinje cell firing and the rapid oscillations of local field potential observed in alert fetal alcohol syndrome mice. Our data strongly suggest that reversal of long-term synaptic plasticity and increased firing rates of Purkinje cells in vivo are major contributors to the ataxia and motor learning deficits observed in fetal alcohol syndrome. Our results show that calcium-related neuronal dysfunction is central to the pathogenesis of the neurological manifestations of fetal alcohol syndrome and suggest new methods for treatment of this disorder