An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation)

<p>Abstract</p> <p>Background</p> <p>Microarray gene expression time-course experiments provide the opportunity to observe the evolution of transcriptional programs that cells use to respond to internal and external stimuli. Most commonly used methods for identifying differentially expressed genes treat each time point as independent and ignore important correlations, including those within samples and between sampling times. Therefore they do not make full use of the information intrinsic to the data, leading to a loss of power.</p> <p>Results</p> <p>We present a flexible random-effects model that takes such correlations into account, improving our ability to detect genes that have sustained differential expression over more than one time point. By modeling the joint distribution of the samples that have been profiled across all time points, we gain sensitivity compared to a marginal analysis that examines each time point in isolation. We assign each gene a probability of differential expression using an empirical Bayes approach that reduces the effective number of parameters to be estimated.</p> <p>Conclusions</p> <p>Based on results from theory, simulated data, and application to the genomic data presented here, we show that BETR has increased power to detect subtle differential expression in time-series data. The open-source R package <it>betr </it>is available through Bioconductor. BETR has also been incorporated in the freely-available, open-source MeV software tool available from <url>http://www.tm4.org/mev.html</url>.</p

In silico and In vitro analysis of MAP3773c protein from Mycobacterium avium subsp. Paratuberculosis

Paratuberculosis is a disease caused by Mycobacterium avium subsp. paratuberculosis (MAP). It is of great interest to better understand the proteins involved in the pathogenicity of this organism in order to be able to identify potential therapeutic targets and design new vaccines. The protein of interest–MAP3773c–was investigated, and molecular modeling in silico, docking, cloning, expression, purification, and partial characterization of the recombinant protein were achieved. In the in silico study, it was shown that MAP3773c of MAP has 34% sequence similarity with Mycobacterium tuberculosis (MTB) FurB, which is a zinc uptake regulator (Zur) protein. The docking data showed that MAP3773c exhibits two metal-binding sites. The presence of structural Zn2+ in the purified protein was confirmed by SDS-PAGE PAR staining. The purification showed one band that corresponded to a monomer, which was confirmed by liquid chromatography–mass spectrometry (LC-MS). The presence of a monomer was verified by analyzing the native protein structure through BN-SDS-PAGE (Native Blue (BN) Two-Dimensional Electrophoresis) and BN–Western blotting. The MAP3773c protein contains structural zinc. In conclusion, our results show that MAP3773c displays the features of a Fur-type protein with two metal-binding sites, one of them coordinating structural Zn2+

Association of immune responses of Zebu and Holstein-Friesian cattle and resistance to mycobacteria in a BCG challenge model

Mycobacterium bovis is the main cause of bovine tuberculosis (BTB) in cattle and can also infect humans. Zebu cattle are considered more resistant to some infectious diseases compared with Holstein‐Friesian (HF) cattle, including BTB. However, epidemiological studies may not take into account usage differences of the two types of cattle. HF cattle may suffer greater metabolic stress due to their more or less exclusive dairy use, whereas Zebu cattle are mainly used for beef production. In experiments conducted so far, the number of animals has been too small to draw statistically robust conclusions on the resistance differences between these cattle breeds. Here, we used a BCG challenge model to compare the ability of naïve and vaccinated Zebu and HF cattle to control/kill mycobacteria. Young cattle of both breeds with similar ages were housed in the same accommodation for the duration of the experiment. After correcting for multiple comparisons, we found no difference between naïve HF and Zebu (ρ = 0.862) cattle. However, there was a trend for vaccinated HF cattle to have lower cfu numbers than non‐vaccinated HF cattle (ρ = 0.057); no such trend was observed between vaccinated and non‐vaccinated Zebu cattle (ρ = 0.560). Evaluation of antigen‐specific IFNγ secretion by PBMC indicated that Zebu and HF cattle differed in their response to mycobacteria. Thus, whilst there may be difference in immune responses, our data indicate that with the number of animals included in the study and under the conditions used in this work, we were unable to measure any differences between Zebu and HF cattle in the overall control of mycobacteria. Whilst determination of different susceptibilities between Zebu and HF cattle using the BCG challenge model will require larger numbers of animals than the number of animals used in this experiment, these data should inform future experiments

Nitric Oxide Not Apoptosis Mediates Differential Killing of Mycobacterium bovis in Bovine Macrophages

To identify the resistance phenotype against Mycobacterium bovis in cattle, we used a bactericidal assay that has been considered a marker of this trait. Three of 24 cows (12.5%) were phenotyped as resistant and 21 as susceptible. Resistance of bovine macrophages (MΦ) to BCG challenge was evaluated for its association with SLC11A1 GT microsatellite polymorphisms within 3′UTR region. Twenty-three cows (95.8%) had a GT(13) genotype, reported as resistant, consequently the SLC11A1polymorphism was not in agreement with our bactericidal assay results. MΦ of cows with resistant or susceptible phenotype were challenged in vitro with virulent M. bovis field strain or BCG, and nitric oxide production, bacterial killing and apoptosis induction were measured in resting and LPS-primed states. M. bovis field strain induced more apoptosis than BCG, although the difference was not significant. Resistant MΦ controlled better the replication of M. bovis (P<0.01), produced more nitric oxide (P<0.05) and were slightly more prone to undergo apoptosis than susceptible cells. LPS pretreatment of MΦ enhanced all the functional parameters analyzed. Inhibition of nitric oxide production with n (G)-monomethyl-L-arginine monoacetate enhanced replication of M. bovis but did not modify apoptosis rates in both resistant and susceptible MΦ. We conclude that nitric oxide production not apoptosis is a major determinant of macrophage resistance to M. bovis infection in cattle and that the influence of SLC11A1 gene 3′UTR polymorphism is not associated with this event

Apoptosis-Inducing Factor Participation in Bovine Macrophage Mycobacterium bovis-Induced Caspase-Independent Cell Death

Mycobacterium tuberculosis complex species survive and replicate in phagosomes of the host cell. Cell death (CD) has been highlighted as one of the probable outcomes in this host-pathogen interaction. Previously, our group demonstrated macrophage apoptosis as a consequence of Mycobacterium bovis infection. In this study, we aimed to identify the contribution of apoptotic effector elements in M. bovis-induced CD. Bovine macrophages were either infected with M. bovis (multiplicity of infection, 10:1) or treated with an M. bovis cell extract (CFE). Structural changes compatible with CD were evaluated. Chromatin condensation was increased three times by the CFE. On the other hand, a terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) assay demonstrated that levels of DNA fragmentation induced by M. bovis and CFE were 53.7% ± 24% and 38.9% ± 14%, respectively, whereas control cells had a basal proportion of 8.9% ± 4.1%. Rates of DNA fragmentation were unaffected by the presence of the pan-caspase inhibitor N-benzyloxycarbonyl-Val-Ala-Asp (z-VAD). Cells treated with 100 μg of CFE for 12 h had a fivefold decrease in the level of mitochondrial outer membrane permeabilization compared to that of untreated cells. Neither M. bovis infection nor CFE treatment induced activation of caspase 3, 8, or 9. Translocation of apoptosis-inducing factor (AIF) to the nucleus was identified in 32% ± 3.5% and 26.3% ± 4.9% of M. bovis-infected and CFE-treated cells, respectively. Incubation of macrophages with z-VAD prior to infection did not alter the percentage of cells showing AIF translocation. Our data suggest that M. bovis-induced CD in bovine macrophages is caspase independent with AIF participation

Specificity of the tuberculin skin test is modified by use of a protein cocktail containing eSAT-6 and CFP-10 in cattle naturally infected with Mycobacterium bovis

The mycobacterial immunodominant ESAT-6 and CFP-10 antigens are strongly recognizable in tuberculosis-infected cattle, and they do not elicit a response in cattle without infection. In addition, they are absent in most environmental mycobacterial species, and therefore, their use can be an alternative to purified protein derivative (PPD) tuberculin in the development of a more specific skin diagnostic test in cattle. The aim of the current study was to assess the potential of an ESAT-6 and CFP-10 (E6-C10) protein cocktail in a skin test format in naturally tuberculosis-infected and paratuberculosis-infected cattle. We also included MPB83 as a third component in one of the protein cocktail preparations. The protein cocktail was tested at different dose concentrations (5, 10, and 15 μg per protein). The best skin response to the E6-C10 protein cocktail was obtained with 10 μg. Subsequently, this concentration was tested in 2 herds with high and low bovine tuberculosis prevalence, the latter with paratuberculosis coinfection. Our data show that the E6-C10 cocktail allows identification of an important proportion of animals that PPDB is not able to recognize, especially in low-prevalence herds. The protein cocktail did not induce reactions in tuberculosis-free cattle or in paratuberculosis-infected cattle. Addition of MPB83 to the protein cocktail did not make any difference in the skin reaction

<i>Mycobacterium bovis</i> induction of bovine macrophage DNA fragmentation is time dependent.

<p>Adherent-macrophages (MØ) were cultured with media alone or with camptothecin (10 µg/mL for 48 h) as negative and positive controls, respectively (A). Also macrophages were cultured in absence (B) or presence of purified <i>E. coli</i> 026:B6 LPS (100 ng/mL) for 22 h (C), and infected with BCG or <i>M. bovis</i> field strain 9926 (MOI of 10 for 4 h), washed and cultured again for 16 and 24 h and stained with TUNEL (BrdUTP-FITC). Histograms are frequency distributions of 1×10⁵ macrophages along FITC signal (log₁₀ scale). Values are percentages of true BrdU-FITC TUNEL-positive cells (M1 gate) of one experiment, representative of two independent experiments with macrophages of three susceptible and three resistant cows. One-way ANOVA showed significant variation in infected versus uninfected controls (<i>P</i><0.05) but not between phenotype (<i>P</i> = 0.4544) regardless of <i>M. bovis</i> strain.</p

Bovine macrophage BCG growth control as an indicatior of a natural disease resistance phenotype.

<p>Adherent-macrophages were infected with BCG Danish strain or <i>M. bovis</i> field strain 9926 (MOI of 10) for 4 h, washed and cultured again for 24 h. Bacterial intracellular growth was calculated by dividing the number of intracellular CFU at 24 h post-infection by the number of intracellular CFU at the start of the assay. The figure shows the percentage of <i>M. bovis</i> growth in macrophages of 24 cows. For BCG values below or equal to the cut-off point of 65% growth (dotted line) are indicative of resistant cattle (white symbols) while values higher than 65% are a sign of susceptibility (black symbols). Plots are mean of triplicates of two independent experiments of each animal.</p

Kinetics of apoptosis induction in resistant and susceptible <i>Mycobacterium bovis</i>–infected bovine macrophages, expressed as percentage (mean ± SD) of cells showing chromatin condensation after infection.

a<p>Macrophages were pre-cultured with or without LPS for 18 h then infected with BCG or <i>M. bovis</i> field strain for 4 h, washed and cultured again for indicated times and then stained with propidium iodide. Two hundred macrophages were analyzed per slide in triplicate cultures and those with chromatin condensation were counted. Results are representative of two independent experiments with macrophages of three susceptible (S) and three resistant (R) cattle.</p>*<p>Significant differences (<i>P</i><0.05) are among phenotypes.</p