The contrast maps for group and regression analyses were thresholded at P < 0.001 without correction for multiple comparisons, and the extent threshold for significant clusters was set to 40 voxels. We were aware that the application of an uncorrected threshold would

certainly limit the impact of possible results as it increases the probability of false positive findings. To justify the selection of an uncorrected threshold in our analyses, we provide the following issues. Taking into account the results of previous Fulvestrant mw findings in DTI studies in ADHD (Ashtari et al., 2005; Makris et al., 2008), we only expected discrete microstructural abnormalities in ADHD that may not be detectable adopting a corrected threshold with

a much higher risk of false negative findings. In this context, it is noteworthy that the only published voxel-based DTI study in ADHD – like a large number of imaging studies in the neuropsychiatric field – also used an uncorrected (P < 0.001) Stem Cell Compound Library ic50 threshold (Ashtari et al., 2005). T1-weighted templates were then overlaid with the statistically significant SPM clusters using MRIcro software for graphical presentation in neurological convention. The MRI atlas of human WM (Mori et al., 2005) was used for the identification of subcortical WM structures. The MNI coordinates and t-statistic of the peak voxel, the cluster size and the corresponding anatomical structures were determined (Mori et al., 2005). The mean FA and MD values of the peak voxel resulting from the voxel-based group analysis as well as from the voxel-based regression analyses were correlated with the measures for attentional performance (ADHD score), impulsivity (number of commission errors) and total ADHD symptomatology (BADDS score). Significance was set to P < 0.05 (uncorrected) for these regression analyses. Gender, age and IQ did not differ between groups (Table 1). Among patients, 16 (43%) were regular smokers, compared with 6 (18%) regular smokers in the control group. As expected,

L-gulonolactone oxidase we found significant group differences in ADHD semi-quantitative measures WURS and BADDS (Table 1). The ADHD score (TOVA) was significantly lower in patients with ADHD (−4.4 ± 5.7) than in controls (1.7 ± 2.0). RT was significantly longer and RT variability was significantly higher in patients with ADHD (Table 1). Patients’ performance was significantly poorer in the TMT-A, in the TMT-B, in the AVLT and in the WMS-R (Table 1). In the remaining neuropsychological tests (MWT, WCST), performance in the patient group was also poorer, but the differences did not achieve statistical significance (Table 1). As the tests examined different categories of neuropsychological performance and executive function, we did not use a Bonferroni correction for multiple comparisons.

e. at approximately 6 weeks after initiation of treatment for

the opportunistic infection [73]. Whilst this study supports early treatment, it does not show whether immediate treatment at time of PCP diagnosis or waiting for a response to PCP treatment (usually within 4–7 days) is the best strategy. Furthermore, recruitment to the study excluded those with severe laboratory abnormalities and required patients to be able to take oral medication – suggesting possible pre-screening selection bias in favour of less sick patients. Cabozantinib research buy Case reports of acute inflammatory syndromes, predominantly in the first 2 weeks of HAART, exist [74] but although IRIS has been reported following early use of HAART post-PCP selleck chemicals llc [75], this appears to be relatively infrequent. Based on this information, some clinicians would treat immediately whilst others may prefer to see a clinical response to PCP treatment. The improvements in systemic and local immunity following continuous use of HAART translate

into a very low risk of PCP if prophylaxis is discontinued in populations with CD4 T-cell counts sustained >200 cells/μL for more than 3 months [76,77]. In practice this is usually undertaken when an individual’s plasma HIV viral load is persistently at undetectable levels. If the peripheral CD4 count falls below 200 cells/μL, PCP prophylaxis should be recommenced. A recent observational study involving over 23 000 individuals has suggested that episodes of PCP are no more frequent in individuals with CD4 T-cell counts of 100–200 cells/μL Casein kinase 1 and an undetectable HIV viral load

(defined in the COHERE study as <400 copies/mL) who do not receive prophylaxis than in those who do [78]. A second smaller observational study also suggested that PCP prophylaxis could be stopped in individuals with a CD4 T-cell count <200 cells/μL when the viral load is undetectable. This study did not define the CD4 T-cell count threshold at which this could be performed [79]. On the basis of these findings some providers may consider stopping PCP prophylaxis in individuals with CD4 counts 100–200 cells/μL, persistently undetectable HIV viral loads (<50 copies/mL) and maximal adherence to their HAART regimen. Healthcare providers should be aware that this is an evolving area and there are no randomised clinical studies to inform clinical practice and a formal recommendation to stop therapy in most cases in this range cannot currently be made. This option should therefore only be considered in selected individuals where there is felt to be some clear advantage to stopping prophylaxis at a CD4 T-cell count 100–200 cells/μL, generally for reasons of treatment toxicity or to improve adherence to other medications.

Transcriptional analysis was performed by real-time PCR to confirm whether the increment of MnP production was caused by the bee2 promoter-regulated expression. gpd, the only housekeeping gene cloned from this strain, was

used as an internal control. For native mnp4, the transcription level at day 4 was the highest selleck products in each strain and markedly decreased from day 8 (Fig. 5a). Janse et al. (1998) reported that transcription of all MnP isozymes at 2 weeks was higher than the transcription of those at 8 weeks in P. chrysosporium grown on hardwood meal. This observation was consistent with the results of our present transcriptional analysis of native mnp4 in P. sordida YK-624. In contrast to native mnp4, http://www.selleckchem.com/products/ABT-263.html we observed high levels of recombinant mnp4 transcription from days 4 to 16 days in BM-65 (Fig. 5b). These results suggest that the transcription of recombinant mnp4 is involved in the increase in MnP production in beech wood meal. Thus, the bee2 promoter is more useful than the GPD promoter under

wood-rotting conditions. To conclude, we identified a protein BUNA2, which was highly produced by P. sordida YK-624 under wood-rotting conditions. The promoter region of the BUNA2 gene, designated bee2, was successfully cloned and demonstrated to be a www.selleck.co.jp/products/cobimetinib-gdc-0973-rg7420.html useful regulator for the high expression of genes under conditions suitable for lignin degradation. In addition, we found that the overexpression of mnp4 under the control of the bee2 promoter is effective for improving the ligninolytic properties in this fungus. Thus, the molecular breeding of superior lignin-degrading fungi for the pretreatment of woody biomass in the production

of bioethanol is possible by the high expression of multiple ligninolytic enzyme genes driven by the bee2 promoter. This work was partially supported by a Grant-in-Aid for Scientific Research (A) (No. 21248023) from the Ministry of Education, Culture, Sports, Science and Technology of Japan. “
“Sortase A (SrtA), a transpeptidase, anchors surface proteins with an LPXTG-motif sorting signal to the cell envelope. To determine the role of SrtA in the pathogenesis of Staphylococcus aureus, we constructed a mutant strain, ∆SrtA, by genetic techniques and identified its functions in a S. aureus-induced mastitis mouse model. The histological and myeloperoxidase (MPO) level results showed that the ∆SrtA strain attenuated the inflammatory reaction in the mammary tissue of mice compared with wild-type S. aureus challenge.

, 2010), where we showed marked differences in saccadic vs. neck electromyographic (EMG) thresholds depending on the size of the characteristic vector. Given this variability, we opted for a fixed stimulation current, and adopted the level used in our previous SEF work (Chapman et al., 2012). Our general experimental setup has been described previously (Chapman et al., 2012). Briefly, the Selleck ERK inhibitor animals were seated in a primate chair with either the head restrained or unrestrained, facing an array of tri-colored (red, green or orange), equiluminant LEDs. The monkeys were trained

as described previously (Chapman & Corneil, 2011) to generate a pro-saccade or an anti-saccade to a peripheral cue depending on the color of a central fixation point (FP; Fig. 1A) for a liquid reward delivered through a head-fixed sipper tube. Trials began with the removal of a diffuse, white background light that prevented dark adaptation. A red or a green FP was then presented directly in front of the monkey. The monkey was required to look at the FP within 1000 ms and hold gaze within a computer-controlled window (radius of 2.5°) for 1250 ms. A red stimulus (the peripheral cue) was then presented randomly to the left or the right of the FP. Cue locations

were fixed at either 10, 15 or 20°, with the eccentricity chosen to be the closest match to the horizontal component of the saccade selleck inhibitor evoked with longer-duration SEF stimulation. The monkeys

had 1000 ms to either look toward (if the FP was red) or away (if the FP was green) from the cue, and fixate for a subsequent 600 ms. The radius of acceptance windows around the correct goal location was 40% of cue eccentricity, to allow for the inaccuracy of anti-saccades in the dark. On anti-saccade trials, an additional green stimulus was illuminated at the correct goal location 300 ms after the correct anti-saccade as reinforcement. A 1000-ms inter-trial interval was provided between each trial. These behavioral constraints were identical for trials with or without ICMS-SEF. Pro- and anti-saccade trials were presented with equal probability with replacement Histidine ammonia-lyase for incorrectly performed trials (i.e. trials where the monkeys did not obtain a reward). Short-duration ICMS-SEF was delivered on two-thirds of all trials, with the other trials designated as control trials. On a given stimulation trial, ICMS-SEF was delivered at a single time-point relative to cue presentation (−1150, −817, −483, −150, 10, 43, 77 or 110 ms, with negative numbers meaning that stimulation preceded cue presentation; Fig. 1A). We define the time preceding cue presentation as the fixation interval, and the time after cue presentation as the post-cue interval.

, 2010), where we showed marked differences in saccadic vs. neck electromyographic (EMG) thresholds depending on the size of the characteristic vector. Given this variability, we opted for a fixed stimulation current, and adopted the level used in our previous SEF work (Chapman et al., 2012). Our general experimental setup has been described previously (Chapman et al., 2012). Briefly, the Linsitinib nmr animals were seated in a primate chair with either the head restrained or unrestrained, facing an array of tri-colored (red, green or orange), equiluminant LEDs. The monkeys were trained

as described previously (Chapman & Corneil, 2011) to generate a pro-saccade or an anti-saccade to a peripheral cue depending on the color of a central fixation point (FP; Fig. 1A) for a liquid reward delivered through a head-fixed sipper tube. Trials began with the removal of a diffuse, white background light that prevented dark adaptation. A red or a green FP was then presented directly in front of the monkey. The monkey was required to look at the FP within 1000 ms and hold gaze within a computer-controlled window (radius of 2.5°) for 1250 ms. A red stimulus (the peripheral cue) was then presented randomly to the left or the right of the FP. Cue locations

were fixed at either 10, 15 or 20°, with the eccentricity chosen to be the closest match to the horizontal component of the saccade Alpelisib mw evoked with longer-duration SEF stimulation. The monkeys

had 1000 ms to either look toward (if the FP was red) or away (if the FP was green) from the cue, and fixate for a subsequent 600 ms. The radius of acceptance windows around the correct goal location was 40% of cue eccentricity, to allow for the inaccuracy of anti-saccades in the dark. On anti-saccade trials, an additional green stimulus was illuminated at the correct goal location 300 ms after the correct anti-saccade as reinforcement. A 1000-ms inter-trial interval was provided between each trial. These behavioral constraints were identical for trials with or without ICMS-SEF. Pro- and anti-saccade trials were presented with equal probability with replacement Rebamipide for incorrectly performed trials (i.e. trials where the monkeys did not obtain a reward). Short-duration ICMS-SEF was delivered on two-thirds of all trials, with the other trials designated as control trials. On a given stimulation trial, ICMS-SEF was delivered at a single time-point relative to cue presentation (−1150, −817, −483, −150, 10, 43, 77 or 110 ms, with negative numbers meaning that stimulation preceded cue presentation; Fig. 1A). We define the time preceding cue presentation as the fixation interval, and the time after cue presentation as the post-cue interval.

Two interactions were significant. First, the sound type (voice, music) by stimulus type (standard, deviant) interaction (F1,34 = 4.298, P = 0.046, ηp2 = 0.112) revealed that participants responded equally fast to vocal and musical standards (F1,35 < 1), but were faster to respond to vocal, rather than musical, deviants (F1,35 = 4.913, P = 0.033, ηp2 = 0.123). Second, the naturalness (NAT, ROT) by sound type (voice, learn more music)

interaction was also significant (F1,34 = 9.464, P < 0.01, ηp2 = 0.218) due to faster RTs to vocal as compared with musical sounds in the NAT condition (F1,35 = 9.395, P < 0.01, ηp2 = 0.212). In summary, musicians were overall more accurate at the temporal discrimination task and tended to be distracted less by irrelevant timbre change. Additionally, while musicians were equally accurate in their responses to vocal and musical deviants, non-musicians were significantly less accurate and more distracted when classifying musical as compared with vocal deviants. Event-related potentials collected from both groups displayed the expected ERP components. In Figs 3 and 4, ERPs elicited by standards are overlaid with ERPs elicited by deviants, separately for NAT (Fig. 3) and ROT (Fig. 4) check details conditions. Figures 5 and 6 directly compare ERPs elicited in musicians and non-musicians for NAT (Fig. 5) and ROT (Fig. 6) sounds in order to better visualize group differences. The N1 and P3a components

are marked on the Cz site, P3b – on the Pz site, and RON – on the F8 site. Below we present ERP results separately for each of the components of interest, which is followed by a summary with an emphasis on the effect of group and its interactions with other factors. Musicians had a significantly larger N1 peak amplitude compared with non-musicians. This effect was present across all

sites in the midline analysis (F1,34 = 5.205, P = 0.029, ηp2 = 0.133), over frontal, fronto-central and central sites in the mid-lateral analysis (group by site, F4,136 = 3.729, P = 0.038, ηp2 = 0.099; group, F1,34 = 4.314–7.84, P = 0.008–0.045, ηp2 = 0.113–0.187), and over frontal and fronto-temporal sites in the lateral analysis (group by site, F3,102 = 3.701, P = 0.04, ηp2 = 0.098; group, F1,34 = 3.58–7.372, P = 0.01–0.055, ηp2 = 0.104–0.178). The BCKDHB effect of group did not interact with naturalness (group by naturalness: midline F1,34 < 1; mid-lateral, F1,34 < 1; lateral, F1,34 = 1.423, P = 0.241). Additionally, deviants elicited a significantly larger N1 peak amplitude compared with standards (stimulus type: midline, F1,34 = 86.22, P < 0.001, ηp2 = 0.717; mid-lateral, F1,34 = 130.727, P < 0.001, ηp2 = 0.794; lateral, F1,34 = 118.833, P < 0.001, ηp2 = 0.778). Lastly, there were several significant results involving the effect of hemisphere over mid-lateral and lateral sites. In mid-lateral sites, the peak amplitude of N1 was overall larger over the right than over the left hemisphere sites (hemisphere, F1,34 = 4.277, P = 0.

Alkaline extraction of NADH was carried out using the protocol of Caruso et al. (2004), with some modifications. Briefly, a 20-mL aliquot from Xcg cultures grown in LB or RSB for 18 h was centrifuged at 12 500 g for 10 min at 4 °C. The cell pellet was DAPT order washed once with 20 mL phosphate-buffered saline (PBS; 10 mM, pH 7.5) and suspended in 2 mL of chilled KOH (0.5 M). Two volumes of cold milliQ water was added to this alkaline suspension, which was then vortexed for 2 min. The mixture was centrifuged at 12 500 g for 40 min at 4 °C. The supernatant was collected and neutralized by adding 10% volume of KH2PO4 (1 M, pH 6.5). The sample was filtered through a 0.22-μm

filter (Millipore, Bedford, MA) and analyzed using HPLC (Waters, Milford, MA). The C18 column (dimension: 150 × 4 mm) was used for analysis. The sample was loaded into a vial of the autosampler. The mobile phase consisted of buffers A and B [A: 0.1 M KH2PO4, pH 6.0; and B: 0.1 M KH2PO4 (pH 6.0) having 10% (v/v) methanol)]. Buffers were filtered through a 0.22-μm filter

(Millipore) and degassed. Before beginning the analysis of samples, the HPLC system was equilibrated with 50% buffer A/50% buffer B for 30 min. The flow rate was adjusted to 1 mL min−1. The samples were analyzed using the binary gradient (Caruso et al., 2004): 100% buffer A for 2 min, followed by sample injection, 100% buffer A for 5 min, 0–25% buffer B for 6 min, 25–60% buffer B for 2.5 min, 60–100% buffer B for 5 min, 100% buffer B for 7.5 min, and, lastly, 100% selleck kinase inhibitor buffer A for 2 min to

equilibrate the system for the next analysis. The detection of NADH was carried out by measuring the absorbance at 254 nm (Waters 996 Photodiode array detector). Acid extraction of ATP and ADP was carried out based on the method of Giannattasio et al. (2003). Briefly, a 20-mL aliquot from Xcg cultures grown in LB or RSB for 18 h was centrifuged at 12 500 g for 10 min at 4 °C. The cells were washed once with 20 mL PBS (10 mM, pH 7.5) and the pellet was suspended in 4 mL of chilled perchloric acid (0.5 M). The cell suspension was sonicated for 3 min and incubated for a further 45 min with vigorous shaking at 10-min intervals. The acid extract was neutralized with 0.8 × 0.5 M KOH and 0.2 × 1 M KH2PO4 (pH 7.5) and kept MTMR9 on ice for 15 min. The potassium perchlorate precipitate was finally removed by centrifugation (12 500 g for 30 min at 4 °C). The supernatant was filtered through a 0.22-μm filter (Millipore) and subjected to HPLC analysis (Waters) using the C18 column (dimension: 150 × 4 mm). Samples were loaded into a vial of the autosampler. The mobile phase consisted of buffers A [0.1 M KH2PO4, pH 6.0; and 8 mM tetrabutylammonium hydrogen sulfate (TBA)] and B [0.1 M KH2PO4, pH 6.0; 8 mM TBA, and 30% (v/v) acetonitrile].

, 2010). Regulation

of rRNA transcription remains particularly cryptic, as most current approaches specifically exclude stable RNAs, including rRNA (e.g. Wurtzel et al., 2010). We used an SSV1-based find more reporter gene system in the model archaeon S. solfataricus (Jonuscheit et al., 2003) to determine whether the S. solfataricus core 16S/23S rRNA gene promoter (−41 to +1) is functional and regulated in vivo in response to the growth phase. The core TF55α and the wild-type lacS promoters from S. solfataricus were used as controls. Viral vector pKMSW72 containing the wild-type lacS gene in SSV1 was constructed in two steps (primers and plasmids listed in Table 1). First, the lacS gene plus 200 bp of upstream DNA was amplified from S. solfataricus P2 (DSM1617) DNA via PCR using Pfu DNA polymerase and primers BG840 and BG841, thereby introducing BamHI sites.

The BamHI-cut PCR product was ligated into similarly Talazoparib in vitro cut pUC28, yielding plasmid pKMSW70. Plasmid pKMSW70 was cut with PstI, dephosphorylated, and ligated to PstI-cut SSV1 to create pKMSW72 (Fig. 1). Vector pMAD107, containing the core 16S/23S rRNA gene promoter–lacS fusion, was constructed in three steps. First, the lacS promoter in pKMSW70 was deleting using long-inverse PCR (Clore & Stedman, 2007) using primers pKMSW70MasterF and pKMSW70MasterR. The PCR product was phosphorylated and ligated to produce pMT95. This plasmid was cut with PstI and PacI, dephosphorylated, and ligated to annealed oligonucleotides p16S/23SrRNAF and p16S/23SrRNAR. For annealing, oligonucleotides were incubated at 94 °C for 10 min followed by slow cooling to room temperature. The resulting plasmid, pMAD106, was digested with PstI, dephosphorylated, and ligated into SSV1 cut with PstI to yield

pMAD107. In the same RAS p21 protein activator 1 manner, primers pTF55αF and pTF55αR were annealed then ligated to pMT95 to produce the TF55α promoter-lacS construct pMAD109. This plasmid was inserted into PstI-cut SSV1 to create pMAD110. All constructions were confirmed by restriction endonuclease digestion and sequencing of the promoter and part of the lacS gene (data not shown). XL-10 Gold supercompetent Escherichia coli cells (Stratagene) were utilized for all steps in vector construction. The pMAD107, pMAD110, and pKMSW72 plasmids, purified from E. coli by alkaline lysis (Feliciello & Chinali 1993), were electroporated into S. solfataricus PH1 as described previously (Albers & Driessen, 2008). Successful transformation was confirmed by PCR using SSV1-specific primers UnivSSV#7F and UnivSSV#8R (Snyder et al., 2004) or B49F and B49R. For UnivSSV#7F and UnivSSV#8R, PCR conditions were as follows: 95 °C 1 min, then 35 cycles, 95 °C, 30 s, 46 °C, 30 s, 72 °C, 1 min, and then 7 min at 72 °C. For B49F and B49R, 95 °C 1 min, then 35 cycles, 95, 60, and 72 °C for 30 s each, then 4 min at 72 °C. Sulfolobus solfataricus strains were grown aerobically at 76 °C on plates or in liquid media, both as in Jonuscheit et al. (2003).

e. FgGFP1 (male) × Z3643 (female)]. Availability of individual MAT

transcript expression profiles in various fungal strains provides clues to the variation in self-fertility among the Fg complex at the level of MAT loci. The differing expression pattern of individual MAT genes in all F. asiaticum strains compared with F. graminearum strains can be attributable to the defect in self-fertility in these strains. Failure to up-regulate MAT1-1-2 and MAT1-1-3, and reduced up-regulation of MAT1-1-1, MAT1-2-1, and MAT1-2-3 during the entire sexual cycle may cause a putative set of genes under the control of these MAT genes to be abnormally or not properly expressed, leading to self-sterility in F. asiaticum. Nevertheless, similarity in expression patterns of MAT1-1-1, MAT1-2-1, GKT137831 molecular weight and MAT1-2-3 in all F. graminearum and F. asiaticum strains

examined cannot exclude the possibility that the early induction pathway of sexual development controlled by these genes is PI3K inhibitor not responsible for the self-fertility differences in these Fg complex strains. To test these postulates, a comparison of genome-wide expression profiles using combinations of wild-type F. graminearum and F. asiaticum strains and their MAT-deleted strains would be necessary. To date, several approaches have been used to identify the target genes of MAT loci in several filamentous fungi (Qi et al., 2006; Hallen et al., 2007; Keszthelyi et al., 2007; Klix et al., 2010; Bidard et al., 2011). For example, comparing transcription profiles during sexual development, or between a fertile fungal strain and its transgenic strain lacking a MAT gene (e.g. in P. anserina, F. verticillioides, Beta adrenergic receptor kinase and S. macrospora), provided several sets of genes

differentially regulated in the mutant strains. However, the genes directly regulated by individual MAT genes remain undetermined. The developmental up-regulation pattern and transcript abundance in two sets of MAT genes (a set of MAT1-1-1, MAT1-2-1, and MAT1-2-3, and the other of MAT1-1-2 and MAT1-1-3) provide new insight into functional role(s) of individual MAT genes for sexual development in F. graminearum, which are also supported by the phenotypic changes in the gene deletion strains. The former set of MAT genes can be considered key regulators of sexual development, particularly required for the early sexual stage for the following reasons. First, the gene expressions peaked at 2 dai, and the transcripts were more (at least 65-fold higher) abundant than those of the latter set of MAT genes at 2 dai. Secondly, the absence of perithecium-like structures in ΔMAT1-2-1 strain or the presence of barren perithecia in the ΔMAT1-1-1 strain, which were even smaller than those in the ΔMAT1-1-2 and ΔMAT1-2-3 strains, on carrot agar could be attributable to blockage of early events such as internuclear recognition, formation of ascogenous hyphae, and nuclear fusion.

DNA and RNA were quantified

and purity determined using the NanoDrop 8000 spectrophotometer (Thermo Scientific). cDNA samples were analyzed using an Agilent 2100 Bioanalyzer. Double-stranded cDNA for microarray analysis was produced according to a protocol provided by Roche NimbleGen® Inc. (http://www.nimblegen.com/products/lit/expression/index.html) with the Wee1 inhibitor modifications. Briefly, cDNA was synthesized using the Superscript Double-Stranded cDNA Synthesis kit (Invitrogen) using 10 µg of total RNA and 3 µg of random primers. The cDNA was incubated with 10 µg of RNaseA Solution (Novagen) for 10 min at 37 °C to eliminate remaining RNA. MaXtract Low Density tubes (Qiagen) were used to purify the cDNA. The final DNA pellet was dried in a SpeedVac and rehydrated in 20 μL of nuclease-free water. cDNAs (2.5 μg per sample; two technical replicates for calf 220) were sent to Roche NimbleGen (Reykjavik, Iceland), for Cy3 labeling, hybridization, scanning, and preliminary data processing using the M. hemolytica custom array (081107_Mannheimia_haem_expr_X4), which is based on the draft sequence of strain ATCC BAA-410 (Gioia et al., 2006). The array is designed as a four-plex (four arrays per slide). Each array contains

18 000 60-mer oligonucleotide probes; these represent up to seven Tm matched probes per gene (2548 of 2695 predicted open reading frames annotated in the genome) plus random and cross-hybridization controls. Details about the array are Fulvestrant cell line available at NimbleGen.com. Gene expression summary values for each gene were generated using quantile normalization (Bolstad et al., 2003) and Robust Multichip Average (RMA) analysis (Irizarry et al., 2003a, b). Normalized data were analyzed using the arraystar v2.1 software (DNAStar, Madison, WI). Replicate sets of expression data for each gene were averaged. Student’s t-test was used to calculate the 99% confidence level for differentially

expressed genes (P < 0.01). Differentially expressed genes were placed into functional classification groups using the clusters of orthologous groups (COGs). Sequence similarity ROS1 assessments were performed using blast. The in vivo samples were collected from calves experimentally challenged with M. hemolytica A1. At necropsy, the lungs were scored for percent pneumonic tissue; calf 220 and 299 had 9% and 18% pneumonic scores, respectively. RNA samples were tested for DNA contamination using two rounds of standard PCR. All samples assessed were deemed to be free of DNA contamination. As the RNA preparations contained both bacterial and host RNA, concentration values are not a direct reflection of the amount of bacterial transcripts. Samples that were converted to ds cDNA were evaluated using an Agilent 2100 Bioanalyzer and were determined to be the product of good quality, non-degraded RNA. In addition, any residue host DNA should have minimal interference with hybridization with the array as the conditions were optimized for specific binding.