Venn diagram showing the relationship of present calls between PBMC, PAX and PAX-GR in SCD samples.

<p>Venn diagram showing the relationship of present calls between PBMC, PAX and PAX-GR in SCD samples.</p

Detection of expressed transcripts in PBMC, PAX and PAX-GR in control (Grey bars) and SCD (Black bars) as determined by the present calls for the samples (n = 5) analyzed by microarrays.

<p>Values are given as mean±SD for the number of present transcripts in each of the groups in each sample type.</p

Figure 2

<p>A. Expression of 18s, globin transcripts α, β by RT-PCR in PAX and PAX-GR from control and SCD samples. Ct values in the expression of globins are given as mean±SD for each group. Red bar - PAX-Control; Green bar - PAX-GR Control; Yellow bar - PAX-SCD; Blue bar - PAX-GR-SCD. B. Normalized signal intensities for β globin probe sets from microarrays for control and SCD samples. Values are given as mean±SD. Grey bar - PAX; Black bar - PAX-GR. C. Normalized signal intensities for α globin probesets from microarrays for control and SCD samples. Values are given as mean±SD. Grey bar - PAX; Black bar - PAX-GR.</p

List of selected genes that overlap between PAX and PAX-GR.

<p>List of selected genes that overlap between PAX and PAX-GR.</p

Heat Map of differential gene expression in PAX-GR in sickle cell disease (n = 5) in comparison to control subjects (n = 5).

<p>Cluster analysis was applied to gene expression data derived from all probes on HG-U133 plus 2.0 at FDR 10% and FC >5.0. The level of expression of each gene in each sample relative to the median level of expression of that gene across all samples is represented using a red, black and green color scale (green – below median; black – equal to median; red - above median). The dendrogram displays the unsupervised clustering of patients and control subjects using the differentially expressed gene list.</p

Validation of microarray data by RT-PCR.

<p>Validation of microarray data by RT-PCR.</p

Gene ontology classification for genes common to PAX and PAX – GR.

<p>Many genes have multiple gene ontology descriptions.</p

A Characterization of the Oral Microbiome in Allogeneic Stem Cell Transplant Patients

<div><h3>Background</h3><p>The mouth is a complex biological structure inhabited by diverse bacterial communities. The purpose of this study is to describe the effects of allogeneic stem cell transplantation on the oral microbiota and to examine differences among those patients who acquired respiratory complications after transplantation.</p> <h3>Methodology/Principal Findings</h3><p>All patients were consented at the National Institutes of Health, Clinical Center. Bacterial DNA was analyzed from patients' oral specimens using the Human Oral Microbe Identification Microarray. The specimens were collected from four oral sites in 45 allogeneic transplantation patients. Specimens were collected at baseline prior to transplantation, after transplantation at the nadir of the neutrophil count and after myeloid engraftment. If respiratory signs and symptoms developed, additional specimens were obtained. Patients were followed for 100 days post transplantation. Eleven patients' specimens were subjected to further statistical analysis. Many common bacterial genera, such as <em>Streptococcus, Veillonella, Gemella</em>, <em>Granulicatella</em> and <em>Camplyobacter</em> were identified as being present before and after transplantation. Five of 11 patients developed respiratory complications following transplantation and there was preliminary evidence that the oral microbiome changed in their oral specimens. Cluster analysis and principal component analysis revealed this change in the oral microbiota.</p> <h3>Conclusions/Significance</h3><p>After allogeneic transplantation, the oral bacterial community's response to a new immune system was not apparent and many of the most common core oral taxa remained unaffected. However, the oral microbiome was affected in patients who developed respiratory signs and symptoms after transplantation. The association related to the change in the oral microbiota and respiratory complications after transplantation will be validated by future studies using high throughput molecular methods.</p> </div

Sampling information.

<p>Sample descriptions including time and site obtained for each patient and totals. Specimens obtained from plaque (P), saliva (S), buccal brushings (B) and tongue brushings (T). Baseline specimens obtained at start of study. Nadir of absolute neutrophil count (ANC) is after transplant when ANC is at its lowest point. Engraftment is after transplant when ANC remained at 0.5×109/liter for two days. RSS represents patients that developed respiratory signs and symptoms after transplant and NoRSS represents patients who did not develop this complication.</p

Genera Factor Loading of Principal Component Analysis.

<p>Factor loading plot of proportion of positive probes further illustrates the PCA plot from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047628#pone-0047628-g004" target="_blank">Figure 4</a>. The loading of the 43 genera show how each genus contributed to the score plot.</p