Locations of the Turkish archaeological sites.

<p>Locations of the Turkish archaeological sites where the ancient wheat samples were obtained. [Image is for representative purpose only. [Source—<a href="http://sedac.ciesin.columbia.edu/gpw" target="_blank">http://sedac.ciesin.columbia.edu/gpw</a>. Licensed under Creative Commons 3.0 Attribution License.]</p

Archaeological wheat samples analyzed in this study.

<p>Archaeological wheat samples analyzed in this study.</p

The hand drawn pictures of ancient seeds from Çatalhöyük and Imamogğlu Höyük.

<p>a) Typical einkorn; hulled domesticated diploid wheat (<i>T</i>. <i>monococcum</i>: identified by EOD & DM); A single seed from Çatalhöyük, originally labeled as an einkorn sample (<i>T</i>. <i>monococcum</i>) (EVI.17, 1962. b) Typical einkorn; hulled domesticated diploid wheat (<i>T</i>. <i>monococcum</i>; identified by EOD & DM); A single seed from Çatalhöyük, originally labeled as an einkorn sample (<i>T</i>. <i>monococcum</i>) (EVI.17, 1962). c) Atypical einkorn; a transition type between einkorn (diploid) and naked wheat (tetra/hexaploid). A single seed from the Çatalhöyük62 sample (<i>T</i>. <i>monococcum</i>) (EVI.17, 1962), identified by D. Martinoli. d) Naked wheat; tetraploid or hexaploid free treshing wheat (<i>T</i>. <i>durum/aestivum</i>). A single seed from the Çatalhöyük62 sample (<i>T</i>. <i>monococcum</i>) (EVI.17, 1962), identified by D. Martinoli. e) Typical emmer; hulled domesticated tetraploid wheat (<i>T</i>. <i>dicoccum</i>; identified by DM); A single seed from Çatalhöyük, originally labelled as an emmer sample, E IV.4, 1961 (<i>T</i>. <i>dicoccum</i>). f) Atypical emmer; a transition type between emmer (tetraploid) and naked wheat (tetra/hexaploid: identified by DM); A single seed from Çatalhöyük originally labeled as an emmer sample E IV.4, 1961 (<i>T</i>. <i>dicoccum</i>) g) Naked wheat; tetraploid or hexaploid free threshing wheat (<i>T</i>. <i>durum/T</i>. <i>aestivum</i>; identified by DM); A single seed from Çatalhöyük, originally labeled as an emmer sample E IV.4, 1961 (<i>T</i>. <i>dicoccum</i>). h) Naked wheat; tetraploid or hexaploid free threshing wheat (<i>T</i>. <i>durum/T</i>. <i>aestivum</i>; identified by EOD); A single seed from the İmamoğlu Höyük sample. i) Naked wheat; tetraploid or hexaploid free threshing wheat (<i>T</i>. <i>durum/T</i>. <i>aestivum</i>; identified by EOD); A single seed from the Patnos sample. EOD: E. O. Dönmez of Department of Biology, Haccettepe University and DM: D. Martinoli, Swiss Biodiversity Forum, Switzerland, Botany (drawn by a commercial graphic artist and further cross-checked by the scientists involved in the study).</p

Autoradiograph of the radioactively labeled PCR amplification products of the Çatalhöyük samples separated on DNA sequencing gel.

<p>1) Modern <i>T</i>. <i>durum</i> targeting 243 bp long PCR amplification product of Glu locus. 2) No DNA, negative control of PCR loaded on lane 1. 3) PCR with Çatalhöyük samples extraction blank. 4) PCR with Çatalhöyük62 and 5) Emmer DNA isolates. 6) PCR with Baklatepe sample extraction blank. 7) PCR with a Baklatepe sample. 8) Modern <i>T</i>. <i>durum</i>. 9) No DNA, negative control of PCR loaded on lane 8. 10) PCR with extraction blank. 11) PCR with Çatalhöyük62 and 12) Çatalhöyük61 DNA isolates. 13) PCR with a Baklatepe sample extraction blank. 14) PCR with a Baklatepe sample. B) Blank lanes. Lanes A) DNA sequencing reaction products with ddATP and G) DNA are sequencing reaction products with ddGTP of M13mp18 ssDNA using a T7 primer. The arrows on the left indicate the lengths in bp, the arrows on the right (lanes 11 and 12) indicate the top and bottom alleles in the Çatalhöyük samples.</p

Target regions Nuclear-HMW glutenin promoter and sequences of the PCR primers utilized in the ancient DNA amplifications in the current study.

<p>Target regions Nuclear-HMW glutenin promoter and sequences of the PCR primers utilized in the ancient DNA amplifications in the current study.</p

A Neighbor-Joining tree showing the genetic similarity between Çatalhöyük (CH) and contemporary wheat species (<i>Triticum</i> sp.).

<p><b>A</b> Neighbor-Joining tree showing the genetic similarity between the Çatalhöyük (CH) and contemporary wheat species (<i>Triticum</i> sp.) based on the DNA sequences excluding the PCR primer sites. CH_M (Çatalhöyük61) and CH_E (Çatalhöyük62) denote the sequences obtained from samples previously classified as emmer (CH61 E.IV, ~6200 BC_calibrated) and einkorn (CH62 E.VI, ~6400 BC_calibrated), respectively; parentheses denote multiple clone copies of the same allele. Genomic compositions are presented as the subscript to each species, including two hexaploid forms, naked (<i>T</i>. <i>aestivum</i>) and hulled (<i>T</i>. <i>spelta</i>) wheat. The Bootstrap values are printed next to the branches. The sequences have been deposited in to GenBank under the accession numbers AF528823-AF528844.</p

Type I IRGs are slightly enriched before onset of symptoms, but some IRGs show no change.

<p>(A) Superarray analysis by qPCR was performed on 70 timepoints from 52 subjects to assess the time course of gene expression. Average fold changes for three groups of genes (Type I IRG, Type II IRG, and Cell Cycle as defined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085422#pone.0085422.s001" target="_blank">Figure S1</a>) were determined for samples collected within the indicated time blocks. Fold changes are compared with healthy baselines. Error bars show the standard deviation. All three gene groupings had a p-value<0.05 when evaluated by ANOVA. (−20 days to −1 days N = 11; 0 days to 3 days N = 12; 4 days to 7 days N = 17; 8 days to 10 days N = 16). (B) The table shows the average fold change for nine select type I IRGs derived from microarray analysis for SLE, YFV, Flu, HRV, RSV, DENV, Poly IC, and EBV. (C) Heatmaps showing fold change as determined by qPCR for <i>OAS1</i>, <i>MX1</i>, and <i>HERC5</i> at multiple timepoints in EBV infection (top panel) or in other situations (bottom panel).</p

Type II IRG gene expression correlates with CD8 lymphocytosis in primary EBV infection.

<p>Data show the correlation between IRG gene expression and CD8 lymphocytosis in 42 subjects at timepoints within the first two weeks after symptom onset during primary EBV infection. The number of CD8 T cells per mL of peripheral blood was determined by flow cytometry (note: average at baseline was 0.25×10⁶). Superarray analysis by qPCR was performed to determine average fold changes for groups of Type I IRGs and Type II IRGs. Pearson correlation coefficients (r-values) and p-values are shown.</p

A distinct gene expression profile is apparent during acute EBV infection, but not latent infection.

<p>(A) Microarray analysis was performed on pre-infection, acute, and latent timepoints for the 10 subjects with primary EBV infection (listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085422#pone.0085422.s005" target="_blank">Table S1</a>). 464 genes were shown to be significantly changed during the primary response to EBV at a fold change of ≥2 and a p-value ≤0.05. No genes were significantly changed during the latent phase of infection using the same criteria. (B) Ingenuity Pathway Analysis of the 464 acute genes revealed 14 pathways that were enriched amongst the genes that changed during primary EBV. These had a significant p-value (the negative log is shown) following evaluation with the Benjamini-Hochberg multiple tests correction. (C) A heatmap representation of the highest (≥3 fold) gene changes during the acute and latent stages of EBV infection.</p

Primary EBV Infection Induces an Expression Profile Distinct from Other Viruses but Similar to Hemophagocytic Syndromes

<div><p>Epstein-Barr Virus (EBV) causes infectious mononucleosis and establishes lifelong infection associated with cancer and autoimmune disease. To better understand immunity to EBV, we performed a prospective study of natural infection in healthy humans. Transcriptome analysis defined a striking and reproducible expression profile during acute infection but no lasting gene changes were apparent during latent infection. Comparing the EBV response profile to multiple other acute viral infections, including influenza A (influenza), respiratory syncytial virus (RSV), human rhinovirus (HRV), attenuated yellow fever virus (YFV), and Dengue fever virus (DENV), revealed similarity only to DENV. The signature shared by EBV and DENV was also present in patients with hemophagocytic syndromes, suggesting these two viruses cause uncontrolled inflammatory responses. Interestingly, while EBV induced a strong type I interferon response, a subset of interferon induced genes, including <i>MX1, HERC5</i>, and <i>OAS1</i>, were not upregulated, suggesting a mechanism by which viral antagonism of immunity results in a profound inflammatory response. These data provide an important first description of the response to a natural herpesvirus infection in humans.</p></div