Correction: TGFß-activation by dendritic cells drives Th17 induction and intestinal contractility and augments the expulsion of the parasite Trichinella spiralis in mice.

[This corrects the article DOI: 10.1371/journal.ppat.1007657.].

Multiregional origins of the domesticated tetraploid wheats.

We used genotyping-by-sequencing (GBS) to investigate the evolutionary history of domesticated tetraploid wheats. With a panel of 189 wild and domesticated wheats, we identified 1,172,469 single nucleotide polymorphisms (SNPs) with a read depth ≥3. Principal component analyses (PCAs) separated the Triticum turgidum and Triticum timopheevii accessions, as well as wild T. turgidum from the domesticated emmers and the naked wheats, showing that SNP typing by GBS is capable of providing robust information on the genetic relationships between wheat species and subspecies. The PCAs and a neighbour-joining analysis suggested that domesticated tetraploid wheats have closest affinity with wild emmers from the northern Fertile Crescent, consistent with the results of previous genetic studies on the origins of domesticated wheat. However, a more detailed examination of admixture and allele sharing between domesticates and different wild populations, along with genome-wide association studies (GWAS), showed that the domesticated tetraploid wheats have also received a substantial genetic input from wild emmers from the southern Levant. Taking account of archaeological evidence that tetraploid wheats were first cultivated in the southern Levant, we suggest that a pre-domesticated crop spread from this region to southeast Turkey and became mixed with a wild emmer population from the northern Fertile Crescent. Fixation of the domestication traits in this mixed population would account for the allele sharing and GWAS results that we report. We also propose that feralization of the component of the pre-domesticated population that did not acquire domestication traits has resulted in the modern wild population from southeast Turkey displaying features of both the domesticates and wild emmer from the southern Levant, and hence appearing to be the sole progenitor of domesticated tetraploids when the phylogenetic relationships are studied by methods that assume a treelike pattern of evolution.

Diversity of a cytokinin dehydrogenase gene in wild and cultivated barley.

The cytokinin dehydrogenase gene HvCKX2.1 is the regulatory target for the most abundant heterochromatic small RNAs in drought-stressed barley caryopses. We investigated the diversity of HvCKX2.1 in 228 barley landraces and 216 wild accessions and identified 14 haplotypes, five of these with ten or more members, coding for four different protein variants. The third largest haplotype was abundant in wild accessions (51 members), but absent from the landrace collection. Protein structure predictions indicated that the amino acid substitution specific to haplotype 3 could result in a change in the functional properties of the HvCKX2.1 protein. Haplotypes 1-3 have overlapping geographical distributions in the wild population, but the average rainfall amounts at the collection sites for haplotype 3 plants are significantly higher during November to February compared to the equivalent data for plants of haplotypes 1 and 2. We argue that the likelihood that haplotype 3 plants were excluded from landraces by sampling bias that occurred when the first wild barley plants were taken into cultivation is low, and that it is reasonable to suggest that plants with haplotype 3 are absent from the crop because these plants were less suited to the artificial conditions associated with cultivation. Although the cytokinin signalling pathway influences many aspects of plant development, the identified role of HvCKX2.1 in the drought response raises the possibility that the particular aspect of cultivation that mitigated against haplotype 3 relates in some way to water utilization. Our results therefore highlight the possibility that water utilization properties should be looked on as a possible component of the suite of physiological adaptations accompanying the domestication and subsequent evolution of cultivated barley.

Diversity of a wall-associated kinase gene in wild and cultivated barley.

Domestication of barley and other cereals was accompanied by an increase in seed size which has been ascribed to human selection, large seeds being preferred by early farmers or favoured by cultivation practices such as deep sowing. An alternative suggestion is that the increase in seed size was an indirect consequence of selection for plants with more vigorous growth. To begin to address the latter hypothesis we studied the diversity of HvWAK1, a wall-associated kinase gene involved in root proliferation, in 220 wild barley accessions and 200 domesticated landraces. A 3655-bp sequence comprising the gene and upstream region contained 69 single nucleotide polymorphisms (SNPs), one indel and four short tandem repeats. A network of 50 haplotypes revealed a complex evolutionary relationship, but with landraces largely restricted to two parts of the topology. SNPs in the HvWAK1 coding region resulted in nonsynonymous substitutions at nine positions in the translation product, but none of these changes were predicted to have a significant effect on the protein structure. In contrast, the region upstream of the coding sequence contained five SNPs that were invariant in the domesticated population, fixation of these SNPs decreasing the likelihood that the upstream of a pair of TATA boxes and transcription start sites would be used to promote transcription of HvWAK1. The sequence diversity therefore suggests that the cis-regulatory region of HvWAK1 might have been subject to selection during barley domestication. The extent of root proliferation has been linked with traits such as above-ground biomass, so selection for particular cis-regulatory variants of HvWAK1 would be consistent with the hypothesis that seed size increases during domestication were the indirect consequence of selection for plants with increased growth vigour.

A discriminatory test for the wheat B and G genomes reveals misclassified accessions of Triticum timopheevii and Triticum turgidum.

The tetraploid wheat species Triticum turgidum and Triticum timopheevii are morphologically similar, and misidentification of material collected from the wild is possible. We compared published sequences for the Ppd-A1, Ppd-B1 and Ppd-G1 genes from multiple accessions of T. turgidum and T. timopheevii and devised a set of four polymerase chain reactions (PCRs), two specific for Ppd-B1 and two for Ppd-G1. We used these PCRs with 51 accessions of T. timopheevii and 20 of T. turgidum. Sixty of these accessions gave PCR products consistent with their taxon identifications, but the other eleven accessions gave anomalous results: ten accessions that were classified as T. turgidum were identified as T. timopheevii by the PCRs, and one T. timopheevii accession was typed as T. turgidum. We believe that these anomalies are not due to errors in the PCR tests because the results agree with a more comprehensive analysis of genome-wide single nucleotide polymorphisms, which similarly suggest that these eleven accessions have been misclassified. Our results therefore show that the accepted morphological tests for discrimination between T. turgidum and T. timopheevii might not be entirely robust, but that species identification can be made cheaply and quickly by PCRs directed at the Ppd-1 gene.

TGFß-activation by dendritic cells drives Th17 induction and intestinal contractility and augments the expulsion of the parasite Trichinella spiralis in mice.

Helminths are highly prevalent metazoan parasites that infect over a billion of the world's population. Hosts have evolved numerous mechanisms to drive the expulsion of these parasites via Th2-driven immunity, but these responses must be tightly controlled to prevent equally devastating immunopathology. However, mechanisms that regulate this balance are still unclear. Here we show that the vigorous Th2 immune response driven by the small intestinal helminth Trichinella spiralis, is associated with increased TGFß signalling responses in CD4+ T-cells. Mechanistically, enhanced TGFß signalling in CD4+ T-cells is dependent on dendritic cell-mediated TGFß activation which requires expression of the integrin αvß8. Importantly, mice lacking integrin αvß8 on DCs had a delayed ability to expel a T. spiralis infection, indicating an important functional role for integrin αvß8-mediated TGFß activation in promoting parasite expulsion. In addition to maintaining regulatory T-cell responses, the CD4+ T-cell signalling of this pleiotropic cytokine induces a Th17 response which is crucial in promoting the intestinal muscle hypercontractility that drives worm expulsion. Collectively, these results provide novel insights into intestinal helminth expulsion beyond that of classical Th2 driven immunity, and highlight the importance of IL-17 in intestinal contraction which may aid therapeutics to numerous diseases of the intestine.

Loss of the TGFß-activating integrin αvß8 on dendritic cells protects mice from chronic intestinal parasitic infection via control of type 2 immunity.

Chronic intestinal parasite infection is a major global health problem, but mechanisms that promote chronicity are poorly understood. Here we describe a novel cellular and molecular pathway involved in the development of chronic intestinal parasite infection. We show that, early during development of chronic infection with the murine intestinal parasite Trichuris muris, TGFß signalling in CD4+ T-cells is induced and that antibody-mediated inhibition of TGFß function results in protection from infection. Mechanistically, we find that enhanced TGFß signalling in CD4+ T-cells during infection involves expression of the TGFß-activating integrin αvß8 by dendritic cells (DCs), which we have previously shown is highly expressed by a subset of DCs in the intestine. Importantly, mice lacking integrin αvß8 on DCs were completely resistant to chronic infection with T. muris, indicating an important functional role for integrin αvß8-mediated TGFß activation in promoting chronic infection. Protection from infection was dependent on CD4+ T-cells, but appeared independent of Foxp3+ Tregs. Instead, mice lacking integrin αvß8 expression on DCs displayed an early increase in production of the protective type 2 cytokine IL-13 by CD4+ T-cells, and inhibition of this increase by crossing mice to IL-4 knockout mice restored parasite infection. Our results therefore provide novel insights into how type 2 immunity is controlled in the intestine, and may help contribute to development of new therapies aimed at promoting expulsion of gut helminths.

Regulation of TGFß in the immune system: an emerging role for integrins and dendritic cells.

Regulation of an immune response requires complex crosstalk between cells of the innate and adaptive immune systems, via both cell-cell contact and secretion of cytokines. An important cytokine with a broad regulatory role in the immune system is transforming growth factor-ß (TGF-ß). TGF-ß is produced by and has effects on many different cells of the immune system, and plays fundamental roles in the regulation of immune responses during homeostasis, infection and disease. Although many cells can produce TGFß, it is always produced as an inactive complex that must be activated to bind to the TGFß receptor complex and promote downstream signalling. Thus, regulation of TGFß activation is a crucial step in controlling TGFß function. This review will discuss how TGFß controls diverse immune responses and how TGFß function is regulated, with a focus on recent work highlighting a critical role for the integrin αvß8 expressed by dendritic cells in activating TGFß.

Intestinal dendritic cells specialize to activate transforming growth factor-ß and induce Foxp3+ regulatory T cells via integrin αvß8.

BACKGROUND & AIMS: The intestinal immune system is tightly regulated to prevent responses against the many nonpathogenic antigens in the gut. Transforming growth factor (TGF)-ß is a cytokine that maintains intestinal homeostasis, in part by inducing Foxp3(+) regulatory T cells (Tregs) that suppress immune responses. TGF-ß is expressed at high levels in the gastrointestinal tract as a latent complex that must be activated. However, the pathways that control TGF-ß activation in the intestine are poorly defined. We investigated the cellular and molecular pathways that control activation of TGF-ß and induction of Foxp3(+) Tregs in the intestines of mice to maintain immune homeostasis. METHODS: Subsets of intestinal dendritic cells (DCs) were examined for their capacity to activate TGF-ß and induce Foxp3(+) Tregs in vitro. Mice were fed oral antigen, and induction of Foxp3(+) Tregs was measured. RESULTS: A tolerogenic subset of intestinal DCs that express CD103 were specialized to activate latent TGF-ß, and induced Foxp3(+) Tregs independently of the vitamin A metabolite retinoic acid. The integrin αvß8, which activates TGF-ß, was significantly up-regulated on CD103(+) intestinal DCs. DCs that lack expression of integrin αvß8 had reduced ability to activate latent TGF-ß and induce Foxp3(+) Tregs in vitro and in vivo. CONCLUSIONS: CD103(+) intestinal DCs promote a tolerogenic environment in the intestines of mice via integrin αvß8-mediated activation of TGF-ß.