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Targeted toxins (TT) for cancer treatment are a class of hybrid biologic comprised of a targeting domain coupled chemically or genetically to a proteinaceous toxin payload. The targeting domain of the TT recognises and binds to a defined target molecule on the cancer cell surface, thereby delivering the toxin that is then required to internalise to an appropriate intracellular compartment in order to kill the target cancer cell. Toxins from several different sources have been investigated over the years, and the two TTs that have so far been licensed for clinical use in humans; both utilise bacterial toxins. Relatively few clinical studies have, however, been undertaken with TTs that utilise single-chain type I ribosome inactivating proteins (RIPs). This paper reviews the clinical experience that has so far been obtained for a range of TTs based on five different type I RIPs and concludes that the majority studied in early phase trials show significant clinical activity that justifies further clinical investigation. A range of practical issues relating to the further clinical development of TT’s are also covered briefly together with some suggested solutions to outstanding problems.

Meiotic recombination rates vary considerably between species, populations and individuals. The genetic exchange between homologous chromosomes plays a major role in evolution by breaking linkage between advantageous and deleterious alleles in the case of introgressions. Identifying recombination rate modifiers is thus of both fundamental and practical interest to understand and utilize variation in meiotic recombination rates. We investigated recombination rate variation in a large intraspecific hybrid population (named HEB-25) derived from a cross between domesticated barley and 25 wild barley accessions. We observed quantitative variation in total crossover number with a maximum of a 1.4-fold difference between subpopulations and increased recombination rates across pericentromeric regions. The meiosis-specific α-kleisin cohesin subunit REC8 was identified as a candidate gene influencing crossover number and patterning. Furthermore, we quantified wild barley introgression patterns and revealed how local and genome-wide recombination rate variation shapes patterns of introgression. The identification of allelic variation in REC8 in combination with the observed changes in crossover patterning suggest a difference in how chromatin loops are tethered to the chromosome axis, resulting in reduced crossover suppression across pericentromeric regions. Local and genome-wide recombination rate variation is shaping patterns of introgressions and thereby directly influences the consequences of linkage drag.

The continuing growth of the human population creates an inevitable necessity for higher crop yields, which are mandatory for the supply with adequate amounts of food. However, increasing grain yield may lead to a reduction of grain quality, such as a decline in protein and mineral nutrient concentrations causing the so-called hidden hunger. To assess the interdependence between quantity and quality and to evaluate the biofortification potential of wild barley, we conducted field studies, examining the interplay between plant development, yield, and nutrient concentrations, using HEB-YIELD, a subset of the wild barley nested association mapping population HEB-25. A huge variation of nutrient concentration in grains was obtained, since we identified lines with a more than 50% higher grain protein, iron, and zinc concentration in comparison to the recurrent parent ‘Barke’. We observed a negative relationship between grain yield and nutritional value in barley, indicated by predominantly negative correlations between yield and nutrient concentrations. Analyzing the genetic control of nutrient concentration in mature grains indicated that numerous genomic regions determine the final nutritional value of grains and wild alleles were frequently associated with higher nutrient concentrations. The targeted introgression of wild barley alleles may enable biofortification in future barley breeding.

Since the dawn of agriculture, crop yield has always been impaired through abiotic stresses. In a field trial across five locations worldwide, we tested three abiotic stresses, nitrogen deficiency, drought and salinity, using HEB-YIELD, a selected subset of the wild barley nested association mapping population HEB-25. We show that barley flowering time genes Ppd-H1, Sdw1, Vrn-H1 and Vrn-H3 exert pleiotropic effects on plant development and grain yield. Under field conditions, these effects are strongly influenced by environmental cues like day length and temperature. For example, in Al-Karak, Jordan, the day length-sensitive wild barley allele of Ppd-H1 was associated with an increase of grain yield by up to 30% compared to the insensitive elite barley allele. The observed yield increase is accompanied by pleiotropic effects of Ppd-H1 resulting in shorter life cycle, extended grain filling period and increased grain size. Our study indicates that the adequate timing of plant development is crucial to maximize yield formation under harsh environmental conditions. We provide evidence that wild barley alleles, introgressed into elite barley cultivars, can be utilized to support grain yield formation. The presented knowledge may be transferred to related crop species like wheat and rice securing the rising global food demand for cereals.

Cholesterol seems to play a central role in the augmentation of saporin-based immunotoxin (IT) cytotoxicity by triterpenoid saponins. Endolysosomal escape has been proposed as one mechanism for the saponin-mediated enhancement of targeted toxins. We investigated the effects of lipid depletion followed by repletion on Saponinum album (SA)-induced endolysosomal escape of Alexa Fluor labelled saporin and the saporin-based immunotoxin OKT10-SAP, directed against CD38, in Daudi lymphoma cells. Lipid deprived cells showed reduced SA-induced endolysosomal escape at two concentrations of SA, as determined by a flow cytometric method. The repletion of membrane cholesterol by low density lipoprotein (LDL) restored SA-induced endolysosomal escape at a concentration of 5 &micro, g/mL SA but not at 1 &micro, g/mL SA. When LDL was used to restore the cholesterol levels in lipid deprived cells, the SA augmentation of OKT10-SAP cytotoxicity was partially restored at 1 &micro, g/mL SA and fully restored at 5 &micro, g/mL SA. These results suggest that different mechanisms of action might be involved for the two different concentrations of SA and that endosomal escape may not be the main mechanism for the augmentation of saporin IT cytotoxicity by SA at the sub-lytic concentration of 1 &micro, g/mL SA.

Discovering QTL hotspots for yield-related grain traits in a population developed from 25 diverse wild barley lines reveals new opportunities for improving cultivated barley., To explore wild barley as a source of useful alleles for yield improvement in breeding, we have carried out a genome-wide association scan using the nested association mapping population HEB-25, which contains 25 diverse exotic barley genomes superimposed on an ~70% genetic background of cultivated barley. A total of 1420 HEB-25 lines were trialled for nine yield-related grain traits for 2 years in Germany and Scotland, with varying N fertilizer application. The phenotypic data were related to genotype scores for 5398 gene-based single nucleotide polymorphism (SNP) markers. A total of 96 quantitative trait locus (QTL) regions were identified across all measured traits, the majority of which co-localize with known major genes controlling flowering time (Ppd-H2, HvCEN, HvGI, VRN-H1, and VRN-H3) and spike morphology (VRS3, VRS1, VRS4, and INT-C) in barley. Fourteen QTL hotspots, with at least three traits coinciding, were also identified, several of which co-localize with barley orthologues of genes controlling grain dimensions in rice. Most of the allele effects are specific to geographical location and/or exotic parental genotype. This study shows the existence of beneficial alleles for yield-related traits in exotic barley germplasm and provides candidate alleles for future improvement of these traits by the breeder.

Plant development in a barley nested association mapping population is controlled by interacting genotypic (wild donor alleles) and environmental (geographical location) effects., Barley is cultivated more widely than the other major world crops because it adapts well to environmental constraints, such as drought, heat, and day length. To better understand the genetic control of local adaptation in barley, we studied development in the nested association mapping population HEB-25, derived from crossing 25 wild barley accessions with the cultivar ‘Barke’. HEB-25 was cultivated in replicated field trials in Dundee (Scotland) and Halle (Germany), differing in regard to day length, precipitation, and temperature. Applying a genome-wide association study, we located 60 and 66 quantitative trait locus (QTL) regions regulating eight plant development traits in Dundee and Halle, respectively. A number of QTLs could be explained by known major genes such as PHOTOPERIOD 1 (Ppd-H1) and FLOWERING LOCUS T (HvFT-1) that regulate plant development. In addition, we observed that developmental traits in HEB-25 were partly controlled via genotype × environment and genotype × donor interactions, defined as location-specific and family-specific QTL effects. Our findings indicate that QTL alleles are available in the wild barley gene pool that show contrasting effects on plant development, which may be deployed to improve adaptation of cultivated barley to future environmental changes.

PurposeThe aim of this work was to develop a quantitative, flow cytometric method for tracking the endolysosomal escape of a fluorescently labelled saporin toxin.MethodsFlow cytometric measurements of fluorescent pulse width and height were used to track the endocytic uptake into Daudi cells of a fluorescently labelled saporin toxin and the saporin based immunotoxin, OKT10-SAP. Subsequently, measurement of changes in pulse width were used to investigate the effect of a triterpenoid saponin on the endolysosomal escape of internalised toxin into the cytosol. Live cell confocal microscopy was used to validate the flow cytometry data.ResultsIncreased endolysosomal escape of saporin and OKT10-SAP was observed by confocal microscopy in cells treated with saponin. Fluorescent pulse width measurements were also able to detect and quantify escape more sensitively than confocal microscopy. Saponin induced endolysosomal escape could be abrogated by treatment with chloroquine, an inhibitor of endolysosomal acidification. Chloroquine abrogation of escape was also mirrored by a concomitant abrogation of cytotoxicity.ConclusionsPoor endolysosomal escape is often a rate limiting step for the cytosolic delivery of protein toxins and other macromolecules. Pulse width analysis offers a simple method to semi-quantify the endolysosomal escape of this and similar molecules into the cytosol.

Triterpenoid saponins augment the cytotoxicity of saporin based immunotoxins. It is postulated that this results from a saponin-mediated increase in the endolysosomal escape of the toxin to the cytosol, but this remains to be confirmed. To address this issue, we used a number of pharmacological inhibitors of endocytic processes as probes to investigate the role played by saponin in the endolysosomal escape of fluorescently labeled saporin and a saporin based immunotoxin targeted against CD38 on human lymphoma and leukemia cell lines. Endolysosomal escape of the toxin was measured by flow cytometric pulse shape analysis. These results were compared to the effects of the various inhibitors on the saponin-mediated augmentation of toxin and immunotoxin cytotoxicity. Inhibitors of clathrin-mediated endocytosis, micropinocytosis, and endosomal acidification abrogated the saponin-induced increase in the endolysosomal escape of the toxin into the cytosol, suggesting that these processes may be involved in the internalization of saponin to the same endolysosomal vesicle as the toxin. Alternatively, these processes may play a direct role in the mechanism by which saponin promotes toxin escape from the endolysosomal compartment to the cytosol. Correlation with the effects of these inhibitors on the augmentation of cytotoxicity provides additional evidence that endolysosomal escape is involved in driving augmentation.

Summary Combinations of histones carrying different covalent modifications are a major component of epigenetic variation. We have mapped nine modified histones in the barley seedling epigenome by chromatin immunoprecipitation next‐generation sequencing (ChIP‐seq). The chromosomal distributions of the modifications group them into four different classes, and members of a given class also tend to coincide at the local DNA level, suggesting that global distribution patterns reflect local epigenetic environments. We used this peak sharing to define 10 chromatin states representing local epigenetic environments in the barley genome. Five states map mainly to genes and five to intergenic regions. Two genic states involving H3K36me3 are preferentially associated with constitutive gene expression, while an H3K27me3‐containing genic state is associated with differentially expressed genes. The 10 states display striking distribution patterns that divide barley chromosomes into three distinct global environments. First, telomere‐proximal regions contain high densities of H3K27me3 covering both genes and intergenic DNA, together with very low levels of the repressive H3K27me1 modification. Flanking these are gene‐rich interior regions that are rich in active chromatin states and have greatly decreased levels of H3K27me3 and increasing amounts of H3K27me1 and H3K9me2. Lastly, H3K27me3‐depleted pericentromeric regions contain gene islands with active chromatin states separated by extensive retrotransposon‐rich regions that are associated with abundant H3K27me1 and H3K9me2 modifications. We propose an epigenomic framework for barley whereby intergenic H3K27me3 specifies facultative heterochromatin in the telomere‐proximal regions and H3K27me1 is diagnostic for constitutive heterochromatin elsewhere in the barley genome., Significance Statement Triticeae cereals are among the most important crops worldwide yet their epigenomics are largely unstudied. Here we have used ChIP‐Seq to explore the epigenome of barley, identifying and mapping chromatin states of nine modified histones at both gene and genome levels.

In this chapter, we refer to the expressed portion of the barley genome as the relatively small fraction of the total cellular DNA that either contains the genes that ultimately produce proteins, or that directly/indirectly controls the level, location and/or timing of when these genes are expressed and proteins are produced. We start by describing the dynamics of tissue and time-dependent gene expression and how common patterns across multiple samples can provide clues about gene networks involved in common biological processes. We then describe some of the complexities of how a single mRNA template can be differentially processed by alternative splicing to generate multiple different proteins or provide a mechanism to regulate the amount of functional gene product in a cell at a given point in time. We extend our analysis, using a number of biological examples, to address how diverse families of small non-coding microRNAs specifically regulate gene expression, and complete our appraisal by looking at the physical/molecular environment around genes that can result in either the promotion or repression of gene expression. We conclude by assessing some of the issues that remain around our ability to fully exploit the depth and power of current approaches for analysing gene expression and propose improvements that could be made using new but available sequencing and bioinformatics technologies.

Saponinum album (SA) is a complex mixture of triterpenoid saponins previously shown to augment the cytotoxicity of the type I ribosome-inactivating protein saporin and an EGF-saporin target toxin that could potentially be used to improve the therapeutic window of targeted toxins.To investigate the augmentative property of SA on saporin and saporin-based immunotoxins (IT) directed against five different cell surface target molecules on human leukemia and lymphoma cells.After determining the optimum dose of SA for each cell line, the extent of SA-mediated augmentation was established for saporin and five saporin-based ITs using XTT and an annexin V apoptosis assay. Immunospecificity was investigated using three different blocking assays. Dose-scheduling was also investigated using the XTT assay.Uncorrected SA-mediated augmentation ranged at best from 31.5 million-fold to, at worse, 174-fold. However, when the calculated fold-increases were adjusted for the non-immunospecific effects of SA on an off-target IT, the true augmentative effects of SA were found to be largely non-immunospecific. Antibody blocking studies demonstrated that the augmentative effect of SA was only partially immunospecific. Separate exposure of target cells to IT and SA at different times demonstrated that immunospecific augmentation of IT by SA could be achieved but only if cells were exposed to IT first and SA second.SA significantly, although variably, augments the cytotoxicity of saporin and saporin-based immunotoxins. Concomitant exposure to both IT and SA can result in non-immunospecific cytotoxicity that can be overcome by temporally separating exposure to each.

Frost tolerance is the main component of winter hardiness for cereals and is largely dependent on the plant's ability to cold acclimate by means of a slow adaptive response induced by low, non-freezing temperatures. In the present work, a Genome-Wide Association mapping study has been performed, looking for the genetic determinants of frost tolerance in a panel of European spring 2-row barley cultivars. Frost damage was evaluated by measuring chlorophyll fluorescence (Fv/Fm) and membrane integrity (Electrolyte Leakage) and considerable variation for this trait was discovered. Genetic association of the trait was sought with >5000 gene-based mapped SNP markers using a Mixed Linear Model approach. A simple genetic architecture was revealed for frost tolerance in this population, with a principal role for the Fr-H1/Vrn-H1 and Fr-H2 loci already detected in previous linkage and association mapping studies. Allelic richness might exist at these loci, not only between winter and spring barley, but also within the spring germplasm, thus offering the opportunity for future development of new spring barley lines with improved resilience in the face of emerging climate change.

Membranes are vital barriers by which cells control the flux of molecules and energy between their exterior and interior and also between their various intracellular compartments. While numerous transport systems exist for ions and small molecules, the cytosolic uptake of larger biological molecules and in particular antibody-targeted drugs, is a big challenge. Inducing leakage of the plasma membrane is unfavorable since the target cell specificity mediated by the antibody would likely be lost in this case. After binding and internalization, the antibody drug conjugates reach the endosomes. Thus, enforcing the endosomal escape of anti-tumor toxins without affecting the integrity of other cellular membranes is of paramount importance. Different strategies have been developed in the last decades to overcome endosomal accumulation and subsequent lysosomal degradation of targeted protein-based drugs. In this review we summarize the various efforts made to establish efficient techniques to disrupt the endosomal membrane barrier including the use of molecular ferries such as cell penetrating peptides or viral membrane fusion proteins, endosomal leakage inducing molecules such as saponins or monensin and physicochemical methods as represented by photochemical internalization.

Triterpenoid saponins from Saponinum Album (SA) exert potent lytic effects on eukaryotic cell plasma membranes and, when used at sub-lytic concentrations, significantly augment the cytotoxicity of saporin-based immunotoxins (IT). To help elucidate the mechanism(s) behind these two phenomena we investigated the role of cholesterol to both. Human Daudi lymphoma cells were lipid deprived using a combination of three different approaches. Following treatment, the total cellular lipid content was analyzed by electrospray ionization mass spectrometry (ESI-MS) and plasma membrane (PM) cholesterol content measured using the lipophilic fluorescent probe NR12S. Maximal lipid deprivation of cells resulted in a complete loss of sensitivity to lysis by SA. Similarly augmentation of the anti-CD19 immunotoxin (IT) BU12-SAPORIN by SA was lost but without a concomitant loss of intrinsic IT cytotoxicity. The lytic activity of SA was restored following incubation of lipid deprived Daudi cells with Synthecol or LDL. The augmentative effect of SA on IT cytotoxicity for Daudi cells was restored following repletion of PM cholesterol levels with LDL. NR12S fluorescence and ESI-MS analysis of cellular lipids demonstrated that restoration of SA lytic activity by Synthecol was entirely due to increased PM cholesterol levels. Restoration of cellular and PM cholesterol levels by LDL also restored the augmentative effect of SA for IT, an effect associated with repletion of PM cholesterol with minor changes in some phospholipid species. These results indicate that the lytic and IT augmentative properties of SA are cholesterol-dependent in contrast to intrinsic IT cytotoxicity that is at least partially cholesterol independent.

A novel family of dispersed repeat sequences from Drosophila melanogaster is described. Sequence analysis of two members of this family show them to contain greater than 75% GC bases. These are comprised of multiple repeats of GGX triplets interspersed occasionally with CGPy and TTPy. Southern blotting shows that these repeats are not transposable elements. Twenty four homologous recombinants have been localised by in situ hybridization to seven sites in the Drosophila genome. Polyadenylated RNAs homologous to this repeat family are expressed in a complex pattern which is developmentally regulated. We suggest that this family encodes a set of glycine-rich domains in Drosophila proteins.

The entry of antibody-based drugs into mainstream medicine has provided the oncologist with new therapeutic tools that have begun to transform the treatment of cancer (Scott et al, 2012; Lee et al, 2013). Toxicity profiles and cell killing mechanism(s) exhibited by antibody and small-molecule cytotoxic therapies are largely non-overlapping, thus providing positive clinical advantages relating to drug resistance and therapy side effects. Additionally, in some instances, combinations of antibody given together with conventional chemotherapy show synergistic activity manifest as significant improvements in treatment outcomes (Hallek et al, 2010). However, not all naked antibodies possess therapeutic activity per se, a property that is determined in part by the antibody's particular target molecule. In instances where the antibody has only weak or no observable therapeutic activity, the strategy has been to ‘arm' the antibody with a protein toxin or a highly potent small-molecule cytotoxic drug to create two closely related classes of therapeutic, namely immunotoxins (IT) and antibody drug conjugates, respectively (Kreitman, 2006; Lambert, 2013). Immunogenicity presents challenges for all antibody-based therapies where multiple administrations of drug over a protracted period are required to achieve a therapeutic effect (Kuus-Reichel et al, 1994). Immunogenicity in this context is defined as the property of the therapeutic to elicit an unwanted immune response when the patient's immune system recognises epitopes displayed by the drug as non-self. The first generation of therapeutic antibodies were based on mouse monoclonal antibodies whose non-human peptide sequences proved highly immunogenic, provoking an immune response in the patient and the resultant production of human anti-mouse antibodies (HAMA) (Norman et al, 1993). The clinical consequences of HAMA responses are variable. HAMA can be inconsequential, but can also lead to a reduction in antibody therapeutic efficacy due to the generation of neutralising antibodies by the host that block the antigen binding site of the therapeutic antibody and/or an increase blood clearance rates. HAMA responses may also have immunopathological consequences that contribute to the drug's dose-limiting toxicity with immune hypersensitivity reactions being frequently observed (Baldo, 2013). Devising strategies that avoid these problems are a necessary prerequisite to the successful development of any antibody-based therapy. Humanisation of murine antibodies is one way of overcoming the HAMA problem where murine polypeptide sequences are replaced with human ones. This was achieved initially through the generation of chimeric antibodies in which the entire constant region of the murine antibody was replaced with the corresponding human constant region while the entire murine variable domain (Fv) was retained (Morrison et al, 1984). This still left significant amounts of murine sequence in the Fv region that remained immunogenic, and so this prompted the next evolutionary step with generation of ‘humanised' antibody molecules where only the murine complementarity-determining regions (CDRs) are grafted onto a wholly human immunoglobulin framework (Jones et al, 1986). Further advances came with the production of entirely human antibodies using phage display technology (McCafferty et al, 1990) or transgenic mice carrying human immunoglobulin genes (Lonberg et al, 1994). While the full humanisation of therapeutic antibodies has succeeded in dramatically reducing the incidence and extent of human anti-human antibody (HAHA) responses (Foon et al, 2004), idiotypic paratopes that are unique to each and every antibody of defined specificity reside in the CDR regions of the antigen binding site and are still capable of provoking a humoral anti-idiotype immune response (Harding et al, 2010). It is therefore general opinion that complete elimination of HAHA responses will be difficult to achieve through antibody engineering alone and that other strategies will be needed. As a class of antibody-based drug, ITs present additional special challenges when it comes to immunogenicity. Being comprised of two separate protein components, an antibody and a toxin linked covalently either through a chemical bond or as a genetic fusion means that there are potentially two macromolecular structures displaying epitopes that may be recognised as non-self. The resultant highly immunogenic nature of IT severely limits their clinical usefulness where repeated treatments may be necessary to achieve a therapeutic effect. Various approaches have been adopted to overcome this and include a variety of immunosuppressive agents given concomitantly with IT. These include cyclophosphamide (Oratz et al, 1990), cyclosporine A (Selvaggi et al, 1993), anti-CTLA4 Ig (Siegall et al, 1997), 15-deoxyspergulin (Pai et al, 1990), anti-CD4 antibody (Jin et al, 1991) and rituximab (Saleh et al, 2002). Site-specific modification of IT with polyethylene glycol has also been shown to reduce immunogenicity and increase the plasma half-life (Tsutsumi et al, 2000). More recently de-immunisation of ITs based on either Pseudomonas exotoxin or diphtheria toxin by engineering out epitopes identified as likely to provoke an immune response (Liu et al, 2012; Schmohl et al, 2015) have proven largely successful and this approach would seem the most likely way ahead in the further clinical development of these chimeric therapeutic molecules. Andersson et al (2015) describe the effects of oral or i.v. administered cyclosporine (Sandimmune) on the development of neutralising antibodies in cancer patients receiving the anti-EpCAM IT MOC31PE. MOC31PE is based on the anti-EpCAM (CD326) IgG1 murine monoclonal antibody MOC31 linked covalently via a thioether bond to Pseudomonas exotoxin A and is designed to target EpCAM-positive epithelial cancers. The MOC31PE molecule utilises unmodified murine antibody and PE, and is therefore expected to be highly immunogenic in humans, affected only by the immune status of the individual patients. Attempts to use immunosuppressant doses of CsA to reduce the immune response against IT is not new, having first been used in combination with the ricin-based anti-melanoma IT XOMAZYME-MEL, but with little success in this instance (Selvaggi et al, 1993). Andersson et al (2009) have previously shown in preclinical studies that cyclosporine also augments the cytotoxic and therapeutic activity of MOC31PE in preclinical models of human cervical cancer. The phase I dose-escalation study reported by Andersson et al (2015) was undertaken to firstly establish how well the combination of MOC31PE plus CsA was tolerated in patients with EpCAM-positive epithelial cancers and secondly to evaluate the extent to which CsA inhibited the generation of neutralising anti-MOC31PE antibodies. In this dose-escalation study, a total of 34 patients received MOC31PE alone in escalating doses, while 29 received a combination of MOC31PE plus CsA (23 patients received CsA i.v. and 6 orally). Within the patient groups, there were a total of ten grade 3 and three grade 4 adverse events (AE) in the MOC31PE monotherapy-treated group compared with twelve grade 3 and six grade 4 AEs in the MOC31PE plus CsA combination group. The authors used an in vitro MTS cytotoxicity assay to determine whether serum from MOC31PE-treated patients contained antibodies that neutralised the IT. Their assay was not capable of discriminating between anti-MOC31PE antibodies that blocked MOC31PE binding to its EpCAM target or those which neutralised the catalytic activity of PE. After three cycles of treatment (each cycle given every 14 days), 93% of patients treated with MOC31PE alone developed neutralising antibodies compared with only 50% treated with the combination of MOC31PE plus CsA given on a 5-day schedule commencing 1 day before MOC31PE administration. The authors therefore conclude that CsA given on this schedule had an acceptable toxicity/safety profile and was capable of reducing the incidence of anti-IT antibody responses that should allow for multiple doses of IT to be given effectively. While the relatively small patient numbers reported in this dose-escalation study with MOC31PE IT do not allow for any meaningful analysis of any therapeutic benefits of using CsA in combination with the IT, it has provided important safety information that paves the way ahead for subsequent phase II and III trials to explore this very issue.

The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter-mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analysing a collection of 896 wild barley accessions (Barley1K) from Israel and all available Israeli H. vulgare accessions from the Israeli gene bank. We compared the performance of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) marker data genotyped over a core collection in estimating population parameters. Estimates of gene flow rates with SSR markers indicated a high level of introgression from cultivated barley into wild barley. After removing accessions from the wild barley sample that were recently admixed with cultivated barley, the inference of population structure improved significantly. Both SSR and SNP markers showed that the genetic population structure of wild barley in Israel corresponds to the three major ecogeographic regions: the coast, the Mediterranean north and the deserts in the Jordan valley and the South. Gene flow rates were estimated to be higher from north to south than in the opposite direction. As has been observed in other crop species, there is a significant exchange of alleles between the wild species and domesticated varieties that needs to be accounted for in the population genetic analysis of domestication.

Barley is cultivated both in highly productive agricultural systems and also in marginal and subsistence environments. Its distribution is worldwide and is of considerable economic importance for animal feed and alcohol production. The overall importance of barley as a human food is minor but there is much potential for new uses exploiting the health benefits of whole grain and beta-glucans. The barley supply chains are complex and show added value at many stages. Germplasm resources for barley are considerable, with much potential for exploitation of its biodiversity available through the use of recently developed genomic and breeding tools. Consequently, substantial gains in crucial sustainability characteristics should be achievable in the future, together with increased understanding of the physiological basis of many agronomic traits, particularly water and nutrient use efficiency. Barley’s ability to adapt to multiple biotic and abiotic stresses will be crucial to its future exploitation and increased emphasis on these traits in elite germplasm is needed to equip the crop for environmental change. Similarly, resource use efficiency should become a higher priority to ensure the crop’s sustainability in the long-term. Clearly barley is a resilient crop with much potential which can be realised in the future.

Gene escape from crops has gained much attention in the last two decades, as transgenes introgressing into wild populations could affect the latter’s ecological characteristics. However, different genes have different likelihoods of introgression. The mixture of selective forces provided by natural conditions creates an adaptive mosaic of alleles from both parental species. We investigated segregation patterns after hybridization between lettuce (Lactuca sativa) and its wild relative, L. serriola. Three generations of hybrids (S1, BC1, and BC1S1) were grown in habitats mimicking the wild parent’s habitat. As control, we harvested S1 seedlings grown under controlled conditions, providing very limited possibility for selection. We used 89 AFLP loci, as well as more recently developed dominant markers, 115 retrotransposon markers (SSAP), and 28 NBS loci linked to resistance genes. For many loci, allele frequencies were biased in plants exposed to natural field conditions, including over-representation of crop alleles for various loci. Furthermore, Linkage disequilibrium was locally changed, allegedly by selection caused by the natural field conditions, providing ample opportunity for genetic hitchhiking. Our study indicates that when developing genetically modified crops, a judicious selection of insertion sites, based on knowledge of selective (dis)advantages of the surrounding crop genome under field conditions, could diminish transgene persistence.

The tribeFabeae(formerlyVicieae) contains some of humanity's most important grain legume crops, namelyLathyrus(grass pea/sweet pea/chickling vetches; about 160 species);Lens(lentils; 4 species);Pisum(peas; 3 species);Vicia(vetches; about 140 species); and the monotypic genusVavilovia.Reconstructing the phylogenetic relationships within this group is essential for understanding the origin and diversification of these crops. Our study, based on molecular data, has positionedPisumgenetically betweenViciaandLathyrusand shows it to be closely allied toVavilovia.A study of phylogeography, using a combination of plastid and nuclear markers, suggested that wild pea spread from its centre of origin, the Middle East, eastwards to the Caucasus, Iran and Afghanistan, and westwards to the Mediterranean. To allow for direct data comparison, we utilized model-based Bayesian Analysis of Population structure (BAPS) software on 4429Pisumaccessions from three large world germplasm collections that include both wild and domesticated pea analyzed by retrotransposon-based markers. An analysis of genetic diversity identified separate clusters containing wild material, distinguishingPisum fulvum,P. elatiusandP. abyssinicum, supporting the view of separate species or subspecies. Moreover, accessions of domesticated peas of Afghan, Ethiopian and Chinese origin were distinguished. In addition to revealing the genetic relationships, these results also provided insight into geographical and phylogenetic partitioning of genetic diversity. This study provides the framework for defining globalPisumgermplasm diversity as well as suggesting a model for the domestication of the cultivated species. These findings, together with gene-based sequence analysis, show that although introgression from wild species has been common throughout pea domestication, much of the diversity still resides in wild material and could be used further in breeding. Moreover, although existing collections contain over 10,000 pea accessions, effort should be directed towards collecting more wild material in order to preserve the genetic diversity of the species.

We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley ( Hordeum vulgare ) gene pool extends, on average, for

Eryngium maritimum L. is a wild plant species threatened or endangered in most of Northern Europe, where species is on the northern margin of its distribution range. Recent studies have found reduction of size and even extinction of many populations. Assessment of genetic diversity in natural populations of endangered wild plant species can reflect condition and fitness of particular population and inform decisions on appropriate conservation measures. Application of inter simple sequence repeat markers and chloroplast DNA sequencing could not resolve genetic relationship between E. maritimum populations in Northern Europe. Therefore, the more sensitive retrotransposon-sequence-specific amplification polymorphism (SSAP) molecular marker system was developed. Six Ty1-copia long terminal repeat retrotransposons were isolated from E. maritimum genome (Tem1–Tem6) and assessed for their utility as molecular markers in this species. Two retrotransposons – Tem2 and Tem5 – were recognized as most informative based on the level of polymorphism and SSAP banding pattern quality. On average, 20.4% of SSAP bands were polymorphic for the five most informative primer combinations in a set of 150 Northern European E. maritimum plants from 13 locations, providing a useful tool for assessment of genetic diversity in this endangered species.

The capability of molecular markers to provide information of genetic structure is influenced by their number and the way they are chosen. This study evaluates the effects of single nucleotide polymorphism (SNP) number and selection strategy on estimates of germplasm diversity and population structure for different types of barley germplasm, namely cultivar and landrace. One hundred and sixty-nine barley landraces from Syria and Jordan and 171 European barley cultivars were genotyped with 1536 SNPs. Different subsets of 384 and 96 SNPs were selected from the 1536 set, based on their ability to detect diversity in landraces or cultivated barley in addition to corresponding randomly chosen subsets. All SNP sets except the landrace-optimised subsets underestimated the diversity present in the landrace germplasm, and all subsets of SNP gave similar estimates for cultivar germplasm. All marker subsets gave qualitatively similar estimates of the population structure in both germplasm sets, but the 96 SNP sets showed much lower data resolution values than the larger SNP sets. From these data we deduce that pre-selecting markers for their diversity in a germplasm set is very worthwhile in terms of the quality of data obtained. Second, we suggest that a properly chosen 384 SNP subset gives a good combination of power and economy for germplasm characterization, whereas the rather modest gain from using 1536 SNPs does not justify the increased cost and 96 markers give unacceptably low performance. Lastly, we propose a specific 384 SNP subset as a standard genotyping tool for middle-eastern landrace barley.

A critical problem in studying ribosome-inactivating proteins (RIPs) lies in the very limited possibility to produce them in heterologous systems. In fact, their inherent toxicity for the producing organism nearly always prevents their recombinant expression. In this study, we designed, expressed and characterized an engineered form of the RIP saporin (SapVSAV), bearing a C-terminal extra sequence that is recognized and bound by the second PDZ domain from murine PTP-BL protein (PDZ2). The co-expression of SapVSAV and PDZ2 in Escherichia coli BL21 cells greatly enhances the production of the toxin in a soluble form. The increase of production was surprisingly not due to protection from bacterial intoxication, but may arise from a stabilization effect of PDZ2 on the toxin molecule during biosynthesis. We found that once purified, SapVSAV is stable but is not toxic to free ribosomes, while it is fully active against human cancer cells. This strategy of co-expression of a toxin moiety and a soluble PDZ domain may represent a new system to increase the production of recombinant toxic proteins and could allow the selection of new extra sequences to target PDZ domains inside specific mammalian cellular domains.

The resistance genes Lr9, Lr24, Lr25, Lr29, Lr35 and Lr37, which were not previously utilised in Hungary, have been incorporated into four Martonvasar winter wheat cultivars using marker-assisted selection with PCR-based markers. In the course of a backcross programme, the genes were transferred into Martonvasar wheat varieties and various BC generations were produced. Work aimed at pyramiding resistance genes is currently underway in Martonvasar, and plants containing the gene combinations Lr9 + Lr24, Lr9 + Lr25 and Lr9 + Lr29 are now available. From the BC2F4 generation of the ‘Mv Emma’*3/’R.L.6010’ combination (‘R.L.6010’ is the donor of the Lr9 gene) 287 lines were tested for leaf rust resistance in an artificially inoculated nursery. A co-dominant primer combination was designed to identify both resistant and susceptible offsprings. The results of resistance tests and molecular marker detection agreed in most cases. Designated leaf rust resistance genes were identified with molecular markers in wheat varieties and breeding lines. The Lr26 and Lr34 resistance genes occur frequently in the Martonvasar gene pool, and the presence of the Lr37 gene has also been detected in a number of Hungarian genotypes.

Twelve different Ty1-copia and Ty3-gypsy group LTR retrotransposons were compared for their usefulness in SSAP marker development in two agriculturally important Vicia species. Three of the retrotransposons, PDR1, Tps19 and Tvf4, yielded useful SSAP marker systems in V. faba, and V. narbonensis. Another, Tvf1 was a good source of SSAP markers in V. narbonensis alone. The optimized SSAP marker systems were applied to the analysis of two diverse Vicia germplasm sets. Two hundred and two polymorphic Tvf1 SSAP markers were scored in 56 V. narbonensis samples and 196 polymorphic markers derived from the other three most useful retrotransposons were scored in a collection of 20 V. faba samples. The marker data were then used to construct phylogenetic trees. The trees for both species tend to show long-branch lengths, with rather little fine structure. Some V. narbonensis accessions cluster by geographical origin but many do not and a given geographical region is often represented by multiple diverse groups in the tree, suggesting a deep and ancient structure for the diversity of V. narbonensis that spans its current geographic range. The tree for the V. faba accessions also shows very limited clustering with geographical origin and no obvious correlation between diversity and morphology-based taxonomic groupings for the species.

Several protein toxins, such as the potent plant toxin ricin, enter mammalian cells by endocytosis and undergo retrograde transport via the Golgi complex to reach the endoplasmic reticulum (ER). In this compartment the catalytic moieties exploit the ER-associated degradation (ERAD) pathway to reach their cytosolic targets. Bacterial toxins such as cholera toxin or Pseudomonas exotoxin A carry KDEL or KDEL-like C-terminal tetrapeptides for efficient delivery to the ER. Chimeric toxins containing monomeric plant ribosome-inactivating proteins linked to various targeting moieties are highly cytotoxic, but it remains unclear how these molecules travel within the target cell to reach cytosolic ribosomes. We investigated the intracellular pathways of saporin, a monomeric plant ribosome-inactivating protein that can enter cells by receptor-mediated endocytosis. Saporin toxicity was not affected by treatment with Brefeldin A or chloroquine, indicating that this toxin follows a Golgi-independent pathway to the cytosol and does not require a low pH for membrane translocation. In intoxicated Vero or HeLa cells, ricin but not saporin could be clearly visualized in the Golgi complex using immunofluorescence. The saporin signal was not evident in the Golgi, but was found to partially overlap with that of a late endosome/lysosome marker. Consistently, the toxicities of saporin or saporin-based targeted chimeric polypeptides were not enhanced by the addition of ER retrieval sequences. Thus, the intracellular movement of saporin differs from that followed by ricin and other protein toxins that rely on Golgi-mediated retrograde transport to reach their retrotranslocation site.

The (non-LTR) LINE and Ty3-gypsy-type LTR retrotransposon populations of three Vicia species that differ in genome size (Vicia faba, Vicia melanops and Vicia sativa) have been characterised. In each species the LINE retrotransposons comprise a complex, very heterogeneous set of sequences, while the Ty3-gypsy elements are much more homogeneous. Copy numbers of all three retrotransposon groups (Ty1-copia, Ty3-gypsy and LINE) in these species have been estimated by random genomic sequencing and Southern hybridisation analysis. The Ty3-gypsy elements are extremely numerous in all species, accounting for 18-35% of their genomes. The Ty1-copia group elements are somewhat less abundant and LINE elements are present in still lower amounts. Collectively, 20-45% of the genomes of these three Vicia species are comprised of retrotransposons. These data show that the three retrotransposon groups have proliferated to different extents in members of the Vicia genus and high proliferation has been associated with homogenisation of the retrotransposon population.

Carbon monoxide (CO), one of the products of heme oxygenase action on heme, prevents arteriosclerotic lesions that occur following aorta transplantation; pre-exposure to 250 parts per million of CO for 1 hour before injury suppresses stenosis after carotid balloon injury in rats as well as in mice. The protective effect of CO is associated with a profound inhibition of graft leukocyte infiltration/activation as well as with inhibition of smooth muscle cell proliferation. The anti-proliferative effect of CO in vitro requires the activation of guanylate cyclase, the generation of cGMP, the activation of p38 mitogen-activated protein kinases and the expression of the cell cycle inhibitor p21Cip1. These findings demonstrate a protective role for CO in vascular injury and support its use as a therapeutic agent.

A collection of 112 winter barley varieties (Hordeum vulgare L.) was grown in the field for two years (2008/09 and 2009/10) in northern Italy and grain and straw yields recorded. In the first year of the trial, a severe attack of barley yellow mosaic virus (BaYMV) strongly influenced final performances with an average reduction of ~ 50% for grain and straw harvested in comparison to the second year. The genetic determination (GD) for grain yield was 0.49 and 0.70, for the two years respectively, and for straw yield GD was low in 2009 (0.09) and higher in 2010 (0.29). Cell wall polymers in culms were quantified by means of the monoclonal antibodies LM6, LM11, JIM13 and BS-400-3 and the carbohydrate-binding module CBM3a using the high-throughput CoMPP technique. Of these, LM6, which detects arabinan components, showed a relatively high GD in both years and a significantly negative correlation with grain yield (GYLD). Overall, heritability (H2) was calculated for GYLD, LM6 and JIM and resulted to be 0.42, 0.32 and 0.20, respectively. A total of 4,976 SNPs from the 9K iSelect array were used in the study for the analysis of population structure, linkage disequilibrium (LD) and genome-wide association study (GWAS). Marker-trait associations (MTA) were analyzed for grain yield and cell wall determination by LM6 and JIM13 as these were the traits showing significant correlations between the years. A single QTL for GYLD containing three MTAs was found on chromosome 3H located close to the Hv-eIF4E gene, which is known to regulate resistance to BaYMV. Subsequently the QTL was shown to be tightly linked to rym4, a locus for resistance to the virus. GWAs on arabinans quantified by LM6 resulted in the identification of major QTLs closely located on 3H and hypotheses regarding putative candidate genes were formulated through the study of gene expression levels based on bioinformatics tools.

The low-recombining pericentromeric region of the barley genome contains roughly a quarter of the genes of the species, embedded in low-recombining DNA that is rich in repeats and repressive chromatin signatures. We have investigated the effects of pericentromeric region residency upon the expression, diversity and evolution of these genes. We observe no significant difference in average transcript level or developmental RNA specificity between the barley pericentromeric region and the rest of the genome. In contrast, all of the evolutionary parameters studied here show evidence of compromised gene evolution in this region. First, genes within the pericentromeric region of wild barley show reduced diversity and significantly weakened purifying selection compared with the rest of the genome. Second, gene duplicates (ohnolog pairs) derived from the cereal whole-genome duplication event ca. 60MYa have been completely eliminated from the barley pericentromeric region. Third, local gene duplication in the pericentromeric region is reduced by 29% relative to the rest of the genome. Thus, the pericentromeric region of barley is a permissive environment for gene expression but has restricted gene evolution in a sizeable fraction of barley's genes.

In order to further define the factors associated with the observed variations in the Epstein-Barr virus-positive rate in childhood Hodgkin's disease, we have studied the effect of material deprivation (measured by the Townsend score) and ethnic origin on the frequency of Epstein-Barr virus-positivity in 55 cases of childhood Hodgkin's disease, diagnosed between 1981 and 1999, from a multi-ethnic region of the United Kingdom. Epstein-Barr virus status was determined by immunohistochemistry for the Epstein-Barr virus-encoded latent membrane protein-1. 62% of cases were Epstein-Barr virus-positive. Ethnic group was the strongest predictor of Epstein-Barr virus-positivity, with South Asians having a more than 20-fold risk of being Epstein-Barr virus-positive compared with non-South Asians. An increased risk was still present after adjusting for deprivation. Townsend scores were significantly higher (indicating more deprivation) in the Epstein-Barr virus-positive group, particularly in males. The relative risk of Epstein-Barr virus-positivity showed a gradient with increasing Townsend score; the risk being 7-times higher in the most deprived quartile compared with the least deprived group. Although the association between Townsend score and Epstein-Barr virus-positivity was reduced after adjusting for ethnic group, the risk of Epstein-Barr virus-positivity was still 3-times higher in the most deprived compared with the least deprived quartile. In addition, cases having 2 or more siblings were 5-times as likely to be Epstein-Barr virus-positive as those from smaller families. These results provide the first evidence of a strong association between Epstein-Barr virus-positive Hodgkin's disease and South Asian children from the United Kingdom. In addition, deprivation may increase the likelihood of Epstein-Barr virus-positive disease independently of ethnicity. © 2001 Cancer Research Campaign http://www.bjcancer.com