B cell profiles, antibody repertoire and reactivity reveal dysregulated responses with autoimmune features in melanoma

B cells are known to contribute to the anti-tumor immune response, especially in immunogenic tumors such as melanoma, yet humoral immunity has not been characterized in these cancers to detail. Here we show comprehensive phenotyping in samples of circulating and tumor-resident B cells as well as serum antibodies in melanoma patients. Memory B cells are enriched in tumors compared to blood in paired samples and feature distinct antibody repertoires, linked to specific isotypes. Tumor-associated B cells undergo clonal expansion, class switch recombination, somatic hypermutation and receptor revision. Compared with blood, tumor-associated B cells produce antibodies with proportionally higher levels of unproductive sequences and distinct complementarity determining region 3 properties. The observed features are signs of affinity maturation and polyreactivity and suggest an active and aberrant autoimmune-like reaction in the tumor microenvironment. Consistent with this, tumor-derived antibodies are polyreactive and characterized by autoantigen recognition. Serum antibodies show reactivity to antigens attributed to autoimmune diseases and cancer, and their levels are higher in patients with active disease compared to post-resection state. Our findings thus reveal B cell lineage dysregulation with distinct antibody repertoire and specificity, alongside clonally-expanded tumor-infiltrating B cells with autoimmune-like features, shaping the humoral immune response in melanoma

Quantitative trait loci analysis of zinc efficiency and grain zinc concentration in wheat using whole genome average interval mapping

Zinc (Zn) deficiency is a widespread problem which reduces yield and grain nutritive value in many cereal growing regions of the world. While there is considerable genetic variation in tolerance to Zn deficiency (also known as Zn efficiency), phenotypic selection is difficult and would benefit from the development of molecular markers. A doubled haploid population derived from a cross between the Zn inefficient genotype RAC875-2 and the moderately efficient genotype Cascades was screened in three experiments to identify QTL linked to growth under low Zn and with the concentrations of Zn and iron (Fe) in leaf tissue and in the grain. Two experiments were conducted under controlled conditions while the third examined the response to Zn in the field. QTL were identified using an improved method of analysis, whole genome average interval mapping. Shoot biomass and shoot Zn and Fe concentrations showed significant negative correlations, while there were significant genetic correlations between grain Zn and Fe concentrations. Shoot biomass, tissue and grain Zn concentrations were controlled by a number of genes, many with a minor effect. Depending on the traits and the site, the QTL accounted for 12–81% of the genetic variation. Most of the QTL linked to seedling growth under Zn deficiency and to Zn and Fe concentrations were associated with height genes with greater seedling biomass associated with lower Zn and Fe concentrations. Four QTL for grain Zn concentration and a single QTL for grain Fe concentration were also identified. A cluster of adjacent QTL related to the severity of symptoms of Zn deficiency, shoot Zn concentration and kernel weight was found on chromosome 4A and a cluster of QTL associated with shoot and grain Fe concentrations and kernel weight was found on chromosome 3D. These two regions appear promising areas for further work to develop markers for enhanced growth under low Zn and for Zn and Fe uptake. Although there was no significant difference between the parents, the grain Zn concentration ranged from 29 to 43 mg kg−1 within the population and four QTL associated with grain Zn concentration were identified. These were located on chromosomes 3D, 4B, 6B and 7A and they described 92% of the genetic variation. Each QTL had a relatively small effect on grain Zn concentration but combining the four high Zn alleles increased the grain Zn by 23%. While this illustrates the potential for pyramiding genes to improve grain Zn, breeding for increased grain Zn concentration requires identification of individual QTL with large effects, which in turn requires construction and testing of new mapping populations in the future

Mapping of a QTL contributing to cereal cyst nematode tolerance and resistance in wheat

Cereal cyst nematode (CCN; Heterodera avenae Woll.) is a root pathogen of cereals that can cause severe yield losses in intolerant wheat cultivars. Tolerance to CCN, measured as early vigour in CCN-infested plots, was mapped in a Trident/Molineux doubled-haploid (DH) population. A locus accounting for a significant proportion of the tolerance to CCN was mapped to chromosome 6B of Molineux by association with RFLP loci Xcdo347-6B and Xbcd1 and also by nullisomic/tetrasomic substitution line analysis, and has been designated Cre8. The linkage of CCN tolerance with Xcdo347-6B was validated using a Barunga/Suneca DH population. The Cre8 locus also contributed to CCN resistance in the Trident/Molineux population. The RFLP locus Xbcd175, which is diagnostic for the Aegilops ventricosa segment VPM1 of Trident, explained up to 18% of the variation for early vigour in CCN-infested soils in the Trident/Molineux population. However, the Trident/Molineux population also segregated for early vigour in the absence of CCN, with Xbcd175 explaining up to 7% of the variation for this trait. The VPM1 segment of Trident therefore provides early vigour that may contribute to CCN tolerance in this cultivar.K. J. Williams, J. G. Lewis, P. Bogacki, M. A. Pallotta, K. L. Willsmore, H. Kuchel and H. Wallwor

A comparison of the genetics of seedling and adult plant resistance to the spot form of net blotch (Pyrenophora teres f. maculata)

Spot form of net blotch (SFNB) (Pyrenophora teres f. maculata) is an economically damaging foliar disease of barley in many of the world's cereal-growing areas. The gene Rpt4 that confers seedling resistance to SFNB has been mapped on the long arm of chromosome 7H, but no genes for adult plant resistance (APR) have been identified. A lack of field resistance to SFNB in breeders' lines selected for Rpt4 led us to investigate the genetics of APR to this disease. Five doubled-haploid populations were phenotyped for seedling and adult plant reaction. Markers linked to Rpt4 explained a large part of the seedling variation, but little of the APR. In 2 mapped populations, major quantitative trait loci (QTLs) for APR distal to Rpt4 on chromosome 7H were identified. QTLs contributing to APR on chromosomes 4H or 5H were also identified in each population. Association of the 5H QTL with a gene for cereal cyst nematode resistance and the probable effect of this linkage on the historical development of cultivars with adult plant resistance to SFNB is discussed.K. J. Williams , G. J. Platz, A. R. Barr, J. Cheong, K. Willsmore, M. Cakir and H. Wallwor

Mapping genes for resistance to the spot form of net blotch

No abstract availabl

The use of high resolution melting (HRM) to map single nucleotide polymorphism markers linked to a covered smut resistance gene in barley

Using an established genetic map, a single gene conditioning covered smut resistance, Ruh.7H, was mapped to the telomere region of chromosome 7HS in an Alexis/ Sloop doubled haploid barley population. The closest marker to Ruh.7H, abg704 was 7.5 cM away. Thirteen loci on the distal end of 7HS with potential to contain single nucleotide polymorphisms (SNPs) were identiWed by applying a comparative genomics approach using rice sequence data. Of these, one locus produced polymorphic co-dominant bands of diVerent size while two further loci contained SNPs that were identiWed using the recently developed high resolution melting (HRM) technique. Two of these markers Xanked Ruh.7H with the proximal marker located 3.8 cM and the distal marker 2.7 cM away. This is the Wrst report on the application of the HRM technique to SNP detection and to rapid scoring of known cleaved ampliWed polymorphic sequence (CAPS) markers in plants. This simple, precise post-PCR technique should Wnd widespread use in the Wne-mapping of genetic regions of interest in complex cereal and other plant genomes

Titanium wire implants with nanotube arrays: a study model for localized cancer treatment

Abstract not availableGagandeep Kaur, Tamsyn Willsmore, Karan Gulati, Irene Zinonos, Ye Wang, Mima Kurian, Shelley Hay, Dusan Los ic, Andreas Evdokio

New eSSR and gSSR markers added to Australian barley maps

To enhance genetic maps of barley previously developed in Australia for identifying markers useable in molecular breeding, a new set of simple sequence repeat (SSR) and indel markers was added to the maps. These markers were developed through (i) database mining of barley expressed sequence tag (EST) sequences, (ii) comparative barley-rice genome analysis, and (iii) screening of a genomic library with SSR probes. The primer set selected for this study comprised 216 EST-SSR (eSSR) and 25 genomic SSR (gSSR) markers, which were screened for polymorphism on 4 doubled haploid (DH) or recombinant inbred line (RIL) populations. In total, 81 new markers were added to the maps, with good coverage on all 7 chromosomes, except 6H, which only had 2 new markers added. The marker order of previously published maps was re-evaluated by comparing recombination fractions calculated by 2 methods to discover the best position for each marker. The new SSR markers were then added to the updated maps. Several of these new markers are linked to important barley disease resistance genes such as those for cereal cyst nematode, spot form of net blotch, and leaf scald resistance, and are readily useable for marker-assisted barley breeding. The new maps are available on-line at www.genica.net.au.Kerrie L. Willsmore, Paul Eckermann, Rajeev K. Varshney, Andreas Graner, Peter Langridge, Margaret Pallotta, Judy Cheong and Kevin J. William

Black point formation in barley: environmental influences and quantitative trait loci

© CSIRO 2008Black point and kernel discoloration of barley both appear to occur under conditions of high humidity at grain fill. Both of these traits are likely to result from the enzymatic oxidation of phenolic compounds to quinones and the transformation of those oxidation products to brown or black pigments during high humidity. However, even though black point symptoms are quite distinct from other types of kernel discoloration, black point of barley has not previously been the sole focus of environmental studies or quantitative trait locus (QTL) analysis. We have evaluated black point tolerance in doubled haploid progeny of Alexis/Sloop and mapped QTLs on chromosomes 2H and 3H. We have also established that the occurrence of low vapour pressure deficit, high humidity, and low temperatures is associated with the formation of black point in susceptible varieties. These environmental conditions probably create a moist environment during grain development so that the developing grain cannot dry out. Stress or wounding to the embryo caused by this environment might then lead to black point formation. The results of this study will enable the use of comprehensive genetic and biochemical approaches to develop a more detailed understanding of this disorder.K. Ryan Walker, Jason A. Able, Diane E. Mather and Amanda J. Abl

Mapping of a novel QTL for resistance to cereal cyst nematode in wheat

K. J. Williams, K. L. Willsmore, S. Olson, M. Matic, H. Kuche