Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker ‘HC’, which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the ‘HC’ marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Oval cell proliferation in p16INK4a expressing mouse liver is triggered by chronic growth stimuli.

Terminal differentiation requires molecules also involved in aging such as the cell cycle inhibitor p16(INK4a).Like other organs, the adult liver represents a quiescent organ with terminal differentiated cells, hepatocytes and cholangiocytes. These cells retain the ability to proliferate in response to liver injury or reduction of liver mass. However, under conditions which prevent mitotic activation of hepatocytes, regeneration can occur instead from facultative hepatic stem cells.For therapeutic application a non-toxic activation of this stem cell compartment is required. We have established transgenic mice with conditional overexpression of the cell cycle inhibitor p16(INK4a) in hepatocytes and have provoked and examined oval cell activation in adult liver in response to a range of proliferative stimuli.We could show that the liver specific expression of p16(INK4a) leads to a faster differentiation of hepatocytes and an activation of oval cells already in postnatal mice without negative consequences on liver function.     

Group-theoretic models of the inversion process in bacterial genomes

The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent than longer, and those that move the terminus of replication are less probable than those that do not. Current methods for establishing the inversion distance between two bacterial genomes are unable to incorporate such information. In this paper we suggest a group-theoretic framework that in principle can take these constraints into account. In particular, we show that by lifting the problem from circular permutations to the affine symmetric group, the inversion distance can be found in polynomial time for a model in which inversions are restricted to acting on two regions. This requires the proof of new results in group theory, and suggests a vein of new combinatorial problems concerning permutation groups on which group theorists will be needed to collaborate with biologists. We apply the new method to inferring distances and phylogenies for published Yersinia pestis data.     

Distinct APC Subtypes Drive Spatially Segregated CD4+ and CD8+ T-Cell Effector Activity during Skin Infection with HSV-1

Efficient infection control requires potent T-cell responses at sites of pathogen replication. However, the regulation of T-cell effector function in situ remains poorly understood. Here, we show key differences in the regulation of effector activity between CD4⁺ and CD8⁺ T-cells during skin infection with HSV-1. IFN-γ-producing CD4⁺ T cells disseminated widely throughout the skin and draining lymph nodes (LN), clearly exceeding the epithelial distribution of infectious virus. By contrast, IFN-γ-producing CD8⁺ T cells were only found within the infected epidermal layer of the skin and associated hair follicles. Mechanistically, while various subsets of lymphoid- and skin-derived dendritic cells (DC) elicited IFN-γ production by CD4⁺ T cells, CD8⁺ T cells responded exclusively to infected epidermal cells directly presenting viral antigen. Notably, uninfected cross-presenting DCs from both skin and LNs failed to trigger IFN-γ production by CD8⁺ T-cells. Thus, we describe a previously unappreciated complexity in the regulation of CD4⁺ and CD8⁺ T-cell effector activity that is subset-specific, microanatomically distinct and involves largely non-overlapping types of antigen-presenting cells (APC).     

Managing potato wart: a review of present research status and future perspective

Key message

Identification of resistance genes to potato wart disease caused by Synchytrium endobioticum is the key for developing diagnostic markers for breeding resistant cultivars. We present an overview on the current knowledge of this host-pathogen system and molecular advances while highlighting future research focus.

Abstract

Potato wart is a quarantined disease of cultivated potato (Solanum tuberosum L.) caused by the obligate biotrophic, soil-borne fungus Synchytrium endobioticum (Schilb.) Perc. Since its discovery by Schilberszky in 1896, the management of wart disease was enabled by research efforts focusing on understanding and classifying the causative agent, its mode of infection, pathogenesis, geographical distribution, detection and chemical control, on developing screening methods for host resistance and on genetic analyses, which led to the development of resistant cultivars. These early successes are currently challenged by new S. endobioticum pathotypes evolving and the increased risk of dissemination by potato tuber trade. New research efforts are therefore required to ensure continuation of effective and sustainable management of the potato wart disease. Advances in molecular biology and genomic tools offer potential for innovations. This review presents an overview on what we know about this complex host-pathogen interaction, highlights recent molecular work and embarks on an outlook towards future research directions.     

In Situ μGISAXS: I. Experimental Setup for Submicron Study of Protein Nucleation and Growth

In this study, we used microbeam grazing-incidence small-angle x-ray scattering (μGISAXS) to investigate in situ protein nucleation and crystal growth assisted by a protein nanotemplate, and introduced certain innovations to improve the method. Our aim was to understand the protein nanotemplate method in detail, as this method has been shown to be capable of accelerating and increasing crystal size and quality, as well as inducing crystallization of proteins that are not crystallizable by classical methods. The nanotemplate experimental setup was used for drops containing growing protein crystals at different stages of nucleation and growth. Two model proteins, lysozyme and thaumatin, were used under unique flow conditions to differentially probe protein crystal nucleation and growth.     

Differential effect of growth factors on growth stimulation and phenotypic stability of glutamine-synthetase-positive and -negative hepatocytes in primary culture

In rat liver parenchyma, two subpopulations of hepatocytes can be distinguished by the absence or presence of the marker enzyme, glutamine synthetase (GS). Hepatocytes in the perivenous zone immediately adjacent to the hepatic venules in the liver acinus are positive for GS. Using autoradiography in combination with immunocytochemistry, the response of these two hepatocyte populations (GS positive and GS negative) to a variety of growth factors (defined compounds or complex stimuli) was investigated in vitro. Irrespective of the individual growth-promoting activity (which varied considerably), all stimuli led to much higher labeling indices in GS-negative cells as compared to GS-positive cells. In GS-negative cells, the strongest effect was exerted by serum obtained from partially hepatectomized rats (labeling index, 67%) and the conditioned media of JM1 and JM2 hepatoma cells (63%-82%), followed by a combination of insulin and either norepinephrine (46%) or epidermal growth factor (EGF; 42%). In contrast, serum had the weakest influence on GS-positive cells (0.3%), while the other potent stimuli enhanced the labeling index of these cells by between 6% and 15% within 48 h. The percentage of labeled nuclei was higher in mononucleated than in binucleated GS-positive hepatocytes. The time course of thymidine incorporation was also different for the two subpopulations. Under all growth-promoting conditions, the stimulation of GS-negative cells peaked between 72 and 96 h, while it increased continuously in GS-positive cells for at least 120 h, particularly in the case of serum. In proliferating cultures, both the absolute and the relative number of GS-positive hepatocytes decreased, while no such effect was found in various nonproliferating control cultures maintained at low and high cell density. Similar results were found for GS activity. In contrast, the hormonal induction of tyrosine aminotransferase (TAT) was not affected. It is suggested that these differences in the growth response of GS-positive and -negative cells contribute to the acinar gradient in hepatocyte proliferation that occurs during liver regeneration. Furthermore, the striking phenotypic instability of GS-positive cells that have undergone DNA synthesis and mitosis supports the hypothesis that cellular reprogramming depends on passage through the cell cycle.     

Renewable resources in the chemical industry – Breaking away from oil?

Rising prices for fossil-based raw materials suggest that sooner or later renewable raw materials will, in principle, become economically viable. This paper examines this widespread paradigm. Price linkages like those seen for decades particularly in connection with petrochemical raw materials are now increasingly affecting renewable raw materials. The main driving force is the competing utilisation as an energy source because both fossil-based and renewable raw materials are used primarily for heat, electrical power and mobility. As a result, prices are determined by energy utilisation. Simple observations show how prices for renewable carbon sources are becoming linked to the crude oil price. Whether the application calls for sugar, starch, virgin oils or lignocellulose, the price for the raw material rises with the oil price. Consequently, expectations regarding price trends for fossil-based energy sources can also be utilised for the valuation of alternative processes. However, this seriously calls into question the assumption that a rising crude oil price will favour the economic viability of alternative products and processes based on renewable raw materials. Conversely, it follows that these products and processes must demonstrate economic viability today. Especially in connection with new approaches in white biotechnology, it is evident that, under realistic assumptions, particularly in terms of achievable yields and the optimisation potential of the underlying processes, the route to utilisation is economically viable. This makes the paradigm mentioned at the outset at least very questionable.     

Reaction norms for developmental time and weight at eclosion in Drosophila mercatorum

We determined reaction norms for developmental time and weight at eclosion for 2 isozygous and 11 genetically mixed strains of Drosophila mercatorum in four culture media differing in yeast concentration. With decreasing yeast concentration, development was delayed, the weight of emerging flies decreased, and the phenotypic variance of both variables increased. Differences among stocks and significant stock × yeast interactions indicated genetic variance for both variables within environment and different phenotypic responses of stocks across environments. The phenotypic correlation between developmental time and weight was negative at low yeast concentrations and disappeared gradually with increasing yeast. The comparison of completely homozygous with genetically heterogenous stocks showed that most of the increase of variability with deteriorating environment was due to the changing expression of genetic variance. The genetic correlation between developmental time and weight turned from negative in poor to positive in rich medium, while the environmental covariance was negative in all media. Plotting the reaction norms in the developmental time-weight plane rather than separately for each trait reveals most of these results at a glance. It also suggests that much of the genetic variance might be additive, because an effect of the half-sib family structure inherent in the design is clearly visible in the plot. We interpret the pattern of changing variances and covariances, pointing out that the special growth physiology of Drosophila and the way environmental factors affect it must be taken into account. We briefly discuss the implications of changing genetic correlations among traits for the evolution of phenotypic plasticity in general.     

Establishment, graft union characteristics and growth of Prunus micrografts

A micrografting technique for use on shoots derived by shoot-tip culture is described. Autografts of Prunus domestica cv. Hauszwetsche as well as heterografts of several sour cherry cultivars ( Prunus cerasus L. cvs Schattenmorelle, Weiroot 158, Köröser) were established. Successful graft formation in vitro was confirmed by translation of ⁸⁶Rb⁺ from the stock root into growing scion tissues. A mechanically strong graft union was formed during the course of a 3-week subculture of micrografts in a liquid medium without the addition of growth regulators. In the case of graft rejection, ⁸⁶Rb⁺ was mainly attracted to new developing shoots from lateral meristems of the stock plant. Histological examination of the graft union revealed callus formation, cytodifferentiation and xylogenesis leading to the formation of vascular connections. Stem elongation after micrografting was related to vigour of the stock and scion genotypes. Early stem elongation could be used as a criterion for preselection of growth vigour in graft combinations. Micrografts were transferred to soil and grown in the greenhouse.