Acid stress in Rumex hydrolapathum (Polygonaceae) and its influence on the phytophage Lycaena dispar (Lepidoptera; Lycaenidae)

Summary The relationship of insect growth to host condition was tested on host plants grown by hydroculture with a standard nutrient solution, but under different acidities, ranging from pH 3.5–7.5. The indirect effect of the host on the development of the phytophage was tested in the pupal stage. The host plant Rumex hydrolapathum had its highest nitrogen content in the range pH 5.5–6.5; pupal weight of Lycaena dispar was correlated with nitrogen concentration, ash weight and water content. There is a remarkable difference in element concentration between young and old leaves of the host, which varies with acidity of the rooting substrate.In this experiment a negative relationship was detected between reproduction of the phytophage and stress of the host.     

Identity-by-Descent Matrix Decomposition Using Latent Ancestral Allele Models

Genetic linkage and association studies are empowered by proper modeling of relatedness among individuals. Such relatedness can be inferred from marker and/or pedigree information. In this study, the genetic relatedness among n inbred individuals at a particular locus is expressed as an n × n square matrix Q. The elements of Q are identity-by-descent probabilities, that is, probabilities that two individuals share an allele descended from a common ancestor. In this representation the definition of the ancestral alleles and their number remains implicit. For human inspection and further analysis, an explicit representation in terms of the ancestral allele origin and the number of alleles is desirable. To this purpose, we decompose the matrix Q by a latent class model with K classes (latent ancestral alleles). Let P be an n × K matrix with assignment probabilities of n individuals to K classes constrained such that every element is nonnegative and each row sums to 1. The problem then amounts to approximating Q by PP^T, while disregarding the diagonal elements. This is not an eigenvalue problem because of the constraints on P. An efficient algorithm for calculating P is provided. We indicate the potential utility of the latent ancestral allele model. For representative locus-specific Q matrices constructed for a set of maize inbreds, the proposed model recovered the known ancestry.HIGH-THROUGHPUT techniques allow extensive genotyping of individuals for thousands of SNP markers (Gibbs et al. 2003) and thereby provide accurate information about the genetic diversity within a population at many chromosomal loci. If two individuals within this population carry the same DNA sequence at a locus, and this sequence can be traced to the same common ancestor, the individuals are said to be identical by descent (IBD) for this segment (Chapman and Thompson 2003). Quite often, however, the ancestral source of a chromosomal segment is ambiguous and thus IBD relationships between haplotypes are given as probabilities. Various methods have been described to estimate the IBD probability of pairs of chromosomal segments (Meuwissen and Goddard 2001; Leutenegger et al. 2003). When pedigree relationships are known, these can be included to estimate IBD probabilities (Wang et al. 1995; Heath 1997; George et al. 2000; Meuwissen and Goddard 2000; Besnier and Carlborg 2007).In quantitative genetic analysis we seek to find and characterize associations between the large number of SNPs that are now available for many organisms and phenotypic variation for traits of interest (e.g., grain yield and time to flowering). Many current methods developed for this purpose make use of IBD information. For example, a locus-specific matrix of IBD probabilities can be incorporated into restricted maximum-likelihood (REML) procedures for fine mapping quantitative trait loci (Bink and Meuwissen 2004) as well as for marker-based genetic evaluation (Fernando and Grossman 1989) using mixed models. The IBD matrix takes the role of a covariance matrix in the REML procedure.Other approaches, however, require that chromosome segments (also referred to here as haplotypes or alleles) are assigned to independent ancestors. These approaches include regression approaches with genetic predictors (Malosetti et al. 2006) and Bayesian oligo-allelic approaches that sample the ancestral origin of each chromosomal segment (Heath 1997; Uimari and Sillanpaa 2001; Bink et al. 2008a). In the IBD matrix representation the ancestral alleles and their number remain implicit. For these approaches, the locus-specific matrix of IBD probabilities must therefore be decomposed into a matrix that links the chromosomal segments to independent ancestral alleles. This decomposition is addressed in this article.The individuals that we consider in this article are inbred. For n inbred individuals the IBD matrix at a given chromosomal position is thus n × n, because there is no need to distinguish between identical chromosomes. In diploid, outbred populations, each individual would be represented by two haplotypes (alleles) and the matrix would be 2n × 2n (Fernando and Grossman 1989). This is feasible if any phase ambiguity can be resolved. From now on, the term “individual” thus means chromosomal segment or haplotype. Analogously, ancestor will be shorthand for ancestral allele (ancestral haplotype).We propose two models of IBD matrix decomposition, a simple threshold model (TIBD) and a more sophisticated latent ancestral allele model (LAAM), that provide (1) an estimate of the number of independent ancestral alleles, (2) a concise, easy-to-interpret, summary of the relatedness, (3) an explicit (probabilistic) representation of the descent of alleles, and (4) the ability to sample alleles for each individual from a set of ancestral alleles in such a way that the probability that a pair of individuals shares the same allele corresponds to their IBD probability.The last two features of the model are essential for its use in Bayesian oligo-allelic approaches to quantitative trait locus (QTL) analysis (Uimari and Sillanpaa 2001; Bink et al. 2008a).     

Fucosebeta-1-P-Ser is a new type of glycosylation: using antibodies to identify a novel structure in Dictyostelium discoideum and study multiple types of fucosylation during growth and development

Three antibodies that recognize distinct fucose epitopes were used to study fucosylation during growth and development of Dictyostelium discoideum. mAb83.5 is known to recognize an undefined "fucose epitope" on several proteins with serine-rich domains, while mAb CAB4, and a component of anti-horse-radish peroxidase, specifically recognize Fucalpha1,6GlcNAc and Fucalpha1,3GlcNAc residues respectively in the core of N-linked oligosaccharides. We show that mAb 83.5 defines a new type of O-glycosylation. Serine-containing peptides incubated with GDPbeta[3H]Fuc and microsomes formed two fucosylated products. A neutral product accounting for 30% of the label did not react with the antibody, while the rest of the label was incorporated into a charged product which contained all the mAb83.5 reactive material. beta- Elimination of the labeled peptide or endogenous products produced [3H]Fuc-1-P, indicating phosphodiester linkage to serine. Fucbeta-1-P and GDP-betaFuc at 100 microM blocked mAb83.5 binding to endogenous and peptide products, but their alpha-linked anomers did not. Electrospray ionization mass spectra of the neutral and anionic labeled products showed major peaks of mass units corresponding to O-Fuc-Ser peptide and O-Fuc-phospho-Ser peptide, respectively. The activity of Fuc- phosphotransferase exactly paralleled the accumulation of reactive glycans during growth and development. The expressions of N-glycan core Fucalpha1,6GlcNAc and Fucalpha1,3GlcNAc and their respective fucosyl transferase activities were also synchronous, but their developmental regulation differed from one another. Fucalpha1, 6GlcNAc was expressed maximally during growth but declined during development. In contrast core Fucalpha1,3GlcNAc epitopes were expressed almost exclusively during development. These findings provide direct evidence for a novel type of O-phosphofucosylation, demonstrate the existence of an O- fucosyl transferase, and identify two different types of core fucosylation in the N-glycans of Dictyostelium.      

Crystal structure of an empty capsid of turnip yellow mosaic virus

Empty capsids (artificial top component) of turnip yellow mosaic virus were co-crystallized with an encapsidation initiator RNA hairpin. No clear density was observed for the RNA, but there were clear differences in the conformation of a loop of the coat protein at the opening of the pentameric capsomer (formed by five A-subunits) protruding from the capsid, compared to the corresponding loop in the intact virus. Further differences were found at the N terminus of the A-subunit. These differences have implications for the mechanism of decapsidation of the virus, required for infection.     

On flexible finite polygenic models for multiple-trait evaluation

Finite polygenic models (FPM) might be an alternative to the infinitesimal model (TIM) for the genetic evaluation of pedigreed multiple-generation populations for multiple quantitative traits. I present a general flexible Bayesian method that includes the number of genes in the FPM as an additional random variable. Markov-chain Monte Carlo techniques such as Gibbs sampling and the reversible jump sampler are used for implementation. Sampling of genotypes of all genes in the FPM is done via the use of segregation indicators. A broad range of FPM models, some combined with TIM, are empirically tested for the estimation of variance components and the number of genes in the FPM. Four simulation scenarios were studied, including genetic models with 5 or 50 additive independent diallelic genes affecting the traits, and random selection or selection on one of the traits was performed. The results in this study were based on ten replicates per simulation scenario. In the case of random selection, uniform priors on additive gene effects led to posterior mean estimates of genetic variance that were positively correlated with the number of genes fitted in the FPM. In the case of trait selection, assuming normal priors on gene effects also led to genetic variance estimates for the selected trait that were negatively correlated with the number of genes in the FPM. This negative correlation was not observed for the unselected trait. Treating the number of genes in the FPM as random revealed a positive correlation between prior and posterior mean estimates of this number, but the prior hardly affected the posterior estimates of genetic variance. Posterior inferences about the number of genes should be considered to be indicative where trait selection seems to improve the power of distinguishing between TIM and FPM. Based on the results of this study, I suggest not replacing TIM by the FPM, but combining TIM and FPM with the number of genes treated as random, to facilitate a highly flexible and thereby robust method for variance component estimation in pedigreed populations. Further study is required to explore the full potential of these models under different genetic model assumptions.     

Heterogeneous nuclear ribonucleoproteins C1/C2 identified as autoantigens by biochemical and mass spectrometric methods

The antigenic specificity of an unusual antinuclear antibody pattern in three patient sera was identified after separating HeLa-cell nuclear extracts by two-dimensional (2D) gel electrophoresis and localizing the antigens by immunoblotting with patient serum. Protein spots were excised from the 2D gel and their contents were analyzed by matrix-assisted laser desorption-ionization (MALDI) or nanoelectrospray ionization time-of-flight (TOF) tandem mass spectrometry (MS) after in-gel digestion with trypsin. A database search identified the proteins as the C1 and C2 heterogeneous nuclear ribonucleoproteins. The clinical spectrum of patients with these autoantibodies includes arthritis, psoriasis, myositis, and scleroderma. None of 59 patients with rheumatoid arthritis, 19 with polymyositis, 33 with scleroderma, and 10 with psoriatic arthritis had similar antibodies. High-resolution protein-separation methods and mass-spectrometric peptide mapping in combination with database searches are powerful tools in the identification of novel autoantigen specificities.     

Evaluation of APOE polymorphisms and the risk for age-related macular degeneration in a Southeastern Brazilian population

This study aimed to evaluate the role of APOE polymorphisms (rs429358 and rs7412) in the risk of age-related macular degeneration in a sample of the Southeastern Brazilian population. Seven hundred and five unrelated individuals were analyzed, 334 with age-related macular degeneration (case group), and 371 without the disease (control group). In the case group, patients were further stratified according to disease phenotypes, divided into dry and wet age-related macular degeneration, and non-advanced and advanced age-related macular degeneration. APOE polymorphisms (rs429358 and rs7412) were evaluated through polymerase chain reaction and direct sequencing. In the comparison of cases vs. controls, none of the associations reached statistical significance, considering the Bonferroni-adjusted P-value, although there was a suggestive protection for the E3/E4 genotype (OR = 0.626; P-value = 0.037) and E4 carriers (OR = 0.6515; P-value = 0.047). Statistically significant protection for both the E3/E4 genotype and E4 carriers was observed in the comparisons: advanced age-related macular degeneration vs. controls (OR = 0.3665, P-value = 0.491 × 10⁻³ and OR = 0.4031, P-value = 0.814 × 10⁻³, respectively), advanced age-related macular degeneration vs. non-advanced age-related macular degeneration (OR = 0.2529, P-value = 0.659 × 10⁻⁴ and OR = 0.2692, P-value = 0.631 × 10⁻⁴, respectively). In the comparison of wet age-related macular degeneration vs. control, protection was statistically significant only for E3/E4 (OR = 0.4052, P-value = 0.001). None of the comparisons demonstrated any significant association for E2 genotypes or E2 carriers in age-related macular degeneration risk in this study. Findings suggest a protective role of the E4 haplotype in the APOE gene in the risk for advanced and wet forms of age-related macular degeneration, in a sample of the Brazilian population. To our knowledge, this is the first Brazilian study to show the association between APOE polymorphisms and age-related macular degeneration.     

Modern techniques for the diagnostic evaluation of the trephine bone marrow biopsy: methodological aspects and applications

Histopathological examination of a bone marrow (BM) trephine biopsy is an integral part of the diagnostic work-up of patients with haematological disorders and other diseases which may afflict hematopoiesis. Until recently, the dramatic increase in modern immunological and molecular techniques which have been added to the diagnostic repertoire of clinical haematology has largely bypassed the BM trephine. In recent years, however, many of the technical obstacles preventing application of these techniques to BM biopsies have been surmounted, and immunohistochemistry, fluorescence in situ hybridization and polymerase chain reaction (PCR)-based molecular techniques for examination of DNA and RNA have successfully been applied to conventionally processed BM trephines. This review tries to give an overview of techniques suitable for trephine biopsies, as well as diagnostic and research applications.     

Extracellular signal-regulated kinase 1/2 plays a pro-life role in experimental brain stem death via MAPK signal-interacting kinase at rostral ventrolateral medulla

Background  

As the origin of a life-and-death signal detected from systemic arterial pressure, which sequentially increases (pro-life) and decreases (pro-death) to reflect progressive dysfunction of central cardiovascular regulation during the advancement towards brain stem death in critically ill patients, the rostral ventrolateral medulla (RVLM) is a suitable neural substrate for mechanistic delineation of this fatal phenomenon. The present study assessed the hypothesis that extracellular signal-regulated kinase 1/2 (ERK1/2), a member of the mitogen-activated protein kinases (MAPKs) that is important for cell survival and is activated specifically by MAPK kinase 1/2 (MEK1/2), plays a pro-life role in RVLM during brain stem death. We further delineated the participation of MAPK signal-interacting kinase (MNK), a novel substrate of ERK in this process.