The relationship between capsid protein (VP2) sequence and pathogenicity of Aleutian mink disease parvovirus (ADV): a possible role for raccoons in the transmission of ADV infections.

Aleutian mink disease parvovirus (ADV) DNA was identified by PCR in samples from mink and raccoons on commercial ranches during an outbreak of Aleutian disease (AD). Comparison of DNA sequences of the hypervariable portion of VP2, the major capsid protein of ADV, indicated that both mink and raccoons were infected by a new isolate of ADV, designated ADV-TR. Because the capsid proteins of other parvoviruses play a prominent role in the determination of viral pathogenicity and host range, we decided to examine the relationship between the capsid protein sequences and pathogenicity of ADV. Comparison of the ADV-TR hypervariable region sequence with sequences of other isolates of ADV revealed that ADV-TR was 94 to 100% related to the nonpathogenic type 1 ADV-G at both the DNA and amino acid levels but less than 90% related to other pathogenic ADVs like the type 2 ADV-Utah, the type 3 ADV-ZK8, or ADV-Pullman. This finding indicated that a virus with a type 1 hypervariable region could be pathogenic. To perform a more comprehensive analysis, the complete VP2 sequence of ADV-TR was obtained and compared with that of the 647-amino-acid VP2 of ADV-G and the corresponding VP2 sequences of the pathogenic ADV-Utah, ADV-Pullman, and ADV-ZK8. Although the hypervariable region amino acid sequence of ADV-TR was identical to that of ADV-G, there were 12 amino acid differences between ADV-G and ADV-TR. Each of these differences was at a position where other pathogenic isolates also differed from ADV-G. Thus, although ADV-TR had the hypervariable sequence of the nonpathogenic type 1 ADV-G, the remainder of the VP2 sequence resembled sequences of other pathogenic ADVs. Under experimental conditions, ADV-TR and ADV-Utah were highly pathogenic and induced typical AD in trios of both Aleutian and non-Aleutian mink, whereas ADV-Pullman was pathogenic only for Aleutian mink and ADV-G was noninfectious. Trios of raccoons experimentally inoculated with ADV-TR and ADV-Utah all became infected with ADV, but only a single ADV-Pullman-inoculated raccoon showed evidence of infection. Furthermore, none of the ADV isolates induced pathological findings of AD in raccoons. Finally, when a preparation of ADV-TR prepared from infected raccoon lymph nodes was inoculated into mink and raccoons, typical AD was induced in Aleutian and non-Aleutian mink, but raccoons failed to show serological or pathological evidence of infection. These results indicated that raccoons can become infected with ADV and may have a role in the transmission of virus to mink but that raccoon-to-raccoon transmission of ADV is unlikely.     

Production of laccase, manganese peroxidase and lignin peroxidase by Brazilian marine-derived fungi

Marine-derived fungi are a potential for the search of new compounds with relevant features. Among these, the ligninolytic enzymes have potential applications in a large number of fields, including the environmental and industrial sectors. This is the work aimed to evaluate the enzymatic activities of three marine-derived fungi (Aspergillus sclerotiorum CBMAI 849, Cladosporium cladosporioides CBMAI 857 and Mucor racemosus CBMAI 847) under different carbon sources and salinity conditions by using statistical experimental design. MnP, LiP and laccase were detected when these fungi were cultured in malt extract, however when grown on basal medium containing glucose and wheat bran LiP was not detected and yet an increase in MnP and laccase was observed. Statistical analysis through surface responses was performed and results showed high values of MnP and laccase activities under 12.5% and 23% (w/v) salinity, highlighting the potential use of these fungi for industrial applications and in bioremediation of contaminated sites having high salt concentrations. The highest values for LiP (75376.34 UI L⁻¹), MnP (4484.30 IU L⁻¹) and laccase (898.15 UI L⁻¹) were obtained with the fungus M. racemosus CBMAI 847 and it is the first report concerning ligninolytic enzymes production by a zygomycete from this genus.     

Comparative analysis of Histophilus somni immunoglobulin-binding protein A (IbpA) with other fic domain-containing enzymes reveals differences in substrate and nucleotide specificities

A new family of adenylyltransferases, defined by the presence of a Fic domain, was recently discovered to catalyze the addition of adenosine monophosphate (AMP) to Rho GTPases (Yarbrough, M. L., Li, Y., Kinch, L. N., Grishin, N. V., Ball, H. L., and Orth, K. (2009) Science 323, 269-272; Worby, C. A., Mattoo, S., Kruger, R. P., Corbeil, L. B., Koller, A., Mendez, J. C., Zekarias, B., Lazar, C., and Dixon, J. E. (2009) Mol. Cell 34, 93-103). This adenylylation event inactivates Rho GTPases by preventing them from binding to their downstream effectors. We reported that the Fic domain(s) of the immunoglobulin-binding protein A (IbpA) from the pathogenic bacterium Histophilus somni adenylylates mammalian Rho GTPases, RhoA, Rac1, and Cdc42, thereby inducing host cytoskeletal collapse, which allows H. somni to breach alveolar barriers and cause septicemia. The IbpA-mediated adenylylation occurs on a functionally critical tyrosine in the switch 1 region of these GTPases. Here, we conduct a detailed characterization of the IbpA Fic2 domain and compare its activity with other known Fic adenylyltransferases, VopS (Vibrio outer protein S) from the bacterial pathogen Vibrio parahaemolyticus and the human protein HYPE (huntingtin yeast interacting protein E; also called FicD). We also included the Fic domains of the secreted protein, PfhB2, from the opportunistic pathogen Pasteurella multocida, in our analysis. PfhB2 shares a common domain architecture with IbpA and contains two Fic domains. We demonstrate that the PfhB2 Fic domains also possess adenylyltransferase activity that targets the switch 1 tyrosine of Rho GTPases. Comparative kinetic and phylogenetic analyses of IbpA-Fic2 with the Fic domains of PfhB2, VopS, and HYPE reveal important aspects of their specificities for Rho GTPases and nucleotide usage and offer mechanistic insights for determining nucleotide and substrate specificities for these enzymes. Finally, we compare the evolutionary lineages of Fic proteins with those of other known adenylyltransferases.     

Complement decay accelerating factor (DAF)/CD55 in cancer

The complement system is a powerful innate mechanism involved in protection of the host against pathogens. It also has a role in the clearance of apoptotic cells and has been implicated in a range of pathologies including autoimmunity and graft rejection. The control of complement is mediated through the complement regulatory proteins (CRPs). These are present on most cells and protect normal cells from complement-mediated attack during innate activation. However, in a range of pathologies and cancer, these molecules are up or down regulated, sometimes secreted and even lost. We will review the expression of CRPs in cancer, focussing on CD55 and highlight other roles of the CRPs and their involvement in leukocyte function. We will also provide some data providing a potential mechanism by which soluble CD55 can inhibit T-cell function and discuss some of the implications of this data.This article is a symposium paper from the “Robert Baldwin Symposium: 50 years of Cancer Immunotherapy”, held in Nottingham, Great Britain, on 30 June 2005.     

The effects of fertilizers on two subsequent generations of winter wheat

Summary The effects of all combinations of nitrogen, phosphorus and potassium, with two different sowing dates, were studied using two varieties of winter wheat grown in pots. As well as studying the direct effects of these treatments on mean grain weight (1000 K weight) and grain yield, particular attention was paid to investigating any possible after-effects of these treatments in the first and second generations of the treated plants.The fertilizer treatments were applied in liquid form to the two varieties at intervals during the growing season. Seed was taken from the fertilizer treated plants and sown in uniform soil of high fertility. Grain yield and 1000 K weight were recorded from the treated plants and from their offspring (first generation) grown in the uniform soil. A second generation of offspring was grown in uniform soil with seed taken from the first generation.Potassium had a depressant after-effect on grain yield in one of two tests with the first generation offspring. There were no significant after-effects in the second generation. The 1000 K weight of seed from the treated with the grain yield of the first generation plants grown from this seed. Highly significant yield differences were obtained among the first generation offspring when offspring from plants differently treated were crowded together in pots and competition was presumably severe.

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Zusammenfassung Die Wirkung aller Kombinationen von Stickstoff-, Phosphor- und Kali-Gaben mit zwei verschiedenen Aussaatterminen wurde an zwei in Gefäßen angezogenen Winterweizensorten untersucht. Die Prüfung erstreckte sich auf die direkte Wirkung dieser Behandlungen auf das durchschnittliche Korngewicht (Tausendkorngewicht) und den Kornertrag, besonders aber auf etwaige Nachwirkungen in der 1. und 2. Generation.Die beiden Sorten erhielten die Düngergaben in flüssiger Form in bestimmten Zeitabständen während der Wachstumsperiode. Kornertrag und Tausendkorngewicht der behandelten Pflanzen und ihrer Nachkommenschaft (1. Generation), die aus Samen der behandelten Pflanzen in einheitlichem, gutem Boden angezogen wurde, werden mitgeteilt. Aus Samen der 1. Generation wurde noch eine 2. Generation aufgezogen.Bei der 1. Generation zeigte sich in einem von zwei Versuchen eine depressive Nachwirkung des Kaliums auf den Kornertrag, in der 2. Generation jedoch blieben signifikante Nachwirkungen aus. Das Tausendkorngewicht der Samen der behandelten Pflanzen war in einem von 2 Versuchen mit dem Kornertrag der aus diesen Samen aufgewachsenen Pflanzen der 1. Generation negativ korreliert. Hochsignifikante Ertragsdifferenzen ergaben sich in der 1. Generation, wenn die Nachkommenschaften verschieden behandelter Pflanzen im Gemisch in Gefäßen kultiviert wurden und die Konkurrenz vermutlich stark war.

     

Emergence of a Novel Avian Pox Disease in British Tit Species

Avian pox is a viral disease with a wide host range. In Great Britain, avian pox in birds of the Paridae family was first diagnosed in a great tit (Parus major) from south-east England in 2006. An increasing number of avian pox incidents in Paridae have been reported each year since, indicative of an emergent infection. Here, we utilise a database of opportunistic reports of garden bird mortality and morbidity to analyse spatial and temporal patterns of suspected avian pox throughout Great Britain, 2006–2010. Reports of affected Paridae (211 incidents) outnumbered reports in non-Paridae (91 incidents). The majority (90%) of Paridae incidents involved great tits. Paridae pox incidents were more likely to involve multiple individuals (77.3%) than were incidents in non-Paridae hosts (31.9%). Unlike the small wart-like lesions usually seen in non-Paridae with avian pox in Great Britain, lesions in Paridae were frequently large, often with an ulcerated surface and caseous core. Spatial analyses revealed strong clustering of suspected avian pox incidents involving Paridae hosts, but only weak, inconsistent clustering of incidents involving non-Paridae hosts. There was no spatial association between Paridae and non-Paridae incidents. We documented significant spatial spread of Paridae pox from an origin in south-east England; no spatial spread was evident for non-Paridae pox. For both host clades, there was an annual peak of reports in August/September. Sequencing of the avian poxvirus 4b core protein produced an identical viral sequence from each of 20 great tits tested from Great Britain. This sequence was identical to that from great tits from central Europe and Scandinavia. In contrast, sequence variation was evident amongst virus tested from 17 non-Paridae hosts of 5 species. Our findings show Paridae pox to be an emerging infectious disease in wild birds in Great Britain, apparently originating from viral incursion from central Europe or Scandinavia.     

Laccase activity and putative laccase genes in marine-derived basidiomycetes

Studies of laccases from marine-derived fungi are limited. In the present work, putative laccase genes from three marine-derived basidiomycetes and their laccase activities were evaluated. High amounts of laccase were produced by the fungal strains Marasmiellus sp. CBMAI 1062 (971.2 U L⁻¹) and Peniophora sp. CBMAI 1063 (709.03 U L⁻¹) when grown for 21 d at 28 °C in MA2ASW medium prepared with artificial seawater. Marine-derived basidiomycetes produced multiple distinct laccase sequences of about 200 bp with 73–90 % similarity to terrestrial basidiomycete laccases. Marasmiellus sp. CBMAI 1062 and Tinctoporellus sp. CBMAI 1061 showed the greatest laccase gene diversity with three and four distinct putative laccase sequences, respectively. This is the first report of laccase genes from marine-derived fungi, and our results revealed new putative laccases produced by three basidiomycetes.     

Bayesian Quantitative Trait Locus Mapping Using Inferred Haplotypes

We describe a fast hierarchical Bayesian method for mapping quantitative trait loci by haplotype-based association, applicable when haplotypes are not observed directly but are inferred from multiple marker genotypes. The method avoids the use of a Monte Carlo Markov chain by employing priors for which the likelihood factorizes completely. It is parameterized by a single hyperparameter, the fraction of variance explained by the quantitative trait locus, compared to the frequentist fixed-effects model, which requires a parameter for the phenotypic effect of each combination of haplotypes; nevertheless it still provides estimates of haplotype effects. We use simulation to show that the method matches the power of the frequentist regression model and, when the haplotypes are inferred, exceeds it for small QTL effect sizes. The Bayesian estimates of the haplotype effects are more accurate than the frequentist estimates, for both known and inferred haplotypes, which indicates that this advantage is independent of the effect of uncertainty in haplotype inference and will hold in comparison with frequentist methods in general. We apply the method to data from a panel of recombinant inbred lines of Arabidopsis thaliana, descended from 19 inbred founders.AS the power of haplotypic association has become better appreciated, studies using inferred multiallelic loci (i.e., haplotypes or pairs of haplotypes) are becoming more common. This is because single-nucleotide polymorphisms (SNPs), which are the most commonly used type of marker, are very susceptible to a loss of power to detect QTL, due to a mismatch in allele frequencies between the SNP and the causative variant. While multiallelic markers contain more information and have greater power than SNPs for QTL mapping, they are more costly and cumbersome. Consequently a major analytical advance has been the combination of multiple SNP marker information, either to infer haplotypes as in many human association studies or to infer the mosaic of ancestral founder haplotypes in synthetic populations descended from multiple founder strains. The latter scenario includes crosses between inbred strains of mice or rats or inbred accessions of plants.However, there are two potential difficulties with haplotypic association. First, in a fixed-effects framework, a parameter is estimated for each haplotype, which is undesirable when the number of haplotypes is large. In a synthetic population descended from N inbred strains, up to N haplotypes may segregate; for the mouse collaborative cross (Threadgill et al. 2002) N = 8 and for the Arabidopsis thaliana multiparent advanced generation intercross (MAGIC) population of recombinant inbred lines, N = 19 (Kover et al. 2009). For complex traits, where many QTL are expected to segregate, multiple QTL mapping only exacerbates problems with the numbers of parameters.Second, one must account for uncertainty in the inference of haplotypes, which depends on the marker density and how well one can distinguish between all founders at a locus. At some loci the founders'' haplotypes may be identical, for example, in crosses descended from inbred strains of mice.These problems are well known in haplotype association mapping involving human populations, where in general fixed-effects regression modeling is used. Consequently methods have been developed to reduce the number of haplotype groups at a marker locus, using hierarchical clustering and Bayesian partitioning algorithms (Molitor et al. 2003; Durrant et al. 2004; Bardel et al. 2006; Morris 2006; Tzeng et al. 2006; Waldron et al. 2006; Igo et al. 2007; Liu et al. 2007; Tachmazidou et al. 2007; Knight et al. 2008).Bayesian methods are increasingly the approach of choice for QTL mapping, particularly for multiple QTL mapping and the modeling of interactions (Yi and Shriner 2008). The hierarchical Bayesian framework can accommodate more complicated models with more parameters, even when there are many more parameters than observations (Meuwissen et al. 2001; Xu 2003). The Bayesian approach has an additional advantage when the inferred haplotypes are not all identifiable. Reliable estimates of haplotype effects can be determined because the shrinkage effect of the prior distribution restricts the posterior. However, these methods must be fast if these complex analyses are to be practical.In a hierarchical model the key problem is how to model the distribution of the variance attributable to a QTL and its prior. Meuwissen et al. (2001) consider a hierarchical Bayesian random-effects model (HBREM) for observed multiallelic marker loci. They choose normal priors centered at zero for the individual genotype effects, with different variances for each locus. The prior distributions for the variance parameters are scaled inverse chi square, with parameters chosen to give the mean and variance preestimated from the data. However, this prior has a tiny probability of a QTL effect being equal to zero, whereas that is clearly very likely in a genome scan. Hence they also showed an alternative prior, a mixture of a point mass at zero and a scaled inverse chi-square distribution, which gave better results.Xu (2003) considers a noninformative Jeffrey''s prior on the locus variance. The model fits all markers simultaneously and can detect large-effect QTL with little noise at other markers, despite the negligible probability of zero locus variance. However, the model is limited to markers with two or three possible genotypes. Wang et al. (2005) extend this approach to inferred genotypes, but still with only two or three possible genotypes per locus and the method is very computationally intensive.Yi and Xu (2008) argue that the noninformative Jeffrey''s prior on the locus variance induces constant shrinkage on the haplotype effects and that it would be preferable to vary shrinkage according to the data. They compare exponential and scaled inverse chi-square priors on the locus variance, using hyperparameters with vague hyperpriors. They also consider a second prior on the haplotype effects (first proposed by Park and Casella 2008), of a normal distribution with variance proportional to the residual error variance. The four models performed equally when tested on populations with only two genotypes segregating at a locus.There are several frequentist approaches to dealing with haplotype uncertainty in QTL mapping. One is to perform a fixed-effects multiple linear regression or generalized linear regression of the phenotype, treating the haplotype probabilities at the locus as the design matrix (Haley and Knott 1992; Mott et al. 2000). Another is to use multiple imputation to draw samples of haplotypes from the haplotype probabilities (Sen and Churchill 2001). A third is to use the EM algorithm to estimate the haplotypes (Excoffier and Slatkin 1995; Hawley and Kidd 1995; Long et al. 1995; Qin et al. 2002; Lin et al. 2005, 2008; Lin and Zeng 2006; Zeng et al. 2006). An alternative is data expansion, where instead of multiple imputation, the data set is expanded by drawing 10–20 replicate haplotype pairs for every individual from their inferred probability distribution, assigning the same value of the response variable to each, and analyzing the expanded data set. However, this may alter the characteristics of the data, such as the haplotype frequencies.In a Bayesian setting, haplotype uncertainty can be accommodated either by including the predictor variables as unknowns in the updating procedure or by multiple imputation. In a fully Bayesian treatment, the unknown haplotype pair assignments are assigned priors and estimated along with the model parameters. However, Markov chain Monte Carlo (MCMC) is then needed to fit the model, updating the parameters on the basis of the haplotype pairs and then updating the haplotype pairs on the basis of the parameters. Updating the haplotype assignments by MCMC is slow and suffers from the label-switching problem among others (Jasra et al. 2005), so an alternative approach would be preferable.In this article, we present a new HBREM for QTL mapping applicable to observed or inferred haplotypes. It does not require costly MCMC techniques, since the joint posterior distribution factorizes. It parameterizes the variance terms in the model, focusing on the proportion of the variance due to the QTL. We compare its performance with that of the frequentist fixed-effects model for both observed and inferred multiallelic loci. We show first that the posterior mode of the proportion of variance due to a locus is a better outcome measure than two standard Bayesian test statistics and second that the Bayesian estimates of the individual haplotype effects are much more accurate than the corresponding frequentist estimates. Finally we analyze real data from A. thaliana recombinant inbred lines descended from 19 parental lines.