t2prhd: a tool to study the patterns of repeat evolution

BACKGROUND: The models developed to characterize the evolution of multigene families (such as the birth-and-death and the concerted models) have also been applied on the level of sequence repeats inside a gene/protein. Phylogenetic reconstruction is the method of choice to study the evolution of gene families and also sequence repeats in the light of these models. The characterization of the gene family evolution in view of the evolutionary models is done by the evaluation of the clustering of the sequences with the originating loci in mind. As the locus represents positional information, it is straightforward that in the case of the repeats the exact position in the sequence should be used, as the simple numbering according to repeat order can be misleading. RESULTS: We have developed a novel rapid visual approach to study repeat evolution, that takes into account the exact repeat position in a sequence. The "pairwise repeat homology diagram" visualizes sequence repeats detected by a profile HMM in a pair of sequences and highlights their homology relations inferred by a phylogenetic tree. The method is implemented in a Perl script (t2prhd) available for downloading at http://t2prhd.sourceforge.net and is also accessible as an online tool at http://t2prhd.brc.hu. The power of the method is demonstrated on the EGF-like and fibronectin-III-like (Fn-III) domain repeats of three selected mammalian Tenascin sequences. CONCLUSION: Although pairwise repeat homology diagrams do not carry all the information provided by the phylogenetic tree, they allow a rapid and intuitive assessment of repeat evolution. We believe, that t2prhd is a helpful tool with which to study the pattern of repeat evolution. This method can be particularly useful in cases of large datasets (such as large gene families), as the command line interface makes it possible to automate the generation of pairwise repeat homology diagrams with the aid of script

Sexual dimorphism in immune function and oxidative physiology across birds: The role of sexual selection

Sex-specific physiology is commonly reported in animals, often indicating lower immune indices and higher oxidative stress in males than in females. Sexual selection is argued to explain these differences, but empirical evidence is limited. Here, we explore sex differences in immunity, oxidative physiology and packed cell volume of wild, adult, breeding birds (97 species, 1997 individuals, 14 230 physiological measurements). We show that higher female immune indices are most common across birds (when bias is present), but oxidative physiology shows no general sex-bias and packed cell volume is generally male-biased. In contrast with predictions based on sexual selection, male-biased sexual size dimorphism is associated with male-biased immune measures. Sexual dichromatism, mating system and parental roles had no effect on sex-specificity in physiology. Importantly, female-biased immunity remained after accounting for sexual selection indices. We conclude that cross-species differences in physiological sex-bias are largely unrelated to sexual selection and alternative explanations should be explored

The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity

We have previously demonstrated that the replacement of the S gene from an avirulent strain (Beaudette) of infectious bronchitis virus (IBV) with an S gene from a virulent strain (M41) resulted in a recombinant virus (BeauR-M41(S)) with the in vitro cell tropism of the virulent virus but that was still avirulent. In order to investigate whether any of the other structural or accessory genes played a role in pathogenicity we have now replaced these from the Beaudette strain with those from M41. The recombinant IBV was in effect a chimaeric virus with the replicase gene derived from Beaudette and the rest of the genome from M41. This demonstrated that it is possible to exchange a large region of the IBV genome, approximately 8.4 kb, using our transient dominant selection method. Recovery of a viable recombinant IBV also demonstrated that it is possible to interchange a complete replicase gene as we had in effect replaced the M41 replicase gene with the Beaudette derived gene. Analysis of the chimaeric virus showed that it was avirulent indicating that none of the structural or accessory genes derived from a virulent isolate of IBV were able to restore virulence and that therefore, the loss of virulence associated with the Beaudette strain resides in the replicase gene

Molecular characterization of a lizard adenovirus reveals the first atadenovirus with two fiber genes and the first adenovirus with either one short or three long fibers per penton

Although adenoviruses (AdVs) have been found in a wide variety of reptiles, including numerous squamate species, turtles, and crocodiles, the number of reptilian adenovirus isolates is still scarce. The only fully sequenced reptilian adenovirus, snake adenovirus 1 (SnAdV-1), belongs to the Atadenovirus genus. Recently, two new atadenoviruses were isolated from a captive Gila monster (Heloderma suspectum) and Mexican beaded lizards (Heloderma horridum). Here we report the full genomic and proteomic characterization of the latter, designated lizard adenovirus 2 (LAdV-2). The double-stranded DNA (dsDNA) genome of LAdV-2 is 32,965 bp long, with an average G+C content of 44.16%. The overall arrangement and gene content of the LAdV-2 genome were largely concordant with those in other atadenoviruses, except for four novel open reading frames (ORFs) at the right end of the genome. Phylogeny reconstructions and plesiomorphic traits shared with SnAdV-1 further supported the assignment of LAdV-2 to the Atadenovirus genus. Surprisingly, two fiber genes were found for the first time in an atadenovirus. After optimizing the production of LAdV-2 in cell culture, we determined the protein compositions of the virions. The two fiber genes produce two fiber proteins of different sizes that are incorporated into the viral particles. Interestingly, the two different fiber proteins assemble as either one short or three long fiber projections per vertex. Stoichiometry estimations indicate that the long fiber triplet is present at only one or two vertices per virion. Neither triple fibers nor a mixed number of fibers per vertex had previously been reported for adenoviruses or any other virus

Study on the emergence of the raspberry cane midge (Resseliella theobaldi Barnes) on the basis of temperature data and catches of sex pheromone traps

Effective chemical protection against the raspberry cane midge (Resseliella theobaldi) should be based on the monitoring of the emergence of the pest. Before the application of sex pheromone traps, the results of several international studies carried out to determine the accumulated temperature needed by the larvae to become adults showed differences in the calculated data. The aim of this paper was to give information on the time of cane midge emergence by using sex pheromone traps and different methods of accumulated temperature calculations. On the basis of three years' results, the use of accumulated soil temperatures turned out to be reliable for the prediction of cane midge flight, and the relative standard deviation was the smallest in the case of 0 °C compared with other values applied as supposed biological zero points. According to our studies, 665 day °C are required for the development of one generation of the raspberry cane midge during the vegetation period. The emergence of the first generation was found at 451 day °C

The role of plant characteristics in the resistance of white cabbage to onion thrips: preliminary results

The onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae) has been recognized as a severe worldwide pest of white cabbage (Brassica oleracea L. convar. capitata provar. capitata Duch.) for almost three decades. Although the most effective control measure is the use of resistant varieties, little is known about the resistance mechanism(s) involved. In 2007, a study at Tordas, Hungary, was carried out with 6 varieties to confirm that antixenosis is at least partly responsible for the resistance against onion thrips. The number of adult thrips and their progeny was counted on the outer ten head leaves at one-third of the heading process.At the same time, the light reflectance of old and outer head leaves was measured. The onion thrips damage was also assessed at full maturity. Antixenosis was found to be responsible for the resistance of ‘Balashi’, ‘Bloktor’ and ‘Riana’ varieties, since the number of adults and offspring found on head leaves was significantly lower than that of ‘Green gem’, ‘Hurricane’ and ‘Quisto’. The resistant varieties (‘Balashi’, ‘Bloktor’ and ‘Riana’) similarly suffered significantly lower damage than the susceptible ones (‘Green gem’, ‘Hurricane’ and ‘Quisto’). The light reflectance spectra of all six varieties were almost identical in the case of the old leaves, but a difference was found between the susceptible and resistant varieties when the reflectance of the outer head-forming leaves was measured. Similarly, the colour of the old leaves was not greatly different, but that of the outer head-forming leaves was correlated to the number of thrips adults found in the cabbage heads