Transcription of a β-1,3-glucanase gene in grape berries in a late developmental period, or earlier after wounding treatments

The hydrolytic enzymes β-1,3-glucanases (EC3.2.1.39) an known to be involved in plant defense reactions against pathogens and in developmental events. We have obtained two partial cDNA clones, corresponding to Vitis vinifera β-1,3-glucanase gene sequences (VvGlu1/7 and VvGlu26). The expression of VvGlu1/7 was studied in grape berries at different developmental stages and in wounded berries with or without salicylic acid elicitation. No constitutive expression was observed in young berries, whereas the induction of VvGlu1/7 transcription was detected during fruit ripening. By contrast, synthesis of mRNA coding for this isoform was generated in the first stage of rapid berry growth in response to wounding treatments with and without salicylic acid

Can habitat specialisation maintain a mosaic hybrid zone in marine bivalves?

Maintaining the integrity of differentiated genomes in marine organisms needs efficient isolation mechanisms, because planktonic larval dispersion provides contacts between taxa. Habitat specialisation is interesting in this respect, because it can both prevent interspecific crosses (each taxon reproduces in its own habitat) and eliminate hybrids (typically less fit than a parental taxon in each habitat). The contact zone between smooth-shelled mussels Mytilus edulis and M. galloprovincialis in Europe is a good example, as allozyme genotypes typical of both taxa seem to segregate into different habitats. However, allozymes may be selected directly and it is not known whether the same pattern can be extended to the whole genome. Here, we used 6 presumably neutral PCR markers to investigate habitat specialisation, focussing on the Bay of Quiberon, a small region in the midst of the contact zone between the 2 taxa. Confirming allozyme findings, our results indicate that habitat specialisation is apparent at the genomic scale, as M, edulis-like genotypes are found in sheltered or open-sea sites under freshwater influence, whereas M, galloprovincialis-like genotypes occupy exposed sites. Hybrid (or mixed) populations are found in open-sea or sheltered areas without freshwater influence. Therefore, habitat specialisation does contribute to the interspecific barrier. However, this mechanism seems insufficient to completely prevent the mixing of the 2 genomes, as mixed populations exist and provide opportunity for further hybridisation. Large gametic disequilibria within hybrid populations indicate the existence of restrictions to genetic exchange between the 2 taxa, even within a single habitat. Habitat-independent isolation mechanisms must, therefore, exist in addition

Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome of Oncidium Gower Ramsey

Oncidium Gower Ramsey is a fascinating and important ornamental flower in floral industry. In this research, the complete nucleotide sequence of the chloroplast genome in Oncidium Gower Ramsey was studied, then analyzed using Codonw software. Correspondence analysis and method of effective number of codon as Nc-plot were conducted to analyze synonymous codon usage. According to the corresponding analysis, codon bias in the chloroplast genome of Oncidium Gower Ramsey is related to their gene length, mutation bias, gene hydropathy level of each protein, gene function and selection or gene expression only subtly affect codon usage. This study will provide insights into the molecular evolution study and high-level transgene expression

Fluctuating selection models and Mcdonald-Kreitman type analyses

It is likely that the strength of selection acting upon a mutation varies through time due to changes in the environment. However, most population genetic theory assumes that the strength of selection remains constant. Here we investigate the consequences of fluctuating selection pressures on the quantification of adaptive evolution using McDonald-Kreitman (MK) style approaches. In agreement with previous work, we show that fluctuating selection can generate evidence of adaptive evolution even when the expected strength of selection on a mutation is zero. However, we also find that the mutations, which contribute to both polymorphism and divergence tend, on average, to be positively selected during their lifetime, under fluctuating selection models. This is because mutations that fluctuate, by chance, to positive selected values, tend to reach higher frequencies in the population than those that fluctuate towards negative values. Hence the evidence of positive adaptive evolution detected under a fluctuating selection model by MK type approaches is genuine since fixed mutations tend to be advantageous on average during their lifetime. Never-the-less we show that methods tend to underestimate the rate of adaptive evolution when selection fluctuates

Evidence for variation in the effective population size of animal mitochondrial DNA

Background: It has recently been shown that levels of diversity in mitochondrial DNA are remarkably constant across animals of diverse census population sizes and ecologies, which has led to the suggestion that the effective population of mitochondrial DNA may be relatively constant. Results: Here we present several lines of evidence that suggest, to the contrary, that the effective population size of mtDNA does vary, and that the variation can be substantial. First, we show that levels of mitochondrial and nuclear diversity are correlated within all groups of animals we surveyed. Second, we show that the effectiveness of selection on non-synonymous mutations, as measured by the ratio of the numbers of non-synonymous and synonymous polymorphisms, is negatively correlated to levels of mitochondrial diversity. Finally, we estimate the effective population size of mitochondrial DNA in selected mammalian groups and show that it varies by at least an order of magnitude. Conclusions: We conclude that there is variation in the effective population size of mitochondria. Furthermore we suggest that the relative constancy of DNA diversity may be due to a negative correlation between the effective population size and the mutation rate per generation

Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow

Speciation often involves repeated episodes of genetic contact between divergent populations before reproductive isolation (RI) is complete. Whole-genome sequencing (WGS) holds great promise for unravelling the genomic bases of speciation. We have studied two ecologically divergent, hybridizing species of the ‘model tree’ genus Populus (poplars, aspens, cottonwoods), Populus alba and P. tremula, using >8.6 million single nucleotide polymorphisms (SNPs) from WGS of population pools. We used the genomic data to (i) scan these species’ genomes for regions of elevated and reduced divergence, (ii) assess key aspects of their joint demographic history based on genomewide site frequency spectra (SFS) and (iii) infer the potential roles of adaptive and deleterious coding mutations in shaping the genomic landscape of divergence. We identified numerous small, unevenly distributed genome regions without fixed polymorphisms despite high overall genomic differentiation. The joint SFS was best explained by ancient and repeated gene flow and allowed pinpointing candidate interspecific migrant tracts. The direction of selection (DoS) differed between genes in putative migrant tracts and the remainder of the genome, thus indicating the potential roles of adaptive divergence and segregating deleterious mutations on the evolution and breakdown of RI. Genes affected by positive selection during divergence were enriched for several functionally interesting groups, including well-known candidate ‘speciation genes’ involved in plant innate immunity. Our results suggest that adaptive divergence affects RI in these hybridizing species mainly through intrinsic and demographic processes. Integrating genomic with molecular data holds great promise for revealing the effects of particular genetic pathways on speciation

Rampant Adaptive Evolution in Regions of Proteins with Unknown Function in Drosophila simulans

Adaptive protein evolution is pervasive in Drosophila. Genomic studies, thus far, have analyzed each protein as a single entity. However, the targets of adaptive events may be localized to particular parts of proteins, such as protein domains or regions involved in protein folding. We compared the population genetic mechanisms driving sequence polymorphism and divergence in defined protein domains and non-domain regions. Interestingly, we find that non-domain regions of proteins are more frequent targets of directional selection. Protein domains are also evolving under directional selection, but appear to be under stronger purifying selection than non-domain regions. Non-domain regions of proteins clearly play a major role in adaptive protein evolution on a genomic scale and merit future investigations of their functional properties

Differential spatial repositioning of activated genes in Biomphalaria glabrata snails infected with Schistosoma mansoni

Copyright @ 2014 Arican-Goktas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.This article has been made available through the Brunel Open Access Publishing Fund.Schistosomiasis is an infectious disease infecting mammals as the definitive host and fresh water snails as the intermediate host. Understanding the molecular and biochemical relationship between the causative schistosome parasite and its hosts will be key to understanding and ultimately treating and/or eradicating the disease. There is increasing evidence that pathogens that have co-evolved with their hosts can manipulate their hosts' behaviour at various levels to augment an infection. Bacteria, for example, can induce beneficial chromatin remodelling of the host genome. We have previously shown in vitro that Biomphalaria glabrata embryonic cells co-cultured with schistosome miracidia display genes changing their nuclear location and becoming up-regulated. This also happens in vivo in live intact snails, where early exposure to miracidia also elicits non-random repositioning of genes. We reveal differences in the nuclear repositioning between the response of parasite susceptible snails as compared to resistant snails and with normal or live, attenuated parasites. Interestingly, the stress response gene heat shock protein (Hsp) 70 is only repositioned and then up-regulated in susceptible snails with the normal parasite. This movement and change in gene expression seems to be controlled by the parasite. Other differences in the behaviour of genes support the view that some genes are responding to tissue damage, for example the ferritin genes move and are up-regulated whether the snails are either susceptible or resistant and upon exposure to either normal or attenuated parasite. This is the first time host genome reorganisation has been seen in a parasitic host and only the second time for any pathogen. We believe that the parasite elicits a spatio-epigenetic reorganisation of the host genome to induce favourable gene expression for itself and this might represent a fundamental mechanism present in the human host infected with schistosome cercariae as well as in other host-pathogen relationships.NIH and Sandler Borroughs Wellcome Travel Fellowshi

Differential immunity as a factor influencing mussel hybrid zone structure

Interspecific hybridisation can alter fitness-related traits, including the response to pathogens, yet immunity is rarely investigated as a potential driver of hybrid zone dynamics, particularly in invertebrates. We investigated the immune response of mussels from a sympatric population at Croyde Bay, within the hybrid zone of Mytilus edulis and Mytilus galloprovincialis in Southwest England. The site is characterised by size-dependent variation in genotype frequencies, with a higher frequency of M. galloprovincialis alleles in large mussels, largely attributed to selective mortality in favour of the M. galloprovincialis genotype. To determine if differences in immune response may contribute to this size-dependent variation in genotype frequencies, we assessed the two pure species and their hybrids in their phagocytic abilities when subject to immune challenge as a measure of immunocompetence and measured the metabolic cost of mounting an antigen-stimulated immune response. Mussels identified as M. galloprovincialis had a greater immunocompetence response at a lower metabolic cost compared to mussels identified as M. edulis. Mussels identified as hybrids had intermediate values for both parameters, providing no evidence for heterosis but suggesting that increased susceptibility compared to M. galloprovincialis may be attributed to the M. edulis genotype. The results indicate phenotypic differences in the face of pathogenic infection, which may be a contributing factor to the differential mortality in favour of M. galloprovincialis, and the size-dependent variation in genotype frequencies associated with this contact zone. We propose that immunity may contribute to European mussel hybrid zone dynamics

Coxiella burnetii Phagocytosis Is Regulated by GTPases of the Rho Family and the RhoA Effectors mDia1 and ROCK

The GTPases belonging to the Rho family control the actin cytoskeleton rearrangements needed for particle internalization during phagocytosis. ROCK and mDia1 are downstream effectors of RhoA, a GTPase involved in that process. Coxiella burnetii, the etiologic agent of Q fever, is internalized by the host´s cells in an actin-dependent manner. Nevertheless, the molecular mechanism involved in this process has been poorly characterized. This work analyzes the role of different GTPases of the Rho family and some downstream effectors in the internalization of C. burnetii by phagocytic and non-phagocytic cells. The internalization of C. burnetii into HeLa and RAW cells was significantly inhibited when the cells were treated with Clostridium difficile Toxin B which irreversibly inactivates members of the Rho family. In addition, the internalization was reduced in HeLa cells that overexpressed the dominant negative mutants of RhoA, Rac1 or Cdc42 or that were knocked down for the Rho GTPases. The pharmacological inhibition or the knocking down of ROCK diminished bacterium internalization. Moreover, C. burnetii was less efficiently internalized in HeLa cells overexpressing mDia1-N1, a dominant negative mutant of mDia1, while the overexpression of the constitutively active mutant mDia1-ΔN3 increased bacteria uptake. Interestingly, when HeLa and RAW cells were infected, RhoA, Rac1 and mDia1 were recruited to membrane cell fractions. Our results suggest that the GTPases of the Rho family play an important role in C. burnetii phagocytosis in both HeLa and RAW cells. Additionally, we present evidence that ROCK and mDia1, which are downstream effectors of RhoA, are involved in that processFil: Salinas Ojeda, Romina Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Ortiz Flores, Rodolfo Matias. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Distel, Jesús Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Aguilera, Milton Osmar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Colombo, Maria Isabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; ArgentinaFil: Beron, Walter. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Cienicas Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; Argentin