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DNA Sequence Comparisons (dna + sequence_comparison)
Selected AbstractsWithin-breed heterozygosity of canine single nucleotide polymorphisms identified by across-breed comparisonANIMAL GENETICS, Issue 6 2002J. A. Brouillette Summary Identification of single nucleotide polymorphisms (SNPs) by DNA sequence comparison across breeds is a strategy for developing genetic markers that are useful for many breeds. However, the heterozygosity of SNPs identified in this way might be severely reduced within breeds by inbreeding or genetic drift in the small effective population size of a breed (population subdivision). The effect of inbreeding and population subdivision on heterozygosity of SNPs in dog breeds has never been investigated in a systematic way. We determined the genotypes of dogs from three divergent breeds for SNPs in four canine genes (ACTC, LMNA, SCGB, and TYMS) identified by across-breed DNA sequence comparison, and compared the genotype frequencies to those expected under Hardy,Weinberg equilibrium (HWE). Although population subdivision significantly skewed allele frequencies across breeds for two of the SNPs, the deviations of observed heterozygosities compared with those expected within breeds were minimal. These results indicate that across-breed DNA sequence comparison is a reasonable strategy for identifying SNPs that are useful within many canine breeds. [source] Botryosphaeriaceae associated with Eucalyptus canker diseases in ColombiaFOREST PATHOLOGY, Issue 2 2009C. A. Rodas Summary The identities of Botryosphaeriaceae causing cankers on Eucalyptus in Colombia were investigated using morphological and DNA sequence comparisons. The pathogenicity of the species was also assessed on 42 Eucalyptus grandis clones planted at four different sites. Two species of the Botryosphaeriaceae were found to occur on E. grandis in Colombia. Neofusicoccum ribis was the more common species, and also the most pathogenic. Botryosphaeria dothidea was found only in one zone of Colombia, and was also less pathogenic than N. ribis. These two species could be distinguished easily based on DNA sequences of the ITS1/ITS2 rDNA region and EF1-,, in addition to conidial sizes. Significant differences in resistance of clones to these pathogens were also evident from the various trials. [source] Sirococcus shoot blight on Picea spinulosa in BhutanFOREST PATHOLOGY, Issue 1 2007T. Kirisits Summary During a recent survey of forest tree diseases in Western and Central Bhutan, Sirococcus shoot blight and an associated Sirococcus sp. were found on saplings and mature trees of Eastern Himalayan spruce (Picea spinulosa). Based on morphological characteristics and DNA sequence comparisons of the ITS region of the rDNA operon, representative isolates from Bhutan were unequivocally identified as Sirococcus conigenus. The DNA sequence data also showed that these isolates belong to the P group of S. conigenus. To our best knowledge, this is the first report of Sirococcus shoot blight from the Himalayas or any other part of Asia. Sirococcus conigenus does not appear to cause dramatic damage at the moment, but this fungus has the potential to cause severe disease problems on P. spinulosa in Bhutan. [source] Identification of evolutionarily conserved regulatory elements in the mouse Fgf8 locusGENESIS: THE JOURNAL OF GENETICS AND DEVELOPMENT, Issue 1 2006Friedrich Beermann Abstract The secreted signaling molecule fibroblast growth factor 8 (Fgf8) is an essential component of certain embryonic signaling centers including the mid-hindbrain (isthmic) organizer, the first branchial arch (BA1), and the apical ectodermal ridge (AER). In these signaling centers Fgf8 transcripts are expressed in a dynamic and transient fashion, but the mechanism by which this highly specific expression pattern is established remains largely unknown. We used DNA sequence comparisons coupled to transgenic approaches to obtain insight into the structure and function of regulatory elements in the Fgf8 locus. First, a bacterial artificial chromosome (BAC) containing the mouse Fgf8 gene partially rescues the embryonic lethality of Fgf8- deficient mice and controls Fgf8 -specific gene expression of a coinjected lacZ reporter transgene. Second, sequence comparison of vertebrate Fgf8 loci revealed evolutionarily highly conserved noncoding sequences that were unexpectedly located mainly 3, of the Fgf8 coding region. Third, in transgenic mice some of these elements were sufficient to target expression to the AER, tail bud, and brain, including the isthmic organizer, indicating that they may represent Fgf8 cis-acting elements. Collectively, these data identify novel regulatory elements of the Fgf8 gene sufficient to drive expression to regions of known Fgf8 activity. genesis 44:1,6, 2006. © 2006 Wiley-Liss, Inc. [source] The selection and evolution of viral quasispecies in HIV-1 infected childrenHIV MEDICINE, Issue 1 2002P Nowak Objectives To analyse the diversity and divergence of the viral populations in three mother,child pairs in longitudinally obtained samples for up to 7 years. Methods Peripheral blood mononuclear cells were obtained from three mothers at delivery and three to four samples were obtained from each of their children from 1.5 months up to 78 months of age. The V3 region of HIV-1 was amplified by polymerase chain reaction, cloned and sequenced. HIV-1 DNA sequence comparisons were performed by phylogenetic analysis. Results The viral population was initially homogenous in two children but highly heterogeneous in one child. Three patterns of vertical transmission seemed to have occurred: transmission of the most prevalent maternal strain, of a minor maternal strain and of multiple maternal strains. In one child, a possible reappearance of a maternal sequence was observed at 34 months of age. Conclusions Children may become infected with the most prevalent maternal strain, a minor maternal variant or multiple maternal quasispecies. Maternal viral variants may reappear in children after several years of infection and could possibly be derived from a reservoir of founder quasispecies established during the children's primary HIV-1 infection. [source] Phytophthora pinifolia sp. nov. associated with a serious needle disease of Pinus radiata in ChilePLANT PATHOLOGY, Issue 4 2008A. Durán During the course of the past three years, a new disease of Pinus radiata, referred to as ,Daño Foliar del Pino' (DFP) has appeared in the Arauco province of Chile and subsequently spread to other areas. The disease is typified by needle infections, exudation of resin at the bases of the needle brachyblasts and, in younger trees, necrotic lesions in the cambium, which eventually girdle the branches. The disease causes the death of young seedlings and mature trees can also succumb after a few years of successive infection, probably hastened by opportunistic fungi such as Diplodia pinea. Isolations on selective medium for Phytophthora spp. led to the consistent isolation of a Phytophthora sp. from needle tissue. DNA sequence comparisons for the ITS rDNA and cox II gene regions, and morphological observation showed that this oomycete represents a previously undescribed species for which the name Phytophthora pinifolia sp. nov. is provided. This new species is characterized by unbranched sporangiophores, and non-papillate, sub-globose to ovoid sporangia that are occasionally free from the sporangiophore with medium length pedicels. Despite using a number of oospore inducing techniques, oogonia/antheridia were not observed in isolates of P. pinifolia. Pathogenicity trials with P. pinifolia showed that it is pathogenic to P. radiata and causes rapid death of the succulent apical parts of young plants. Phytophthora pinifolia is the first Phytophthora known to be associated with needles and shoots of a Pinus sp. and its aerial habit is well matched with the occurrence and symptoms of DFP in Chile. [source] | ||||||||||