Isolation of polymorphic tetranucleotide microsatellite markers in the satin bowerbird, Ptilonorhynchus violaceus

We isolated 13 polymorphic microsatellite markers from the satin bowerbird, Ptilonorhynchus violaceus from a genomic library enriched in (AAGG)(n) repetitive elements and characterized them in 20 individuals. The number of alleles ranged from two to 18 per locus with the observed heterozygosity ranging from 0.15 to 1.00. These markers will be useful for analysing questions concerning parentage, population genetic structure and models of speciation.

Isolation of polymorphic tetranucleotide microsatellite for the large-billed scrubwren (Sericomis magnirostris)

We isolated 12 polymorphic microsatellite markers for the large-billed scrubwren Sericornis magnirostris from genomic libraries enriched for (AAGG)(n) and (AACC)(n) repetitive elements and characterized them in 11 individuals. The number of alleles ranged from four to 15 per locus with the observed heterozygosity ranging from 0.14 to 0.91. These markers will be useful to address questions concerning population genetic structure and models of speciation.

Isolation of polymorphic tetranucleotide microsatellite markers for the grey-headed robin (Poecilodryas albispecularis)

We isolated 12 polymorphic microsatellite markers for the grey-headed robin Poecilodryas albispecularis from genomic libraries enriched for (AAGG)n and (AACC)n repetitive elements and characterized them in 12 individuals. The number of alleles ranges from three to nine per locus with the observed heterozygosity ranging from 0.33 to 0.90. These markers will be useful for analysis of questions concerning population genetic structure and testing models of speciation.

Isolation of polymorphic tetranucleotide microsatellite markers for the green-eyed tree frog (Litoria genimaculata)

We have isolated 16 polymorphic microsatellite markers for the green-eyed tree frog, Litoria genimaculata, from genomic libraries enriched for (AAGG)(n) and (AAAG)(n) repetitive elements. The number of alleles ranges from four to 14 per locus with the observed heterozygosity ranging from 0.36 to 1.00. These markers will be useful for analysis of questions concerning population genetic structure and speciation.

Isolation of polymorphic tetranucleotide microsatellite markers for the ornate nursery frog Cophixalus ornatus

We have isolated 18 polymorphic microsatellite loci for Cophixalus ornatus from genomic libraries enriched for (AAAG)(n), (AACC)(n) and (AAGG)(n) repetitive elements. The number of alleles ranges from five to 22 per locus with the observed heterozygosity ranging from 0.10 to 0.92. These markers will be useful for the analysis of population structure in C. ornatus and testing alternative models of speciation.

Capturing strategy as an everyday practice:quantitative methodologies for analysing practice data

Few works address methodological issues of how to conduct strategy-as-practice research and even fewer focus on how to analyse the subsequent data in ways that illuminate strategy as an everyday, social practice. We address this gap by proposing a quantitative method for analysing observational data, which can complement more traditional qualitative methodologies. We propose that rigorous but context-sensitive coding of transcripts can render everyday practice analysable statistically. Such statistical analysis provides a means for analytically representing patterns and shifts within the mundane, repetitive elements through which practice is accomplished. We call this approach the Event Database (EDB) and it consists of five basic coding categories that help us capture the stream of practice. Indexing codes help to index or categorise the data, in order to give context and offer some basic information about the event under discussion. Indexing codes are descriptive codes, which allow us to catalogue and classify events according to their assigned characteristics. Content codes are to do with the qualitative nature of the event; this is the essence of the event. It is a description that helps to inform judgements about the phenomenon. Nature codes help us distinguish between discursive and tangible events. We include this code to acknowledge that some events differ qualitatively from other events. Type events are codes abstracted from the data in order to help us classify events based on their description or nature. This involves significantly more judgement than the index codes but consequently is also more meaningful. Dynamics codes help us capture some of the movement or fluidity of events. This category has been included to let us capture the flow of activity over time.

Capturing strategy as an everyday practice:quantitative methodologies for analysing practice data

Few works address methodological issues of how to conduct strategy-as-practice research and even fewer focus on how to analyse the subsequent data in ways that illuminate strategy as an everyday, social practice. We address this gap by proposing a quantitative method for analysing observational data, which can complement more traditional qualitative methodologies. We propose that rigorous but context-sensitive coding of transcripts can render everyday practice analysable statistically. Such statistical analysis provides a means for analytically representing patterns and shifts within the mundane, repetitive elements through which practice is accomplished. We call this approach the Event Database (EDB) and it consists of five basic coding categories that help us capture the stream of practice. Indexing codes help to index or categorise the data, in order to give context and offer some basic information about the event under discussion. Indexing codes are descriptive codes, which allow us to catalogue and classify events according to their assigned characteristics. Content codes are to do with the qualitative nature of the event; this is the essence of the event. It is a description that helps to inform judgements about the phenomenon. Nature codes help us distinguish between discursive and tangible events. We include this code to acknowledge that some events differ qualitatively from other events. Type events are codes abstracted from the data in order to help us classify events based on their description or nature. This involves significantly more judgement than the index codes but consequently is also more meaningful. Dynamics codes help us capture some of the movement or fluidity of events. This category has been included to let us capture the flow of activity over time.

Splitting of a prevalent Mycobacterium bovis spoligotype by variable-number tandem-repeat typing reveals high heterogeneity in an evolving clonal group

Mycobacterium bovis populations in countries with persistent bovine tuberculosis usually show a prevalent spoligotype with a wide geographical distribution. This study applied mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing to a random panel of 115 M. bovis isolates that are representative of the most frequent spoligotype in the Iberian Peninsula, SB0121. VNTR typing targeted nine loci: ETR-A (alias VNTR2165), ETR-B (VNTR2461), ETR-D (MIRU4, VNTR580), ETR-E (MIRU31, VNTR3192), MIRU26 (VNTR2996), QUB11a (VNTR2163a), QUB11b (VNTR2163b), QUB26 (VNTR4052), and QUB3232 (VNTR3232). We found a high degree of diversity among the studied isolates (discriminatory index [D] = 0.9856), which were split into 65 different MIRU-VNTR types. An alternative short-format MIRU-VNTR typing targeting only the four loci with the highest variability values was found to offer an equivalent discriminatory index. Minimum spanning trees using the MIRU-VNTR data showed the hypothetical evolution of an apparent clonal group. MIRU-VNTR analysis was also applied to the isolates of 176 animals from 15 farms infected by M. bovis SB0121; in 10 farms, the analysis revealed the coexistence of two to five different MIRU types differing in one to six loci, which highlights the frequency of undetected heterogeneity.

A LINE2 repetitive DNA sequence from the cichlid fish, Oreochromis niloticus: sequence analysis and chromosomal distribution

We report the cloning and characterization of a long interspersed nucleotide element (LINE) fi-om a cichlid fish, Oreochromis niloticus, and show the distribution of this element, called CiLINE2 for cichlid LINE2, in the chromosomes of this species. The identification of an open reading frame in CiLINE2 with amino acid sequence similarity to reverse transcriptases encoded by LINE-like elements in Caenorhabditis elegans, Platemys spixii, Schistosoma mansoni, Gallus gallus (CRI), Drosophila melanogaster (I factor), and Homo sapiens (LINE2), as well as the structure of the element, suggest it is a member of this family of non-long terminal repeat-containing retrotransposons. Search of a DNA sequence database identified sequences similar to CiLINE2 in four other fish species (Haplotaxodon microlepis, Oreochromis mossambicus, Pseudotropheus zebra, and Fugu rubripes). Southern blot hybridization experiments revealed the presence of sequences similar to CiLINE2 in all Tilapiini species analyzed from the genera Oreochromis, Tilapia, and Sarotherodon, and gave an estimated copy number of about 5500 for the haploid genome of O. niloticus. Fluorescent in situ hybridization showed that CiLINE2 sequences were organized in small clusters dispersed over all chromosomes of O. niloticus, with a higher concentration near chromosome ends. Furthermore the long arm of chromosome 1 was strikingly enriched with this sequence. The distribution of LINE2-related elements might underlie the difference in chromosome banding patterns observed between cold-blooded vertebrates and mammals.

Short interspersed CAN SINE elements as prognostic markers in canine mammary neoplasia

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evolution of cis-regulatory elements in a repetitive sequence adjacent to a sea urchin aboral ectoderm -specific gene

The creation, preservation, and degeneration of cis-regulatory elements controlling developmental gene expression are fundamental genome-level evolutionary processes about which little is known. In this study, critical differences in cis-regulatory elements controlling the expression of the sea urchin aboral ectoderm-specific spec genes were identified and explored. In genomes of species within the Strongylocentrotidae family, multiple copies of a repetitive sequence element termed RSR were present, but RSRs were not detected in genomes of species outside Strongylocentrotidae. RSRs are invariably associated with spec genes, and in Strongylocentrotus purpuratus, the spec2a RSR functioned as a transcriptional enhancer displaying greater activity than RSRs from the spec1 or spec2c paralogs. Single base-pair differences at two cis-regulatory elements within the spec2a RSR greatly increased the binding affinities of four transcription factors: SpCCAAT-binding factor at one element and SpOtx, SpGoosecoid, and SpGATA-E at another. The cis-regulatory elements to which SpCCAAT-binding factor, SpOtx, SpGoosecoid, and SpGATA-E bound were recent evolutionary acquisitions that could act either to activate or repress transcription, depending on the cell type. These elements were found in the spec2a RSR ortholog in Strongylocentrotus pallidus but not in the RSR orthologs of Strongylocentrotus droebachiensis or Hemicentrotus pulcherrimus. These results indicate that spec genes exhibit a dynamic pattern of cis-regulatory element evolution while stabilizing selection preserves their aboral ectoderm expression domain. ^

Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes

The positions of ≈4,800 individual miniature inverted-repeat transposable element (MITE)-like repeats from four families were mapped on the Caenorhabditis elegans chromosomes. These families represent 1–2% of the total sequence of the organism. The four MITE families (Cele1, Cele2, Cele14, and Cele42) displayed distinct chromosomal distribution profiles. For example, the Cele14 MITEs were observed clustering near the ends of the autosomes. In contrast, the Cele2 MITEs displayed an even distribution through the central autosome domains, with no evidence for clustering at the ends. Both the number of elements and the distribution patterns of each family were conserved on all five C. elegans autosomes. The distribution profiles indicate chromosomal polarity and suggest that the current genetic and physical maps of chromosomes II, III, and X are inverted with respect to the other chromosomes. The degree of conservation of both the number and distribution of these elements on the five autosomes suggests a role in defining specific chromosomal domains.

Elements of medical jurisprudence, interspersed with a copious selection of curious and instructive cases ans analyses of opinions delivered at coroners inquests /

Mode of access: Internet.

Adiposity, Sex Hormones, and Repetitive Element DNA Methylation in Healthy Postmenopausal Women

INTRODUCTION: Low levels of methylation within repetitive DNA elements, such as long interspersed nuclear element-1 (LINE-1) and Alu repeats, are believed to epigenetically predispose an individual to cancer and other diseases. The extent to which lifestyle factors affect the degree of DNA methylation within these genomic regions has yet to be fully understood. Adiposity and sex hormones are established risk factors for certain types of cancer and other illnesses, particularly amongst postmenopausal women. The aim of the current investigation is to assess the impact of adiposity and sex hormones on LINE-1 and Alu methylation in healthy postmenopausal women. METHODS: A cross-sectional study was conducted using baseline data from an ancillary study of the Alberta Physical Activity and Breast Cancer Prevention (ALPHA) Trial. Current adiposity was measured using a dual-energy x-ray absorptiometry (DXA) scan, computed tomography (CT) scan, and balance beam scale. Historical weights were self-reported in a questionnaire. Current endogenous sex hormone concentrations were measured in fasting blood serum. Estimated lifetime number of menstrual cycles was used as a proxy for cumulative exposure to ovarian sex hormones. Repetitive element methylation was quantified in white blood cells using a pyrosequencing assay. Linear regression was used to model the relations of interest while adjusting for important confounders. RESULTS: Adiposity and serum estrogen concentrations were positively related to LINE-1 methylation but were not associated with Alu methylation. Cumulative ovarian sex hormone exposure had a “U-shaped” relation with LINE-1 regardless of folate intake and a negative relation with Alu methylation amongst low folate consumers. Androgens were not associated with repetitive element DNA methylation in this population. CONCLUSION: Adiposity and estrogens appear to play a role in maintaining high levels of repetitive element DNA methylation in healthy postmenopausal women. LINE-1 methylation may be a mechanism whereby estrogen exposure protects against cardiovascular and neurodegenerative illnesses. These results add to the growing body of literature showing how the epigenome is shaped by our lifestyle choices. Future prospective studies assessing the relation between levels of repetitive element DNA methylation in healthy individuals and subsequent disease risk are needed to better understand the clinical significance of these results.

Occurrence of LINE, gypsy-like, and copia-like retrotransposons in the clonally propagated sweet potato (Ipomoea batatas L.)

Retrotransposons are a class of transposable elements that represent a major fraction of the repetitive DNA of most eukaryotes. Their abundance stems from their expansive replication strategies. We screened and isolated sequence fragments of long terminal repeat (LTR), gypsy-like reverse transcriptase (rt) and gypsy-like envelope (env) domains, and two partial sequences of non-LTR retrotransposons, long interspersed element (LINE), in the clonally propagated allohexaploid sweet potato (Ipomoea batatas (L.) Lam.) genome. Using dot-blot hybridization, these elements were found to be present in the ~1597 Mb haploid sweet potato genome with copy numbers ranging from ~50 to ~4100 as observed in the partial LTR (IbLtr-1) and LINE (IbLi-1) sequences, respectively. The continuous clonal propagation of sweet potato may have contributed to such a multitude of copies of some of these genomic elements. Interestingly, the isolated gypsy-like env and gypsy-like rt sequence fragments, IbGy-1 (~2100 copies) and IbGy-2 (~540 copies), respectively, were found to be homologous to the Bagy-2 cDNA sequences of barley (Hordeum vulgare L.). Although the isolated partial sequences were found to be homologous to other transcriptionally active elements, future studies are required to determine whether they represent elements that are transcriptionally active under normal and (or) stressful conditions.