A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system

BACKGROUND: The genome of Protochlamydia amoebophila UWE25, a Parachlamydia-related endosymbiont of free-living amoebae, was recently published, providing the opportunity to search for genomic islands (GIs). RESULTS: On the residual cumulative G+C content curve, a G+C-rich 19-kb region was observed. This sequence is part of a 100-kb chromosome region, containing 100 highly co-oriented ORFs, flanked by two 17-bp direct repeats. Two identical gly-tRNA genes in tandem are present at the proximal end of this genetic element. Several mobility genes encoding transposases and bacteriophage-related proteins are located within this chromosome region. Thus, this region largely fulfills the criteria of GIs. The G+C content analysis shows that several modules compose this GI. Surprisingly, one of them encodes all genes essential for F-like conjugative DNA transfer (traF, traG, traH, traN, traU, traW, and trbC), involved in sex pilus retraction and mating pair stabilization, strongly suggesting that, similarly to the other F-like operons, the parachlamydial tra unit is devoted to DNA transfer. A close relatedness of this tra unit to F-like tra operons involved in conjugative transfer is confirmed by phylogenetic analyses performed on concatenated genes and gene order conservation. These analyses and that of gly-tRNA distribution in 140 GIs suggest a proteobacterial origin of the parachlamydial tra unit. CONCLUSIONS: A GI of the UWE25 chromosome encodes a potentially functional F-like DNA conjugative system. This is the first hint of a putative conjugative system in chlamydiae. Conjugation most probably occurs within free-living amoebae, that may contain hundreds of Parachlamydia bacteria tightly packed in vacuoles. Such a conjugative system might be involved in DNA transfer between internalized bacteria. Since this system is absent from the sequenced genomes of Chlamydiaceae, we hypothesize that it was acquired after the divergence between Parachlamydiaceae and Chlamydiaceae, when the Parachlamydia-related symbiont was an intracellular bacteria. It suggests that this heterologous DNA was acquired from a phylogenetically-distant bacteria sharing an amoebal vacuole. Since Parachlamydiaceae are emerging agents of pneumonia, this GI might be involved in pathogenicity. In future, conjugative systems might be developed as genetic tools for Chlamydiales

Characterization and mutations in the human sex determining factor SRY

Available from British Library Document Supply Centre-DSC:DXN021834 / BLDSC - British Library Document Supply CentreSIGLEGBUnited Kingdo

Transfer from English for Academic Purposes to Disciplinary Modules

Transfer has been defined as learning in one context impacting performance in another context and is considered a priority aim for education. Transfer is critical for English for Academic Purposes (EAP) programmes in tertiary settings and yet it remains poorly understood. Research into EAP transfer rarely explores how transfer operates in various disciplinary contexts, and mostly focusses on students’ general perceptions of this transfer rather than on textual evidence. This study investigated transfer operated by twelve participants from a Systemic Functional Linguistics (SFL)/Genre informed English for General Academic Purposes (EGAP) module to Life Science, Maths, Chemistry, and Engineering modules. The methods involved a triangulated perspective addressing students’ perception of transfer, textual evidence of transfer and the discipline lecturer’s evaluation of an assignment. Student texts from the EAP module and the discipline were analysed using a broad SFL framework; semi-structured interviews with the participants were conducted and analysed with a multi-framework approach, including Legitimation Code Theory and SFL. Results indicate that an SFL/Genre approach to EGAP course design impacts transfer positively by making linguistic resources visible to the students and enabling them to analyse and make appropriate language decisions in the new contexts of their discipline. Most participants applied their EAP knowledge judiciously in the disciplinary writing context. Results also reveal that not all knowledge was transferred equally; moreover, three of the twelve participants reported minimal transfer. Further analysis of the interview data showed that students’ dispositions towards knowledge in the EAP module may play a role in transfer. Beyond investigating transfer from an SFL/Genre EAP module, the thesis, therefore, also revisits the notion that motivation is an important factor in transfer and proposes a deeper orientation to disciplinary knowledge structures and the concept of affiliation as a more satisfactory explanation for a lack of transfe

Comparative mapping for positional cloning and defining homology regions between the mouse and human genomes

The goal of this dissertation project was to utilize genetic and physical mapping methods as a means to define genomic homology between human and mouse genomes, as well as to use this information to define functional relationships between the two species. The Comparative mapping studies were designed to expand upon the current knowledge of comparative mapping and homology regions between mouse and man, and to begin to study the homology region borders. Positional cloning research was initiated to localize the translocation breakpoints in a mutant mouse associated with a neurological defect as a first step toward isolation of genes that could be involved in the phenotype of this animal.Comparative mapping of human chromosome 19 and related regions of the mouse genome represents one major focus of this research. Human chromosome 19 was a good target for comparative studies due to the extensive physical mapping of the chromosome,and availability of conserved, mapped gene markers to use for these studies. Comparative Studies involved both the 19q- and 19p-arms of the chromosome, and helped lay the foundation of a chromosome-wide comparative map. One region, 19pl3.1, was investigated in detail. This region is shown to be prone to rearrangements during evolution, as indicated by the homology groups associated within both the mouse and human genomes. These studies revealed the need for more fine mapping of the genome for both species, demonstrating that examination of specific homology groups at a higher resolution reveals that both similarities and surprising differences between related mouse and human regions. These studies provided data suggesting that repeated sequences are associated with at least some homology region borders, a concept that may serve as a guide for future comparative mapping between human, mouse, and other species.One application of comparative mapping is its ability to link functional information derived from mouse mutations to specific genes and disease within the human genome. As part of this effort, research focused upon localizing and physical mapping a region surrounding the breakpoint in IGso, a mouse mutation associated with a reciprocal translocation. Homozygosity for the translocation causes developmental lethality. Animals That are heterozygous display neurological defects including the inability to swim and abnormal startle responses. A genetic map of the region surrounding one of the translocation breakpoints was established on mouse chromosome 2. Fluorescence in situ hybridization (FISH) techniques were used to localize translocation breakpoints to a small interval less than IcM in length. This region shows remarkable linkage conservation with a well-characterized region of human chromosome lip 13, which harbors genes responsible for the WAGR syndrome (Wilms tumor, aniridia, genitourinary malformations, and mental retardation). Comparative mapping information was used to narrow down the translocation interval, and establish a contig consisting of yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), and Pl-derived artificial chromosomes (PACs), which covered approximately 600 kb throughout the breakpoint region. This allowed the breakpoint to be isolated within a single PAC clone of 150 kb in length.Together these studies have set the stage for future investigations of genes located on chromosome 19, and for the cloning of gene(s) associated with the IGso phenotype in mice

Conjugation of extrachromosomal replicons of Rhodococcus erythropolis AN12

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2006.Includes bibliographical references.Bacteria belonging to the Gram-positive actinomycete species, Rhodococcus erythropolis, are diverse not only in terms of metabolic potentials but the plasmids they encode. Pulsed-field gel electrophoresis (PFGE) revealed three previously uncharacterized megaplasmids in the genome of Rhodococcus erythropolis AN12. These megaplasmids, pREA400, pREA250 and pREA100, migrate at approximately 400 kb, 250 kb and 100 kb, respectively. Genetic screening of an AN12 transposon insertion library showed that two megaplasmids, pREA400 and pREA250, are conjugative. It is known for other bacterial systems that a relaxase encoded by the traA gene is required to initiate DNA transfer during plasmid conjugation. Sequences adjacent to the transposon insertion in megaplasmid pREA400 revealed a putative traA-like open reading frame. A novel site-specific gene disruption method was developed to generate a traA mutation in AN12, which allowed us to address the role of the traA gene for Rhodococcus megaplasmid conjugation. We found that the AN12 traA mutant is no longer capable of transferring the pREA400 megaplasmid to Rhodococcus erythropolis SQ1. It was shown previously that the R. erythropolis AN12 genome harbors a 6.3 kb cryptic plasmid called pAN12.(cont.) Here we show that pAN12 is conjugatively mobilizable into other rhodococcal strains. A series of plasmid deletion constructs were tested for loss of mobility to identify the pAN12 cis-acting conjugation requirement. In this way, an approximately 700 bp region was found to be required for plasmid transmission. A small 61 bp element within this region exhibited sequence similarity to the minimal 54 bp clt region known to be required for the conjugation of the streptomycete plasmid, pIJ101. The functionality of these cis-acting elements appears to be conserved, as the addition of this pAN12 clt-like region confers mobility to an otherwise non-conjugative plasmid. However, unlike pJI 101 which encodes all necessary factors for transfer, pAN12 mobility is dependent on the presence of the AN12 megaplasmid, pREA400.by Joyce Chun-Yi Yang.Ph.D