Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome

<p>Abstract</p> <p>Background</p> <p>Flax (<it>Linum usitatissimum </it>L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome.</p> <p>Results</p> <p>The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding.</p> <p>Conclusion</p> <p>The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps. The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly.</p

We're in this Together: Sensation of the Host Cell Environment by Endosymbiotic Bacteria

Bacteria inhabit diverse environments, including the inside of eukaryotic cells. While a bacterial invader may initially act as a parasite or pathogen, a subsequent mutualistic relationship can emerge in which the endosymbiotic bacteria and their host share metabolites. While the environment of the host cell provides improved stability when compared to an extracellular environment, the endosymbiont population must still cope with changing conditions, including variable nutrient concentrations, the host cell cycle, host developmental programs, and host genetic variation. Furthermore, the eukaryotic host can deploy mechanisms actively preventing a bacterial return to a pathogenic state. Many endosymbionts are likely to use two-component systems (TCSs) to sense their surroundings, and expanded genomic studies of endosymbionts should reveal how TCSs may promote bacterial integration with a host cell. We suggest that studying TCS maintenance or loss may be informative about the evolutionary pathway taken toward endosymbiosis, or even toward endosymbiont-to-organelle conversion.Peer reviewe

p53 inactivating mutations in Chinese nasopharyngeal carcinomas

Previously a low frequency of p53 mutations was detected in nasopharyngeal carcinoma (NPC) using molecular techniques to screen for mutations, yet immunohistochemical staining revealed a high frequency of p53 aberrant proteins. These findings might be attributed to the occurrence of p53 mutations outside the common hot spots and/or the inactivation of the protein through interactions with cellular or viral proteins. Using a previously established simple and sensitive p53 yeast functional assay, we blindly screened 25 nasopharyngeal biopsies for p53 mutations from exons 4 to 11, p53 was mutated in 27.3\% of NPC specimens and in 0\% of the nasopharyngeal biopsies from patients with non-malignant diseases. Two p53 mutations were detected in exon 7 and two were detected in exon 8. Interestingly, the exon 8 mutations observed in NPC lie in codons which appear to be hot spots for mutations in other head and neck cancers. (C) 1998 Elsevier Science Ireland Ltd. All rights reserved

A contribution to the pathobiology of Biomphalaria glabrata hemocytes

This study attempts to investigate the relationship between the hemocytes in the two compartments: circulating peripheral lymph and the connective tissues. The hemocytes are compared with the vertebrate macrophages and constitute the principal line of defense against external aggression. The hemocytes were counted in circulating hemolymph and their phagocytic capability was evaluated in Schistosoma mansoni-infected Biomphalaria glabrata and the results were compared with those obtained from normal intact control snails. Although the number of circulating hemocytes revealed a mild increase in snails at the 6th week of infection, the overall findings were similar and pointed out that the cells in the two compartments are not functionally connected. However, the hemocytes found within the connective tissues of infected snails showed definite ultrastructural differences in the number and disposition of cytoplasmic prolongations and organelles in comparison with the hemocytes from non-infected snails. Histochemically, the staining for acid phosphatase activity served as a marker to hemocytes, sometimes being found in extracellular material at the foci of parasite-hemocyte interactions