Variability in LTR-retrotransposon redundancy and proximity to genes between sunflower cultivars and wild accessions.

The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long-terminal-repeat retrotransposons. Being knowledge on the retrotransposon-related variability within this species still limited, we performed a quantitative and qualitative survey of intraspecific variation of LTR-retrotransposon fraction of the genome across different genotypes of H. annuus, using next generation sequencing technologies. First, we characterized the repetitive component of a sunflower homozygous experimental line, using 454 reads, and prepared a library of retrotransposon-related sequences. Then, we analysed the LTRretrotransposon fraction of 7 wild accessions and 8 cultivars of sunflowerby mapping Illumina reads of the 15 genotypes onto the library. We observed large variations in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads of the 15 genotypes onto two sets of sequences, i.e. retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the 15 genomes by counting the number of paired reads of which one mapped onto a retrotransposon and the other onto a gene. Large variability among genotypes was ascertained also for retrotransposonproximity to genes. Both retrotransposon redundancy and proximity to genes showed different behaviour among retrotransposon families and also between cultivated and wild genotypes, indicating a possible involvement in sunflower domestication

A survey of variability in LTR-retrotransposon abundance and proximity to genes between wild and cultivated sunflower genotypes

Sunflower (Helianthus annuus) is an important crop species of the Asteraceae family. Recent characterization of sunflower repetitive fraction has shown that the genome of this species contains a very large proportion of transposable elements, especially long-terminal-repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next generation sequencing technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across different genotypes of H. annuus. First, we characterized the repetitive component of a sunflower homozygous experimental line, using 454 reads, and prepared a library of retrotransposon-related sequences. Then, we analysed the retrotransposon fraction of 7 wild accessions and 8 cultivars of H. annuus by mapping Illumina reads of the 15 genotypes onto the library. We observed large variations in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads of the 15 genotypes onto two sets of sequences, i.e. retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the 15 genomes by counting the number of paired reads of which one mapped onto a retrotransposon and the other onto a gene. Large variability among genotypes was ascertained also for retrotransposon proximity to genes. Both retrotransposon redundancy and proximity to genes showed different behaviour among retrotransposon families and also between cultivated and wild genotypes, indicating a possible involvement in sunflower domestication

Repetitive DNA and plant domestication: variation in copy number and proximity to genes of LTR-retrotransposons among wild and cultivated sunflower (Helianthus annuus) genotypes.

The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next generation sequencing technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes - 7 wild accessions and 8 cultivars - of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis we mapped Illumina paired reads to two sets of sequences, i.e. long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was ascertained also for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower

An insight into structure and composition of the fig genome

Ficus carica L. is a diploid species, with a genome size of 0.36 pg/2C, still poorly characterized at genetic and genomic level. With the aim of analysing the fig genome structure, we used Illumina technology to produce 25.64 genome equivalents of 35-511 nt long MiSeq sequences and 12.96 genome equivalents of 25-100 nt long HiSeq paired-end reads. The two libraries were subject to a first assembly run separately, then a hybrid assembly was performed; finally, contigs and supercontigs were scaffolded. This first rough assembly is composed of 264,088 scaffolds, up to 41,760 nt in length, covering 323,708,138 nt, that corresponds to 87.5% of the fig genome, with N50 = 2,523. Masking the scaffolds with a transcriptome of Rosaceae, from which sequences related to repetitive elements were removed, allowed us to establish that coding genes account for at least 6.8% of the fig genome. Gene prediction analysis produced 44,419 putative genes. A sample of around 5,000 predicted genes were annotated with regard to gene ontology and function. Concerning the repetitive component, the fig genome resulted composed for 58.3% of repeated sequences, of which none was especially redundant. Among identified repeats, the most represented were LTR-retrotransposons, with Gypsy elements more frequent than Copia

Clinical Efficacy of A Nutraceutical Approach for the Management of Dyslipidemia in Metabolic Disorders: A One-Year Treatment With Armolipid Plus

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The Peculiar Landscape of Repetitive Sequences in the Olive (Olea europaea L.) Genome

Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome

Z-alpha1-antitrypsin polymers and small airways disease: a new paradigm in alfa-1 anti-trypsin deficiency-related COPD development?

The presence of Alpha1-Antitrypsin (AAT) polymers, known to promote a sustained pro-inflammatory activity, has been previously demonstrated in bronchial biopsies of subjects with Z-AAT deficiency (AATD) suggesting a possible role in the development of COPD through a small airway disease impairment. The study aimed to assess the presence of small airways dysfunction and the potential correlation with the presence of Z-AAT polymers obtained by Exhaled Breath Condensate (EBC) collection in PiZZ subjects, as compared with matched healthy PiMM subjects. We enrolled 19 asymptomatic, never smoker subjects: 9 PiZZ and 10 PiMM as controls, without obstructive ventilatory defect (i.e., normal FEV1/VC% ratio). All subjects underwent complete pulmonary function tests (PFT). EBC was collected in all subjects. ELISA test was applied to search for Z-AAT polymers. The PiZZ subjects showed normal lung volumes and DLCO values. However, in comparison with PiMM subjects, the single breath test N2 wash-out revealed significant differences regarding the phase III slope (1.45±0.35 N2/L vs. 0.96±0.40 N2/L) (p<0.02) in the PiZZ subjects, while the closing volume/vital capacity ratio (14.3±4.5 % vs. 11.3±6.3 %) was not significantly increased. The ELISA test detected the presence of Z-AAT polymers in 44% of PiZZ patients. Asymptomatic, never smoker PiZZ subjects with normal spirometry and lung diffusion capacity showed airways impairment when compared to PiMM subjects. Although Z-AAT polymers were found only in 44% of PiZZ subjects, these findings suggest the possibility that chronic bronchiolitis can develop as a result of the long-term pro-inflammatory activity of Z-AAT polymers in subjects with Z-related AATD

Impaired NK-cell-mediated cytotoxic activity and cytokine production in patients with endometriosis: A possible role for PCBs and DDE

Endometriosis is a gynaecological disorder characterized by the presence and growth of endometrial tissue in ectopic sites. In this study we examined the immunological functions of patients with endometriosis and serum level of PCBs and p,p'-DDE to verify the impact of these environmental contaminants on the dysregulation of immune functions. We found that proliferative responses and immunoglobulin production were not dysregulated in patients with endometriosis while NK cell activity was significantly down-regulated in these patients. Moreover, a significant down-regulation of IL-1 beta and IL-12 production was found in patients with respect to controls. Serum levels of PCBs and p,p'-DDE were found to be significantly higher in women with endometriosis than in the control group, with respect to the sum of the congeners most prominent in human tissues. In particular, total PCBs concentration in patients with endometriosis and controls was respectively 330 and 160 ng/g fat with respect to the most abundant congeners, while pp-DDE concentration was of 770 and 3 10 ng/g fat. Moreover, we found that normal human PBMC pulsed with PCBs p,p'-DDE and their combination showed a significant down-regulation of NK cell cytotoxic activity and IL-1 beta and IL-12 production. These findings suggest that changes in specific immune parameters correlate with elevated serum PCBs and DDE levels and endometriosis. (c) 2006 Elsevier Inc. All rights reserved

Biosurfactant from vaginal Lactobacillus crispatus BC1 as a promising agent to interfere with Candida adhesion

Lactobacillus spp. dominating the vaginal microbiota of healthy women contribute to the prevention of urogenital and sexually transmitted infections. Their protective role in the vagina can be mediated by Lactobacillus cells themselves, metabolites or bacterial components, able to interfere with pathogen adhesion and infectivity. Vulvovaginal candidiasis (VVC) is a common genital infection, caused by the overgrowth of opportunistic Candida spp. including C. albicans, C. glabrata, C. krusei and C. tropicalis. Azole antifungal drugs are not always efcient in resolv ing VVC and preventing recurrent infections, thus alternative anti-Candida agents based on vaginal probiotics have gained more importance. The present work aims to chemically characterize the biosurfactant (BS) isolated from a vaginal Lactobacillus crispatus strain, L. crispatus BC1, and to investigate its safety and antiadhesive/antimicrobial activ ity against Candida spp., employing in vitro and in vivo assays. Results: BS isolated from vaginal L. crispatus BC1 was characterised as non-homogeneous lipopeptide molecules with a critical micellar concentration value of 2 mg/mL, and good emulsifcation and mucoadhesive properties. At 1.25 mg/mL, the BS was not cytotoxic and reduced Candida strains? ability to adhere to human cervical epithelial cells, mainly by exclusion mechanism. Moreover, intravaginal (i.va.) inoculation of BS in a murine experimental model was safe and did not perturb vaginal cytology, histology and cultivable vaginal microbiota. In the case of i.va. challenge of mice with C. albicans, BS was able to reduce leukocyte infux. Conclusions: These results indicate that BS from vaginal L. crispatus BC1 is able to interfere with Candida adhesion in vitro and in vivo, and suggest its potential as a preventive agent to reduce mucosal damage occasioned by Candida during VVC.Fil: de Gregorio, Priscilla Romina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Parolin, Carola. Universidad de Bologna; ItaliaFil: Abruzzo, Angela. Universidad de Bologna; ItaliaFil: Luppi, Barbara. Universidad de Bologna; ItaliaFil: Protti, Michele. Universidad de Bologna; ItaliaFil: Mercolini, Laura. Universidad de Bologna; ItaliaFil: Silva, Jessica Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Giordani, Barbara. Universidad de Bologna; ItaliaFil: Marangoni, Antonella. Universidad de Bologna; ItaliaFil: Nader, Maria Elena Fatima. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Vitali, Beatrice. Universidad de Bologna; Itali

Notulae to the Italian flora of algae, bryophytes, fungi and lichens: 7

In this contribution, new data concerning algae, bryophytes, fungi, and lichens of the Italian flora are presented. It includes new records and confirmations for the algae genus Chara, the bryophyte genera Cephalozia, Conardia, Conocephalum, Didymodon, Sphagnum, Tetraplodon, and Tortula, the fungal genera Endophyllum, Gymnosporangium, Microbotryum, Phragmidium, and Pluteus, and the lichen genera Candelariella, Cladonia, Flavoplaca, Lichenothelia, Peltigera, Placolecis, Rinodina, Scytinium, and Solenopsora