Exposure diversity as a design principle for recommender systems

Personalized recommendations in search engines, social media and also in more traditional media increasingly raise concerns over potentially negative consequences for diversity and the quality of public discourse. The algorithmic filtering and adaption of online content to personal preferences and interests is often associated with a decrease in the diversity of information to which users are exposed. Notwithstanding the question of whether these claims are correct or not, this article discusses whether and how recommendations can also be designed to stimulate more diverse exposure to information and to break potential ‘filter bubbles’ rather than create them. Combining insights from democratic theory, computer science and law, the article makes suggestions for design principles and explores the potential and possible limits of ‘diversity sensitive design’.Peer reviewe

Copia and Gypsy retrotransposons activity in sunflower (Helianthus annuus L.)

<p>Abstract</p> <p>Background</p> <p>Retrotransposons are heterogeneous sequences, widespread in eukaryotic genomes, which refer to the so-called mobile DNA. They resemble retroviruses, both in their structure and for their ability to transpose within the host genome, of which they make up a considerable portion. <it>Copia</it>- and <it>Gypsy</it>-like retrotransposons are the two main classes of retroelements shown to be ubiquitous in plant genomes. Ideally, the retrotransposons life cycle results in the synthesis of a messenger RNA and then self-encoded proteins to process retrotransposon mRNA in double stranded extra-chromosomal cDNA copies which may integrate in new chromosomal locations.</p> <p>Results</p> <p>The RT-PCR and IRAP protocol were applied to detect the presence of <it>Copia </it>and <it>Gypsy </it>retrotransposon transcripts and of new events of integration in unstressed plants of a sunflower (<it>Helianthus annuus </it>L.) selfed line. Results show that in sunflower retrotransposons transcription occurs in all analyzed organs (embryos, leaves, roots, and flowers). In one out of sixty-four individuals analyzed, retrotransposons transcription resulted in the integration of a new element into the genome.</p> <p>Conclusion</p> <p>These results indicate that the retrotransposon life cycle is firmly controlled at a post transcriptional level. A possible silencing mechanism is discussed.</p

Different histories of two highly variable LTR retrotransposons in sunflower species

In the Helianthus genus, very large intra- and interspecific variability related to two specific retrotransposons of Helianthus annuus (Helicopia and SURE) exists. When comparing these two sequences to sunflower sequence databases recently produced by our lab, the Helicopia family was shown to belong to the Maximus/SIRE lineage of the Sirevirus genus of the Copia superfamily, whereas the SURE element (whose superfamily was not even previously identified) was classified as a Gypsy element of the Ogre/Tat lineage of the Metavirus genus. Bioinformatic analysis of the two retrotransposon families revealed their genomic abundance and relative proliferation timing. The genomic abundance of these families differed significantly among 12 Helianthus species. The ratio between the abundance of long terminal repeats and their reverse transcriptases suggested that the SURE family has relatively more solo long terminal repeats than does Helicopia. Pairwise comparisons of Illumina reads encoding the reverse transcriptase domain indicated that SURE amplification may have occurred more recently than that of Helicopia. Finally, the analysis of population structure based on the SURE and Helicopia polymorphisms of 32 Helianthus species evidenced two subpopulations, which roughly corresponded to species of the Helianthus and Divaricati/Ciliares sections. However, a number of species showed an admixed structure, confirming the importance of interspecific hybridisation in the evolution of this genus. In general, these two retrotransposon families differentially contributed to interspecific variability, emphasising the need to refer to specific families when studying genome evolution

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

A survey of Gypsy and Copia LTR-retrotransposon superfamilies and lineages and their distinct dynamics in the Populus trichocarpa (L.) genome

In this work, we report a comprehensive study of long terminal repeat retrotransposons of Populus trichocarpa. Our research group studied the retrotransposon component of the poplar genome in 2012, isolating 1479 putative full-length elements. However, in that study, it was not possible to identify the superfamily to which the majority of isolated full-length elements belonged. Moreover, during recent years, the genome sequence of P. trichocarpa has been updated, deciphering thek sequences of a number of previously unresolved loci. In this work, we performed a complete scan of the updated version of the genome sequence to isolate full-length retrotransposons based on sequence and structural features. The new dataset showed a reduced number of elements (958), and 21 fulllength elements were discovered for the first time. The majority of retroelements belonged to the Gypsy superfamily (57%), while Copia elements amounted to 41.1% of the dataset. Fulllength elements were dispersed throughout the chromosomes. However, Gypsy and, to a lesser extent, Copia elements accumulated preferentially at putative centromeres. Gypsy elements were more active in retrotransposition than Copia elements, with the exception of during the past million years, in which Copia elements were the most active. Improved annotation procedures also allowed us to determine the specific lineages to which isolated elements belonged. The three Gypsy lineages, Athila, OGRE, and Chromovirus (in the decreasing order), were by far the most abundant. On the other hand, each identified Copia lineage represented less than 1 % of the genome. Significant differences in the insertion age were found among lineages, suggesting specific activation mechanisms. Moreover, different chromosomal regions were affected by retrotransposition in different ages. In all chromosomes, putative pericentromeric regions were filled with elements older than themean insertion age. Overall, results demonstrate structural and functional differences among plant retrotransposon lineages and further support the view of retrotransposons as a community of different organisms in the genome

Genome editing: il futuro (prossimo) del miglioramento genetico delle piante

Genome editing, or genome editing with engineered nucleases, is a technology that, using engineered nucleases, allows site-specific single-base mutations or the insertion, deletion or replacement of DNA sequences in a specific site in the genome of an organism. Genome editing is based on the induction of double strand breaks (DSBs) in the DNA in the locus of interest to introduce mutations in that locus. In fact, after DSB induction, the damage will be repaired by processes (the non-homologous end joining and/or the homology-directed repair), that occur naturally in the cells and during which mutations may occur. DSBs can be induced by different nucleases, all capable of specifically recognising a locus in the genome. The most promising is the CRISPR/Cas system, for ease of designing nucleases with sequence specificity and for the fact that it can be used in nearly every organism. In the CRISPR/Cas9 system, the recognition of the DNA sequence to be modified is operated by an RNA sequence. After successful DNA DSB, the cell proceeds with the repair of DNA. Generally, the cell uses non-homologous end joining, which produces substitutions, insertions and deletions of nucleotides in the damaged DNA site, and usually leads to loss of function of the target gene. When using this mode, the genome editing can be considered a biological site-specific mutagenesis, different from the mutagenesis induced by physical or chemical agents which randomly induce mutations through the entire genome. On the contrary, when homologydirected repair is involved, genome editing can be considered a predetermined biological mutagenesis that modifies or corrects the target gene in the sense determined by the investigator. Applying genome editing to plants requires also ancillary technologies, according to the species and cell types. First, in vitro culture techniques, especially protoplast cultures, might be necessary for the production of cells that can be subjected to the nuclease treatment. Then, transformation vectors (Agrobacterium, viruses or biolistic methods) are needed to enable the transfer of the components required for genome editing to the plant cell. The vectors may be stable or transient; in the latter case, both the possible cytotoxicity of constitutively expressed nucleases and the production of transgenic plants would be avoided. Concerning the first results obtained using this technology, mutations in target genes of cultivated plants were obtained mostly through non-homologous end joining for traits related to morphology, quality and to the resistance to pathogens and herbicides, in both herbaceous and woody species. Results were also reported exploiting the homology-directed repair. Overall, the genome editing technology proved suitable to introduce precise and predictable gene mutations directly into elite cultivars, reducing the duration of traditional crossing and backcrossing breeding, with the possibility to modi fy more than one genes per experiment . Although many advances in genome editing technology have been achieved in recent years, some technical problems remain to be solved, including the need for increasing the efficiency of the system, the production of off-target mutations, the influence of chromatin structure on the editing efficiency, the possible side effects on genes lying close to target genes and the efficiency of the technology in polyploid species (where many copies of target genes occur). In conclusion, the CRISPR/Cas system has emerged as the most important tool for the future of genetics because of its simplicity, versatility and efficiency. It will have a major impact on both basic and applied research and will be used to produce cultivars with improved disease resistance, with a higher nutritional value, and able to survive climate changes, more suitable as bioenergy crops, producing useful chemicals and biomolecule

Mimicking the Hierarchical Organization of Natural Collagen: Toward the Development of Ideal Scaffolding Material for Tissue Regeneration

Biological materials found in living organisms, many of which are proteins, feature a complex hierarchical organization. Type I collagen, a fibrous structural protein ubiquitous in the mammalian body, provides a striking example of such a hierarchical material, with peculiar architectural features ranging from the amino acid sequence at the nanoscale (primary structure) up to the assembly of fibrils (quaternary structure) and fibers, with lengths of the order of microns. Collagen plays a dominant role in maintaining the biological and structural integrity of various tissues and organs, such as bone, skin, tendons, blood vessels, and cartilage. Thus, "artificial" collagen-based fibrous assemblies, endowed with appropriate structural properties, represent ideal substrates for the development of devices for tissue engineering applications. In recent years, with the ultimate goal of developing three-dimensional scaffolds with optimal bioactivity able to promote both regeneration and functional recovery of a damaged tissue, numerous studies focused on the capability to finely modulate the scaffold architecture at the microscale and the nanoscale in order to closely mimic the hierarchical features of the extracellular matrix and, in particular, the natural patterning of collagen. All of these studies clearly show that the accurate characterization of the collagen structure at the submolecular and supramolecular levels is pivotal to the understanding of the relationships between the nanostructural/microstructural properties of the fabricated scaffold and its macroscopic performance. Several studies also demonstrate that the selected processing, including any crosslinking and/or sterilization treatments, can strongly affect the architecture of collagen at various length scales. The aim of this review is to highlight the most recent findings on the development of collagen-based scaffolds with optimized properties for tissue engineering. The optimization of the scaffolds is particularly related to the modulation of the collagen architecture, which, in turn, impacts on the achieved bioactivity

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