Examples of PCR amplification with three individual polymorphic Alu-containing loci (MLS 19, MLS 50 and MLS 65) in ten tracer (lines t1–t10) and one driver (line Dr) DNA samples

<p><b>Copyright information:</b></p><p>Taken from "Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach"</p><p>Nucleic Acids Research 2005;33(2):e16-e16.</p><p>Published online 26 Jan 2005</p><p>PMCID:PMC548376.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> Lines K+ and K− represent positive and negative controls, respectively. M, DNA fragments of a 100 bp ladder length marker (SybEnzime). Gray and white arrows to the left of the electrophoregrams indicate the predicted locations of the Alu containing and Alu-free PCR products, respectively. Scheme of genomic primers location is represented at the bottom

Edizione Nazionale del Carteggio di L.A. Muratori, vol. 11, Carteggi con Cacciago .... Capilupi

Questo carteggio conferma, al pari degli altri volumi, la straordinaria capacit\ue0 dell\u2019erudito modenese di tessere una rete di contatti e scambi culturali che andava dagli angoli pi\uf9 remoti della Penisola alle grandi sedi della cultura europea. Tra i carteggi raccolti nel presente volume \u2013 in tutto cinquantasei \u2013 spiccano, per consistenza e interesse, quelli con il veneto Angelo Caloger\ue0, esponente di rilievo del giornalismo scientifico, il filosofo siciliano Tommaso Campailla, l\u2019erudito marchigiano Filippo Camerini, l\u2019abate Pietro Canneti e il geografo Giacomo Cantelli. Non mancano inoltre lettere che gettano luce sulla multiforme personalit\ue0 muratoriana, i cui interessi spaziavano dalla medicina (carteggio con P. Capilupi), alla pratica pastorale (Campi Cervelli), al diritto canonico (C.L. Calcagnini), ai molti volti della storia. Interessanti infine i contatti pi\uf9 o meno occasionali di quanti si rivolsero al modenese per ricevere consigli in materia di genealogia, educazione e linguistica

The oligonucleotides used for the preparation of the DNA libraries.

<p>The oligonucleotides used for the preparation of the DNA libraries.</p

Number of the retroelement insertions detected within genes and promoters (for each library, predictions are derived from 1000 simulations of coordinates sample sets).

<p>Error bars show 1 SD. (A)—L1 in genes; (B)—L1 in promoters; (C)—Alu in genes; (D)—Alu in promoters.</p

Validation of the potentially somatic retroelement insertions.

<p>Black arrows show the primers. GP primers are complementary to the flanking sequences, RE primers are complementary to the retroelement sequence (RE).</p

The number of potentially somatic L1 and Alu insertions detected in different tissue samples and the data on their distribution in genome.

<p>The number of potentially somatic L1 and Alu insertions detected in different tissue samples and the data on their distribution in genome.</p

Retroelements flanking sequences library preparation.

<p>Small vertical arrows show the restriction sites. Horizontal arrows show PCR primers.</p

The orientation of somatic L1 and Alu insertions relative to nearby genes.

<p>*—p-value based on Monte-Carlo test, 1000 permutations (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117854#sec007" target="_blank">Materials and Methods</a> for details), NS—non-significant (p>0.05)</p><p>The orientation of somatic L1 and Alu insertions relative to nearby genes.</p

TCR out-of-frame repertoire sharing in monozygous twins is higher than in unrelated individuals, or than predicted by stochastic models of recombination.

<p>The number of shared out-of-frame alpha TCR clonotypes between all 15 pairs among 6 donors consisting of 3 twin pairs (ordinate) is compared to the model prediction (abscissa). To be able to compare pairs of datasets of different sizes, the sharing number was normalized by the product of the cloneset sizes. The three outstanding red circles represent the twin pairs, while the black circles refer to the 12 pairs of unrelated individuals among the 6 twins. The model prediction is based on a generative stochastic model of VJ recombination [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005572#pcbi.1005572.ref013" target="_blank">13</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005572#pcbi.1005572.ref014" target="_blank">14</a>], inferred separately for each donor to account for differences between individuals. It agrees well with the data from unrelated individuals up to a common multiplicative factor, but systematically underestimates sharing in twins. Error bars show one standard deviation.</p

TCR nucleotide sequences shared between twins are statistically different from sequences shared between unrelated individuals.

<p>Distribution of log₁₀ <i>P</i>_gen, with <i>P</i>_gen the probability that a sequence is generated by the VJ recombination process, for shared out-of-frame TCR alpha clonotypes between one individual and the other five. While the distribution of shared sequences between unrelated individuals (red curves) is well explained by coincidental convergent recombination as predicted by our stochastic model (blue), sequences shared between two twins (green) have an excess of low probability sequences: 31 sequences with log₁₀ <i>P</i>_gen < −10. For comparison the distribution of <i>P</i>_gen in regular (not necessarily shared) sequences is shown in black.</p