Data_Sheet_1_Analysis of the 16S rRNA gene for the characterization of the bacterial community of the Lambro river (Italy).PDF

Characterization of the microbial community of a river can provide various indications, such as its general state of health or the presence of contamination. Furthermore, the study of Bacteroidetes, which have a high degree of host specificity, can provide information on the species involved in any fecal contamination. The analysis of the 16S rRNA was used to characterize the bacterial community of the Lambro river (Italy) through. The results, which were obtained by analyzing water from 15 sampling points, show a reduction in the complexity of the bacterial community as the river enters a densely populated region. The cause could be a source of chemical or physical contamination that carries out a positive selection toward some bacterial species and negative toward others. In addition, a notable increase in the percentage of Bacteroidetes was reported, especially when the river enters regions characterized by high agricultural and livestock activity, such as cattle and pig farming. However, in the samples taken from this area, no Bacteroidetes ascribable to these two species or to the other species considered (i.e., human, dog, and cat) were found. Surprisingly, suspected bacterial contamination of swine origin was identified in a sparsely populated region characterized by small family farms. Finally, the efficient treatment of urban wastewater was confirmed as no markers of fecal pollution of human origin were identified.</p

Histological examination of the new cases reported.

<p>Case C61: Histologic section of the right (A) and left (B) gonad showing seminiferous tubules with diffuse atrophy of the seminal line. Case C64: Right Ovotestis (C): The gonads were surrounded by ovarian bursa and shown some follicular structures and corpora lutea (white arrow). In the medulla hypoplastic seminiferous tubules were present (black arrow). Case C65 (D): Dog ovotestis. In the gonad, follicular structures including oocytes (arrow) coexist with testicular tubuli lined by Setoli cells (asterisc) (Courtesy of Valeria Grieco, University of Milan).</p

Q-RT PCR results.

<p>Histograms represent the copy numbers ratio of a non-polymorphic probe within Sox9 gene in the two duplicated dogs (dog10 and dog44, red bars) relative to five normal control dogs (blue bars). The data have been normalized against two different reference sequences (Abs17, Bglr2).</p

List of CNVs identified with array-CGH in the seven cases with the indication of their code, type, location and size (CanFam2 assembly).

<p>CNVs were checked for occurrence in the Database of Genomic Copy Number Variants in the dog genome (<a href="http://dogs.genouest.org/LUPA.dir/CNV.html" target="_blank">http://dogs.genouest.org/LUPA.dir/CNV.html</a>) and in several papers <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101244#pone.0101244-Chen1" target="_blank">[29]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101244#pone.0101244-Berglund1" target="_blank">[33]</a>.</p

Graphical representation of the SOX9 locus duplications discovered.

<p>The figure shows a 1,6(canFam2 assembly) and magnified views of the two SOX9 duplications detected, by array-CGH, in cases C10 (left) and C44 (right), respectively. The shaded areas indicate a gain in DNA copy number (duplication, average log2 ratios: +0, 5) detected by red dots. Asterisks indicate the 168 bp repeats.</p