Pecularities of immunoglobulin gene structures as a basis for somatic mutation emergence

AbstractUsing the method of contextual analysis, we have studied the collection of somatic mutations in immunoglobulin genes. It has been found that the emergence of somatic mutations can be based on the reparation of complementarity violations in the heteroduplexes corresponding to complementary palindromes or direct repeats of DNA

Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite <i>Leishmania</i>.

Knowledge of viral diversity is expanding greatly, but many lineages remain underexplored. We surveyed RNA viruses in 52 cultured monoxenous relatives of the human parasite &lt;i&gt;Leishmania&lt;/i&gt; ( &lt;i&gt;Crithidia&lt;/i&gt; and &lt;i&gt;Leptomonas&lt;/i&gt; ), as well as plant-infecting &lt;i&gt;Phytomonas&lt;/i&gt; &lt;i&gt;Leptomonas pyrrhocoris&lt;/i&gt; was a hotbed for viral discovery, carrying a virus (Leptomonas pyrrhocoris ostravirus 1) with a highly divergent RNA-dependent RNA polymerase missed by conventional BLAST searches, an emergent clade of tombus-like viruses, and an example of viral endogenization. A deep-branching clade of trypanosomatid narnaviruses was found, notable as &lt;i&gt;Leptomonas seymouri&lt;/i&gt; bearing Narna-like virus 1 (LepseyNLV1) have been reported in cultures recovered from patients with visceral leishmaniasis. A deep-branching trypanosomatid viral lineage showing strong affinities to bunyaviruses was termed " &lt;i&gt;Leishbunyavirus&lt;/i&gt; " (LBV) and judged sufficiently distinct to warrant assignment within a proposed family termed " &lt;i&gt;Leishbunyaviridae&lt;/i&gt; " Numerous relatives of trypanosomatid viruses were found in insect metatranscriptomic surveys, which likely arise from trypanosomatid microbiota. Despite extensive sampling we found no relatives of the totivirus &lt;i&gt;Leishmaniavirus&lt;/i&gt; (LRV1/2), implying that it was acquired at about the same time the &lt;i&gt;Leishmania&lt;/i&gt; became able to parasitize vertebrates. As viruses were found in over a quarter of isolates tested, many more are likely to be found in the &gt;600 unsurveyed trypanosomatid species. Viral loss was occasionally observed in culture, providing potentially isogenic virus-free lines enabling studies probing the biological role of trypanosomatid viruses. These data shed important insights on the emergence of viruses within an important trypanosomatid clade relevant to human disease

The Distribution of Inversion Lengths in Bacteria

The distribution of the lengths of genomic segments inverte during the evolutionary divergence of two species cannot be inferred d rectly from the output of genome rearrangement algorithms, due to th rapid loss of signal from all but the shortest inversions. The numb of short inversions produced by these algorithms, however, particular those involving a single gene, is relatively reliable. To gain some insig into the shape of the inversion-length distribution we first apply a genom rearrangement algorithm to each of 32 pairs of bacterial genomes. F each pair we then simulate their divergence using a test distribution generate the inversions and use the simulated genomes as input to th reconstruction algorithm. It is the comparison between the algorith output for the real pair of genomes and the simulated pair which is use to assess the test distribution. We find that simulations based on th exponential distribution cannot provide a good fit, but that simulatio based on a gamma distribution can account for both single-gene inve sions and short inversions involving at most 20 genes, and we conclud that the shape of latter distribution corresponds well to the true distr bution at least for small inversion lengths