DCJ-indel and DCJ-substitution distances with distinct operation costs

BACKGROUND: Classical approaches to compute the genomic distance are usually limited to genomes with the same content and take into consideration only rearrangements that change the organization of the genome (i.e. positions and orientation of pieces of DNA, number and type of chromosomes, etc.), such as inversions, translocations, fusions and fissions. These operations are generically represented by the double-cut and join (DCJ) operation. The distance between two genomes, in terms of number of DCJ operations, can be computed in linear time. In order to handle genomes with distinct contents, also insertions and deletions of fragments of DNA – named indels – must be allowed. More powerful than an indel is a substitution of a fragment of DNA by another fragment of DNA. Indels and substitutions are called content-modifying operations. It has been shown that both the DCJ-indel and the DCJ-substitution distances can also be computed in linear time, assuming that the same cost is assigned to any DCJ or content-modifying operation. RESULTS: In the present study we extend the DCJ-indel and the DCJ-substitution models, considering that the content-modifying cost is distinct from and upper bounded by the DCJ cost, and show that the distance in both models can still be computed in linear time. Although the triangular inequality can be disrupted in both models, we also show how to efficiently fix this problem a posteriori

Microplastic in angling baits as a cryptic source of contamination in European freshwaters.

High environmental microplastic pollution, and its largely unquantified impacts on organisms, are driving studies to assess their potential entry pathways into freshwaters. Recreational angling, where many anglers release manufactured baits into freshwater ecosystems, is a widespread activity with important socio-economic implications in Europe. It also represents a potential microplastic pathway into freshwaters that has yet to be quantified. Correspondingly, we analysed three different categories of industrially-produced baits ('groundbait', 'boilies' and 'pellets') for their microplastic contamination (particles 700 µm to 5 mm). From 160 samples, 28 microplastics were identified in groundbait and boilies, with a mean concentration of 17.4 (± 48.1 SD) MP kg-1 and 6.78 (± 29.8 SD) mg kg-1, yet no microplastics within this size range were recorded in the pellets. Microplastic concentrations significantly differed between bait categories and companies, but microplastic characteristics did not vary. There was no correlation between microplastic contamination and the number of bait ingredients, but it was positively correlated with C:N ratio, indicating a higher contamination in baits with higher proportion of plant-based ingredients. We thus reveal that bait microplastics introduced accidentally during manufacturing and/or those originating from contaminated raw ingredients might be transferred into freshwaters. However, further studies are needed to quantify the relative importance of this cryptic source of contamination and how it influences microplastic levels in wild fish

Restricted DCJ-indel model: sorting linear genomes with DCJ and indels

Abstract Background The double-cut-and-join (DCJ) is a model that is able to efficiently sort a genome into another, generalizing the typical mutations (inversions, fusions, fissions, translocations) to which genomes are subject, but allowing the existence of circular chromosomes at the intermediate steps. In the general model many circular chromosomes can coexist in some intermediate step. However, when the compared genomes are linear, it is more plausible to use the so-called restricted DCJ model, in which we proceed the reincorporation of a circular chromosome immediately after its creation. These two consecutive DCJ operations, which create and reincorporate a circular chromosome, mimic a transposition or a block-interchange. When the compared genomes have the same content, it is known that the genomic distance for the restricted DCJ model is the same as the distance for the general model. If the genomes have unequal contents, in addition to DCJ it is necessary to consider indels, which are insertions and deletions of DNA segments. Linear time algorithms were proposed to compute the distance and to find a sorting scenario in a general, unrestricted DCJ-indel model that considers DCJ and indels. Results In the present work we consider the restricted DCJ-indel model for sorting linear genomes with unequal contents. We allow DCJ operations and indels with the following constraint: if a circular chromosome is created by a DCJ, it has to be reincorporated in the next step (no other DCJ or indel can be applied between the creation and the reincorporation of a circular chromosome). We then develop a sorting algorithm and give a tight upper bound for the restricted DCJ-indel distance. Conclusions We have given a tight upper bound for the restricted DCJ-indel distance. The question whether this bound can be reduced so that both the general and the restricted DCJ-indel distances are equal remains open.</p