Complete assembly of circular and chloroplast genomes based on global optimization.

This paper focuses on the last two stages of genome assembly, namely, scaffolding and gap-filling, and shows that they can be solved as part of a single optimization problem. Our approach is based on modeling genome assembly as a problem of finding a simple path in a specific graph that satisfies as many distance constraints as possible encoding the insert-size information. We formulate it as a mixed-integer linear programming (MILP) problem and apply an optimization solver to find the exact solutions on a benchmark of chloroplasts. We show that the presence of repetitions in the set of unitigs is the main reason for the existence of multiple equivalent solutions that are associated to alternative subpaths. We also describe two sufficient conditions and we design efficient algorithms for identifying these subpaths. Comparisons of the results achieved by our tool with the ones obtained with recent assemblers are presented.

Characterization of an air-spun poly(L-lactic acid) nanofiber mesh.

It was previously showed that PLLA nanofiber mesh promoted good endothelial cell proliferation. A new technique was developed to produce nanofibers by air jet spinning inside the tubular shape of vascular prostheses and to characterize this nanofiber mesh. Polymer macromolecule stability was assessed by gel permeation chromatography. Thermal analyses were conducted with differential scanning calorimetry and dynamic mechanical analysis on PLLA nanofibers obtained with 4% and 7% solutions (w/v) in chloroform. Polyethylene terephthalate (PET) was also treated with atmospheric pressure dielectric barrier discharge under air or nitrogen atmosphere to optimize PLLA nanofiber adherence, assessed by peel tests. Air spinning induced a reduction of number-average molecular weight (M(n)) for the 7% PLLA solution but not for the 4% solution. The nanofibers were more crystalline and less sensible to viscoelastic relaxation as a function of aging in the 4% solution than in the 7% solution. Discharge treatment of the PET promoted identical surface modification on PET film and PET textile surfaces. Moreover, the best PLLA nanofibers adhesion results were obtained under nitrogen atmosphere. This study demonstrates that it is possible to coat the internal side of tubular vascular prostheses with PLLA nanofibers, and provides a better understanding of the air spinning process as well as optimizing nanofibers adhesion.

A poly(L-lactic acid) nanofibre mesh scaffold for endothelial cells on vascular prostheses.

The absence of neoendothelium covering the intimal surface of small-diameter PET vascular prostheses is known to be one cause of failure following implantation in humans. Protein coatings currently used to seal porous textile structures have not shown evidence of in vivo neoendothelium formation. In this study, we covered the inner wall of textile prostheses with a biodegradable synthetic scaffold made of poly(l-lactic) acid (PLLA) nanofibres obtained by an air-spinning process we developed that produces nanofibres by stretching a solution of polymer with a high-speed compressed air jet. The air spinning was designed to process a scaffold that would support good endothelial cell proliferation. Our innovative process enabled us to very rapidly cover textile samples with PLLA nanofibres to determine the influence of air pressure, polymer solution flow rate and polymer concentration on fibre quality. High air pressure was shown to induce a significant number of ruptures. High polymer flow rate stimulated the formation of polymer droplets, and the fibre diameter mean increased for the 4% and 7% polymer concentrations. The adherence and proliferation of bovine aortic endothelial cells was assessed to compare prosthesis samples with or without the PLLA nanofibre scaffold and PET film. The PLLA nanofibres displayed a significantly better proliferation rate, and enabled endothelial cells to proliferate in the monolayer. Our novel approach therefore opens the door to the development of partially degradable textile prostheses with a blood/textile interface that supports endothelial cell proliferation.