Beyond representing orthology relations by trees

Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple relations on a set of sequences called orthology relations may be employed. In addition to being interesting from a practical point of view they are also attractive from a theoretical perspective in that e.\,g.\,a characterization is known for when such a relation is representable by a certain type of phylogenetic tree. For an orthology relation inferred from real biological data it is however generally too much to hope for that it satisfies that characterization. Rather than trying to correct the data in some way or another which has its own drawbacks, as an alternative, we propose to represent an orthology relation $\delta$ in terms of a structure more general than a phylogenetic tree called a phylogenetic network. To compute such a network in the form of a level-1 representation for $\delta$, we formalize an orthology relation in terms of the novel concept of a symbolic 3- dissimilarity which is motivated by the biological concept of a ``cluster of orthologous groups'', or COG for short. For such maps which assign symbols rather that real values to elements, we introduce the novel {\sc Network-Popping} algorithm which has several attractive properties. In addition, we characterize an orthology relation $\delta$ on some set $X$ that has a level-1 representation in terms of eight natural properties for $\delta$ as well as in terms of level-1 representations of orthology relations on certain subsets of $X$

Computational Cancer Biology: An Evolutionary Perspective

ISSN:1553-734XISSN:1553-735

Reconstruction of time-consistent species trees

Background The history of gene families—which are equivalent to event-labeled gene trees—can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The question then arises as whether inferred event-labeled gene trees are “biologically feasible” which is the case if one can find a species tree with which the gene tree can be reconciled in a time-consistent way. Results In this contribution, we consider event-labeled gene trees that contain speciations, duplications as well as horizontal gene transfer (HGT) and we assume that the species tree is unknown. Although many problems become NP-hard as soon as HGT and time-consistency are involved, we show, in contrast, that the problem of finding a time-consistent species tree for a given event-labeled gene can be solved in polynomial-time. We provide a cubic-time algorithm to decide whether a “time-consistent” species tree for a given event-labeled gene tree exists and, in the affirmative case, to construct the species tree within the same time-complexity

The <it>in vivo</it> performance of small-caliber nanofibrous polyurethane vascular grafts

<p>Abstract</p> <p>Background</p> <p>In a previous <it>in vitro</it> study, we confirmed that small-caliber nanofibrous polyurethane (PU) vascular grafts have favorable mechanical properties and biocompatibility. In the present study, we examined the <it>in vivo</it> biocompatibility and stability of these grafts.</p> <p>Methods</p> <p>Forty-eight adult male beagle dogs were randomly divided into two groups receiving, respectively, polyurethane (PU) or polytetrafluoroethylene (PTFE) grafts (n = 24 animals / group). Each group was studied at 4, 8, 12, and 24 weeks after graft implantation. Blood flow was analyzed by color Doppler ultrasound and computed tomography angiography. Patency rates were judged by animal survival rates. Coverage with endothelial and smooth muscle cells was characterized by hematoxylin-eosin and immunohistological staining, and scanning electron microscopy (SEM).</p> <p>Results</p> <p>Patency rates were significantly higher in the PU group (p = 0.02 vs. PTFE group). During the first 8 weeks, endothelial cells gradually formed a continuous layer on the internal surface of PU grafts, whereas coverage of PTFE graft by endothelial cells was inhomogeneous. After 12 weeks, neointimal thickness remained constant in the PU group, while PTFE group showed neointimal hyperplasia. At 24 weeks, some anastomotic sites of PTFE grafts became stenotic (p = 0.013 vs. PU group). Immunohistological staining revealed a continuous coverage by endothelial cells and an orderly arrangement of smooth muscle cells on PU grafts. Further, SEM showed smooth internal surfaces in PU grafts without thrombus or obvious neointimal hyperplasia.</p> <p>Conclusions</p> <p>Small-caliber nanofibrous PU vascular grafts facilitate the endothelialization process, prevent excessive neointimal hyperplasia, and improve patency rates.</p