Drying dynamics of pellet feces.

Pellet feces are generated by a number of animals important to science or agriculture, including mice, rats, goats, and wombats. Understanding the factors that lead to fecal shape may provide a better understanding of animal health and diet. In this combined experimental and theoretical study, we test the hypothesis that pellet feces are formed by drying processes in the intestine. Inspirational to our work is the formation of hexagonal columnar jointings in cooling lava beds, in which the width L of the hexagon scales as L ∼ J-1 where J is the heat flux from the bed. Across 22 species of mammals, we report a transition from cylindrical to pellet feces if fecal water content drops below 0.65. Using a mathematical model that accounts for water intake rate and intestinal dimensions, we show pellet feces length L scales as L ∼ J-2.08 where J is the flux of water absorbed by the intestines. We build a mimic of the mammalian intestine using a corn starch cake drying in an open trough, finding that corn starch pellet length scales with water flux-0.46. The range of exponents does not permit us to conclude that formation of columnar jointings is similar to the formation of pellet feces. Nevertheless, the methods and physical picture shown here may be of use to physicians and veterinarians interested in using feces length as a marker of intestinal health.

Intestines of non-uniform stiffness mold the corners of wombat feces.

The bare-nosed wombat (Vombatus ursinus) is a fossorial, herbivorous, Australian marsupial, renowned for its cubic feces. However, the ability of the wombat's soft intestine to sculpt flat faces and sharp corners in feces is poorly understood. In this combined experimental and numerical study, we show one mechanism for the formation of corners in a highly damped environment. Wombat dissections show that cubes are formed within the last 17 percent of the intestine. Using histology and tensile testing, we discover that the cross-section of the intestine exhibits regions with a two-fold increase in thickness and a four-fold increase in stiffness, which we hypothesize facilitates the formation of corners by contractions of the intestine. Using a mathematical model, we simulate a series of azimuthal contractions of a damped elastic ring composed of alternating stiff and soft regions. Increased stiffness ratio and higher Reynolds number yield shapes that are more square. The corners arise from faster contraction in the stiff regions and relatively slower movement in the center of the soft regions. These results may have applications in manufacturing, clinical pathology, and digestive health.

xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria.

BACKGROUND: Genomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. A variety of computational methods, both genome-composition based and comparative, have been developed to identify them. Some of these methods are explicitly designed to work in single strains, while others make use of multiple strains. In general, existing methods do not identify islands in the context of the phylogeny in which they evolved. Even multiple strain approaches are best suited to identifying genomic islands that are present in one strain but absent in others. They do not automatically recognize islands which are shared between some strains in the clade or determine the branch on which these islands inserted within the phylogenetic tree. RESULTS: We have developed a software package, xenoGI, that identifies genomic islands and maps their origin within a clade of closely related bacteria, determining which branch they inserted on. It takes as input a set of sequenced genomes and a tree specifying their phylogenetic relationships. Making heavy use of synteny information, the package builds gene families in a species-tree-aware way, and then attempts to combine into islands those families whose members are adjacent and whose most recent common ancestor is shared. The package provides a variety of text-based analysis functions, as well as the ability to export genomic islands into formats suitable for viewing in a genome browser. We demonstrate the capabilities of the package with several examples from enteric bacteria, including an examination of the evolution of the acid fitness island in the genus Escherichia. In addition we use output from simulations and a set of known genomic islands from the literature to show that xenoGI can accurately identify genomic islands and place them on a phylogenetic tree. CONCLUSIONS: xenoGI is an effective tool for studying the history of genomic island insertions in a clade of microbes. It identifies genomic islands, and determines which branch they inserted on within the phylogenetic tree for the clade. Such information is valuable because it helps us understand the adaptive path that has produced living species.