Detecting sex-linked genes using genotyped individuals sampled in natural populations

We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows to statistically test for the presence or absence of sex chromosomes, and to infer sex-linked genes based on the posterior probabilities in the model. Furthermore, for gametologous sequences, the haplotype and level of nucleotide polymorphism of each copy can be inferred, as well as the divergence between both. We test the method using simulated and human sequencing data, and show that, for most cases, robust predictions are obtained with 5 to 10 individuals per sex

Detecting sex-linked genes using genotyped individuals sampled in natural populations

We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows to statistically test for the presence or absence of sex chromosomes, and to infer sex-linked genes based on the posterior probabilities in the model. Furthermore, for gametologous sequences, the haplotype and level of nucleotide polymorphism of each copy can be inferred, as well as the divergence between both. We test the method using simulated and human sequencing data, and show that, for most cases, robust predictions are obtained with 5 to 10 individuals per sex

Moving Forward Moving Backward: Directional Sorting of Chemotactic Cells due to Size and Adhesion Differences

Differential movement of individual cells within tissues is an important yet poorly understood process in biological development. Here we present a computational study of cell sorting caused by a combination of cell adhesion and chemotaxis, where we assume that all cells respond equally to the chemotactic signal. To capture in our model mesoscopic properties of biological cells, such as their size and deformability, we use the Cellular Potts Model, a multiscale, cell-based Monte Carlo model. We demonstrate a rich array of cell-sorting phenomena, which depend on a combination of mescoscopic cell properties and tissue level constraints. Under the conditions studied, cell sorting is a fast process, which scales linearly with tissue size. We demonstrate the occurrence of “absolute negative mobility”, which means that cells may move in the direction opposite to the applied force (here chemotaxis). Moreover, during the sorting, cells may even reverse the direction of motion. Another interesting phenomenon is “minority sorting”, where the direction of movement does not depend on cell type, but on the frequency of the cell type in the tissue. A special case is the cAMP-wave-driven chemotaxis of Dictyostelium cells, which generates pressure waves that guide the sorting. The mechanisms we describe can easily be overlooked in studies of differential cell movement, hence certain experimental observations may be misinterpreted

Statistical mechanics of two-dimensional shuffled foams: Geometry-topology correlation in small or large disorder limits

Bubble monolayers are model systems for experiments and simulations of two-dimensional packing problems of deformable objects. We explore the relation between the distributions of the number of bubble sides (topology) and the bubble areas (geometry) in the low liquid fraction limit. We use a statistical model [M. Durand, Europhys. Lett. 90, 60002 (2010)] which takes into account Plateau laws. We predict the correlation between geometrical disorder (bubble size dispersity) and topological disorder (width of bubble side number distribution) over an extended range of bubble size dispersities. Extensive data sets arising from shuffled foam experiments, surface evolver simulations, and cellular Potts model simulations all collapse surprisingly well and coincide with the model predictions, even at extremely high size dispersity. At moderate size dispersity, we recover our earlier approximate predictions [M. Durand, J. Kafer, C. Quilliet, S. Cox, S. A. Talebi, and F. Graner, Phys. Rev. Lett. 107, 168304 (2011)]. At extremely low dispersity, when approaching the perfectly regular honeycomb pattern, we study how both geometrical and topological disorders vanish. We identify a crystallization mechanism and explore it quantitatively in the case of bidisperse foams. Due to the deformability of the bubbles, foams can crystallize over a larger range of size dispersities than hard disks. The model predicts that the crystallization transition occurs when the ratio of largest to smallest bubble radii is 1.4

A Fly in the Ointment: Evaluation of Traditional Use of Plants to Repel and Kill Blowfly Larvae in Fermented Fish

Introduction: In rural areas in Laos, fly larvae infestations are common in fermenting fish. Blowflies (Chrysomyamegacephala, Diptera: Calliphoridae) are attracted to oviposit (and/or larviposit) onto fermenting fish which results ininfestations with fly larvae. Knowledge of traditional use of plants to repel larvae during the production of fermented fish iscommon and widespread in Lao PDR. Research Questions: How effective are the most salient species in repelling, and killing fly larvae in fermenting fish? Material and Methods: The three plant species most frequently reported to repel fly larvae during an ethnobotanical surveythroughout Lao PDR were tested for repellence and larvicidal activity of fly larvae infesting fermented fish. The lethality andrepellence of Tadehagi triquetrum (L.) H. Ohashi (Fabaceae), Uraria crinita (L.) Desv. ex DC. (Fabaceae) and Bambusa multiplex(Lour.) Raeusch. ex Schult. & Schult. f. (Poaceae) were tested in an experimental design using fermenting fish in Vientiane,Lao PDR. Results: The repellent effect of fresh material of T. triquetrum and U. crinita, and the larvicidal effect of fresh B. multiplex, issignificantly more effective than that of dried material of the same species, and the total effect (repellence and larvicidaleffect combined) for each of the three species was significantly more effective for fresh than for dry material. Fresh materialof T. triquetrum, U. crinita, or B. multiplex added on top of the fermenting fish repelled 50%, 54%, 37%, and killed 22%, 28%,and 40% of fly larvae. The total effect was not significantly different per species at 72%, 82%, and 77%, respectively. Discussion and Conclusions: The three most salient species are effective in repelling and killing fly larvae in the productionof fermented fish, and may be essential to augment food safety during traditional fermentation in open jars

Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus Silene

In the plant genus Silene, separate sexes and sex chromosomes are believed to have evolved twice. Silene species that are wholly or largely hermaphroditic are assumed to represent the ancestral state from which dioecy evolved. This assumption is important for choice of outgroup species for inferring the genetic and chromosomal changes involved in the evolution of dioecy, but is mainly based on data from a single locus (ITS). To establish the order of events more clearly, and inform outgroup choice, we therefore carried out (i) multi-nuclear-gene phylogenetic analyses of 14 Silene species (including 7 hermaphrodite or gynodioecious species), representing species from both Silene clades with dioecious members, plus a more distantly related outgroup, and (ii) a BayesTraits character analysis of the evolution of dioecy. We confirm two origins of dioecy within this genus in agreement with recent work on comparing sex chromosomes from both clades with dioecious species. We conclude that sex chromosomes evolved after the origin of Silene and within a clade that includes only S. latifolia and its closest relatives. We estimate that sex chromosomes emerged soon after the split with the ancestor of S. viscosa, the probable closest non-dioecious S. latifolia relative among the species included in our study

Des cellules aux tissus : modélisation physique du comportement collectif des cellules embryonnaires

To understand how cellular mechanical properties act on the level of a tissue, where they are implied in morphogenesis, it has been proposed that cells act as soap bubbles or molecules in a liquid. We test these analogies between tissues and physical systems with a computational model, in collaboration with experimentalists.In the retina of Drosophila, the packing of cells has been compared to soap bubble packing. We find that the resemblance is not due to the physical resemblance of cells and bubbles, but to a similar organisation on the collective level: cells in a tissue tile the space, like bubbles in a foam, thereby influencing each other's shapes.The spontaneous sorting of cells of different types has been compared to the demixing of liquids. While in liquids this behaviour is due to the attraction between molecules, we find that in aggregates of zebrafish germlayer cells differential contraction of the cytoskeleton plays a role as well.Compression of an aggregate of cells has been analysed as if the aggregate behaved as a liquid drop, where only the surface tension determines its properties. However, individual cells in the aggregate deform and rearrange, and solid-like stresses inside the aggregate co-determine its shape and forces.The widely used physical analogies prove thus to be incomplete, but interesting. We propose a distinctive description, in which an aggregate or tissue is a collection of closely packed living cells that change shape and rearrange. This approach allows to study how cell adhesion, cortical tension and the cellular fluctuations govern the behaviour on the collective level, and on morphogenesis.Pour comprendre comment les propriétés mécaniques des cellules jouent au niveau d'un tissu et déterminent la morphogénèse, il a été proposé que les cellules se comportent comme les bulles de savon, ou comme des molécules dans un liquide. Nous testons numériquement ces analogies entre tissus et systèmes physiques, en collaboration avec des experimentateurs.Dans la rétine de la Drosophile, les cellules ont été comparées aux bulles de savon. On trouve que la ressemblance entre les cellules et bulles de savon n'est pas due à leur propriétés physiques, mais à leur structure collective: les cellules dans un tissu pavent l'espace, comme les bulles dans une mousse, donc elles influencent leur formes entre elles.Le tri spontané des cellules de types différents est souvent comparé à la démixion de liquides. Pour les liquides, ce comportement est produit par des différences d'attraction entre les molécules, alors qu'on trouve que pour les cellules embryonnaires du poisson zèbre la contraction différentielle du cortex des cellules est le facteur le plus important.La compression d'un agrégat de cellules a été analysé comme si c'était une goutte liquide, où les propriétés sont déterminées uniquement par la tension de surface. Mais, les cellules dans un agrégat peuvent se déformer et se réarranger, et des contraintes plutôt solides co-déterminent la forme et les forces de l'agrégat.Ces analogies physiques sont donc incomplètes, mais intéressantes. A partir d'elles, nous proposons ici une description propre aux cellules: un agrégat ou tissu est une collection de cellules vivantes qui peuvent changer leur forme et se réarranger. Cette approche nous permet d'étudier l'effet de l'adhésion cellulaire, la tension corticale, et les fluctuations des cellules sur le comportement collectif et la morphogénèse

How sex chromosomes get trapped into nonrecombination

International audienceSuppression of recombination along the Y chromosome leads to its degeneration, so why does a process with such potentially deleterious consequences arise? In this issue of PLOS Biology, a new model reveals how and why this might be

How sex chromosomes get trapped into nonrecombination

Suppression of recombination along the Y chromosome leads to its degeneration, so why does a process with such potentially deleterious consequences arise? In this issue of PLOS Biology, a new model reveals how and why this might be. We know that suppression of recombination leads to degeneration of Y chromosomes, but it has remained difficult to understand how features with such strong negative effects actually arise. This Primer explores a new model published in PLOS Biology that reveals how this could happen