Analysis of the Development of a Morphological Phenotype as a Function of Protein Concentration in Budding Yeast

Gene deletion and protein overexpression are common methods for studying functions of proteins. In this article, we describe a protocol for analysis of phenotype development as a function of protein concentration at population and single-cell levels in Saccharomyces cerevisiae. Although this protocol is based on the overexpression of a protein, it can easily be adapted for morphological phenotypes dependent on suppression of protein expression. Our lab is interested in studying the signaling properties of the endocytic adaptor protein epsin. To that purpose we used a dominant negative approach in which we over-expressed the conserved Epsin N-Terminal Homology (ENTH) domain in order to interfere with the functions of endogenous epsin-2 (Ent2 or YLR206W). We observed that overexpression of the ENTH domain of Ent2 (ENTH2) in wild type cells led to a cell division defect that is dependent on the mislocalization of a family of scaffolding proteins, septins.Download video file.^{(167M, mp4)}     

Morphological Bases for Evolution of Functions

The morphological and morphometrical changes in the renal proximal tubular cells of the salmonOncorhynchus gorbuscha during spawning migration are described for the first time. The evaluation of the ultrastructural changes in the kidney of the adult humpback salmon allows concluding that the proximal tubular cells are affected by significant osmotic loads during spawning migration. Various destructive processes in the proximal tubular cells indicate a decrease of their functional activity in the fresh water. The analysis of the results of the study of the humpback salmon kidney ultrastructure during the anadromous migration allow suggesting that reduction of the amount of the most active cell organelles in the proximal tubule, such as mitochondria and the basolateral membrane system, is associated with a decrease of the number of ion pumps that operate less intensively in the fresh water. Such mechanism of the kidney functioning in the euryhaline fish appears to be formed in the course of evolution as an adaptation to the freshwater environment. The morphological and morphometrical changes in the proximal tubules of nephrons were described for the first time in Pacific salmon smoltsOncorhynchus keta, O. gorbuscha,O. Kisutch, andO. masou in environments with different salinity. The most marked response to the transfer to the sea water or to the calcium-enriched sea water was observed in the chum salmon smolts. In 48 h, the tubular diameter reached its peak, more than 72 μm, the tubular lumen also was very large, while the epithelium height was only slightly greater than that in the fresh water control. In spite of the considerable morphological changes, as soon as in 24 h (the Ca²⁺-enriched sea water) and in 48 h (the sea water) the ion content in smolt carcasses was within the physiological norm for the environment with enhanced salinity. These results indicate a high efficiency of the osmoregulatory system in smolts during their transfer from the fresh to the sea water.     

Morphological variation of species through time

Ten measurements, taken from each of 700 shells or four biologically distinct shallow marine gastropod species, were used to define the appropriate phenotypes in multidimensional space. Canonical discriminant analysis was performed on the data and a set of allocatory rules was derived. These allocatory rules, derived from extant specimens, were than applied to 644 fossil specimens of three of these biological species. Fossil individuals occupy the appropriate phenotypic space as defined by their modern descendants. The variation of fossil sample means about the modern means is illustrated. This variation is in the form of oscillations around the modern mean values and is correlated with climate. The distinction between taxonomic and biological species is discussed. The results of a number of previous studies are re-examined in the light of this discussion. It is argued that biological groupings can only be reliably determined when the appropriate data are available for extant organisms. Extant organisms, which have good fossil records, should therefore from the basis of paleontological evolutionary studies.     

Morphological and Physical Analysis of Natural Phospholipids-Based Biomembranes

Background

Liposomes are currently an important part of biological, pharmaceutical, medical and nutritional research, as they are considered to be among the most effective carriers for the introduction of various types of bioactive agents into target cells.

Scope of Review

In this work, we study the lipid organization and mechanical properties of biomembranes made of marine and plant phospholipids. Membranes based on phospholipids extracted from rapeseed and salmon are studied in the form of liposome and as supported lipid bilayer. Dioleylphosphatidylcholine (DOPC) and dipalmitoylphosphatidylcholine (DPPC) are used as references to determine the lipid organization of marine and plant phospholipid based membranes. Atomic force microscopy (AFM) imaging and force spectroscopy measurements are performed to investigate the membranes'' topography at the micrometer scale and to determine their mechanical properties.

Major Conclusions

The mechanical properties of the membranes are correlated to the fatty acid composition, the morphology, the electrophoretic mobility and the membrane fluidity. Thus, soft and homogeneous mechanical properties are evidenced for salmon phospholipids membrane containing various polyunsaturated fatty acids. Besides, phase segregation in rapeseed membrane and more important mechanical properties were emphasized for this type of membranes by contrast to the marine phospholipids based membranes.

General Significance

This paper provides new information on the nanomechanical and morphological properties of membrane in form of liposome by AFM. The originality of this work is to characterize the physico-chemical properties of the nanoliposome from the natural sources containing various fatty acids and polar head.     

Evolution of Collective Behaviors for a Real Swarm of Aquatic Surface Robots

Swarm robotics is a promising approach for the coordination of large numbers of robots. While previous studies have shown that evolutionary robotics techniques can be applied to obtain robust and efficient self-organized behaviors for robot swarms, most studies have been conducted in simulation, and the few that have been conducted on real robots have been confined to laboratory environments. In this paper, we demonstrate for the first time a swarm robotics system with evolved control successfully operating in a real and uncontrolled environment. We evolve neural network-based controllers in simulation for canonical swarm robotics tasks, namely homing, dispersion, clustering, and monitoring. We then assess the performance of the controllers on a real swarm of up to ten aquatic surface robots. Our results show that the evolved controllers transfer successfully to real robots and achieve a performance similar to the performance obtained in simulation. We validate that the evolved controllers display key properties of swarm intelligence-based control, namely scalability, flexibility, and robustness on the real swarm. We conclude with a proof-of-concept experiment in which the swarm performs a complete environmental monitoring task by combining multiple evolved controllers.     

The Significance of Non-vertical Transmission of Phenotype for the Evolution of Altruism

My aim in this paper is to demonstrate that a very simple learning rule based on imitation can help to sustain altruism as a culturally transmitted pattern or behaviour among agents playing a standard prisoner’s dilemma game. The point of this demonstration is not to prove that imitation is single-handedly responsible for existing levels of altruism (a thesis that is false), nor is the point to show that imitation is an important factor in explanations for the evolution of altruism (a thesis already prominent in the existing literature). The point is to show that imitation contributes to the evolution of altruism in a particular way that is not always fairly represented by evolutionary game theory models. Specifically, the paper uses a simple model to illustrate that cultural transmission includes mechanisms that do not transmit phenotype vertically (i.e. from parent to related offspring) and that these mechanisms can promote altruism in the absence of any direct biological propensity favouring such behaviour. This is a noteworthy result because it shows that evolutionary models can be built to explicitly reflect the contribution of non-vertical transmission in our explanations for the evolution of altruism among humans and other social species.     

Morphological and Physiological Aspects of Evolution in Common Buckwheat

Comparative morphological and physiological studies of the ancestral forms (Fagopyrum homotropicumO. and F. esculentumssp. ancestraleO.) and the various morphogenotypes of common buckwheat (F. esculentumMoench.) were carried out in glasshouse experiments in a soil culture. A considerable reduction of plant morphogenesis, a restriction of the growth of the vegetative organs, and the ecological and agricultural specialization (accompanied by the change in the primary adaptive life strategy from competitive (c) to ruderal (r) or to combined c/rtype) occurred in the evolution of common buckwheat. The reduction of morphogenesis was accompanied by changes in some of the morphological and anatomical structures and their functions, primarily, the source–sink relationships among plant organs. Compensatory mechanisms were developed, and the nutritional compounds became reutilized as an additional source for fruit formation and ripening.     

Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree

The distribution of a phenotype on a phylogenetic tree is often a quantity of interest. Many phenotypes have imperfect heritability, so that a measurement of the phenotype for an individual can be thought of as a single realization from the phenotype distribution of that individual. If all individuals in a phylogeny had the same phenotype distribution, measured phenotypes would be randomly distributed on the tree leaves. This is, however, often not the case, implying that the phenotype distribution evolves over time. Here we propose a new model based on this principle of evolving phenotype distribution on the branches of a phylogeny, which is different from ancestral state reconstruction where the phenotype itself is assumed to evolve. We develop an efficient Bayesian inference method to estimate the parameters of our model and to test the evidence for changes in the phenotype distribution. We use multiple simulated data sets to show that our algorithm has good sensitivity and specificity properties. Since our method identifies branches on the tree on which the phenotype distribution has changed, it is able to break down a tree into components for which this distribution is unique and constant. We present two applications of our method, one investigating the association between HIV genetic variation and human leukocyte antigen and the other studying host range distribution in a lineage of Salmonella enterica, and we discuss many other potential applications.     

Evolution of cooperation through indirect reciprocity

How can cooperation through indirect reciprocity evolve and what would it be like? This problem has previously been studied by simulating evolution in a small group of interacting individuals, assuming no gene flow between groups. In these simulations, certain ''image scoring'' strategies were found to be the most successful. However, analytical arguments show that it would not be in an individual''s interest to use these strategies. Starting with this puzzle, we investigate indirect reciprocity in simulations based on an island model. This has an advantage in that the role of genetic drift can be examined. Our results show that the image scoring strategies depend on very strong drift or a very small cost of giving help. As soon as these factors are absent, selection eliminates image scoring. We also consider other possibilities for the evolution of indirect reciprocity. In particular, we find that the strategy of aiming for ''good standing'' has superior properties. It can be an evolutionarily stable strategy and, even if not, it usually beats image scoring. Furthermore, by introducing quality variation among individuals into the model, we show that the standing strategy can be quality revealing, adding a new dimension to indirect reciprocity. Finally, we discuss general problems with currently popular modelling styles.