Maximal ecological diversity exceeds evolutionary diversity in model ecosystems

Understanding community saturation is fundamental to ecological theory. While investigations of the diversity of evolutionary stable states (ESSs) are widespread, the diversity of communities that have yet to reach an evolutionary endpoint is poorly understood. We use Lotka–Volterra dynamics and trait-based competition to compare the diversity of randomly assembled communities to the diversity of the ESS. We show that, with a large enough founding diversity (whether assembled at once or through sequential invasions), the number of long-time surviving species exceeds that of the ESS. However, the excessive founding diversity required to assemble a saturated community increases rapidly with the dimension of phenotype space. Additionally, traits present in communities resulting from random assembly are more clustered in phenotype space compared to random, although still markedly less ordered than the ESS. By combining theories of random assembly and ESSs we bring a new viewpoint to both the saturation and random assembly literature.     

A Highlights from MBoC Selection: Cell shape impacts on the positioning of the mitotic spindle with respect to the substratum

All known mechanisms of mitotic spindle orientation rely on astral microtubules. We report that even in the absence of astral microtubules, metaphase spindles in MDCK and HeLa cells are not randomly positioned along their x-z dimension, but preferentially adopt shallow β angles between spindle pole axis and substratum. The nonrandom spindle positioning is due to constraints imposed by the cell cortex in flat cells that drive spindles that are longer and/or wider than the cell''s height into a tilted, quasidiagonal x-z position. In rounder cells, which are taller, fewer cortical constraints make the x-z spindle position more random. Reestablishment of astral microtubule–mediated forces align the spindle poles with cortical cues parallel to the substratum in all cells. However, in flat cells, they frequently cause spindle deformations. Similar deformations are apparent when confined spindles rotate from tilted to parallel positions while MDCK cells progress from prometaphase to metaphase. The spindle disruptions cause the engagement of the spindle assembly checkpoint. We propose that cell rounding serves to maintain spindle integrity during its positioning.     

Giant Enhancement of Transmitted Light and Its Localization Due to Elastic Surface Plasmon–Polariton Scattering by a Thin Dielectric Diffraction Grating

The enhancement factor for surface plasmon–polaritons scattering by a thin dielectric grating was measured experimentally. Scattering of a p-polarized wave may be up to 30,000 times stronger than the non-resonant scattering of an s-polarized wave by the same grating. A detailed comparison between the theoretical calculations and experimental measurements was performed. Strong localization of the scattered field near the edges of diffraction grating grooves was found. Such localization is very promising for numerous applications, e.g., biological sensors, optical tweezers for catching particles, or viruses, etc.     

Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks

Background  

Uncovering cellular roles of a protein is a task of tremendous importance and complexity that requires dedicated experimental work as well as often sophisticated data mining and processing tools. Protein functions, often referred to as its annotations, are believed to manifest themselves through topology of the networks of inter-proteins interactions. In particular, there is a growing body of evidence that proteins performing the same function are more likely to interact with each other than with proteins with other functions. However, since functional annotation and protein network topology are often studied separately, the direct relationship between them has not been comprehensively demonstrated. In addition to having the general biological significance, such demonstration would further validate the data extraction and processing methods used to compose protein annotation and protein-protein interactions datasets.     

Spectroscopy analysis for simultaneous determination of lycopene and β-carotene in fungal biomass of Blakeslea trispora

Blakeslea trispora is a good alternative source for producing such carotenoids as lycopene and β-carotene. The objective of this research was to elaborate a method for the simultaneous determination of lycopene and β-carotene in Blakeslea trispora products using a usual UV-vis spectrophotometer. The standard solutions of the mixture of different concentrations of β-carotene and lycopene were measured with the UV-vis method and correlation formula for the extinction coefficients of 1% standard solution of lycopene in the solvent (hexane) and the ratios of the optical densities at the character peaks of 470 and 502 nm was elaborated. This gives a possibility to calculate the concentrations of lycopene and β-carotene in the mixture. The prediction quality of the UV-vis method was sufficient and the obtained results were very close to the ones, being measured with the HPLC technique. The proposed method can be used for both routine industrial work and academic research, providing the rapid analysis for simultaneous measurements of lycopene and β-carotene.     

Genetic polymorphism of the erythrocytic enzymes in the Buryat populations

Polymorphism of seven erythrocytic enzymes PGM1, ESD, CLO1, PGD and PGP were studied in five samples of Buryats. The main investment into differentiation between populations has been made by the following systems: CLO1, PGD and PGM1. Analysis of genetic distances between populations demonstrated that there was some parallelism among the genetic and anthropological differentiation in the Buryat populations. The groups of the Agingsky county (the area to the east from the Baikal Lake) have probably the largest proportion of the Caucasian genes as compared to other populations studied. One of the characteristics of the Buryats, especially for the population to the east from the Baikal Lake, is high frequency of the PGD allele. The rate of the genetic variability on the intra-population level is higher than the difference between populations. This means that the divergence between the Buryats populations is not very strong. Consideration of the genetic variability on the intra-population level seems to be more perspective for ecogenetic estimation of the adaptive genetic processes than analysis of the differences between populations studied.     

Study of interlocus interactions using a series of gene markers in samples from groups with different health status]

Interloci equilibrium between pairs of gene markers in the samples of different health rate in the population of Buryats of Chitinskaya Province was tested. The following methods were used: calculation of interloci correlation coefficients, chi 2-testing of the hypothesis of interloci equilibrium and the modification of principal components analysis on the basis of the matrix of Pearson's coefficients of contingency. In the groups of "extreme" health rate the tendency to increase in interloci disequilibrium was discovered. The reason for this effect is the increase in some phenotype combination frequencies that can be considered as markers of non-specific individual resistance in the environmental condition of the populations studied.     

A Model for the Self-Organization of Vesicular Flux and Protein Distributions in the Golgi Apparatus

The generation of two non-identical membrane compartments via exchange of vesicles is considered to require two types of vesicles specified by distinct cytosolic coats that selectively recruit cargo, and two membrane-bound SNARE pairs that specify fusion and differ in their affinities for each type of vesicles. The mammalian Golgi complex is composed of 6–8 non-identical cisternae that undergo gradual maturation and replacement yet features only two SNARE pairs. We present a model that explains how distinct composition of Golgi cisternae can be generated with two and even a single SNARE pair and one vesicle coat. A decay of active SNARE concentration in aging cisternae provides the seed for a cis trans SNARE gradient that generates the predominantly retrograde vesicle flux which further enhances the gradient. This flux in turn yields the observed inhomogeneous steady-state distribution of Golgi enzymes, which compete with each other and with the SNAREs for incorporation into transport vesicles. We show analytically that the steady state SNARE concentration decays exponentially with the cisterna number. Numerical solutions of rate equations reproduce the experimentally observed SNARE gradients, overlapping enzyme peaks in cis, medial and trans and the reported change in vesicle nature across the Golgi: Vesicles originating from younger cisternae mostly contain Golgi enzymes and SNAREs enriched in these cisternae and extensively recycle through the Endoplasmic Reticulum (ER), while the other subpopulation of vesicles contains Golgi proteins prevalent in older cisternae and hardly reaches the ER.     

What do we know about gliotransmitter release from astrocytes?

Astrocytes participate in information processing by actively modulating synaptic properties via gliotransmitter release. Various mechanisms of astrocytic release have been reported, including release from storage organelles via exocytosis and release from the cytosol via plasma membrane ion channels and pumps. It is still not fully clear which mechanisms operate under which conditions, but some of them, being Ca²⁺-regulated, may be physiologically relevant. The properties of Ca²⁺-dependent transmitter release via exocytosis or via ion channels are different and expected to produce different extracellular transmitter concentrations over time and to have distinct functional consequences. The molecular aspects of these two release pathways are still under active investigation. Here, we discuss the existing morphological and functional evidence in support of either of them. Transgenic mouse models, specific antagonists and localization studies have provided insight into regulated exocytosis, albeit not in a systematic fashion. Even more remains to be uncovered about the details of channel-mediated release. Better functional tools and improved ultrastructural approaches are needed in order fully to define specific modalities and effects of astrocytic gliotransmitter release pathways.     

SPECIATION DUE TO HYBRID NECROSIS IN PLANT–PATHOGEN MODELS

We develop a model for speciation due to postzygotic incompatibility generated by autoimmune reactions. The model is based on frequency‐dependent interactions between host plants and their pathogens, which can generate disruptive selection and give rise to speciation if distant phenotypes become reproductively isolated. Based on recent experimental evidence from Arabidopsis, we assume that at the molecular level, incompatibility between host strains is caused by epistatic interactions between two proteins in the plant immune system—the guard and the guardee. Within each plant strain, immune reactions occur when the guardee protein is modified by a pathogen effector, and the guard subsequently binds to the guardee, thus precipitating an immune response. When guard and guardee proteins come from phenotypically distant parents, a hybrid's immune system can be triggered by erroneous interactions between these proteins even in the absence of pathogen attack, leading to severe autoimmune reactions in hybrids. This generates a Dobzhnasky–Muller incompatibility due to immune reactions. Our model shows how phenotypic variation generated by frequency‐dependent host–pathogen interactions can lead to such postzygotic incompatibilities between extremal types, and hence to speciation.