Using Von Mises-fisher Distribution for Polymer Conformation Analysis in Multi-scale Framework

AbstractIn this study we consider the statistical representation of polymer conformations, which is very important when modeling rheology at macroscopic scales. It is impossible to track all relevant microscopic variables for each polymer in a polymer-laden solution due to the huge number degrees of freedom associated with such fluids. We applied this approach to one of the most descriptive kinetic models of polymer, Kramers bead-rod model, where the probability density function models the angle of each rod with respect to the fixed coordinate axes. Towards this goal we apply mixture of von Mises-Fisher distribution for modeling a polymer conformation. The Expectation-Maximization based clustering algorithms are used to estimate the conformation given the ensemble of polymers. Both distribution sampling and parameters estimation have been implemented in parallel using CPU and GPU based platforms

Novel regulation of the homeotic gene Scr associated with a crustacean leg-to-maxilliped appendage transformation.

Homeotic genes are known to be involved in patterning morphological structures along the antero-posterior axis of insects and vertebrates. Because of their important roles in development, changes in the function and expression patterns of homeotic genes may have played a major role in the evolution of different body plans. For example, it has been proposed that during the evolution of several crustacean lineages, changes in the expression patterns of the homeotic genes Ultrabithorax and abdominal-A have played a role in transformation of the anterior thoracic appendages into mouthparts termed maxillipeds. This homeotic-like transformation is recapitulated at the late stages of the direct embryonic development of the crustacean Porcellio scaber (Oniscidea, Isopoda). Interestingly, this morphological change is associated with apparent novelties both in the transcriptional and post-transcriptional regulation of the Porcellio scaber ortholog of the Drosophila homeotic gene, Sex combs reduced (Scr). Specifically, we find that Scr mRNA is present in the second maxillary segment and the first pair of thoracic legs (T1) in early embryos, whereas protein accumulates only in the second maxillae. In later stages, however, high levels of SCR appear in the T1 legs, which correlates temporally with the transformation of these appendages into maxillipeds. Our observations provide further insight into the process of the homeotic leg-to-maxilliped transformation in the evolution of crustaceans and suggest a novel regulatory mechanism for this process in this group of arthropods.Organismic and Evolutionary Biolog

Correction: Sarsekova D, Ayan S, Talgat A, 2020. Ectomycorrhizal Flora Formed by Main Forest Trees in the Irtysh River Region of Central and Northeastern Kazakhstan

The authors wish to make the correction of the paper of Sarsekova et al. (2020). In the original paper, there was a mistake in the order of the first and the second name of the author Talghat Abbzhabnov. The correct order is Talghat Abbzhabnov. The original paper published on 11 May 2020 has been updated and both versions will be available on the paper webpage. The authors emphasize that this change does not affect the results of this research, and they apologize for any inconvenience this change may cause

Ectomycorrhizal Flora Formed by Main Forest Trees in the Irtysh River Region of Central and Northeastern Kazakhstan

In this study, the aim was to determine and identify symbiotically living ectomycorrhizas of the main tree species forming forests in central and northeastern Kazakhstan. Surveys were conducted on the right bank of the Irtysh River in a mixed forest of Pinus sylvestris, Picea obovata and Betula pendula trees. The collection was formed and the primary identification of voucher samples of fruiting bodies of macromycetes collected as ectomycorrhiza forming fungi was completed. In the collection and species identification of fruiting bodies, standard methods were used. A total of 30 ectomycorrhizas belonging to Agaricomycetes were identified. The distribution of 30 species into families is as follows: Suillaceae (8), Russulaceae (7), Cortinariaceae (4), Boletaceae (3), Tricholomataceae (2), Amanitaceae (1), Cantharellaceae (1), Gomphaceae (1), Gomphidiaceae (1), Paxillaceae (1), and Bankeraceae (1). The richest genus on account of the number of species was Suillus (8). Concerning the woody host species, 17 mycorrhizas were determined to build symbiosis with P. sylvestris, 8 mycorrhizas with B. pendula, 6 mycorrhizas with Populus tremula, 1 mycorrhiza with P. obovata, 1 mycorrhiza with Quercus robur, 1 mycorrhiza with Salix sp., and 1 mycorrhiza with Pinus densiflora Siebold and Zuccarini. Ectomycorrhizas should be used as a major performance-enhancing tool in afforestation and restoration studies in the Irtysh River basin under extreme ecological conditions and under climate change effects

The old and new faces of morphology: the legacy of D'Arcy Thompson's 'theory of transformations' and 'laws of growth'

In 1917, the publication of On Growth and Form by D'Arcy Wentworth Thompson challenged both mathematicians and naturalists to think about biological shapes and diversity as more than a confusion of chaotic forms generated at random, but rather as geometric shapes that could be described by principles of physics and mathematics. Thompson's work was based on the ideas of Galileo and Goethe on morphology and of Russell on functionalism, but he was first to postulate that physical forces and internal growth parameters regulate biological forms and could be revealed via geometric transformations in morphological space. Such precise mathematical structure suggested a unifying generative process, as reflected in the title of the book. To Thompson it was growth that could explain the generation of any particular biological form, and changes in ontogeny, rather than natural selection, could then explain the diversity of biological shapes. Whereas adaptationism, widely accepted in evolutionary biology, gives primacy to extrinsic factors in producing morphological variation, Thompson's ‘laws of growth' provide intrinsic directives and constraints for the generation of individual shapes, helping to explain the ‘profusion of forms, colours, and other modifications' observed in the living world

GPU accelerated shake and rattle algorithms for systems with holonomic constraints

The dynamic of complex fluid can be described by including viscoelastic stress tensor into the equation of Non-Newtonian fluid. Different models are used to evaluate the stress tensor at various levels, with the multi-scale model being the most effective

Recapitulating cranial osteogenesis with neural crest cells in 3-D microenvironments

The experimental systems that recapitulate the complexity of native tissues and enable precise control over the microenvironment are becoming essential for the pre-clinical tests of therapeutics and tissue engineering. Here, we described a strategy to develop an in vitro platform to study the developmental biology of craniofacial osteogenesis. In this study, we directly osteo-differentiated cranial neural crest cells (CNCCs) in a 3-D in vitro bioengineered microenvironment. Cells were encapsulated in the gelatin-based photo-crosslinkable hydrogel and cultured up to three weeks. We demonstrated that this platform allows efficient differentiation of p75 positive CNCCs to cells expressing osteogenic markers corresponding to the sequential developmental phases of intramembranous ossification. During the course of culture, we observed a decrease in the expression of early osteogenic marker Runx2, while the other mature osteoblast and osteocyte markers such as Osterix, Osteocalcin, Osteopontin and Bone sialoprotein increased. We analyzed the ossification of the secreted matrix with alkaline phosphatase and quantified the newly secreted hydroxyapatite. The Field Emission Scanning Electron Microscope (FESEM) images of the bioengineered hydrogel constructs revealed the native-like osteocytes, mature osteoblasts, and cranial bone tissue morphologies with canaliculus-like intercellular connections. This platform provides a broadly applicable model system to potentially study diseases involving primarily embryonic craniofacial bone disorders, where direct diagnosis and adequate animal disease models are limited

GPU accelerated shake and rattle algorithms for systems with holonomic constraints

The dynamic of complex fluid can be described by including viscoelastic stress tensor into the equation of Non-Newtonian fluid. Different models are used to evaluate the stress tensor at various levels, with the multi-scale model being the most effective

Convergent Evolution of Sexual Dimorphism in Skull Shape Using Distinct Developmental Strategies

Studies integrating evolutionary and developmental analyses of morphological variation are of growing interest to biologists as they promise to shed fresh light on the mechanisms of morphological diversification. Sexually dimorphic traits tend to be incredibly divergent across taxa. Such diversification must arise through evolutionary modifications to sex differences during development. Nevertheless, few studies of dimorphism have attempted to synthesize evolutionary and developmental perspectives. Using geometric morphometric analysis of head shape for 50 Anolis species, we show that two clades have converged on extreme levels of sexual dimorphism through similar, male-specific changes in facial morphology. In both clades, males have evolved highly elongate faces whereas females retain faces of more moderate proportion. This convergence is accomplished using distinct developmental mechanisms; one clade evolved extreme dimorphism through the exaggeration of a widely shared, potentially ancestral, developmental strategy whereas the other clade evolved a novel developmental strategy not observed elsewhere in the genus. Together, our analyses indicate that both shared and derived features of development contribute to macroevolutionary patterns of morphological diversity among Anolis lizards.Organismic and Evolutionary Biolog

Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs

The astonishing variation in the shape and size of bird beaks reflects a wide range of dietary specializations that played an important role in avian diversification. Among Darwin's finches, ground finches (Geospiza spp.) have beaks that represent scaling variations of the same shape, which are generated by alterations in the signaling pathways that regulate growth of the two skeletal components of the beak: the prenasal cartilage (pnc) and the premaxillary bone (pmx). Whether this developmental mechanism is responsible for variation within groups of other closely related bird species, however, has remained unknown. Here, we report that the Caribbean bullfinches (Loxigilla spp.), which are closely related to Darwin's finches, have independently evolved beaks of a novel shape, different from Geospiza, but also varying from each other only in scaling. However, despite sharing the same beak shape, the signaling pathways and tissues patterning Loxigilla beaks differ among the three species. In Loxigilla noctis, as in Geospiza, the pnc develops first, shaped by Bmp4 and CaM signaling, followed by the development of the pmx, regulated by TGFβIIr, β-catenin, and Dkk3 signaling. In contrast, beak morphogenesis in Loxigilla violacea and Loxigilla portoricensis is generated almost exclusively by the pmx through a mechanism in which Ihh and Bmp4 synergize to promote expansion of bone tissue. Together, our results demonstrate high flexibility in the relationship between morphology and underlying developmental causes, where different developmental programs can generate identical shapes, and similar developmental programs can pattern different shapes.Organismic and Evolutionary Biolog