Structural conservation of WEE1 and its role in cell cycle regulation in plants

The WEE1 kinase is ubiquitous in plant development and negatively regulates the cell cycle through phosphorylations. However, analogies with the control of the human cell cycle by tyrosine- (Tyr-) phosphorylation of cyclin-dependent kinases (CDKs) are sometimes questioned. In this in silico study, we assessed the structural conservation of the WEE1 protein in the plant kingdom with a particular focus on agronomically valuable plants, the legume crops. We analyzed the phylogenetic distribution of amino-acid sequences among a large number of plants by Bayesian analysis that highlighted the general conservation of WEE1 proteins. A detailed sequence analysis confirmed the catalytic potential of WEE1 proteins in plants. However, some substitutions of an arginine and a glutamate at the entrance of the catalytic pocket, illustrated by 3D structure predictions, challenged the specificity of this protein toward the substrate and Tyr-phosphorylation compared to the human WEE1. The structural differences, which could be responsible for the loss of specificity between human and plants, are highlighted and suggest the involvement of plant WEE1 in more cell regulation processes.

Non-biodegradable objects may boost microbial growth in water bodies by harnessing bubbles

Given the ubiquity of bubbles and non-biodegradable wastes in aqueous environments, their transport through bubbles should be widely extant in water bodies. In this study, we investigate the effect of bubble-induced waste transport on microbial growth by using yeasts as model microbes and a silicone rubber object as model waste. Noteworthily, this object repeatedly rises and sinks in fluid through fluctuations in bubble-acquired buoyant forces produced by cyclic nucleation, growth and release of bubbles from object's surface. The rise–sink movement of the object gives rise to a strong bulk mixing and an enhanced resuspension of cells from the floor. Such spatially dynamic contaminant inside a nutrient-rich medium also leads to an increment in the total microbe concentration in the fluid. The enhanced concentration is caused by strong nutrient mixing generated by the object's movement which increases the nutrient supply to growing microbes and thereby, prolonging their growth phases. We confirm these findings through a theoretical model for cell concentration and nutrient distribution in fluid medium. The model is based on the continuum hypothesis and it uses the general conservation law which takes an advection–diffusion growth form. We conclude the study with the demonstration of bubble-induced digging of objects from model sand.

Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence

Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.

Heritage of (non-)existing cities – on the Polish examples of medieval Świecie and Renaissance Krasiczyn

This article analyses the urban heritage protection and spatial development policies of two model historical urban centres in Poland, whose spatial layout has been erased: medieval Świecie nad Wisłą (the Pomeranian region) and Renaissance Krasiczyn (the Subcarpathian region). Their urban layouts had a significant compositional factor (a town and castle complex in axial plan). The second element important in terms of landscape protection and spatial planning is their history: at the end of the eighteenth century and during the nineteenth century they had to be relocated. The analysis covers the spatial form during the period of their founding, the reasons for transformation, their present-day state of preservation, and the current spatial conservation and development policy. General conservation conclusions have also been formulated.

The bubble-induced population dynamics of fermenting yeasts

Bubble-induced transport is a ubiquitous natural and industrial phenomenon. In brewery, such transport occurs due to gas bubbles generated through anaerobic fermentation by yeasts. Two major kinds of fermentation viz. top (ale) and bottom (lager) fermentation, display a difference in their yeast distributions inside a sugar broth. The reason for this difference is believed to be yeast–bubble adhesion arising due to surface hydrophobicity of the yeast cell wall; however, the physical mechanism is still largely a mystery. In this report, through in vivo experiments, we develop a novel theoretical model for yeast distribution based on the general conservation law. This work clarifies that bubble-induced diffusion is the dominant transport mechanism in bottom-fermentation by lagers whereas, yeast–bubble adhesion plays a leading role in transporting ales in top-fermentation, thereby corroborating the centuries-old belief regarding distribution difference in yeast population in two kinds of fermentation.

Theoretical Foundation of Rapid Distortion Theory on Transversely Sheared Mean Flows

The focus of this paper is on Rapid Distortion Theory on transversely sheared mean flows, which is often used to investigate turbulence-solid surface interactions. The main purpose of the paper is to bring together and present in a consistent fashion a general theory that has been developed in several different papers that have been published in the Journal of Fluid Mechanics. The equations for the unsteady pressure and velocity flections (which decouple from the entropy fluctuations) are rewritten in terms of a gauge function in order to obtain expressions that involve two arbitrarily convected quantities. A pair of very general conservation laws are used to derive upstream boundary conditions that relate these quantities to the actual physical variables. The entropy fluctuations can be determined after the fact once the solutions for the pressure and velocity fluctuations are known. The result involves a third arbitrary convected quantity that is equal to the entropy fluctuations at upstream infinity and can, therefore, be specified as an additional upstream boundary condition. A secondary purpose of the paper is to summarize a number of applications of the theory that have also appeared in the literature and show how they compare with an experiment.

Onsager's conjecture in bounded domains for the conservation of entropy and other companion laws

We show that weak solutions of general conservation laws in bounded domains conserve their generalized entropy, and other respective companion laws, if they possess a certain fractional differentiability of order one-third in the interior of the domain, and if the normal component of the corresponding fluxes tend to zero as one approaches the boundary. This extends various recent results of the authors.