Drosophila melanogaster Transcriptome Response to Different Wolbachia Strains.

Wolbachia is a maternally inherited, intercellular bacterial symbiont of insects and some other invertebrates. Here, we investigated the effect of two different Wolbachia strains, differing in a large chromosomal inversion, on the differential expression of genes in D. melanogaster females. We revealed significant changes in the transcriptome of the infected flies compared to the uninfected ones, as well as in the transcriptome of flies infected with the Wolbachia strain, wMelPlus, compared to flies infected with the wMelCS112 strain. We linked differentially expressed genes (DEGs) from two pairwise comparisons, "uninfected-wMelPlus-infected" and "uninfected-wMelCS112-infected", into two gene networks, in which the following functional groups were designated: "Proteolysis", "Carbohydrate transport and metabolism", "Oxidation-reduction process", "Embryogenesis", "Transmembrane transport", "Response to stress" and "Alkaline phosphatases". Our data emphasized similarities and differences between infections by different strains under study: a wMelPlus infection results in more than double the number of upregulated DEGs and half the number of downregulated DEGs compared to a wMelCS112 infection. Thus, we demonstrated that Wolbachia made a significant contribution to differential expression of host genes and that the bacterial genotype plays a vital role in establishing the character of this contribution.

Wolbachia Effect on Drosophila melanogaster Lipid and Carbohydrate Metabolism.

The effect of maternally inherited endosymbiotic bacteria Wolbachia on triglyceride and carbohydrate metabolism, starvation resistance and feeding behavior of Drosophila melanogaster females was studied. Eight D. melanogaster lines of the same nuclear background were investigated; one had no infection and served as the control, and seven others were infected with different Wolbachia strains pertaining to wMel and wMelCS groups of genotypes. Most of the infected lines had a higher overall lipid content and triglyceride level than the control line and their expression of the bmm gene regulating triglyceride catabolism was reduced. The glucose content was higher in the infected lines compared to that in the control, while their trehalose levels were similar. It was also found that the Wolbachia infection reduced the level of tps1 gene expression (coding for enzyme for trehalose synthesis from glucose) and had no effect on treh gene expression (coding for trehalose degradation enzyme). The infected lines exhibited lower appetite but higher survival under starvation compared to the control. The data obtained may indicate that Wolbachia foster their hosts' energy exchange through increasing its lipid storage and glucose content to ensure the host's competitive advantage over uninfected individuals. The scheme of carbohydrate and lipid metabolism regulation under Wolbachia's influence was suggested.

New Wolbachia pipientis Genotype Increasing Heat Stress Resistance of Drosophila melanogaster Host Is Characterized by a Large Chromosomal Inversion.

The maternally transmitted endocellular bacteria Wolbachia is a well-known symbiont of insects, demonstrating both negative and positive effects on host fitness. The previously found Wolbachia strain wMelPlus is characterized by a positive effect on the stress-resistance of its host Drosophila melanogaster, under heat stress conditions. This investigation is dedicated to studying the genomic underpinnings of such an effect. We sequenced two closely related Wolbachia strains, wMelPlus and wMelCS112, assembled their complete genomes, and performed comparative genomic analysis engaging available Wolbachia genomes from the wMel and wMelCS groups. Despite the two strains under study sharing very close gene-composition, we discovered a large (>1/6 of total genome) chromosomal inversion in wMelPlus, spanning through the region that includes the area of the inversion earlier found in the wMel group of Wolbachia genotypes. A number of genes in unique inversion blocks of wMelPlus were identified that might be involved in the induction of a stress-resistant phenotype in the host. We hypothesize that such an inversion could rearrange established genetic regulatory-networks, causing the observed effects of such a complex fly phenotype as a modulation of heat stress resistance. Based on our findings, we propose that wMelPlus be distinguished as a separate genotype of the wMelCS group, named wMelCS3.

Easy and Effective Method for Extracting and Purifying Wolbachia Genomic DNA.

A number of methods for extracting the DNA of maternally inherited obligate intracellular bacteria Wolbachia from an insect host and its subsequent purification have been described in previous scholarship. As Wolbachia is present in the hosts' organisms in rather low quantities, these techniques used to be quite labor-intensive. For this paper, we analyzed them in detail, searched for a possibility to simplify and accelerate the protocol, and proposed an easy and effective method for isolating Wolbachia DNA from Drosophila melanogaster with a purity sufficient for genomic sequencing. Our method involves the centrifugation of homogenized flies or just their ovaries, as the most Wolbachia-enriched tissue, followed by the filtration of homogenate and extraction of DNA using a modified version of the Livak buffer protocol. The proportion of Wolbachia DNA in the total DNA was quantified based on the results of sequencing with the use of the Illumina MiSeq platform and a pipeline of bioinformatic analysis. For the two analyzed D. melanogaster lines infected with two different Wolbachia strains, the proportion was at least 68 and 94%, respectively.

Aspect Ratio Dependence of Heat Transfer in a Cylindrical Rayleigh-Bénard Cell.

While the heat transfer and the flow dynamics in a cylindrical Rayleigh-Bénard (RB) cell are rather independent of the aspect ratio Γ (diameter/height) for large Γ, a small-Γ cell considerably stabilizes the flow and thus affects the heat transfer. Here, we first theoretically and numerically show that the critical Rayleigh number for the onset of convection at given Γ follows Ra_{c,Γ}∼Ra_{c,∞}(1+CΓ^{-2})^{2}, with C≲1.49 for Oberbeck-Boussinesq (OB) conditions. We then show that, in a broad aspect ratio range (1/32)≤Γ≤32, the rescaling Ra→Ra_{ℓ}≡Ra[Γ^{2}/(C+Γ^{2})]^{3/2} collapses various OB numerical and almost-OB experimental heat transport data Nu(Ra,Γ). Our findings predict the Γ dependence of the onset of the ultimate regime Ra_{u,Γ}∼[Γ^{2}/(C+Γ^{2})]^{-3/2} in the OB case. This prediction is consistent with almost-OB experimental results (which only exist for Γ=1, 1/2, and 1/3) for the transition in OB RB convection and explains why, in small-Γ cells, much larger Ra (namely, by a factor Γ^{-3}) must be achieved to observe the ultimate regime.

Periodically Modulated Thermal Convection.

Many natural and industrial turbulent flows are subjected to time-dependent boundary conditions. Despite being ubiquitous, the influence of temporal modulations (with frequency f) on global transport properties has hardly been studied. Here, we perform numerical simulations of Rayleigh-Bénard convection with time periodic modulation in the temperature boundary condition and report how this modulation can lead to a significant heat flux (Nusselt number Nu) enhancement. Using the concept of Stokes thermal boundary layer, we can explain the onset frequency of the Nu enhancement and the optimal frequency at which Nu is maximal, and how they depend on the Rayleigh number Ra and Prandtl number Pr. From this, we construct a phase diagram in the 3D parameter space (f, Ra, Pr) and identify the following: (i) a regime where the modulation is too fast to affect Nu; (ii) a moderate modulation regime, where Nu increases with decreasing f, and (iii) slow modulation regime, where Nu decreases with further decreasing f. Our findings provide a framework to study other types of turbulent flows with time-dependent forcing.

Multiple States in Turbulent Large-Aspect-Ratio Thermal Convection: What Determines the Number of Convection Rolls?

Wall-bounded turbulent flows can take different statistically stationary turbulent states, with different transport properties, even for the very same values of the control parameters. What state the system takes depends on the initial conditions. Here we analyze the multiple states in large-aspect ratio (Γ) two-dimensional turbulent Rayleigh-Bénard flow with no-slip plates and horizontally periodic boundary conditions as model system. We determine the number n of convection rolls, their mean aspect ratios Γ_{r}=Γ/n, and the corresponding transport properties of the flow (i.e., the Nusselt number Nu), as function of the control parameters Rayleigh (Ra) and Prandtl number. The effective scaling exponent ß in Nu∼Ra^{ß} is found to depend on the realized state and thus Γ_{r}, with a larger value for the smaller Γ_{r}. By making use of a generalized Friedrichs inequality, we show that the elliptical shape of the rolls and viscous damping determine the Γ_{r} window for the realizable turbulent states. The theoretical results are in excellent agreement with our numerical finding 2/3≤Γ_{r}≤4/3, where the lower threshold is approached for the larger Ra. Finally, we show that the theoretical approach to frame Γ_{r} also works for free-slip boundary conditions.

Elliptical Instability and Multiple-Roll Flow Modes of the Large-Scale Circulation in Confined Turbulent Rayleigh-Bénard Convection.

The large-scale circulation (LSC) of fluid is one of the main concepts in turbulent thermal convection as it is known to be important in global heat and mass transport in the system. In turbulent Rayleigh-Bénard convection (RBC) in slender containers, the LSC is formed of several dynamically changing convective rolls that are stacked on top of each other. The present study reveals the following two important facts: (i) the mechanism which causes the twisting and breaking of a single-roll LSC into multiple rolls is the elliptical instability and (ii) the heat and momentum transport in RBC, represented by the Nusselt (Nu) and Reynolds (Re) numbers, is always stronger (weaker) for smaller (larger) number n of the rolls in the LSC structure. Direct numerical simulations support the findings for n=1,…,4 and the diameter-to-height aspect ratio of the cylindrical container Γ=1/5, the Prandtl number Pr=0.1 and Rayleigh number Ra=5×10^{5}. Thus, Nu and Re are, respectively, 2.5 and 1.5 times larger for a single-roll LSC (n=1) than for a LSC with n=4 rolls.

Boundary Zonal Flow in Rotating Turbulent Rayleigh-Bénard Convection.

For rapidly rotating turbulent Rayleigh-Bénard convection in a slender cylindrical cell, experiments and direct numerical simulations reveal a boundary zonal flow (BZF) that replaces the classical large-scale circulation. The BZF is located near the vertical side wall and enables enhanced heat transport there. Although the azimuthal velocity of the BZF is cyclonic (in the rotating frame), the temperature is an anticyclonic traveling wave of mode one, whose signature is a bimodal temperature distribution near the radial boundary. The BZF width is found to scale like Ra^{1/4}Ek^{2/3} where the Ekman number Ek decreases with increasing rotation rate.

Momentum and heat transport scalings in laminar vertical convection.

We derive the dependence of the Reynolds number Re and the Nusselt number Nu on the Rayleigh number Ra and the Prandtl number Pr in laminar vertical convection (VC), where a fluid is confined between two differently heated isothermal vertical walls. The boundary layer equations in laminar VC yield two limiting scaling regimes: Nu∼Pr^{1/4}Ra^{1/4}, Re∼Pr^{-1/2}Ra^{1/2} for Pr≪1 and Nu∼Pr^{0}Ra^{1/4}, Re∼Pr^{-1}Ra^{1/2} for Pr≫1. These theoretical results are in excellent agreement with direct numerical simulations for Ra from 10^{5} to 10^{10} and Pr from 10^{-2} to 30. The transition between the regimes takes place for Pr around 10^{-1}.

Prandtl-Number Dependence of Heat Transport in Laminar Horizontal Convection.

We report the Prandtl-number (Pr) and Rayleigh-number (Ra) dependencies of the Reynolds number (Re) and mean convective heat transport, measured by the Nusselt number (Nu), in horizontal convection (HC) systems, where the heat supply and removal are provided exclusively through a lower horizontal surface of a fluid layer. For laminar HC, we find that Re∼Ra^{2/5}Pr^{-4/5}, Nu∼Ra^{1/5}Pr^{1/10} with a transition to Re∼Ra^{1/2}Pr^{-1}, Nu∼Ra^{1/4}Pr^{0} for large Pr. The results are based on direct numerical simulations for Ra from 3×10^{8} to 5×10^{10} and Pr from 0.05 to 50 and are explained by applying the Grossmann-Lohse approach [J. Fluid Mech. 407, 27 (2000)] transferred from the case of Rayleigh-Bénard convection to the case of laminar HC.

Thermal boundary layer equation for turbulent Rayleigh-Bénard convection.

We report a new thermal boundary layer equation for turbulent Rayleigh-Bénard convection for Prandtl number Pr>1 that takes into account the effect of turbulent fluctuations. These fluctuations are neglected in existing equations, which are based on steady-state and laminar assumptions. Using this new equation, we derive analytically the mean temperature profiles in two limits: (a) Pr≳1 and (b) Pr≫1. These two theoretical predictions are in excellent agreement with the results of our direct numerical simulations for Pr=4.38 (water) and Pr=2547.9 (glycerol), respectively.

Influence of the angle between the wind and the isothermal surfaces on the boundary layer structures in turbulent thermal convection.

We derive the asymptotes for the ratio of the thermal to viscous boundary layer thicknesses for infinite and infinitesimal Prandtl numbers Pr as functions of the angle ß between the large-scale circulation and an isothermal heated or cooled surface for the case of turbulent thermal convection with laminar-like boundary layers. For this purpose, we apply the Falkner-Skan ansatz, which is a generalization of the Prandtl-Blasius one to a nonhorizontal free-stream flow above the viscous boundary layer. Based on our direct numerical simulations (DNS) of turbulent Rayleigh-Bénard convection for Pr=0.1, 1, and 10 and moderate Rayleigh numbers up to 108 we evaluate the value of ß that is found to be around 0.7π for all investigated cases. Our theoretical predictions for the boundary layer thicknesses for this ß and the considered Pr are in good agreement with the DNS results.