Hairpin-like Structure Research Articles

Vortex-shedding modes of a pair of side-by-side thin pitching plates

We have conducted three-dimensional (3D) direct numerical simulations to analyze vortex-shedding modes past vertically arranged, side-by-side 3D pitching plates, considering cases where the plates are in the same, opposite, and different phases. The simulations are performed at a Reynolds number Re=1000, with a dimensionless pitching frequency St=1, and a maximum pitching angle θmax=15°. The vortex-shedding modes reveal horseshoe vortices transforming into distorted hairpin-like structures in the far wake for in-phase plates. Opposite phase plates exhibit helical distortion and core bifurcation, while different phase angles produce meridionally twisted, entangled hairpins. We observe a reverse von Kármán vortex street for in- and different-phase plates, while the opposite shows a reverse Kármán vortex street for the upper plate and a Kármán vortex street for the lower plate. The streakline visualizations reveal wake compression and spoke-like structures symmetrically emanating from the shear layer extremities around the plates' central region. We find leapfrog-like cross-stream vortex interaction when the plates are in phase. The line-time diagram reveals alternating patches of low-intensity cells, switching between negative and positive, alongside continuous bands of both positive and negative cells. Both plates produce similar thrust for the parameters examined in this study.

Statistics and evolution of Reynolds shear stress structure in cylinder-wake/boundary-layer interaction

The three-dimensional structures based on the quadrant classification of the tangential Reynolds stress (Qs), are studied in direct numerical simulations of cylinder-wake/boundary-layer interaction with a moderate gap ratio (G/D=1.0) and low or middle Reynolds numbers. In this paper, direct numerical simulations are performed using the immersed boundary lattice Boltzmann method (LBM). We utilize a three-dimensional clustering method to identify Reynolds shear stress structures (Qs-structures) associated with intense events. The kinematic characteristics of coherent structures are discussed through the statistical properties of Qs-structures. The spatial relationship of between vortex clusters and Qs-structures (mainly Q2-structures as well as Q4-structures) is explained by their evolution characteristics. The spatial distribution of Qs-structures, determined by the volume distribution of the minimum and maximum wall distances (ymin and ymax), are found to be similar to that of vortex clusters in the cylinder/wall interaction. In the near-wall statistical region, the secondary vortex clusters are surrounded by the parallel Q2 and Q4 pairs, and mostly lodged within the Q2. During the evolution process of coherent structures, the Q2-structures and the secondary vortex clusters developed into hairpin-like structures, respectively. The conditional average results demonstrated that the generated hairpin vortex structures are attributed to the momentum transfers.

Variation of vortical structures across shock-wave/turbulent boundary-layer interaction region in a compression ramp flow

This paper describes direct numerical simulations of a shock-wave/turbulent boundary-layer interaction (STBLI) process in a compression-ramp flow with a ramp angle of 24° and a free-stream Mach number of Ma∞=2.9. Spectral analysis, two-point cross correlation, convection velocity statistics, and individual vortex identification are used to elucidate the streamwise variation of multiscale turbulent structures in the STBLI process. Typical Lagrangian coherent structures in the turbulent boundary layer before the STBLI region are characterized as hairpin-like vortical structures, with heads that rise together with the separated mean flow in the STBLI region. In the downstream region, the reattached turbulent boundary layer has a two-layer structure. The outer layer is characterized as an intensification of large-scale velocity structures, which is attributed to the shock-wave-induced compression effect on vortical structures. A viscous-dominated layer develops independently in the vicinity of the wall, leading to a gradual restoration of the wall-shear effect that accumulates the inner-layer dynamics of small-to-moderate-scale turbulent motions.

Elimination of zero-repeat subunit in allergenic seed protein 13S globulin using the novel allele GlbNB2 in common buckwheat (Fagopyrum esculentum Moench)

Common buckwheat (Fagopyrum esculentum Moench) seeds contain 13S globulin, the zero-repeat subunit of which is trypsin-resistant and allergenic. Here, its two novel alleles were analyzed for development of hypoallergenic plants. The GlbNC allele has a Miniature Inverted-repeat Transposable Element (MITE)-like insertion in the 4th exon. However, most of the insertion was spliced-out, resulting in accumulation of zero-repeat subunit in GlbNC homozygotes. Meanwhile, the GlbNB2 has a 164-bp insertion in the 3rd exon, resulting in no accumulation of zero-repeat subunit in GlbNB2 homozygotes (NB2_homo). Both the insertion sequences were predicted to form a hairpin-like structure, and that of GlbNB2 was more rigid than that of GlbNC. Trypsin digestion in NB2_homo showed that the α polypeptide of Met-rich subunit is also hard to digest, that is a next target to eliminate for hypoallergenic buckwheat development.

Composition and Conformation of Hetero- versus Homo-Fluorinated Triazolamers Influence their Activity on Islet Amyloid Polypeptide Aggregation.

Novel fluorinated foldamers based on aminomethyl-1,4-triazolyl-difluoroacetic acid (1,4-Tz-CF2) units were synthesized and their conformational behaviour was studied by NMR and molecular dynamics. Their activity on the aggregation of the human islet amyloid polypeptide (hIAPP) amyloid protein was evaluated by fluorescence spectroscopy and mass spectrometry. The fluorine labelling of these foldamers allowed the analysis of their interaction with the target protein. We demonstrated that the preferred extended conformation of homotriazolamers of 1,4-Tz-CF2 unit increases the aggregation of hIAPP, while the hairpin-like conformation of more flexible heterotriazolamers containing two 1,4-Tz-CF2 units mixed with natural amino acids from the hIAPP sequence reduces it, and more efficiently than the parent natural peptide. The longer heterotriazolamers having three 1,4-Tz-CF2 units adopting more folded hairpin-like and ladder-like structures similar to short multi-stranded β-sheets have no effect. This work demonstrates that a good balance between the structuring and flexibility of these foldamers is necessary to allow efficient interaction with the target protein.

Adsorption Isotherm and Mechanism of Ca2+ Binding to Polyelectrolyte.

Polyelectrolytes, such as poly(acrylic acid) (PAA), can effectively mitigate CaCO3 scale formation. Despite their success as antiscalants, the underlying mechanism of binding of Ca2+ to polyelectrolyte chains remains unresolved. Through all-atom molecular dynamics simulations, we constructed an adsorption isotherm of Ca2+ binding to sodium polyacrylate (NaPAA) and investigated the associated binding mechanism. We find that the number of calcium ions adsorbed [Ca2+]ads to the polymer saturates at moderately high concentrations of free calcium ions [Ca2+]aq in the solution. This saturation value is intricately connected with the binding modes accessible to Ca2+ ions when they bind to the polyelectrolyte chain. We identify two dominant binding modes: the first involves binding to at most two carboxylate oxygens on a polyacrylate chain, and the second, termed the high binding mode, involves binding to four or more carboxylate oxygens. As the concentration of free calcium ions [Ca2+]aq increases from low to moderate levels, the polyelectrolyte chain undergoes a conformational transition from an extended coil to a hairpin-like structure, enhancing the accessibility to the high binding mode. At moderate concentrations of [Ca2+]aq, the high binding mode accounts for at least one-third of all binding events. The chain's conformational change and its consequent access to the high binding mode are found to increase the overall Ca2+ ion binding capacity of the polyelectrolyte chain.

Probing RNA structural landscapes across Candida yeast genomes.

Understanding the intricate roles of RNA molecules in virulence and host-pathogen interactions can provide valuable insights into combatting infections and improving human health. Although much progress has been achieved in understanding transcriptional regulation during host-pathogen interactions in diverse species, more is needed to know about the structure of pathogen RNAs. This is particularly true for fungal pathogens, including pathogenic yeasts of the Candida genus, which are the leading cause of hospital-acquired fungal infections. Our work addresses the gap between RNA structure and their biology by employing genome-wide structure probing to comprehensively explore the structural landscape of mRNAs and long non-coding RNAs (lncRNAs) in the four major Candida pathogens. Specifically focusing on mRNA, we observe a robust correlation between sequence conservation and structural characteristics in orthologous transcripts, significantly when sequence identity exceeds 50%, highlighting structural feature conservation among closely related species. We investigate the impact of single nucleotide polymorphisms (SNPs) on mRNA secondary structure. SNPs within 5' untranslated regions (UTRs) tend to occur in less structured positions, suggesting structural constraints influencing transcript regulation. Furthermore, we compare the structural properties of coding regions and UTRs, noting that coding regions are generally more structured than UTRs, consistent with similar trends in other species. Additionally, we provide the first experimental characterization of lncRNA structures in Candida species. Most lncRNAs form independent subdomains, similar to human lncRNAs. Notably, we identify hairpin-like structures in lncRNAs, a feature known to be functionally significant. Comparing hairpin prevalence between lncRNAs and protein-coding genes, we find enrichment in lncRNAs across Candida species, humans, and Arabidopsis thaliana, suggesting a conserved role for these structures. In summary, our study offers valuable insights into the interplay between RNA sequence, structure, and function in Candida pathogens, with implications for gene expression regulation and potential therapeutic strategies against Candida infections.

Boundary layer transition of hypersonic flow over a delta wing

Cross-flow transition over a delta wing is systematically studied in a Mach 6.5 hypersonic wind tunnel, employing the Rayleigh scattering flow visualisation, high-speed schlieren and fast-response pressure sensors. Direct numerical simulations and analysis based on linear stability theory under the same flow conditions are applied to analyse the transition mechanism. Three unstable modes are identified: the travelling cross-flow instabilities, the second mode and the low-frequency waves. It is shown that the travelling cross-flow vortices first appear in the cross-flow region near the leading edge of the model. These vortices can modulate the mean profile of the flow, which benefits the growth of second mode. A phase-locked interaction mechanism transfers energy from the cross-flow instabilities to the high-frequency second mode, leading to amplification at the expense of the cross-flow instability. As the second mode grows to a critical amplitude, it triggers a $z$ -type secondary instability within a similar frequency range, which introduces secondary finger-like structures connecting to the cross-flow vortex. It is further found that the generation of these finger-like structures is related to the expansion and compression of the second mode. These finger vortices further evolve along the streamwise direction into low-frequency waves and corresponding hairpin-like structures that finally trigger turbulence. An interaction mechanism likely exists between the secondary instability and the low-frequency waves, since their phase speeds are approaching each other. These observations of the interaction mechanism are consistent with those of previous studies on hypersonic boundary layers (Zhang et al., Phys. Fluids, vol. 32 (7), 2020, 071702; Li et al., Phys. Fluids, vol. 32 (5), 2020, 051701).

Flow transitions of head-on vortex ring collisions with contaminated air–water interfaces

An experimental study was conducted on head-on collisions of Re = 2000 and 4000 vortex rings upon air–water interfaces to study the vortex dynamics and the effects of different vortex ring Reynolds numbers on the key vortex flow mechanisms. Unfiltered tap water was used where surface contaminants were present; hence, the interfacial stress levels are lower but not entirely zero like an idealized free surface. Results demonstrate that the vortex dynamics involve first, the resulting secondary and tertiary vortex rings transitioning into wavy states, before their upper loops disconnect/reconnect to the interface to form U-shaped vortex loops along the inner and outer peripheries of the primary vortex ring, respectively, in an alternating pattern. Second, tertiary vortex loops entangle around the primary vortex ring to produce counter-rotating vortex pairs that reorganize themselves along the primary vortex ring outer periphery, between the primary vortex ring and secondary vortex loops, as well as hairpin-like structures that aid ejection of primary vortex ring momentum. Third, secondary vortex loops rotate toward the collision axis before their lower segments are entrained by the primary vortex ring. A higher Reynolds number primary vortex ring would confer additional flow changes, such as a higher wave number for the secondary and tertiary vortex rings/loops, pairings of secondary vortex loops “side-arms” that reduce their instances by about half and formations of Tsai–Widnall–Moore–Saffman instabilities induced by flow perturbations. Finally, vortex flow models proposed to explain the flow mechanism at different flow stages are found to be in good agreements with the experimental visualizations.

Evolutionary Spread of Distinct O-methyltransferases Guides the Discovery of Unique Isoaspartate-Containing Peptides, Pamtides.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse class of natural products with a distinct biosynthetic logic, the enzymatic modification of genetically encoded precursor peptides. Although their structural and biosynthetic diversity remains largely underexplored, the identification of novel subclasses with unique structural motifs and biosynthetic pathways is challenging. Here, it is reported that peptide/protein L-aspartyl O-methyltransferases (PAMTs) present in several RiPP subclasses are highly homologous. Importantly, it is discovered that the apparent evolutionary transmission of the PAMT gene to unrelated RiPP subclasses can serve as a basis to identify a novel RiPP subclass. Biochemical and structural analyses suggest that homologous PAMTs convert aspartate to isoaspartate via aspartyl-O-methyl ester and aspartimide intermediates, and often require cyclic or hairpin-like structures for modification. By conducting homology-based bioinformatic analysis of PAMTs, over 2,800 biosynthetic gene clusters (BGCs) are identified for known RiPP subclasses in which PAMTs install a secondary modification, and over 1,500 BGCs where PAMTs function as a primary modification enzyme, thereby defining a new RiPP subclass, named pamtides. The results suggest that the genome mining of proteins with secondary biosynthetic roles can be an effective strategy for discovering novel biosynthetic pathways of RiPPs through the principle of "guilt by association".

Structure and Conformation of Hydroxypropylmethyl Cellulose with a Wide Range of Molar Masses in Aqueous Solution─Effects of Hydroxypropyl Group Addition.

The structure of hydroxypropylmethyl cellulose (HpMC) samples with a wide range of weight average molar masses (Mw) from 23 to 5000 kg mol-1, a controlled degree of substitution (DS) of 1.9 by methyl groups, and a molar substitution number (MS) of 0.25 by hydroxypropyl groups dissolved in aqueous solution was examined using static light scattering (SLS), dynamic light scattering (DLS), small-to-wide angle neutron scattering (S-WANS) techniques, and intrinsic viscosity ([η]) measurements. The determined Mw and the radius of gyration (Rg) showed the relationships Rg ∝ Mw1.0 and [η] ∝ Mw1.7 in a range of Mw < 100 kg mol-1, similar to rigid rod molecules in solution. However, exponents in the relationships decreased gradually with increasing Mw and reached ∼0.5 in a high Mw region, which is a typical value of flexible chain molecules for both Rg and [η]. These observations suggest that the HpMC samples behave as semiflexible rods with a certain persistence length (lp). The ratios of the hydrodynamic radius via DLS measurements to Rg also supported semiflexible rod behavior. Particle form factors and the average lengths (L) resulting from SLS and S-WANS experiments are well described with rigid rod particles in the range of Mw < 100 kg mol-1 and semiflexible rods with lp ∼ 100 nm in Mw > 100 kg mol-1. Because the average contour length (lc) calculated from Mw is approximately twice as long as L in the Mw range < 100 kg mol-1, the formed HpMC particles possess a folded hairpin-like elongated rigid rod structure. However, the lc/L value increases gradually in the range Mw > 200 kg mol-1, where the formed HpMC particles behave as semiflexible rods. The formed particle structure was substantially different from that found in methyl cellulose samples with a similar DS value, which showed rod-like behavior over a wide Mw range. The addition of hydroxypropyl groups only at MS = 0.25 effectively changed the formed particle structure.

On the motion of hairpin filaments in the atmospheric boundary layer

A recent work of Harikrishnan et al. [“Geometry and organization of coherent structures in stably stratified atmospheric boundary layers,” arXiv:2110.02253 (2021)] has revealed an abundance of hairpin-like vortex structures, oriented in a similar direction, in the turbulent patches of a stably stratified Ekman flow. In this study, hairpin-like structures are investigated by treating them as slender vortex filaments, i.e., a vortex filament whose diameter d is small when compared to its radius of curvature R. The corrected thin-tube model of Klein and Knio [“Asymptotic vorticity structure and numerical simulation of slender vortex filaments,” J. Fluid Mech. 284, 275 (1995)] is used to compute the motion of these filaments with the atmospheric boundary layer as a background flow. Our results suggest that the orientation of the hairpin filament in the spanwise direction is linked to its initial starting height under stable stratification, whereas no such dependency can be observed with the neutrally stratified background flow. An improved feature tracking scheme based on spatial overlap for tracking Q-criterion vortex structures on the direct numerical simulation data is also developed. It overcomes the limitation of using a constant threshold in time by dynamically adjusting the thresholds to accommodate the growth or deterioration of a feature. A comparison between the feature tracking and the filament simulation reveals qualitatively similar temporal developments. Finally, an extension of the asymptotic analysis of Callegari and Ting [“Motion of a curved vortex filament with decaying vortical core and axial velocity,” J. Appl. Math. 35, 148–175 (1978)] is carried out to include the effect of gravity. The results show that, in the regime considered here, a contribution from the gravity term occurs only when the tail of an infinitely long filament is tilted at an angle relative to the wall.

Characteristics and causes of voltage observed at the current feeder of high-temperature superconducting WISE conductor

The HTS (high-temperature superconducting) conductor is a feasible candidate for constructing magnets for next-generation fusion devices because of its higher critical current in a high magnetic field. A new concept of the HTS-WISE (Wound and Impregnated Stacked Elastic tapes) conductor has been studied aiming to apply the fusion reactor magnet. Here, the WISE-U conductor is composed of stacked thirty REBCO tapes (10 mm width, 65 μm thickness, I c = 370 A @77 K, s.f.) wrapped by a stainless-steel coil tube which is inserted into the metal pipe. The 4 m-long REBCO tapes are folded with a radius of curvature of 35 mm in a hairpin-like structure. A low-melting-point metal U-Alloy 60 whose melting point is 60°C is poured into the pipe for impregnation to make the non-insulation conductor. The REBCO tapes and the current feeder made of oxygen-free copper were also impregnated with the U-Alloy 60 to connect. This fabrication method has the advantage of being easier to fabricate than the technique of connecting each tape using indium foil. The energization test results showed that a maximum current value of 16.9 kA was recorded at B = 5 T and T = 30 K, however, a burnout occurred in the current feeder before the critical current was determined. Then, the improved WISE conductor has been designed and tested which showed a maximum of 19kA was reached in the self-field and 20K. However, burnout still occurred in the current feeder section. In those experiments, the superconducting section has not been damaged at all. If this burnout had been avoided, a higher current-carrying capacity could have been obtained. Identifying the cause of burnout and improving the current feeder is required.

Hairpin-like structure and Jahn–Teller distortions in adenosine monophosphate copper coordination polymers: synthesis and chirality

Hairpin-like structure and Jahn–Teller distortions in adenosine monophosphate copper coordination polymers: synthesis and chirality

Gallocin A, an Atypical Two-Peptide Bacteriocin with Intramolecular Disulfide Bonds Required for Activity.

Streptococcus gallolyticus subsp. gallolyticus (SGG) is an opportunistic gut pathogen associated with colorectal cancer. We previously showed that colonization of the murine colon by SGG in tumoral conditions was strongly enhanced by the production of gallocin A, a two-peptide bacteriocin. Here, we aimed to characterize the mechanisms of its action and resistance. Using a genetic approach, we demonstrated that gallocin A is composed of two peptides, GllA1 and GllA2, which are inactive alone and act together to kill "target" bacteria. We showed that gallocin A can kill phylogenetically close relatives of the pathogen. Importantly, we demonstrated that gallocin A peptides can insert themselves into membranes and permeabilize lipid bilayer vesicles. Next, we showed that the third gene of the gallocin A operon, gip, is necessary and sufficient to confer immunity to gallocin A. Structural modeling of GllA1 and GllA2 mature peptides suggested that both peptides form alpha-helical hairpins stabilized by intramolecular disulfide bridges. The presence of a disulfide bond in GllA1 and GllA2 was confirmed experimentally. Addition of disulfide-reducing agents abrogated gallocin A activity. Likewise, deletion of a gene encoding a surface protein with a thioredoxin-like domain impaired the ability of gallocin A to kill Enterococcus faecalis. Structural modeling of GIP revealed a hairpin-like structure strongly resembling those of the GllA1 and GllA2 mature peptides, suggesting a mechanism of immunity by competition with GllA1/2. Finally, identification of other class IIb bacteriocins exhibiting a similar alpha-helical hairpin fold stabilized with an intramolecular disulfide bridge suggests the existence of a new subclass of class IIb bacteriocins. IMPORTANCE Streptococcus gallolyticus subsp. gallolyticus (SGG), previously named Streptococcus bovis biotype I, is an opportunistic pathogen responsible for invasive infections (septicemia, endocarditis) in elderly people and is often associated with colon tumors. SGG is one of the first bacteria to be associated with the occurrence of colorectal cancer in humans. Previously, we showed that tumor-associated conditions in the colon provide SGG with an ideal environment to proliferate at the expense of phylogenetically and metabolically closely related commensal bacteria such as enterococci (1). SGG takes advantage of CRC-associated conditions to outcompete and substitute commensal members of the gut microbiota using a specific bacteriocin named gallocin, recently renamed gallocin A following the discovery of gallocin D in a peculiar SGG isolate. Here, we showed that gallocin A is a two-peptide bacteriocin and that both GllA1 and GllA2 peptides are required for antimicrobial activity. Gallocin A was shown to permeabilize bacterial membranes and kill phylogenetically closely related bacteria such as most streptococci, lactococci, and enterococci, probably through membrane pore formation. GllA1 and GllA2 secreted peptides are unusually long (42 and 60 amino acids long) and have very few charged amino acids compared to well-known class IIb bacteriocins. In silico modeling revealed that both GllA1 and GllA2 exhibit a similar hairpin-like conformation stabilized by an intramolecular disulfide bond. We also showed that the GIP immunity peptide forms a hairpin-like structure similar to GllA1/GllA2. Thus, we hypothesize that GIP blocks the formation of the GllA1/GllA2 complex by interacting with GllA1 or GllA2. Gallocin A may constitute the first class IIb bacteriocin which displays disulfide bridges important for its structure and activity and might be the founding member of a subtype of class IIb bacteriocins.

An enzyme-responsive electrochemical DNA biosensor achieving various dynamic range by using only-one immobilization probe

Developing a simple and easy-to-operate biosensor with tunable dynamic range would provide enormous opportunities to promote the diagnostic applications. Herein, an enzyme-responsive electrochemical DNA biosensor is developed by using only-one immobilization probe. The immobilization probe was designed with a two-loop hairpin-like structure that contained the mutually independent target recognition and enzyme (EcoRI restriction endonuclease) responsive domains. The target recognition was based on a toehold-mediated strand displacement reaction strategy. The toehold region was initially caged in the loop of the immobilization probe and showed a relatively low binding affinity with target, which was improved via EcoRI cleavage of immobilization probe to liberate the toehold region. The EcoRI cleavage operation for immobilization probe demonstrated the well regulation ability in detection performance. It showed a largely extended dynamic range, a significantly lowered detection limit and better discrimination ability toward the mismatched sequences whether in two buffers (with high or low salt concentrations) or in the serum system. The advantages also includes simplicity in probe design, and facile biosensor fabrication and operation. It thus opens a new avenue for the development of the modulated DNA biosensor and hold a great potential for the diagnostic applications and drug monitoring.

Direct numerical simulations of turbulent jets: vortex–interface–surfactant interactions

We study the effect of insoluble surfactants on the spatio-temporal evolution of turbulent jets. We use three-dimensional numerical simulations and employ an interface-tracking/level-set method that accounts for surfactant-induced Marangoni stresses. The present study builds on our previous work (Constante-Amores et al., J. Fluid Mech., vol. 922, 2021, A6) in which we examined in detail the vortex–surface interaction in the absence of surfactants. Numerical solutions are obtained for a wide range of Weber and elasticity numbers in which vorticity production is generated by surface deformation and surfactant-induced Marangoni stresses. The present work demonstrates, for the first time, the crucial role of Marangoni stresses, brought about by surfactant concentration gradients, in the formation of coherent, hairpin-like vortex structures. These structures have a profound influence on the development of the three-dimensional interfacial dynamics. We also present theoretical expressions for the mechanisms that influence the rate of production of circulation in the presence of surfactants for a general, three-dimensional, two-phase flow, and highlight the dominant contribution of surfactant-induced Marangoni stresses.

The unsteady wake transition behind a wall-mounted large-depth-ratio prism

The wake of a long rectangular wall-mounted prism is investigated at Reynolds numbers of $Re=250\unicode{x2013}1200$ by directly solving the Navier–Stokes equations. The aim of this study was to examine the unsteady transition mechanism in the wake of a large-depth-ratio (streamwise length to width) prism as well as to characterize the unsteady wake evolution at low Reynolds numbers. The results highlighted that increasing Reynolds number significantly altered the dominance of upwash and downwash flows in the time-averaged flow and changed the characteristics of coherent structures, including their size, dominant frequency and interaction with other structures in the flow. The wake is, therefore, categorized into three regimes within the transition process: steady regime at $Re \leq 625$ , regular unsteady regime at $625 &lt; Re &lt; 750$ and irregular unsteady regime at $Re \geq 750$ . Particularly, the wake started to exhibit unsteady features at $Re=625\unicode{x2013}650$ , which transitioned to an early irregular unsteady wake topology at $Re=750$ . At $Re \geq 675$ , horseshoe vortices transformed to vortex loops. There were hairpin-like structures formed on the upper and side faces of the long prism. The results further indicated that the transition to unsteadiness is attributed to separated leading-edge shear-layer instabilities and interactions of the shear layer with the horseshoe structures. The wake was more complex due to the interactions of multiple coherent structures in the flow, which resulted in a multiple-periodicity wake system. A skeleton model is proposed for a large-depth-ratio prism, to incorporate details of the unsteady flow features and specify various flow coherent structures at low Reynolds numbers.

Is the Intergenic Region of Aedes aegypti Totivirus a Recombination Hotspot?

The genus totivirus in the family Totiviridae contains double-stranded RNA viruses. Their genome has two open reading frames (ORFs) that encode capsid protein (CP) and RNA-dependent RNA polymerase (RdRp). The toti-like viruses recently identified in Anopheles sp. and Aedes aegypti mosquitoes (AaTV) share the same genome organization as other totiviruses. The AaTVs that have been described in distinct geographical regions are monophyletic. In this study, we show that AaTV sequences can be grouped into at least three phylogenetic clades (named A, B, and C). Clades A and B are composed of AaTV sequences from mosquitoes collected in the Caribbean region (Guadeloupe), and clade C contains sequences from the USA. These clades may represent AaTV lineages that are locally adapted to their host populations. We also identified three recombinant AaTV strains circulating in mosquitoes in Guadeloupe. Although these strains have different chimeric patterns, the position of the recombination breakpoint was identical in all strains. Interestingly, this breakpoint is located in a hairpin-like structure in the intergenic region of the AaTV genome. This RNA structure may stall RNA polymerase processivity and consequently induce template switching. In vitro studies should be conducted to further investigate the biological significance of AaTV's intergenic region as a recombination hotspot.

The evolution of coherent vortical structures in increasingly turbulent stratified shear layers

We study the morphology of Eulerian vortical structures and their interaction with density interfaces in increasingly turbulent stably stratified shear layers. We analyse the three-dimensional, simultaneous velocity and density fields obtained in the stratified inclined duct laboratory experiment (SID). We track, across 15 datasets, the evolution of coherent structures from pre-turbulent Holmboe waves, through intermittent turbulence, to full turbulence and mixing. We use the rortex–shear decomposition of the local vorticity vectors into a rortex vector capturing rigid-body rotation and a shear vector. We describe the morphology of ubiquitous hairpin-like vortical structures (revealed by the rortex), similar to those commonly observed in boundary-layer turbulence. These are born as relatively weak vortices around the strong three-dimensional shearing structures of confined Holmboe waves, and gradually strengthen and deform under increasing turbulence, transforming into pairs of upward- and downward-pointing hairpins propagating in opposite directions on the top and bottom edge of the shear layer. The pair of legs for each hairpin are counter-rotating and entrain fluid laterally and vertically, whereas their arched-up ‘heads’, which are transverse vortices, entrain fluid vertically. We then elucidate how this large-scale vortex morphology stirs and mixes the density field. Essentially, vortices located at the sharp density interface on either edge of the mixing layer (mostly hairpin heads) engulf blobs of unmixed fluid into the mixing layer, whereas vortices inside the mixing layer (mostly hairpin legs) further stir it, generating strong, small-scale shear, enhancing mixing. These findings provide new insights into the role of turbulent coherent structures in shear-driven stratified mixing.