Rewiring of the Fruit Metabolome in Tomato Breeding.

Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how breeding globally altered fruit metabolite content. Selection for alleles of genes associated with larger fruits altered metabolite profiles as a consequence of linkage with nearby genes. Selection of five major loci reduced the accumulation of anti-nutritional steroidal glycoalkaloids in ripened fruits, rendering the fruit more edible. Breeding for pink tomatoes modified the content of over 100 metabolites. The introgression of resistance genes from wild relatives in cultivars also resulted in major and unexpected metabolic changes. The study reveals a multi-omics view of the metabolic breeding history of tomato, as well as provides insights into metabolome-assisted breeding and plant biology.

(ADP-ribosyl)hydrolases: structure, function, and biology.

ADP-ribosylation is an intricate and versatile posttranslational modification involved in the regulation of a vast variety of cellular processes in all kingdoms of life. Its complexity derives from the varied range of different chemical linkages, including to several amino acid side chains as well as nucleic acids termini and bases, it can adopt. In this review, we provide an overview of the different families of (ADP-ribosyl)hydrolases. We discuss their molecular functions, physiological roles, and influence on human health and disease. Together, the accumulated data support the increasingly compelling view that (ADP-ribosyl)hydrolases are a vital element within ADP-ribosyl signaling pathways and they hold the potential for novel therapeutic approaches as well as a deeper understanding of ADP-ribosylation as a whole.

Emergence of threefold symmetric helical photocurrents in epitaxial low twinned Bi2Se3.

We present evidence of a strong circular photon drag effect (PDE) in topological insulators (TIs) through the observation of helicity-dependent topological photocurrents with threefold rotational symmetry using THz spectroscopy in epitaxially-grown Bi2Se3 with reduced crystallographic twinning. We establish how twinned domains introduce competing nonlinear optical (NLO) responses inherent to the crystal structure that obscure geometry-sensitive optical processes through the introduction of a spurious mirror symmetry. Minimizing the twinning defect reveals strong NLO response currents whose magnitude and direction depend on the alignment of the excitation to the crystal axes and follow the threefold rotational symmetry of the crystal. Notably, photocurrents arising from helical light reverse direction for left/right circular polarizations and maintain a strong azimuthal dependence-a result uniquely attributable to the circular PDE, where the photon momentum acts as an applied in-plane field stationary in the laboratory frame. Our results demonstrate new levels of control over the magnitude and direction of photocurrents in TIs and that the study of single-domain films is crucial to reveal hidden phenomena that couple topological order and crystal symmetries.

A single parameter can predict surfactant impairment of superhydrophobic drag reduction.

Recent experimental and computational investigations have shown that trace amounts of surfactants, unavoidable in practice, can critically impair the drag reduction of superhydrophobic surfaces (SHSs), by inducing Marangoni stresses at the air-liquid interface. However, predictive models for realistic SHS geometries do not yet exist, which has limited the understanding and mitigation of these adverse surfactant effects. To address this issue, we derive a model for laminar, three-dimensional flow over SHS gratings as a function of geometry and soluble surfactant properties, which together encompass 10 dimensionless groups. We establish that the grating length g is the key geometric parameter and predict that the ratio between actual and surfactant-free slip increases with g2. Guided by our model, we perform synergistic numerical simulations and microfluidic experiments, finding good agreement with the theory as we vary surfactant type and SHS geometry. Our model also enables the estimation, based on velocity measurements, of a priori unknown properties of surfactants inherently present in microfluidic systems. For SHSs, we show that surfactant effects can be predicted by a single parameter, representing the ratio between the grating length and the interface length scale beyond which the flow mobilizes the air-water interface. This mobilization length is more sensitive to the surfactant chemistry than to its concentration, such that even trace-level contaminants may significantly increase drag if they are highly surface active. These findings advance the fundamental understanding of realistic interfacial flows and provide practical strategies to maximize superhydrophobic drag reduction.

The genomics of linkage drag in inbred lines of sunflower.

Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here, we analyzed the genomic and phenotypic impacts of wild introgressions in inbred lines of cultivated sunflower to estimate the impacts of linkage drag. First, we generated reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge-regression best linear unbiased prediction (BLUP) model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including >3,000 new genes. While introgressions reduced genetic load at protein-coding sequences, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low-frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.

Self-propulsion via slipping: Frictional swimming in multilegged locomotors.

Locomotion is typically studied either in continuous media where bodies and legs experience forces generated by the flowing medium or on solid substrates dominated by friction. In the former, centralized whole-body coordination is believed to facilitate appropriate slipping through the medium for propulsion. In the latter, slip is often assumed minimal and thus avoided via decentralized control schemes. We find in laboratory experiments that terrestrial locomotion of a meter-scale multisegmented/legged robophysical model resembles undulatory fluid swimming. Experiments varying waves of leg stepping and body bending reveal how these parameters result in effective terrestrial locomotion despite seemingly ineffective isotropic frictional contacts. Dissipation dominates over inertial effects in this macroscopic-scaled regime, resulting in essentially geometric locomotion on land akin to microscopic-scale swimming in fluids. Theoretical analysis demonstrates that the high-dimensional multisegmented/legged dynamics can be simplified to a centralized low-dimensional model, which reveals an effective resistive force theory with an acquired viscous drag anisotropy. We extend our low-dimensional, geometric analysis to illustrate how body undulation can aid performance in non-flat obstacle-rich terrains and also use the scheme to quantitatively model how body undulation affects performance of biological centipede locomotion (the desert centipede Scolopendra polymorpha) moving at relatively high speeds (∼0.5 body lengths/sec). Our results could facilitate control of multilegged robots in complex terradynamic scenarios.

Ultrahigh efficient emulsification with drag-reducing liquid gating interfacial behavior.

Emulsification is a crucial technique for mixing immiscible liquids into droplets in numerous areas ranging from food to medicine to chemical synthesis. Commercial emulsification methods are promising for high production, but suffer from high energy input. Here, we report a very simple and scalable emulsification method that employs the drag-reducing liquid gating structure to create a smooth liquid-liquid interface for the reduction of resistance and tunable generation of droplets with good uniformity. Theoretical modeling and experimental results demonstrate that our method exhibits ultrahigh efficiency, which can reach up to more than 4 orders of magnitude greater energy-saving compared to commercial methods. For temperature-sensitive biological components, such as enzymes, proteins, and bacteria, it can offer a comfortable environment to avoid exposure to high temperatures during emulsifying, and the interface also enables the suppression of fouling. This unique drag-reducing liquid gating interfacial emulsification mechanism promotes the efficiency of droplet generation and provides fresh insight into the innovation of emulsifications that can be applied in many fields, including the food industry, the daily chemical industry, biomedicine, material fabrication, the petrochemical industry, and beyond.

Phonon drag thermal Hall effect in metallic strontium titanate.

SrTiO3, a quantum paralectric, displays a detectable phonon thermal Hall effect (THE). Here, we show that the amplitude of the THE is extremely sensitive to stoichiometry. It drastically decreases upon substitution of a tiny fraction of Sr atoms with Ca, which stabilizes the ferroelectric order. It drastically increases by an even lower density of oxygen vacancies, which turn the system to a dilute metal. The enhancement in the metallic state exceeds by far the sum of the electronic and the phononic contributions. We explain this observation as an outcome of three features: 1) Heat is mostly transported by phonons; 2) the electronic Hall angle is extremely large; and 3) there is substantial momentum exchange between electrons and phonons. Starting from Herring's picture of phonon drag, we arrive to a quantitative account of the enhanced THE. Thus, phonon drag, hitherto detected as an amplifier of thermoelectric coefficients, can generate a purely thermal transverse response in a dilute metal with a large Hall angle. Our results reveal a hitherto-unknown consequence of momentum-conserving collisions between electrons and phonons.

Electron Drag Effect on Thermal Conductivity in Two-Dimensional Semiconductors.

Two-dimensional (2D) materials have shown great potential in applications as transistors, where thermal dissipation becomes crucial because of the increasing energy density. Although the thermal conductivity of 2D materials has been extensively studied, interactions between nonequilibrium electrons and phonons, which can be strong when high electric fields and heat current coexist, are not considered. In this work, we systematically study the electron drag effect, where nonequilibrium electrons impart momenta to phonons and influence the thermal conductivity, in 2D semiconductors using ab initio simulations. We find that, at room temperature, electron drag can significantly increase thermal conductivity by decreasing phonon-electron scattering in 2D semiconductors while its impact in three-dimensional semiconductors is negligible. We attribute this difference to the large electron-phonon scattering phase space and larger contribution to thermal conductivity by drag-active phonons. Our work elucidates the fundamental physics underlying coupled electron-phonon transport in materials of various dimensionalities.

Assessing the Settling Velocity of Biofilm-Encrusted Microplastics: Accounting for Biofilms as an Equivalent to Surface Roughness.

While it is well established that a biofilm contributes to the sinking of plastics, the underlying mechanisms of how it influences the vertical transport of plastics have not been well explained. In this context, our study dives into the intricate effects of biofouling on the settling velocity (Ws) of microplastics (MPs) within the fluid. We adopt the perspective that the biofilm is a form of surface roughness impacting the drag coefficient (Cd) and vertical settling of MPs. By advancing the biofouling process model, we simulate the temporal variations of density and biofilm thickness of biofouled floating MPs, accounting for realistic parameters and assuming a layer-by-layer growth of biofilm on plastisphere surfaces. MPs of polyethylene (PE) exhibit a quicker initiation of descent compared to their polypropylene (PP) counterparts. Furthermore, leveraging computational fluid dynamics (CFD) simulation, the method to predict the Cd of spherical MPs with surface roughness is established. By treating the thickness of the biofilm as roughness height, an explicit method to predict the Ws of biofouled MPs is derived. The settling experiments for biofouled MPs conducted not only support the combination of the biofouling model and the explicit method to predict the Ws of biofouled MPs but also enhance the prediction accuracy by introducing a ratio parameter Co to better relate the equivalent surface roughness height (k) to the biofilm thickness (σ), i.e., k = Co·σ, where the recommended value of Co for spherical PP and PE MPs is between 0.5 to 0.8. This study, thus, provides new insights into the dynamics of biofouled MPs in hydraulic ecosystems.

In memory of Kelvin Kiptum: a reflection on his record-breaking marathon and the future outlook for a sub 2-h race from a drafting perspective.

BACKGROUND: Drafting is a common technique to reduce the drag experienced by elite runners on races, leading to faster finish times. The tactic has been successfully used in previous marathon world records. In the 2023 Chicago Marathon, Kenyan runner Kelvin Kiptum broke the marathon record after a 2:00:35 finish. This feat is impressive considering the lack of use of drafting, despite the availability of two pacers for the majority of the race. METHODS: In this study, the drag faced by Kiptum and his pacers during the race is calculated by means of computational fluid dynamics (CFD). The performance of each runner is evaluated from an energetic standpoint, and the analysis is extended to include more efficient drafting formations. RESULTS: Running in proper formations results in drag reductions in excess of 70% for the main runner. Our results indicate that, by properly using the advantages of drafting, Kiptum could have finished the race at a staggering 1:57:34, a full three minutes better than his own record and 215 s better than the previous world record. CONCLUSION: Proper use of drafting does indeed improve the energetic performance of a runner, allowing for lower race times and potentially helping elite runners in breaking the 2-h barrier for a marathon.

Experimental observation of the origin and structure of elastoinertial turbulence.

Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, "elastoinertial turbulence" (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the "maximum drag reduction limit," and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number.

Aerodynamic integration produces a vehicle shape with a negative drag coefficient.

Negative drag coefficients are normally associated with a vessel outfitted with a sail to extract energy from the wind and propel the vehicle forward. Therefore, the notion of a heavy vehicle, that is, a semi truck, that generates negative aerodynamic drag without a sail or any external appendages may seem implausible, especially given the fact that these vehicles have some of the largest drag coefficients on the road today. However, using both wind tunnel measurements and computational fluid dynamics simulations, we demonstrate aerodynamically integrated vehicle shapes that generate negative body-axis drag in a crosswind as a result of large negative frontal pressures that effectively "pull" the vehicle forward against the wind, much like a sailboat. While negative body-axis drag exists only for wind yaw angles above a certain analytical threshold, the negative frontal pressures exist at smaller yaw angles and subsequently produce body-axis drag coefficients that are significantly less than those of modern heavy vehicles. The application of this aerodynamic phenomenon to the heavy vehicle industry would produce sizable reductions in petroleum use throughout the United States.

Towards an accurate rolling resistance: Estimating intra-cycle load distribution between front and rear wheels during wheelchair propulsion from inertial sensors.

Accurate assessment of rolling resistance is important for wheelchair propulsion analyses. However, the commonly used drag and deceleration tests are reported to underestimate rolling resistance up to 6% due to the (neglected) influence of trunk motion. The first aim of this study was to investigate the accuracy of using trunk and wheelchair kinematics to predict the intra-cyclical load distribution, more particularly front wheel loading, during hand-rim wheelchair propulsion. Secondly, the study compared the accuracy of rolling resistance determined from the predicted load distribution with the accuracy of drag test-based rolling resistance. Twenty-five able-bodied participants performed hand-rim wheelchair propulsion on a large motor-driven treadmill. During the treadmill sessions, front wheel load was assessed with load pins to determine the load distribution between the front and rear wheels. Accordingly, a machine learning model was trained to predict front wheel load from kinematic data. Based on two inertial sensors (attached to the trunk and wheelchair) and the machine learning model, front wheel load was predicted with a mean absolute error (MAE) of 3.8% (or 1.8 kg). Rolling resistance determined from the predicted load distribution (MAE: 0.9%, mean error (ME): 0.1%) was more accurate than drag test-based rolling resistance (MAE: 2.5%, ME: -1.3%).

Inducing Electric Current in Graphene Using Ionic Flow.

Classical nanofluidic frameworks account for the confined fluid and ion transport under an electrostatic field at the solid-liquid interface, but the electronic property of the solid is often overlooked. Harvesting the interaction of the nanofluidic transport with the electron transport in solid requires a route effectively coupling ion and electron dynamics. Here we report a nanofluidic analogy of Coulomb drag for exploring the dynamic ion-electron interactions at the liquid-graphene interface. An induced electric current in graphene by ionic flow with no bias directly applied to the graphene channel is observed experimentally, featuring an opposite electron current direction to the ion current. Our experiments and ab initio calculations show that the current generation stems from the confined ion-electron interactions via a nanofluidic Coulomb drag mechanism. Our findings may open up a new dimension for nanofluidics and transport control by ion-electron coupling.

A chromosome scale tomato genome built from complementary PacBio and Nanopore sequences alone reveals extensive linkage drag during breeding.

The assembly and scaffolding of plant crop genomes facilitate the characterization of genetically diverse cultivated and wild germplasm. The cultivated tomato (Solanum lycopersicum) has been improved through the introgression of genetic material from related wild species, including resistance to pandemic strains of tobacco mosaic virus (TMV) from Solanum peruvianum. Here we applied PacBio HiFi and ONT Nanopore sequencing to develop independent, highly contiguous and complementary assemblies of an inbred TMV-resistant tomato variety. We show specific examples of how HiFi and ONT datasets can complement one another to improve assembly contiguity. We merged the HiFi and ONT assemblies to generate a long-read-only assembly where all 12 chromosomes were represented as 12 contiguous sequences (N50 = 68.5 Mbp). This chromosome scale assembly did not require scaffolding using an orthogonal data type. The merged assembly was validated by chromosome conformation capture data and is highly consistent with previous tomato genome assemblies that made use of genetic maps and Hi-C for scaffolding. Our long-read-only assembly reveals that a complex series of structural variants linked to the TMV resistance gene likely contributed to linkage drag of a 64.1-Mbp region of the S. peruvianum genome during tomato breeding. Through marker studies and ONT-based comprehensive haplotyping we show that this minimal introgression region is present in six cultivated tomato hybrid varieties developed in three commercial breeding programs. Our results suggest that complementary long read technologies can facilitate the rapid generation of near-complete genome sequences.

E-cadherin adhesion dynamics as revealed by an accelerated force ramp are dependent upon the presence of α-catenin.

Tissue remodeling and shape changes often rely on force-induced cell rearrangements occurring via cell-cell contact dynamics. Epithelial cell-cell contact shape changes are particularly dependent upon E-cadherin adhesion dynamics which are directly influenced by cell-generated and external forces. While both the mobility of E-cadherin adhesions and their adhesion strength have been reported before, it is not clear how these two aspects of E-cadherin adhesion dynamics are related. Here, using magnetic pulling cytometry, we applied an accelerated force ramp on the E-cadherin adhesion between an E-cadherin-coated magnetic microbead and an epithelial cell to ascertain this relationship. Our approach enables the determination of the adhesion strength and force-dependent mobility of individual adhesions, which revealed a direct correlation between these key characteristics. Since α-catenin has previously been reported to play a role in both E-cadherin mobility and adhesion strength when studied independently, we also probed epithelial cells in which α-catenin has been knocked out. We found that, in the absence of α-catenin, E-cadherin adhesions not only had lower adhesion strength, as expected, but were also more mobile. We observed that α-catenin was required for the recovery of strained cell-cell contacts and propose that the adhesion strength and force-dependent mobility of E-cadherin adhesions act in tandem to regulate cell-cell contact homeostasis. Our approach introduces a method which relates the force-dependent adhesion mobility to adhesion strength and highlights the morphological role played by α-catenin in E-cadherin adhesion dynamics.

Still air resistance during walking and running.

In everyday life during terrestrial locomotion our body interacts with two media opposing the forward movement of the body: the ground and the air. Whereas the work done to overcome the ground reaction force has been extensively studied, the work done to overcome still air resistance has been only indirectly estimated by means of theoretical studies and by measurements of the force exerted on puppets simulating the geometry of the human body. In this study, we directly measured the force exerted by still air resistance on eight male subjects during walking and running on an instrumented treadmill with a belt moving at the same speed of a flow of laminar air facing the subject. Overall, the coefficient of proportionality between drag and velocity squared (Aeff) was smaller during running than walking. During running Aeff decreased progressively with increasing average velocity up to an apparently constant, velocity independent value, similar to that predicted in the literature using indirect methods. A predictive equation to estimate drag as a function of the speed and the height of the running subject is provided.

Hydrofoil-like legs help stream mayfly larvae to stay on the ground.

Adaptations to flow have already been in the focus of early stream research, but till today morphological adaptations of stream insects are hardly understood. While most previous stream research focused on drag, the effects of lift on ground-living stream insects have been often overlooked. Stream mayfly larvae Ecdyonurus sp. graze on algae on top of the stones and therefore inhabit current exposed places in streams. They have a dorso-ventrally flattened body shape, which is known to reduce drag. However, this body shape enhances lift too, increasing the danger for the animal of getting detached from the substrate. Using microscopic techniques, 3D-printing, and drag and lift measurements in a wind tunnel, our experiments show that the widened femora of Ecdyonurus sp. can generate negative lift, contributing to counterbalance the (positive) lift of the overall body shape. The larvae can actively regulate the amount of lift by adjusting the femur's tilt or optimizing the distance to the ground. This shows that morphological adaptations of benthic stream insects can be very elaborate and can reach far beyond adaptations of the overall body shape. In the presented case, Ecdyonurus sp. takes advantage of the flow to overcome the flow's challenges.

Rapid manoeuvre of fan worms (Annelida: Sabellidae) through tubes.

Multiple variables determine the success of an escape response of an animal, and the rapidity of the escape manoeuvre is often the most important. Fan worms (Annelida: Sabellidae) can rapidly withdraw their tentacles, which are covered in heavily ciliated ramifications called pinnules, into their tubes to protect them from approaching threats. Here, we explore the dynamic and mechanistic features behind this escape manoeuvre. The escape responses of fan worms were recorded by high-speed videography and quantified by computerized motion analysis, showing an ultrahigh retraction speed of 272±135 mm s-1 (8±4 body lengths s-1). We found that fan worms possess powerful muscle-driven systems, which can generate contractive forces up to 36 times their body weight. In order to achieve these rapid, forceful movements through seawater without damaging their tentacles, fan worms have developed functional morphological adaptations to reduce fluidic drag, including the flattening of their radiolar pinnules and the deformation of bodily segmental ridges. Our hydrodynamic models indicate that these mechanical processes can decrease fluidic drag by 47%, trapped mass by 75% and friction coefficient by 89%. These strategies allow fan worms to execute rapid escape responses and could inspire the design of fast in-pipe robots.