A Simplified Model for the Study of Film-Boiling Droplet Motion on Microscale Ratchets.

In this work, we explore a simplified model based on both analytical and computational methods for the study of film-boiling droplet motion on microscale ratchets. We consider a specific ratchet design with the length periods and depth of ratchets much smaller than the size of the droplet. We conclude based on our modeling that for the ratchet configuration considered in this paper, the conduction within the vapor film is the dominant means of heat transfer in comparison with convection and radiation. Furthermore, we demonstrate a more manageable two-dimensional model in which analytical approaches coupled with computational approaches yield reasonably accurate results in comparison to the actual experiments.

Rewinding the Ratchet: Rare Recombination Locally Rescues Neo-W Degeneration and Generates Plateaus of Sex-Chromosome Divergence.

Natural selection is less efficient in the absence of recombination. As a result, nonrecombining sequences, such as sex chromosomes, tend to degenerate over time. Although the outcomes of recombination arrest are typically observed after many millions of generations, recent neo-sex chromosomes can give insight into the early stages of this process. Here, we investigate the evolution of neo-sex chromosomes in the Spanish marbled white butterfly, Melanargia ines, where a Z-autosome fusion has turned the homologous autosome into a nonrecombining neo-W chromosome. We show that these neo-sex chromosomes are likely limited to the Iberian population of M. ines, and that they arose around the time when this population split from North-African populations, around 1.5 million years ago. Recombination arrest of the neo-W chromosome has led to an excess of premature stop-codons and frame-shift mutations, and reduced gene expression compared to the neo-Z chromosome. Surprisingly, we identified two regions of ∼1 Mb at one end of the neo-W that are both less diverged from the neo-Z and less degraded than the rest of the chromosome, suggesting a history of rare but repeated genetic exchange between the two neo-sex chromosomes. These plateaus of neo-sex chromosome divergence suggest that neo-W degradation can be locally reversed by rare recombination between neo-W and neo-Z chromosomes.

STAG2-RAD21 complex: A unidirectional DNA ratchet mechanism in loop extrusion.

DNA loop extrusion plays a key role in the regulation of gene expression and the structural arrangement of chromatin. Most existing mechanistic models of loop extrusion depend on some type of ratchet mechanism, which should permit the elongation of loops while preventing their collapse, by enabling DNA to move in only one direction. STAG2 is already known to exert a role as DNA anchor, but the available structural data suggest a possible role in unidirectional DNA motion. In this work, a computational simulation framework was constructed to evaluate whether STAG2 could enforce such unidirectional displacement of a DNA double helix. The results reveal that STAG2 V-shape allows DNA sliding in one direction, but blocks opposite DNA movement via a linear ratchet mechanism. Furthermore, these results suggest that RAD21 binding to STAG2 controls its flexibility by narrowing the opening of its V-shape, which otherwise remains widely open in absence of RAD21. Therefore, in the proposed model, in addition to its already described role as a DNA anchor, the STAG2-RAD21 complex would be part of a ratchet mechanism capable of exerting directional selectivity on DNA sliding during loop extrusion. The identification of the molecular basis of the ratchet mechanism of loop extrusion is a critical step in unraveling new insights into a broad spectrum of chromatin activities and their implications for the mechanisms of chromatin-related diseases.

Muller's ratchet in a near-critical regime: Tournament versus fitness proportional selection.

Muller's ratchet, in its prototype version, models a haploid, asexual population whose size N is constant over the generations. Slightly deleterious mutations are acquired along the lineages at a constant rate, and individuals carrying less mutations have a selective advantage. The classical variant considers fitness proportional selection, but other fitness schemes are conceivable as well. Inspired by the work of Etheridge et al. (2009) we propose a parameter scaling which fits well to the "near-critical" regime that was in the focus of Etheridge et al. (2009) (and in which the mutation-selection ratio diverges logarithmically as N→∞). Using a Moran model, we investigate the"rule of thumb" given in Etheridge et al. (2009) for the click rate of the "classical ratchet" by putting it into the context of new results on the long-time evolution of the size of the best class of the ratchet with (binary) tournament selection. This variant of Muller's ratchet was introduced in González Casanova et al. (2023), and was analysed there in a subcritical parameter regime. Other than that of the classical ratchet, the size of the best class of the tournament ratchet follows an autonomous dynamics up to the time of its extinction. It turns out that, under a suitable correspondence of the model parameters, this dynamics coincides with the so called Poisson profile approximation of the dynamics of the best class of the classical ratchet.

Comparison of Four Different Dental Implant Removal Techniques in Terms of the Weight and Volume of Bone Loss.

PURPOSE: Several approaches have been suggested for implant removal. However, further research is necessary to review data regarding the amount of bone removed and the duration of removal time for different procedures. This study evaluates and compares various implant removal techniques.  Materials and methods: A polyurethane block was scanned to create an implant surgical guide. Afterward, implant-guided surgery was performed on 60 simulated bone blocks. The implants were then separated into four groups and removed utilizing the counter-torque ratchet, trephine drills, burs, and piezosurgery. RESULTS: For the weight of bone loss, there were significant differences in the median between the counter-torque ratchet technique (CTRT) and trephine (p < 0.01), CTRT and bur (p < 0.01), trephine and piezo (p < 0.01), and bur and piezo (p = 0.04). All groups, except CTRT and the piezo group, demonstrated a statistically significant difference (p < 0.01) in the procedure durations. Regarding the volume of bone loss, a statistically significant difference (p < 0.01) was found between each group.  Conclusions: CTRT showed the least amount of bone loss. On the other hand, the trephine technique was demonstrated to be the fastest. It is essential to consider the limitations and risks when choosing the approach for implant removal.

Transmissible cancers, the genomes that do not melt down.

Evolutionary theory predicts that the accumulation of deleterious mutations in asexually reproducing organisms should lead to genomic decay. Clonally reproducing cell lines, i.e., transmissible cancers, when cells are transmitted as allografts/xenografts, break these rules and survive for centuries and millennia. The currently known 11 transmissible cancer lineages occur in dogs (canine venereal tumour disease), in Tasmanian devils (devil facial tumor diseases, DFT1 and DFT2), and in bivalves (bivalve transmissible neoplasia). Despite the mutation loads of these cell lines being much higher than observed in human cancers, they have not been eliminated in space and time. Here, we provide potential explanations for how these fascinating cell lines may have overcome the fitness decline due to the progressive accumulation of deleterious mutations and propose that the high mutation load may carry an indirect positive fitness outcome. We offer ideas on how these host-pathogen systems could be used to answer outstanding questions in evolutionary biology. The recent studies on the evolution of these clonal pathogens reveal key mechanistic insight into transmissible cancer genomes, information that is essential for future studies investigating how these contagious cancer cell lines can repeatedly evade immune recognition, evolve, and survive in the landscape of highly diverse hosts.

Anthrax Toxin: Model System for Studying Protein Translocation.

Dedicated translocase channels are nanomachines that often, but not always, unfold and translocate proteins through narrow pores across the membrane. Generally, these molecular machines utilize external sources of free energy to drive these reactions, since folded proteins are thermodynamically stable, and once unfolded they contain immense diffusive configurational entropy. To catalyze unfolding and translocate the unfolded state at appreciable timescales, translocase channels often utilize analogous peptide-clamp active sites. Here we describe how anthrax toxin has been used as a biophysical model system to study protein translocation. The tripartite bacterial toxin is composed of an oligomeric translocase channel, protective antigen (PA), and two enzymes, edema factor (EF) and lethal factor (LF), which are translocated by PA into mammalian host cells. Unfolding and translocation are powered by the endosomal proton gradient and are catalyzed by three peptide-clamp sites in the PA channel: the α clamp, the ϕ clamp, and the charge clamp. These clamp sites interact nonspecifically with the chemically complex translocating chain, serve to minimize unfolded state configurational entropy, and work cooperatively to promote translocation. Two models of proton gradient driven translocation have been proposed: (i) an extended-chain Brownian ratchet mechanism and (ii) a proton-driven helix-compression mechanism. These models are not mutually exclusive; instead the extended-chain Brownian ratchet likely operates on ß-sheet sequences and the helix-compression mechanism likely operates on α-helical sequences. Finally, we compare and contrast anthrax toxin with other related and unrelated translocase channels.

Apomixis and the paradox of sex in plants.

BACKGROUND: The predominance of sex in eukaryotes, despite the high costs of meiosis and mating, remains an evolutionary enigma. Many theories have been proposed, none of them being conclusive on its own, and they are, in part, not well applicable to land plants. Sexual reproduction is obligate in embryophytes for the great majority of species. SCOPE: This review compares the main forms of sexual and asexual reproduction in ferns and angiosperms, based on the generation cycling of sporophyte and gametophyte (leaving vegetative propagation aside). The benefits of sexual reproduction for maintenance of genomic integrity in comparison to asexuality are discussed in the light of developmental, evolutionary, genetic and phylogenetic studies. CONCLUSIONS: Asexual reproduction represents modifications of the sexual pathway, with various forms of facultative sexuality. For sexual land plants, meiosis provides direct DNA repair mechanisms for oxidative damage in reproductive tissues. The ploidy alternations of meiosis-syngamy cycles and prolonged multicellular stages in the haploid phase in the gametophytes provide a high efficiency of purifying selection against recessive deleterious mutations. Asexual lineages might buffer effects of such mutations via polyploidy and can purge the mutational load via facultative sexuality. The role of organelle-nuclear genome compatibility for maintenance of genome integrity is not well understood. In plants in general, the costs of mating are low because of predominant hermaphroditism. Phylogenetic patterns in the archaeplastid clade suggest that high frequencies of sexuality in land plants are concomitant with a stepwise increase of intrinsic and extrinsic stress factors. Furthermore, expansion of genome size in land plants would increase the potential mutational load. Sexual reproduction appears to be essential for keeping long-term genomic integrity, and only rare combinations of extrinsic and intrinsic factors allow for shifts to asexuality.

A dynamical limit to evolutionary adaptation.

Natural selection makes evolutionary adaptation possible even if the overwhelming majority of new mutations are deleterious. However, in rapidly evolving populations where numerous linked mutations occur and segregate simultaneously, clonal interference and genetic hitchhiking can limit the efficiency of selection, allowing deleterious mutations to accumulate over time. This can in principle overwhelm the fitness increases provided by beneficial mutations, leading to an overall fitness decline. Here, we analyze the conditions under which evolution will tend to drive populations to higher versus lower fitness. Our analysis focuses on quantifying the boundary between these two regimes, as a function of parameters such as population size, mutation rates, and selection pressures. This boundary represents a state in which adaptation is precisely balanced by Muller's ratchet, and we show that it can be characterized by rapid molecular evolution without any net fitness change. Finally, we consider the implications of global fitness-mediated epistasis and find that under some circumstances, this can drive populations toward the boundary state, which can thus represent a long-term evolutionary attractor.

A model for collagen secretion by intercompartmental continuities.

Newly synthesized secretory proteins are exported from the endoplasmic reticulum (ER) at specialized subcompartments called exit sites (ERES). Cargoes like procollagen are too large for export by the standard COPII-coated vesicle of 60 nm average diameter. We have previously suggested that procollagen is transported from the ER to the next secretory organelle, the ER-Golgi intermediate compartment (ERGIC), in TANGO1-dependent interorganelle tunnels. In the theoretical model presented here, we suggest that intrinsically disordered domains of TANGO1 in the ER lumen induce an entropic contraction, which exerts a force that draws procollagen toward the ERES. Within this framework, molecular gradients of pH and/or HSP47 between the ER and ERGIC create a force in the order of tens of femto-Newtons. This force is substantial enough to propel procollagen from the ER at a speed of approximately 1 nm · s-1. This calculated speed and the quantities of collagen secreted are similar to its observed physiological secretion rate in fibroblasts, consistent with the proposal that ER export is the rate-limiting step for procollagen secretion. Hence, the mechanism we propose is theoretically adequate to explain how cells can utilize molecular gradients and export procollagens at a rate commensurate with physiological needs.

Electric Tuning of Vortex Ratchet Effect in NbSe2.

Inversion symmetry breaking has played an important role in recent discoveries of nonreciprocal charge transport. Niobium diselenide, for example, lacks an inversion center in the monolayer form and can host prominent nonreciprocal transport property. Here, however, we observe a nonreciprocal transport signal in the second-harmonic channel of bulk-like NbSe2, in which inversion symmetry of the lattice seems preserved. The second-harmonic signal occurs along different in-plane current orientations and appears not only in the vortex-liquid regime but also even in the superconducting fluctuation regime without an applied magnetic field. By adding a direct current (DC) bias, we quantify the symmetry breaking effect in the vortex-liquid regime. The DC bias also suggests that the rectification effect at the contacts may account for the seemingly nonreciprocal transport at zero magnetic field. Our results demonstrate that DC biasing is a useful knob for addressing nonreciprocal charge transport in a wide range of materials.

An analysis of a rural hospital's investment decision under different payment systems.

From an economic perspective, large investments in medical equipment are justifiable only when many patients benefit. Although rural hospitals play a crucial role locally, the treatments they can offer are limited. In this study, I characterize investment level that maximizes the total surplus, encompassing patients' welfare and producer surplus, and subtracting treatment costs. Specifically, I account for economic externalities generated by the investment in the rural hospital and for different utility losses that patients suffer when they cannot be treated locally. I demonstrate that the optimal investment level can be implemented if the Health Authority has the power to set specific prices for each disease. Additionally, I explore a decentralized situation wherein the investment decision lies with the rural hospital manager, and the Health Authority can only make a discrete decision between two payment systems: Fee-for-service, which covers all treatment costs, or Diagnosis-Related-Groups, which reimburses a price per patient based on the overall average cost. I find that the Diagnosis-Related-Groups system outperforms the Fee-for-service in terms of total surplus when the treatment cost at the rural hospital is lower. However, when the rural hospital has higher costs and the Health Authority seeks to incentivize investment, the Fee-for-service system is superior.

Mutational meltdown in asexual populations doomed to extinction.

Asexual populations are expected to accumulate deleterious mutations through a process known as Muller's ratchet. Lynch and colleagues proposed that the ratchet eventually results in a vicious cycle of mutation accumulation and population decline that drives populations to extinction. They called this phenomenon mutational meltdown. Here, we analyze mutational meltdown using a multi-type branching process model where, in the presence of mutation, populations are doomed to extinction. We analyse the change in size and composition of the population and the time of extinction under this model.

Bidirectional Droplet Manipulation on Magnetically Actuated Superhydrophobic Ratchet Surfaces.

Droplet manipulation has garnered significant attention in various fields due to its wide range of applications. Among many different methods, magnetic actuation has emerged as a promising approach for remote and instantaneous droplet manipulation. In this study, we present the bidirectional droplet manipulation on a magnetically actuated superhydrophobic ratchet surface. The surface consists of silicon strips anchored on elastomer ridges with superhydrophobic black silicon structures on the top side and magnetic layers on the bottom side. The soft magnetic properties of the strips enable their bidirectional tilting to form a ratchet surface and thus bidirectional droplet manipulation upon varying external magnetic field location and strength. Computational multiphysics models were developed to predict the tilting of the strips, demonstrating the concept of bidirectional tilting along with a tilting angle hysteresis theory. Experimental results confirmed the soft magnetic hysteresis and consequential bidirectional tilting of the strips. The superhydrophobic ratchet surface formed by the tilting strips induced the bidirectional self-propulsion of dispensed droplets through the Laplace pressure gradient, and the horizontal acceleration of the droplets was found to be positively correlated with the tilting angle of the strips. Additionally, a finite element analysis was conducted to identify the critical conditions for dispensed droplet penetration through the gaps between the strips, which hinder the droplet's self-propulsion. The models and findings here provide substantial insights into the design and optimization of magnetically actuated superhydrophobic ratchet surfaces to manipulate droplets in the context of digital microfluidic applications.

Human deleterious mutation rate implies high fitness variance, with declining mean fitness compensated by rarer beneficial mutations of larger effect.

Each new human has an expected Ud = 2 - 10 new deleterious mutations. This deluge of deleterious mutations cannot all be purged, and therefore accumulate in a declining fitness ratchet. Using a novel simulation framework designed to efficiently handle genome-wide linkage disequilibria across many segregating sites, we find that rarer, beneficial mutations of larger effect are sufficient to compensate fitness declines due to the fixation of many slightly deleterious mutations. Drift barrier theory posits a similar asymmetric pattern of fixations to explain ratcheting genome size and complexity, but in our theory, the cause is Ud > 1 rather than small population size. In our simulations, Ud ~2 - 10 generates high within-population variance in relative fitness; two individuals will typically differ in fitness by 15-40%. Ud ~2 - 10 also slows net adaptation by ~13%-39%. Surprisingly, fixation rates are more sensitive to changes in the beneficial than the deleterious mutation rate, e.g. a 10% increase in overall mutation rate leads to faster adaptation; this puts to rest dysgenic fears about increasing mutation rates due to rising paternal age.

Current working models of SMC-driven DNA-loop extrusion.

Structural maintenance of chromosome (SMC) proteins play a key roles in the chromosome organization by condensing two meters of DNA into cell-sized structures considered as the SMC protein extrudes DNA loop. Recent sequencing-based high-throughput chromosome conformation capture technique (Hi-C) and single-molecule experiments have provided direct evidence of DNA-loop extrusion. However, the molecular mechanism by which SMCs extrude a DNA loop is still under debate. Here, we review DNA-loop extrusion studies with single-molecule assays and introduce recent structural studies of how the ATP-hydrolysis cycle is coupled to the conformational changes of SMCs for DNA-loop extrusion. In addition, we explain the conservation of the DNA-binding sites that are vital for dynamic DNA-loop extrusion by comparing Cryo-EM structures of SMC complexes. Based on this information, we compare and discuss four compelling working models that explain how the SMC complex extrudes a DNA loop.

Trapping metastatic cancer cells with mechanical ratchet arrays.

Current treatments for cancer, such as chemotherapy, radiotherapy, immunotherapy, and surgery, have positive results but are generally ineffective against metastatic tumors. Treatment effectiveness can be improved by employing bioengineered cancer traps, typically utilizing chemoattractant-loaded materials, to attract infiltrating cancer cells preventing their uncontrolled spread and potentially enabling eradication. However, the encapsulated chemical compounds can have adverse effects on other cells causing unwanted responses, and the generated gradients can evolve unpredictably. Here, we report the development of a cancer trap based on mechanical ratchet structures to capture metastatic cells. The traps use an array of asymmetric local features to mechanically attract cancer cells and direct their migration for prolonged periods. The trapping efficiency was found to be greater than isotropic or inverse anisotropic ratchet structures on either disseminating cancer cells and tumor spheroids. Importantly, the traps exhibited a reduced effectiveness when targeting non-metastatic and non-tumorigenic cells, underscoring their particular suitability for capturing highly invasive cancer cells. Overall, this original approach may have therapeutic implications for fighting cancer, and may also be used to control cell motility for other biological processes. STATEMENT OF SIGNIFICANCE: Current cancer treatments have limitations in treating metastatic tumors, where cancer cells can invade distant organs. Biomaterials loaded with chemoattractants can be implanted to attract and capture metastatic cells preventing uncontrolled spread. However, encapsulated chemical compounds can have adverse effects on other cells, and gradients can evolve unpredictably. This paper presents an original concept of "cancer traps" based on using mechanical ratchet-based structures to capture metastatic cancer cells, with greater trapping efficiency and stability than previously studied methods. This innovative approach has significant potential clinical implications for fighting cancer, particularly in treating metastatic tumors. Additionally, it could be applied to control cell motility for other biological processes, opening new possibilities for biomedicine and tissue engineering.

Life's Mechanism.

The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of 'being alive'. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic of intrinsic functioning. Empirical studies demonstrate that biomolecules including ratcheting or rotating enzymes and ribozymes undergo repetitive conformation state changes driven either directly or indirectly by thermodynamic gradients. They exhibit disparate structures, but govern processes relying on directional physical motion (DNA transcription, translation, cytoskeleton transport) and share the principle of repetitive uniplanar conformation changes driven by thermodynamic gradients, producing dependable unidirectional motion: 'heat engines' exploiting thermodynamic disequilibria to perform work. Recognition that disparate biological molecules demonstrate conformation state changes involving directional motion, working in self-regulating networks, allows a mechanistic definition: life is a self-regulating process whereby matter undergoes cyclic, uniplanar conformation state changes that convert thermodynamic disequilibria into directed motion, performing work that locally reduces entropy. 'Living things' are structures including an autonomous network of units exploiting thermodynamic gradients to drive uniplanar conformation state changes that perform work. These principles are independent of any specific chemical environment, and can be applied to other biospheres.

The Mechanism by Which Umbrella-Shaped Ratchet Trichomes on the Elaeagnus angustifolia Leaf Surface Collect Water and Reflect Light.

Leaves are essential for plants, enabling photosynthesis and transpiration. In arid regions, water availability limits plant growth. Some plants, like Elaeagnus angustifolia, a sandy sub-tree species widely distributed in arid and semi-arid regions, have unique leaf structures to reduce water loss and solar radiation. Here, we describe the leaves of Elaeagnus angustifolia L., with special functioning trichomes. Through leaf submicroscopic structure observation, in situ water collection experiments, photosynthesis measurements, and reflection spectrum analysis, we investigated E. angustifolia leaves, focusing on their functioning trichomes. These trichomes capture water vapor, reflect UV and NIR light, and possess a 3D interface structure composed of 1D and 2D structures. The 1D conical structure captures water droplets, which are then gathered by the radial conical structure and guided towards the stomata through wedge-shaped grooves on the 2D umbrella structure. The trichomes also reflect sunlight, with micropapillae reflecting UV light and the umbrella structure reflecting NIR light. These mechanisms reduce leaf temperature, respiration, and water transpiration, protecting against solar radiation damage. This study provides insights into water collection and light-reflection mechanisms, revealing adaptive strategies of plants with large leaves in arid regions.

ATP Drives the Formation of a Catalytic Hydrazone through an Energy Ratchet Mechanism.

An energy ratchet mechanism is exploited for the synthesis of a molecule. In the presence of adenosine triphosphate (ATP), hydrazone-bond formation between an aldehyde and hydrazide is accelerated and the composition at thermodynamic equilibrium is shifted towards the hydrazone. Enzymatic hydrolysis of ATP installs a kinetically stable state, at which hydrazone is present at a higher concentration compared to the composition at thermodynamic equilibrium in the presence of the degradation products of ATP. It is shown that the kinetic state has an enhanced catalytic activity in the hydrolysis of an RNA-model compound.