Modeling the Evolution of S. pombe Populations with Multiple Killer Meiotic Drivers.

Meiotic drivers are selfish genetic loci that can be transmitted to more than half of the viable gametes produced by a heterozygote. This biased transmission gives meiotic drivers an evolutionary advantage that can allow them to spread over generations until all members of a population carry the driver. This evolutionary power can also be exploited to modify natural populations using synthetic drivers known as 'gene drives.' Recently, it has become clear that natural drivers can spread within genomes to birth multicopy gene families. To understand intragenomic spread of drivers, we model the evolution of two or more distinct meiotic drivers in a population. We employ the wtf killer meiotic drivers from Schizosaccharomyces pombe, which are multicopy in all sequenced isolates, as models. We find that a duplicate wtf driver identical to the parent gene can spread in a population unless, or until, the original driver is fixed. When the duplicate driver diverges to be distinct from the parent gene, we find that both drivers spread to fixation under most conditions, but both drivers can be lost under some conditions. Finally, we show that stronger drivers make weaker drivers go extinct in most, but not all, polymorphic populations with absolutely linked drivers. These results reveal the strong potential for natural meiotic drive loci to duplicate and diverge within genomes. Our findings also highlight duplication potential as a factor to consider in the design of synthetic gene drives.

Quartz Crystal Microbalance Frequency Response to Discrete Adsorbates in Liquids.

Quartz crystal microbalance with dissipation monitoring (QCM-D) has become a major tool enabling accurate investigation of the adsorption kinetics of nanometric objects such as DNA fragments, polypeptides, proteins, viruses, liposomes, polymer, and metal nanoparticles. However, in liquids, a quantitative analysis of the experimental results is often intricate because of the complex interplay of hydrodynamic and adhesion forces varying with the physicochemical properties of adsorbates and functionalized QCM-D sensors. In the present paper, we dissect the role of hydrodynamics for the analytically tractable case of stiff contact, whereas the adsorbed rigid particles oscillate with the resonator without rotation. Under the assumption of the low surface coverage, we theoretically study the excess shear force exerted on the resonator, which has two contributions: (i) the fluid-mediated force due to flow disturbance created by the particle and (ii) the force exerted on the particle by the fluid and transmitted to the sensor via contact. The theoretical analysis enables an accurate interpretation of the QCM-D impedance measurements. It is demonstrated inter alia that for particles of the size comparable with protein molecules, the hydrodynamic force dominates over the inertial force and that the apparent mass derived from QCM independently of the overtone is about 10 times the Sauerbrey (inertial) mass. The theoretical results show excellent agreement with the results of experiments and advanced numerical simulations for a wide range of particle sizes and oscillation frequencies.

Microglial Rac1 is essential for experience-dependent brain plasticity and cognitive performance.

Microglia, the largest population of brain immune cells, continuously interact with synapses to maintain brain homeostasis. In this study, we use conditional cell-specific gene targeting in mice with multi-omics approaches and demonstrate that the RhoGTPase Rac1 is an essential requirement for microglia to sense and interpret the brain microenvironment. This is crucial for microglia-synapse crosstalk that drives experience-dependent plasticity, a fundamental brain property impaired in several neuropsychiatric disorders. Phosphoproteomics profiling detects a large modulation of RhoGTPase signaling, predominantly of Rac1, in microglia of mice exposed to an environmental enrichment protocol known to induce experience-dependent brain plasticity and cognitive performance. Ablation of microglial Rac1 affects pathways involved in microglia-synapse communication, disrupts experience-dependent synaptic remodeling, and blocks the gains in learning, memory, and sociability induced by environmental enrichment. Our results reveal microglial Rac1 as a central regulator of pathways involved in the microglia-synapse crosstalk required for experience-dependent synaptic plasticity and cognitive performance.

Phase plane dynamics of ERK phosphorylation.

The extracellular signal-regulated kinase (ERK) controls multiple critical processes in the cell and is deregulated in human cancers, congenital abnormalities, immune diseases, and neurodevelopmental syndromes. Catalytic activity of ERK requires dual phosphorylation by an upstream kinase, in a mechanism that can be described by two sequential Michaelis-Menten steps. The estimation of individual reaction rate constants from kinetic data in the full mechanism has proved challenging. Here, we present an analytically tractable approach to parameter estimation that is based on the phase plane representation of ERK activation and yields two combinations of six reaction rate constants in the detailed mechanism. These combinations correspond to the ratio of the specificities of two consecutive phosphorylations and the probability that monophosphorylated substrate does not dissociate from the enzyme before the second phosphorylation. The presented approach offers a language for comparing the effects of mutations that disrupt ERK activation and function in vivo. As an illustration, we use phase plane representation to analyze dual phosphorylation under heterozygous conditions, when two enzyme variants compete for the same substrate.

Gas-assisted microfluidic step-emulsification for generating micron- and submicron-sized droplets.

Micron- and submicron-sized droplets have extensive applications in biomedical diagnosis and drug delivery. Moreover, accurate high-throughput analysis requires a uniform droplet size distribution and high production rates. Although the previously reported microfluidic coflow step-emulsification method can be used to generate highly monodispersed droplets, the droplet diameter (d) is constrained by the microchannel height (b), d≳3b, while the production rate is limited by the maximum capillary number of the step-emulsification regime, impeding emulsification of highly viscous liquids. In this paper, we report a novel, gas-assisted coflow step-emulsification method, where air serves as the innermost phase of a precursor hollow-core air/oil/water emulsion. Air gradually diffuses out, producing oil droplets. The size of the hollow-core droplets and the ultrathin oil layer thickness both follow the scaling laws of triphasic step-emulsification. The minimal droplet size attains d≈1.7b, inaccessible in standard all-liquid biphasic step-emulsification. The production rate per single channel is an order-of-magnitude higher than that in the standard all-liquid biphasic step-emulsification and is also superior to alternative emulsification methods. Due to low gas viscosity, the method can also be used to generate micron- and submicron-sized droplets of high-viscosity fluids, while the inert nature of the auxiliary gas offers high versatility.

Recombination between heterologous human acrocentric chromosomes.

The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications1,2. Although the resolution of these regions in the first complete assembly of a human genome-the Telomere-to-Telomere Consortium's CHM13 assembly (T2T-CHM13)-provided a model of their homology3, it remained unclear whether these patterns were ancestral or maintained by ongoing recombination exchange. Here we show that acrocentric chromosomes contain pseudo-homologous regions (PHRs) indicative of recombination between non-homologous sequences. Utilizing an all-to-all comparison of the human pangenome from the Human Pangenome Reference Consortium4 (HPRC), we find that contigs from all of the SAACs form a community. A variation graph5 constructed from centromere-spanning acrocentric contigs indicates the presence of regions in which most contigs appear nearly identical between heterologous acrocentric chromosomes in T2T-CHM13. Except on chromosome 15, we observe faster decay of linkage disequilibrium in the pseudo-homologous regions than in the corresponding short and long arms, indicating higher rates of recombination6,7. The pseudo-homologous regions include sequences that have previously been shown to lie at the breakpoint of Robertsonian translocations8, and their arrangement is compatible with crossover in inverted duplications on chromosomes 13, 14 and 21. The ubiquity of signals of recombination between heterologous acrocentric chromosomes seen in the HPRC draft pangenome suggests that these shared sequences form the basis for recurrent Robertsonian translocations, providing sequence and population-based confirmation of hypotheses first developed from cytogenetic studies 50 years ago9.

The Poynting Vector Field Generic Singularities in Resonant Scattering of Plane Linearly Polarized Electromagnetic Waves by Subwavelength Particles.

We present the results of a study of the Poynting vector field generic singularities at the resonant light scattering of a plane monochromatic linearly polarized electromagnetic wave by a subwavelength particle. We reveal the impact of the problem symmetry, the spatial dimension, and the energy conservation law on the properties of the singularities. We show that, in the cases when the problem symmetry results in the existence of an invariant plane for the Poynting vector field lines, a formation of a standing wave in the immediate vicinity of a singularity gives rise to a saddle-type singular point. All other types of singularities are associated with vanishing at the singular points, either (i) magnetic field, for the polarization plane parallel to the invariant plane, or (ii) electric field, at the perpendicular orientation of the polarization plane. We also show that in the case of two-dimensional problems (scattering by a cylinder), the energy conservation law restricts the types of possible singularities only to saddles and centers in the non-dissipative media and to saddles, foci, and nodes in dissipative. Finally, we show that dissipation affects the (i)-type singularities much stronger than the (ii)-type. The same conclusions are valid for the imaginary part of the Poynting vector in problems where the latter is regarded as a complex quantity. The singular points associated with the formation of standing waves are different for real and imaginary parts of this complex vector field, while all other singularities are common. We illustrate the general discussion by analyzing singularities at light scattering by a subwavelength Germanium cylinder with the actual dispersion of its refractive index.

Nature of the Poynting Vector Field Singularities in Resonant Light Scattering by Nanoparticles.

Singularities of the Poynting vector field subwavelength patterns in resonant light scattering by nanoparticles are discussed and classified. There are two generic types of the singularities, namely, (i) the singularities related to the vanishing of the magnetic (and/or electric) field at the singular points and (ii) the singularities related to the formation of standing waves in proximity to the singular points. The connection of these types of singularities to the topology of the singular points, space dimension (3D vs. 2D), and energy conservation law are revealed. In particular, it is shown that in 2D cases in non-dissipative media, the energy conservation reduces the possible types of generic singular points to saddles and centers only. In 3D cases, a universal expression connecting different components of the Poynting vector and valid for any generic singularities is derived and numerically checked for various types of singular points.

Correction: Shape-controlled anisotropy of superparamagnetic micro-/nanohelices.

Correction for 'Shape-controlled anisotropy of superparamagnetic micro-/nanohelices' by Alexander M. Leshansky et al., Nanoscale, 2016, 8, 14127-14138, https://doi.org/10.1039/C6NR01803C.

The architecture and operating mechanism of a cnidarian stinging organelle.

The stinging organelles of jellyfish, sea anemones, and other cnidarians, known as nematocysts, are remarkable cellular weapons used for both predation and defense. Nematocysts consist of a pressurized capsule containing a coiled harpoon-like thread. These structures are in turn built within specialized cells known as nematocytes. When triggered, the capsule explosively discharges, ejecting the coiled thread which punctures the target and rapidly elongates by turning inside out in a process called eversion. Due to the structural complexity of the thread and the extreme speed of discharge, the precise mechanics of nematocyst firing have remained elusive7. Here, using a combination of live and super-resolution imaging, 3D electron microscopy, and genetic perturbations, we define the step-by-step sequence of nematocyst operation in the model sea anemone Nematostella vectensis. This analysis reveals the complex biomechanical transformations underpinning the operating mechanism of nematocysts, one of nature's most exquisite biological micro-machines. Further, this study will provide insight into the form and function of related cnidarian organelles and serve as a template for the design of bioinspired microdevices.

Calculating absorption dose when X-ray irradiation modifies material quantity and chemistry.

X-ray absorption is a sensitive and versatile tool for chemical speciation. However, when high doses are used, the absorbed energy can change the composition, amount and structure of the native material, thereby changing the aspects of the absorption process on which speciation is based. How can one calculate the dose when X-ray irradiation affects the chemistry and changes the amount of the material? This paper presents an assumption-free approach which can retrieve from the experimental data all dose-sensitive parameters - absorption coefficients, composition (elemental molecular units), material densities - which can then be used to calculate accurate doses as a function of irradiation. This approach is illustrated using X-ray damage to a solid film of a perfluorosulfonic acid fluoropolymer in a scanning transmission soft X-ray microscope. This new approach is compared against existing dose models which calculate the dose by making simplifying assumptions regarding the material quantity, density and chemistry. While the detailed measurements used in this approach go beyond typical methods to experimental analytical X-ray absorption, they provide a more accurate quantitation of radiation dose, and help to understand mechanisms of radiation damage.

Double emulsions with ultrathin shell by microfluidic step-emulsification.

Double emulsions with ultrathin shells are important in some biomedical applications, such as controlled drug release. However, the existing production techniques require two or more manipulation steps, or more complicated channel geometry, to form thin-shell double emulsions. This work presents a novel microfluidic tri-phasic step-emulsification device, with an easily fabricated double-layer PDMS channel, for production of oil-in-oil-in-water and water-in-water-in-oil double emulsions in a single step. The shell thickness is controlled by the flow rates and can reach 1.4% of the µm-size droplet diameter. Four distinct emulsification regimes are observed depending on the experimental conditions. A theoretical model for the tri-phasic step-emulsification is proposed to predict the boundaries separating the four regimes of emulsification in plane of two dimensionless capillary numbers, Ca. The theory yields two coupled nonlinear differential equations that can be solved numerically to find the approximate shape of the free interfaces in the shallow (Hele-Shaw) microfluidic channel. This approximation is then used as the initial guess for the more accurate finite element method solution, showing very good agreement with the experimental findings. This study demonstrates the feasibility of co-flow step-emulsification as a promising method to production of double (and multiple) emulsions and micro-capsules with ultrathin shells of controllable thickness.

DNA replication, transcription, and H3K56 acetylation regulate copy number and stability at tandem repeats.

Tandem repeats are inherently unstable and exhibit extensive copy number polymorphisms. Despite mounting evidence for their adaptive potential, the mechanisms associated with regulation of the stability and copy number of tandem repeats remain largely unclear. To study copy number variation at tandem repeats, we used two well-studied repetitive arrays in the budding yeast genome, the ribosomal DNA (rDNA) locus, and the copper-inducible CUP1 gene array. We developed powerful, highly sensitive, and quantitative assays to measure repeat instability and copy number and used them in multiple high-throughput genetic screens to define pathways involved in regulating copy number variation. These screens revealed that rDNA stability and copy number are regulated by DNA replication, transcription, and histone acetylation. Through parallel studies of both arrays, we demonstrate that instability can be induced by DNA replication stress and transcription. Importantly, while changes in stability in response to stress are observed within a few cell divisions, a change in steady state repeat copy number requires selection over time. Further, H3K56 acetylation is required for regulating transcription and transcription-induced instability at the CUP1 array, and restricts transcription-induced amplification. Our work suggests that the modulation of replication and transcription is a direct, reversible strategy to alter stability at tandem repeats in response to environmental stimuli, which provides cells rapid adaptability through copy number variation. Additionally, histone acetylation may function to promote the normal adaptive program in response to transcriptional stress. Given the omnipresence of DNA replication, transcription, and chromatin marks like histone acetylation, the fundamental mechanisms we have uncovered significantly advance our understanding of the plasticity of tandem repeats more generally.

Fluid-Mediated Force on a Particle Due to an Oscillating Plate and Its Effect on Deposition Measurements by a Quartz Crystal Microbalance.

Interaction of particles with boundaries is a fundamental problem in many fields of physics. In this Letter, we theoretically examine the fluid-mediated interaction between a horizontally oscillating plate and a spherical particle, revealing emergence of the novel nonlinear vertical force exerted on the particle. Although we demonstrate that the phenomenon only slightly alters deposition of colloidal (sub-)µm-sized particles measured by quartz crystal microbalance, it can result in levitation of larger particles above the plate, considerably hindering their deposition.

Pushing myelination - developmental regulation of myosin expression drives oligodendrocyte morphological differentiation.

Oligodendrocytes are the central nervous system myelin-forming cells providing axonal electrical insulation and higher-order neuronal circuitry. The mechanical forces driving the differentiation of oligodendrocyte precursor cells into myelinating oligodendrocytes are largely unknown, but likely require the spatiotemporal regulation of the architecture and dynamics of the actin and actomyosin cytoskeletons. In this study, we analyzed the expression pattern of myosin motors during oligodendrocyte development. We report that oligodendrocyte differentiation is regulated by the synchronized expression and non-uniform distribution of several members of the myosin network, particularly non-muscle myosins 2B and 2C, which potentially operate as nanomechanical modulators of cell tension and myelin membrane expansion at different cell stages.This article has an associated First Person interview with the first author of the paper.

The membrane periodic skeleton is an actomyosin network that regulates axonal diameter and conduction.

Neurons have a membrane periodic skeleton (MPS) composed of actin rings interconnected by spectrin. Here, combining chemical and genetic gain- and loss-of-function assays, we show that in rat hippocampal neurons the MPS is an actomyosin network that controls axonal expansion and contraction. Using super-resolution microscopy, we analyzed the localization of axonal non-muscle myosin II (NMII). We show that active NMII light chains are colocalized with actin rings and organized in a circular periodic manner throughout the axon shaft. In contrast, NMII heavy chains are mostly positioned along the longitudinal axonal axis, being able to crosslink adjacent rings. NMII filaments can play contractile or scaffolding roles determined by their position relative to actin rings and activation state. We also show that MPS destabilization through NMII inactivation affects axonal electrophysiology, increasing action potential conduction velocity. In summary, our findings open new perspectives on axon diameter regulation, with important implications in neuronal biology.

Modeling Propulsion of Soft Magnetic Nanowires.

The emergent interest in artificial nanostructures that can be remotely navigated a specific location in a fluidic environment is motivated by the enormous potential this technology offers to biomedical applications. Originally, bio-inspired micro-/nanohelices driven by a rotating magnetic field were proposed. However, fabrication of 3D helical nanostructures is complicated. One idea to circumvent complex microfabrication is to use 1D soft magnetic nanowires that acquire chiral shape when actuated by a rotating field. The paper describes the comprehensive numerical approach for modeling propulsion of externally actuated soft magnetic nanowires. The proposed bead-spring model allows for arbitrary filament geometry and flexibility and takes rigorous account of intra-filament hydrodynamic interactions. The comparison of the numerical predictions with the previous experimental results on propulsion of composite two-segment (Ni-Ag) nanowires shows an excellent agreement. Using our model we could substantiate and rationalize important and previously unexplained details, such as bidirectional propulsion of three-segment (Ni-Ag-Au) nanowires.

Protrusion membrane pearling emerges during 3D cell division.

Cell division is accompanied by dramatic changes in shape that ultimately lead to the physical separation of one cell into two. In 2D microenvironments, cells round up and remain adhered onto the substrate by thin retraction fibers during division. In contrast, in 3D environments, cells divide exhibiting long protrusions that guide the orientation of the division axis. However, the mechanism of cell division in three dimensions still remains poorly understood. Here we report the spontaneous formation of transient quasiperiodic membrane pearling on extended mitotic protrusions during 3D cell division. Protrusion membrane pearling may be initiated by the non-uniform distribution of focal adhesions and consequent stationary instability of the protrusive membrane. Overall, membrane pearling emergence may provide insights into a novel modality of 3D cell division with potential physiological relevance.

Robustness and evolvability of heterogeneous cell populations.

Biological systems are endowed with two fundamental but seemingly contradictory properties: robustness, the ability to withstand environmental fluctuations and genetic variability; and evolvability, the ability to acquire selectable and heritable phenotypic changes. Cell populations with heterogeneous genetic makeup, such as those of infectious microbial organisms or cancer, rely on their inherent robustness to maintain viability and fitness, but when encountering environmental insults, such as drug treatment, these populations are also poised for rapid adaptation through evolutionary selection. In this study, we develop a general mathematical model that allows us to explain and quantify this fundamental relationship between robustness and evolvability of heterogeneous cell populations. Our model predicts that robustness is, in fact, essential for evolvability, especially for more adverse environments, a trend we observe in aneuploid budding yeast and breast cancer cells. Robustness also compensates for the negative impact of the systems' complexity on their evolvability. Our model also provides a mathematical means to estimate the number of independent processes underlying a system's performance and identify the most generally adapted subpopulation, which may resemble the multi-drug-resistant "persister" cells observed in cancer.

First-principles X-ray absorption dose calculation for time-dependent mass and optical density.

A dose integral of time-dependent X-ray absorption under conditions of variable photon energy and changing sample mass is derived from first principles starting with the Beer-Lambert (BL) absorption model. For a given photon energy the BL dose integral D(e, t) reduces to the product of an effective time integral T(t) and a dose rate R(e). Two approximations of the time-dependent optical density, i.e. exponential A(t) = c + aexp(-bt) for first-order kinetics and hyperbolic A(t) = c + a/(b + t) for second-order kinetics, were considered for BL dose evaluation. For both models three methods of evaluating the effective time integral are considered: analytical integration, approximation by a function, and calculation of the asymptotic behaviour at large times. Data for poly(methyl methacrylate) and perfluorosulfonic acid polymers measured by scanning transmission soft X-ray microscopy were used to test the BL dose calculation. It was found that a previous method to calculate time-dependent dose underestimates the dose in mass loss situations, depending on the applied exposure time. All these methods here show that the BL dose is proportional to the exposure time D(e, t) ≃ K(e)t.