Right in two: capabilities of ion mobility spectrometry for untargeted metabolomics

This mini review focuses on the opportunities provided by current and emerging separation techniques for mass spectrometry metabolomics. The purpose of separation technologies in metabolomics is primarily to reduce complexity of the heterogeneous systems studied, and to provide concentration enrichment by increasing sensitivity towards the quantification of low abundance metabolites. For this reason, a wide variety of separation systems, from column chemistries to solvent compositions and multidimensional separations, have been applied in the field. Multidimensional separations are a common method in both proteomics applications and gas chromatography mass spectrometry, allowing orthogonal separations to further reduce analytical complexity and expand peak capacity. These applications contribute to exponential increases in run times concomitant with first dimension fractionation followed by second dimension separations. Multidimensional liquid chromatography to increase peak capacity in metabolomics, when compared to the potential of running additional samples or replicates and increasing statistical confidence, mean that uptake of these methods has been minimal. In contrast, in the last 15 years there have been significant advances in the resolution and sensitivity of ion mobility spectrometry, to the point where high-resolution separation of analytes based on their collision cross section approaches chromatographic separation, with minimal loss in sensitivity. Additionally, ion mobility separations can be performed on a chromatographic timescale with little reduction in instrument duty cycle. In this review, we compare ion mobility separation to liquid chromatographic separation, highlight the history of the use of ion mobility separations in metabolomics, outline the current state-of-the-art in the field, and discuss the future outlook of the technology. "Where there is one, you're bound to divide it. Right in two", James Maynard Keenan.

Lumbar multiunit activity power spectrum during air-stepping in the spinal cat: evidence for a flexor dominated rostrocaudally distributed locomotor center

Clues about the organization of spinal networks responsible for rhythmic motor behaviors have come from examination of reflex circuitry, lesioning studies and single cell recordings. Recently, more attention has been paid to extracellularly recorded multiunit signals thought to represent the general activity of local cellular potentials. Focusing on the gross localization of spinal locomotor networks, we used multiunit signals of the lumbar cord to classify the activation and organization of those networks. We employed power spectral analysis to compare multiunit power across rhythmic conditions and locations and to infer patterns of activation based upon coherence and phase measures. We found greater multiunit power in mid-lumbar segments during stepping, supportive of previous lesioning studies isolating rhythm generating capabilities to these segments. We also found much greater multiunit power during the flexion phase of stepping than during the extension phase for all lumbar segments. Greater multiunit power at flexion indicates increased neural activity during this phase and is suggestive of previously reported asymmetries between flexor and extensor related interneuronal populations of the spinal rhythm generating network. Finally, the multiunit power showed no phase lag at coherent frequencies throughout the lumbar enlargement indicative of a longitudinal standing wave of neural activation. Our results suggest that the multiunit activity may be representative of the spinal rhythm generating activity that is distributed in a rostrocaudal gradient. Additionally, our results indicate that this multiunit activity may operate as a flexor dominant standing wave of activation that is synchronized throughout the rostrocaudal extent of the lumbar enlargement.

Modelling of Tissue Invasion in Epithelial Monolayers

Mathematical and computational models are used to describe biomechanical processes in multicellular systems. Here, we develop a model to analyse how two types of epithelial cell layers interact during tissue invasion depending on their cellular properties, i.e., simulating cancer cells expanding into a region of normal cells. We model the tissue invasion process using the cellular Potts model and implement our two-dimensional computational simulations in the software package CompuCell3D. The model predicts that differences in mechanical properties of cells can lead to tissue invasion, even if the division rates and death rates of the two cell types are the same. We also show how the invasion speed varies depending on the cell division and death rates and the mechanical properties of the cells.

Antigenic escape is accelerated by the presence of immunocompromised hosts

The repeated emergence of SARS-CoV-2 escape mutants from host immunity has obstructed the containment of the current pandemic and poses a serious threat to humanity. Prolonged infection in immunocompromised patients has received increasing attention as a driver of immune escape, and accumulating evidence suggests that viral genomic diversity and emergence of immune-escape mutants are promoted in immunocompromised patients. However, because immunocompromised patients comprise a small proportion of the host population, whether they have a significant impact on antigenic evolution at the population level is unknown. We consider an evolutionary epidemiological model that combines antigenic evolution and epidemiological dynamics. Applying this model to a heterogeneous host population, we study the impact of immunocompromised hosts on the evolutionary dynamics of pathogen antigenic escape from host immunity. We derived analytical formulae of the speed of antigenic evolution in heterogeneous host populations and found that even a small number of immunocompromised hosts in the population significantly accelerates antigenic evolution. Our results demonstrate that immunocompromised hosts play a key role in viral adaptation at the population level and emphasize the importance of critical care and surveillance of immunocompromised hosts.

Travelling-Wave Electrophoresis, Electro-Hydrodynamics, Electro-Rotation, and Symmetry- Breaking of a Polarizable Dimer in Non-Uniform Fields

A theoretical framework is presented for calculating the polarization, electro-rotation, travelling-wave dielectrophoresis, electro-hydrodynamics and induced-charge electroosmotic flow fields around a freely suspended conducting dimer (two touching spheres) exposed to non-uniform direct current (DC) or alternating current (AC) electric fields. The analysis is based on employing the classical (linearized) Poisson–Nernst–Planck (PNP) formulation under the standard linearized ‘weak-field’ assumption and using the tangent-sphere coordinate system. Explicit expressions are first derived for the axisymmetric AC electric potential governed by the Robin (mixed) boundary condition applied on the dimer surface depending on the resistance–capacitance circuit (RC) forcing frequency. Dimer electro-rotation due to two orthogonal (out-of-phase) uniform AC fields and the corresponding mobility problem of a polarizable dimer exposed to a travelling-wave electric excitation are also analyzed. We present an explicit solution for the non-linear induced-charge electroosmotic (ICEO) flow problem of a free polarized dimer in terms of the corresponding Stokes stream function determined by the Helmholtz–Smoluchowski velocity slip. Next, we demonstrate how the same framework can be used to obtain an exact solution for the electro-hydrodynamic (EHD) problem of a polarizable sphere lying next to a conducting planar electrode. Finally, we present a new solution for the induced-charge mobility of a Janus dimer composed of two fused spherical colloids, one perfectly conducting and one dielectrically coated. So far, most of the available electrokinetic theoretical studies involving polarizable nano/micro shapes dealt with convex configurations (e.g., spheres, spheroids, ellipsoids) and as such the newly obtained electrostatic AC solution for a dimer provides a useful extension for similar concave colloids and engineered particles.

Influence of the basilar membrane shape and mechanical properties in the cochlear response: A numerical study

Hearing impairment is one of the most common health disorders, affecting individuals of all ages, reducing considerably their quality of life. At present, it is known that during an acoustic stimulation a travelling wave is developed inside the cochlea. Existing mathematical and numerical models available in the literature try to describe the shape of this travelling wave, the majority of them present a set of approaches based on some limitations either or both of the mechanical properties used and the geometrical description of the realistic representation. The present numerical study highlights the distinctions of using a spiral model of the cochlea, by comparing the obtained results with a straight, or simplified model. The influence of the implantation of transversely isotropic mechanical models was also studied, by comparing the basilar membrane with isotropic and transversely isotropic mechanical properties. Values of the root mean square error calculated for all models show a greater proximity of the cochlear mapping to the Greenwood function when the basilar membrane is assumed with transversely isotropic mechanical properties for both straight and spiral model. The root-mean square errors calculated were: 2.05, 1.70, 2.72, 2.08 mm, for the straight-isotropic, straight-transversely isotropic, spiral-isotropic and spiral-transversely isotropic model, respectively.

Comparative micromechanics of bushcricket ears with and without a specialized auditory fovea region in the crista acustica

In some insects and vertebrate species, the specific enlargement of sensory cell epithelium facilitates the perception of particular behaviourally relevant signals. The insect auditory fovea in the ear of the bushcricket Ancylecha fenestrata (Tettigoniidae: Phaneropterinae) is an example of such an expansion of sensory epithelium. Bushcricket ears developed in convergent evolution anatomical and functional similarities to mammal ears, such as travelling waves and auditory foveae, to process information by sound. As in vertebrate ears, sound induces a motion of this insect hearing organ (crista acustica), which can be characterized by its amplitude and phase response. However, detailed micromechanics in this bushcricket ear with an auditory fovea are yet unknown. Here, we fill this gap in knowledge for bushcricket, by analysing and comparing the ear micromechanics in Ancylecha fenestrata and a bushcricket species without auditory fovea (Mecopoda elongata, Tettigoniidae: Mecopodinae) using laser-Doppler vibrometry. We found that the increased size of the crista acustica, expanded by a foveal region in A. fenestrata, leads to higher mechanical amplitudes and longer phase delays in A. fenestrata male ears. Furthermore, area under curve analyses of the organ oscillations reveal that more sensory units are activated by the same stimuli in the males of the auditory fovea-possessing species A. fenestrata. The measured increase of phase delay in the region of the auditory fovea supports the conclusion that tilting of the transduction site is important for the effective opening of the involved transduction channels. Our detailed analysis of sound-induced micromechanics in this bushcricket ear demonstrates that an increase of sensory epithelium with foveal characteristics can enhance signal detection and may also improve the neuronal encoding.

Bidirectional Linear Motion by Travelling Waves on Legged Piezoelectric Microfabricated Plates

This paper reports the design, fabrication and performance of MEMS-based piezoelectric bidirectional conveyors featuring 3D printed legs, driven by linear travelling waves (TW). The structures consisted of an aluminium–nitride (AlN) piezoelectric film on top of millimetre-sized rectangular thin silicon bridges and two electrode patches. The position and size of the patches were analytically optimised for TW generation in three frequency ranges: 19, 112 and 420 kHz, by the proper combination of two contiguous flexural modes. After fabrication, the generated TW were characterized by means of Laser–Doppler vibrometry to obtain the relevant tables of merit, such as the standing wave ratio and the average amplitude. The experimental results agreed with the simulation, showing the generation of a TW with an amplitude as high as 6 nm/V and a standing wave ratio as low as 1.46 for a device working at 19.3 kHz. The applicability of the fabricated linear actuator device as a conveyor was investigated. Its kinetic performance was studied with sliders of different mass, being able to carry a 35 mg silicon slider, 18 times its weight, with 6 V of continuous sinusoidal excitation and a speed of 0.65 mm/s. A lighter slider, weighting only 3 mg, reached a mean speed of 1.7 mm/s at 6 V. In addition, by applying a burst sinusoidal excitation comprising 10 cycles, the TW generated in the bridge surface was able to move a 23 mg slider in discrete steps of 70 nm, in both directions, which is a promising result for a TW piezoelectric actuator of this size.

Revisiting the Fisher-Kolmogorov-Petrovsky-Piskunov equation to interpret the spreading-extinction dichotomy

The Fisher-Kolmogorov-Petrovsky-Piskunov model, also known as the Fisher-KPP model, supports travelling wave solutions that are successfully used to model numerous invasive phenomena with applications in biology, ecology and combustion theory. However, there are certain phenomena that the Fisher-KPP model cannot replicate, such as the extinction of invasive populations. The Fisher-Stefan model is an adaptation of the Fisher-KPP model to include a moving boundary whose evolution is governed by a Stefan condition. The Fisher-Stefan model also supports travelling wave solutions; however, a key additional feature of the Fisher-Stefan model is that it is able to simulate population extinction, giving rise to a spreading-extinction dichotomy. In this work, we revisit travelling wave solutions of the Fisher-KPP model and show that these results provide new insight into travelling wave solutions of the Fisher-Stefan model and the spreading-extinction dichotomy. Using a combination of phase plane analysis, perturbation analysis and linearization, we establish a concrete relationship between travelling wave solutions of the Fisher-Stefan model and often-neglected travelling wave solutions of the Fisher-KPP model. Furthermore, we give closed-form approximate expressions for the shape of the travelling wave solutions of the Fisher-Stefan model in the limit of slow travelling wave speeds, c≪1.

Reversible signal transmission in an active mechanical metamaterial

Mechanical metamaterials are designed to enable unique functionalities, but are typically limited by an initial energy state and require an independent energy input to function repeatedly. Our study introduces a theoretical active mechanical metamaterial that incorporates a biological reaction mechanism to overcome this key limitation of passive metamaterials. Our material allows for reversible mechanical signal transmission, where energy is reintroduced by the biologically motivated reaction mechanism. By analysing a coarse-grained continuous analogue of the discrete model, we find that signals can be propagated through the material by a travelling wave. Analysis of the continuum model provides the region of the parameter space that allows signal transmission, and reveals similarities with the well-known FitzHugh-Nagumo system. We also find explicit formulae that approximate the effect of the time scale of the reaction mechanism on the signal transmission speed, which is essential for controlling the material.

Spatial synchrony in sub-arctic geometrid moth outbreaks reflects dispersal in larval and adult life cycle stages

Spatial synchrony in population dynamics can be caused by dispersal or spatially correlated variation in environmental factors like weather (Moran effect). Distinguishing between these mechanisms is challenging for natural populations, and the study of dispersal-induced synchrony in particular has been dominated by theoretical modelling and laboratory experiments. The goal of the present study was to evaluate the evidence for dispersal as a cause of meso-scale (distances of tens of kilometres) spatial synchrony in natural populations of the two cyclic geometrid moths Epirrita autumnata and Operophtera brumata in sub-arctic mountain birch forest in northern Norway. To infer the role of dispersal in geometrid synchrony, we applied three complementary approaches, namely estimating the effect of design-based dispersal barriers (open sea) on synchrony, comparing the strength of synchrony between E. autumnata (winged adults) and the less dispersive O. brumata (wingless adult females), and relating the directionality (anisotropy) of synchrony to the predominant wind directions during spring, when geometrid larvae engage in windborne dispersal (ballooning). The estimated effect of dispersal barriers on synchrony was almost three times stronger for the less dispersive O. brumata than E. autumnata. Inter-site synchrony was also weakest for O. brumata at all spatial lags. Both observations argue for adult dispersal as an important synchronizing mechanism at the spatial scales considered. Further, synchrony in both moth species showed distinct anisotropy and was most spatially extensive parallel to the east-west axis, coinciding closely to the overall dominant wind direction. This argues for a synchronizing effect of windborne larval dispersal. Congruent with most extensive dispersal along the east-west axis, E. autumnata also showed evidence for a travelling wave moving southwards at a speed of 50-80 km/year. Our results suggest that dispersal processes can leave clear signatures in both the strength and directionality of synchrony in field populations, and highlight wind-driven dispersal as promising avenue for further research on spatial synchrony in natural insect populations.

Stability of combustion waves in a simplified gas-solid combustion model in porous media

We study the stability of the combustion waves that occur in a simplified model for injection of air into a porous medium that initially contains some solid fuel. We determine the essential spectrum of the linearized system at a travelling wave. For certain waves, we are able to use a weight function to stabilize the essential spectrum. We perform a numerical computation of the Evans function to show that some of these waves have no unstable discrete spectrum. The system is partly parabolic, so the linearized operator is not sectorial, and the weight function decays at one end. We use an extension of a recent result about partly parabolic systems that are stabilized by such weight functions to show nonlinear stability.This article is part of the theme issue 'Stability of nonlinear waves and patterns and related topics'.

A mathematical model of marine bacteriophage evolution

To explore how particularities of a host cell-virus system, and in particular host cell replication, affect viral evolution, in this paper we formulate a mathematical model of marine bacteriophage evolution. The intrinsic simplicity of real-life phage-bacteria systems, and in particular aquatic systems, for which the assumption of homogeneous mixing is well justified, allows for a reasonably simple model. The model constructed in this paper is based upon the Beretta-Kuang model of bacteria-phage interaction in an aquatic environment (Beretta & Kuang 1998 Math. Biosci.149, 57-76. (doi:10.1016/S0025-5564(97)10015-3)). Compared to the original Beretta-Kuang model, the model assumes the existence of a multitude of viral variants which correspond to continuously distributed phenotypes. It is noteworthy that the model is mechanistic (at least as far as the Beretta-Kuang model is mechanistic). Moreover, this model does not include any explicit law or mechanism of evolution; instead it is assumed, in agreement with the principles of Darwinian evolution, that evolution in this system can occur as a result of random mutations and natural selection. Simulations with a simplistic linear fitness landscape (which is chosen for the convenience of demonstration only and is not related to any real-life system) show that a pulse-type travelling wave moving towards increasing Darwinian fitness appears in the phenotype space. This implies that the overall fitness of a viral quasi-species steadily increases with time. That is, the simulations demonstrate that for an uneven fitness landscape random mutations combined with a mechanism of natural selection (for this particular system this is given by the conspecific competition for the resource) lead to the Darwinian evolution. It is noteworthy that in this system the speed of propagation of this wave (and hence the rate of evolution) is not constant but varies, depending on the current viral fitness and the abundance of susceptible bacteria. A specific feature of the original Beretta-Kuang model is that this model exhibits a supercritical Hopf bifurcation, leading to the loss of stability and the rise of self-sustained oscillations in the system. This phenomenon corresponds to the paradox of enrichment in the system. It is remarkable that under the conditions that ensure the bifurcation in the Beretta-Kuang model, the viral evolution model formulated in this paper also exhibits a rise in self-sustained oscillations of the abundance of all interacting populations. The propagation of the travelling wave, however, remains stable under these conditions. The only visible impact of the oscillations on viral evolution is a lower speed of the evolution.

The travelling wave of Gray-Scott systems - existence, multiplicity and stability

This article studies existence and stability of travelling wave of unstirred Gray-Scott system in biological pattern formation which models an isothermal chemical reaction [Formula: see text] involving two chemical species, a reactant A and an auto-catalyst B, and a linear decay [Formula: see text], where C is an inert product. Our result shows a new and very distinctive feature of Gray-Scott type of models in generating rich and structurally different travelling pulses than related models in the literature. In particular, the existence of multiple travelling waves which have distinctive number of local maxima is proved. Furthermore, the stability of travelling wave of the reaction-diffusion system of isothermal diffusion system [Formula: see text], is also studied.

Non-invasive biophysical measurement of travelling waves in the insect inner ear

Frequency analysis in the mammalian cochlea depends on the propagation of frequency information in the form of a travelling wave (TW) across tonotopically arranged auditory sensilla. TWs have been directly observed in the basilar papilla of birds and the ears of bush-crickets (Insecta: Orthoptera) and have also been indirectly inferred in the hearing organs of some reptiles and frogs. Existing experimental approaches to measure TW function in tetrapods and bush-crickets are inherently invasive, compromising the fine-scale mechanics of each system. Located in the forelegs, the bush-cricket ear exhibits outer, middle and inner components; the inner ear containing tonotopically arranged auditory sensilla within a fluid-filled cavity, and externally protected by the leg cuticle. Here, we report bush-crickets with transparent ear cuticles as potential model species for direct, non-invasive measuring of TWs and tonotopy. Using laser Doppler vibrometry and spectroscopy, we show that increased transmittance of light through the ear cuticle allows for effective non-invasive measurements of TWs and frequency mapping. More transparent cuticles allow several properties of TWs to be precisely recovered and measured in vivo from intact specimens. Our approach provides an innovative, non-invasive alternative to measure the natural motion of the sensilla-bearing surface embedded in the intact inner ear fluid.

More than Skew: Asymmetric Wave Propagation in a Reaction-Diffusion-Convection System

Convection-induced instability in reaction-diffusion systems produces complicated patterns of oscillations behind propagating wavefronts. We transform the system twice: into lambda-omega form, then into polar variables. We find analytical estimates for the wavefront speed which we confirm numerically. Our previous work examined a simpler system [E. H. Flach, S. Schnell, and J. Norbury, Phys. Rev. E 76, 036216 (2007)]; the onset of instability is qualitatively different in numerical solutions of this system. We modify our estimates and connect the two different behaviours. Our estimate explains how the Turing instability fits with pattern found in reaction-diffusion-convection systems. Our results can have important applications to the pattern formation analysis of biological systems.

Modelling the spread of Wolbachia in spatially heterogeneous environments

The endosymbiont Wolbachia infects a large number of insect species and is capable of rapid spread when introduced into a novel host population. The bacteria spread by manipulating their hosts' reproduction, and their dynamics are influenced by the demographic structure of the host population and patterns of contact between individuals. Reaction-diffusion models of the spatial spread of Wolbachia provide a simple analytical description of their spatial dynamics but do not account for significant details of host population dynamics. We develop a metapopulation model describing the spatial dynamics of Wolbachia in an age-structured host insect population regulated by juvenile density-dependent competition. The model produces similar dynamics to the reaction-diffusion model in the limiting case where the host's habitat quality is spatially homogeneous and Wolbachia has a small effect on host fitness. When habitat quality varies spatially, Wolbachia spread is usually much slower, and the conditions necessary for local invasion are strongly affected by immigration of insects from surrounding regions. Spread is most difficult when variation in habitat quality is spatially correlated. The results show that spatial variation in the density-dependent competition experienced by juvenile host insects can strongly affect the spread of Wolbachia infections, which is important to the use of Wolbachia to control insect vectors of human disease and other pests.

Improved RF performance of travelling wave MR with a high permittivity dielectric lining of the bore

Application of travelling wave MR to human body imaging is restricted by the limited peak power of the available RF amplifiers. Nevertheless, travelling wave MR advantages like a large field of view excitation and distant location of transmit elements would be desirable for whole body MRI. In this work, improvement of the B1+ efficiency of travelling wave MR is demonstrated. High permittivity dielectric lining placed next to the scanner bore wall effectively reduces attenuation of the travelling wave in the longitudinal direction and at the same time directs the radial power flow toward the load. First, this is shown with an analytical model of a metallic cylindrical waveguide with the dielectric lining next to the wall and loaded with a cylindrical phantom. Simulations and experiments also reveal an increase of B1+ efficiency in the center of the bore for travelling wave MR with a dielectric lining. Phantom experiments show up to a 2-fold gain in B1+ with the dielectric lining. This corresponds to a 4-fold increase in power efficiency of travelling wave MR. In vivo experiments demonstrate an 8-fold signal-to-noise ratio gain with the dielectric lining. Overall, it is shown that dielectric lining is a constructive method to improve efficacy of travelling wave MR.

Coaxial waveguide for travelling wave MRI at ultrahigh fields

At high magnetic fields the performance of a volume-type body coil inside a human sized MR-scanner is influenced by the waveguide action of the scanner's bore. This can result in undesirable strong radio frequency fields B1+) outside the coil's target volume. A radio frequency (RF) transmit system, exploiting this waveguide action of the bore, is proposed in this work. A coaxial waveguide section is introduced between the antenna and the imaging region. It is shown that the coaxial waveguide has several advantages over the initially proposed travelling wave setup based on the cylindrical waveguide. First, a novel radio frequency matching principle (based on the transmission line impedance matching) is feasible with the coaxial waveguide achieving better radio frequency transmission characteristics, such as homogeneity and power efficiency of B1+ field. In case of body torso imaging, the coaxial waveguide prevents unwanted specific absorptive rate (SAR) deposition outside the target region and thus, effectively decreases local peak SAR values by factor of 5. A 3-fold B1+ gain in the prostate can be achieved with the coaxial waveguide in comparison with the initially proposed travelling wave setup.