Seppe Kuehn

Advances in mechanical detection of magnetic resonance

The invention and initial demonstration of magnetic resonance force microscopy (MRFM) in the early 1990s launched a renaissance of mechanical approaches to detecting magnetic resonance. This article reviews progress made in MRFM in the last decade, including the demonstration of scanned probe detection of magnetic resonance (electron spin resonance, ferromagnetic resonance, and nuclear magnetic resonance) and the mechanical detection of electron spin resonance from a single spin. Force and force-gradient approaches to mechanical detection are reviewed and recent related work using attonewton sensitivity cantilevers to probe minute fluctuating electric fields near surfaces is discussed. Given recent progress, pushing MRFM to single proton sensitivity remains an exciting possibility. We will survey some practical and fundamental issues that must be resolved to meet this challenge.

Force-gradient detected nuclear magnetic resonance

We have detected nuclear magnetic resonance in GaAs by selectively inverting 71Ga spins to create a local force gradient which shifts the mechanical resonance frequency of a nearby magnet tipped microcantilever. Employing a low spring constant cantilever (60 μN/m) at 4.4 K and 7 T, we demonstrate a magnetic moment sensitivity of 7.5×10−21 J/T, equal to the Curie Law magnetization from 7.1×108 71Ga spins. The method obviates the need to spin-lock sample magnetization during detection, allowing the signal to be collected for a time approaching the full spin-lattice relaxation time.

Batch fabrication and characterization of ultrasensitive cantilevers with submicron magnetic tips

We have batch fabricated ultrasensitive silicon cantilevers with integrated submicron magnetic tips and have characterized both their mechanical and magnetic properties. Cantilevers with spring constants as small as 10−5 N/m were fabricated, with quality factors in the range of 2.5–3.5×104 and a force sensitivity as good as 64×10−18 N Hz−1/2 at room temperature in vacuum. Cantilever spring constants were measured by observing thermomechanical position fluctuations with a fiber optic interferometer, while resonance frequencies and quality factors were inferred from cantilever ring down transients. Polycrystalline nickel tips as small as 1.2 μm×0.4 μm×0.2 μm were fabricated on the cantilevers by electron beam lithography, thermal evaporation, and lift-off. Tip magnetic moments were inferred from the shift of the cantilever frequency versus magnetic field and show a 0.60±0.12 T saturation magnetization, indicating that less than 28 nm of oxide forms on the tips during processing. Force sensitivity was demons...

Quantifying Electric Field Gradient Fluctuations over Polymers Using Ultrasensitive Cantilevers

An ultrasensitive cantilever, oscillating parallel to a surface in vacuum, is used to probe weak thermal electric field gradient fluctuations over thin polymer films. We measure the power spectrum of cantilever frequency fluctuations as a function of cantilever height and voltage over polymers of various compositions and thicknesses. The data are well described by a linear-response theory that calculates stochastic electric fields arising from thermally driven dielectric fluctuations.

Behavioral diversity in microbes and low-dimensional phenotypic spaces.

Systematic studies of phenotypic diversity—required for understanding evolution—lag behind investigations of genetic diversity. Here we develop a quantitative approach to studying behavioral diversity, which we apply to swimming of the ciliate Tetrahymena. We measure the full-lifetime behavior of hundreds of individual organisms at high temporal resolution, over several generations and in diverse nutrient conditions. To characterize population diversity and temporal variability we introduce a unique statistical framework grounded in the notion of a phenotypic space of behaviors. We show that this space is effectively low dimensional with dimensions that correlate with a two-state “roaming and dwelling” model of swimming behavior. Temporal variability over the lifetime of an individual is correlated with the fraction of time spent roaming whereas diversity between individuals is correlated with the speed of roaming. Quantifying the dynamics of behavioral variation shows that behavior over the lifetime of an individual is strongly nonstationary. Analysis of behavioral dynamics between generations reveals complex patterns of behavioral heritability that point to the importance of considering correlations beyond mothers and daughters. Our description of a low-dimensional behavioral space should enable the systematic study of the evolutionary and ecological bases of phenotypic constraints. Future experimental and theoretical studies of behavioral diversity will have to account for the possibility of nonstationary and environmentally dependent behavioral dynamics that we observe.

Microbial population dynamics by digital in-line holographic microscopy

Measurements of population dynamics are ubiquitous in experiments with microorganisms. Studies with microbes elucidating adaptation, selection, and competition rely on measurements of changing populations in time. Despite this importance, quantitative methods for measuring population dynamics microscopically, with high time resolution, across many replicates remain limited. Here we present a new noninvasive method to precisely measure microbial spatiotemporal population dynamics based on digital in-line holographic (DIH) microscopy. Our inexpensive, replicate DIH microscopes imaged hundreds of swimming algae in three dimensions within a volume of several microliters on a time scale of minutes over periods of weeks.

Environment determines evolutionary trajectory in a constrained phenotypic space

Constraints on phenotypic variation limit the capacity of organisms to adapt to the multiple selection pressures encountered in natural environments. To better understand evolutionary dynamics in this context, we select Escherichia coli for faster migration through a porous environment, a process which depends on both motility and growth. We find that a trade-off between swimming speed and growth rate constrains the evolution of faster migration. Evolving faster migration in rich medium results in slow growth and fast swimming, while evolution in minimal medium results in fast growth and slow swimming. In each condition parallel genomic evolution drives adaptation through different mutations. We show that the trade-off is mediated by antagonistic pleiotropy through mutations that affect negative regulation. A model of the evolutionary process shows that the genetic capacity of an organism to vary traits can qualitatively depend on its environment, which in turn alters its evolutionary trajectory. DOI: http://dx.doi.org/10.7554/eLife.24669.001

Quantitative high-throughput population dynamics in continuous-culture by automated microscopy

We present a high-throughput method to measure abundance dynamics in microbial communities sustained in continuous-culture. Our method uses custom epi-fluorescence microscopes to automatically image single cells drawn from a continuously-cultured population while precisely controlling culture conditions. For clonal populations of Escherichia coli our instrument reveals history-dependent resilience and growth rate dependent aggregation.

Dynamic structure of locomotor behavior in walking fruit flies

The function of the brain is unlikely to be understood without an accurate description of its output, yet the nature of movement elements and their organization remains an open problem. Here, movement elements are identified from dynamics of walking in flies, using unbiased criteria. On one time scale, dynamics of walking are consistent over hundreds of milliseconds, allowing elementary features to be defined. Over longer periods, walking is well described by a stochastic process composed of these elementary features, and a generative model of this process reproduces individual behavior sequences accurately over seconds or longer. Within elementary features, velocities diverge, suggesting that dynamical stability of movement elements is a weak behavioral constraint. Rather, long-term instability can be limited by the finite memory between these elementary features. This structure suggests how complex dynamics may arise in biological systems from elements whose combination need not be tuned for dynamic stability. DOI: http://dx.doi.org/10.7554/eLife.26410.001

Hitchhiking, collapse and contingency in phage infections of migrating bacterial populations

Natural bacterial populations are subject to constant predation pressure by phages. Bacteria use a variety of well-studied molecular mechanisms to defend themselves from phage predation. However, since phage are non-motile, perhaps the simplest defense against phage would be for bacteria to outrun their predators. In particular, chemotaxis, the active migration of bacteria up attractant gradients, may help the bacteria escape slowly diffusing phages. Here we study phage infection dynamics in migrating bacterial populations driven by chemotaxis through low viscosity agar plates. We find that expanding phage-bacteria populations support two migrating fronts, an outermost “bacterial” front driven by nutrient uptake and chemotaxis and an inner “phage” front at which bacterial population collapses due to phage predation. We show that with increasing adsorption rate and initial phage population, the rate of migration of the phage front increases, eventually overtaking the bacterial front and driving the system across a “phage transition” from a regime where bacteria outrun a phage infection to one where they must evolve phage resistance to survive. We confirm experimentally that this process requires phages to “surf” the bacterial front by repeatedly reinfecting the fastest moving bacteria. A deterministic model recapitulates the transition. Macroscopic fluctuations in bacterial densities at the phage front suggest that a feedback mechanism, possibly due to growth rate dependent phage infection rates, drives millimeter scale spatial structure in phage-bacteria populations. Our work opens a new, spatiotemporal, line of investigation into the eco-evolutionary struggle between bacteria and their phage predators. Significance Statement The infection of bacteria by phage requires physical contact. This fact means that motile bacteria may avoid non-motile phage by simply running away. By this mechanism bacterial chemotaxis may help bacteria to escape phages. Here we show that when phage infect bacteria moving in soft agar plates, high phage populations or infectivity rates result in phages stopping and killing all bacteria. Conversely, when initial phage numbers or infectivity rates are low, bacteria are able to migrate away from phage successfully, despite phage ability to “surf” bacterial fronts for more than 24 hours. Between these regimes we document a “phage transition” where bacterial physiology and contingency in phage infection manifest through large-scale fluctuations in spatio-temporal dynamics.