The hessian blob algorithm : precise particle detection in atomic force microscopy imagery

"Received: 20 October 2017; Accepted: 29 December 2017; Published online: 17 January 2018."Imaging by atomic force microscopy (AFM) offers high-resolution descriptions of many biological systems; however, regardless of resolution, conclusions drawn from AFM images are only as robust as the analysis leading to those conclusions. Vital to the analysis of biomolecules in AFM imagery is the initial detection of individual particles from large-scale images. Threshold and watershed algorithms are conventional for automatic particle detection but demand manual image preprocessing and produce particle boundaries which deform as a function of user-defined parameters, producing imprecise results subject to bias. Here, we introduce the Hessian blob to address these shortcomings. Combining a scalespace framework with measures of local image curvature, the Hessian blob formally defines particle centers and their boundaries, both to subpixel precision. Resulting particle boundaries are independent of user defined parameters, with no image preprocessing required. We demonstrate through direct comparison that the Hessian blob algorithm more accurately detects biomolecules than conventional AFM particle detection techniques. Furthermore, the algorithm proves largely insensitive to common imaging artifacts and noise, delivering a stable framework for particle analysis in AFM

Single-molecule observation of nucleotide induced conformational changes in basal SecA-ATP hydrolysis

11 pages ; illustrationsSecA is the critical adenosine triphosphatase that drives preprotein transport through the translocon, SecYEG, in Escherichia coli. This process is thought to be regulated by conformational changes of specific domains of SecA, but real-time, real-space measurement of these changes is lacking. We use single-molecule atomic force microscopy (AFM) to visualize nucleotide-dependent conformations and conformational dynamics of SecA. Distinct topographical populations were observed in the presence of specific nucleotides. AFM investigations during basal adenosine triphosphate (ATP) hydrolysis revealed rapid, reversible transitions between a compact and an extended state at the ~100-ms time scale. A SecA mutant lacking the precursor-binding domain (PBD) aided interpretation. Further, the biochemical activity of SecA prepared for AFM was confirmed by tracking inorganic phosphate release. We conclude that ATP-driven dynamics are largely due to PBD motion but that other segments of SecA contribute to this motion during the transition state of the ATP hydrolysis cycle.Funding: This work was supported by the National Science Foundation (CAREER award number 1054832 to G.M.K.) and a Burroughs Wellcome Fund Career Award at the Scientific Interface (to G.M.K.)Nagaraju Chada1*, Kanokporn Chattrakun1, Brendan P. Marsh1†, Chunfeng Mao2, Priya Bariya2, Gavin M. King1,2‡: 1Department of Physics and Astronomy, University of Missouri–Columbia, Columbia, MO 65211, USA. 2Department of Biochemistry, University of Missouri–Columbia, Columbia, MO 65211, USA. *Present address: Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA. †Present address: Department of Applied Physics, Stanford University, Stanford, CA 94305 USA. ‡Corresponding author.Nagaraju Chada (1*), Kanokporn Chattrakun (1), Brendan P. Marsh (1†), Chunfeng Mao (2), Priya Bariya (2), Gavin M. King (1,2‡) -- References: 1) Department of Physics and Astronomy, University of Missouri–Columbia, Columbia,MO 65211, USA ; 2) Department of Biochemistry, University of Missouri–Columbia, Columbia, MO 65211, USA ; *) Present address: Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA ; †) Present address: Department of Applied Physics, Stanford University, Stanford, CA 94305 USA ; ‡) Corresponding author

An optical lattice with sound

Funding: We acknowledge funding support from the Army Research Office. Y.G. and B.M. acknowledge funding from the Stanford Q-FARM Graduate Student Fellowship and the NSF Graduate Research Fellowship, respectively. S.G. acknowledges support from NSF Grant No. DMR-1653271.Quantized sound waves—phonons—govern the elastic response of crystalline materials, and also play an integral part in determining their thermodynamic properties and electrical response (for example, by binding electrons into superconducting Cooper pairs). The physics of lattice phonons and elasticity is absent in simulators of quantum solids constructed of neutral atoms in periodic light potentials: unlike real solids, traditional optical lattices are silent because they are infinitely stiff. Optical-lattice realizations of crystals therefore lack some of the central dynamical degrees of freedom that determine the low-temperature properties of real materials. Here, we create an optical lattice with phonon modes using a Bose–Einstein condensate (BEC) coupled to a confocal optical resonator. Playing the role of an active quantum gas microscope, the multimode cavity QED system both images the phonons and induces the crystallization that supports phonons via short-range, photon-mediated atom–atom interactions. Dynamical susceptibility measurements reveal the phonon dispersion relation, showing that these collective excitations exhibit a sound speed dependent on the BEC–photon coupling strength. Our results pave the way for exploring the rich physics of elasticity in quantum solids, ranging from quantum melting transitions to exotic ‘fractonic’ topological defects in the quantum regime.PostprintPeer reviewe

Enhancing associative memory recall and storage capacity using confocal cavity QED

Funding: Y.G. and B.M. acknowledgefunding from the Stanford Q-FARM Graduate Student Fellowship and the NSF Graduate Research Fellowship, respectively. J.K. acknowledges support from the Leverhulme Trust (IAF-2014-025), and S.G. acknowledges funding from the James S. McDonnell and Simons Foundations and an NSF Career Award.We introduce a near-term experimental platform for realizing an associative memory. It can simultaneously store many memories by using spinful bosons coupled to a degenerate multimode optical cavity. The associative memory is realized by a confocal cavity QED neural network, with the modes serving as the synapses, connecting a network of superradiant atomic spin ensembles,which serve as the neurons. Memories are encoded in the connectivity matrix between the spins and can be accessed through the input and output of patterns of light. Each aspect of the scheme is based on recently demonstrated technology using a confocal cavity and Bose-condensed atoms. Our scheme has two conceptually novel elements. First, it introduces a new form of random spin system that interpolates between a ferromagnetic and a spin glass regime as a physical parameter is tuned—the positions of ensembles within the cavity. Second, and more importantly, the spins relax via deterministic steepest-descent dynamics rather than Glauber dynamics. We show that this nonequilibrium quantum-optical scheme has significant advantages for associative memory over Glauber dynamics: These dynamics can enhance the network’s ability to store and recall memories beyond that of the standard Hopfield model. Surprisingly, the cavity QED dynamics can retrieve memories even when the system is in the spin glass phase. Thus, the experimental platform provides a novel physical instantiation of associative memories and spin glasses as well as provides an unusual form of relaxational dynamics that is conducive to memory recall even in regimes where it was thought to be impossible.Publisher PDFPeer reviewe

Glass : a multi-platform specimen supporting substrate for precision single molecule studies of membrane proteins : [abstract]

Abstract only."852-Pos Board B632.""Page 170a, Sunday, February 8, 2015."--At top of page.Abstract in program book: High resolution (~ 1 nm lateral resolution) biological AFM imaging has been carried out almost exclusively using freshly cleaved mica as a specimen supporting surface, but mica suffers from a fundamental limitation that has hindered AFM’s broader integration with many modern optical methods. Mica exhibits biaxial birefringence; indeed, this naturally occurring material is used commercially for constructing optical wave plates. In general, propagation through birefringent material alters the polarization state and bifurcates the propagation direction of light in a manner which varies with thickness. This makes it challenging to incorporate freshly cleaved mica substrates with modern optical methods, many of which employ highly focused and polarized laser beams passing through then specimen plane. Using bacteriorhodopsin from Halobacterium salinarum and the translocon SecYEG from Escherichia coli, we demonstrate that faithful images of 2D crystalline and non-crystalline membrane proteins in lipid bilayers can be obtained on common microscope cover glass following a straight-forward cleaning procedure. Direct comparison between data obtained on glass and on mica show no significant differences in AFM image fidelity. This work opens the door for combining high resolution biological AFM with powerful optical methods that require optically isotropic substrates such as ultra-stable1 and direct 3D AFM2. In turn, this capability should enable long timescale conformational dynamics measurements of membrane proteins in near-native conditions

Integrating Survey and Molecular Approaches to Better Understand Wildlife Disease Ecology

Infectious wildlife diseases have enormous global impacts, leading to human pandemics, global biodiversity declines and socio-economic hardship. Understanding how infection persists and is transmitted in wildlife is critical for managing diseases, but our understanding is limited. Our study aim was to better understand how infectious disease persists in wildlife populations by integrating genetics, ecology and epidemiology approaches. Specifically, we aimed to determine whether environmental or host factors were stronger drivers of Salmonella persistence or transmission within a remote and isolated wild pig (Sus scrofa) population. We determined the Salmonella infection status of wild pigs. Salmonella isolates were genotyped and a range of data was collected on putative risk factors for Salmonella transmission. We a priori identified several plausible biological hypotheses for Salmonella prevalence (cross sectional study design) versus transmission (molecular case series study design) and fit the data to these models. There were 543 wild pig Salmonella observations, sampled at 93 unique locations. Salmonella prevalence was 41% (95% confidence interval [CI]: 37-45%). The median Salmonella DICE coefficient (or Salmonella genetic similarity) was 52% (interquartile range [IQR]: 42-62%). Using the traditional cross sectional prevalence study design, the only supported model was based on the hypothesis that abundance of available ecological resources determines Salmonella prevalence in wild pigs. In the molecular study design, spatial proximity and herd membership as well as some individual risk factors (sex, condition score and relative density) determined transmission between pigs. Traditional cross sectional surveys and molecular epidemiological approaches are complementary and together can enhance understanding of disease ecology: abundance of ecological resources critical for wildlife influences Salmonella prevalence, whereas Salmonella transmission is driven by local spatial, social, density and individual factors, rather than resources. This enhanced understanding has implications for the control of diseases in wildlife populations. Attempts to manage wildlife disease using simplistic density approaches do not acknowledge the complexity of disease ecology

Demonstration of a positron beam-driven hollow channel plasma wakefield accelerator

International audiencePlasma wakefield accelerators have been used to accelerate electron and positron particle beams with gradients that are orders of magnitude larger than those achieved in conventional accelerators. In addition to being accelerated by the plasma wakefield, the beam particles also experience strong transverse forces that may disrupt the beam quality. Hollow plasma channels have been proposed as a technique for generating accelerating fields without transverse forces. Here we demonstrate a method for creating an extended hollow plasma channel and measure the wakefields created by an ultrarelativistic positron beam as it propagates through the channel. The plasma channel is created by directing a high-intensity laser pulse with a spatially modulated profile into lithium vapour, which results in an annular region of ionization. A peak decelerating field of 230 MeV/m is inferred from changes in the beam energy spectrum, in good agreement with theory and particle-in-cell simulations

Long- and short-term outcomes in renal allografts with deceased donors: A large recipient and donor genome-wide association study.

Improvements in immunosuppression have modified short-term survival of deceased-donor allografts, but not their rate of long-term failure. Mismatches between donor and recipient HLA play an important role in the acute and chronic allogeneic immune response against the graft. Perfect matching at clinically relevant HLA loci does not obviate the need for immunosuppression, suggesting that additional genetic variation plays a critical role in both short- and long-term graft outcomes. By combining patient data and samples from supranational cohorts across the United Kingdom and European Union, we performed the first large-scale genome-wide association study analyzing both donor and recipient DNA in 2094 complete renal transplant-pairs with replication in 5866 complete pairs. We studied deceased-donor grafts allocated on the basis of preferential HLA matching, which provided some control for HLA genetic effects. No strong donor or recipient genetic effects contributing to long- or short-term allograft survival were found outside the HLA region. We discuss the implications for future research and clinical application

Translating Marine Animal Tracking Data into Conservation Policy and Management

There have been efforts around the globe to track individuals of many marine species and assess their movements and distribution with the putative goal of supporting their conservation and management. Determining whether, and how, tracking data have been successfully applied to address real-world conservation issues is however difficult. Here, we compile a broad range of case studies from diverse marine taxa to show how tracking data have helped inform conservation policy and management, including reductions in fisheries bycatch and vessel strikes, and the design and administration of marine protected areas and important habitats. Using these examples, we highlight pathways through which the past and future investment in collecting animal tracking data might be better used to achieve tangible conservation benefits

Global Conservation Priorities for Marine Turtles

Where conservation resources are limited and conservation targets are diverse, robust yet flexible priority-setting frameworks are vital. Priority-setting is especially important for geographically widespread species with distinct populations subject to multiple threats that operate on different spatial and temporal scales. Marine turtles are widely distributed and exhibit intra-specific variations in population sizes and trends, as well as reproduction and morphology. However, current global extinction risk assessment frameworks do not assess conservation status of spatially and biologically distinct marine turtle Regional Management Units (RMUs), and thus do not capture variations in population trends, impacts of threats, or necessary conservation actions across individual populations. To address this issue, we developed a new assessment framework that allowed us to evaluate, compare and organize marine turtle RMUs according to status and threats criteria. Because conservation priorities can vary widely (i.e. from avoiding imminent extinction to maintaining long-term monitoring efforts) we developed a “conservation priorities portfolio” system using categories of paired risk and threats scores for all RMUs (n = 58). We performed these assessments and rankings globally, by species, by ocean basin, and by recognized geopolitical bodies to identify patterns in risk, threats, and data gaps at different scales. This process resulted in characterization of risk and threats to all marine turtle RMUs, including identification of the world's 11 most endangered marine turtle RMUs based on highest risk and threats scores. This system also highlighted important gaps in available information that is crucial for accurate conservation assessments. Overall, this priority-setting framework can provide guidance for research and conservation priorities at multiple relevant scales, and should serve as a model for conservation status assessments and priority-setting for widespread, long-lived taxa