P.C. Doerschuk

Cornell University, Ithaca, New York, United States

Are you P.C. Doerschuk?

Claim your profile

Publications (105)148.66 Total impact

  • [show abstract] [hide abstract]
    ABSTRACT: Quasi-equivalent viruses that infect animals and bacteria require a maturation process in which particles transition from initially assembled procapsids to infectious virions. Nudaurelia capensis ω virus (NωV) is a T = 4, eukaryotic, single-stranded ribonucleic acid virus that has proved to be an excellent model system for studying the mechanisms of viral maturation. Structures of NωV procapsids (diameter = 480 Å), a maturation intermediate (410 Å), and the mature virion (410 Å) were determined by electron cryo-microscopy and three-dimensional image reconstruction (cryoEM). The cryoEM density for each particle type was analyzed with a recently developed maximum likelihood variance (MLV) method for characterizing microstates occupied in the ensemble of particles used for the reconstructions. The procapsid and the mature capsid had overall low variance (i.e., uniform particle populations) while the maturation intermediate (that had not undergone post-assembly autocatalytic cleavage) had roughly two to four times the variance of the first two particles. Without maturation cleavage, the particles assume a variety of microstates, as the frustrated subunits cannot reach a minimum energy configuration. Geometric analyses of subunit coordinates provided a quantitative description of the particle reorganization during maturation. Superposition of the four quasi-equivalent subunits in the procapsid had an average root mean square deviation (RMSD) of 3 Å while the mature particle had an RMSD of 11 Å, showing that the subunits differentiate from near equivalent environments in the procapsid to strikingly non-equivalent environments during maturation. Autocatalytic cleavage is clearly required for the reorganized mature particle to reach the minimum energy state required for stability and infectivity. Copyright © 2014 John Wiley & Sons, Ltd.
    Journal of Molecular Recognition 04/2014; 27(4). · 3.01 Impact Factor
  • [show abstract] [hide abstract]
    ABSTRACT: We generalize the concept of allostery from the traditional non active-site control of enzymes to virus maturation. Virtually all animal viruses transition from a procapsid, non infectious state, to a mature infectious state. The procapsid contains an encoded chemical program that is executed following an environmental cue. We developed an exceptionally accessible virus system for the study of the activators of maturation and the down stream consequences that result in particle stability and infectivity.Nudaurelia Capensis Omegavirus (NωV) is a T=4 icosahedral virus that undergoes a dramatic maturation in which the 490Å spherical procapsid condenses to a 400Å icosahedral shaped capsid with associated specific auto-proteolysis and stabilization. Employing X-ray crystallography, time resolved electron cryo-microscopy and hydrogen/deuterium exchange as well as biochemistry it was possible to define the mechanisms of allosteric communication among the 4 quasi-equivalent subunits in the icosahedral asymmetric unit. These gene products undergo proteolysis at different rates, dependent on quaternary structure environment, while particle stability is conferred globally following only a few local subunit transitions. We show that there is a close similarity between the concepts of tensegrity, associated with geodesic domes and mechanical engineering, and allostery, associated with biochemical control mechanisms.
    Journal of Molecular Biology 02/2013; · 3.91 Impact Factor
  • [show abstract] [hide abstract]
    ABSTRACT: CryoEM data capture the dynamic character associated with biological macromolecular assemblies by preserving the various conformations of the individual specimens at the moment of flash freezing. Regions of high variation in the data set are apparent in the image reconstruction due to the poor density that results from the lack of superposition of these regions. These observations are qualitative and, to date, only preliminary efforts have been made to quantitate the heterogeneity in the ensemble of particles that are individually imaged. We developed and tested a quantitative method for simultaneously computing a reconstruction of the particle and a map of the space-varying heterogeneity of the particle based on an entire data set. The method uses a maximum likelihood algorithm that explicitly takes into account the continuous variability from one instance to another instance of the particle. The result describes the heterogeneity of the particle as a variance to be plotted at every voxel of the reconstructed density. The test, employing time resolved data sets of virus maturation, not only recapitulated local variations obtained with difference map analysis, but revealed a remarkable time dependent reduction in the overall particle dynamics that was unobservable with classical methods of analysis.
    Journal of Structural Biology 12/2012; · 3.36 Impact Factor
  • Yili Zheng, Qiu Wang, Peter C Doerschuk
    [show abstract] [hide abstract]
    ABSTRACT: An estimation problem for statistical reconstruction of heterogeneous three-dimensional objects from two-dimensional tomographic data (single-particle cryoelectron microscope images) is posed as the problem of estimating class probabilities, means, and covariances for a Gaussian mixture where both the mean and covariance are stochastically structured. Both discrete (i.e., classes) and continuous heterogeneity is included. A maximum likelihood solution computed by a generalized expectation-maximization algorithm is presented and demonstrated on experimental images of Flock House Virus.
    Journal of the Optical Society of America A 06/2012; 29(6):959-70. · 1.67 Impact Factor
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: The instantaneous rate of change of alcohol exposure (slope) may contribute to changes in measures of brain function following administration of alcohol that are usually attributed to breath alcohol concentration (BrAC) acting alone. To test this proposition, a 2-session experiment was designed in which carefully prescribed, constant-slope trajectories of BrAC intersected at the same exposure level and time since the exposure began. This paper presents the methods and limitations of the experimental design. Individualized intravenous infusion rate profiles of 6% ethanol (EtOH) that achieved the constant-slope trajectories for an individual were precomputed using a physiologically based pharmacokinetic model. Adjusting the parameters of the model allowed each infusion profile to account for the subject's EtOH distribution and elimination kinetics. Sessions were conducted in randomized order and made no use of feedback of BrAC measurements obtained during the session to modify the precalculated infusion profiles. In one session, an individual's time course of exposure, BrAC(t), was prescribed to rise at a constant rate of 6.0 mg% per minute until it reached 68 mg% and then descend at -1.0 mg% per minute; in the other, to rise at a rate of 3.0 mg% per minute. The 2 exposure trajectories were designed to intersect at a BrAC (t = 20 minutes) = 60 mg% at an experimental time of 20 minutes. Intersection points for 54 of 61 subjects were within prescribed deviations (range of ± 3 mg% and ± 4 minutes from the nominal intersection point). Results confirmed the feasibility of applying the novel methods for achieving the intended time courses of the BrAC, with technical problems limiting success to 90% of the individuals tested.
    Alcoholism Clinical and Experimental Research 04/2012; 36(6):1042-9. · 3.42 Impact Factor
  • Qiu Wang, Yili Zheng, Peter C. Doerschuk
    [show abstract] [hide abstract]
    ABSTRACT: Instances of biological macromolecular complexes that have identical chemical constituents may not have the same geometry due to, for example, flexibility. Cryo electron microscopy provides one noisy projection image of each of many instances of a complex where the projection directions for the different instances are random. The noise is sufficient severe (SNR << 1) that the projection direction for a particular image cannot be easily estimated from the individual image. The goal is to determine the 3-D geometry of the complex (the 3-D distribution of electron scattering intensity) which requires fusing information from these many images of many complexes. In order to describe the geometric heterogeneity of the complexes, the complex is described as a weighted sum of basis functions where the weights are random. In order to get tractable algorithms, the weights are modeled as Gaussian random variables with unknown statistics and the noise is modeled as additive Gaussian random variables with unknown covariance. The statistics of the weights and the statistics of the noise are jointly estimated by maximum likelihood by a generalized expectation maximization algorithm. The method has been developed to the point where it appears able to solve problems of interest to the structural biology community.
    Proc SPIE 02/2012;
  • Cory J. Prust, Qiu Wang, Peter C. Doerschuk, John E. Johnson
    [show abstract] [hide abstract]
    ABSTRACT: A highly scalable method for determining the projection orientation of each image in a set of cryo electron microscopy images of a labeled particle is proposed. The method relies on the presence of a label that is a sufficiently strong scatterer such that its 2-D location in each image can be restricted to at most a small number of sites by processing applied to each image individually. It is not necessary to know the 3-D location of the label on the particle. After first determining the possible locations of the label in the 2-D images in parallel, the information from all images is fused to determine the 3-D location of the label on the particle and then the 3-D location is used to determine the projection orientation for each image by processing each image individually. With projection orientations, many algorithms exist for computing the 3-D reconstruction. The performance of the algorithm is studied as a function of the label SNR.
    Proc SPIE 02/2012;
  • [show abstract] [hide abstract]
    ABSTRACT: Subtle alterations in cerebral blood flow can impact the health and function of brain cells and are linked to cognitive decline and dementia. To understand hemodynamics in the three-dimensional vascular network of the cerebral cortex, we applied two-photon excited fluorescence microscopy to measure the motion of red blood cells (RBCs) in individual microvessels throughout the vascular hierarchy in anesthetized mice. To resolve heartbeat- and respiration-dependent flow dynamics, we simultaneously recorded the electrocardiogram and respiratory waveform. We found that centerline RBC speed decreased with decreasing vessel diameter in arterioles, slowed further through the capillary bed, and then increased with increasing vessel diameter in venules. RBC flow was pulsatile in nearly all cortical vessels, including capillaries and venules. Heartbeat-induced speed modulation decreased through the vascular network, while the delay between heartbeat and the time of maximum speed increased. Capillary tube hematocrit was 0.21 and did not vary with centerline RBC speed or topological position. Spatial RBC flow profiles in surface vessels were blunted compared with a parabola and could be measured at vascular junctions. Finally, we observed a transient decrease in RBC speed in surface vessels before inspiration. In conclusion, we developed an approach to study detailed characteristics of RBC flow in the three-dimensional cortical vasculature, including quantification of fluctuations in centerline RBC speed due to cardiac and respiratory rhythms and flow profile measurements. These methods and the quantitative data on basal cerebral hemodynamics open the door to studies of the normal and diseased-state cerebral microcirculation.
    AJP Heart and Circulatory Physiology 01/2012; 302(7):H1367-77. · 3.63 Impact Factor
  • Qiu Wang, P.C. Doerschuk
    [show abstract] [hide abstract]
    ABSTRACT: Instances of biological macromolecular complexes that have identical chemical constituents may not have the same geometry due to, for example, flexibility. Cryo electron microscopy provides one noisy projection image of each of many instances of a complex where the projection directions for the different instances are random. The noise is sufficient severe (SNR ≪ 1) that the projection direction for a particular image cannot be easily estimated from the individual image. The goal is to determine the 3-D geometry of the complex (the 3-D distribution of electron scattering intensity) which requires fusing information from these many images of many complexes. In order to describe the geometric heterogeneity of the complexes, the complex is described as a weighted sum of basis functions where the weights are random. In order to get tractable algorithms, the weights are modeled as Gaussian random variables with unknown statistics and the noise is modeled as additive Gaussian random variables with unknown covariance. The statistics of the weights and the statistics of the noise are jointly estimated by maximum likelihood by a generalized expectation maximization algorithm. The method has been developed to the point where it appears to be able to solve problems of interest to the structural biology community.
    Statistical Signal Processing Workshop (SSP), 2012 IEEE; 01/2012
  • [show abstract] [hide abstract]
    ABSTRACT: The influence of family history and genetics on the risk for the development of abuse or dependence is a major theme in alcoholism research. Recent research have used endophenotypes and behavioral paradigms to help detect further genetic contributions to this disease. Electronic tasks, essentially video games, which provide alcohol as a reward in controlled environments and with specified exposures have been developed to explore some of the behavioral and subjective characteristics of individuals with or at risk for alcohol substance use disorders. A generative model (containing parameters with unknown values) of a simple game involving a progressive work paradigm is described along with the associated point process signal processing that allows system identification of the model. The system is demonstrated on human subject data. The same human subject completing the task under different circumstances, e.g., with larger and smaller alcohol reward values, is assigned different parameter values. Potential meanings of the different parameter values are described.
    Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 08/2011; 2011:2699-702.
  • Source
    Seunghee Lee, P.C. Doerschuk, J.E. Johnson
    [show abstract] [hide abstract]
    ABSTRACT: Many micro- to nano-scale 3-D biological objects have a helical symmetry. Cryo electron microscopy provides 2-D projection images where, however, the images have low SNR and unknown projection directions. The object is described as a helical array of identical motifs, where both the parameters of the helical symmetry and the motif are unknown. Using a detailed image formation model, a maximum-likelihood estimator for the parameters of the symmetry and the 3-D motif based on images of many objects and algorithms for computing the estimate are described. The possibility that the objects are not identical but rather come from a small set of homogeneous classes is included. The first example is based on 316 128 ×100 pixel experimental images of Tobacco Mosaic Virus, has one class, and achieves 12.40-Å spatial resolution in the reconstruction. The second example is based on 400 128 ×128 pixel synthetic images of helical objects constructed from NaK ion channel pore macromolecular complexes, has two classes differing in helical symmetry, and achieves 7.84- and 7.90-Å spatial resolution in the reconstructions for the two classes.
    IEEE Transactions on Image Processing 08/2011; · 3.20 Impact Factor
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: The cortical microvasculature plays a key role in cortical tissue health by transporting important molecules via blood. Disruptions to blood flow in the microvasculature due to events such as stroke can thus induce damage to the cortex. Recent developments in two-photon microscopy have enabled in vivo imaging of anesthetized rat cortex in three dimensions. The microscopy data provide information about the geometry of the cortical microvasculature, length and diameter of the vessels in the imaged microvasculature network, and blood flow through a subset of those vessels. We demonstrate a model that achieves three goals. First, given a network of interconnected vessels and flow measurements on a subset of those vessels, we can estimate the flows in the remaining vessels. Second, we can determine which and how many vessels should have blood flow measurements taken to provide sufficient information to predict the unmeasured flows. Finally, the model enables us to predict effects of blockages in one or more vessels, indicating which vessels are most important to overall flow in the network.
    Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 08/2011; 2011:174-7.
  • Kang Wang, P.C. Doerschuk
    [show abstract] [hide abstract]
    ABSTRACT: Cryo electron microscopy (cryo EM) imaging experiments can lead to stochastic models for biological macromolecular complexes. However, interpreting the statistical variability is difficult. In some situations, the variability in the original complexes is due primarily to thermal fluctuations which are snap frozen in place during the preparation of the specimen. In this case the images are images of samples of the equilibrium statistical mechanics ensemble of the complex. Based on representing the complex by a spring-mass mechanical model, an estimation problem for determining the masses and spring constants is described and demonstrated on synthetic data. With a model, quantities such as normal modes can be computed, which provide insight into the dynamics of biological complexes.
    Biomedical Imaging: From Nano to Macro, 2011 IEEE International Symposium on; 05/2011
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: Sulfolobus Turreted Icosahedral Virus (STIV) experiences an extra-cellular environment of near boiling acid (80°C, pH 3) and particles purified under these conditions were previously analyzed by cryo electron microscopy and image reconstruction. Here we describe cryo-tomograms of Solfolobus cells infected with STIV and the maximum likelihood algorithm employed to compute reconstructions of virions within the cell. Virions in four different tomograms were independently reconstructed with an average of 91 particles per tomogram and their structures compared with each other and with the higher resolution single-particle reconstruction from purified virions. The algorithm described here automatically classified and oriented two different particle types within each cell and generated reconstructions of full and empty particles. Because the particles are randomly oriented within the cell, the reconstructions do not suffer from the missing wedge of data absent from the reciprocal-space tomogram. The fact that the particles have icosahedral symmetry is used to dramatically improve the signal to noise ratio in the reconstructions. The reconstructions have approximately 60Å resolution (based on Fourier Shell Correlation analysis among reconstructions computed by the algorithm described here from four different tomograms).
    Journal of Structural Biology 03/2011; 174(3):425-33. · 3.36 Impact Factor
  • Qiu Wang, Peter C. Doerschuk
    [show abstract] [hide abstract]
    ABSTRACT: Instances of biological macromolecular complexes that have identical chemical constituents may not have the same geometry due to, for example, flexibility. Cryo electron microscopy provides one noisy projection image of each of many instances of a complex where the projection directions for the different instances are random. The noise is sufficient severe (SNR
    Proc SPIE 02/2011;
  • Yili Zheng, Qiu Wang, Peter C. Doerschuk
    [show abstract] [hide abstract]
    ABSTRACT: Different instances of a biological macromolecular complex need not share the same 3-D electron scattering distribution function due to stoichiometric variability, flexibility and vibrations, etc. Cryo electron microscopy provides 2-D images of each of many such complexes where each image is roughly a projection. A statistical estimation problem is described and demonstrated for determining a statistical description of the complex from such imagery.
    Proceedings of the 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2011, March 30 - April 2, 2011, Chicago, Illinois, USA; 01/2011
  • I. Ozil, M.H. Plawecki, P.C. Doerschuk, S.J. O'Connor
    [show abstract] [hide abstract]
    ABSTRACT: Recent research on alcoholism explores the influence of family history and genetics on the risk of developing abuse or dependence. Endophenotypes and behavioral paradigms have been used to help detect genetic contributions to this disease. Electronic tasks, which can be considered video games, that provide alcohol as a reward in controlled environments have been developed to explore some of the behaviors and characteristics of individuals with or at risk for alcohol substance use disorders. One such game involves a progressive work paradigm where subjects receive larger or smaller alcohol rewards for completing the task. A generative model for this game is described along with the signal processing needed to characterize the subjects' behavior by system identification. Statistical performance of the algorithm is described and evaluated for the human data. Potential meanings of the different parameter values and the performance results are described.
    Signals, Systems and Computers (ASILOMAR), 2011 Conference Record of the Forty Fifth Asilomar Conference on; 01/2011
  • Source
    [show abstract] [hide abstract]
    ABSTRACT: We applied whole-cell electron cryotomography to the archaeon Sulfolobus infected by Sulfolobus turreted icosahedral virus (STIV), which belongs to the PRD1-Adeno lineage of dsDNA viruses. STIV infection induced the formation of pyramid-like protrusions with sharply defined facets on the cell surface. They had a thicker cross-section than the cytoplasmic membrane and did not contain an exterior surface protein layer (S-layer). Intrapyramidal bodies often occupied the volume of the pyramids. Mature virions, procapsids without genome cores, and partially assembled particles were identified, suggesting that the capsid and inner membrane coassemble in the cytoplasm to form a procapsid. A two-class reconstruction using a maximum likelihood algorithm demonstrated that no dramatic capsid transformation occurred upon DNA packaging. Virions tended to form tightly packed clusters or quasicrystalline arrays while procapsids mostly scattered outside or on the edges of the clusters. The study revealed vivid images of STIV assembly, maturation, and particle distribution in cell.
    Structure 12/2010; 18(12):1579-86. · 5.99 Impact Factor
  • [show abstract] [hide abstract]
    ABSTRACT: Cryo electron microscopy is frequently used on biological specimens that show a mixture of different types of object. Because the electron beam rapidly destroys the specimen, the beam current is minimized which leads to noisy images (SNR substantially less than 1) and only one projection image per object (with an unknown projection direction) is collected. For situations where the objects can reasonably be described as coming from a finite set of classes, an approach based on joint maximum likelihood estimation of the reconstruction of each class and then use of the reconstructions to label the class of each image is described and demonstrated on two challenging problems: an assembly mutant of Cowpea Chlorotic Mottle Virus and portals of the bacteriophage P22.
    Proc SPIE 08/2010;
  • Yili Zheng, Peter C. Doerschuk
    [show abstract] [hide abstract]
    ABSTRACT: A statistical estimation problem for determining 3-D reconstructions from a single 2-D projection image of each of multiple objects when the objects are heterogeneous is described. The method is based on a Gaussian mixture description of the heterogeneity and is motivated by cryo electron microscopy of biological objects.
    Proc SPIE 08/2010;

Publication Stats

355 Citations
148.66 Total Impact Points

Institutions

  • 2009–2014
    • Cornell University
      • Department of Biomedical Engineering
      Ithaca, New York, United States
    • Milwaukee School of Engineering
      • Department of Electrical Engineering and Computer Science
      Milwaukee, WI, United States
    • Indiana University-Purdue University Indianapolis
      • Department of Medicine
      Indianapolis, IN, United States
  • 2005–2013
    • The Scripps Research Institute
      • • Department of Integrative Structural and Computational Biology
      • • Department of Cell and Molecular Biology
      • • Center for Integrative Molecular Biosciences
      La Jolla, CA, United States
  • 1991–2012
    • Purdue University
      • School of Electrical and Computer Engineering
      West Lafayette, IN, United States
  • 1995
    • The IT Process Institute
      Eugene, Oregon, United States