Publications by Year: 2010

2010
Clouse R, de Bivort BL, Giribet G. Phylogenetic signals in morphometric data. Cladistics 2010;27:1-4.
de Bivort BL, Clouse RM, Giribet G. A morphometrics-based phylogeny of the temperate Gondwanan mite harvestmen (Opiliones, Cyphophthalmi, Pettalidae). Journal of Zoological Systematics and Evolutionary Research 2010;In press 2010_de_bivort_.pdf
de Bivort BL, Giribet G. A systematic revision of South African Pettalidae (Arachnida : Opiliones : Cyphophthalmi) based on a combined analysis of discrete and continuous characters with the description of seven new species. Invertebrate Systematics 2010;24:371-406. 2010_giribet_csiro.pdf
Richards CT. Kinematics and hydrodynamics analysis of swimming anurans reveals striking inter-specific differences in the mechanism for producing thrust. J Exp Biol 2010;213(4):621-34.Abstract

This study aimed to compare the swimming kinematics and hydrodynamics within and among aquatic and semi-aquatic/terrestrial frogs. High-speed video was used to obtain kinematics of the leg joints and feet as animals swam freely across their natural range of speeds. Blade element analysis was then used to model the hydrodynamic thrust as a function of foot kinematics. Two purely aquatic frogs, Xenopus laevis and Hymenochirus boettgeri, were compared with two semi-aquatic/terrestrial frogs, Rana pipiens and Bufo americanus. The four species performed similarly. Among swimming strokes, peak stroke velocity ranged from 3.3+/-1.1 to 20.9+/-2.5, from 6.8+/-2.1 to 28.6+/-3.7 and from 4.9+/-0.5 to 20.9+/-4.1 body lengths per second (BL s(-1)) in X. laevis, H. boettgeri and R. pipiens, respectively (means +/- s.d.; N=4 frogs for each). B. americanus swam much more slowly at 3.1+/-0.3 to 7.0+/-2.0 BL s(-1) (N=3 frogs). Time-varying joint kinematics patterns were superficially similar among species. Because foot kinematics result from the cumulative motion of joints proximal to the feet, small differences in time-varying joint kinematics among species resulted in species-specific foot kinematics (therefore hydrodynamics) patterns. To obtain a simple measure of the hydrodynamically useful motion of the foot, this study uses 'effective foot velocity' (EFV): a measure of the component of foot velocity along the axis of swimming. Resolving EFV into translational and rotational components allows predictions of species-specific propulsion strategies. Additionally, a novel kinematic analysis is presented here that enables the partitioning of translational and rotational foot velocity into velocity components contributed by extension at each individual limb joint. Data from the kinematics analysis show that R. pipiens and B. americanus translated their feet faster than their body moved forward, resulting in positive net translational EFV. Conversely, translational EFV was slower than the body velocity in H. boettgeri and X. laevis, resulting in negative net translational EFV. Consequently, the translational component of thrust (caused mostly by hip, knee and ankle extension) was twofold higher than rotational thrust in Rana pipiens. Likewise, rotational components of thrust were nearly twofold higher than translational components in H. boettgeri. X. laevis, however, was the most skewed species observed, generating nearly 100% of total thrust by foot rotation generated by hip, ankle and tmt extension. Thus, this study presents a simple kinematics analysis that is predictive of hydrodynamic differences among species. Such differences in kinematics reveal a continuum of different propulsive strategies ranging from mostly rotation-powered (X. laevis) to mostly translation-powered (R. pipiens) swimming.

2010_richards_jrnl.pdf
Roy S, Prasad M, Topolancik J, Vollmer F. All-optical switching with bacteriorhodopsin protein coated microcavities and its application to low power computing circuits. Journal of Applied Physics 2010;107:053115. 2010_roy_aip.pdf
Gabrielse G, Klothammer WS, McConnell R, Richerme P, Wrubel J, Kalra R, Novitski D, Grzonka D, Oelert W, Sefzick T, Zielinski M, Borbely JS, George MC, Hessels EA, Storry CH, Weel M, Mullers A, Walz J, Speck A. Centrifugal Separation of Antiprotons and Electrons. Phys. Rev. Lett. 2010;105:213002. 2010_gabrielse_prl.pdf
Spicer R, Groover A. Evolution of development of vascular cambia and secondary growth. New Phytol 2010;186(3):577-92.Abstract

Secondary growth from vascular cambia results in radial, woody growth of stems. The innovation of secondary vascular development during plant evolution allowed the production of novel plant forms ranging from massive forest trees to flexible, woody lianas. We present examples of the extensive phylogenetic variation in secondary vascular growth and discuss current knowledge of genes that regulate the development of vascular cambia and woody tissues. From these foundations, we propose strategies for genomics-based research in the evolution of development, which is a next logical step in the study of secondary growth.

2010_spicer_rev._new_phytologist.pdf
Speck A, Mandal P. Half-cycle-pulse-train induced state redistribution of Rydberg atoms. Physical Review A 2010;81:013401. 2010_mandal_pr.pdf
Okada K, Bartolini F, Deaconescu AM, Moseley JB, Dogic Z, Grigorieff N, Gundersen GG, Goode BL. Adenomatous polyposis coli protein nucleates actin assembly and synergizes with the formin mDia1. J Cell Biol 2010;189(7):1087-96.Abstract

The tumor suppressor protein adenomatous polyposis coli (APC) regulates cell protrusion and cell migration, processes that require the coordinated regulation of actin and microtubule dynamics. APC localizes in vivo to microtubule plus ends and actin-rich cortical protrusions, and has well-documented direct effects on microtubule dynamics. However, its potential effects on actin dynamics have remained elusive. Here, we show that the C-terminal "basic" domain of APC (APC-B) potently nucleates the formation of actin filaments in vitro and stimulates actin assembly in cells. Nucleation is achieved by a mechanism involving APC-B dimerization and recruitment of multiple actin monomers. Further, APC-B nucleation activity is synergistic with its in vivo binding partner, the formin mDia1. Together, APC-B and mDia1 overcome a dual cellular barrier to actin assembly imposed by profilin and capping protein. These observations define a new function for APC and support an emerging view of collaboration between distinct actin assembly-promoting factors with complementary activities.

2010_okada_jrnl.pdf
Narayana S, Sato Y. Compact miniature high-resolution thermometer. IEEE Transactions on Applied Superconductivity 2010;20:2402. 2010_sato_ieee.pdf
Narayana S, Sato Y. Direct observation of dynamical bifurcation in a superfluid Josephson junction. Phys Rev Lett 2010;105(20):205302.Abstract

We report a direct observation of dynamical bifurcation between two plasma oscillation states of a superfluid Josephson junction. We excite the superfluid plasma resonance into a nonlinear regime by driving below the natural plasma frequency and observe a clear transition between two dynamical states. We also demonstrate bifurcation by changing the potential well with temperature variations.

2010_narayana_prl.pdf
Barry E, Dogic Z. Entropy driven self-assembly of nonamphiphilic colloidal membranes. Proc Natl Acad Sci U S A 2010;107(23):10348-53.Abstract

We demonstrate that homogeneous monodisperse rods in the presence of attractive interactions assemble into equilibrium 2D fluid-like membranes composed of a one-rod length thick monolayer of aligned rods. Unique features of our system allow us to simultaneously investigate properties of these membranes at both continuum and molecular lengthscales. Analysis of thermal fluctuations at continuum lengthscales yields the membranes' lateral compressibility and bending rigidity and demonstrates that the properties of colloidal membranes are comparable to those of traditional lipid bilayers. Fluctuations at molecular lengthscales, in which single rods protrude from the membrane surface, are directly measured by comparing the positions of individual fluorescently labeled rods within a membrane to that of the membrane's continuum conformation. As two membranes approach each other in suspension, protrusion fluctuations are suppressed leading to effective repulsive interactions. Motivated by these observations, we propose an entropic mechanism that explains the stability of colloidal membranes and offers a general design principle for the self-assembly of 2D nanostructured materials from rod-like molecules.

2010_dogic_pnas.pdf
Sato Y. Fiske-amplified superfluid interferometry. Physical Review B 2010;81:172502. 2010_sato_pr.pdf
Fischer P, Ghosh A, Premasiri WR, Ziegler LD. Nanostructured Plasmonic Surfaces for Surface Enhanced Raman Scattering   of Bacteria. XXII International Conference on Raman Spectroscopy 2010;1267:994-995.
Pinto N, Cox DD. An Evaluation of the Invariance Properties of a Biologically-Inspired System for Unconstrained Face Recognition. ICST Conference on Biologically Inspired Network, Information, and Computing Systems 2010;
Sriram V, Tsoi K, Luk W, Cox DD. A Design-Space Exploration of Biologically-Inspired Visual Object Recognition Algorithms Using CPUs, GPUs and FPGAs. Many-Core and Reconfigurable Supercomputing 2010; 2010_sriram_.pdf
Halvorsen K, Wong WP. Massively parallel single-molecule manipulation using centrifugal force. Biophys J 2010;98(11):L53-5.Abstract

Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology, and medicine. However, widespread adoption of single-molecule techniques has been impeded by equipment cost and the laborious nature of making measurements one molecule at a time. We have solved these issues by developing an approach that enables massively parallel single-molecule force measurements using centrifugal force. This approach is realized in an instrument that we call the centrifuge force microscope in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force-field while their micro-to-nanoscopic motions are observed. We demonstrate high-throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Additionally, we verify the force accuracy of the instrument by measuring the well-established DNA overstretching transition at 66 +/- 3 pN. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems.

2010_halvorsen_jrnl.pdf
Fischer P, Salam A. Molecular QED of coherent and incoherent sum-frequency and second-harmonic generation in chiral liquids in the presence of a static electric field. Molecular Physics 2010;108(14):1857-1868. 2010_fischer_mp.pdf
Cheng D, Halvorsen K, Wong WP. Note: High-precision microsphere sorting using velocity sedimentation. Rev Sci Instrum 2010;81(2):026106.Abstract

Monodisperse populations of microspheres are desirable for a variety of research and industrial applications, but many desirable sizes and materials can be difficult to synthesize and have limited commercial availability. In this paper, we present an effective, straightforward, and low cost method for sorting polydisperse microspheres into many separate monodisperse samples. The basic approach is to use velocity sedimentation through a density gradient in a long vertical column, followed by carefully targeted extraction. We demonstrate this technique by reducing the coefficient of variation of melamine microspheres from 13% to 1%-4% and glass microspheres from 35% to 3%-8%. This simple and inexpensive method can be used to sort microspheres of many sizes and materials, and is easily scalable, opening the possibility of cheap, monodisperse microspheres.

2010_cheng_apl.pdf
Zoccolan D, Graham BJ, Cox DD. A self-calibrating, camera-based eye tracker for the recording of rodent eye movements. Front Neurosci 2010;4:193.Abstract

Much of neurophysiology and vision science relies on careful measurement of a human or animal subject's gaze direction. Video-based eye trackers have emerged as an especially popular option for gaze tracking, because they are easy to use and are completely non-invasive. However, video eye trackers typically require a calibration procedure in which the subject must look at a series of points at known gaze angles. While it is possible to rely on innate orienting behaviors for calibration in some non-human species, other species, such as rodents, do not reliably saccade to visual targets, making this form of calibration impossible. To overcome this problem, we developed a fully automated infrared video eye-tracking system that is able to quickly and accurately calibrate itself without requiring co-operation from the subject. This technique relies on the optical geometry of the cornea and uses computer-controlled motorized stages to rapidly estimate the geometry of the eye relative to the camera. The accuracy and precision of our system was carefully measured using an artificial eye, and its capability to monitor the gaze of rodents was verified by tracking spontaneous saccades and evoked oculomotor reflexes in head-fixed rats (in both cases, we obtained measurements that are consistent with those found in the literature). Overall, given its fully automated nature and its intrinsic robustness against operator errors, we believe that our eye-tracking system enhances the utility of existing approaches to gaze-tracking in rodents and represents a valid tool for rodent vision studies.

2010_graham_frontiers_in_neuroscience.pdf