Publications by Year: 2009

2009
Bar-Yam Y, Harmon D, de Bivort B. Systems biology. Attractors and democratic dynamics. . Science 2009;323:1016-7.
de Bivort BL, Perlstein EO, Kunes S, Schreiber SL. Amino acid metabolic origin as an evolutionary influence on protein sequence in yeast. . J Mol Evol 2009;68:490-7.Abstract
The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their respective yeast metabolic cycle phases. Typically, the amino acids themselves are most abundant at the end of their precursor's phase. We show that this metabolic cycling has likely biased the amino acid composition of proteins across the S. cerevisiae genome. In particular, we observed that the metabolic source of amino acids is the single most important source of variation in the amino acid compositions of functionally related proteins and that this signal appears only in (facultative) organisms using both oxidative and reductive metabolism. Periodically expressed proteins are enriched for amino acids generated in the preceding phase of the metabolic cycle. Proteins expressed during the oxidative phase contain more glycolysis-derived amino acids, whereas proteins expressed during the reductive phase contain more respiration-derived amino acids. Rare amino acids (e.g., tryptophan) are greatly overrepresented or underrepresented, relative to the proteomic average, in periodically expressed proteins, whereas common amino acids vary by a few percent. Genome-wide, we infer that 20,000 to 60,000 residues have been modified by this previously unappreciated pressure. This trend is strongest in ancient proteins, suggesting that oscillating endogenous amino acid availability exerted genome-wide selective pressure on protein sequences across evolutionary time.
de Bivort BL, Guo H-FF, Zhong Y. Notch signaling is required for activity-dependent synaptic plasticity at the Drosophila neuromuscular junction. . J Neurogenet 2009;23:395-404.Abstract
The cell-surface-signaling protein Notch, is required for numerous developmental processes and typically specifies which of two adjacent cells will adopt a non-neuronal developmental fate. It has recently been implicated in long-term memory formation in mammals and Drosophila. Here, we investigated whether activity-dependent synaptic plasticity at the neuromuscular junctions (NMJs) of third instar Drosophila larvae depends on Notch signaling. The length and number of axonal branches and number of presynaptic sites (boutons) in NMJ vary with the level of synaptic activity, so we increased activity at the NMJ by two complementary methods: increasing the chronic growth temperature of third instar larvae from 18 to 28 degrees C and using the double-mutant ether-a-gogo,Shaker (eagSh), both of which increase NMJ size and bouton count. Animals homozygous for the functionally null, temperature-sensitive Notch alleles, N(ts1) and N(ts2), displayed no activity-dependent increase in NMJ complexity when reared at the restrictive temperature. Dominant-negative Notch transgenic expression also blocked activity-dependent plasticity. Ectopic expression of wild-type Notch and constitutively active truncated Notch transgenes also reduced activity-dependent plasticity, suggesting that there is a "happy medium" level of Notch activity in mediating NMJ outgrowth. Last, we show that endogenous Notch is primarily expressed in the presynaptic cell bodies where its expression level is positively correlated with motor neuron activity.
Clouse R, de Bivort BL, Giribet G. A phylogenetic analysis for the South-east Asian mite harvestman family Stylocellidae (Opiliones : Cyphophthalmi) - a combined analysis using morphometric and molecular data . Invertebrate Systematics 2009;23:515-529.
Arnold S, Keng D, Shopova SI, Holler S, Zurawsky W, Vollmer F. Whispering gallery mode carousel--a photonic mechanism for enhanced nanoparticle detection in biosensing . Opt. Express 2009;17:6230-6238.
Vollmer F, Arnold S. Optical microcavities: single virus detection and nanoparticle trapping  . Proc. of SPIE 2009;7397:739702.
Topolancik J, Vollmer F, Ilic R, Crescimanno M. Out-of-plane scattering from vertically asymmetric photonic crystal slab waveguides with in-plane disorder. . Opt Express 2009;17(15):12470-80.Abstract
We characterize optical wave propagation along line defects in two-dimensional arrays of air-holes in free-standing silicon slabs. The fabricated waveguides contain random variations in orientation of the photonic lattice elements which perturb the in-plane translational symmetry. The vertical slab symmetry is also broken by a tilt of the etched sidewalls. We discuss how these lattice imperfections affect out-of-plane scattering losses and introduce a mechanism for high-Q cavity excitation related to polarization mixing.
Husale S, Persson HHJ, Sahin O. DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets. . Nature 2009;462(7276):1075-8.Abstract
Techniques to detect and quantify DNA and RNA molecules in biological samples have had a central role in genomics research. Over the past decade, several techniques have been developed to improve detection performance and reduce the cost of genetic analysis. In particular, significant advances in label-free methods have been reported. Yet detection of DNA molecules at concentrations below the femtomolar level requires amplified detection schemes. Here we report a unique nanomechanical response of hybridized DNA and RNA molecules that serves as an intrinsic molecular label. Nanomechanical measurements on a microarray surface have sufficient background signal rejection to allow direct detection and counting of hybridized molecules. The digital response of the sensor provides a large dynamic range that is critical for gene expression profiling. We have measured differential expressions of microRNAs in tumour samples; such measurements have been shown to help discriminate between the tissue origins of metastatic tumours. Two hundred picograms of total RNA is found to be sufficient for this analysis. In addition, the limit of detection in pure samples is found to be one attomolar. These results suggest that nanomechanical read-out of microarrays promises attomolar-level sensitivity and large dynamic range for the analysis of gene expression, while eliminating biochemical manipulations, amplification and labelling.
Dong M, Husale S, Sahin O. Determination of protein structural flexibility by microsecond force spectroscopy. . Nat Nanotechnol 2009;4(8):514-7.Abstract
Proteins are dynamic molecular machines having structural flexibility that allows conformational changes. Current methods for the determination of protein flexibility rely mainly on the measurement of thermal fluctuations and disorder in protein conformations and tend to be experimentally challenging. Moreover, they reflect atomic fluctuations on picosecond timescales, whereas the large conformational changes in proteins typically happen on micro- to millisecond timescales. Here, we directly determine the flexibility of bacteriorhodopsin -- a protein that uses the energy in light to move protons across cell membranes -- at the microsecond timescale by monitoring force-induced deformations across the protein structure with a technique based on atomic force microscopy. In contrast to existing methods, the deformations we measure involve a collective response of protein residues and operate under physiologically relevant conditions with native proteins.
Huang F, Addas K, Ward A, Flynn TN, Velasco E, Hagan MF, Dogic Z, Fraden S. Pair Potential of Charged Colloidal Stars . Phys. Rev. Lett. 2009;102:108302.
Lau AWC, Prasad A, Dogic Z. Condensation of isolated semi-flexible filaments driven by depletion interactions . EPL 2009;87:48006.
Barry E, Dogic Z, Meyer RB, Pelcovits RA, Oldenbourg R. Direct measurement of the twist penetration length in a single smectic A layer of colloidal virus particles. . J Phys Chem B 2009;113(12):3910-3.Abstract
In the 1970s, deGennes discussed the fundamental geometry of smectic liquid crystals and established an analogy between the smectic A phase and superconductors. It follows that smectic layers expel twist deformations in the same way that superconductors expel magnetic field. We make a direct observation of the penetration of twist at the edge of a single isolated smectic A layer composed of chiral fd virus particles subjected to a depletion interaction. Using the LC-PolScope, we make quantitative measurements of the spatial dependence of the birefringence due to molecular tilt near the layer edges. We match data to theory for the molecular tilt penetration profile and determine the twist penetration length for this system.
Koenderink GH, Dogic Z, Nakamura F, Bendix PM, MacKintosh FC, Hartwig JH, Stossel TP, Weitz DA. An active biopolymer network controlled by molecular motors. . Proc Natl Acad Sci U S A 2009;106(36):15192-7.Abstract
We describe an active polymer network in which processive molecular motors control network elasticity. This system consists of actin filaments cross-linked by filamin A (FLNa) and contracted by bipolar filaments of muscle myosin II. The myosin motors stiffen the network by more than two orders of magnitude by pulling on actin filaments anchored in the network by FLNa cross-links, thereby generating internal stress. The stiffening response closely mimics the effects of external stress applied by mechanical shear. Both internal and external stresses can drive the network into a highly nonlinear, stiffened regime. The active stress reaches values that are equivalent to an external stress of 14 Pa, consistent with a 1-pN force per myosin head. This active network mimics many mechanical properties of cells and suggests that adherent cells exert mechanical control by operating in a nonlinear regime where cell stiffness is sensitive to changes in motor activity. This design principle may be applicable to engineering novel biologically inspired, active materials that adjust their own stiffness by internal catalytic control.
Ghosh A, Fischer P. Controlled propulsion of artificial magnetic nanostructured propellers. . Nano Lett 2009;9(6):2243-5.Abstract
For biomedical applications, such as targeted drug delivery and microsurgery, it is essential to develop a system of swimmers that can be propelled wirelessly in fluidic environments with good control. Here, we report the construction and operation of chiral colloidal propellers that can be navigated in water with micrometer-level precision using homogeneous magnetic fields. The propellers are made via nanostructured surfaces and can be produced in large numbers. The nanopropellers can carry chemicals, push loads, and act as local probes in rheological measurements.
Fratz M, Fischer P, Giel DM. Full phase and amplitude control in computer-generated holography. . Opt Lett 2009;34(23):3659-61.Abstract
We report what we believe to be the first realization of a computer-generated complex-valued hologram recorded in a single film of photoactive polymer. Complex-valued holograms give rise to a diffracted optical field with control over its amplitude and phase. The holograms are generated by a one-step direct laser writing process in which a spatial light modulator (SLM) is imaged onto a polymer film. Temporal modulation of the SLM during exposure controls both the strength of the induced birefringence and the orientation of the fast axis. We demonstrate that complex holograms can be used to impart arbitrary amplitude and phase profiles onto a beam and thereby open new possibilities in the control of optical beams.
Wong WP, Springer TA. Mechanoenzymatic cleavage of the ultralarge vascular protein, von Willebrand factor . Science 2009;324(5932):1330-1334.
Wong WP, Halvorsen K. Beyond the frame rate: measuring high-frequency fluctuations with light-intensity modulation. . Opt Lett 2009;34(3):277-9.Abstract
Power-spectral-density measurements of any sampled signal are typically restricted by both acquisition rate and frequency response limitations of instruments, which can be particularly prohibitive for video-based measurements. We have developed a new method called intensity modulation spectral analysis that circumvents these limitations, dramatically extending the effective detection bandwidth. We demonstrate this by video tracking an optically trapped microsphere while oscillating an LED illumination source. This approach allows us to quantify fluctuations of the microsphere at frequencies over 10 times higher than the Nyquist frequency, mimicking a significantly higher frame rate.
Pinto N, DiCarlo JJ, Cox DD. How far can you get with a modern face recognition test set using only simple features? . IEEE Computer Vision and Pattern Recognition 2009;
Mujica-Parodi L, Strey H, Frederick B, Savoy RL, Cox DD, Botanov Y, Tolkunov D, Rubin D, Weber J. Chemosensory Cues to Conspecific Emotional Stress Activate the Amygdala in Humans . PLoS One 2009;4(7):e6415.
Pinto N, Doukhan D, DiCarlo JJ, Cox DD. A high-throughput screening approach to discovering good forms of biologically inspired visual representation. . PLoS Comput Biol 2009;5(11):e1000579.Abstract
While many models of biological object recognition share a common set of "broad-stroke" properties, the performance of any one model depends strongly on the choice of parameters in a particular instantiation of that model--e.g., the number of units per layer, the size of pooling kernels, exponents in normalization operations, etc. Since the number of such parameters (explicit or implicit) is typically large and the computational cost of evaluating one particular parameter set is high, the space of possible model instantiations goes largely unexplored. Thus, when a model fails to approach the abilities of biological visual systems, we are left uncertain whether this failure is because we are missing a fundamental idea or because the correct "parts" have not been tuned correctly, assembled at sufficient scale, or provided with enough training. Here, we present a high-throughput approach to the exploration of such parameter sets, leveraging recent advances in stream processing hardware (high-end NVIDIA graphic cards and the PlayStation 3's IBM Cell Processor). In analogy to high-throughput screening approaches in molecular biology and genetics, we explored thousands of potential network architectures and parameter instantiations, screening those that show promising object recognition performance for further analysis. We show that this approach can yield significant, reproducible gains in performance across an array of basic object recognition tasks, consistently outperforming a variety of state-of-the-art purpose-built vision systems from the literature. As the scale of available computational power continues to expand, we argue that this approach has the potential to greatly accelerate progress in both artificial vision and our understanding of the computational underpinning of biological vision.