Publications by Year: 2012

Collins B, Kane EA, Reeves DC, Akabas MH, Blau J. Balance of activity between LN(v)s and glutamatergic dorsal clock neurons promotes robust circadian rhythms in Drosophila. Neuron 2012;74(4):706-718. 2012_collins_nih.pdf
Gershow M, Berck M, Matthew D, Luo L, Kane EA, Carlson J, Samuel A. Controlling airborne chemical cues for studying navigation in small animals. Nature Methods 2012; 2012_gershow_nih.pdf
Song E, de Bivort B, Dan C, Kunes S. Determinants of the Drosophila odorant receptor pattern. Dev Cell 2012;22:363-76.Abstract

In most olfactory systems studied to date, neurons that express the same odorant receptor (Or) gene are scattered across sensory epithelia, intermingled with neurons that express different Or genes. In Drosophila, olfactory sensilla that express the same Or gene are dispersed on the antenna and the maxillary palp. Here we show that Or identity is specified in a spatially stereotyped pattern by the cell-autonomous activity of the transcriptional regulators Engrailed and Dachshund. Olfactory sensilla then become highly motile and disperse beneath the epidermis. Thus, positional information and cell motility underlie the dispersed patterns of Drosophila Or gene expression.

Raz, Graham S, and, Cohen JH, and, de Bivort A, and, Grishkan BL, and, Nevo I, and, Eviatar. Growth and Asymmetry of Soil Microfungal Colonies from Evolution Canyon, Lower Nahal Oren, Mount Carmel, Israel [Internet]. PLoS ONE 2012;7:e34689. Publisher's VersionAbstract


Fluctuating asymmetry is a contentious indicator of stress in populations of animals and plants. Nevertheless, it is a measure of developmental noise, typically obtained by measuring asymmetry across an individual organism's left-right axis of symmetry. These individual, signed asymmetries are symmetrically distributed around a mean of zero. Fluctuating asymmetry, however, has rarely been studied in microorganisms, and never in fungi.

Objective and Methods

We examined colony growth and random phenotypic variation of five soil microfungal species isolated from the opposing slopes of Evolution Canyon, Mount Carmel, Israel. This canyon provides an opportunity to study diverse taxa inhabiting a single microsite, under different kinds and intensities of abiotic and biotic stress. The south-facing African slope of Evolution Canyon is xeric, warm, and tropical. It is only 200 m, on average, from the north-facing European slope, which is mesic, cool, and temperate. Five fungal species inhabiting both the south-facing African slope, and the north-facing European slope of the canyon were grown under controlled laboratory conditions, where we measured the fluctuating radial asymmetry and sizes of their colonies.


Different species displayed different amounts of radial asymmetry (and colony size). Moreover, there were highly significant slope by species interactions for size, and marginally significant ones for fluctuating asymmetry. There were no universal differences (i.e., across all species) in radial asymmetry and colony size between strains from African and European slopes, but colonies of Clonostachys rosea from the African slope were more asymmetric than those from the European slope.

Conclusions and Significance

Our study suggests that fluctuating radial asymmetry has potential as an indicator of random phenotypic variation and stress in soil microfungi. Interaction of slope and species for both growth rate and asymmetry of microfungi in a common environment is evidence of genetic differences between the African and European slopes of Evolution Canyon.

Kain JS, Stokes C, de Bivort BL. Phototactic personality in fruit flies and its suppression by serotonin and white. Proc Natl Acad Sci U S A 2012;109:19834-9.Abstract

Drosophila typically move toward light (phototax positively) when startled. The various species of Drosophila exhibit some variation in their respective mean phototactic behaviors; however, it is not clear to what extent genetically identical individuals within each species behave idiosyncratically. Such behavioral individuality has indeed been observed in laboratory arthropods; however, the neurobiological factors underlying individual-to-individual behavioral differences are unknown. We developed "FlyVac," a high-throughput device for automatically assessing phototaxis in single animals in parallel. We observed surprising variability within every species and strain tested, including identically reared, isogenic strains. In an extreme example, a domesticated strain of Drosophila simulans harbored both strongly photopositive and strongly photonegative individuals. The particular behavior of an individual fly is not heritable and, because it persists for its lifetime, constitutes a model system for elucidating the molecular mechanisms of personality. Although all strains assayed had greater than expected variation (assuming binomial sampling), some had more than others, implying a genetic basis. Using genetics and pharmacology, we identified the metabolite transporter White and white-dependent serotonin as suppressors of phototactic personality. Because we observed behavioral idiosyncrasy in all experimental groups, we suspect it is present in most behaviors of most animals.

Richards CT, Clemente CJ. A bio-robotic platform for integrating internal and external mechanics during muscle-powered swimming. Bioinspir Biomim 2012;7(1):016010.Abstract

To explore the interplay between muscle function and propulsor shape in swimming animals, we built a robotic foot to mimic the morphology and hind limb kinematics of Xenopus laevis frogs. Four foot shapes ranging from low aspect ratio (AR = 0.74) to high (AR = 5) were compared to test whether low-AR feet produce higher propulsive drag force resulting in faster swimming. Using feedback loops, two complementary control modes were used to rotate the foot: force was transmitted to the foot either from (1) a living plantaris longus (PL) muscle stimulated in vitro or (2) an in silico mathematical model of the PL. To mimic forward swimming, foot translation was calculated in real time from fluid force measured at the foot. Therefore, bio-robot swimming emerged from muscle-fluid interactions via the feedback loop. Among in vitro-robotic trials, muscle impulse ranged from 0.12 ± 0.002 to 0.18 ± 0.007 N s and swimming velocities from 0.41 ± 0.01 to 0.43 ± 0.00 m s(-1), similar to in vivo values from prior studies. Trends in in silico-robotic data mirrored in vitro-robotic observations. Increasing AR caused a small (∼10%) increase in peak bio-robot swimming velocity. In contrast, muscle force-velocity effects were strongly dependent on foot shape. Between low- and high-AR feet, muscle impulse increased ∼50%, while peak shortening velocity decreased ∼50% resulting in a ∼20% increase in net work. However, muscle-propulsion efficiency (body center of mass work/muscle work) remained independent of AR. Thus, we demonstrate how our experimental technique is useful for quantifying the complex interplay among limb morphology, muscle mechanics and hydrodynamics.

Clemente CJ, Richards CT. Determining the influence of muscle operating length on muscle performance during frog swimming using a bio-robotic model. Bioinspiration & Biomimetics 2012;7:036018. 2012_clemente_bioinspiration_biometics.pdf
Richards CT, Sawicki GS. Elastic recoil can either amplify or attenuate muscle-tendon power, depending on inertial vs. fluid dynamic loading. J Theor Biol 2012;313:68-78.Abstract

Frog jumps exceed muscle power limits. To achieve this, a muscle may store elastic energy in tendon before it is released rapidly, producing 'power amplification' as tendon recoil assists the muscle to accelerate the load. Do the musculoskeletal modifications conferring power amplification help or hinder frog swimming? We used a Hill-type mathematical model of a muscle-tendon (MT) with contractile element (CE) and series elastic element (SEE) properties of frogs. We varied limb masses from 0.3 to 30 g, foot-fin areas from 0.005 to 50 cm(2) and effective mechanical advantage (EMA=in-lever/out-lever) from 0.025 to 0.1. 'Optimal' conditions produced power amplification of ~19% greater than the CE limit. Yet, other conditions caused ~80% reduction of MT power (power attenuation) due to SEE recoil absorbing power from (rather than adding to) the CE. The tendency for elastic recoil to cause power amplification vs. attenuation was load dependent: low fluid drag loads, high limb mass and EMA=0.1 caused power amplification whereas high drag, low mass and low EMA (=0.025) caused attenuation. Power amplification emerged when: (1) CE shortening velocity is 1/3V(max), (2) elastic energy storage is neither too high nor too low, and (3). peak inertial-drag force ratio ≥ ~1.5. Excessive elastic energy storage delayed the timing of recoil, causing power attenuation. Thus our model predicts that for fluid loads, the benefit from a compliant tendon is modest, and when the system is 'poorly tuned' (i.e., inappropriate EMA), MT power attenuation can be severe.

Schonbrun E, Gorthi SS, Schaak D. Microfabricated multiple field of view imaging flow cytometry. Lab Chip 2012;12(2):268-73.Abstract

The combination of microscopy and flow cytometry enables image based screening of large collections of cells. Despite the proposition more than thirty years ago, adding high resolution wide-field imaging to flow cytometers remains challenging. The velocity of cells in flow cytometry can surpass a meter per second, requiring either sub-microsecond exposure times or other sophisticated photodetection techniques. Instead of faster detectors and brighter sources, we demonstrate that by imaging multiple channels simultaneously, a high throughput can be maintained with a flow velocity reduced in proportion to the degree of parallelization. The multi-field of view imaging flow cytometer (MIFC) is implemented with parallel arrays of microfluidic channels and diffractive lenses that produce sixteen wide field images with a magnification of 45 and submicron resolution. Using this device, we have imaged latex beads, red blood cells, and acute myeloid leukemia cells at rates of 2,000-20,000 per second.

Gorthi SS, Schonbrun E. Phase imaging flow cytometry using a focus-stack collecting microscope. Opt Lett 2012;37(4):707-9.Abstract

This letter introduces a fluidics-based focus-stack collecting microscope. A microfluidic device transports cells through the focal plane of a microscope, resulting in an efficient method to collect focus stacks of large collections of single cells. Images from the focus stacks are used to reconstruct the quantitative phase of cells with the transport-of-intensity-equation method. Using the phase imaging flow cytometer, we measure three-dimensional shape variations of red blood and leukemia cells.

Carraro N, Tisdale-Orr TE, Clouse RM, Knöller AS, Spicer R. Diversification and Expression of the PIN, AUX/LAX, and ABCB Families of Putative Auxin Transporters in Populus. Front Plant Sci 2012;3:17.Abstract

Intercellular transport of the plant hormone auxin is mediated by three families of membrane-bound protein carriers, with the PIN and ABCB families coding primarily for efflux proteins and the AUX/LAX family coding for influx proteins. In the last decade our understanding of gene and protein function for these transporters in Arabidopsis has expanded rapidly but very little is known about their role in woody plant development. Here we present a comprehensive account of all three families in the model woody species Populus, including chromosome distribution, protein structure, quantitative gene expression, and evolutionary relationships. The PIN and AUX/LAX gene families in Populus comprise 16 and 8 members respectively and show evidence for the retention of paralogs following a relatively recent whole genome duplication. There is also differential expression across tissues within many gene pairs. The ABCB family is previously undescribed in Populus and includes 20 members, showing a much deeper evolutionary history, including both tandem and whole genome duplication as well as probable gene loss. A striking number of these transporters are expressed in developing Populus stems and we suggest that evolutionary and structural relationships with known auxin transporters in Arabidopsis can point toward candidate genes for further study in Populus. This is especially important for the ABCBs, which is a large family and includes members in Arabidopsis that are able to transport other substrates in addition to auxin. Protein modeling, sequence alignment and expression data all point to ABCB1.1 as a likely auxin transport protein in Populus. Given that basipetal auxin flow through the cambial zone shapes the development of woody stems, it is important that we identify the full complement of genes involved in this process. This work should lay the foundation for studies targeting specific proteins for functional characterization and in situ localization.

Wilson L, Zhang R. 3D Localization of weak scatterers in digital holographic microscopy using Rayleigh-Sommerfeld back-propagation. Opt. Express 2012;20:16735-16744. 2012_wilson_optics_express.pdf
Narayana S, Sato Y. DC magnetic cloak. Adv Mater 2012;24(1):71-4. 2012_narayana_communication.pdf
Martinez VA, Besseling R, Croze OA, Tailleur J, Reufer M, Schwarz-Linek J, Wilson LG, Bees MA, Poon WCK. Differential dynamic microscopy: a high-throughput method for characterizing the motility of microorganisms. Biophys J 2012;103(8):1637-47.Abstract

We present a fast, high-throughput method for characterizing the motility of microorganisms in three dimensions based on standard imaging microscopy. Instead of tracking individual cells, we analyze the spatiotemporal fluctuations of the intensity in the sample from time-lapse images and obtain the intermediate scattering function of the system. We demonstrate our method on two different types of microorganisms: the bacterium Escherichia coli (both smooth swimming and wild type) and the biflagellate alga Chlamydomonas reinhardtii. We validate the methodology using computer simulations and particle tracking. From the intermediate scattering function, we are able to extract the swimming speed distribution, fraction of motile cells, and diffusivity for E. coli, and the swimming speed distribution, and amplitude and frequency of the oscillatory dynamics for C. reinhardtii. In both cases, the motility parameters were averaged over ∼10(4) cells and obtained in a few minutes.

Narayana S, Sato Y. Heat flux manipulation with engineered thermal materials. Phys Rev Lett 2012;108(21):214303.Abstract

Utilizing a multilayered composite approach, we have designed and constructed a new class of artificial materials for thermal conduction. We show that an engineered material can be utilized to control the diffusive heat flow in ways inconceivable with naturally occurring materials. By shielding, concentrating, and inverting heat current, we experimentally demonstrate the unique potential and the utility of guiding heat flux.

Sahin O, Yong EH, Driks A, Mahadevan L. Physical basis for the adaptive flexibility of Bacillus spore coats. J R Soc Interface 2012;9(76):3156-60.Abstract

Bacillus spores are highly resistant dormant cells formed in response to starvation. The spore is surrounded by a structurally complex protein shell, the coat, which protects the genetic material. In spite of its dormancy, once nutrient is available (or an appropriate physical stimulus is provided) the spore is able to resume metabolic activity and return to vegetative growth, a process requiring the coat to be shed. Spores dynamically expand and contract in response to humidity, demanding that the coat be flexible. Despite the coat's critical biological functions, essentially nothing is known about the design principles that allow the coat to be tough but also flexible and, when metabolic activity resumes, to be efficiently shed. Here, we investigated the hypothesis that these apparently incompatible characteristics derive from an adaptive mechanical response of the coat. We generated a mechanical model predicting the emergence and dynamics of the folding patterns uniformly seen in Bacillus spore coats. According to this model, spores carefully harness mechanical instabilities to fold into a wrinkled pattern during sporulation. Owing to the inherent nonlinearity in their formation, these wrinkles persist during dormancy and allow the spore to accommodate changes in volume without compromising structural and biochemical integrity. This characteristic of the spore and its coat may inspire design of adaptive materials.

Sato Y, Packard RE. Superfluid helium interferometers. 2012;10:31. 2012_packard_physics_today.pdf
Sato Y, Packard RE. Superfluid helium quantum interference devices: physics and applications. Rep Prog Phys 2012;75(1):016401.Abstract

We present an overview of recent developments related to superfluid helium quantum interference devices (SHeQUIDs). We discuss the physics of two reservoirs of superfluid helium coupled together and describe the quantum oscillations that result from varying the coupling strength. We explain the principles behind SHeQUIDs that can be built based on these oscillations and review some techniques and applications.

Sato Y, Packard RE. Superfluid helium quantum interference devices: present status & future prospects. In: Journal of Physics: Conference Series 400. 2012 p. 052030. 2012_sato_bioinspiration_biometics.pdf
Halvorsen K, Wong WP. Binary DNA nanostructures for data encryption. PLoS One 2012;7(9):e44212.Abstract

We present a simple and secure system for encrypting and decrypting information using DNA self-assembly. Binary data is encoded in the geometry of DNA nanostructures with two distinct conformations. Removing or leaving out a single component reduces these structures to an encrypted solution of ssDNA, whereas adding back this missing "decryption key" causes the spontaneous formation of the message through self-assembly, enabling rapid read out via gel electrophoresis. Applications include authentication, secure messaging, and barcoding.