Clemente CJ, Richards CT. Muscle power limits speed: muscle function and hydrodynamics constrains power in swimming frogs. Nature Communications 2013;4Abstract

Studies of the muscle force–velocity relationship and its derived n-shaped power–velocity curve offer important insights into muscular limits of performance. Given the power is maximal at 1/3 Vmax, geometric scaling of muscle force coupled with fluid drag force implies that this optimal muscle-shortening velocity for power cannot be maintained across the natural body-size range. Instead, muscle velocity may decrease with increasing body size, conferring a similar n-shaped power curve with body size. Here we examine swimming speed and muscle function in the aquatic frog Xenopus laevis. Swimming speed shows an n-shaped scaling relationship, peaking at 47.35 g. Further, in vitro muscle function of the ankle extensor plantaris longus also shows an optimal body mass for muscle power output (47.27 g), reflecting that of swimming speed. These findings suggest that in drag-based aquatic systems, muscle–environment interactions vary with body size, limiting both the muscle’s potential to produce power and the swimming speed.

Yun H, Hur SC. Sequential multi-molecule delivery using vortex-assisted electroporation. Lab on a Chip 2013;13:2764-2772.Abstract

We developed an on-chip microscale electroporation system that enables sequential delivery of multiple molecules with precise and independent dosage controllability into pre-selected identical populations of target cells. The ability to trap cells with uniform size distribution contributed to enhanced molecular delivery efficiency and cell viability. Additionally, the system provides real-time monitoring ability of the entire delivery process, allowing timely and independent modification of cell- and molecule-specific electroporation parameters. The precisely controlled amount of inherently membrane-impermeant molecules was transferred into human cancer cells by varying electric field strengths and molecule injection durations. The proposed microfluidic electroporation system's improved viability and comparable gene transfection efficiency to that of commercial systems suggest that the current system has great potential to expand the research fields that on-chip electroporation techniques can be used in.

Sato Y. Viewpoint: A SQUID analog with a Bose-Einstein condensate. Physics 2013;6:123. 2013_sato_physics.pdf
Gaudry Q, Hong EJ, Kain J, de Bivort BL, Wilson RI. Asymmetric neurotransmitter release enables rapid odour lateralization in Drosophila. Nature 2013;493:424-8.Abstract

In Drosophila, most individual olfactory receptor neurons (ORNs) project bilaterally to both sides of the brain. Having bilateral rather than unilateral projections may represent a useful redundancy. However, bilateral ORN projections to the brain should also compromise the ability to lateralize odours. Nevertheless, walking or flying Drosophila reportedly turn towards the antenna that is more strongly stimulated by odour. Here we show that each ORN spike releases approximately 40% more neurotransmitter from the axon branch ipsilateral to the soma than from the contralateral branch. As a result, when an odour activates the antennae asymmetrically, ipsilateral central neurons begin to spike a few milliseconds before contralateral neurons, and at a 30to50% higher rate than contralateral neurons. We show that a walking fly can detect a 5% asymmetry in total ORN input to its left and right antennal lobes, and can turn towards the odour in less time than it requires the fly to complete a stride. These results demonstrate that neurotransmitter release properties can be tuned independently at output synapses formed by a single axon onto two target cells with identical functions and morphologies. Our data also show that small differences in spike timing and spike rate can produce reliable differences in olfactory behaviour.

Gorthi SS, Schaak D, Schonbrun E. Fluorescence imaging of flowing cells using a temporally coded excitation. Opt Express 2013;21(4):5164-70.Abstract

Imaging fluorescence in moving cells is fundamentally challenging because the exposure time is constrained by motion-blur, which limits the available signal. We report a method to image fluorescently labeled leukemia cells in fluid flow that has an effective exposure time of up to 50 times the motion-blur limit. Flowing cells are illuminated with a pseudo-random excitation pulse sequence, resulting in a motion-blur that can be computationally removed to produce near diffraction-limited images. This method enables observation of cellular organelles and their behavior in a fluid environment that resembles the vasculature.

Spicer R, Tisdale-Orr TE, Talavera C. Auxin-responsive DR5 promoter coupled with transport assays suggest separate but linked routes of auxin transport during woody stem development in Populus. PLOS ONE 2013; 2013_spicer_plos.pdf
SatoY. On the manipulation of heat current with thermal metamaterials. Parity (Japan) 2013;2:46.
Sato Y. Manipulation of heat flow. In: McGraw-Hill Yearbook of Science & Technology. 2013 p. in press.
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