Effects of salt concentrations and bending energy on the extent of ejection of phage genomes

Recent work has shown that pressures inside dsDNA phage capsids can be as high as many tens of atmospheres; it is this pressure that is responsible for initiation of the delivery of phage genomes to host cells. The forces driving ejection of the genome have been shown to decrease monotonically as ejection proceeds, and hence to be strongly dependent on the genome length. Here we investigate the effects of ambient salts on the pressures inside phage-λ, for the cases of mono-, di-, and tetravalent cations, and measure how the extent of ejection against a fixed osmotic pressure (mimicking the bacterial cytoplasm) varies with cation concentration. We find, for example, that the ejection fraction is halved in 30 mM Mg²⁺ and is decreased by a factor of 10 upon addition of 1 mM spermine. These effects are calculated from a simple model of genome packaging, using DNA-DNA repulsion energies as determined independently from x-ray diffraction measurements on bulk DNA solutions. By comparing the measured ejection fractions with values implied from the bulk DNA solution data, we predict that the bending energy makes the d-spacings inside the capsid larger than those for bulk DNA at the same osmotic pressure.     

Membrane-assisted viral DNA ejection

Genome packaging and delivery are fundamental steps in the replication cycle of all viruses. Icosahedral viruses with linear double-stranded DNA (dsDNA) usually package their genome into a preformed, rigid procapsid using the power generated by a virus-encoded packaging ATPase. The pressure and stored energy due to this confinement of DNA at a high density is assumed to drive the initial stages of genome ejection. Membrane-containing icosahedral viruses, such as bacteriophage PRD1, present an additional architectural complexity by enclosing their genome within an internal membrane vesicle. Upon adsorption to a host cell, the PRD1 membrane remodels into a proteo-lipidic tube that provides a conduit for passage of the ejected linear dsDNA through the cell envelope. Based on volume analyses of PRD1 membrane vesicles captured by cryo-electron tomography and modeling of the elastic properties of the vesicle, we propose that the internal membrane makes a crucial and active contribution during infection by maintaining the driving force for DNA ejection and countering the internal turgor pressure of the host. These novel functions extend the role of the PRD1 viral membrane beyond tube formation or the mere physical confinement of the genome. The presence and assistance of an internal membrane might constitute a biological advantage that extends also to other viruses that package their linear dsDNA to high density within an internal vesicle.     

Ion-Dependent Dynamics of DNA Ejections for Bacteriophage λ

We studied the control parameters that govern the dynamics of in vitro DNA ejection in bacteriophage λ. Previous work demonstrated that bacteriophage DNA is highly pressurized, and this pressure has been hypothesized to help drive DNA ejection. Ions influence this process by screening charges on DNA; however, a systematic variation of salt concentrations to explore these effects has not been undertaken. To study the nature of the forces driving DNA ejection, we performed in vitro measurements of DNA ejection in bulk and at the single-phage level. We present measurements on the dynamics of ejection and on the self-repulsion force driving ejection. We examine the role of ion concentration and identity in both measurements, and show that the charge of counterions is an important control parameter. These measurements show that the mobility of ejecting DNA is independent of ionic concentrations for a given amount of DNA in the capsid. We also present evidence that phage DNA forms loops during ejection, and confirm that this effect occurs using optical tweezers.     

Energy of electrons emitted as a result of separation of surfaces

Experiments indicating acceleration of charged particles as a result of separation of solid surfaces are analyzed. As a possible mechanism of such acceleration, generation of surface charge on the separated surfaces of a cleaved ionic crystal is considered. The maximum electric field generated due to the charging of the separated surfaces and the energy of electrons accelerated in such a field are estimated. It is shown that, for the maximum attainable electric field, conditions are created for the generation of runaway electrons that, even at atmospheric pressure, electrons are accelerated to high energies, not experiencing collisions with gas particles.     

Real-time imaging of DNA ejection from single phage particles

Infection by tailed dsDNA phages is initiated by release of the viral DNA from the capsid and its polarized injection into the host. The driving force for the genome transport remains poorly defined. Among many hypothesis [1], it has been proposed that the internal pressure built up during packaging of the DNA in the capsid is responsible for its injection [2-4]. Whether the energy stored during packaging is sufficient to cause full DNA ejection or only to initiate the process was tested on phage T5 whose DNA (121,400 bp) can be released in vitro by mere interaction of the phage with its E. coli membrane receptor FhuA [5-7]. We present a fluorescence microscopy study investigating in real time the dynamics of DNA ejection from single T5 phages adsorbed onto a microfluidic cell. The ejected DNA was fluorescently stained, and its length was measured at different stages of the ejection after being stretched in a hydrodynamic flow. We conclude that DNA release is not an all-or-none process but occurs in a stepwise fashion and at a rate reaching 75,000 bp/sec. The relevance of this stepwise ejection to the in vivo DNA transfer is discussed.     

Dependence of the ion energy on the parameters of the laser pulse and target in the radiation-pressure-dominated regime of acceleration

When the dominant mechanism for ion acceleration is the laser radiation pressure, the conversion efficiency of the laser energy into the energy of relativistic ions may be very high. Stability analysis of a thin plasma layer accelerated by the radiation pressure shows that Raleigh-Taylor instability may enhance plasma inhomogeneity. In the linear stage of instability, the plasma layer decays into separate bunches, which are accelerated by the radiation pressure similarly to clusters accelerated under the action of an electromagnetic wave. The energy and luminosity of an ion beam accelerated in the radiation-pressure-dominated regime are calculated.     

Effects of substrate structure on speed and acceleration capacity in climbing geckos

We studied the effects of substrate structure on locomotor performance in a climbing gecko, Hemidactylus garnoti . We quantified three performance traits (acceleration capacity, instantaneous speed, and final speed) on three substrates: (i) smooth wood, (ii) a cloth surface, and (iii) a wire mesh. While acceleration capacity and instantaneous speed were highest on the wooden surface, final speed did not differ significantly among substrates. Using scanning electron microscopy (SEM) pictures, we estimated that 98% of the wooden surface is available for adhesion by the setae on the toepads, while this percentage is much lower for the mesh and cloth (41 and 37%, respectively). We suggest that when a gecko climbs up a gap-filled substrate, such as the wire mesh or cloth, adhesion will only happen between part of the toepad and the substrate, resulting in a diminished acceleration capacity. The higher acceleration capacity on the wooden substrate and the fact that the geckos tend to slip less often on this particular surface, may explain the difference in instantaneous speed. As for final speed, geckos might achieve similar final speeds on all three substrates by employing different locomotor strategies. Our results suggest that microhabitat use in nature might have a profound effect on locomotor performance and survival for climbing lizards such as geckos.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 385–393.     

A power equation for the sprint in speed skating.

An analysis of the start of the 500 m speed skating races during the 1988 Olympic Winter Games showed a remarkably high correlation between the acceleration of the skater in the first second of the sprint and the final time (r = -0.75). In this study a power equation is used to explain this high coefficient of correlation. The performance in speed skating is determined by the capability of external power production by the speed skater. This power is necessary to overcome the air and ice friction and to increase the kinetic energy of the skater. Numerical values of the power dissipated to air and ice friction, both dependent on speed, are obtained from ice friction and wind tunnel experiments. Using aerobic and anaerobic power production as measured during supra maximal bicycle tests of international-level speed skaters, a model of the kinetics of power production is obtained. Simulation of power production and power dissipation yields values of speed and acceleration and, finally, the performance time of the sprint during speed skating. The mean split time at 100 m and the final time at 500 m in these races, derived from simulation, were 10.57 s (+/- 0.31) and 37.82 s (+/- 0.96), respectively. The coefficient of correlation between the simulated 500 m times and the actual 500 m times was 0.90. From the results of this study it can be concluded that the distribution of the available anaerobic energy is an important factor in the short lasting events. For the same amount of anaerobic energy the better sprinters appear to be able to liberate considerably more energy at the onset of the race than skaters of lower performance level.     

The locomotory function of the fins in the squid Loligo pealei

Kinematic data of high spatial and temporal resolution, acquired from image sequences of adult long-finned squid, Loligo pealei, during steady swimming in a flume, were used to examine the role of fins and the coordination between fin and jet propulsion in squid locomotion. Fin shape and body outlines were digitized and used to calculate fin wave speed, amplitude, frequency, angle of attack, body deformation, speed, and acceleration. L. pealei were observed to have two fin gait patterns with a transition at 1.4-1.8 mantle lengths per second (Lm s-1) marked by alternation between the two patterns. Fin motion in L. pealei exhibited characteristics of both traveling waves and flapping wings. At low speeds, fin motion was more wave-like; at high speeds, fin motion was more flap-like and was marked by regular periods during which the fins were wrapped tightly against the mantle. Fin cycle frequencies were dependent on swimming speed and gait, and obvious coordination between the fins and jet were observed. Fin wave speed, angle of attack, and body acceleration confirmed the role of fins in thrust production and revealed a role of fins at all swimming speeds by a transition from drag-based to lift-based thrust when fin wave speed dropped below swimming speed. Estimates of peak fin thrust were as high as 0.44-0.96 times peak jet thrust in steady swimming over the range of swimming speeds observed. Fin downstrokes generally contributed more to thrust than did upstrokes, especially at high speeds.     

风速变化对草原生态系统的影响研究进展

在全球风速呈下降趋势的大背景下,研究风速变化对生态系统的影响具有重要意义,尤其是其重要组成部分——草原生态系统。近年来大量学者开始研究风速变化对草原生态系统的影响,主要集中在以下几个方面并得出相关的结论,(1)风速变化会影响植物的生长速率和叶片形态,适当的风速能够促进植物生长发育、提高植被初级生产力,而强风或持续大风不仅会对植物产生破坏作用,还会影响其生长发育;(2)风会最先带走地表细小颗粒,从而导致土壤质地变粗、水分下降、营养成分重新分配;(3)风引起地表边界层和大气边界层物质和能量的转移和交换,热量和水汽的交换导致地表微气候发生变化,如风速降低会导致地表温度升高;(4)风力作用使得土壤水分亏缺、营养成分变化,导致草原生态系统结构变化、草地覆盖度降低、物种生活型复杂化、耐旱植物增加;(5)大气稳定性、CO2交换速率和碳排放都会随着风速的增加而增加,碳吸收则相反,碳通量也因此发生变化。综上,风速降低对于草原生态系统的影响复杂且利弊相当,未来的发展趋势会更加侧重于以下几个方面的发展:研究对象的多样化、加强控制实验的定量化研究、综合多要素的相互作用机理研究、整体结构和功能性的研究。     

The mechanics of hopping by kangaroos (Macropodidae)

Force platform records and films have been made of kangaroos and a wallaby hopping.
The maximum forces exerted on the ground were about six times body weight. The force exerted on the ground changes direction, throughout the period when the feet are on the ground, so that it is always more or less in line with the centre of mass. Consequently the animal decelerates a little and then accelerates again, during the contact phase.
The fluctuations of potential energy which occur in each hop are slightly smaller at high speeds than at low ones. Fluctuations of external kinetic energy increase with speed and account for most of the energy cost of hopping at high speeds. Fluctuations of internal kinetic energy (due to acceleration and deceleration of the limbs) are relatively small. While the feet are on the ground the extensor muscles of the hip do positive work, those of the knee negative work and those of the ankle negative work followed by positive work. The energy cost of hopping is reduced substantially by elastic storage of energy in the Achilles tendon. In the case of a wallaby hopping at moderate speed the calculated saving was 40%. The maximum stresses developed in leg muscles, tendons and the tibia have been calculated and are discussed in relation to the known properties of muscle, tendon and bone. The trunk pitches as the animal hops because the two legs swing forwards and back simultaneously. Appropriate tail movements reduce, but do not eliminate, this effect. A mathematical theory of hopping is presented and used to investigate the merits of different hopping techniques.
Dawson & Taylor's (1973) discovery that the rate of oxygen consumption of kangaroos decreases a little, as hopping speed increases, is probably to be explained by the increased role of elastic storage of energy at high speeds.     

On Higher Ground: How Well Can Dynamic Body Acceleration Determine Speed in Variable Terrain?

Introduction

Animal travel speed is an ecologically significant parameter, with implications for the study of energetics and animal behaviour. It is also necessary for the calculation of animal paths by dead-reckoning. Dead-reckoning uses heading and speed to calculate an animal’s path through its environment on a fine scale. It is often used in aquatic environments, where transmission telemetry is difficult. However, its adoption for tracking terrestrial animals is limited by our ability to measure speed accurately on a fine scale. Recently, tri-axial accelerometers have shown promise for estimating speed, but their accuracy appears affected by changes in substrate and surface gradients. The purpose of the present study was to evaluate four metrics of acceleration; Overall dynamic body acceleration (ODBA), vectorial dynamic body acceleration (VDBA), acceleration peak frequency and acceleration peak amplitude, as proxies for speed over hard, soft and inclined surfaces, using humans as a model species.

Results

A general linear model (GLM) showed a significant difference in the relationships between the metrics and speed depending on substrate or surface gradient. When the data from all surface types were considered together, VeDBA had the highest coefficient of determination.

Conclusions

All of the metrics showed some variation in their relationship with speed according to the surface type. This indicates that changes in the substrate or surface gradient during locomotion by animals would produce errors in speed estimates, and also in dead-reckoned tracks if they were calculated from speeds based entirely on a priori calibrations. However, we describe a method by which the relationship between acceleration metrics and speed can be corrected ad hoc, until tracks accord with periodic ground truthed positions, obtained via a secondary means (e.g. VHF or GPS telemetry). In this way, dead-reckoning provides a means to obtain fine scale movement data for terrestrial animals, without the need for additional data on substrate or gradient.     

Compensatory reactions during lower body negative pressure (LBNP) exposure, head-up tilt (HUT) and +Gz tolerance

The effects of lower body negative pressure (LBNP) on acceleration tolerance and head-up tilt were investigated. Healthy male subjects underwent LBNP protocols of various pressures and acceleration tolerance tests; some subjects additionally underwent head-up tilt tests. All subjects were measured for hemodynamic changes and plasma hormonal level changes. The results of these studies showed acceleration tolerance to depend on plasma renin activity, left ventricular ejection time, cardiac output, preejection period, plasma aldosterone levels, and heart rate. The significance of this result is discussed.     

Bacteriophage T5 DNA ejection under pressure

The transfer of the bacteriophage genome from the capsid into the host cell is a key step of the infectious process. In bacteriophage T5, DNA ejection can be triggered in vitro by simple binding of the phage to its purified Escherichia coli receptor FhuA. Using electrophoresis and cryo-electron microscopy, we measure the extent of DNA ejection as a function of the external osmotic pressure. In the high pressure range (7-16 atm), the amount of DNA ejected decreases with increasing pressure, as theoretically predicted and observed for λ and SPP1 bacteriophages. In the low and moderate pressure range (2-7 atm), T5 exhibits an unexpected behavior. Instead of a unique ejected length, multiple populations coexist. Some phages eject their complete genome, whereas others stop at some nonrandom states that do not depend on the applied pressure. We show that contrarily to what is observed for the phages SPP1 and λ, T5 ejection cannot be explained as resulting from a simple pressure equilibrium between the inside and outside of the capsid. Kinetics parameters and/or structural characteristics of the ejection machinery could play a determinant role in T5 DNA ejection.     

Two distinct visual motion mechanisms for smooth pursuit: evidence from individual differences

Smooth-pursuit eye velocity to a moving target is more accurate after an initial catch-up saccade than before, an enhancement that is poorly understood. We present an individual-differences-based method for identifying mechanisms underlying a physiological response and use it to test whether visual motion signals driving pursuit differ pre- and postsaccade. Correlating moment-to-moment measurements of pursuit over time with two psychophysical measures of speed estimation during fixation, we find two independent associations across individuals. Presaccadic pursuit acceleration is predicted by the precision of low-level (motion-energy-based) speed estimation, and postsaccadic pursuit precision is predicted by the precision of high-level (position-tracking) speed estimation. These results provide evidence that a low-level motion signal influences presaccadic acceleration and an independent high-level motion signal influences postsaccadic precision, thus presenting a plausible mechanism for postsaccadic enhancement of pursuit.     

The locomotory function of the fins in the squid Loligo pealei

Kinematic data of high spatial and temporal resolution, acquired from image sequences of adult long-finned squid, Loligo pealei, during steady swimming in a flume, were used to examine the role of fins and the coordination between fin and jet propulsion in squid locomotion. Fin shape and body outlines were digitized and used to calculate fin wave speed, amplitude, frequency, angle of attack, body deformation, speed, and acceleration. L. pealei were observed to have two fin gait patterns with a transition at 1.4-1.8 mantle lengths per second (L_m s^-1) marked by alternation between the two patterns. Fin motion in L. pealei exhibited characteristics of both traveling waves and flapping wings. At low speeds, fin motion was more wave-like; at high speeds, fin motion was more flap-like and was marked by regular periods during which the fins were wrapped tightly against the mantle. Fin cycle frequencies were dependent on swimming speed and gait, and obvious coordination between the fins and jet were observed. Fin wave speed, angle of attack, and body acceleration confirmed the role of fins in thrust production and revealed a role of fins at all swimming speeds by a transition from drag-based to lift-based thrust when fin wave speed dropped below swimming speed. Estimates of peak fin thrust were as high as 0.44-0.96 times peak jet thrust in steady swimming over the range of swimming speeds observed. Fin downstrokes generally contributed more to thrust than did upstrokes, especially at high speeds.     

Dynamics of double stranded DNA reptation from bacteriophage.

The dynamics of dsDNA release process from a phage head has been analyzed theoretically. The process was considered as dsDNA reptation through the phage tail. The driving force is assumed to be the decrease of the DNA globule free energy on its releasing from the head in the surrounding medium. The results of the equilibrium theory on an intraphage DNA globule were applied. Three possible sources of friction were examined. The first one is in the inner channel of the tail. The second is the friction of DNA segments in the whole globule volume, which is essential when the globule decondensation is a collective process, at simultaneous moving of all the turns (mechanism 1). The third is the globule friction with the capsid inner surface, that is most important when decondensation proceeds via the globule rotation as a whole spool (mechanism 2). Mechanism 1 would require a lot of time for ejection. Mechanism 2 would lead to different ejection dynamics of short- and long-tailed phages. Comparison of the theoretical results with the published experimental data argues in favor of mechanism 2.     

The fluid mechanics of bolus ejection from the oral cavity

The squeezing action of the tongue against the palate provides driving forces to propel swallowed material out of the mouth and through the pharynx. Transport in respose to these driving forces, however, is dependent on the material properties of the swallowed bolus. Given the complex geometry of the oral cavity and the unsteady nature of this process, the mechanics governing the oral phase of swallowing are not well understood. In the current work, the squeezing flow between two approaching parallel plates is used as a simplified mathematical model to study the fluid mechanics of bolus ejection from the oral cavity. Driving forces generated by the contraction of intrinsic and extrinsic lingual muscles are modeled as a spatially uniform pressure applied to the tongue. Approximating the tongue as a rigid body, the motion of tongue and fluid are then computed simultaneously as a function of time. Bolus ejection is parameterized by the time taken to clear half the bolus from the oral cavity, t_1/2. We find that t_1/2 increases with increased viscosity and density and decreases with increased applied pressure. In addition, for low viscosity boluses (μapproximately 1000 cP), viscosity dominates. A transition region between these two regimes is found in which both properties affect the solution characteristics. The relationship of these results to the assessment and treatment of swallowing disorders is discussed.     

Measurements of single DNA molecule packaging dynamics in bacteriophage lambda reveal high forces, high motor processivity, and capsid transformations

Molecular motors drive genome packaging into preformed procapsids in many double-stranded (ds)DNA viruses. Here, we present optical tweezers measurements of single DNA molecule packaging in bacteriophage lambda. DNA-gpA-gpNu1 complexes were assembled with recombinant gpA and gpNu1 proteins and tethered to microspheres, and procapsids were attached to separate microspheres. DNA binding and initiation of packaging were observed within a few seconds of bringing these microspheres into proximity in the presence of ATP. The motor was observed to generate greater than 50 picoNewtons (pN) of force, in the same range as observed with bacteriophage phi29, suggesting that high force generation is a common property of viral packaging motors. However, at low capsid filling the packaging rate averaged approximately 600 bp/s, which is 3.5-fold higher than phi29, and the motor processivity was also threefold higher, with less than one slip per genome length translocated. The packaging rate slowed significantly with increasing capsid filling, indicating a buildup of internal force reaching 14 pN at 86% packaging, in good agreement with the force driving DNA ejection measured in osmotic pressure experiments and calculated theoretically. Taken together, these experiments show that the internal force that builds during packaging is largely available to drive subsequent DNA ejection. In addition, we observed an 80 bp/s dip in the average packaging rate at 30% packaging, suggesting that procapsid expansion occurs at this point following the buildup of an average of 4 pN of internal force. In experiments with a DNA construct longer than the wild-type genome, a sudden acceleration in packaging rate was observed above 90% packaging, and much greater than 100% of the genome length was translocated, suggesting that internal force can rupture the immature procapsid, which lacks an accessory protein (gpD).     

Locomotion in copepods: pattern of movements and energetics of Cyclops

The cost of swimming in copepods has generally been estimated through the application of fluid dynamics theory to data on velocity and acceleration obtained by means of movies. It has also been estimated through the changes in fat content of copepods after sustained swimming (i.e. vertical migration). However, the range of estimated costs of locomotion is exceedingly large (from 0.1% to 95% of total metabolism). This communication studies the pattern of swimming movements and the work done by Cyclops, using high speed cinematographic techniques. The contribution of swimming to the energy expenditure of the individual is estimated, and consideration of the possible role of rubber-like proteins in the cuticle of copepods is made.