Death odour changes movement pattern of a Collembola

We used video-tracking of individuals of a Collembola, Protaphorura armata, on a clay surface in a petri dish to analyse their movement pattern in an environment with attractive and repellent cues. An area with dead conspecifics was repellent whilst live conspecifics made the area attractive. An area which had been occupied for 24 hours by the predatory mite, Hypoaspis aculeifer, was avoided only if the mite had preyed upon P. armata before it was placed in the area. P. armata lost their looping behaviour, moved faster and more straightened out (decreased turning rate) in the presence of attractive or repellent odours. The resulting net squared displacement was faster than in the control and best described as a correlated random walk. Our results emphasise the importance of considering varying movement pattern in response to environmental cues when predicting dispersal and spatial distribution of an animal.     

Modelling the movement of a soil insect

We use a linear autoregressive model to describe the movement of a soil-living insect, Protaphorura armata (Collembola). Models of this kind can be viewed as extensions of a random walk, but unlike a correlated random walk, in which the speed and turning angles are independent, our model identifies and expresses the correlations between the turning angles and a variable speed. Our model uses data in x- and y-coordinates rather than in polar coordinates, which is useful for situations in which the resolution of the observations is limited. The movement of the insect was characterized by (i) looping behaviour due to autocorrelation and cross correlation in the velocity process and (ii) occurrence of periods of inactivity, which we describe with a Poisson random effects model. We also introduce obstacles to the environment to add structural heterogeneity to the movement process. We compare aspects such as loop shape, inter-loop time, holding angles at obstacles, net squared displacement, number, and duration of inactive periods between observed and predicted movement. The comparison demonstrates that our approach is relevant as a starting-point to predict behaviourally complex moving, e.g. systematic searching, in a heterogeneous landscape.     

Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics

Measurements of protein-mediated DNA looping reveal that in vivo conditions favor the formation of loops shorter than those that occur in vitro, yet the precise physical mechanisms underlying this shift remain unclear. To understand the extent to which in vivo supercoiling may explain these shifts, we develop a theoretical model based on coarse-grained molecular simulation and analytical transition state theory, enabling us to map out looping energetics and kinetics as a function of two key biophysical parameters: superhelical density and loop length. We show that loops on the scale of a persistence length respond to supercoiling over a much wider range of superhelical densities and to a larger extent than longer loops. This effect arises from a tendency for loops to be centered on the plectonemic end region, which bends progressively more tightly with superhelical density. This trend reveals a mechanism by which supercoiling favors shorter loop lengths. In addition, our model predicts a complex kinetic response to supercoiling for a given loop length, governed by a competition between an enhanced rate of looping due to torsional buckling and a reduction in looping rate due to chain straightening as the plectoneme tightens at higher superhelical densities. Together, these effects lead to a flattening of the kinetic response to supercoiling within the physiological range for all but the shortest loops. Using experimental estimates for in vivo superhelical densities, we discuss our model’s ability to explain available looping data, highlighting both the importance of supercoiling as a regulatory force in genetics and the additional complexities of looping phenomena in vivo.     

Development of left/right handedness in the chick heart.

The chick heart tube develops from the fusion of the right and left areas of precardiac mesoderm and in almost all cases loops to the embryo's right-hand side. We have investigated whether any intrinsic difference exists in the right and left areas of precardiac mesoderm, that influences the direction of looping of the heart tube. Chick embryos incubated to stages 4,5 and 6 were cultured by the New method. Areas of precardiac mesoderm were exchanged between donor and host embryos of the same stage and different stages to form control, double-right and double-left sided embryos. Overall, double-right sided embryos formed many more left-hand loops than double-left sided embryos. At stages 4 and 5 a small percentage of double-right embryos formed left-hand loops (13%) whereas at stage 6 almost 50% of hearts had left-hand loops. Control embryos formed right-hand loops in 97% of cases. The stability of right-hand heart looping by double-left sided embryos, may be related to the process of 'conversion', whereas the direction of looping by double-right sided embryos has become randomised. There is some indication that an intrinsic change occurred in the precardiac mesoderm between stages 5 and 6 that later influenced the direction of looping of the heart tube. The direction of body turning is suggested to be linked to the direction of heart looping.     

MODELS OF MUSCLE Z-BAND FINE STRUCTURE BASED ON A LOOPING FILAMENT CONFIGURATION

The fine architecture of skeletal muscle Z bands is considered in view of stereo electron microscopical evidence and current biochemical and immunological concepts, and a new Z-band model is proposed. This model is based on a looping, interlinking configuration, within the Z band, of strands which emanate from I-band (actin) filaments of adjacent sarcomeres. Two versions of the model seem presently feasible: one in which the Z-band lattice is composed of actin loops; and another in which the same pattern is derived from tropomyosin. Either version satisfies actual electron micrograph images as well as or better than prior Z-band models. Moreover, the principle of looping linkage in filament-to-filament attachment can be related to similar filament patterns seen in several adhesion sites where intracellular filaments insert on cell membranes.     

Gene repression by minimal lac loops in vivo

The inflexibility of double-stranded DNA with respect to bending and twisting is well established in vitro. Understanding apparent DNA physical properties in vivo is a greater challenge. Here, we exploit repression looping with components of the Escherichia coli lac operon to monitor DNA flexibility in living cells. We create a minimal system for testing the shortest possible DNA repression loops that contain an E. coli promoter, and compare the results to prior experiments. Our data reveal that loop-independent repression occurs for certain tight operator/promoter spacings. When only loop-dependent repression is considered, fits to a thermodynamic model show that DNA twisting limits looping in vivo, although the apparent DNA twist flexibility is 2- to 4-fold higher than in vitro. In contrast, length-dependent resistance to DNA bending is not observed in these experiments, even for the shortest loops constraining <0.4 persistence lengths of DNA. As observed previously for other looping configurations, loss of the nucleoid protein heat unstable (HU) markedly disables DNA looping in vivo. Length-independent DNA bending energy may reflect the activities of architectural proteins and the structure of the DNA topological domain. We suggest that the shortest loops are formed in apical loops rather than along the DNA plectonemic superhelix.     

Computational analysis of looping of a large family of highly bent DNA by LacI

Sequence-dependent intrinsic curvature of DNA influences looping by regulatory proteins such as LacI and NtrC. Curvature can enhance stability and control shape, as observed in LacI loops formed with three designed sequences with operators bracketing an A-tract bend. We explore geometric, topological, and energetic effects of curvature with an analysis of a family of highly bent sequences, using the elastic rod model from previous work. A unifying straight-helical-straight representation uses two phasing parameters to describe sequences composed of two straight segments that flank a common helically supercoiled segment. We exercise the rod model over this two-dimensional space of phasing parameters to evaluate looping behaviors. This design space is found to comprise two subspaces that prefer parallel versus anti-parallel binding topologies. The energetic cost of looping varies from 4 to 12 kT. Molecules can be designed to yield distinct binding topologies as well as hyperstable or hypostable loops and potentially loops that can switch conformations. Loop switching could be a mechanism for control of gene expression. Model predictions for linking numbers and sizes of LacI-DNA loops can be tested using multiple experimental approaches, which coupled with theory could address whether proteins or DNA provide the observed flexibility of protein-DNA loops.     

Interaction between descending input and thoracic reflexes for joint coordination in cockroach. II Comparative studies on tethered turning and searching

Tethered cockroaches turn from unilateral antennal contact using asymmetrical movements of mesothoracic (T2) legs (Mu and Ritzmannin J Comp Physiol A 191:1037–1054, 2005). During the turn, the leg on the inside of the turn (the inside T2 leg) has distinctly different motor patterns from those in straight walking. The transformation from walking to inside leg turning could be triggered by descending commands that alter a few critical reflexes that start a cascade of physical changes in leg movement or posture, leading to further alterations. This hypothesis has two implications: First, the descending activities must be able to influence thoracic reflexes. Second, one should be able to initiate the turning motor pattern in the absence of descending signals by mimicking a point farther down in the reflex cascade. We addressed the first implication in the companion paper. To examine the second implication, we compared kinematics and motor activities of the T2 leg during searching with that of inside leg turning. The reaching movements made during searching were found to be similar to the movements made by the inside leg during turning. Moreover, even after disconnecting the brain from the thoracic ganglia the reaching movements were similar. This observation is consistent with the second implication from the hypothesis.     

Leg coordination during turning on an extremely narrow substrate in a bug, Mesocerus marginatus (Heteroptera, Coreidae)

The turning movement of a bug, Mesocerus marginatus, is observed when it walks upside-down below a horizontal beam and, at the end of the beam, performs a sharp turn by 180 degrees . The turn at the end of the beam is accomplished in three to five steps, without strong temporal coordination among legs. During the stance, leg endpoints (tarsi) run through rounded trajectories, rotating to the same side in all legs. During certain phases of the turn, a leg is strongly depressed and the tarsus crosses the midline. Swing movements rotate to the same side as do leg endpoints in stance, in strong contrast to the typical swing movements found in turns or straight walk on a flat surface. Terminal location is found after the search through a trajectory that first moves away from the body and then loops back to find substrate. When a leg during stance has crossed the midline, in the following swing movement the leg may move even stronger on the contralateral side, i.e. is stronger depressed, in contrast to swing movements in normal walking, where the leg is elevated. These results suggest that the animals apply a different control strategy compared to walking and turning on a flat surface.     

Search orientation of Musca domestica in patches of sucrose drops

ABSTRACT. The searching tactics of the housefly, Musca dormestica L. (Diptera: Muscidae), have been delineated from digitized pathways of flies walking in patches of sucrose drops arranged in linear (ROW) and hexagonal (HEX) arrays. The areas covered by flies in ROW and HEX patches are distinctly different, but flies seem not to employ different tactics for the two types of resource arrays. The number of drops located, if at least one drop is found, does not differ between ROW and HEX. Most quantitative measures of local search remain constant after the first interdrop interval, although feeding time decreases as flies sample successive drops. Local search intensifies after each drop is ingested, with locomotory rate decreasing and turning rate increasing, followed by decay of both measures toward ranging levels. Searching can be characterized by two movement tendencies resulting from specific, definable, locomotory functions: a forward-moving tendency is expressed by the fly as it leaves a resource in approximately the same direction as it arrives; and local search is characterized by looping, rather than straight walking, with a variable turning rate that generates a rough ‘zigzag’ superimposed on looping. The two movement tendencies, combined, allow flies to locate resources in a linear arrangement, because of the forward-moving tendency, and to locate resources not arranged in a linear array because of the ‘noisy’ loop. M. domestica does not appear to retain and use information gained from one patch of drops in another, so the search tactic of the fly seems therefore to be a compromise between straight movement and circular movement that may be adaptive for an environment subject to frequent changes in the spatial distribution of resources. Giving-up-time, the period between ingesting the last drop and leaving the patch, is a function of the rate of change in the transition from local search to ranging, which is constant in our experiments. If a fly does not encounter another drop while ranging, during which it walks relatively straight, the fly moves out of and away from the patch.     

The morphology and ecology of Dipolydora armata (Polychaeta, Spionidae) from the western Mediterranean Sea

Bick. A. 2001. The morphology and ecology of Dipolydora armata (Polychaeta, Spionidae) from the western Mediterranean Sea. — Acta Zoologica (Stockholm) 82 : 177–187
The cosmopolitan spionid Dipolydora armata is a dominant species of epifauna on Thais haemastoma shells in the western Mediterranean Sea. Some characters, particularly number, thickness and arrangement of notopodial spines, were extremely variable among specimens. Three morphological forms were distinguished based on the general appearance of the bundles of spines; one form possesses at least one bundle of stout spines, whereas bundles of medium spines or thinner acicular spines characterise the other forms. Differences in prostomial shape, as well as in the extension and form of the caruncle, were artefacts (preservation or angle of observation). The present study supports D. rogeri as a junior synonym of D. armata. D. armata was regularly found on shells inhabited by hermit crabs ( Calcinus tubularis , Clibanarius erythropus ) and on damaged, empty shells. Abundance, dominance, size frequency, occurrence of larvae and occurrence of regenerated specimens varied, possibly as a result of fouling strategy and recurrent settlements.     

Norovirus P particle, a novel platform for vaccine development and antibody production

The norovirus P particle is an octahedral nanoparticle formed by 24 copies of the protrusion (P) domain of the norovirus capsid protein. This P particle is easily produced in Escherichia coli, extremely stable, and highly immunogenic. There are three surface loops per P domain, making a total of 72 loops per particle, and these are potential sites for foreign antigen presentation for immune enhancement. To prove this concept, a small peptide (His tag, 7 amino acids [aa]) and a large antigen (rotavirus VP8, 159 aa) were inserted into one of the loops. Neither insertion affects P particle formation, while both antigens were presented well on the P particle surface. The immune-enhancement effect of the P particle was demonstrated by significantly increased antibody titers induced by the P particle-presented antigens compared to the titers induced by free antigens. In addition, the measured neutralization antibody titers and levels of protection against rotavirus shedding in mice immunized with the VP8 chimeric P particles were significantly higher than those of mice immunized with the free VP8 antigen. Sera from P particle-VP8 chimera-vaccinated animals also blocked norovirus virus-like particle (VLP) binding to the histo-blood group antigen (HBGA) receptors. From these data, the P particle appears to be an excellent vaccine platform for antigen presentation. The readily available three surface loops and the great capacity for foreign antigen insertion make this platform attractive for wide application in vaccine development and antibody production. The P particle-VP8 chimeras may serve as a dual vaccine against both rotavirus and norovirus.     

Step response of lung surface-to-volume ratio by light-scattering stereology

By means of backscattered light from a pointlike source on the pleural surface, we investigated the dynamic behavior of the surface-to-volume ratio (S/V) in excised dog lobes subjected to small volume steps both in and out on both the inflation and deflation limb of standard pressure-volume maneuvers. The technique utilizes the established correlation of the pattern of backscattered light with morphometric mean linear intercept and is suitable for dynamic studies. We hypothesized that 1) there would be a difference in the timing of stress relaxation or recovery between alveolar septa and the fibromuscular tissue in the alveolar duct that would reveal itself as a temporally changing S/V after a step-volume change and 2) that geometric hysteresis (looping of S/V with volume), as seen with large volume excursion histories, would be similarly present in small tidal volume loops. Our experimental results contradicted both hypotheses. In particular, we found virtually no change in S/V after a step-volume change, even in the presence of substantial stress adaptation. In addition, when geometric hysteresis of small loops was present, it was always in the sense opposite to the geometric hysteresis of large loops. We conclude that 1) there is a functional "matching" of the stress-adaptive timing between alveolar septa and ductal mouths and 2) during small volume looping, the stress hysteresis (looping of stress with volume) in the ductal tissue may be larger than that of the septa, including surface tension.     

Modeling a self-avoiding chromatin loop: relation to the packing problem, action-at-a-distance, and nuclear context

There is now convincing evidence that genomes are organized into loops, and that looping brings distant genes together so that they can bind to local concentrations of polymerases in "factories" or "hubs." As there remains no systematic analysis of how looping affects the probability that a gene can access binding sites in such factories/hubs, we used an algorithm that we devised and Monte Carlo methods to model a DNA or chromatin loop as a semiflexible (self-avoiding) tube attached to a sphere; we examine how loop thickness, rigidity, and contour length affect where particular segments of the loop lie relative to binding sites on the sphere. Results are compared with those obtained with the traditional model of an (infinitely thin) freely jointed chain. They provide insights into the packing problem (how long genomes are packed into small nuclei), and action-at-a-distance (how firing of one origin or gene can prevent firing of an adjacent one).     

Search strategy of sex pheromone-stimulated male German cockroaches

Stimulation of the male German cockroach, Blattella germanica, with contact sex pheromone releases courtship behaviour and then area-restricted local search. Servosphere-recorded search patterns, compared to pre-stimulus pathways, are characterised by increased looping and path crossing and a relatively high rate of turning. Search behaviour can be performed in the absence of visual cues, including information relative to the site of stimulation. Information controlling search motor patterns is at least in part genetic; certain pattern components are generally similar from trial to trial, whereas specific pattern components vary widely.     

Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI

Many restriction enzymes require binding of two copies of a recognition sequence for DNA cleavage, thereby introducing a loop in the DNA. We investigated looping dynamics of Type IIE restriction enzymes NaeI and NarI by tracking the Brownian motion of single tethered DNA molecules. DNA containing two endonuclease recognition sites spaced a few 100 bp apart connect small polystyrene beads to a glass surface. The position of a bead is tracked through video microscopy. Protein-mediated looping and unlooping is then observed as a sudden specific change in Brownian motion of the bead. With this method we are able to directly follow DNA looping kinetics of single protein–DNA complexes to obtain loop stability and loop formation times. We show that, in the absence of divalent cations, NaeI induces DNA loops of specific size. In contrast, under these conditions NarI mainly creates non-specific loops, resulting in effective DNA compaction for higher enzyme concentrations. Addition of Ca²⁺ increases the NaeI-DNA loop lifetime by two orders of magnitude and stimulates specific binding by NarI. Finally, for both enzymes we observe exponentially distributed loop formation times, indicating that looping is dominated by (re)binding the second recognition site.