Geometric estimates of heritability in biological shape

The recently developed geometric morphometrics methods represent an important contribution of statistics and geometry to the study of biological shapes. We propose simple protocols using shape distances that incorporate geometric techniques into linear quantitative genetic models that should provide insights into the contribution of genetics to shape variation in organisms. The geometric approaches use Procrustes distances in a curved shape space and distances in tangent spaces within and among families to estimate shape heritability. We illustrate the protocols with an example of wing shape variation in the honeybee, Apis mellifera. The heritability of overall shape variation was small, but some localized components depicting shape changes on distal wing regions showed medium to large heritabilities. The genetic variance-covariance matrix of the geometric shape variables was significantly correlated with the phenotypic shape variance-covariance matrix. A comparison of the results of geometric methods with the traditional multivariate analysis of interlandmark distances indicated that even with a larger dimensionality, the interlandmark distances were not as rich in shape information as the landmark coordinates. Quantitative genetics studies of shape should greatly benefit from the application of geometric methods.     

Otolith shape in juvenile cod (Gadus morhua): Ontogenetic and environmental effects

The objectives of this study were to describe the otolith shape development of cod from post-metamorphosis larvae to juveniles and to examine whether shape development is an ontogenetically determined process. Fish were reared under three different temperature regimes and two feeding levels. I examined shape by the length~width relationship of the otolith as well as the number and size of the lobes formed. Otolith size and crenulation is exclusively linked to fish size, indicating an ontogenetically determined development. Otolith shape is closely associated with the spatial development of the lobes. This process is linked with food consumption. Higher food consumption leads to a higher number of larger lobes, resulting in a more rectangular otolith. In conclusion: Otolith shape development consists of an ontogenetic component in the form of increasing size and crenulation and an environmental component impacting on the size and number of the lobes formed.     

Learning to use illumination gradients as an unambiguous cue to three dimensional shape

The luminance and colour gradients across an image are the result of complex interactions between object shape, material and illumination. Using such variations to infer object shape or surface colour is therefore a difficult problem for the visual system. We know that changes to the shape of an object can affect its perceived colour, and that shading gradients confer a sense of shape. Here we investigate if the visual system is able to effectively utilise these gradients as a cue to shape perception, even when additional cues are not available. We tested shape perception of a folded card object that contained illumination gradients in the form of shading and more subtle effects such as inter-reflections. Our results suggest that observers are able to use the gradients to make consistent shape judgements. In order to do this, observers must be given the opportunity to learn suitable assumptions about the lighting and scene. Using a variety of different training conditions, we demonstrate that learning can occur quickly and requires only coarse information. We also establish that learning does not deliver a trivial mapping between gradient and shape; rather learning leads to the acquisition of assumptions about lighting and scene parameters that subsequently allow for gradients to be used as a shape cue. The perceived shape is shown to be consistent for convex and concave versions of the object that exhibit very different shading, and also similar to that delivered by outline, a largely unrelated cue to shape. Overall our results indicate that, although gradients are less reliable than some other cues, the relationship between gradients and shape can be quickly assessed and the gradients therefore used effectively as a visual shape cue.     

Agonist-induced changes in cell shape during regulated secretion in rat pancreatic acini

The actin cytoskeleton plays an important role in the mediation of exocytosis and the determination of cell shape. Experimentally induced changes in cell shape have been shown to affect stimulated secretion in pancreatic acini. In this study, we have examined whether physiologic agonists induce changes in acinar cell shape to modulate secretion. Computer-enhanced video microscopy, immunofluorescence confocal microscopy, and quantitative Western blotting were used to study cell shape changes and cytoskeletal dynamics in rat pancreatic acini. Amylase assays were performed to study the effect of the actin-myosin cytoskeletal antagonists latrunculin A, BDM, and ML-9 on secretion. We found that pancreatic acini underwent a prominent and reversible shape change in response to the physiologic secretory agonist cholecystokinin. This was accompanied by an apical activation of myosin II as well as a basolateral redistribution of both actin and myosin II. Cytoskeletal antagonists inhibited this shape change and attenuated stimulated amylase secretion. Therefore, in addition to acting as a barrier at the apex, the actin-myosin cytoskeleton may also function to modulate cell shape to further regulate stimulated secretion.     

When Geometry Constrains Vision: Systematic Misperceptions within Geometrical Configurations

How accurate are we in reproducing a point within a simple shape? This is the empirical question we addressed in this work. Participants were presented with a tiny disk embedded in an empty circle (Experiment 1 and 3) or in a square (Experiment 2). Shortly afterwards the disk vanished and they had to reproduce the previously seen disk position within the empty shape by means of the mouse cursor, as accurately as possible. Several loci inside each shape were tested. We found that the space delimited by a circle and by a square is not homogeneous and the observed distortion appears to be consistent across observers and specific for the two tested shapes. However, a common pattern can be identified when reproducing geometrical loci enclosed in a shape: errors are shifted toward the periphery in the region around the center and toward the center in the region nearby the edges. The error absolute value declines progressively as we approach an equilibrium contour line between the center and the outline of the shape where the error is null. These results suggest that enclosing an empty space within a shape imposes an organization to it and warps its metrics: not only the perceived loci inside a shape are not the same as the geometrical loci, but they are misperceived in a systematic way that is functional to the correct identification of the center of the shape. Eye movements recordings (Experiment 3) are consistent with this interpretation of the data.     

Effects of Caricaturing in Shape or Color on Familiarity Decisions for Familiar and Unfamiliar Faces

Recent evidence suggests that while reflectance information (including color) may be more diagnostic for familiar face recognition, shape may be more diagnostic for unfamiliar face identity processing. Moreover, event-related potential (ERP) findings suggest an earlier onset for neural processing of facial shape compared to reflectance. In the current study, we aimed to explore specifically the roles of facial shape and color in a familiarity decision task using pre-experimentally familiar (famous) and unfamiliar faces that were caricatured either in shape-only, color-only, or both (full; shape + color) by 15%, 30%, or 45%. We recorded accuracies, mean reaction times, and face-sensitive ERPs. Performance data revealed that shape caricaturing facilitated identity processing for unfamiliar faces only. In the ERP data, such effects of shape caricaturing emerged earlier than those of color caricaturing. Unsurprisingly, ERP effects were accentuated for larger levels of caricaturing. Overall, our findings corroborate the importance of shape for identity processing of unfamiliar faces and demonstrate an earlier onset of neural processing for facial shape compared to color.     

Involvement of a calcium-independent pathway in plasmin-induced platelet shape change

Plasmin-induced platelet activation is considered to be a cause of reocclusion after thrombolytic therapy with plasminogen activators. However, little is known regarding its mechanism and regulation, particularly with respect to the initial step shape change. We here demonstrate that a Ca2+-independent pathway is involved in plasmin-induced human platelet shape change, and that Rho-kinase plays an important role in this pathway. When the increase in cytosolic Ca2+ was prevented by an intracellular Ca2+ chelator, 5,5'-dimethyl-BAPTA, plasmin-induced platelet shape change was partially inhibited but still occurred. In the presence of 5,5'-dimethyl-BAPTA, a specific Rho-kinase inhibitor, Y-27632, completely inhibited the shape change. Phosphorylation of myosin light chain, a key regulator of platelet shape change, was completely inhibited by Y-27632 in 5,5'-dimethyl-BAPTA-treated platelets. Although plasmin caused tyrosine phosphorylation of the 80 kDa protein during the shape change, it did not seem to have a critical role. cAMP-elevating agents inhibited plasmin-induced shape change in 5,5'-dimethyl-BAPTA- or Y-27632-treated platelets with similar efficiency. These results indicated that plasmin causes platelet shape change by activating Ca2+-dependent and Ca2+-independent-Rho-kinase-dependent pathways, both of which are sensitive to cAMP.     

Computer-aided design and manufacture of an above-knee amputee socket

This paper describes the initial test results obtained from a newly developed computer-aided socket design (CASD) and manufacturing (CASM) process for above-knee amputees. Anthropometric measures taken from an amputee provided input information to a CASD system. Using these measurements, data from a reference shape library stored in the computer were selected and modified to create a unique socket shape reflecting the particular characteristics of the amputation stump. The resultant shape was produced as a ‘primitive’ test socket by a CASM process. Numerical shape data were then transferred to a CNC milling machine to construct a negative cast, from which the primitive socket was produced by a vacuum-forming procedure. The resultant primitive socket shape was fitted and the amputee was able to load the socket without discomfort. Some shape discrepancies were identified and the shape data were modified interactively by the CASD system to create a final socket shape. The final socket shape was manufactured and worn by the amputee during a 35 min walking trial. Subjective evaluation was that the socket provided comfort and control comparable with that of the conventional socket, and proved to be acceptable to the amputee. This was followed by a 2-month home trial which was also successful. The CASD socket shapes were compared numerically in area, shape and volume with data taken from the original socket worn by the amputee, a new socket made by conventional methods and a topographic model of the amputation stump. The final CASD socket shape compared favourably with that of a socket manufactured by conventional methods. Results indicated that by the use of the CASD/CASM process, it was possible to produce an above-knee prosthetic socket which provided comfort and control for the amputee.     

Visual Cues of Object Properties Differentially Affect Anticipatory Planning of Digit Forces and Placement

Studies on anticipatory planning of object manipulation showed initial task failure (i.e., object roll) when visual object shape cues are incongruent with other visual cues, such as weight distribution/density (e.g., symmetrically shaped object with an asymmetrical density). This suggests that shape cues override density cues. However, these studies typically only measured forces, with digit placement constrained. Recent evidence suggests that when digit placement is unconstrained, subjects modulate digit forces and placement. Thus, unconstrained digit placement might be modulated on initial trials (since it is an explicit process), but not forces (since it is an implicit process). We tested whether shape and density cues would differentially influence anticipatory planning of digit placement and forces during initial trials of a two-digit object manipulation task. Furthermore, we tested whether shape cues would override density cues when cues are incongruent. Subjects grasped and lifted an object with the aim of preventing roll. In Experiment 1, the object was symmetrically shaped, but with asymmetrical density (incongruent cues). In Experiment 2, the object was asymmetrical in shape and density (congruent cues). In Experiment 3, the object was asymmetrically shaped, but with symmetrical density (incongruent cues). Results showed differential modulation of digit placement and forces (modulation of load force but not placement), but only when shape and density cues were congruent. When shape and density cues were incongruent, we found collinear digit placement and symmetrical force sharing. This suggests that congruent and incongruent shape and density cues differentially influence anticipatory planning of digit forces and placement. Furthermore, shape cues do not always override density cues. A continuum of visual cues, such as those alluding to shape and density, need to be integrated.     

Influence of body mass on the shape of forelimb in musteloid carnivorans

In the majority of mammals, the limbs are positioned under the body and play an important role in gravitational support, allowing the transfer of the load and providing stability to the animal. For this reason, an animal's body mass likely has a significant effect on the shape of its limb bones. In the present study, we investigate the influence of body mass variation on the shape of the three long bones of the forelimb in a group of closely‐related species of mammals: the musteloid carnivorans. We use geometric morphometric techniques to quantify forelimb shape; then estimate phylogenetic signal in the shape of each long bone; and, finally, we apply an independent contrasts approach to assess evolutionary associations between forelimb shape and body mass. The results obtained show that body mass evolution is tightly coordinated with the evolution of forelimb shape, although not equally in all elements. In particular, the humeral and radial shapes of heavier species appear better suited for load bearing and load transmission than the ulna. Nevertheless, our results also show that body mass influences only part of forelimb long bone shape and that other factors, such as locomotor ecology, must be considered to fully understand forelimb evolution. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 91–103.     

Characterization of <Emphasis Type="Italic">fs10.1</Emphasis>, a major QTL controlling fruit elongation in <Emphasis Type="Italic">Capsicum</Emphasis>

We previously identified fs10.1 as a major QTL controlling fruit shape (index of length to width) in an interspecific F₂ cross of Capsicum annuum (round fruit) × C. chinense (elongated fruit) in pepper. To more precisely map and characterize the QTL, we constructed near-isogenic lines for fs10.1 and mapped it in a BC₄F₂ population. In this population, fs10.1 segregated as a Mendelian locus and mapped 0.3 cM away from the closest molecular marker. We further verified the effect of fs10.1 in an F₂ population from an independent cross between elongated- and conical-fruited parents. To identify additional allelic variation at fruit shape loci, we screened an EMS-mutagenized population of the blocky-fruited cv. Maor and identified the mutant E-1654 with elongated fruit. This fruit shape mutation was mapped to the fs10.1 region and was determined to be allelic to the QTL. By measuring fruit shape of near-isogenic lines for fs10.1 during fruit development, we found that the shape of the fruit is determined primarily in the first 2 weeks after anthesis. Histological measurements of cell size and cell shape in pericarp sections of fruits of the isogenic lines throughout fruit development indicated that the shape of the fruit is determined primarily by cell shape and that the development of fruit shape is correlated with cell shape.     

Time-related shape control modifications during erythrocyte storage with additive solutions

To obtain more detailed information on the reversibility of shape alterations in blood bank stored erythrocytes, we have studied shape recovery after chemical crenation and rheological properties in 8 PAGGS-sorbitol preserved erythrocyte concentrates during a five week storage period under blood bank conditions. Our results show that red cell capability to regain a normal discoid shape after chemical crenation decreases during storage but is not lost over a five week period. Moreover there is a significant but weak correlation between red cell ATP content and both shape recovery capability and viscosity. Our results confirm suspicious that red cell shape perturbations following blood bank storage are widely reversible. Two different mechanisms may be involved in reducing shape recovery capability during storage, namely an ATP-dependent mechanism and an energy-independent one. The energy dependent mechanism may be preserved by the previous addition of solutions which maintain higher energy levels during storage.     

Low-temperature induction of calcium-dependent protein phosphorylation in blood platelets

Exposure to low temperature causes platelets to change shape in a manner similar to the shape change that precedes secretagogue-induced serotonin release. Previous studies have shown that two proteins, of approximately 20,000 and approximately 40,000 Mr, become phosphorylated before secretion. We have investigated whether low temperature can induce phosphorylation of these proteins and/or serotonin secretion. The data indicate that low-temperature-induced shape change has no requirement for extracellular calcium, whereas phosphorylation of the two proteins and subsequent serotonin release both have strong calcium requirements. Because cold treatment is thought to influence platelet shape through an effect on microtubules, the events in the shape change- release sequence would seem to be ordered as follows: microtubule disassembly leads to shape change leads to protein phosphorylation leads to secretion.     

Factors determining persistent asymmetry and egg shape in birds: A hypothesis

The shape of birds' eggs has fascinated scientists for many years. It is now possible mathematically to describe shape accurately, allowing exploration of the physical and ecological factors driving the evolution of egg shape. However, there has been relatively little consideration of how egg shape is established in the oviduct or, given that even without an external calcitic layer eggs retain their shape, how shape is fixed in the isthmus. This paper proposes a hypothesis that attempts to explain how egg shape is established and fixed in the oviduct. The hypothesis suggests that as the egg mass (i.e. yolk and albumen) moves from the magnum into the isthmus, it is squeezed by the physical restriction imposed by the isthmus lumen and cannot easily move into the isthmus. As the leading edge of the egg mass enters the isthmus, the egg mass in the distal magnum is forced to bulge outwards, resulting in an asymmetrical shape. The various egg shapes observed in birds are, hence, produced by the interaction between the size of the egg mass relative to female body mass, and the degree of the restriction of the isthmus. Thus, a large egg mass, i.e. relative to female body mass, entering a narrow isthmus will produce a pointed egg shape. If the egg mass is relatively small, and the isthmus lumen wide, more of the egg mass could enter the isthmus and the degree of asymmetry would be reduced. It is further proposed that egg shape is fixed during the formation of the shell membranes in the isthmus because the constituent protein fibres permanently stick together as they are deposited. For the first time this hypothesis helps explain the pattern of deposition and characteristics of the calcitic egg in relation to the diversity of egg shapes in birds and reptiles.     

The Role of Stress Fibers in the Shape Determination Mechanism of Fish Keratocytes

Crawling cells have characteristic shapes that are a function of their cell types. How their different shapes are determined is an interesting question. Fish epithelial keratocytes are an ideal material for investigating cell shape determination, because they maintain a nearly constant fan shape during their crawling locomotion. We compared the shape and related molecular mechanisms in keratocytes from different fish species to elucidate the key mechanisms that determine cell shape. Wide keratocytes from cichlids applied large traction forces at the rear due to large focal adhesions, and showed a spatially loose gradient associated with actin retrograde flow rate, whereas round keratocytes from black tetra applied low traction forces at the rear small focal adhesions and showed a spatially steep gradient of actin retrograde flow rate. Laser ablation of stress fibers (contractile fibers connected to rear focal adhesions) in wide keratocytes from cichlids increased the actin retrograde flow rate and led to slowed leading-edge extension near the ablated region. Thus, stress fibers might play an important role in the mechanism of maintaining cell shape by regulating the actin retrograde flow rate.     

WIDE AND THICK GRAIN 1, which encodes an otubain‐like protease with deubiquitination activity,influences grain size and shape in rice

Grain size and shape are two crucial traits that influence grain yield and grain appearance in rice. Although several factors that affect grain size have been described in rice, the molecular mechanisms underlying the determination of grain size and shape are still elusive. In this study we report that WIDE AND THICK GRAIN 1 (WTG1) functions as an important factor determining grain size and shape in rice. The wtg1‐1 mutant exhibits wide, thick, short and heavy grains and also shows an increased number of grains per panicle. WTG1 determines grain size and shape mainly by influencing cell expansion. WTG1 encodes an otubain‐like protease, which shares similarity with human OTUB1. Biochemical analyses indicate that WTG1 is a functional deubiquitinating enzyme, and the mutant protein (wtg1‐1) loses this deubiquitinating activity. WTG1 is expressed in developing grains and panicles, and the GFP–WTG1 fusion protein is present in the nucleus and cytoplasm. Overexpression of WTG1 results in narrow, thin, long grains due to narrow and long cells, further supporting the role of WTG1 in determining grain size and shape. Thus, our findings identify the otubain‐like protease WTG1 to be an important factor that determines grain size and shape, suggesting that WTG1 has the potential to improve grain size and shape in rice.