Response to “Critical Assessment of the Evidence for Striped Nanoparticles”

Stirling et al., (10.1371/journal.pone.0108482) presented an analysis on some of our publications on the formation of stripe-like domains on mixed-ligand coated gold nanoparticles. The authors shed doubts on some of our results however no valid argument is provided against what we have shown since our first publication: scanning tunneling microscopy (STM) images of striped nanoparticles show stripe-like domains that are independent of imaging parameters and in particular of imaging speed. We have consistently ruled out the presence of artifacts by comparing sets of images acquired at different tip speeds, finding invariance of the stipe-like domains. Stirling and co-workers incorrectly analyzed this key control, using a different microscope and imaging conditions that do not compare to ours. We show here data proving that our approach is rigorous. Furthermore, we never solely relied on image analysis to draw our conclusions; we have always used the chemical nature of the particles to assess the veracity of our images. Stirling et al. do not provide any justification for the spacing of the features that we find on nanoparticles: ~1 nm for mixed ligand particles and ~ 0.5 nm for homoligand particles. Hence our two central arguments remain unmodified: independence from imaging parameters and dependence on ligand shell chemical composition. The paper report observations on our STM images; none is a sufficient condition to prove that our images are artifacts. We thoroughly addressed issues related to STM artifacts throughout our microscopy work. Stirling et al. provide guidelines for what they consider good STM images of nanoparticles, such images are indeed present in our literature. They conclude that the evidences we provided to date are insufficient, this is a departure from one of the authors’ previous article which concluded that our images were composed of artifacts. Given that four independent laboratories have reproduced our measurements and that no scientifically rigorous argument is presented to invalidate our STM images, and also given that Stirling et al. do not contest the quality of our recent STM images, we re-affirm that specific binary mixture of ligands spontaneously form features in their ligand shell that we describe as stripe-like domains ~1 nm in width.     

Analysis of emergent patterns in crossing flows of pedestrians reveals an invariant of ‘stripe’ formation in human data

When two streams of pedestrians cross at an angle, striped patterns spontaneously emerge as a result of local pedestrian interactions. This clear case of self-organized pattern formation remains to be elucidated. In counterflows, with a crossing angle of 180°, alternating lanes of traffic are commonly observed moving in opposite directions, whereas in crossing flows at an angle of 90°, diagonal stripes have been reported. Naka (1977) hypothesized that stripe orientation is perpendicular to the bisector of the crossing angle. However, studies of crossing flows at acute and obtuse angles remain underdeveloped. We tested the bisector hypothesis in experiments on small groups (18-19 participants each) crossing at seven angles (30° intervals), and analyzed the geometric properties of stripes. We present two novel computational methods for analyzing striped patterns in pedestrian data: (i) an edge-cutting algorithm, which detects the dynamic formation of stripes and allows us to measure local properties of individual stripes; and (ii) a pattern-matching technique, based on the Gabor function, which allows us to estimate global properties (orientation and wavelength) of the striped pattern at a time T. We find an invariant property: stripes in the two groups are parallel and perpendicular to the bisector at all crossing angles. In contrast, other properties depend on the crossing angle: stripe spacing (wavelength), stripe size (number of pedestrians per stripe), and crossing time all decrease as the crossing angle increases from 30° to 180°, whereas the number of stripes increases with crossing angle. We also observe that the width of individual stripes is dynamically squeezed as the two groups cross each other. The findings thus support the bisector hypothesis at a wide range of crossing angles, although the theoretical reasons for this invariant remain unclear. The present results provide empirical constraints on theoretical studies and computational models of crossing flows.     

The adaptive significance of colour pattern polymorphism in the Australian scincid lizard Lampropholis delicata

Females of Lampropholis delicata are dimorphic for colour pattern, the difference between morphs being the presence or absence of a distinct white mid-lateral stripe. A less distinct striped morph occurs also in males. We evaluated alternative hypotheses for the maintenance of this polymorphism by examining temporal and spatial variation in morph frequency, testing for differential selection among morphs using data on body size and reproductive traits from preserved specimens, and experimentally manipulating colour pattern in free-ranging lizards of both sexes, to assess the influence of the lateral stripe on survival rates. We found that the relative frequency of striped individuals varied among populations and decreased from north to south in both sexes, coincident with an increasing incidence of regenerated tails. Morph frequencies did not change through time within a population. Striped gravid females appeared to survive better and produced larger clutches than did non-striped females. In our experimental study, the relationship between survival and colour morph differed between the two sexes; males painted with a white lateral stripe had lower survival than control (brown stripe) males, but survival did not differ between striped and control females. The different response in the two sexes may be due partly to differences in temperature and microhabitat selection. We propose that the white lateral stripe decreases susceptibility to predators in gravid females but increases risk of predation in males, especially in combination with low temperatures. The polymorphism might be maintained by: (1) opposing fitness consequences of the stripe in males and females; (2) sex-specific habitat selection; and (3) gene flow in combination with spatial variation in relative fitness of the two morphs.     

Competition between fixed and moving stripes in the control of orientation by flying Drosophila

ABSTRACT. The direction in which Drosophila hydei Sturtevant flew in response to the movement of a striped pattern beneath them was biased along a direction parallel to the long axis of a stationary stripe between them and the pattern. This was not due to the flies reacting to the movement of the ends of the stripes along the long edges of the stationary one, since a stationary stripe above the flies, not between them and the pattern, similarly biased their flight direction. It was due instead to an optomotor turning reaction induced by the edges of the stationary stripe as the flies were led towards or away from it by their turning and speed control reactions to the moving stripes.     

Spatial distribution of Prosopis glandulosa var. torreyana in vegetation stripes of the southern Chihuahuan Desert

Mosaics consisting of vegetation stripes surrounded by bare areas have been described in several arid and semiarid ecosystems. The dynamics of the system depends on the redistribution of rainwater which is preferentially stored and evapotranspired in the vegetated stripes. A process of plant `colonization' in the upslope fringe of the stripes has been described in some cases and a consequent upslope migration of the stripes has been inferred, but not confirmed in all cases quoted in the literature. In this paper, we studied the spatial distribution of mesquite (Prosopis glandulosa var. torreyana) and the soil parameters in three vegetation stripes and their associated bare areas in the southern Chihuahuan Desert. The spatial distribution of mesquites of different sizes do not coincide with that expected under the hypothesis of an uniform upslope stripe migration, but soil data suggest that current bare areas had been vegetated some time ago. Dispersion and establishment abilities enhanced by overgrazing may explain the observed mesquite distribution, but the presence of trees with high basal diameters in any part of the stripes suggests stripe permanence at the same site and no upslope migration. These results point to the conflicting evidence on stripe migration that has been already found in other areas. The most probable scenario in our study area is that of a general long-term change of form of the stripes taking place at very variable speeds in different stripes, including the possibility that some of them remain stationary for prolonged periods, and showing different histories of colonization according to the life-history of the different species concerned. The speed and regularity of the process would show a very high temporal and spatial variability due to the interaction of climatic, geomorphologic and biotic interactions.     

Pigment cell mechanisms underlying dorsal color‐pattern polymorphism in the japanese four‐lined snake

To provide histological foundation for studying the genetic mechanisms of color‐pattern polymorphisms, we examined light reflectance profiles and cellular architectures of pigment cells that produced striped, nonstriped, and melanistic color patterns in the snake Elaphe quadrivirgata. Both, striped and nonstriped morphs, possessed the same set of epidermal melanophores and three types of dermal pigment cells (yellow xanthophores, iridescent iridophores, and black melanophores), but spatial variations in the densities of epidermal and dermal melanophores produced individual variations in stripe vividness. The densities of epidermal and dermal melanophores were two or three times higher in the dark‐brown‐stripe region than in the yellow background in the striped morph. However, the densities of epidermal and dermal melanophores between the striped and background regions were similar in the nonstriped morph. The melanistic morph had only epidermal and dermal melanophores and neither xanthophores nor iridophores were detected. Ghost stripes in the shed skin of some melanistic morphs suggested that stripe pattern formation and melanism were controlled independently. We proposed complete‐ and incomplete‐dominance heredity models for the stripe‐melanistic variation and striped, pale‐striped, and nonstriped polymorphisms, respectively, according to the differences in pigment‐cell composition and its spatial architecture. J. Morphol. 274:1353–1364, 2013. © 2013 Wiley Periodicals, Inc.     

Pigment cell mechanism of postembryonic stripe pattern formation in the Japanese four‐lined snake

Postembryonic changes in the dermal and epidermal pigment cell architecture of the striped and nonstriped morph of the Japanese four‐lined snake Elaphe quadrivirgata were examined to reveal stripe pattern formation after hatching. The striped and nonstriped morphs were distinguishable at the hatching, suggesting that the basis of stripe pattern was formed during embryonic development. In the striped morph, the color of stripes changed from red‐brown in juveniles to vivid dark‐brown in adults, and density of dermal melanophore increased much more in the stripe than background dorsal scales with growth. This increase in density of dermal melanophore was accompanied not only by the increased epidermal melanophore density but also by the change in vertical structures of dermal melanophore. By contrast, the density of epidermal and dermal melanophore evenly increased over the dorsal scales in the nonstriped morph. Thus, the increased vividness of the stripe pattern after hatching is achieved through localized increase of melanophore density particularly in the stripe region but not over the whole dorsal scales. J. Morphol. 277:196–203, 2016. © 2015 Wiley Periodicals, Inc.     

Correlation between the ripple phase and stripe domains in membranes

We investigate the relationship between stripe domains and the ripple phase in membranes. These have previously been observed separately without being linked explicitly. Past results have demonstrated that solid and ripple phases exhibit rich textural patterns related to the orientational order of tilted lipids and the orientation of ripple corrugations. Here we reveal a highly complex network pattern of ripple and solid domains in DLPC, DPPC bilayers with structures covering length scales from 10 nm to 100 μm. Using spincoated double supported membranes we investigate domains by correlated AFM and fluorescence microscopy. Cooling experiments demonstrate the mode of nucleation and growth of stripe domains enriched in the fluorescent probe. Concurrent AFM imaging reveals that these stripe domains have a one-to-one correspondence with a rippled morphology running parallel to the stripe direction. Both thin and thick stripe domains are observed having ripple periods of 13.5±0.2 nm and 27.4±0.6 nm respectively. These are equivalent to previously observed asymmetric/equilibrium and symmetric/metastable ripple phases, respectively. Thin stripes grow from small solid domains and grow predominantly in length with a speed of ~3 times that of the thick stripes. Thick stripes grow by templating on the sides of thinner stripes or can emerge directly from the fluid phase. Bending and branching angles of stripes are in accordance with an underlying six fold lattice. We discuss mechanisms for the nucleation and growth of ripples and discuss a generic phase diagram that may partly rationalize the coexistence of metastable and stable phases.     

Fine structural analysis of the thoracic longitudinal stripes of Zaprionus vittiger (Diptera)

The structure of the longitudinal zebra stripes on the thorax of adult Zaprionus vittiger has been investigated by light-, polarization-, transmission electron-, and scanning electron microscopy. Each stripe consists of a central white stripe of about 50 μm width and two lateral dark brown stripes about 30 μm wide. Three different types of trichomes occur: Very long bent trichomes of the grooved-type, long bent trichomes of the crested-type, and short straight trichomes. The central white stripe contains neither bristle organs nor short straight trichomes but carries many long bent trichomes most of which are of the grooved type, contain two cavities and polarize the light in the polarization microscope. The dark brown stripes carry bristle organs and many trichomes of the short and straight-type. Bent trichomes of the crested-type are found on the whole zebra stripe at about equal frequencies; they contain no cavities and do not polarize the light. The cuticle of the dark stripes is underlain by pigment cells. It is suggested that the pigment granules in the epidermal cells cause the dark color of the dark brown stripes, whereas the form and structure of the bent grooved type trichomes cause the white color of the central stripe.     

Ultrastructure of the thick ascending limb of Henle in the rat kidney

The thick ascending limb of Henle (TAL) in the rat until recently has been considered a morphologically homogeneous structure despite physiologic and biochemical evidence to the contrary. The present study was designed to examine the ultrastructural characteristics of the TAL in the inner cortex and the outer and inner stripes of the outer medulla using qualitative and quantitative transmission electron microscopy. Kidneys of male Sprague-Dawley rats were preserved by in vivo perfusion with glutaraldehyde for light and electron microscopy. The peritubular diameter and cell height were determined by direct measurements on tubule cross sections. Morphometric analyses were performed on montages of tubule cross sections. The peritubular diameter of the TAL was similar in the three regions under investigation, but the TAL cells were taller in the inner stripe than in the inner cortex and outer stripe. Morphometry revealed significant differences between the three regions with respect to the mean tubular cross-sectional area (AT), the surface density (SV), and the surface area per mm of tubule (ST) of apical and basolateral plasma membranes, and the volume density (VV) of mitochondria. The major morphologic division appeared to be between the inner stripe segment and the remainder of the TAL. These findings document the presence of significant morphologic heterogeneity of the rat TAL.     

Bi-sensory, striped representations: comparative insights from owl and platypus.

Bi-sensory striped arrays are described in owl and platypus that share some similarities with the other variant of bi-sensory striped array found in primate and carnivore striate cortex: ocular dominance columns. Like ocular dominance columns, the owl and platypus striped systems each involve two different topographic arrays that are cut into parallel stripes, and interdigitated, so that higher-order neurons can integrate across both arrays. Unlike ocular dominance stripes, which have a separate array for each eye, the striped array in the middle third of the owl tectum has a separate array for each cerebral hemisphere. Binocular neurons send outputs from both hemispheres to the striped array where they are segregated into parallel stripes according to hemisphere of origin. In platypus primary somatosensory cortex (S1), the two arrays of interdigitated stripes are derived from separate sensory systems in the bill, 40,000 electroreceptors and 60,000 mechanoreceptors. The stripes in platypus S1 cortex produce bimodal electrosensory-mechanosensory neurons with specificity for the time-of-arrival difference between the two systems. This "thunder-and-lightning" system would allow the platypus to estimate the distance of the prey using time disparities generated at the bill between the earlier electrical wave and the later mechanical wave caused by the motion of benthic prey. The functional significance of parallel, striped arrays is not clear, even for the highly-studied ocular dominance system, but a general strategy is proposed here that is based on the detection of temporal disparities between the two arrays that can be used to estimate distance.     

Differentiation in Coprinus lagopus. III. Expansion of excised fruit-bodies.

Fruit-body expansion was studied in Coprinus lagopus (sensu Buller) following surgical procedures. Elongation occurred after denuding mushroom caps of essentially all peripheral scales. Young primordia (1 - 5 mm) failed to develop after vertical bisection. Older primordia (e.g. 10 mm) expanded 3 - 4 fold after vertical bisection or quadrisection, underwent autolysis and basidiospore production. An amorphous brown gel in the stripe lumen disappeared during development of bisected primordia. Stripes isolated from primordia expanded autonomously and exhibited negative geotropism when incubated upside down or when the stripe apex was removed. Displacement of charcoal particles dusted on intact stripes revealed the most active zone of expansion to be the upper mid-region of the stripe. Segmented stripes likewise showed most active elongation in the mid-region. Vertically bisected stripes also expanded.     

Genes that control dorsoventral polarity affect gene expression along the anteroposterior axis of the Drosophila embryo

At least 13 genes control the establishment of dorsoventral polarity in the Drosophila embryo and more than 30 genes control the anteroposterior pattern of body segments. Each group of genes is thought to control pattern formation along one body axis, independently of the other group. We have used the expression of the fushi tarazu (ftz) segmentation gene as a positional marker to investigate the relationship between the dorsoventral and anteroposterior axes. The ftz gene is normally expressed in seven transverse stripes. Changes in the striped pattern in embryos mutant for other genes (or progeny of females homozygous for maternal-effect mutations) can reveal alterations of cell fate resulting from such mutations. We show that in the absence of any of ten maternal-effect dorsoventral polarity gene functions, the characteristic stripes of ftz protein are altered. Normally there is a difference between ftz stripe spacing on the dorsal and ventral sides of the embryo; in dorsalized mutant embryos the ftz stripes appear to be altered so that dorsal-type spacing occurs on all sides of the embryo. These results indicate that cells respond to dorsoventral positional information in establishing early patterns of gene expression along the anteroposterior axis and that there may be more significant interactions between the different axes of positional information than previously determined.     

The interaction of edge-fixation and negative phototaxis in the orientation of walking gypsy moths,Lymantria dispar

Summary The visual orientation towards single black stripes and more complex patterns, comprising smooth gradients of brightness was studied in walking gypsy moths. Depending on the width of a black stripe, up to three walking directions are preferred within one stimulus situation: towards the centre of the stripe and towards a region within the stripe closer to each edge. The observed responses are explained by a compromise between edge-fixation and negative phototaxis. This hypothesis turned out to be also applicable to more complex patterns.     

Adaptive evolution of cryptic coloration: the shape of host plants and dorsal stripes in Timema walking-sticks

The adaptive significance of cryptic colour patterns has seldom been analysed in a phylogenetic context. We mapped data on the presence vs. absence of dorsal stripes, and the use of needle-like vs. broad foliage, onto a recent phylogeny of Timema walking-sticks, in order to infer the evolutionary history of these traits and test the hypothesis that the dorsal stripe is an adaptation for crypsis on needle-like leaves. By maximum parsimony optimization, the dorsal stripe has evolved five or six times in this clade, each time in association with the use of vegetation with needle-like leaves. Maddison's concentrated changes test showed that this association between morphology and habitat was statistically significant. By contrast, results based on Pagel's maximum likelihood analyses did not reach significance, probably because the large number of origins of dorsal stripe introduces statistical uncertainty. These results suggest that the adaptations for crypsis can arise readily and in parallel, in the appropriate selective environment. However, they may also constrain the evolution of host-plant use, as there is no unambiguous case of Timema species with dorsal stripes shifting to broad-leaved plants.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 1–5.