A simple way to compute protein dynamics without a mechanical model

We found that in proteins the average atomic fluctuation is linearly related to the square of the atomic distance from the center of mass of the protein. Using this simple relation, we can accurately compute the temperature factors of proteins of a wide range of sizes and folds, and the correlation of the fluctuations in proteins. This simple relation provides a direct link between protein dynamics and the static protein's geometrical shape and offers a simple way to compute protein dynamics without either long time trajectory integration or any matrix operations.     

Collection of tubal stage bovine embryos by means of endoscopy. A technique report

Here we describe the development and optimization of endoscopy-mediated transvaginal access for collecting ova and embryos from the bovine oviduct. The novel technique was developed in three experimental setups: In Experiment 1 embryos were collected unilaterally from nonstimulated heifers. We flushed the oviducts of superovulated heifers unilaterally (Experiment 2) and bilaterally (Experiment 3). In Experiment 1 the oviducts of 18 heifers were successfully cannulated, which resulted in the collection of twelve 1-cell to 8-cell embryos and one empty zona. Unilateral flushing of 13 animals (Experiment 2) resulted in 84 ova with 6.3 +/- 3.2 observed ovulation sites. Bilateral flushing of 25 animals (Experiment 3) resulted in 293 ova plus 10 empty zonae from 11.8 +/- 5.4 ovulation sites. Given our experience from these studies we optimized the technical equipment by improving the flushing metal catheter (Experiment 4). The novel catheter hermetically sealed the lumen of the ampulla at the moment, the medium was flushed through the oviduct. This resulted in a visible flow of medium via oviducts toward the embryo filter connected to an embryo flushing catheter that was fixed in the uterine horns. Our endoscopy-guided method is minimally invasive and facilitates the flushing of tubal stage embryos.     

Experimental evolution of a novel sexually antagonistic allele

Evolutionary conflict permeates biological systems. In sexually reproducing organisms, sex-specific optima mean that the same allele can have sexually antagonistic expression, i.e. beneficial in one sex and detrimental in the other, a phenomenon known as intralocus sexual conflict. Intralocus sexual conflict is emerging as a potentially fundamental factor for the genetic architecture of fitness, with important consequences for evolutionary processes. However, no study to date has directly experimentally tested the evolutionary fate of a sexually antagonistic allele. Using genetic constructs to manipulate female fecundity and male mating success, we engineered a novel sexually antagonistic allele (SAA) in Drosophila melanogaster. The SAA is nearly twice as costly to females as it is beneficial to males, but the harmful effects to females are recessive and X-linked, and thus are rarely expressed when SAA occurs at low frequency. We experimentally show how the evolutionary dynamics of the novel SAA are qualitatively consistent with the predictions of population genetic models: SAA frequency decreases when common, but increases when rare, converging toward an equilibrium frequency of ～8%. Furthermore, we show that persistence of the SAA requires the mating advantage it provides to males: the SAA frequency declines towards extinction when the male advantage is experimentally abolished. Our results empirically demonstrate the dynamics underlying the evolutionary fate of a sexually antagonistic allele, validating a central assumption of intralocus sexual conflict theory: that variation in fitness-related traits within populations can be maintained via sex-linked sexually antagonistic loci.     

Influence of cell geometry on division-plane positioning

The spatial organization of cells depends on their ability to sense their own shape and size. Here, we investigate how cell shape affects the positioning of the nucleus, spindle and subsequent cell division plane. To manipulate geometrical parameters in a systematic manner, we place individual sea urchin eggs into microfabricated chambers of defined geometry (e.g., triangles, rectangles, and ellipses). In each shape, the nucleus is positioned at the center of mass and is stretched by microtubules along an axis maintained through mitosis and predictive of the future division plane. We develop a simple computational model that posits that microtubules sense cell geometry by probing cellular space and orient the nucleus by exerting pulling forces that scale to microtubule length. This model quantitatively predicts division-axis orientation probability for a wide variety of cell shapes, even in multicellular contexts, and estimates scaling exponents for length-dependent microtubule forces.     

The Effect of Perspective on Presence and Space Perception

In this paper we report two experiments in which the effect of perspective projection on presence and space perception was investigated. In Experiment 1, participants were asked to score a presence questionnaire when looking at a virtual classroom. We manipulated the vantage point, the viewing mode (binocular versus monocular viewing), the display device/screen size (projector versus TV) and the center of projection. At the end of each session of Experiment 1, participants were asked to set their preferred center of projection such that the image seemed most natural to them. In Experiment 2, participants were asked to draw a floor plan of the virtual classroom. The results show that field of view, viewing mode, the center of projection and display all significantly affect presence and the perceived layout of the virtual environment. We found a significant linear relationship between presence and perceived layout of the virtual classroom, and between the preferred center of projection and perceived layout. The results indicate that the way in which virtual worlds are presented is critical for the level of experienced presence. The results also suggest that people ignore veridicality and they experience a higher level of presence while viewing elongated virtual environments compared to viewing the original intended shape.     

Microsatellite loci in eelgrass Zostera marina reveal marked polymorphism within and among populations

Using an enriched genomic library, we developed seven (CT)n/(GA)n microsatellite loci for eelgrass Zostera marina L. Enrichment is described and highly recommended for genomes in which microsatellites are rare, such as in many plants. A test for polymorphism was performed on individuals from three geographically separated populations (N = 15/population) and revealed considerable genetic variation. The number of alleles per locus varied between five and 11 and the observed heterozygosities for single loci ranged from 0.16 to 0.81 within populations. Mean allele lengths were markedly different among populations, indicating that the identified loci will be useful in studying population structure in Z. marina. As the frequency of the most abundant multilocus genotype within populations was always < 1%, these loci have sufficient resolving power to address clone size in predominantly vegetatively reproducing populations.     

Widespread genetic mosaicism in the marine angiosperm <Emphasis Type="Italic">Zostera marina</Emphasis> is correlated with clonal reproduction

Somatic mutations are an underappreciated source of genetic variation within multi-cellular organisms. The resulting genetic mosaicism should be particularly abundant in large clones of vegetatively propagating angiosperms. Little is known on the abundance and ecological correlates of genetic mosaicism in field populations, despite its potential evolutionary significance. Because sexual reproduction restores genetic homogeneity, we predicted that in facultatively clonally reproducing organisms, the prevalence of genetic mosaicism increases with increasing clonality. This was tested among 33 coastal locations colonized by the ecologically important marine angiosperm Zostera marina, ranging from Portugal to Finland. Genetic mosaics were detectable as complex microsatellite genotypes at two hypervariable loci that revealed additional mosaic alleles, suggesting the presence of one or more divergent cell lineages within the same ramet. The proportions of non-mosaic genotypes in a population sharply decreased below a clonal richness of 0.2. Accordingly, more genetic mosaics were found at the southern and northern limit of the distribution of Z. marina in Europe where sexual reproduction is rare or absent. The genetic mosaics observed at neutral microsatellite markers suggest the possibility of within-clone variation at selectively relevant loci and supports the notion that members of clones are seldom genetically identical.     

Binocular Depth Judgments on Smoothly Curved Surfaces

Binocular disparity is an important cue to depth, allowing us to make very fine discriminations of the relative depth of objects. In complex scenes, this sensitivity depends on the particular shape and layout of the objects viewed. For example, judgments of the relative depths of points on a smoothly curved surface are less accurate than those for points in empty space. It has been argued that this occurs because depth relationships are represented accurately only within a local spatial area. A consequence of this is that, when judging the relative depths of points separated by depth maxima and minima, information must be integrated across separate local representations. This integration, by adding more stages of processing, might be expected to reduce the accuracy of depth judgements. We tested this idea directly by measuring how accurately human participants could report the relative depths of two dots, presented with different binocular disparities. In the first, Two Dot condition the two dots were presented in front of a square grid. In the second, Three Dot condition, an additional dot was presented midway between the target dots, at a range of depths, both nearer and further than the target dots. In the final, Surface condition, the target dots were placed on a smooth surface defined by binocular disparity cues. In some trials, this contained a depth maximum or minimum between the target dots. In the Three Dot condition, performance was impaired when the central dot was presented with a large disparity, in line with predictions. In the Surface condition, performance was worst when the midpoint of the surface was at a similar distance to the targets, and relatively unaffected when there was a large depth maximum or minimum present. These results are not consistent with the idea that depth order is represented only within a local spatial area.     

The morphogenesis of liposomes viewed from the aspect of bending energy

It is known that liposomes transform their shapes sequentially through one of several transformation pathways. Using the mechanical principle of the least bending energy of membranes, we investigate the stability and shape transformation of liposomes with geometrical symmetry. We have done this by computer simulations and theoretical analyses, in which three-dimensional liposome shapes have been generated by the modified Cassini equation. We show first that there are energetically stable liposome shapes having intrinsic geometrical symmetry. We find that by reducing the volume, the stable shape can change from a circular biconcave shape as in red blood cells, to elliptical, triangular, square, and other polygonal shapes. It is also found that the preceding two results hold true irrespective of the overall surface area of liposome.     

Attentive mechanisms in visual search

Selective attention can be employed to a restricted region in space or to specific objects. Many properties of this attentional window or spotlight are not well understood. In the present study, we examined the question whether the putative shape of the attentional spotlight can be determined by endogenous cueing within a visual search paradigm. Participants searched for a target among distractors, which were arranged within a vertical or horizontal rectangle. The shape of this rectangle was cued endogenously in a valid or invalid way. Response times (RTs) to correct identification of target orientation were recorded. In Experiment 1, the difference between valid and invalid RTs demonstrated that cueing resulted in elongated attentional areas. This was true only for a group of experienced psychophysical participants, whereas a group of inexperienced participants were not able to use cueing in this way. In Experiment 2, the line motion illusion was used to examine the spatial properties of the attended area. The results confirmed for both experienced and inexperienced participants that attention was confined to the cued elongated area only. We present converging evidence for an attentional spotlight whose shape can be adjusted flexibly by appropriate endogenous cueing.     

Consistent spatial scaling of high-severity wildfire can inform expected future patterns of burn severity

Increasing wildfire activity in forests worldwide has driven urgency in understanding current and future fire regimes. Spatial patterns of area burned at high severity strongly shape forest resilience and constitute a key dimension of fire regimes, yet remain difficult to predict. To characterize the range of burn severity patterns expected within contemporary fire regimes, we quantified scaling relationships relating fire size to patterns of burn severity. Using 1615 fires occurring across the Northwest United States between 1985 and 2020, we evaluated scaling relationships within fire regimes and tested whether relationships vary across space and time. Patterns of high-severity fire demonstrate consistent scaling behaviour; as fire size increases, high-severity patches consistently increase in size and homogeneity. Scaling relationships did not differ substantially across space or time at the scales considered here, suggesting that as fire-size distributions potentially shift, stationarity in patch-size scaling can be used to infer future patterns of burn severity.     

Short‐term variations in gene flow related to cyclic density fluctuations in the common vole

In highly fluctuating populations with complex social systems, genetic patterns are likely to vary in space and time due to demographic and behavioural processes. Cyclic rodents are extreme examples of demographically instable populations that often exhibit strong social organization. In such populations, kin structure and spacing behaviour may vary with density fluctuations and impact both the composition and spatial structure of genetic diversity. In this study, we analysed the multiannual genetic structure of a cyclic rodent, Microtus arvalis, using a sample of 875 individuals trapped over three complete cycles (from 1999 to 2007) and genotyped at 10 microsatellite loci. We tested the predictions that genetic diversity and gene flow intensity vary with density fluctuations. We found evidences for both spatial scale‐dependant variations in genetic diversity and higher gene flow during high density. Moreover, investigation of sex‐specific relatedness patterns revealed that, although dispersal is biased toward males in this species, distances moved by both sexes were lengthened during high density. Altogether, these results suggest that an increase in migration with density allows to restore the local loss of genetic diversity occurring during low density. We then postulate that this change in migration results from local competition, which enhances female colonization of empty spaces and male dispersal among colonies.     

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.     

Likelihood-based inferences under isolation by distance: two-dimensional habitats and confidence intervals

Likelihood-based methods of inference of population parameters from genetic data in structured populations have been implemented but still little tested in large networks of populations. In this work, a previous software implementation of inference in linear habitats is extended to two-dimensional habitats, and the coverage properties of confidence intervals are analyzed in both cases. Both standard likelihood and an efficient approximation are considered. The effects of misspecification of mutation model and dispersal distribution, and of spatial binning of samples, are considered. In the absence of model misspecification, the estimators have low bias, low mean square error, and the coverage properties of confidence intervals are consistent with theoretical expectations. Inferences of dispersal parameters and of the mutation rate are sensitive to misspecification or to approximations inherent to the coalescent algorithms used. In particular, coalescent approximations are not appropriate to infer the shape of the dispersal distribution. However, inferences of the neighborhood parameter (or of the product of population density and mean square dispersal rate) are generally robust with respect to complicating factors, such as misspecification of the mutation process and of the shape of the dispersal distribution, and with respect to spatial binning of samples. Likelihood inferences appear feasible in moderately sized networks of populations (up to 400 populations in this work), and they are more efficient than previous moment-based spatial regression method in realistic conditions.     

Participation of the Classical Speech Areas in Auditory Long-Term Memory

Accumulating evidence suggests that storing speech sounds requires transposing rapidly fluctuating sound waves into more easily encoded oromotor sequences. If so, then the classical speech areas in the caudalmost portion of the temporal gyrus (pSTG) and in the inferior frontal gyrus (IFG) may be critical for performing this acoustic-oromotor transposition. We tested this proposal by applying repetitive transcranial magnetic stimulation (rTMS) to each of these left-hemisphere loci, as well as to a nonspeech locus, while participants listened to pseudowords. After 5 minutes these stimuli were re-presented together with new ones in a recognition test. Compared to control-site stimulation, pSTG stimulation produced a highly significant increase in recognition error rate, without affecting reaction time. By contrast, IFG stimulation led only to a weak, non-significant, trend toward recognition memory impairment. Importantly, the impairment after pSTG stimulation was not due to interference with perception, since the same stimulation failed to affect pseudoword discrimination examined with short interstimulus intervals. Our findings suggest that pSTG is essential for transforming speech sounds into stored motor plans for reproducing the sound. Whether or not the IFG also plays a role in speech-sound recognition could not be determined from the present results.     

Correction method for the physical dose calculated using Clarkson integration at the center of the spread-out Bragg peak for asymmetric field in carbon-ion radiotherapy

PurposeWe previously proposed a calculation method using Clarkson integration to obtain the physical dose at the center of the spread-out Bragg peak (SOBP) for a treatment beam, the measurement point of which agrees with the isocenter [Tajiri et al. Med. Phys. 2013; 40: 071733–1–5]. However, at the measurement point which does not agree with the isocenter, the physical dose calculated by this method might have a large error. For this error, we propose a correction method.Materials and methodsTo confirm whether the error can be corrected using in-air off axis ratio (OAR), we measured the physical dose at the center of an asymmetric square field and a symmetric square field and in-air OAR. For beams of which the measurement point does not agree with the isocenter, as applied to prostate cancer patients, the physical dose calculated using Clarkson integration was corrected with in-air OAR.ResultsThe maximum difference between the physical dose measured at the center of an asymmetric square field and the product of in-air OAR and the physical dose at the center of a symmetric square field was – 0.12%. For beams as applied to prostate cancer patients, the differences between the measured physical doses and the physical doses corrected using in-air OAR were −0.17 ± 0.23%.ConclusionsThe physical dose at the measurement point which does not agree with the isocenter, can be obtained from in-air OAR at the isocenter plane and the physical dose at the center of the SOBP on the beam axis.     

Convergent evolution of floral shape tied to pollinator shifts in Iochrominae (Solanaceae)*

Flower form is one of many floral features thought to be shaped by pollinator‐mediated selection. Although the drivers of variation in flower shape have often been examined in microevolutionary studies, relatively few have tested the relationship between shape evolution and shifts in pollination system across clades. In the present study, we use morphometric approaches to quantify shape variation across the Andean clade Iochrominae and estimate the relationship between changes in shape and shifts in pollination system using phylogenetic comparative methods. We infer multiple shifts from an ancestral state of narrow, tubular flowers toward open, bowl‐shaped, or campanulate flowers as well as one reversal to the tubular form. These transitions in flower shape are significantly correlated with changes in pollination system. Specifically, tubular forms tend to be hummingbird‐pollinated and the open forms tend to be insect‐pollinated, a pattern consistent with experimental work as well as classical floral syndromes. Nonetheless, our study provides one of the few empirical demonstrations of the relationship between flower shape and pollination system at a macroevolutionary scale.     

GENETIC VARIATION IN THE HOMOSPOROUS FERN PELLAEA ANDROMEDIFOLIA

Genetic variability was examined in nine sexual and three apogamous natural populations of the homosporous fern Pellaea andromedifolia by electrophoretic analysis of enzymes specified by eight loci. Genetic interpretations of heterozygous banding patterns were determined by segregational analysis of gametophytes. High levels of segregating heterozygosity characterized the sexually reproducing populations, and genotype frequencies at the five polymorphic loci were consistent with those expected under conditions of random intergametophytic mating. Multiple-banded patterns in the apogamously reproducing populations resembled those of heterozygous sexual individuals, but did not segregate. The results suggest that genetic variation in sexual homosporous vascular plants is produced by cross fertilization of genetically different gametes and may not result from pairing between homoeologous chromosomes carrying duplicated loci as previously thought.