Lis1/dynactin regulates metaphase spindle orientation in Drosophila neuroblasts

Mitotic spindle orientation in polarized cells determines whether they divide symmetrically or asymmetrically. Moreover, regulated spindle orientation may be important for embryonic development, stem cell biology, and tumor growth. Drosophila neuroblasts align their spindle along an apical/basal cortical polarity axis to self-renew an apical neuroblast and generate a basal differentiating cell. It is unknown whether spindle alignment requires both apical and basal cues, nor have molecular motors been identified that regulate spindle movement. Using live imaging of neuroblasts within intact larval brains, we detect independent movement of both apical and basal spindle poles, suggesting that forces act on both poles. We show that reducing astral microtubules decreases the frequency of spindle movement, but not its maximum velocity, suggesting that one or few microtubules can move the spindle. Mutants in the Lis1/dynactin complex strongly decrease maximum and average spindle velocity, consistent with this motor complex mediating spindle/cortex forces. Loss of either astral microtubules or Lis1/dynactin leads to spindle/cortical polarity alignment defects at metaphase, but these are rescued by telophase. We propose that an early Lis1/dynactin-dependent pathway and a late Lis1/dynactin-independent pathway regulate neuroblast spindle orientation.     

Stochastic sampling of the RNA structural alignment space

A novel method is presented for predicting the common secondary structures and alignment of two homologous RNA sequences by sampling the ‘structural alignment’ space, i.e. the joint space of their alignments and common secondary structures. The structural alignment space is sampled according to a pseudo-Boltzmann distribution based on a pseudo-free energy change that combines base pairing probabilities from a thermodynamic model and alignment probabilities from a hidden Markov model. By virtue of the implicit comparative analysis between the two sequences, the method offers an improvement over single sequence sampling of the Boltzmann ensemble. A cluster analysis shows that the samples obtained from joint sampling of the structural alignment space cluster more closely than samples generated by the single sequence method. On average, the representative (centroid) structure and alignment of the most populated cluster in the sample of structures and alignments generated by joint sampling are more accurate than single sequence sampling and alignment based on sequence alone, respectively. The ‘best’ centroid structure that is closest to the known structure among all the centroids is, on average, more accurate than structure predictions of other methods. Additionally, cluster analysis identifies, on average, a few clusters, whose centroids can be presented as alternative candidates. The source code for the proposed method can be downloaded at http://rna.urmc.rochester.edu.     

Three-dimensional kinematic analysis of influence of hand orientation and joint limits on the control of arm postures and movements

The problems related to kinematic redundancy in both task and joint space were investigated for arm prehension movements in this paper. After a detailed analysis of kinematic redundancy of the arm, it is shown that the redundancy problem is ill posed only for the control of hand orientation. An experiment was then designed to investigate the influence of hand orientation on the control of arm movements. Since movements must be made within the limits of the joints, the influence of these limits was also analyzed quantitatively. The results of the experiment confirm that the increase of movement time because of the change of object orientation is due to the lengthening of the deceleration phase disproportionately to the rest of the movement. The variation of hand path due to the change of object orientation was observed as being surprisingly small for some subjects as opposed to the large range of object orientation, implying that hand path and hand orientation could be controlled separately, thus simplifying the computational problem of inverse kinematics. Moreover, the observations from the present experiment strongly suggest that a functional segmentation of the proximal and distal joints exists and that the control of wrist motion is dissociated from the rest of joint motions. The contribution of each joint in the control of arm movements could be determined through the principle of minimum energy and minimum discomfort under the constraints of the joint limits. A simplified inverse kinematics model was tested. It shows that these hypotheses can be easily implemented in a geometric algorithm and be used to predict arm prehension postures reasonably well under the constraints of joint limits. Received: 6 August 1998 / Accepted in revised form: 16 December 1998     

Predicted Secondary Structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Impact on Sequence Alignment and Phylogeny Estimation

We utilize the secondary structural properties of the 28S rRNA D2–D10 expansion segments to hypothesize a multiple sequence alignment for major lineages of the hymenopteran superfamily Ichneumonoidea (Braconidae, Ichneumonidae). The alignment consists of 290 sequences (originally analyzed in Belshaw and Quicke, Syst Biol 51:450–477, 2002) and provides the first global alignment template for this diverse group of insects. Predicted structures for these expansion segments as well as for over half of the 18S rRNA are given, with highly variable regions characterized and isolated within conserved structures. We demonstrate several pitfalls of optimization alignment and illustrate how these are potentially addressed with structure-based alignments. Our global alignment is presented online at (http://hymenoptera.tamu.edu/rna) with summary statistics, such as basepair frequency tables, along with novel tools for parsing structure-based alignments into input files for most commonly used phylogenetic software. These resources will be valuable for hymenopteran systematists, as well as researchers utilizing rRNA sequences for phylogeny estimation in any taxon. We explore the phylogenetic utility of our structure-based alignment by examining a subset of the data under a variety of optimality criteria using results from Belshaw and Quicke (2002) as a benchmark.Access to on-line data: http://hymenoptera.tamu.edu/rna; username, ichs; password, ichzzz     

High resolution imaging of the fibrous microstructure in bovine common carotid artery using optical polarization tractography

The biomechanical properties of artery are primarily determined by the fibrous structures in the vessel wall. Many vascular diseases are associated with alternations in the orientation and alignment of the fibrous structure in the arterial wall. Knowledge on the structural features of the artery wall is crucial to our understanding of the biology of vascular diseases and the development of novel therapies. Optical coherence tomography (OCT) and polarization‐sensitive OCT have shown great promise in imaging blood vessels due to their high resolution, fast acquisition, good imaging depth, and large field of view. However, the feasibility of using OCT based methods for imaging fiber orientation and distribution in the arterial wall has not been investigated. Here we show that the optical polarization tractography (OPT), a technology developed from Jones matrix OCT, can reveal the fiber orientation and alignment in the bovine common carotid artery. The fiber orientation and alignment data obtained in OPT provided a robust contrast marker to clearly resolve the intima and media boundary of the carotid artery wall.

Optical polarization tractography can visualize fiber orientation and alignment in carotid artery.     

A neural model for generating and learning a rapid movement sequence

 In this article, a neural model for generating and learning a rapid ballistic movement sequence in two-dimensional (2D) space is presented and evaluated in the light of some considerations about handwriting generation. The model is based on a central nucleus (called a planning space) consisting of a fully connected grid of leaky integrators simulating neurons, and reading an input vector Ξ (t) which represents the external movement of the end effector. The movement sequencing results in a succession of motor strokes whose instantiation is controlled by the global activation of the planning space as defined by a competitive interaction between the neurons of the grid. Constraints such as spatial accuracy and movement time are exploited for the correct synchronization of the impulse commands. These commands are then fed into a neuromuscular synergy whose output is governed by a delta lognormal equation. Each movement sequence is memorized originally as a symbolic engram representing the sequence of the principal reference points of the 2D movement. These points, called virtual targets, correspond to the targets of each single rapid motor stroke composing the movement sequence. The task during the learning phase is to detect the engram corresponding to a new observed movement; the process is controlled by the dynamics of the neural grid. Received: 16 March 1995/Accepted in revised form: 25 July 1995     

A Shared Intentional Space of Witch-Hunt and Sacrifice

In this article, the issue is whether witch-hunts can be seen to share certain aspects with the realm of sacrifice. With resource to recent developments in the Pacific Island nation of Vanuatu, it is argued that witchcraft is ‘the other side of sacrifice’ in more than one sense: firstly, as the witch is sacrificing its victim and breaking through to the social world from a world beyond and, secondly, as the witch-hunt is a movement with the purpose of sacrificing the accused witch for the healing of the community. The argument hinges on the alignment of the space intended by sacrifice and the space revealed by the appearance of the witch – as both articulating an engagement with ‘the very source of life’ (Hubert & Mauss 1964: 98).     

Murlet: a practical multiple alignment tool for structural RNA sequences

MOTIVATION: Structural RNA genes exhibit unique evolutionary patterns that are designed to conserve their secondary structures; these patterns should be taken into account while constructing accurate multiple alignments of RNA genes. The Sankoff algorithm is a natural alignment algorithm that includes the effect of base-pair covariation in the alignment model. However, the extremely high computational cost of the Sankoff algorithm precludes its application to most RNA sequences. RESULTS: We propose an efficient algorithm for the multiple alignment of structural RNA sequences. Our algorithm is a variant of the Sankoff algorithm, and it uses an efficient scoring system that reduces the time and space requirements considerably without compromising on the alignment quality. First, our algorithm computes the match probability matrix that measures the alignability of each position pair between sequences as well as the base pairing probability matrix for each sequence. These probabilities are then combined to score the alignment using the Sankoff algorithm. By itself, our algorithm does not predict the consensus secondary structure of the alignment but uses external programs for the prediction. We demonstrate that both the alignment quality and the accuracy of the consensus secondary structure prediction from our alignment are the highest among the other programs examined. We also demonstrate that our algorithm can align relatively long RNA sequences such as the eukaryotic-type signal recognition particle RNA that is approximately 300 nt in length; multiple alignment of such sequences has not been possible by using other Sankoff-based algorithms. The algorithm is implemented in the software named 'Murlet'. AVAILABILITY: The C++ source code of the Murlet software and the test dataset used in this study are available at http://www.ncrna.org/papers/Murlet/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

A generalized global alignment algorithm

MOTIVATION: Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions. RESULTS: We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity. AVAILABILITY: The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.     

Rapid Quantification of 3D Collagen Fiber Alignment and Fiber Intersection Correlations with High Sensitivity

Metastatic cancers aggressively reorganize collagen in their microenvironment. For example, radially orientated collagen fibers have been observed surrounding tumor cell clusters in vivo. The degree of fiber alignment, as a consequence of this remodeling, has often been difficult to quantify. In this paper, we present an easy to implement algorithm for accurate detection of collagen fiber orientation in a rapid pixel-wise manner. This algorithm quantifies the alignment of both computer generated and actual collagen fiber networks of varying degrees of alignment within 5°°. We also present an alternative easy method to calculate the alignment index directly from the standard deviation of fiber orientation. Using this quantitative method for determining collagen alignment, we demonstrate that the number of collagen fiber intersections has a negative correlation with the degree of fiber alignment. This decrease in intersections of aligned fibers could explain why cells move more rapidly along aligned fibers than unaligned fibers, as previously reported. Overall, our paper provides an easier, more quantitative and quicker way to quantify fiber orientation and alignment, and presents a platform in studying effects of matrix and cellular properties on fiber alignment in complex 3D environments.     

Diffusion anisotropy in collagen gels and tumors: the effect of fiber network orientation

The interstitial matrix is comprised of cross-linked collagen fibers, generally arranged in nonisotropic orientations. Spatial alignment of matrix components within the tissue can affect diffusion patterns of drugs. In this study, we developed a methodology for the calculation of diffusion coefficients of macromolecules and nanoparticles in collagenous tissues. The tissues are modeled as three-dimensional, stochastic, fiber networks with varying degrees of alignment. We employed a random walk approach to simulate diffusion and a Stokesian dynamics method to account for hydrodynamic hindrance. We performed our analysis for four different structures ranging from nearly isotropic to perfectly aligned. We showed that the overall diffusion coefficient is not affected by the orientation of the network. However, structural anisotropy results in diffusion anisotropy, which becomes more significant with increase in the degree of alignment, the size of the diffusing particle, and the fiber volume fraction. To test our model predictions we performed diffusion measurements in reconstituted collagen gels and tumor xenografts. We measured fiber alignment and diffusion with second harmonic generation and multiphoton fluorescent recovery after photobleaching techniques, respectively. The results showed for the first time in tumors that the structure and orientation of collagen fibers in the extracellular space leads to diffusion anisotropy.     

A memory-efficient algorithm for multiple sequence alignment with constraints

MOTIVATION: Recently, the concept of the constrained sequence alignment was proposed to incorporate the knowledge of biologists about structures/functionalities/consensuses of their datasets into sequence alignment such that the user-specified residues/nucleotides are aligned together in the computed alignment. The currently developed programs use the so-called progressive approach to efficiently obtain a constrained alignment of several sequences. However, the kernels of these programs, the dynamic programming algorithms for computing an optimal constrained alignment between two sequences, run in (gamman2) memory, where gamma is the number of the constraints and n is the maximum of the lengths of sequences. As a result, such a high memory requirement limits the overall programs to align short sequences only. RESULTS: We adopt the divide-and-conquer approach to design a memory-efficient algorithm for computing an optimal constrained alignment between two sequences, which greatly reduces the memory requirement of the dynamic programming approaches at the expense of a small constant factor in CPU time. This new algorithm consumes only O(alphan) space, where alpha is the sum of the lengths of constraints and usually alpha < n in practical applications. Based on this algorithm, we have developed a memory-efficient tool for multiple sequence alignment with constraints. AVAILABILITY: http://genome.life.nctu.edu.tw/MUSICME.     

Myosin Motors Drive Long Range Alignment of Actin Filaments

The bulk alignment of actin filament sliding movement, powered by randomly oriented myosin molecules, has been observed and studied using an in vitro motility assay. The well established, actin filament gliding assay is a minimal experimental system for studying actomyosin motility. Here, we show that when the assay is performed at densities of actin filaments approaching those found in living cells, filament gliding takes up a preferred orientation. The oriented patterns of movement that we have observed extend over a length scale of 10–100 μm, similar to the size of a mammalian cell. We studied the process of filament alignment and found that it depends critically upon filament length and density. We developed a simple quantitative measure of filament sliding orientation and this enabled us to follow the time course of alignment and the formation and disappearance of oriented domains. Domains of oriented filaments formed spontaneously and were separated by distinct boundaries. The pattern of the domain structures changed on the time scale of several seconds and the collision of neighboring domains led to emergence of new patterns. Our results indicate that actin filament crowding may play an important role in structuring the leading edge of migrating cells. Filament alignment due to near-neighbor mechanical interactions can propagate over a length scale of several microns; much greater than the size of individual filaments and analogous to a log drive. Self-alignment of actin filaments may make an important contribution to cell polarity and provide a mechanism by which cell migration direction responds to chemical cues.     

On the alignment of cellulose microfibrils by cortical microtubules: A review and a model

Summary The hypothesis that microtubules align microfibrils, termed the alignment hypothesis, states that there is a causal link between the orientation of cortical microtubules and the orientation of nascent microfibrils. I have assessed the generality of this hypothesis by reviewing what is known about the relation between microtubules and microfibrils in a wide group of examples: in algae of the family Characeae,Closterium acerosum, Oocystis solitaria, and certain genera of green coenocytes and in land plant tip-growing cells, xylem, diffusely growing cells, and protoplasts. The salient features about microfibril alignment to emerge are as follows. Cellulose microfibrils can be aligned by cortical microtubules, thus supporting the alignment hypothesis. Alignment of microfibrils can occur independently of microtubules, showing that an alternative to the alignment hypothesis must exist. Microfibril organization is often random, suggesting that self-assembly is insufficient. Microfibril organization differs on different faces of the same cell, suggesting that microfibrils are aligned locally, not with respect to the entire cell. Nascent microfibrils appear to associate tightly with the plasma membrane. To account for these observations, I present a model that posits alignment to be mediated through binding the nascent microfibril. The model, termed templated incorporation, postulates that the nascent microfibril is incorporated into the cell wall by binding to a scaffold that is oriented; further, the scaffold is built and oriented around either already incorporated microfibrils or plasma membrane proteins, or both. The role of cortical microtubules is to bind and orient components of the scaffold at the plasma membrane. In this way, spatial information to align the microfibrils may come from either the cell wall or the cell interior, and microfibril alignment with and without microtubules are subsets of a single mechanism.Dedicated to Professor Brian E. S. Gunning on the occasion of his 65th birthday     

Migration patterns of sympathetic preganglionic neurons in embryonic rat spinal cord

The displacement of immature neurons from their place of origin in the germinal epithelium toward their adult positions in the nervous system appears to involve migratory pathways or guides. While the importance of radial glial fibers in this process has long been recognized, data from recent investigations have suggested that other mechanisms might also play a role in directing the movement of young neurons. We have labeled autonomic preganglionic cells by microinjections of horseradish peroxidase (HRP) into the sympathetic chain ganglia of embryonic rats in order to study the migration and differentiation of these spinal cord neurons. Our results, in conjunction with previous observations, suggest that the migration pattern of preganglionic neurons can be divided into three distinct phases. In the first phase, the autonomic motor neurons arise in the ventral ventricular zone and migrate radially into the ventral horn of the developing spinal cord, where, together with somatic motor neurons, they form a single, primitive motor column (Phelps P. E., Barber R. P., and Vaughn J. E. (1991). J. Comp. Neurol. 307:77–86). During the second phase, the autonomic motor neurons separate from the somatic motor neurons and are displaced dorsally toward the intermediate spinal cord. When the preganglionic neurons reach the intermediolateral (IML) region, they become progressively more multipolar, and many of them undergo a change in alignment, from a dorsoventral to a mediolateral orientation. In the third phase of autonomic motor neuron development, some of these cells are displaced medially, and occupy sites between the IML and central canal. The primary and tertiary movements of the preganglionic neurons are in alignment with radial glial processes in the embryonic spinal cord, an arrangement that is consistent with a hypothesis that glial elements might guide autonomic motor neurons during these periods of development. In contrast, during the second phase, the dorsal translocation of preganglionic neurons occurs in an orientation perpendicular to radial glial fibers, indicating that glial elements are not involved in the secondary migration of these cells. The results of previous investigations have provided evidence that, in addition to glial processes, axonal pathways might provide a substrate for neuronal migration. Logically, therefore, it is possible that the secondary dorsolateral translocation of autonomic preganglionic neurons could be directed along early forming circumferential axons of spinal association interneurons, and this hypothesis is supported by the fact that such fibers are appropriately arrayed in both developmental time and space to guide this movement.     

Comparison of three standard anatomical reference frames for the tibia-fibula complex

Definition of anatomical reference frames is necessary both for in vitro biomechanical testing, and for in vivo human movement analyses. Different reference frames have been proposed in the literature for the lower limb, and in particular for the tibia–fibula complex. The scope of this work was to compare the three most commonly referred proposals (proposed by [Ruff, C.B., Hayes, W.C., 1983. Cross-sectional geometry at Pecos Pueblo femora and tibiae —A biomechanical investigation: I. method and general patterns of variation. American Journal of Physical Anthropology 60, pp. 359–381.], by [Cappozzo, A., Catani, F., Della Croce, U., Leardini, A., 1995. Position and orientation in space of bones during movement: anatomical frame definition and determination. Clinical Biomechanics (Bristol, Avon) 10, pp. 171–178.], and by the Standardization and Terminology Committee of the International Society of Biomechanics, [Wu, G., Siegler, S., Allard, P., Kirtley, C., Leardini, A., Rosenbaum, D., Whittle, M., D'Lima, D.D., Cristofolini, L., Witte, H., Schmid, O., Stokes, I., 2002. ISB recommendation on definitions of joint coordinate system of various joints for reporting of human joint motion—part I: ankle, hip and spine. International Society of Biomechanics. Journal of Biomechanics 35, pp. 543–548.]). These three frames were identified on six cadaveric tibia–fibula specimens based on the relevant anatomical landmarks, using a high-precision digitizer. The intra-operator (ten repetitions) and inter-operator (three operators) repeatability were investigated in terms of reference frame orientation. The three frames had similar intra-operator repeatability. The reference frame proposed by Ruff et al. had a better inter-operator repeatability (this must be put in relation with the original context of interest, i.e. in vitro measurements on dissected bones). The reference frames proposed by Ruff et al. and by ISB had a similar alignment; the frame proposed by Cappozzo et al. was considerably externally rotated and flexed with respect to the other two. Thus, the reference frame proposed by Ruff et al. is preferable when the full bone surface is accessible (typically during in vitro tests). Conversely, no advantage in terms of repeatability seems to exist between the reference frames proposed by Cappozzo et al. and ISB.     

Comparison of alignment tensors generated for native tRNAVal using magnetic fields and liquid crystalline media

Residual dipolar couplings (RDCs) complement standard NOE distance and J-coupling torsion angle data to improve the local and global structure of biomolecules in solution. One powerful application of RDCs is for domain orientation studies, which are especially valuable for structural studies of nucleic acids, where the local structure of a double helix is readily modeled and the orientations of the helical domains can then be determined from RDC data. However, RDCs obtained from only one alignment media generally result in degenerate solutions for the orientation of multiple domains. In protein systems, different alignment media are typically used to eliminate this orientational degeneracy, where the combination of RDCs from two (or more) independent alignment tensors can be used to overcome this degeneracy. It is demonstrated here for native E. coli tRNA^Val that many of the commonly used liquid crystalline alignment media result in very similar alignment tensors, which do not eliminate the 4-fold degeneracy for orienting the two helical domains in tRNA. The intrinsic magnetic susceptibility anisotropy (MSA) of the nucleobases in tRNA^Val was also used to obtain RDCs for magnetic alignment at 800 and 900 MHz. While these RDCs yield a different alignment tensor, the specific orientation of this tensor combined with the high rhombicity for the tensors in the liquid crystalline media only eliminates two of the four degenerate orientations for tRNA^Val. Simulations are used to show that, in optimal cases, the combination of RDCs obtained from liquid crystalline medium and MSA-induced alignment can be used to obtain a unique orientation for the two helical domains in tRNA^Val. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

RNA global alignment in the joint sequence–structure space using elastic shape analysis

The functions of RNAs, like proteins, are determined by their structures, which, in turn, are determined by their sequences. Comparison/alignment of RNA molecules provides an effective means to predict their functions and understand their evolutionary relationships. For RNA sequence alignment, most methods developed for protein and DNA sequence alignment can be directly applied. RNA 3-dimensional structure alignment, on the other hand, tends to be more difficult than protein structure alignment due to the lack of regular secondary structures as observed in proteins. Most of the existing RNA 3D structure alignment methods use only the backbone geometry and ignore the sequence information. Using both the sequence and backbone geometry information in RNA alignment may not only produce more accurate classification, but also deepen our understanding of the sequence–structure–function relationship of RNA molecules. In this study, we developed a new RNA alignment method based on elastic shape analysis (ESA). ESA treats RNA structures as three dimensional curves with sequence information encoded on additional dimensions so that the alignment can be performed in the joint sequence–structure space. The similarity between two RNA molecules is quantified by a formal distance, geodesic distance. Based on ESA, a rigorous mathematical framework can be built for RNA structure comparison. Means and covariances of full structures can be defined and computed, and probability distributions on spaces of such structures can be constructed for a group of RNAs. Our method was further applied to predict functions of RNA molecules and showed superior performance compared with previous methods when tested on benchmark datasets. The programs are available at http://stat.fsu.edu/ ∼jinfeng/ESA.html.     

BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny

SUMMARY: BAli-Phy is a Bayesian posterior sampler that employs Markov chain Monte Carlo to explore the joint space of alignment and phylogeny given molecular sequence data. Simultaneous estimation eliminates bias toward inaccurate alignment guide-trees, employs more sophisticated substitution models during alignment and automatically utilizes information in shared insertion/deletions to help infer phylogenies. AVAILABILITY: Software is available for download at http://www.biomath.ucla.edu/msuchard/bali-phy.     

Simulation of phototaxis in the flagellateEuglena gracilis

A three-dimensional model of the flagellateEuglena gracilis was developed to simulate phototaxis and movement in space. The simulation of the phototactic behavior was compared with thein vivo behavior in order to determine the mechanism of orientation with respect to light. Phototactic behavior with respect to one light source, can be explained by the shading hypothesis as well as by a dichroic orientation of the absorbing vectors of the photoreceptor pigments. In contrast, the behavior of the cells when exposed to two perpendicular light beams is not compatible with the shading hypothesis. Likewise, the phototactic orientation of stigmaless cells cannot be accounted for on the basis of the shading hypothesis. In contrast, simulations andin vivo observations of the behavior under polarized light strongly indicate the validity of the dichroic orientation of the photoreceptor pigments.