Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing

The cellular process responsible for providing energy for most life on Earth, namely, photosynthetic light-harvesting, requires the cooperation of hundreds of proteins across an organelle, involving length and time scales spanning several orders of magnitude over quantum and classical regimes. Simulation and visualization of this fundamental energy conversion process pose many unique methodological and computational challenges. We present, in two accompanying movies, light-harvesting in the photosynthetic apparatus found in purple bacteria, the so-called chromatophore. The movies are the culmination of three decades of modeling efforts, featuring the collaboration of theoretical, experimental, and computational scientists. We describe the techniques that were used to build, simulate, analyze, and visualize the structures shown in the movies, and we highlight cases where scientific needs spurred the development of new parallel algorithms that efficiently harness GPU accelerators and petascale computers

Cephalopods Between Science, Art, and Engineering: A Contemporary Synthesis

ABSTRACT Cephalopods are outstanding animals. For centuries, they have provided a rich source of inspiration to many aspects of human cultures, from art, history, media and spiritual beliefs to the most exquisite scientific curiosity. Given their high esthetical value and 'mysteriously' rich behavioral repertoire they have functioned as boundary objects (or subjects) connecting seemingly distinct thematic fields. Interesting aspects of their being span from the rapid camouflaging ability inspiring contemporary art practices, to their soft and fully muscular body that curiously enough inspired both gastronomy and (soft) robotics. The areas influenced by cephalopods include ancient mythology, art, behavioural science, neuroscience, genomics, camouflage technology and bespoken robotics. Although these might seem far related fields, in this manuscript we want to show how the increasing scientific and popular interest in this heterogeneous class of animals have indeed prompted a high level of integration between scientific, artistic and sub-popular culture. We will present an overview of the birth and life of cephalopod investigations from the traditional study of ethology, neuroscience, and biodiversity to the more recent and emerging field of genomics, material industry and soft robotics. Within this framework, we will attempt to capture the current interest and progress in cephalopod scientific research that lately met both the public interest and the 'liberal arts' curiosity

Functional colour genes and signals of selection in colour polymorphic salamanders

Coloration has been associated with multiple biologically relevant traits that drive adaptation and diversification in many taxa. However, despite the great diversity of colour patterns present in amphibians the underlying molecular basis is largely unknown. Here, we use insight from a highly colour-variable lineage of the European fire salamander (Salamandra salamandra bernardezi) to identify functional associations with striking variation in colour morph and pattern. The three focal colour morphs—ancestral black-yellow striped, fully yellow and fully brown—differed in pattern, visible coloration and cellular composition. From population genomic analyses of up to 4,702 loci, we found no correlations of neutral population genetic structure with colour morph. However, we identified 21 loci with genotype–phenotype associations, several of which relate to known colour genes. Furthermore, we inferred response to selection at up to 142 loci between the colour morphs, again including several that relate to coloration genes. By transcriptomic analysis across all different combinations, we found 196 differentially expressed genes between yellow, brown and black skin, 63 of which are candidate genes involved in animal coloration. The concordance across different statistical approaches and ‘omic data sets provide several lines of evidence for loci linked to functional differences between colour morphs, including TYR, CAMK1 and PMEL. We found little association between colour morph and the metabolomic profile of its toxic compounds from the skin secretions. Our research suggests that current ecological and evolutionary hypotheses for the origins and maintenance of these striking colour morphs may need to be revisited.This research was supported by a Natural Environment Research Council; a Royal Society Research Grant; a Glasgow Natural History Society grant; a Wellcome Trust ISSF Catalyst Grant and a Spanish Ministry of Science Grant

Octopus Senses: From Genes To Behavior

Octopuses are intelligent, soft-bodied animals, have complex nervous systems with remarkable cognitive abilities and keen senses that perform reliably in a variety of visual and chemo-tactile learning tasks for exploring and sensing the environment. They have the largest nervous system of any invertebrate, with 500 million neurons distributed centrally and peripherally throughout the body. The nervous system of common octopus (Octopus vulgaris), is comprised of central lobes surrounding the esophagus and a pair of optic lobes that together contain approximately a third of the neurons, with the remaining two-thirds distributed within the arms (e.g. in the large axial nerve cords that extends along the center of each of their eight arms). The most obvious characteristic feature of an octopus is its eight long and flexible arms, but these pose a great challenge for achieving the level of motor and sensory information processing necessary for their behaviors. In addition, octopuses have a significant number of lobes of the nervous system dedicated to visual, tactile, and chemosensory perception. In this study, I aimed to provide a comprehensive view on the genetic bases for the tactile form of olfaction, extraocular photoreception in the sucker, localization of photoreceptors molecules in the optic lobe of O. vulgaris, as well as to identify the major genes are involved in the adult neurogenesis and then the cognitive system in O. vulgaris. I have applied a developed whole-mount in situ hybridization, real-time qPCR, and bioinformatic methods, supported by behavioral evidences to provide a comprehensive view on these processes in O. vulgaris, highlight how genomic innovation translates into organismal organization novelties. Results achieved contributed to some extent, and promoted interest in this field

Of bars and stripes : A Malawi cichlid hybrid cross provides insights into genetic modularity and evolution of modifier loci underlying colour pattern diversification

Abstract Understanding the origins of phenotypic diversity among closely related species remains an important largely unsolved question in evolutionary biology. With over 800 species, Lake Malawi haplochromine cichlid fishes are a prominent example of extremely fast evolution of diversity including variation in coloration. Previously, a single major effect gene, agrp2 (asip2b), has been linked to evolutionary losses and gains of horizontal stripe patterns in cichlids, but it remains unknown what causes more fine-scale variation in the number and continuity of the stripes. Also, the genetic basis of the most common color pattern in African cichlids, vertical bars, and potential interactions between the two color patterns remain unknown. Based on a hybrid cross of the horizontally striped Lake Malawi cichlid Pseudotropheus cyaneorhabdos and the vertically barred species Chindongo demasoni we investigated the genetic basis of both color patterns. The distribution of phenotypes in the F2 generation of the cross indicates that horizontal stripes and vertical bars are independently inherited patterns that are caused by two sets of genetic modules. While horizontal stripes are largely controlled by few major effect loci, vertical bars are a highly polygenic trait. Horizontal stripes show substantial variation in the F2 generation that, interestingly, resemble naturally occurring phenotypes found in other Lake Malawi cichlid species. Quantitative trait loci (QTL) mapping of this cross reveals known (agrp2) and unknown loci underlying horizontal stripe patterns. These findings provide novel insights into the incremental fine-tuning of an adaptive trait that diversified through the evolution of additional modifier loci.Peer reviewe

A computational approach to the quantification of animal camouflage

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2014Evolutionary pressures have led to some astonishing camouflage strategies in the animal kingdom. Cephalopods like cuttlefish and octopus mastered a rather unique skill: they can rapidly adapt the way their skin looks in color, texture and pattern, blending in with their backgrounds. Showing a general resemblance to a visual background is one of the many camouflage strategies used in nature. For animals like cuttlefish that can dynamically change the way they look, we would like to be able to determine which camouflage strategy a given pattern serves. For example, does an inexact match to a particular background mean the animal has physiological limitations to the patterns it can show, or is it employing a different camouflage strategy (e.g., disrupting its outline)? This thesis uses a computational and data-driven approach to quantify camouflage patterns of cuttlefish in terms of color and pattern. First, we assess the color match of cuttlefish to the features in its natural background in the eyes of its predators. Then, we study overall body patterns to discover relationships and limitations between chromatic components. To facilitate repeatability of our work by others, we also explore ways for unbiased data acquisition using consumer cameras and conventional spectrometers, which are optical imaging instruments most commonly used in studies of animal coloration and camouflage. This thesis makes the following contributions: (1) Proposes a methodology for scene-specific color calibration for the use of RGB cameras for accurate and consistent data acquisition. (2) Introduces an equation relating the numerical aperture and diameter of the optical fiber of a spectrometer to measurement distance and angle, quantifying the degree of spectral contamination. (3) Presents the first study assessing the color match of cuttlefish (S. officinalis) to its background using in situ spectrometry. (4) Develops a computational approach to pattern quantification using techniques from computer vision, image processing, statistics and pattern recognition; and introduces Cuttlefish72x5, the first database of calibrated raw (linear) images of cuttlefish.Funding was provided by the National Science Foundation, Office of Naval Research, NIH-NEI, and the Woods Hole Oceanographic Institution Academic Programs Office

Testing changes in gene expression profiles in Octopus vulgaris (Mollusca Cephalopoda)

The aim of this thesis is to contribute to the understanding of the molecular machinery involved in learning and memory processes in Octopus vulgaris. Fear is the leitmotif. A fear conditioning training protocol was developed to evaluate behavioural responses in animals negatively conditioned to an artificial stimulus. To test whether interaction with con specifics in a solitary animal induces a form of innate fear, experiments were carried out to test the influence of 'social' interaction on predatory performances. Genomic information available for O.vulgaris is limited, from these data I found a-tubulin, octopressin, cephalotocin, stathmin. I also identified the partial cDNA sequences for TH, uch and dat. Creb and ubi were also considered herein. I studied the pattern of distribution of these genes by in situ hybridization, the analysis of the co-localization of Ov-dat and Ov-THtranscripts allowed to draw a possible distribution of dopaminergic and noradrenergic neurons in the octopus CNS. I analysed the pattern of expression of these genes in response to fear. I showed that CREB phosphorylation levels significantly increased during memory retrieval suggesting that a phenomenon analogue to reconsolidation may occur in octopus. Experiments of qRT-PCR revealed the increased expression of Ov-uch and Ov-stm in the lobes known as centers for learning and memory confirming the involvement of these genes in the processes of synaptic plasticity, learning and LTM. The increased expression of Ov-dat and Ov-TH in response to learned fear suggests that the consolidation of a task with aversive reinforcers is mediated by a dopaminergic pathway. On the contrary, in response to social interaction these genes are down-regulated suggesting that this process is mediated by other neurotransmitters. Finally, this study will provide the basic tools for future experiments where the analysis of the molecular machinery may be correlated with different forms of learning and synaptic plasticity

Ray Tracing Gems

This book is a must-have for anyone serious about rendering in real time. With the announcement of new ray tracing APIs and hardware to support them, developers can easily create real-time applications with ray tracing as a core component. As ray tracing on the GPU becomes faster, it will play a more central role in real-time rendering. Ray Tracing Gems provides key building blocks for developers of games, architectural applications, visualizations, and more. Experts in rendering share their knowledge by explaining everything from nitty-gritty techniques that will improve any ray tracer to mastery of the new capabilities of current and future hardware. What you'll learn: The latest ray tracing techniques for developing real-time applications in multiple domains Guidance, advice, and best practices for rendering applications with Microsoft DirectX Raytracing (DXR) How to implement high-performance graphics for interactive visualizations, games, simulations, and more Who this book is for: Developers who are looking to leverage the latest APIs and GPU technology for real-time rendering and ray tracing Students looking to learn about best practices in these areas Enthusiasts who want to understand and experiment with their new GPU