Mechanisms of photoreceptor mediated responses in photomorphogenesis and phototropism

Photoreceptor facilitated light perception provides plants with critical environmental information from which they can direct their growth. We investigated the early photomorphogenic responses in Glycine max and Glycine soja with the aim of elucidating the effect that domestication has had on early light responses. Our study indicates that G. max exhibits growth in darkness that is more characteristic of growth in light. This finding suggests that domestication has resulted in a crop species that is partially constitutively photomorphogenic. We additionally investigated the effects of blue light-induced ubiquitination sites that were ubiquitinated dependently by NON-PHOTOTROPIC HYPOCOTYL3 (NPH3) in the red light photoreceptor phytochrome A (phyA) in Arabidopsis thaliana. We discovered that transgenic lines expressing phyA with the ubiquitination sites K555 and K603 converted to non-ubiquitinatable arginine residues displayed reduced degradation in blue light and additionally reduced phototropic curvature in high intensity blue light, while functioning normally in other responses tested: very low and low intensity blue light phototropism, far-red light hypocotyl growth inhibition, and red light-induced phyA degradation. This finding suggests a mechanism for a more direct route of blue and red light-signaling crosstalk than has been previously shown.Includes bibliographical reference

Mechanisms of the phototropic pathway

Plants are sessile organisms and therefore are limited in their ability to gather resources. Therefore, they have evolved several mechanisms that aid them in their quest to gather light, water and nutrients. One such mechanism is phototropism, a plants ability to bend towards or away from a light source. This mechanism is mediated by the blue light photoreceptor phototropin (phot). Arabidopsis thaliana contains two phototropins, phot1 which is the primary photoreceptor under low intensity light and phot2, which acts redundantly with phot1 under high intensity light. The perception of blue light by the phototropins (phot1 and phot2) initiates signaling events that lead to a lateral redistribution of the plant hormone auxin; which ultimately results in differential growth and the bending response. In addition to phototropism, these proteins mediate several other growth and developmental responses such as leaf movement, chloroplast movement, and stomatal opening. A second protein which is critical to the phototropic response and interacts with phot1 is NONPHOTOTROPIC HYPOCOTYL3 (NPH3). In addition to phototropism, NPH3 has a role in phot1-mediated leaf movement. NPH3 has been shown to act as a substrate adapter in an E3 ubiquitin ligase complex with the protein CULLIN3 (CUL3). This CRL3NPH3 complex is responsible for ubiquitinating the phot1 photoreceptor in a blue light fashion. This ubiquitination has been shown to be necessary for the bending response, but it's role in receptor ubiquitination is still not fully understood. To better understand this component of phot1-mediated phototropism, we characterized an allelic series of NPH3 mutants to further understand the role of this substrate adapter in this mechanism. Additionally, we characterized several mutant plant lines containing a mutant phot1 protein in which critical ubiquitination sites were mutated in an effort to render the protein unable to be ubiquitinated to further understand phot1 ubiquitination.Includes bibliographical reference

Patterns of Connection in Architecture: The Paradox of Light and Shadow

There exists a dialectical relationship between light and shadow. This relationship reflects the inherent paradoxical qualities of nature. Light and shadow continually move and evolve, never static, as nature continually moves and evolves. The movement of daylight continually generates its opposite, shadow, leading to a reconciliation of opposites. This continual mirroring between light and shadow creates a holistic image that gives dimensionality and life to the illuminated structure. I present this exploration of light and shadow as a set of ideas, as one example of a “poetic map”, to help architects develop an awareness of how to “think about their thinking.” This awareness reflects a way of “Being-in-the-world” that taps into a deeper consciousness of what makes us human. It reflects a way of thinking about who we are, what our fundamental needs are and what our role is in the larger world. It is essential that architects “think about their thinking”. They must reflect on the impact of their thoughts and ideas on their work. They must contemplate a connection to nature through their work and, in turn, a connection to the larger world. Ultimately, every work of architecture reflects this awareness, or lack thereof. Learning how to think and developing this awareness can be taught. A “poetic map”, such as that presented here, suggests a path along which this awareness can be developed. From this “map”, it is up to each of us to explore and develop our own understanding of the “territory”. The “territory” is a way to think and to be. The “territory” is not shown on the map. In nature, light and shadow are one “pattern which connects”. Light and shadow play an important role in our perception of, and response to, space. Furthermore, humans, “are by nature phototropic --- they move toward light, and when stationary, they orient themselves toward the light” according to Christopher Alexander et al in their book Pattern Language.1 It is the paradox of light and shadow that engages our senses, gives architecture life and connects us, through architecture, to nature and to that which is sacred. Unfortunately, architecture has become primarily a visual experience. We have lost our sensory engagement, through architecture, to nature. Because our connection to nature, or to that which is sacred, is fundamental to our being, we have lost a part of ourselves. We must step back and engage all our senses with architecture that highlights nature and becomes “the pattern which connects” us to the “change and flow of climate, season, sun and shadow, constantly tuning our awareness of the natural cycles which support all life.”2 In this DArch project, I clarify the paradox of light and shadow in architecture. I explain the role of our senses in our perception of space, specifically with respect to light and shadow. I also explain how light and shadow influence materiality, memory, wayfinding and cycles of time in architecture. The successful manipulation of light and shadow frames our experience of architecture. Case studies of buildings that manipulate light and shadow to create full sensory engagement are presented to enhance our understanding of the relationship between light and shadow and the impact of that relationship on our experience of architecture. This relationship is critical to man’s connection to nature through architecture. It is this connection to nature that, in turn, enhances our response to the built environment. 1 Christopher Alexander et al., Pattern Language (New York: Oxford University Press, 1977), 645. 2 http://www.ecodesign.org/Porfolio/Commercial/bateson.html accessed 9/17/208

Phototaxic foraging of the archaepaddler, a hypothetical deep-sea species

An autonomous agent (animat, hypothetical animal), called the (archae) paddler, is simulated in sufficient detail to regard its simulated aquatic locomotion (paddling) as physically possible. The paddler is supposed to be a model of an animal that might exist, although it is perfectly possible to view it as a model of a robot that might be built. The agent is assumed to navigate in a simulated deep-sea environment, where it hunts autoluminescent prey. It uses a biologically inspired phototaxic foraging-strategy, while paddling in a layer just above the bottom. The advantage of this living space is that the navigation problem is essentially two-dimensional. Moreover, the deep-sea environment is physically simple (and hence easier to simulate): no significant currents, constant temperature, completely dark. A foraging performance metric is developed that circumvents the necessity to solve the travelling salesman problem. A parametric simulation study then quantifies the influence of habitat factors, such as the density of prey, and the body-geometry (e.g. placement, direction and directional selectivity of the eyes) on foraging success. Adequate performance proves to require a specific body-% geometry adapted to the habitat characteristics. In general performance degrades smoothly for modest changes of the geometric and habitat parameters, indicating that we work in a stable region of 'design space'. The parameters have to strike a compromise between on the one hand the ability to 'fixate' an attractive target, and on the other hand to 'see' as many targets at the same time as possible. One important conclusion is that simple reflex-based navigation can be surprisingly efficient. In the second place, performance in a global task (foraging) depends strongly on local parameters like visual direction-tuning, position of the eyes and paddles, etc. Behaviour and habitat 'mould' the body, and the body-geometry strongly influences performance. The resulting platform enables further testing of foraging strategies, or vision and locomotion theories stemming either from biology or from robotics

Study for identification of beneficial uses of space, phase 1. Volume 1: Executive summary

The technological effects of the Space Shuttle Program are considered in terms of the development of improved products, processes, and services aimed at benefitting the public from economic and sociological points of view. As such, an outline is provided for a large number of private organizations to suggest and identify specific areas of research and development which can most effectively be exploited in an extraterrestrial environment

Phytochrome genes in higher plants: Structure,expression, and evolution

© 2006 Springer. All Rights Reserved. Phytochromes play critical roles in monitoring light quantity, quality, and periodicity in plants and they relay this photosensory information to a large number of signaling pathways that regulate plant growth and development. Given these complex functions, it is not surprising that the phytochrome apoproteins are encoded by small multigene families and that different forms of phytochrome regulate different aspects of photomorphogenesis. Over the course of the last decade, progress has been made in defining the number, molecular properties, and biological activities of the photoreceptors that constitute a plant R/FR sensing system. This chapter summarizes our current understanding of the structure of the genes that encode the phytochrome apoproteins (the PHY genes), the expression patterns of those genes, the nature of the phytochrome apoprotein family, and PHY gene evolution in seed plants. Phytochrome was discovered and its basic photochemical properties were first described through physiological studies of light-sensitive seed germination and photoperiodic effects on flowering (Borthwick, et al., 1948, Borthwick, et al., 1952). The pigment itself was initially isolated from extracts of dark-grown (etiolated) plant tissue in 1959 (Butler, et al., 1959), but it was not until much later that phytochrome was purified to homogeneity in an undegraded form (Vierstra and Quail, 1983). DNA sequences of gene and cDNA clones for oat etiolated-tissue spectroscopically in planta and purified in its native form, this dark-tissue phytochrome (now called phyA) remains the most completely biochemically and spectroscopically characterized form of the receptor. At various times throughout the first 40 years of the study of the abundant etiolated-tissue phytochrome, evidence for the presence and activity of additional forms of phytochrome, often referred to as green-tissue or light-stable phytochromes, was obtained. Initially, in physiological experiments, it was sometimes not possible to correlate specific in vivo phytochrome activities with the phytochrome provided the first complete descriptions of the apoprotein (Hershey et al., 1985). Because it accumulates to levels that permit it to be assayed known spectroscopic properties of the molecule. Later, direct evidence for multiple species of phytochrome in plants and in plant extracts was obtained using both spectroscopic and immunochemical methods (reviewed in Pratt, 1995). The molecular identities of these additional phytochrome forms were ultimately deduced from cDNA clones that were isolated by nucleic acid similarity to etiolated-tissue phytochrome sequences (Sharrock and Quail, 1989). More recently, analysis of a large number of complete and partial PHY gene or cDNA sequences from a broad sampling of plant phylogenetic groups and sequencing of several plant genomes have resulted in a much clearer and more general picture of what constitutes a higher plant R/FR photoreceptor family. It is likely that the major types of long-wavelength photosensing pigments have now been identified and the challenge that lies ahead is to understand how the signalling mechanisms, expression patterns, and interactions of these molecules contribute to plant responses to the R/FR environment. Extending the investigation of phytochrome gene families and their functions to additional angiosperm and gymnosperm genera will be an integral component of this effort and of our ability to utilize this growing understanding of phytochrome function to modify the agricultural properties of plants and to better understand the history of land plants

Phototropic memory in early plant development

Tato diplomová práce byla inspirována publikovanými kontroverzními výsledky o existenci a spolehlivosti paměťové stopy směru posledního osvětlení u mladých jedinců dvouděložných rostlin. Teoretická část této diplomové práce nejprve pojednává o fototropismu, stručně shrnuje dosavadní znalosti o tomto růstovém pohybu, fototropinech a mechanismu vzniku fototropického ohybu, včetně role auxinu a jeho transportérů. Zabývá se také vlivem světla, kterému je rostlina vystavena před samotnou fototropickou stimulací, na výsledný ohyb hypokotylu. Další část literárního přehledu je věnována otázce existence paměti u rostlin. Experimenty provedené v rámci praktické části vychází z předpokladu, že rostliny jsou schopné ukládat paměťovou stopu o předchozí světelné expozici. Po vytvoření systému, který umožnoval získat robustní fototropickou odpověď na modré světlo, bylo na semenáčcích modelové rostliny Lepidium sativum za různých podmínek testováno, jestli a jak směr, ze kterého světlo působí, ovlivňuje odpověď rostlin na následnou fototropickou stimulaci. Výsledky naznačují, že nejméně v jednom případě by se výsledná fototropická odpověď dala interpretovat tak, že u testovaných rostlin došlo k vytvoření specifické paměťové stopy. Nelze však říci, že by v rámci této práce byla existence paměťové stopy o předchozí...This thesis was inspired by controversial published results on the existence and reliability of a memory trace of the direction of the last illumination in young dicots. The theoretical part first covers phototropism, it briefly summarizes current knowledge about this growth movement, phototropins, and the mechanism of phototropic bending, including the role of auxin and its transporters. It also discusses the effect of previous light exposure on hypocotyl bending. Another section of the theoretical part is focused on the question of the existence of memory in plants. The experiments performed in the practical part are based on the assumption that plants are able to store a memory trace of previous light exposure. After the establishment of a system that made it possible to obtain a robust phototropic response to blue light, seedlings of the model plant Lepidium sativum were tested under different conditions to see if and how the direction of light affected the plants' response to subsequent phototropic stimulation. The results suggest that in at least one case, the final phototropic response could be interpreted as a formation of a specific memory trace in the tested plants. However, based on the results of this work, the existence of a memory trace of previous light exposure cannot be...Katedra experimentální biologie rostlinDepartment of Experimental Plant BiologyPřírodovědecká fakultaFaculty of Scienc

Charles M. Breder, Jr.: Dry Tortugas, 1929

During the summer of 1929, Dr. Charles M. Breder, Jr., employed at that time by the New York Aquarium and American Museum of Natural History, visited the Carnegie Laboratory in the Dry Tortugas to study the development and habits of flying fishes and their allies. The diary of the trip was donated to the Mote Marine Laboratory Library by his family. Dr. Breder's meticulous handwritten account gives us the opportunity to see the simple yet great details of his observations and field experiments. His notes reveal the findings and thoughts of one of the world's greatest ichthyologists. The diary was transcribed as part of the Coastal Estuarine Data/Document Rescue and Archeology effort for South Florida. (PDF contains 75 pages

Design analysis: Understanding e-waste recycling by generation Y

This paper aims to understand e-waste recycling behavior of Generation Y. It presents a pilot study that explores this generation’s e-waste recycling practices, their attitudes towards ewaste recycling, and the barriers to e-waste recycling. The findings reveal the complexity of the actual e-waste recycling behavior, many participants in this study hold a positive attitude towards e-waste recycling, yet there is a shortage of convenient recycling options and e-waste recycling information. Based on the Motivation-Opportunity-Abilities model, this paper also uncovers the decision-making process involved in each recycling action. We use these findings to present a preliminary analysis of design implications to provoke design ideas and services that support ewaste recycling, and discuss our further research direction

Method Acting and Pacino\u27s Looking for Richard

In her paper, Method Acting and Pacino\u27s Looking for Richard, Peirui Su explores the influence of method acting on Al Pacino\u27s decision to film Shakespeare\u27s Richard III as an unconventional docudrama. She compares Pacino\u27s film to Laurence Olivier\u27s 1955 film of Richard III and Ian McKellen\u27s 1995 modernized version to show how Pacino\u27s documentary structure solves the problems raised by films that try either to recreate the Elizabethan world or to update Shakespeare, thereby introducing anachronisms. Su argues that Pacino engages US-American audiences by filming interviews and open rehearsals. Su concludes her paper by analyzing the well-known scene of Richard\u27s wooing Lady Anne to show how Pacino\u27s characterization of Richard III relies on the insight that Richard, like Pacino himself, is an actor