Mapping the natural visual world of the zebrafish (Danio rerio): from sensory input to behavioural output

Vision is one of the most crucial senses for animals to catch prey, find mates and stay alive. The tetrachromatic zebrafish (Danio rerio) is a widely used model animal in visual neuroscience with four cone photoreceptors sensitive to UV, blue, green and red light. However, a detailed understanding of how their visual system is adapted to the natural environment, and what is important for the fish to see in their shallow freshwater habitats of the Indian subcontinent, has been missing. Therefore, it also has not been possible to carefully assess the importance of different parts of the light spectrum for their natural behaviours. In this thesis I introduce a new method for natural imaging, characterise the spectral composition of zebrafish’s natural visual world and demonstrate the role of UV light in their prey capture behaviours. To characterise the light conditions in natural environments, I developed and built two hyperspectral scanners to take spectrally detailed light measurements in shallow ponds and slowly moving streams in North-East India. As expected, the spectral profile becomes increasingly monochromatic and red shifted when moving from surface to the bottom. However, the short wavelength dominated surface and long wavelength dominated bottom are separated with colour-rich horizon. These spectral statistics match rather perfectly with the cone densities and colour processing abilities of the bipolar cells in the larval zebrafish retina. Previous work has demonstrated how prey capture behaviours on larval zebrafish can be triggered by small, bright spots. The short wavelength dominated upper part of the visual field projects light from UV bright prey items perfectly to the ventro-temporal part of the retina (“strike zone”) with high density of UV cones. Finally, with my behaviour experiments I demonstrate how prey capture behaviours are strongly driven by UV bright paramecia detected with the strike zone

Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana

Marine diatoms are important primary producers that thrive in diverse and dynamic environments. They do so, in theory, by sensing changing conditions and adapting their physiology accordingly. Using the model species Thalassiosira pseudonana, we conducted a detailed physiological and transcriptomic survey to measure the recurrent transcriptional changes that characterize typical diatom growth in batch culture. Roughly 40% of the transcriptome varied significantly and recurrently, reflecting large, reproducible cell-state transitions between four principal states: (i) "dawn," following 12 h of darkness; (ii ) "dusk," following 12 h of light; (iii ) exponential growth and nutrient repletion; and (iv) stationary phase and nutrient depletion. Increases in expression of thousands of genes at the end of the reoccurring dark periods (dawn), including those involved in photosynthesis (e.g., ribulose-1,5- bisphosphate carboxylase oxygenase genes rbcS and rbcL), imply large-scale anticipatory circadian mechanisms at the level of gene regulation. Repeated shifts in the transcript levels of hundreds of genes encoding sensory, signaling, and regulatory functions accompanied the four cell-state transitions, providing a preliminary map of the highly coordinated gene regulatory program under varying conditions. Several putative light sensing and signaling proteins were associated with recurrent diel transitions, suggesting that these genes may be involved in light-sensitive and circadian regulation of cell state. These results begin to explain, in comprehensive detail, how the diatom gene regulatory program operates under varying environmental conditions. Detailed knowledge of this dynamic molecular process will be invaluable for new hypothesis generation and the interpretation of genetic, environmental, and metatranscriptomic data from field studies

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 333)

This bibliography lists 122 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during January, 1990. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance

Can We Put Photobiology to Work? Using Light to Manipulate the Nutritional and Sensory Properties of Greenhouse Tomatoes

While generally viewed within the context of plant growth and development, different qualities of light are also powerful elicitors of secondary metabolic pathways in plants that affect the nutritional value and flavor of edible tissues. Leveraging fundamental photobiology principles, our studies sought to use different qualities of supplemental light including ultraviolet-B (UV-B), UV-A, blue, red, and far-red as an environmental treatment to restore garden-grown flavor and nutritional attributes to greenhouse-grown tomatoes (Solanum lycopersicum); a commercially important crop that has a poor reputation compared to its garden-grown counterparts. To test our hypotheses, we used a battery of physicochemical analyses that included total soluble solids, citric/ascorbic acid content, pH, and electrical conductivity of tomato fruits. Additionally, phenolic compounds in fruit tissues were quantified broadly using the Folin-Ciocalteu method and specific flavonoids were quantified with a more targeted approach using HPLC-ESI (-)-MS. Lycopene and β-carotene were quantified spectrophotometrically. In one study, qPCR was used to quantify genes involved in light-signal transduction in order to better understand the molecular underpinnings of plant UV-B perception. Two studies included consumer sensory panels to assess the impact of supplemental light quality o

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 299)

This bibliography lists 96 reports, articles, and other documents introduced into the NASA scientific and technical information system in June, 1987

Far-Red Absorbing Rhodopsins, Insights From Heterodimeric Rhodopsin-Cyclases

The recently discovered Rhodopsin-cyclases from Chytridiomycota fungi show completely unexpected properties for microbial rhodopsins. These photoreceptors function exclusively as heterodimers, with the two subunits that have very different retinal chromophores. Among them is the bimodal photoswitchable Neorhodopsin (NeoR), which exhibits a near-infrared absorbing, highly fluorescent state. These are features that have never been described for any retinal photoreceptor. Here these properties are discussed in the context of color-tuning approaches of retinal chromophores, which have been extensively studied since the discovery of the first microbial rhodopsin, bacteriorhodopsin, in 1971 (Oesterhelt et al., Nature New Biology, 1971, 233 (39), 149–152). Further a brief review about the concept of heterodimerization is given, which is widely present in class III cyclases but is unknown for rhodopsins. NIR-sensitive retinal chromophores have greatly expanded our understanding of the spectral range of natural retinal photoreceptors and provide a novel perspective for the development of optogenetic tools.Peer Reviewe

Life as an Explanation of the Measurement Problem

No consensus regarding the universal validity of any particular interpretation of the measurement problem has been reached so far. The problem manifests strongly in various Wigner's-friend-type experiments where different observers experience different realities measuring the same quantum system. But only classical information obeys the second law of thermodynamics and can be perceived solely at the holographic screen of the closed orientable two-dimensional manifold implied by Verlinde's and Landauer's mass-information equivalence equations. I conjecture that biological cell, as a dissipative structure, is the smallest agent capable of processing quantum information through its holographic screen and that this mechanism have been extended by natural evolution to endo- and exosemiosis in multicellular organisms, and further to language of Homo sapiens. Any external stimuli must be measured and classified by the cell in the context of classical information to provide it with an evolutionary gain. Quantum information contained in a pure quantum state cannot be classified, while incoherent mixtures of non-orthogonal quantum states are only partially classifiable. The concept of an unobservable velocity, normal to the holographic screen is introduced. It is shown that it enables to derive the Unruh acceleration as acting normal to the screen, as well as to conveniently relate de Broglie and Compton wavelengths. It follows that the perceived universe, is induced by the set of Pythagorean triples, while all its measurable features, including perceived dimensionality, are set to maximise informational diversity.Comment: This research is incomplete and partially incorrec