Ferrochelatase is a conserved downstream target of the blue light-sensing White collar complex in fungi.

Light is a universal signal perceived by organisms, including fungi, in which light regulates common and unique biological processes depending on the species. Previous research has established that conserved proteins, originally called White collar 1 and 2 from the ascomycete Neurospora crassa, regulate UV/blue light sensing. Homologous proteins function in distant relatives of N. crassa, including the basidiomycetes and zygomycetes, which diverged as long as a billion years ago. Here we conducted microarray experiments on the basidiomycete fungus Cryptococcus neoformans to identify light-regulated genes. Surprisingly, only a single gene was induced by light above the commonly used twofold threshold. This gene, HEM15, is predicted to encode a ferrochelatase that catalyses the final step in haem biosynthesis from highly photoreactive porphyrins. The C. neoformans gene complements a Saccharomyces cerevisiae hem15Delta strain and is essential for viability, and the Hem15 protein localizes to mitochondria, three lines of evidence that the gene encodes ferrochelatase. Regulation of HEM15 by light suggests a mechanism by which bwc1/bwc2 mutants are photosensitive and exhibit reduced virulence. We show that ferrochelatase is also light-regulated in a white collar-dependent fashion in N. crassa and the zygomycete Phycomyces blakesleeanus, indicating that ferrochelatase is an ancient target of photoregulation in the fungal kingdom.

Differential Control of Xanthophylls and Light-Induced Stress Proteins, as Opposed to Light-Harvesting Chlorophyll a/b Proteins, during Photosynthetic Acclimation of Barley Leaves to Light Irradiance

Barley (Hordeum vulgare L.) plants were grown at different photon flux densities ranging from 100 to 1800 μmol m−2 s−1 in air and/or in atmospheres with reduced levels of O2 and CO2. Low O2 and CO2 partial pressures allowed plants to grow under high photosystem II (PSII) excitation pressure, estimated in vivo by chlorophyll fluorescence measurements, at moderate photon flux densities. The xanthophyll-cycle pigments, the early light-inducible proteins, and their mRNA accumulated with increasing PSII excitation pressure irrespective of the way high excitation pressure was obtained (high-light irradiance or decreased CO2 and O2 availability). These findings indicate that the reduction state of electron transport chain components could be involved in light sensing for the regulation of nuclear-encoded chloroplast gene expression. In contrast, no correlation was found between the reduction state of PSII and various indicators of the PSII light-harvesting system, such as the chlorophyll a-to-b ratio, the abundance of the major pigment-protein complex of PSII (LHCII), the mRNA level of LHCII, the light-saturation curve of O2 evolution, and the induced chlorophyll-fluorescence rise. We conclude that the chlorophyll antenna size of PSII is not governed by the redox state of PSII in higher plants and, consequently, regulation of early light-inducible protein synthesis is different from that of LHCII.

Metallic Nanoparticles Arranged in a Helical Geometry: Route Towards Strong and Broadband Chiro-optical Response

Recent advances in nanotechnology have paved ways to various techniques for designing and fabricating novel nanostructures incorporating noble metal nanoparticles, for a wide range of applications. The interaction of light with metal nanoparticles (NPs) can generate strongly localized electromagnetic fields (Localized Surface Plasmon Resonance, LSPR) at certain wavelengths of the incident beam. In assemblies or structures where the nanoparticles are placed in close proximity, the plasmons of individual metallic NPs can be strongly coupled to each other via Coulomb interactions. By arranging the metallic NPs in a chiral (e.g. helical) geometry, it is possible to induce collective excitations, which lead to differential optical response of the structures to right-and left circularly polarized light (e.g. Circular Dichroism - CD). Earlier reports in this field include novel techniques of synthesizing metallic nanoparticles on biological helical templates made from DNA, proteins etc. In the present work, we have developed new ways of fabricating chiral complexes made of metallic NPs, which demonstrate a very strong chiro-optical response in the visible region of the electromagnetic spectrum. Using DDA (Discrete Dipole Approximation) simulations, we theoretically studied the conditions responsible for large and broadband chiro-optical response. This system may be used for various applications, for example those related to polarization control of visible light, sensing of proteins and other chiral bio-molecules, and many more.

Control circuits for avalanche photodiodes

Avalanche Photodiodes (APDs) have been used in a wide range of low light sensing applications such as DNA sequencing, quantum key distribution, LIDAR and medical imaging. To operate the APDs, control circuits are required to achieve the desired performance characteristics. This thesis presents the work on development of three control circuits including a bias circuit, an active quench and reset circuit and a gain control circuit all of which are used for control and performance enhancement of the APDs. The bias circuit designed is used to bias planar APDs for operation in both linear and Geiger modes. The circuit is based on a dual charge pumps configuration and operates from a 5 V supply. It is capable of providing milliamp load currents for shallow-junction planar APDs that operate up to 40 V. With novel voltage regulators, the bias voltage provided by the circuit can be accurately controlled and easily adjusted by the end user. The circuit is highly integrable and provides an attractive solution for applications requiring a compact integrated APD device. The active quench and reset circuit is designed for APDs that operate in Geiger-mode and are required for photon counting. The circuit enables linear changes in the hold-off time of the Geiger-mode APD (GM-APD) from several nanoseconds to microseconds with a stable setting step of 6.5 ns. This facilitates setting the optimal `afterpulse-free' hold-off time for any GM-APD via user-controlled digital inputs. In addition this circuit doesn’t require an additional monostable or pulse generator to reset the detector, thus simplifying the circuit. Compared to existing solutions, this circuit provides more accurate and simpler control of the hold-off time while maintaining a comparable maximum count-rate of 35.2 Mcounts/s. The third circuit designed is a gain control circuit. This circuit is based on the idea of using two matched APDs to set and stabilize the gain. The circuit can provide high bias voltage for operating the planar APD, precisely set the APD’s gain (with the errors of less than 3%) and compensate for the changes in the temperature to maintain a more stable gain. The circuit operates without the need for external temperature sensing and control electronics thus lowering the system cost and complexity. It also provides a simpler and more compact solution compared to previous designs. The three circuits designed in this project were developed independently of each other and are used for improving different performance characteristics of the APD. Further research on the combination of the three circuits will produce a more compact APD-based solution for a wide range of applications.

The Function and Regulation of Photobodies in Phytochrome Signaling

Light is a critical environmental signal that regulates every phase of the plant life cycle, from germination to floral initiation. Of the many light receptors in the model plant Arabidopsis thaliana, the red- and far-red light-sensing phytochromes (phys) are arguably the best studied, but the earliest events in the phy signaling pathway remain poorly understood. One of the earliest phy signaling events is the translocation of photoactivated phys from the cytoplasm to the nucleus, where they localize to subnuclear foci termed photobodies; in continuous light, photobody localization correlates closely with the light-dependent inhibition of embryonic stem growth. Despite a growing body of evidence supporting the biological significance of photobodies in light signaling, photobodies have also been shown to be dispensable for seedling growth inhibition in continuous light, so their physiological importance remains controversial; additionally, the molecular components that are required for phy localization to photobodies are largely unknown. The overall goal of my dissertation research was to gain insight into the early steps of phy signaling by further defining the role of photobodies in this process and identifying additional intragenic and extragenic requirements for phy localization to photobodies.

Even though the domain structure of phys has been extensively studied, not all of the intramolecular requirements for phy localization to photobodies are known. Previous studies have shown that the entire C-terminus of phys is both necessary and sufficient for their localization to photobodies. However, the importance of the individual subdomains of the C-terminus is still unclear. For example a truncation lacking part of the most C-terminal domain, the histidine kinase-related domain (HKRD), can still localize to small photobodies in the light and behaves like a weak allele. However, a point mutation within the HKRD renders the entire molecule completely inactive. To resolve this discrepancy, I explored the hypothesis that this point mutation might impair the dimerization of the HKRD; dimerization has been shown to occur via the C-terminus of phy and is required for more efficient signaling. I show that this point mutation impairs nuclear localization of phy as well as its subnuclear localization to photobodies. Additionally, yeast-two-hybrid analysis shows that the wild-type HKRD can homodimerize but that the HKRD containing the point mutation fails to dimerize with both itself and with wild-type HKRD. These results demonstrate that dimerization of the HKRD is required for both nuclear and photobody localization of phy.

Studies of seedlings grown in diurnal conditions show that photoactivated phy can persist into darkness to repress seedling growth; a seedling's growth rate is therefore fastest at the end of the night. To test the idea that photobodies could be involved in regulating seedling growth in the dark, I compared the growth of two transgenic Arabidopsis lines, one in which phy can localize to photobodies (PBG), and one in which it cannot (NGB). Despite these differences in photobody morphology, both lines are capable of transducing light signals and inhibiting seedling growth in continuous light. After the transition from red light to darkness, the PBG line was able to repress seedling growth, as well as the accumulation of the growth-promoting, light-labile transcription factor PHYTOCHROME INTERACTING FACTOR 3 (PIF3), for eighteen hours, and this correlated perfectly with the presence of photobodies. Reducing the amount of active phy by either reducing the light intensity or adding a phy-inactivating far-red pulse prior to darkness led to faster accumulation of PIF3 and earlier seedling growth. In contrast, the NGB line accumulated PIF3 even in the light, and seedling growth was only repressed for six hours; this behavior was similar in NGB regardless of the light treatment. These results suggest that photobodies are required for the degradation of PIF3 and for the prolonged stabilization of active phy in darkness. They also support the hypothesis that photobody localization of phys could serve as an instructive cue during the light-to-dark transition, thereby fine-tuning light-dependent responses in darkness.

In addition to determining an intragenic requirement for photobody localization and further exploring the significance of photobodies in phy signaling, I wanted to identify extragenic regulators of photobody localization. A recent study identified one such factor, HEMERA (HMR); hmr mutants do not form large photobodies, and they are tall and albino in the light. To identify other components in the HMR-mediated branch of the phy signaling pathway, I performed a forward genetic screen for suppressors of a weak hmr allele. Surprisingly, the first three mutants isolated from the screen were alleles of the same novel gene, SON OF HEMERA (SOH). The soh mutations rescue all of the phenotypes associated with the weak hmr allele, and they do so in an allele-specific manner, suggesting a direct interaction between SOH and HMR. Null soh alleles, which were isolated in an independent, tall, albino screen, are defective in photobody localization, demonstrating that SOH is an extragenic regulator of phy localization to photobodies that works in the same genetic pathway as HMR.

In this work, I show that dimerization of the HKRD is required for both the nuclear and photobody localization of phy. I also demonstrate a tight correlation between photobody localization and PIF3 degradation, further establishing the significance of photobodies in phy signaling. Finally, I identify a novel gene, SON OF HEMERA, whose product is necessary for phy localization to photobodies in the light, thereby isolating a new extragenic determinant of photobody localization. These results are among the first to focus exclusively on one of the earliest cellular responses to light - photobody localization of phys - and they promise to open up new avenues into the study of a poorly understood facet of the phy signaling pathway.

Effect of excitation wavelength on the Raman spectroscopy of the porcine photoreceptor layer from the area centralis.

Raman microscopy, based upon the inelastic scattering (Raman) of light by molecular species, has been applied as a specific structural probe in a wide range of biomedical samples. The purpose of the present investigation was to assess the potential of the technique for spectral characterization of the porcine outer retina derived from the area centralis, which contains the highest proportion of cone:rod cell ratio in the pig retina. METHODS: Retinal cross-sections, immersion-fixed in 4% (w/v) PFA and cryoprotected, were placed on salinized slides and air-dried prior to direct Raman microscopic analysis at three excitation wavelengths, 785 nm, 633 nm, and 514 nm. RESULTS: Raman spectra of each of the photoreceptor inner and outer segments (PIS, POS) and of the outer nuclear layer (ONL) of the retina acquired at 785 nm were dominated by vibrational features characteristic of proteins and lipids. There was a clear difference between the inner and outer domains in the spectroscopic regions, amide I and III, known to be sensitive to protein conformation. The spectra recorded with 633 nm excitation mirrored those observed at 785 nm excitation for the amide I region, but with an additional pattern of bands in the spectra of the PIS region, attributed to cytochrome c. The same features were even more enhanced in spectra recorded with 514 nm excitation. A significant nucleotide contribution was observed in the spectra recorded for the ONL at all three excitation wavelengths. A Raman map was constructed of the major spectral components found in the retinal outer segments, as predicted by principal component analysis of the data acquired using 633 nm excitation. Comparison of the Raman map with its histological counterpart revealed a strong correlation between the two images. CONCLUSIONS: It has been demonstrated that Raman spectroscopy offers a unique insight into the biochemical composition of the light-sensing cells of the retina following the application of standard histological protocols. The present study points to the considerable promise of Raman microscopy as a component-specific probe of retinal tissue.

A biosignal embedded system for physiological computing

Thesis submitted in the fulfilment of the requirements for the Degree of Master in Electronic and Telecomunications Engineering

Phytochrome Kinase Substrate 4 is phosphorylated by the phototropin 1 photoreceptor.

Phototropism allows plants to redirect their growth towards the light to optimize photosynthesis under reduced light conditions. Phototropin 1 (phot1) is the primary low blue light-sensing receptor triggering phototropism in Arabidopsis. Light-induced autophosphorylation of phot1, an AGC-class protein kinase, constitutes an essential step for phototropism. However, apart from the receptor itself, substrates of phot1 kinase activity are less clearly established. Phototropism is also influenced by the cryptochromes and phytochromes photoreceptors that do not provide directional information but influence the process through incompletely characterized mechanisms. Here, we show that Phytochrome Kinase Substrate 4 (PKS4), a known element of phot1 signalling, is a substrate of phot1 kinase activity in vitro that is phosphorylated in a phot1-dependent manner in vivo. PKS4 phosphorylation is transient and regulated by a type 2-protein phosphatase. Moreover, phytochromes repress the accumulation of the light-induced phosphorylated form of PKS4 showing a convergence of photoreceptor activity on this signalling element. Our physiological analyses suggest that PKS4 phosphorylation is not essential for phototropism but is part of a negative feedback mechanism.

Genome-wide association analysis identifies novel loci for chronotype in 100,420 individuals from the UK Biobank

Our sleep timing preference, or chronotype, is a manifestation of our internal biological clock. Variation in chronotype has been linked to sleep disorders, cognitive and physical performance, and chronic disease. Here we perform a genome-wide association study of self-reported chronotype within the UK Biobank cohort (n=100,420). We identify 12 new genetic loci that implicate known components of the circadian clock machinery and point to previously unstudied genetic variants and candidate genes that might modulate core circadian rhythms or light-sensing pathways. Pathway analyses highlight central nervous and ocular systems and fear-response-related processes. Genetic correlation analysis suggests chronotype shares underlying genetic pathways with schizophrenia, educational attainment and possibly BMI. Further, Mendelian randomization suggests that evening chronotype relates to higher educational attainment. These results not only expand our knowledge of the circadian system in humans but also expose the influence of circadian characteristics over human health and life-history variables such as educational attainment.

Light Reflectance Characteristics and Remote Sensing of Waterlettuce

Waterlettuce ( Pistia stratiotes L.) is a free-floating exotic aquatic weed that often invades and clogs waterways in the southeastern United States. A study was conducted to evaluate the potential of using remote sensing technology to distinguish infestations of waterlettuce in Texas waterways. Field reflectance measurements showed that waterlettuce had higher visible green reflectance than associated plant species. Waterlettuce could be detected in both aerial color- infrared (CIR) photography and videography where it had light pink to pinkish-white image tonal responses. Computer analysis of CIR photographic and videographic images had overall accuracy assessments of 86% and 84%, respectively. (PDF contains 6 pages.)

CMOS indoor light energy harvesting system for wireless sensing applications

This book discusses in detail the CMOS implementation of energy harvesting. The authors describe an integrated, indoor light energy harvesting system, based on a controller circuit that dynamically and automatically adjusts its operation to meet the actual light circumstances of the environment where the system is placed. The system is intended to power a sensor node, enabling an autonomous wireless sensor network (WSN). Although designed to cope with indoor light levels, the system is also able to work with higher levels, making it an all-round light energy harvesting system. The discussion includes experimental data obtained from an integrated manufactured prototype, which in conjunction with a photovoltaic (PV) cell, serves as a proof of concept of the desired energy harvesting system. © 2016 Springer International Publishing. All rights are reserved.

Use of Information Visualization Methods Eliminating Cross Talk in Multiple Sensing Units Investigated for a Light-Addressable Potentiometric Sensor

The integration of nanostructured films containing biomolecules and silicon-based technologies is a promising direction for reaching miniaturized biosensors that exhibit high sensitivity and selectivity. A challenge, however, is to avoid cross talk among sensing units in an array with multiple sensors located on a small area. In this letter, we describe an array of 16 sensing units, of a light-addressable potentiometric sensor (LAPS), which was made with layer-by-Layer (LbL) films of a poly(amidomine) dendrimer (PAMAM) and single-walled carbon nanotubes (SWNTs), coated with a layer of the enzyme penicillinase. A visual inspection of the data from constant-current measurements with liquid samples containing distinct concentrations of penicillin, glucose, or a buffer indicated a possible cross talk between units that contained penicillinase and those that did not. With the use of multidimensional data projection techniques, normally employed in information Visualization methods, we managed to distinguish the results from the modified LAPS, even in cases where the units were adjacent to each other. Furthermore, the plots generated with the interactive document map (IDMAP) projection technique enabled the distinction of the different concentrations of penicillin, from 5 mmol L(-1) down to 0.5 mmol L(-1). Data visualization also confirmed the enhanced performance of the sensing units containing carbon nanotubes, consistent with the analysis of results for LAPS sensors. The use of visual analytics, as with projection methods, may be essential to handle a large amount of data generated in multiple sensor arrays to achieve high performance in miniaturized systems.

Fluoro-sensing applied to detection and identification of hydrocarbons in inland waters. Study of the impact of different UV light sources

This paper presents the detection and identification of hydrocarbons through flu oro-sensing by developing a simple and inexpensive detector for inland water, in contrast to current systems, designed to be used for marine waters at large distances and being extremely costly. To validate the proposed system, three test-benches have been mounted, with various UV-Iight sources. Main application of this system would be detect hydrocarbons pollution in rivers, lakes or dams, which in fact, is of growing interest by administrations.