Light-dependent Functions Research Articles

Linking extreme seasonality and gene expression in Arctic marine protists

At high latitudes, strong seasonal differences in light availability affect marine organisms and regulate the timing of ecosystem processes. Marine protists are key players in Arctic aquatic ecosystems, yet little is known about their ecological roles over yearly cycles. This is especially true for the dark polar night period, which up until recently was assumed to be devoid of biological activity. A 12 million transcripts catalogue was built from 0.45 to 10 μm protist assemblages sampled over 13 months in a time series station in an Arctic fjord in Svalbard. Community gene expression was correlated with seasonality, with light as the main driving factor. Transcript diversity and evenness were higher during polar night compared to polar day. Light-dependent functions had higher relative expression during polar day, except phototransduction. 64% of the most expressed genes could not be functionally annotated, yet up to 78% were identified in Arctic samples from Tara Oceans, suggesting that Arctic marine assemblages are distinct from those from other oceans. Our study increases understanding of the links between extreme seasonality and biological processes in pico- and nanoplanktonic protists. Our results set the ground for future monitoring studies investigating the seasonal impact of climate change on the communities of microbial eukaryotes in the High Arctic.

Low-Light Dependence of the Magnetic Field Effect on Cryptochromes: Possible Relevance to Plant Ecology.

Various responses to static magnetic fields (MF) have been reported in plants, and it has been suggested that the geomagnetic field influences plant physiology. Accordingly, diverse mechanisms have been proposed to mediate MF effects in plants. The currently most probable sensor candidates are cryptochromes (Cry) which are sensitive to submillitesla MF. Here, we propose a quantitative approach of the MF effect on Cry depending on light intensity, and try to link it to a possible functional role for magnetic sensitivity in plants. Based on a theoretical evaluation and on a review of relevant data on Arabidopsis thaliana Cry 1, we point out that the MF effect on the signaling state of Cry, as well as the possible consequences of that effect on certain phenotypes (growth in particular) show parallel dependences on light intensity, being most prominent at low light levels. Based on these findings, we propose that Cry magnetosensitivity in plants could represent an ecological adaptation which regulates the amount of Cry signaling state under low light conditions. That hypothesis would preferentially be tested by studying sensitive and specific endpoints, such as the expression of clock proteins that are downregulated by Cry, but under light intensities lower than those used so far. Finally, we highlight that the low-light dependence of the MF effect described here could also apply to light-dependent functions of animal Cry, in particular magnetoreception which, from the present evaluation, would be based on the magnetic sensitivity of the photoreduction reaction, like in plants.

Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes.

We report here the assembly of a northern spotted owl (Strix occidentalis caurina) genome. We generated Illumina paired-end sequence data at 90× coverage using nine libraries with insert lengths ranging from ∼250 to 9,600 nt and read lengths from 100 to 375 nt. The genome assembly is comprised of 8,108 scaffolds totaling 1.26 × 109 nt in length with an N50 length of 3.98 × 106 nt. We calculated the genome-wide fixation index (FST) of S. o. caurina with the closely related barred owl (Strix varia) as 0.819. We examined 19 genes that encode proteins with light-dependent functions in our genome assembly as well as in that of the barn owl (Tyto alba). We present genomic evidence for loss of three of these in S. o. caurina and four in T. alba. We suggest that most light-associated gene functions have been maintained in owls and their loss has not proceeded to the same extent as in other dim-light-adapted vertebrates.

Retinal Waves Modulate an Intraretinal Circuit of Intrinsically Photosensitive Retinal Ganglion Cells.

Before the maturation of rod and cone photoreceptors, the developing retina relies on light detection by intrinsically photosensitive retinal ganglion cells (ipRGCs) to drive early light-dependent behaviors. ipRGCs are output neurons of the retina; however, they also form functional microcircuits within the retina itself. Whether ipRGC microcircuits exist during development and whether they influence early light detection remain unknown. Here, we investigate the neural circuit that underlies the ipRGC-driven light response in developing mice. We use a combination of calcium imaging, tracer coupling, and electrophysiology experiments to show that ipRGCs form extensive gap junction networks that strongly contribute to the overall light response of the developing retina. Interestingly, we found that gap junction coupling was modulated by spontaneous retinal waves, such that acute blockade of waves dramatically increased the extent of coupling and hence increased the number of light-responsive neurons. Moreover, using an optical sensor, we found that this wave-dependent modulation of coupling is driven by dopamine that is phasically released by retinal waves. Our results demonstrate that ipRGCs form gap junction microcircuits during development that are modulated by retinal waves; these circuits determine the extent of the light response and thus potentially impact the processing of early visual information and light-dependent developmental functions. Light-dependent functions in early development are mediated by intrinsically photosensitive retinal ganglion cells (ipRGCs). Here we show that ipRGCs form an extensive gap junction network with other retinal neurons, including other ipRGCs, which shapes the retina's overall light response. Blocking cholinergic retinal waves, which are the primary source of neural activity before maturation of photoreceptors, increased the extent of ipRGC gap junction networks, thus increasing the number of light-responsive cells. We determined that this modulation of ipRGC gap junction networks occurs via dopamine released by waves. These results demonstrate that retinal waves mediate dopaminergic modulation of gap junction networks to regulate pre-vision light responses.

The importance of intrinsically photosensitive retinal ganglion cells and implications for lighting design

We reviewed the role of melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs) in light-dependent functions, including circadian rhythm that is important for health and visual perception. We then discussed the implications for lighting design.

The importance of gold‐electrode‐adjacent stationary high‐field Böer domains for the photoconductivity of CdS

When the electron density decreases stronger than linearly with the electric field in photoconductive CdS due to field quenching, high‐field domains must occur that remain attached to either the cathode or anode in slit electrode geometry with blocking cathodes. These Böer domains1 are easily seen by their shift in optical absorption due to the Franz‐Keldysh effect and offer unique opportunities to analyze field dependent parameters within the range of constant electron density and electric field, such as the carrier density or mobility as a function of the field, and give information of the light dependent work function. They also provide insight why a 200 Å thick cover layer of CdS on top of a CdTe solar cell increases its efficiency from 8 to 16% . The behavior of these Böer domains escapes conventional current voltage analyses except for their visual observation, while other high‐field domains with their current fluctuations or oscillations are easily observed and are the subjects of thousands of publications and many books. In this review we will exclude detailed discussion of dynamic domains, but include some new specifics that help to understand the mechanisms of the Böer domains and their applications. Only properties at low optical excitation intensities are discussed that exclude Joules heating. Within the p‐type regime of the anode‐adjacent domain extremely steep electronic quenching signal becomes visible that could signalize an intrinsic donor level slightly above the middle of the band gap that may be responsible for not allowing CdS to ever become p‐type by doping. image

Circadian and Wake-Dependent Effects on the Pupil Light Reflex in Response to Narrow-Bandwidth Light Pulses

Nonvisual light-dependent functions in humans are conveyed mainly by intrinsically photosensitive retinal ganglion cells, which express melanopsin as photopigment. We aimed to identify the effects of circadian phase and sleepiness across 24 hours on various aspects of the pupil response to light stimulation. We tested 10 healthy adults hourly in two 12-hour sessions covering a 24-hour period. Pupil responses to narrow bandwidth red (635 ± 18 nm) and blue (463 ± 24 nm) light (duration of 1 and 30 seconds) at equal photon fluxes were recorded, and correlated with salivary melatonin concentrations at the same circadian phases and to subjective sleepiness ratings. The magnitude of pupil constriction was determined from minimal pupil size. The post-stimulus pupil response was assessed from the pupil size at 6 seconds following light offset, the area within the redilation curve, and the exponential rate of redilation. Among the measured parameters, the pupil size 6 seconds after light offset correlated with melatonin concentrations (P < 0.05) and showed a significant modulation over 24 hours with maximal values after the nocturnal peak of melatonin secretion. In contrast, the post-stimulus pupil response following red light stimulation correlated with subjective sleepiness (P < 0.05) without significant changes over 24 hours. The post-stimulus pupil response to blue light as a marker of intrinsic melanopsin activity demonstrated a circadian modulation. In contrast, the effect of sleepiness was more apparent in the cone contribution to the pupil response. Thus, pupillary responsiveness to light is under influence of the endogenous circadian clock and subjective sleepiness.

The phosducin-like protein PhLP1 impacts regulation of glycoside hydrolases and light response in Trichoderma reesei.

BackgroundIn the biotechnological workhorse Trichoderma reesei (Hypocrea jecorina) transcription of cellulase genes as well as efficiency of the secreted cellulase mixture are modulated by light. Components of the heterotrimeric G-protein pathway interact with light-dependent signals, rendering this pathway a key regulator of cellulase gene expression.ResultsAs regulators of heterotrimeric G-protein signaling, class I phosducin-like proteins, are assumed to act as co-chaperones for G-protein beta-gamma folding and exert their function in response to light in higher eukaryotes. Our results revealed light responsive transcription of the T. reesei class I phosducin-like protein gene phlp1 and indicate a light dependent function of PhLP1 also in fungi. We showed the functions of PhLP1, GNB1 and GNG1 in the same pathway, with one major output being the regulation of transcription of glycoside hydrolase genes including cellulase genes in T. reesei. We found no direct correlation between the growth rate and global regulation of glycoside hydrolases, which suggests that regulation of growth does not occur only at the level of substrate degradation efficiency.Additionally, PhLP1, GNB1 and GNG1 are all important for proper regulation of light responsiveness during long term exposure. In their absence, the amount of light regulated genes increased from 2.7% in wild type to 14% in Δphlp1. Besides from the regulation of degradative enzymes, PhLP1 was also found to impact on the transcription of genes involved in sexual development, which was in accordance with decreased efficiency of fruiting body formation in Δphlp1. The lack of GNB1 drastically diminished ascospore discharge in T. reesei.ConclusionsThe heterotrimeric G-protein pathway is crucial for the interconnection of nutrient signaling and light response of T. reesei, with the class I phosducin-like protein PhLP1, GNB1 and GNG1 acting as important nodes, which influence light responsiveness, glycoside hydrolase gene transcription and sexual development.

Light-transduction in melanopsin-expressing photoreceptors of Amphioxus

Spatial vision in different organisms is mediated by 2 classes of photoreceptors: microvillar and ciliary. Recently, additional photosensitive cells implicated in nonvisual light-dependent functions have been identified in the mammalian retina. A previously undescribed photopigment, melanopsin, underlies these photoresponses, and it has been proposed that its transduction mechanisms may be akin to the lipid-signaling scheme of invertebrate microvillar receptors, rather than the cyclic-nucleotide cascade of vertebrates. Melanopsin has an ancient origin in deuterostomia, and expresses in 2 morphologically distinct classes of cells in the neural tube of Amphioxus, the most basal extant chordate: pigmented ocelli, and Joseph cells. However, to our knowledge, their physiology and alleged photosensitivity had never been investigated. We dissociated both types of cells, and conclusively demonstrated by patch-electrode recoding that they are primary photoreceptors; their receptor potential is depolarizing, accompanied by an increase in membrane conductance. The action spectrum peaks in the blue region, approximately 470 nm, similar to the absorption of melanopsin in vitro. The light-dependent conductance rectifies inwardly; Na and Ca are differentially implicated in the 2 cell types. Fluorescence Ca imaging reveals that photostimulation rapidly mobilizes calcium from internal stores. Intracellular 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetate severely impairs the photoresponse, indicating that light-evoked Ca elevation is an important event in photoexcitation. These observations support the notion that the lineage of microvillar photoreceptors and its associated light-signaling pathway also evolved in the chordates. Thus, Joseph cells and pigmented ocelli of the Amphioxus may represent a link between ancestral rhabdomeric-like light sensors present in prebilaterians and the circadian photoreceptors of higher vertebrates.

Analysis of the phytochrome gene family in Ceratodon purpureus by gene targeting reveals the primary phytochrome responsible for photo- and polarotropism

Using gene targeting by homologous recombination in Ceratodon purpureus, we were able to knock out four phytochrome photoreceptor genes independently and to analyze their function with respect to red light dependent phototropism, polarotropism, and chlorophyll content. The strongest phenotype was found in knock-out lines of a newly described phytochrome gene termed CpPHY4 lacking photo- and polarotropic responses at moderate fluence rates. Eliminating the atypical phytochrome gene CpPHY1, which is the only known phytochrome-like gene containing a putative C-terminal tyrosine kinase-like domain, affects red light-induced chlorophyll accumulation. This result was surprising, since no light dependent function was ever allocated to this unusual gene.

Shedding Light on Animal Cryptochromes

Shedding Light on Animal Cryptochromes

Optimal primary production model and parameterization in the eastern East China Sea

Integrated primary production (IPP) datasets from the eastern East China Sea (ECS) were used to validate the depth dependent and time integrated model (TIM), the empirical model (EM), and the vertically generalized production model (VGPM). Employing constant maximum chlorophyll-a (Chl-a) specific carbon fixation rate (P opt B ), the original TIM could not explain measured IPP variance, while the low P opt B estimated using P opt B models originally embedded in the EM were responsible for original EM low estimations. The disparity between P opt B expressions originally embedded in the VGPM and that observed in this study was responsible for the low accuracy of the original VGPM. After locally tuning on the P opt B model, TIM and VGPM could predict well, whereas EM still gave low estimates. This was probably due to the fact that, unlike TIM and VGPM, EM employs a constant factor instead of a light dependent function in describing the depth of light-saturation primary production. The high accuracy of TIM was limited by the complexity of estimating many variable inputs. EM, as a simplest model, should be used with caution in the eastern ECS. Global VGPM with locally adjusted P opt B seemed to be an effective model for estimating IPP in the eastern ECS.

Molecular cloning of glutamate dehydrogenase genes of Nicotiana plumbaginifolia: structure analysis and regulation of their expression by physiological and stress conditions

Two Nicotiana plumbaginifolia gdh genes ( gdhA and gdhB) encoding for NADH dependent glutamate dehydrogenase (GDH) were isolated by PCR and I-PCR (inverse-PCR) and sequenced. The coding sequence is interrupted by eight introns that are located in the same positions in both genes. Computer analysis of the promoter regions of gdhA (650 nt) and gdhB (1800 nt) revealed several conserved motifs and, for gdhB, the presence of an I-Box element known to have light dependent regulatory functions in plants. The response of the gdh genes to carbohydrate deprivation and to ammonium feeding and to various stress conditions (salinity, temperature shifts and heavy metals) was examined in callus culture. The results clearly showed that the carbohydrate status of the cell is the main factor affecting gdh genes expression. Stress condition may depress or increase gdh transcript levels, but theses are not always correlated to the corresponding levels of GDH activity. Altogether these results point to the existence of multiple levels of regulation (transcriptional and post-transcriptional) of gdh genes.

Response regulator homologues have complementary, light-dependent functions in the Arabidopsis circadian clock.

TIMING OF CAB EXPRESSION 1 ( TOC1) functions with CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) in a transcriptional feedback loop that is important for the circadian clock in Arabidopsis thaliana (L.) Heynh. TOC1 and its four paralogues, the Arabidopsis PSEUDO-RESPONSE REGULATOR (PRR) genes, are expressed in an intriguing daily sequence. This was proposed to form a second feedback loop, similar to the interlocking clock gene circuits in other taxa. We show that prr9 and prr5 null mutants have reciprocal period defects for multiple circadian rhythms, consistent with subtly altered expression patterns of CCA1 and TOC1. The period defects are conditional on light quality and combine additively in double-mutant plants. Thus PRR9 and PRR5 modulate light input to the circadian clock but are neither uniquely required for rhythm generation nor form a linear series of mutual PRR gene regulation.

Melatonin receptors step into the light: cloning and classification of subtypes

Melatonin, the principal hormone of the pineal gland, has several biological effects’. The hormone regulates the repwlustive alterations that occur in response to chaqges in day length in seasonally breeding mammals!. Melatonin can also alter the timing of mammalian circadian rhythms, and appears to function in concert with light to hold circadian rhythms in phase with prevailing environmental conditions’, Melatonin inhibits the Ca”*-dependent release of dopamine in mammalian retinad, and appears to act in verte brate retina to affect several lightdependent functions, including shedding of photopigment discs and phagocytosis? The pineal hormone can also induce sleep in humans; this hypnotic effect may be separated from its effects on circadian rhythm@. Melatonin appears to exert these effects through pharmacologically specific, high-affinity receptor+? Recent progress in this area has been the cloning of a family oi G protein-coupled ..~eptors for mehtonin,

Dark-induced supersensitivity of dopamine D-1 and D-2 receptors in rat retina

Light deprivation of rat retina leads to a rapid (within 6 h) development of a state of supersensitivity (upregulation) of dopamine D-1 receptors (positively coupled to adenylate cyclase), which are essentially involved in the modulation by light of the electrical activity and communication between horizontal cells. In contrast, the supersensitivity of D-2 receptors (negatively coupled to cAMP generating system) appears to develop only after 2 days (better after 4 days) of dark adaptation, although these receptors are linked to multiple light-dependent retinal functions. These results suggest the existence of different mechanisms of sensory adaptation for these two subtypes of dopamine receptors.