Mechanotransduction, cellular biophotonic activity, and signaling patterns for tissue regeneration.

Signaling molecules exhibit mechanical oscillations, entailing precise vibrational directionalities. These steering signatures have profound functional implications and are intimately connected with the onset of molecular electric oscillations and biophoton emission. We discuss biophotonic activity as a form of endogenous photobiomodulation, orchestrating the mechano-sensing/-transduction in signaling players. We focus on exogenous photobiomodulation in the form of pulsed wave modulation of selected light wavelengths to direct endogenous biophotonic activity and molecular cellular dynamics. We highlight the relevance of this strategy to target and reprogram the developmental potential of tissue-resident stem cells in damaged tissues, affording precision regenerative medicine without the need for cell or tissue transplantation.

Translational photobiology: towards dynamic lighting in indoor horticulture.

Crop productivity depends on the ability of plants to thrive across different growth environments. In nature, light conditions fluctuate due to diurnal and seasonal changes in direction, duration, intensity, and spectrum. Laboratory studies, predominantly conducted with arabidopsis (Arabidopsis thaliana), have provided valuable insights into the metabolic and regulatory strategies that plants employ to cope with varying light intensities. However, there has been less focus on how horticultural crops tolerate dynamically changing light conditions during the photoperiod. In this review we connect insights from photobiology in model plants to the application of dynamic lighting in indoor horticulture. We explore how model species respond to fluctuating light intensities and discuss how this knowledge could be translated for new lighting solutions in controlled environment agriculture.

Plant Phytochrome Interactions Decode Light and Temperature Signals.

Plant phytochromes perceive red and far-red light to elicit adaptations to the changing environment. Downstream physiological responses revolve around red-light-induced interactions with phytochrome-interacting factors (PIF). Phytochromes double as thermoreceptors, owing to the pronounced temperature dependence of thermal reversion from the light-adapted Pfr to the dark-adapted Pr state. Here, we assess whether thermoreception may extend to the phytochrome:PIF interactions. While the association between Arabidopsis (Arabidopsis thaliana) PHYTOCHROME B (PhyB) and several PHYTOCHROME-INTERACTING FACTOR (PIF) variants moderately accelerates with temperature, the dissociation does more so, thus causing net destabilization of the phytochrome:PIF complex. Markedly different temperature profiles of PIF3 and PIF6 might underlie stratified temperature responses in plants. Accidentally, we identify a photoreception mechanism under strong continuous light, where the extent of phytochrome:PIF complexation decreases with red-light intensity rather than increases. Mathematical modeling rationalizes this attenuation mechanism and ties it to rapid red-light-driven Pr⇄Pfr interconversion and complex dissociation out of Pr. Varying phytochrome abundance, e.g., during diurnal and developmental cycles, and interaction dynamics, e.g., across different PIFs, modify the nature and extent of attenuation, thus permitting light-response profiles more malleable than possible for the phytochrome Pr⇄Pfr interconversion alone. Our data and analyses reveal a photoreception mechanism with implications for plant physiology, optogenetics, and biotechnological applications.

Direct detection of the chloride release and uptake reactions of Natronomonas pharaonis halorhodopsin.

Membrane transport proteins undergo multistep conformational changes to fulfill the transport of substrates across biological membranes. Substrate release and uptake are the most important events of these multistep reactions that accompany significant conformational changes. Thus, their relevant structural intermediates should be identified to better understand the molecular mechanism. However, their identifications have not been achieved for most transporters due to the difficulty of detecting the intermediates. Herein, we report the success of these identifications for a light-driven chloride transporter halorhodopsin (HR). We compared the time course of two flash-induced signals during a single transport cycle. One is a potential change of Cl--selective membrane, which enabled us to detect tiny Cl--concentration changes due to the Cl- release and the subsequent Cl--uptake reactions by HR. The other is the absorbance change of HR reflecting the sequential formations and decays of structural intermediates. Their comparison revealed not only the intermediates associated with the key reactions but also the presence of two additional Cl--binding sites on the Cl--transport pathways. The subsequent mutation studies identified one of the sites locating the protein surface on the releasing side. Thus, this determination also clarified the Cl--transport pathway from the initial binding site until the release to the medium.

Dataset of images for visual and non-visual analysis of colour applications in architecture.

This paper describes three datasets which include 443 folders and approximately 4430 images. The images were obtained from the interior of a 1:50 scale model using a fisheye camera connected to a Raspberry Pi microcomputer. This dataset aims to analyze the photobiological effects (visual and non-visual) of the interplay between coloured surfaces and different types of lighting strategies. The experiments were conducted under three types of light sources: simulated daylight through a mirror-box artificial sky simulator, direct daylight, and an electric lighting system that allows for colour temperature modification. This dataset includes low dynamic range images to generate high dynamic range images, which in turn can be used to plot false colour maps concerning photopic luminance, melanopic luminance, CCT of an image, M/P ratio, and brightness distribution maps. This dataset can be useful for architects, interior designers, and building engineers to integrate lighting and colour strategies according to the visual and non-visual needs of the users. This research was partially used in the research of Espinoza-Sanhueza et al. [1,2]. The datasets are published and shared through a Mendeley repository [3].

Activating an invertebrate bistable opsin with the all-trans 6.11 retinal analog.

Animal vision depends on opsins, a category of G protein-coupled receptor (GPCR) that achieves light sensitivity by covalent attachment to retinal. Typically binding as an inverse agonist, 11-cis retinal photoisomerizes to the all-trans isomer and activates the receptor, initiating downstream signaling cascades. Retinal bound to bistable opsins isomerizes back to the 11-cis state after absorption of a second photon, inactivating the receptor. Bistable opsins are essential for invertebrate vision and nonvisual light perception across the animal kingdom. While crystal structures are available for bistable opsins in the inactive state, it has proven difficult to form homogeneous populations of activated bistable opsins either via illumination or reconstitution with all-trans retinal. Here, we show that a nonnatural retinal analog, all-trans retinal 6.11 (ATR6.11), can be reconstituted with the invertebrate bistable opsin, Jumping Spider Rhodopsin-1 (JSR1). Biochemical activity assays demonstrate that ATR6.11 functions as a JSR1 agonist. ATR6.11 binding also enables complex formation between JSR1 and signaling partners. Our findings demonstrate the utility of retinal analogs for biophysical characterization of bistable opsins, which will deepen our understanding of light perception in animals.

Lights, location, action: Shade avoidance signalling over spatial scales.

Plants growing in dense vegetation stands need to flexibly position their photosynthetic organs to ensure optimal light capture in a competitive environment. They do so through a suite of developmental responses referred to as the shade avoidance syndrome. Belowground, root development is also adjusted in response to aboveground neighbour proximity. Canopies are dynamic and complex environments with heterogenous light cues in the far-red, red, blue and UV spectrum, which can be perceived with photoreceptors by spatially separated plant tissues. Molecular regulation of plant architecture adjustment via PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factors and growth-related hormones such as auxin, gibberellic acid, brassinosteroids and abscisic acid were historically studied without much attention to spatial or tissue-specific context. Recent developments and technologies have, however, sparked strong interest in spatially explicit understanding of shade avoidance regulation. Other environmental factors such as temperature and nutrient availability interact with the molecular shade avoidance regulation network, often depending on the spatial location of the signals, and the responding organs. Here, we aim to review recent advances in how plants respond to heterogenous light cues and integrate these with other environmental signals.

Light emitting diode effect of red, blue, and amber light on photosynthesis and plant growth parameters.

The visible light spectrum (400-700 nm) powers plant photosynthesis and innumerable other biological processes. Photosynthesis curves plotted by pioneering photobiologists show that amber light (590-620 nm) induces the highest photosynthetic rates in this spectrum. Yet, both red and blue light are viewed superior in their influence over plant growth. Here we report two approaches for quantifying how light wavelength photosynthesis and plant growth using light emitting diodes (LEDs). Resolved quantum yield spectra of tomato and lettuce plants resemble those acquired earlier, showing high quantum utilization efficiencies in the 420-430 nm and 590-620 nm regions. Tomato plants grown under blue (445 nm), amber (595 nm), red (635 nm), and combined red-blue-amber light for 14 days show that amber light yields higher fresh and dry mass, by at least 20%. Principle component analysis shows that amber light has a more pronounced and direct effect on fresh mass, whereas red light has a major effect on dry mass. These data clarify amber light's primary role in photosynthesis and suggest that bandwidth determines plant growth and productivity under sole amber lighting. Findings set precedence for future work aimed at maximizing plant productivity, with widespread implications for controlled environment agriculture.

Far-red light enrichment affects gene expression and architecture as well as growth and photosynthesis in rice.

Plants use light as a resource and signal. Photons within the 400-700 nm waveband are considered photosynthetically active. Far-red photons (FR, 700-800 nm) are used by plants to detect nearby vegetation and elicit the shade avoidance syndrome. In addition, FR photons have also been shown to contribute to photosynthesis, but knowledge about these dual effects remains scarce. Here, we study shoot-architectural and photosynthetic responses to supplemental FR light during the photoperiod in several rice varieties. We observed that FR enrichment only mildly affected the rice transcriptome and shoot architecture as compared to established model species, whereas leaf formation, tillering and biomass accumulation were clearly promoted. Consistent with this growth promotion, we found that CO2-fixation in supplemental FR was strongly enhanced, especially in plants acclimated to FR-enriched conditions as compared to control conditions. This growth promotion dominates the effects of FR photons on shoot development and architecture. When substituting FR enrichment with an end-of-day FR pulse, this prevented photosynthesis-promoting effects and elicited shade avoidance responses. We conclude that FR photons can have a dual role, where effects depend on the environmental context: in addition to being an environmental signal, they are also a potent source of harvestable energy.

The photophysical, photobiological, and DNA/HSA-binding properties of corroles containing carbazole and phenothiazine moieties.

This study characterized four corrole derivatives, namely Cbz-Cor, MetCbz-Cor, PTz-Cor, and PTzEt-Cor, examining their photophysical, electrochemical, photobiological, and biomolecule-binding properties. Experimental photophysical data of absorption and emission elements correlated with a theoretical analysis obtained through time-dependent density functional theory (TD-DFT). As for the photophysical properties, we observed lower fluorescence quantum yields and discernible differences between the excited and ground states, as indicated by Stokes shift values. Natural Transition Orbit (NTO) plots presented high occupied molecular orbital - low unoccupied molecular orbital (HOMO-LUMO) densities around the tetrapyrrolic macrocycle in all examples. Our findings demonstrate that corroles maintain stability in solution and offer photostability (<20 %), predominantly in DMSO(5 %)/Tris-HCl (pH 7.4) buffer solution. Furthermore, the singlet oxygen (1O2) quantum yield and log POW values underscore their potential application in photoinactivation approaches, as these corroles serve as effective ROS generators with more lipophilic features. We also evaluated their biomolecular binding capacity towards salmon sperm DNA and human serum albumin using spectroscopic techniques and molecular docking analysis for sustenance. Concerning biomolecule interaction profiles, the corrole derivatives showed a propensity for interacting in the minor grooves of the double helix DNA due to secondary forces, which were more pronounced in site III of the human serum protein.

Comparative Study of Healthy Older and Younger Adults Shows They Have the Same Skin Concentration of Vitamin D3 Precursor, 7-Dehydrocholesterol, and Similar Response to UVR.

Vitamin D3 synthesis in human skin is initiated by solar ultraviolet radiation (UVR) exposure of precursor 7-dehydrocholesterol (7DHC), but influence of age on the early stage of vitamin D3 metabolism is uncertain. We performed a prospective standardised study in healthy ambulant adults aged ≥65 and ≤40 years examining (1) if baseline skin 7DHC concentration differs between younger and older adults and (2) the impact of older age on serum vitamin D3 response to solar simulated UVR. Eleven younger (18-40 years) and 10 older (65-89 years) adults, phototype I-III, received low-dose UVR (95% UVA, 5% UVB, 1.3 SED) to ~35% of the body surface area. Biopsies were taken for 7DHC assay from unexposed skin, skin immediately and 24 h post-UVR, and blood sampled at baseline, 24 h and 7 d post-UVR for vitamin D3 assay. Samples were analysed by HPLC-MS/MS. Baseline skin 7DHC (mean ± SD) was 0.22 ± 0.07 and 0.25 ± 0.08 µg/mg in younger versus older adults (no significant difference). Baseline serum vitamin D3 concentration was 1.5 ± 1.5 and 1.5 ± 1.7 nmol/L in younger versus older adults, respectively, and showed a significant increase in both groups post-UVR (no significant differences between age groups). Thus, skin 7DHC concentration was not a limiting factor for vitamin D3 production in older relative to younger adults. This information assists public health guidance on sun exposure/vitamin D nutrition, with particular relevance to the growing populations of healthy ambulant adults ≥65 years.

Convergent mechanism underlying the acquisition of vertebrate scotopic vision.

High sensitivity of scotopic vision (vision in dim light conditions) is achieved by the rods' low background noise, which is attributed to a much lower thermal activation rate (kth) of rhodopsin compared with cone pigments. Frogs and nocturnal geckos uniquely possess atypical rods containing noncanonical cone pigments that exhibit low kth, mimicking rhodopsin. Here, we investigated the convergent mechanism underlying the low kth of rhodopsins and noncanonical cone pigments. Our biochemical analysis revealed that the kth of canonical cone pigments depends on their absorption maximum (λmax). However, rhodopsin and noncanonical cone pigments showed a substantially lower kth than predicted from the λmax dependency. Given that the λmax is inversely proportional to the activation energy of the pigments in the Hinshelwood distribution-based model, our findings suggest that rhodopsin and noncanonical cone pigments have convergently acquired low frequency of spontaneous-activation attempts, including thermal fluctuations of the protein moiety, in the molecular evolutionary processes from canonical cone pigments, which contributes to highly sensitive scotopic vision.

The Influence of Blue Light Exposure on Reconstructed 3-Dimensional Skin Model: Molecular Changes and Gene Expression Profile.

Recent studies have provided information about digital eye strain and the potential damage that blue light from digital devices can cause to the eyes. In this study, we analyzed the influence of blue light exposure on reconstructed 3-dimensional skin model using RNA sequencing to identify the expression of transcripts and abnormal events. Three-dimensional skin was exposed to visible light spectrum and isolated blue wavelength for 1, 2, and 4 hours to represent acute exposure and 1 hour over 4 sequential days to represent repeated exposure, respectively, in this in vitro model. We compared gene expression levels with those of unexposed control. Samples submitted to repeated exposure showed reduced AK2 and DDX47, whereas they showed increased PABPC3 gene expression, revealing a significantly negative impact. RT-PCR validation assay with exposed 3-dimensional skin compared with unexposed control regarding 1 and 4 days of incubation showed increased IL-6 signaling mechanism activation and signal transducer and activator of transcription 3 gene STAT3 gene expression, whereas it showed decreased peroxisome proliferator-activated receptor signaling mechanism activation, suggesting an influence on inflammatory pathways. We also demonstrate upregulated gene expression of KIT, MAPK2, and PI3KC in samples from exposed condition, corroborating previous findings related to pigmentation signaling stimuli. These results reveal, to our knowledge, previously unreported data that enable studies on molecular response correlation of in vitro digital blue light exposure and human skin studies.

From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons.

Over the last decade, the development of time-resolved serial crystallography (TR-SX) at X-ray free-electron lasers (XFELs) and synchrotrons has allowed researchers to study phenomena occurring in proteins on the femtosecond-to-minute timescale, taking advantage of many technical and methodological breakthroughs. Protein crystals of various sizes are presented to the X-ray beam in either a static or a moving medium. Photoactive proteins were naturally the initial systems to be studied in TR-SX experiments using pump-probe schemes, where the pump is a pulse of visible light. Other reaction initiations through small-molecule diffusion are gaining momentum. Here, selected examples of XFEL and synchrotron time-resolved crystallography studies will be used to highlight the specificities of the various instruments and methods with respect to time resolution, and are compared with cryo-trapping studies.

Bathymetric origin shapes the physiological responses of Pterygophora californica (Laminariales, Phaeophyceae) to deep marine heatwaves.

Kelp communities are experiencing exacerbated heat-related impacts from more intense, frequent, and deeper marine heatwaves (MHWs), imperiling the long-term survival of kelp forests in the climate change scenario. The occurrence of deep thermal anomalies is of critical importance, as elevated temperatures can impact kelp populations across their entire bathymetric range. This study evaluates the impact of MHWs on mature sporophytes of Pterygophora californica (walking kelp) from the bathymetric extremes (8-10 vs. 25-27 m) of a population situated in Baja California (Mexico). The location is near the southernmost point of the species's broad distribution (from Alaska to Mexico). The study investigated the ecophysiological responses (e.g., photobiology, nitrate uptake, oxidative stress) and growth of adult sporophytes through a two-phase experiment: warming simulating a MHW and a post-MHW phase without warming. Generally, the effects of warming differed depending on the bathymetric origin of the sporophytes. The MHW facilitated essential metabolic functions of deep-water sporophytes, including photosynthesis, and promoted their growth. In contrast, shallow-water sporophytes displayed metabolic stress, reduced growth, and oxidative damage. Upon the cessation of warming, certain responses, such as a decline in nitrate uptake and net productivity, became evident in shallow-water sporophytes, implying a delay in heat-stress response. This indicates that variation in temperatures can result in more prominent effects than warming alone. The greater heat tolerance of sporophytes in deeper waters shows convincing evidence that deep portions of P. californica populations have the potential to serve as refuges from the harmful impacts of MHWs on shallow reefs.

Distribution of photoactive ß-carboline alkaloids across Passiflora caerulea floral organs.

This study reports valuable information regarding the presence and concentration of a series of photoactive ß-carboline (ßCs) alkaloids (norharmane, harmane, harmine, harmol, harmaline, and harmalol) and their distribution across the floral age and organs of Passiflora caerulea. UHPLC-MS/MS data reported herein reveal that the ßCs' content ranged from 1 to 110 µg kg-1 , depending on the floral organ and age. In certain physiologically relevant organs, such as anthers, ßCs' content was one order of magnitude higher than in other organs, suggesting a special role for ßCs in this specific organ. ßCs' content also varied in a structure-dependent manner. Alkaloids bearing a hydroxyl group at position C(7) of the main ßC ring were present at concentrations one order of magnitude higher than other ßC derivatives investigated. UV-visible and fluorescence spectroscopy of the flower extracts provided complementary information regarding other biologically relevant groups of chromophores (phenolic/indolic derivatives, flavonoids/carotenes, and chlorophylls). Since flowers are constantly exposed to solar radiation, the presence of photoactive ßCs in floral organs may have several (photo)biological implications that are further discussed.

Photophysical, photobiological, and mycobacteria photo-inactivation properties of new meso-tetra-cationic platinum(II) metalloderivatives at meta position.

In this manuscript, we report the photo-inactivation evaluation of new tetra-cationic porphyrins with peripheral Pt(II) complexes ate meta N-pyridyl positions in the antimicrobial photodynamic therapy (aPDT) of rapidly growing mycobacterial strains (RGM). Four different metalloderivatives were synthetized and applied. aPDT experiments in the strains of Mycobacteroides abscessus subsp. Abscessus (ATCC 19977), Mycolicibacterium fortuitum (ATCC 6841), Mycobacteroides abscessus subsp. Massiliense (ATCC 48898), and Mycolicibacterium smegmatis (ATCC 700084) conducted with adequate concentration of photosensitizers (PS) under white-light conditions at 90 min (irradiance of 50 mW cm-2 and a total light dosage of 270 J cm-2) showed that the Zn(II) derivative is the most effective PS significantly reduced the concentration of viable mycobacteria. The effectiveness of the molecule as PS for PDI studies is also clear with mycobacteria, which is strongly related with the porphyrin peripheral charge and coordination platinum(II) compounds and consequently about the presence of metal center ion. This class of PS may be promising antimycobacterial aPDT agents with potential applications in medical clinical cases and bioremediation.

Effect of photobiomodulation therapy on TGF-ß release from dentin, migration and viability of dental pulp stem cells in regenerative endodontics treatment: An ex vivo study.

BACKGROUND AND AIM: Regenerative endodontic procedures (REPs) are oriented by the principles of tissue engineering, incorporating dental pulp stem cells (DPSC), crucial growth factors like Transforming growth factor-ß (TGF-ß1), and scaffolds to facilitate the regeneration of dental pulp tissues. The present study aimed to investigate the effect of photobiomodulation (PBM) therapy, using an 808 nm diode laser on cellular modulation mechanisms in REPs. METHOD AND MATERIAL: A total of 108 human dentin discs obtained from intact single root teeth were randomly assigned into six groups (n = 8): 1. Positive control (EDTA), 2. PBM-1 (3 J/cm2), 3. PBM-2 (5 J/cm2), 4. EDTA+PBM-1, 5. EDTA+PBM-2, and 6. Negative control (NaOCl). Then, an extract solution was prepared from each disc and the concentration of released TGF-ß1 from the discs was measured using enzyme-linked immunosorbent assay (ELISA). Moreover, the extract solution was added to DPSC culture medium to evaluate cell viability and migration through MTT assay and scratch test, respectively. RESULT: The group exposed to PBM-1 showed the highest cell viability, while treatment with EDTA and EDTA+PBM-2 decreased cellular viability. Also, the PBM-treated groups showed significantly higher release of TGF-ß1 compared to the negative control. EDTA and EDTA+PBM-1 showed the highest release among all the groups. No significant difference was found between EDTA and EDTA+PBM-1, as well as between PBM-1 and PBM-2. Moreover, the PBM-1 group exhibited the highest migration after 24 h, which was significantly greater than other groups, except for the PBM-2 group. CONCLUSION: According to the obtained data, 808 nm mediated-PBM (3 J/cm2), both independently and in conjunction with EDTA, enhanced the release of TGF-ß1 from dentin and improved cell viability and migration of DPSCs. It seems that, PBM under the specific parameters employed in this study, could be an effective adjunctive therapy in REPs.

One More for Light-triggered Conformational Changes in Cryptochromes: CryP from Phaeodactylum tricornutum.

Cryptochromes are a ubiquitously occurring class of photoreceptors. Together with photolyases, they form the Photolyase Cryptochrome Superfamily (PCSf) by sharing a common protein architecture and binding mode of the FAD chromophore. Despite these similarities, PCSf members exert different functions. Photolyases repair UV-induced DNA damage by photocatalytically driven electron transfer between FADH¯ and the DNA lesion, whereas cryptochromes are light-dependent signaling molecules and trigger various biological processes by photoconversion of their FAD redox and charge states. Given that most cryptochromes possess a C-terminal extension (CTE) of varying length, the functions of their CTE have not yet been fully elucidated and are hence highly debated. In this study, the role of the CTE was investigated for a novel subclass of the PCSf, the CryP-like cryptochromes, by hydrogen/deuterium exchange and mass-spectrometric analysis. Striking differences in the relative deuterium uptake were observed in different redox states of CryP from the diatom Phaeodactylum tricornutum. Based on these measurements we propose a model for light-triggered conformational changes in CryP-like cryptochromes that differs from other known cryptochrome families like the insect or plant cryptochromes.

Phytoplankton Image Segmentation and Annotation Method Based on Microscopic Fluorescence.

Microscopic phytoplankton segmentation is an important part of water quality assessment. The segmentation of microscopic phytoplankton still faces challenges for computer vision, such as being affected by background impurities and requiring a large number of manual annotation. In this paper, the characteristics of phytoplankton emitting fluorescence under excitation light were utilized to segment and annotate phytoplankton contours by fusing fluorescence images and bright field images. Morphological operations were used to process microscopic fluorescence images to obtain the initial contours of phytoplankton. Then, microscopic bright field images were processed by Active Contour to fine tune the contours. Seven algae species were selected as the experimental objects. Compared with manually labeling the contour in LabelMe, the recall, precision, FI score and IOU of the proposed segmentation method are 85.3%, 84.5%, 84.7%, and 74.6%, respectively. Mask-RCNN was used to verify the correctness of labels annotated by the proposed method. The average recall, precision, F1 score and IOU are 97.0%, 86.5%, 91.1%, and 84.2%, respectively, when the Mask-RCNN is trained with the proposed automatic labeling method. And the results corresponding to manual labeling are 95.3%, 86.1%, 90.3%, and 82.8% respectively. The experimental results show that the proposed method can segment the phytoplankton microscopic image accurately, and the automatically annotated contour data has the same effect as the manually annotated contour data in Mask-RCNN, which greatly reduces the manual annotation workload.