Axially swept open-top light-sheet microscopy for densely labeled clinical specimens.

Open-top light-sheet (OTLS) microscopy offers rapid 3D imaging of large optically cleared specimens. This enables nondestructive 3D pathology, which provides key advantages over conventional slide-based histology including comprehensive sampling without tissue sectioning/destruction and visualization of diagnostically important 3D structures. With 3D pathology, clinical specimens are often labeled with small-molecule stains that broadly target nucleic acids and proteins, mimicking conventional hematoxylin and eosin (H&E) dyes. Tight optical sectioning helps to minimize out-of-focus fluorescence for high-contrast imaging in these densely labeled tissues but has been challenging to achieve in OTLS systems due to trade-offs between optical sectioning and field of view. Here we present an OTLS microscope with voice-coil-based axial sweeping to circumvent this trade-off, achieving 2 µm axial resolution over a 750 × 375 µm field of view. We implement our design in a non-orthogonal dual-objective (NODO) architecture, which enables a 10-mm working distance with minimal sensitivity to refractive index mismatches, for high-contrast 3D imaging of clinical specimens.

Wireless Powered Microwave-Light Conversion Platform with Dual-Stimulus Nanoresponder Coating for Deep-Seated Photodynamic Therapy.

Traditional external field-assisted therapies, e.g., microwave (MW) therapy and phototherapy, cannot effectively and minimally damage eliminate deep-seated infection, owing to the poor penetrability of light and low reactive oxygen species (ROS) stimulation capability of MW. Herein, an implantable and wireless-powered therapeutic platform (CNT-FeTHQ-TS), in which external MW can be converted into internal light via MW wireless-powered light-emitting chips, is designed to eradicate deep-seated tissue infections by MW-induced deep-seated photodynamic therapy. In application, CNT-FeTHQ-TS is implanted at internal lesions, and the chip emits light under external MW irradiation. Subsequently, CNT-FeTHQ coating in the platform can respond to both MW and light simultaneously to generate ROS and MW-hyperthermia for rapid and precise sterilization at focus. Importantly, MW also improves the photodynamic performance of CNT-FeTHQ by introducing vacancies in FeTHQ to facilitate the photoexcitation process and changing the spin state of electrons to inhibit the complexation of photogenerated electron-hole pairs, which were confirmed by simulation calculations and in situ MW-irradiated photoluminescence experiments. In vivo, CNT-FeTHQ-TS can effectively cure mice with Staphylococcus aureus infection in dorsal subcutaneous tissue. This work overcomes the key clinical limitations of safe energy transmission and conversion for treating deep-seated infections.

Rhodopsin-based light-harvesting system for sustainable synthetic biology.

Rhodopsins, a diverse class of light-sensitive proteins found in various life domains, have attracted considerable interest for their potential applications in sustainable synthetic biology. These proteins exhibit remarkable photochemical properties, undergoing conformational changes upon light absorption that drive a variety of biological processes. Exploiting rhodopsin's natural properties could pave the way for creating sustainable and energy-efficient technologies. Rhodopsin-based light-harvesting systems offer innovative solutions to a few key challenges in sustainable engineering, from bioproduction to renewable energy conversion. In this opinion article, we explore the recent advancements and future possibilities of employing rhodopsins for sustainable engineering, underscoring the transformative potential of these biomolecules.

Prefrontal cortex neurons encode ambient light intensity differentially across regions and layers.

While light can affect emotional and cognitive processes of the medial prefrontal cortex (mPFC), no light-encoding was hitherto identified in this region. Here, extracellular recordings in awake mice revealed that over half of studied mPFC neurons showed photosensitivity, that was diminished by inhibition of intrinsically photosensitive retinal ganglion cells (ipRGCs), or of the upstream thalamic perihabenular nucleus (PHb). In 15% of mPFC photosensitive neurons, firing rate changed monotonically along light-intensity steps and gradients. These light-intensity-encoding neurons comprised four types, two enhancing and two suppressing their firing rate with increased light intensity. Similar types were identified in the PHb, where they exhibited shorter latency and increased sensitivity. Light suppressed prelimbic activity but boosted infralimbic activity, mirroring the regions' contrasting roles in fear-conditioning, drug-seeking, and anxiety. We posit that prefrontal photosensitivity represents a substrate of light-susceptible, mPFC-mediated functions, which could be ultimately studied as a therapeutical target in psychiatric and addiction disorders.

Improving adjustment to daylight saving time transitions with light.

Daylight saving time (DST) is currently utilized in many countries with the rationale that it enhances the alignment between daylight hours and activity peaks in the population. The act of transitioning into and out of DST introduces disruptions to the circadian rhythm, thereby impacting sleep and overall health. Despite the substantial number of individuals affected, the consequences of this circadian disruption have often been overlooked. Here, we employ a mathematical model of the human circadian pacemaker to elucidate how the biological clock interacts with daytime and evening exposures to both natural and electrical light. This interaction plays a crucial role in determining the adaptation to the 1 hour time zone shift imposed by the transition to or from DST. In global discussions about DST, there is a prevailing assumption that individuals easily adjust to DST transitions despite a few studies indicating that the human circadian system requires several days to fully adjust to a DST transition. Our study highlights that evening light exposure changes can be the main driving force for re-entrainment, with chronobiological models predicting that people with longer intrinsic period (i.e. later chronotype) entrain more slowly to transitions to or from DST as compared to people with a shorter intrinsic period (earlier chronotype). Moreover, the model forecasts large inter-individual differences in the adaptation speed, in particular during the spring transition. The predictions derived from our model offer circadian biology-based recommendations for light exposure strategies that facilitate a more rapid adaptation to DST-related transitions or travel across a single time zone. As such, our study contributes valuable insights to the ongoing discourse on DST and its implications for human circadian rhythms.

Proton-pumping photoreceptor controls expression of ABC transporter by regulating transcription factor through light.

Light is a significant factor for living organisms with photosystems, like microbial rhodopsin-a retinal protein that functions as an ion pump, channel, and sensory transduction. Gloeobacter violaceus PCC7421, has a proton-pumping rhodopsin gene, the Gloeobacter rhodopsin (GR). The helix-turn-helix family of transcriptional regulators has various motifs, and they regulate gene expression in the presence of various metal ions. Here, we report that active proton outward pumping rhodopsin interacted with the helix-turn-helix transcription regulator and regulated gene expression. This interaction is confirmed using ITC analysis (KD of 8 µM) and determined the charged residues required. During in vitro experiments using fluorescent and luciferase reporter systems, ATP-binding cassette (ABC) transporters and the self-regulation of G. violaceus transcriptional regulator (GvTcR) are regulated by light, and gene regulation is observed in G. violaceus using the real-time polymerase chain reaction. These results expand our understanding of the natural potential and limitations of microbial rhodopsin function.

A rapid aureochrome opto-switch enables diatom acclimation to dynamic light.

Diatoms often outnumber other eukaryotic algae in the oceans, especially in coastal environments characterized by frequent fluctuations in light intensity. The identities and operational mechanisms of regulatory factors governing diatom acclimation to high light stress remain largely elusive. Here, we identified the AUREO1c protein from the coastal diatom Phaeodactylum tricornutum as a crucial regulator of non-photochemical quenching (NPQ), a photoprotective mechanism that dissipates excess energy as heat. AUREO1c detects light stress using a light-oxygen-voltage (LOV) domain and directly activates the expression of target genes, including LI818 genes that encode NPQ effector proteins, via its bZIP DNA-binding domain. In comparison to a kinase-mediated pathway reported in the freshwater green alga Chlamydomonas reinhardtii, the AUREO1c pathway exhibits a faster response and enables accumulation of LI818 transcript and protein levels to comparable degrees between continuous high-light and fluctuating-light treatments. We propose that the AUREO1c-LI818 pathway contributes to the resilience of diatoms under dynamic light conditions.

In vivo photocontrol of orexin receptors with a nanomolar light-regulated analogue of orexin-B.

Orexinergic neurons are critically involved in regulating arousal, wakefulness, and appetite. Their dysfunction has been associated with sleeping disorders, and non-peptide drugs are currently being developed to treat insomnia and narcolepsy. Yet, no light-regulated agents are available to reversibly control their activity. To meet this need, a photoswitchable peptide analogue of the endogenous neuroexcitatory peptide orexin-B was designed, synthesized, and tested in vitro and in vivo. This compound - photorexin - is the first photo-reversible ligand reported for orexin receptors. It allows dynamic control of activity in vitro (including almost the same efficacy as orexin-B, high nanomolar potency, and subtype selectivity to human OX2 receptors) and in vivo in zebrafish larvae by direct application in water. Photorexin induces dose- and light-dependent changes in locomotion and a reduction in the successive induction reflex that is associated with sleep behavior. Molecular dynamics calculations indicate that trans and cis photorexin adopt similar bent conformations and that the only discriminant between their structures and activities is the positioning of the N-terminus. This, in the case of the more active trans isomer, points towards the OX2 N-terminus and extra-cellular loop 2, a region of the receptor known to be involved in ligand binding and recognition consistent with a "message-address" system. Thus, our approach could be extended to several important families of endogenous peptides, such as endothelins, nociceptin, and dynorphins among others, that bind to their cognate receptors through a similar mechanism: a "message" domain involved in receptor activation and signal transduction, and an "address" sequence for receptor occupation and improved binding affinity.

Identifying antibiotic-resistant strains via cell sorting and elastic-light-scatter phenotyping.

The proliferation and dissemination of antimicrobial-resistant bacteria is an increasingly global challenge and is attributed mainly to the excessive or improper use of antibiotics. Currently, the gold-standard phenotypic methodology for detecting resistant strains is agar plating, which is a time-consuming process that involves multiple subculturing steps. Genotypic analysis techniques are fast, but they require pure starting samples and cannot differentiate between viable and non-viable organisms. Thus, there is a need to develop a better method to identify and prevent the spread of antimicrobial resistance. This work presents a novel method for detecting and identifying antibiotic-resistant strains by combining a cell sorter for bacterial detection and an elastic-light-scattering method for bacterial classification. The cell sorter was equipped with safety mechanisms for handling pathogenic organisms and enabled precise placement of individual bacteria onto an agar plate. The patterning was performed on an antibiotic-gradient plate, where the growth of colonies in sections with high antibiotic concentrations confirmed the presence of a resistant strain. The antibiotic-gradient plate was also tested with an elastic-light-scattering device where each colony's unique colony scatter pattern was recorded and classified using machine learning for rapid identification of bacteria. Sorting and patterning bacteria on an antibiotic-gradient plate using a cell sorter reduced the number of subculturing steps and allowed direct qualitative binary detection of resistant strains. Elastic-light-scattering technology is a rapid, label-free, and non-destructive method that permits instantaneous classification of pathogenic strains based on the unique bacterial colony scatter pattern. KEY POINTS: • Individual bacteria cells are placed on gradient agar plates by a cell sorter • Laser-light scatter patterns are used to recognize antibiotic-resistant organisms • Scatter patterns formed by colonies correspond to AMR-associated phenotypes.

Pupillary Light Reflex Reveals Melanopsin System Alteration in the Background of Myopia-26, the Female Limited Form of Early-Onset High Myopia.

Purpose: The purpose of this study was to evaluate pupillary light reflex (PLR) to chromatic flashes in patients with early-onset high-myopia (eoHM) without (myopic controls = M-CTRL) and with (female-limited myopia-26 = MYP-26) genetic mutations in the ARR3 gene encoding the cone arrestin. Methods: Participants were 26 female subjects divided into 3 groups: emmetropic controls (E-CTRL, N = 12, mean age = 28.6 ± 7.8 years) and 2 myopic (M-CTRL, N = 7, mean age = 25.7 ± 11.5 years and MYP-26, N = 7, mean age = 28.3 ± 15.4 years) groups. In addition, one hemizygous carrier and one control male subject were examined. Direct PLRs were recorded after 10-minute dark adaptation. Stimuli were 1-second red (peak wavelength = 621 nm) and blue (peak wavelength = 470 nm) flashes at photopic luminance of 250 cd/m². A 2-minute interval between the flashes was introduced. Baseline pupil diameter (BPD), peak pupil constriction (PPC), and postillumination pupillary response (PIPR) were extracted from the PLR. Group comparisons were performed with ANOVAs. Results: Dark-adapted BPD was comparable among the groups, whereas PPC to the red light was slightly reduced in patients with myopia (P = 0.02). PIPR at 6 seconds elicited by the blue flash was significantly weaker (P < 0.01) in female patients with MYP-26, whereas it was normal in the M-CTRL group and the asymptomatic male carrier. Conclusions: L/M-cone abnormalities due to ARR3 gene mutation is currently claimed to underlie the pathological eye growth in MYP-26. Our results suggest that malfunction of the melanopsin system of intrinsically photosensitive retinal ganglion cells (ipRGCs) is specific to patients with symptomatic MYP-26, and may therefore play an additional role in the pathological eye growth of MYP-26.

The Collapsible Light Trap: a portable Pennsylvania Light Trap for collecting aquatic insects.

A Collapsible Light Trap (CLT) for collecting insects, particularly aquatic insects, is described here. CLT is a modified Pennsylvania Light Trap with the advantage of being collapsible and lightweight to be carried in a small backpack and very easy to set up in the field. CLT is equipped with LED light strip wrapped around a PVC tube and can be connected to a regular 12 V / 7 Ah battery, running for more than 48 uninterrupted hours. Complete CLT weighs 0.8-1.0 kg, depending on the metal used, and the battery weighs around 2 kg, being easily transportable to more remote collecting areas. Over the years, CLTs have been used for collecting and describing the diversity of aquatic insects from Brazil, particularly caddisflies. Depending on the locality, only one trap for one night can collect over a thousand insect specimens and more than 200 individuals of caddisflies.

Protocol for Generating Arabidopsis thaliana Cell Suspension Cultures Under Different Light Conditions.

Plant cell suspension cultures (PCSCs) are in vitro-cultured cells that can divide indefinitely in a sterile growth medium. These PCSCs can be derived from various plant tissues, such as the root, stem, leaves, or seeds, and are maintained in a suitable culture medium containing nutrients, vitamins, hormones, and other essential components necessary for their growth. PCSCs have extensive applications in biotechnology, particularly in producing pharmaceutical and chemical compounds. This chapter presents a protocol for generating cell lines from Arabidopsis thaliana root callus under different light conditions, which can be used to investigate the effects of light on plant cell growth and development. The protocol described in this chapter is a valuable tool for researchers interested in utilizing PCSCs in their studies.

[How to Choose the Best Optogenetic Tool for Your Research].

All-optical methods that provide deeper understanding of neural activity are currently being developed. Optogenetics is a biological technique useful to control neuronal activity or life phenomena using light. Microbial rhodopsins are light-activated membrane proteins used as optogenetic tools. Microbial rhodopsins such as channelrhodopsin2 (ChR2) consist of seven-pass transmembrane proteins with a covalently bound retinal. Light absorption is followed by photoisomerization of the all-trans retinal to a 13-cis configuration and subsequent conformational changes in the molecule, with consequent permeability of the channel structure to ions. Recent studies have reported the discovery of microbial rhodopsins with novel functions. Microbial rhodopsin diversity has also increased. We describe the characteristics of microbial rhodopsins used as optogenetic tools and the latest research in this domain.

Engineered droplet-forming peptide as photocontrollable phase modulator for fused in sarcoma protein.

The assembly and disassembly of biomolecular condensates are crucial for the subcellular compartmentalization of biomolecules in the control of cellular reactions. Recently, a correlation has been discovered between the phase transition of condensates and their maturation (aggregation) process in diseases. Therefore, modulating the phase of condensates to unravel the roles of condensation has become a matter of interest. Here, we create a peptide-based phase modulator, JSF1, which forms droplets in the dark and transforms into amyloid-like fibrils upon photoinitiation, as evidenced by their distinctive nanomechanical and dynamic properties. JSF1 is found to effectively enhance the condensation of purified fused in sarcoma (FUS) protein and, upon light exposure, induce its fibrilization. We also use JSF1 to modulate the biophysical states of FUS condensates in live cells and elucidate the relationship between FUS phase transition and FUS proteinopathy, thereby shedding light on the effect of protein phase transition on cellular function and malfunction.

Methanogenesis in the presence of oxygenic photosynthetic bacteria may contribute to global methane cycle.

Accumulating evidences are challenging the paradigm that methane in surface water primarily stems from the anaerobic transformation of organic matters. Yet, the contribution of oxygenic photosynthetic bacteria, a dominant species in surface water, to methane production remains unclear. Here we show methanogenesis triggered by the interaction between oxygenic photosynthetic bacteria and anaerobic methanogenic archaea. By introducing cyanobacterium Synechocystis PCC6803 and methanogenic archaea Methanosarcina barkeri with the redox cycling of iron, CH4 production was induced in coculture biofilms through both syntrophic methanogenesis (under anoxic conditions in darkness) and abiotic methanogenesis (under oxic conditions in illumination) during the periodic dark-light cycles. We have further demonstrated CH4 production by other model oxygenic photosynthetic bacteria from various phyla, in conjunction with different anaerobic methanogenic archaea exhibiting diverse energy conservation modes, as well as various common Fe-species. These findings have revealed an unexpected link between oxygenic photosynthesis and methanogenesis and would advance our understanding of photosynthetic bacteria's ecological role in the global CH4 cycle. Such light-driven methanogenesis may be widely present in nature.

Assessment of Dormancy Level and Germination Ability of Seeds with Physiological Dormancy.

Germination test is fundamental and commonly used technique for seed dormancy and germination studies, and proper assessment of dormancy level and germination ability of a given set of seeds is prerequisite for most of the studies. However, germination is very sensitive to imbibition conditions, and dormancy development is also sensitive to growth conditions of the mother plants. In this chapter, we describe tips for plant growth and germination test mainly for physiological and molecular genetic studies with Arabidopsis. This protocol can be applied for other plant species with relatively small seeds and for various studies to analyze the effect of light, phytohormones, and other chemicals in seed germination.

Light signaling regulates root-knot nematode infection and development via HY5-SWEET signaling.

BACKGROUND: Meloidogyne incognita is one of the most important plant-parasitic nematodes and causes tremendous losses to the agricultural economy. Light is an important living factor for plants and pathogenic organisms, and sufficient light promotes root-knot nematode infection, but the underlying mechanism is still unclear. RESULTS: Expression level and genetic analyses revealed that the photoreceptor genes PHY, CRY, and PHOT have a negative impact on nematode infection. Interestingly, ELONGATED HYPOCOTYL5 (HY5), a downstream gene involved in the regulation of light signaling, is associated with photoreceptor-mediated negative regulation of root-knot nematode resistance. ChIP and yeast one-hybrid assays supported that HY5 participates in plant-to-root-knot nematode responses by directly binding to the SWEET negative regulatory factors involved in root-knot nematode resistance. CONCLUSIONS: This study elucidates the important role of light signaling pathways in plant resistance to nematodes, providing a new perspective for RKN resistance research.

Light Sensing beyond Vision: Focusing on a Possible Role for the FICZ/AhR Complex in Skin Optotransduction.

Although our skin is not the primary visual organ in humans, it acts as a light sensor, playing a significant role in maintaining our health and overall well-being. Thanks to the presence of a complex and sophisticated optotransduction system, the skin interacts with the visible part of the electromagnetic spectrum and with ultraviolet (UV) radiation. Following a brief overview describing the main photosensitive molecules that detect specific electromagnetic radiation and their associated cell pathways, we analyze their impact on physiological functions such as melanogenesis, immune response, circadian rhythms, and mood regulation. In this paper, we focus on 6-formylindolo[3,2-b]carbazole (FICZ), a photo oxidation derivative of the essential amino acid tryptophan (Trp). This molecule is the best endogenous agonist of the Aryl hydrocarbon Receptor (AhR), an evolutionarily conserved transcription factor, traditionally recognized as a signal transducer of both exogenous and endogenous chemical signals. Increasing evidence indicates that AhR is also involved in light sensing within the skin, primarily due to its ligand FICZ, which acts as both a chromophore and a photosensitizer. The biochemical reactions triggered by their interaction impact diverse functions and convey crucial data to our body, thus adding a piece to the complex puzzle of pathways that allow us to decode and elaborate environmental stimuli.

Daily Light Onset and Plasma Membrane Tethers Regulate Mitochondria Redistribution within the Retinal Pigment Epithelium.

The retinal pigment epithelium (RPE) is an essential component of the retina that plays multiple roles required to support visual function. These include light onset- and circadian rhythm-dependent tasks, such as daily phagocytosis of photoreceptor outer segments. Mitochondria provide energy to the highly specialized and energy-dependent RPE. In this study, we examined the positioning of mitochondria and how this is influenced by the onset of light. We identified a population of mitochondria that are tethered to the basal plasma membrane pre- and post-light onset. Following light onset, mitochondria redistributed apically and interacted with melanosomes and phagosomes. In a choroideremia mouse model that has regions of the RPE with disrupted or lost infolding of the plasma membrane, the positionings of only the non-tethered mitochondria were affected. This provides evidence that the tethering of mitochondria to the plasma membrane plays an important role that is maintained under these disease conditions. Our work shows that there are subpopulations of RPE mitochondria based on their positioning after light onset. It is likely they play distinct roles in the RPE that are needed to fulfil the changing cellular demands throughout the day.

Boosted photocatalytic performance of cobalt ferrite anchored g-C3N4 nanocomposite toward various emerging environmental hazardous pollutants degradation: insights into stability and Z-scheme mechanism.

In this study, a highly efficient CoFe2O4-anchored g-C3N4 nanocomposite with Z-scheme photocatalyst was developed by facile calcination and hydrothermal technique. To evaluate the crystalline structure, sample surface morphology, elemental compositions, and charge conductivity of the as-synthesized catalysts by various characterization techniques. The high interfacial contact of CoFe2O4 nanoparticles (NPs) with g-C3N4 nanosheets reduced the optical bandgap from 2.67 to 2.5 eV, which improved the charge carrier separation and transfer. The photo-degradation of methylene blue (MB) and rhodamine B (Rh B) aqueous pollutant suspension under visible-light influence was used to investigate the photocatalytic degradation activity of the efficient CoFe2O4/g-C3N4 composite catalyst. The heterostructured spinel CoFe2O4 anchored g-C3N4 photocatalysts (PCs) with Z-scheme show better photocatalytic degradation performance for both organic dyes. Meanwhile, the efficiency of aqueous MB and Rh B degradation in 120 and 100 min under visible-light could be up to 91.1% and 73.7%, which is greater than pristine g-C3N4 and CoFe2O4 catalysts. The recycling stability test showed no significant changes in the photo-degradation activity after four repeated cycles. Thus, this work provides an efficient tactic for the construction of highly efficient magnetic PCs for the removal of hazardous pollutants in the aquatic environment.