From Blur to Brilliance: The Ascendance of Advanced Microscopy in Neuronal Cell Biology.

The intricate network of the brain's neurons and synapses poses unparalleled challenges for research, distinct from other biological studies. This is particularly true when dissecting how neurons and their functional units work at a cell biological level. While traditional microscopy has been foundational, it was unable to reveal the deeper complexities of neural interactions. However, an imaging renaissance has transformed our capabilities. Advancements in light and electron microscopy, combined with correlative imaging, now achieve unprecedented resolutions, uncovering the most nuanced neural structures. Maximizing these tools requires more than just technical proficiency. It is crucial to align research aims, allocate resources wisely, and analyze data effectively. At the heart of this evolution is interdisciplinary collaboration, where various experts come together to translate detailed imagery into significant biological insights. This review navigates the latest developments in microscopy, underscoring both the promise of and prerequisites for bending this powerful tool set to understanding neuronal cell biology.

Phosphorylated transcription factor PuHB40 mediates ROS-dependent anthocyanin biosynthesis in pear exposed to high light.

Plants are increasingly vulnerable to environmental stresses because of global warming and climate change. Stress-induced reactive oxygen species (ROS) accumulation results in plant cell damage and even cell death. Anthocyanins are important antioxidants that scavenge ROS to maintain ROS homeostasis. However, the mechanism underlying ROS-induced anthocyanin accumulation is unclear. In this study, we determined that the HD-Zip I family member transcription factor PuHB40 mediates ROS-dependent anthocyanin biosynthesis under high-light stress in pear (Pyrus ussuriensis). Specifically, PuHB40 induces the PuMYB123-like-PubHLH3 transcription factor complex for anthocyanin biosynthesis. PuHB40-mediated transcriptional activation depends on its phosphorylation level, which is regulated by protein phosphatase PP2A. Elevated ROS content maintains high PuHB40 phosphorylation levels, while also enhancing PuHB40-induced PuMYB123-like transcription by decreasing PuPP2AA2 expression, ultimately leading to increased anthocyanin biosynthesis. Our study reveals a pathway regulating ROS-induced anthocyanin biosynthesis in pear, further clarifying the mechanism underlying abiotic stress-induced anthocyanin biosynthesis, which may have implications for improving plant stress tolerance.

The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs.

Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae, whereas no orthologous relationships were found between C. caldarium Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.

Highly selective photoelectrochemical CO2 reduction by crystal phase-modulated nanocrystals without parasitic absorption.

Photoelectrochemical (PEC) carbon dioxide (CO2) reduction (CO2R) holds the potential to reduce the costs of solar fuel production by integrating CO2 utilization and light harvesting within one integrated device. However, the CO2R selectivity on the photocathode is limited by the lack of catalytic active sites and competition with the hydrogen evolution reaction. On the other hand, serious parasitic light absorption occurs on the front-side-illuminated photocathode due to the poor light transmittance of CO2R cocatalyst films, resulting in extremely low photocurrent density at the CO2R equilibrium potential. This paper describes the design and fabrication of a photocathode consisting of crystal phase-modulated Ag nanocrystal cocatalysts integrated on illumination-reaction decoupled heterojunction silicon (Si) substrate for the selective and efficient conversion of CO2. Ag nanocrystals containing unconventional hexagonal close-packed phases accelerate the charge transfer process in CO2R reaction, exhibiting excellent catalytic performance. Heterojunction Si substrate decouples light absorption from the CO2R catalyst layer, preventing the parasitic light absorption. The obtained photocathode exhibits a carbon monoxide (CO) Faradaic efficiency (FE) higher than 90% in a wide potential range, with the maximum FE reaching up to 97.4% at -0.2 V vs. reversible hydrogen electrode. At the CO2/CO equilibrium potential, a CO partial photocurrent density of -2.7 mA cm-2 with a CO FE of 96.5% is achieved in 0.1 M KHCO3 electrolyte on this photocathode, surpassing the expensive benchmark Au-based PEC CO2R system.

A high-light therapy restores the circadian clock and corrects the pathological syndrome generated in restricted-fed mice.

Time-restricted feeding (RF) is known to shift the phasing of gene expression in most primary metabolic tissues, whereas a time misalignment between the suprachiasmatic nucleus circadian clock (SCNCC) and its peripheral CCs (PCC's) is known to induce various pathophysiological conditions, including a metabolic syndrome. We now report that a unique "light therapy," involving different light intensities (TZT0-ZT12150-TZT0-ZT12700 lx, TZT0-ZT1275-TZT0-ZT12150 lx, and TZT0-ZT12350-TZT0-ZT12700 lx), realigns the RF-generated misalignment between the SCNCC and the PCC's. Using such high-light regime, we show that through shifting the SCNCC and its activity, it is possible in a RF and "night-shifted mouse model" to prevent/correct pathophysiologies (e.g., a metabolic syndrome, a loss of memory, cardiovascular abnormalities). Our data indicate that such a "high-light regime" could be used as a unique chronotherapy, for those working on night shifts or suffering from jet-lag, in order to realign their SCNCC and PCC's, thereby preventing the generation of pathophysiological conditions.

Light regulates widespread plant alternative polyadenylation through the chloroplast.

Transcription of eukaryotic protein-coding genes generates immature mRNAs that are subjected to a series of processing events, including capping, splicing, cleavage, and polyadenylation (CPA), and chemical modifications of bases. Alternative polyadenylation (APA) greatly contributes to mRNA diversity in the cell. By determining the length of the 3' untranslated region, APA generates transcripts with different regulatory elements, such as miRNA and RBP binding sites, which can influence mRNA stability, turnover, and translation. In the model plant Arabidopsis thaliana, APA is involved in the control of seed dormancy and flowering. In view of the physiological importance of APA in plants, we decided to investigate the effects of light/dark conditions and compare the underlying mechanisms to those elucidated for alternative splicing (AS). We found that light controls APA in approximately 30% of Arabidopsis genes. Similar to AS, the effect of light on APA requires functional chloroplasts, is not affected in mutants of the phytochrome and cryptochrome photoreceptor pathways, and is observed in roots only when the communication with the photosynthetic tissues is not interrupted. Furthermore, mitochondrial and TOR kinase activities are necessary for the effect of light. However, unlike AS, coupling with transcriptional elongation does not seem to be involved since light-dependent APA regulation is neither abolished in mutants of the TFIIS transcript elongation factor nor universally affected by chromatin relaxation caused by histone deacetylase inhibition. Instead, regulation seems to correlate with changes in the abundance of constitutive CPA factors, also mediated by the chloroplast.

Structures and organizations of PSI-AcpPCI supercomplexes from red tidal and coral symbiotic photosynthetic dinoflagellates.

Marine photosynthetic dinoflagellates are a group of successful phytoplankton that can form red tides in the ocean and also symbiosis with corals. These features are closely related to the photosynthetic properties of dinoflagellates. We report here three structures of photosystem I (PSI)-chlorophylls (Chls) a/c-peridinin protein complex (PSI-AcpPCI) from two species of dinoflagellates by single-particle cryoelectron microscopy. The crucial PsaA/B subunits of a red tidal dinoflagellate Amphidinium carterae are remarkably smaller and hence losing over 20 pigment-binding sites, whereas its PsaD/F/I/J/L/M/R subunits are larger and coordinate some additional pigment sites compared to other eukaryotic photosynthetic organisms, which may compensate for the smaller PsaA/B subunits. Similar modifications are observed in a coral symbiotic dinoflagellate Symbiodinium species, where two additional core proteins and fewer AcpPCIs are identified in the PSI-AcpPCI supercomplex. The antenna proteins AcpPCIs in dinoflagellates developed some loops and pigment sites as a result to accommodate the changed PSI core, therefore the structures of PSI-AcpPCI supercomplex of dinoflagellates reveal an unusual protein assembly pattern. A huge pigment network comprising Chls a and c and various carotenoids is revealed from the structural analysis, which provides the basis for our deeper understanding of the energy transfer and dissipation within the PSI-AcpPCI supercomplex, as well as the evolution of photosynthetic organisms.

Direct-write 3D printing of plasmonic nanohelicoids by circularly polarized light.

Chiral plasmonic surfaces with 3D "forests" from nanohelicoids should provide strong optical rotation due to alignment of helical axis with propagation vector of photons. However, such three-dimensional nanostructures also demand multi-step nanofabrication, which is incompatible with many substrates. Large-scale photonic patterns on polymeric and flexible substrates remain unattainable. Here, we demonstrate the substrate-tolerant direct-write printing and patterning of silver nanohelicoids with out-of-plane 3D orientation using circularly polarized light. Centimeter-scale chiral plasmonic surfaces can be produced within minutes using inexpensive medium-power lasers. The growth of nanohelicoids is driven by the symmetry-broken site-selective deposition and self-assembly of the silver nanoparticles (NPs). The ellipticity and wavelength of the incident photons control the local handedness and size of the printed nanohelicoids, which enables on-the-fly modulation of nanohelicoid chirality during direct writing and simple pathways to complex multifunctional metasurfaces. Processing simplicity, high polarization rotation, and fine spatial resolution of the light-driven printing of stand-up helicoids provide a rapid pathway to chiral plasmonic surfaces, accelerating the development of chiral photonics for health and information technologies.

Ultrafast generation of hidden phases via energy-tuned electronic photoexcitation in magnetite.

Phase transitions occurring in nonequilibrium conditions can evolve through high-energy intermediate states inaccessible via equilibrium adiabatic conditions. Because of the subtle nature of such hidden phases, their direct observation is extremely challenging and requires simultaneous visualization of matter at subpicoseconds and subpicometer scales. Here, we show that a magnetite crystal in the vicinity of its metal-to-insulator transition evolves through different hidden states when controlled via energy-tuned ultrashort laser pulses. By directly monitoring magnetite's crystal structure with ultrafast electron diffraction, we found that upon near-infrared (800 nm) excitation, the trimeron charge/orbital ordering pattern is destroyed in favor of a phase-separated state made of cubic-metallic and monoclinic-insulating regions. On the contrary, visible light (400 nm) activates a photodoping charge transfer process that further promotes the long-range order of the trimerons by stabilizing the charge density wave fluctuations, leading to the reinforcement of the monoclinic insulating phase. Our results demonstrate that magnetite's structure can evolve through completely different metastable hidden phases that can be reached long after the initial excitation has relaxed, breaking ground for a protocol to control emergent properties of matter.

Diagnostic potential of blood plasma longitudinal viscosity measured using Brillouin light scattering.

Blood plasma viscosity (PV) is an established biomarker for numerous diseases. Measurement of the shear PV using conventional rheological techniques is, however, time consuming and requires significant plasma volumes. Here, we show that Brillouin light scattering (BLS) and angle-resolved spectroscopy measurements of the longitudinal PV from microliter-sized plasma volumes can serve as a proxy for the shear PV measured using conventional viscometers. This is not trivial given the distinct frequency regime probed and the longitudinal viscosity, a combination of the shear and bulk viscosity, representing a unique material property on account of the latter. We demonstrate this for plasma from healthy persons and patients suffering from different severities of COVID-19 (CoV), which has been associated with an increased shear PV. We further show that the additional information contained in the BLS-measured effective longitudinal PV and its temperature scaling can provide unique insight into the chemical constituents and physical properties of plasma that can be of diagnostic value. In particular, we find that changes in the effective longitudinal viscosity are consistent with an increased suspension concentration in CoV patient samples at elevated temperatures that is correlated with disease severity and progression. This is supported by results from rapid BLS spatial-mapping, angle-resolved BLS measurements, changes in the elastic scattering, and anomalies in the temperature scaling of the shear viscosity. Finally, we introduce a compact BLS probe to rapidly perform measurements in plastic transport tubes. Our results open a broad avenue for PV diagnostics based on the high-frequency effective longitudinal PV and show that BLS can provide a means for its implementation.

A circadian clock output functions independently of phyB to sustain daytime PIF3 degradation.

The circadian clock is an endogenous oscillator, and its importance lies in its ability to impart rhythmicity on downstream biological processes, or outputs. Our knowledge of output regulation, however, is often limited to an understanding of transcriptional connections between the clock and outputs. For instance, the clock is linked to plant growth through the gating of photoreceptors via rhythmic transcription of the nodal growth regulators, PHYTOCHROME-INTERACTING FACTORs (PIFs), but the clock's role in PIF protein stability is less clear. Here, we identified a clock-regulated, F-box type E3 ubiquitin ligase, CLOCK-REGULATED F-BOX WITH A LONG HYPOCOTYL 1 (CFH1), that specifically interacts with and degrades PIF3 during the daytime. Additionally, genetic evidence indicates that CFH1 functions primarily in monochromatic red light, yet CFH1 confers PIF3 degradation independent of the prominent red-light photoreceptor phytochrome B (phyB). This work reveals a clock-mediated growth regulation mechanism in which circadian expression of CFH1 promotes sustained, daytime PIF3 degradation in parallel with phyB signaling.

Electroluminescent vertical tunneling junctions based on WSe2 monolayer quantum emitter arrays: Exploring tunability with electric and magnetic fields.

We experimentally demonstrate the creation of defects in monolayer WSe2 via nanopillar imprinting and helium ion irradiation. Based on the first method, we realize atomically thin vertical tunneling light-emitting diodes based on WSe2 monolayers hosting quantum emitters at deterministically specified locations. We characterize these emitters by investigating the evolution of their emission spectra in external electric and magnetic fields, as well as by inducing electroluminescence at low temperatures. We identify qualitatively different types of quantum emitters and classify them according to the dominant electron-hole recombination paths, determined by the mechanisms of intervalley mixing occurring in fundamental conduction and/or valence subbands.

Resolving the overlooked photochemical nitrophenol transformation mechanism induced by nonradical species under visible light.

Nitrophenols present on the surface of particulates are ubiquitous in the atmosphere. However, its atmospheric photochemical transformation pathway remains unknown, for which the crucial effect of visible light is largely overlooked, resulting in an incomplete understanding of the effects of nitrophenols in the atmospheric environment. This study delves into the photolysis mechanism of 4-nitrophenol (4NP), one of the most abundant atmospheric nitrophenol compounds, on the surface of photoactive particulates under visible light irradiation. Unexpectedly, the nonradical species (singlet oxygen, 1O2) was identified as a dominant factor in driving the visible photolysis of 4NP. The pathways of HONO and p-benzoquinone (C6H4O2) generation were clarified by acquiring direct evidence of C-N and O-H bond breakage in the nitro (-NO2) and hydroxyl (-OH) groups of 4NP. The further decomposition of HONO results in the generation of NO and hydroxyl radicals, which could directly contribute to atmospheric oxidizing capacity and complicate the PM2.5 composition. Significantly, the behavior of 1O2-induced visible photolysis of 4NP was universal on the surface of common particulates in the atmosphere, such as A1 dust and Fe2O3. This work advances the understanding of the photochemical transformation mechanism of particulate-phase atmospheric nitrophenols, which is indispensable in elucidating the role of nitrophenols in atmospheric chemistry.

Light-induced insulator-metal transition in Sr2IrO4 reveals the nature of the insulating ground state.

Sr2IrO4 has attracted considerable attention due to its structural and electronic similarities to La2CuO4, the parent compound of high-Tc superconducting cuprates. It was proposed as a strong spin-orbit-coupled Jeff = 1/2 Mott insulator, but the Mott nature of its insulating ground state has not been conclusively established. Here, we use ultrafast laser pulses to realize an insulator-metal transition in Sr2IrO4 and probe the resulting dynamics using time- and angle-resolved photoemission spectroscopy. We observe a gap closure and the formation of weakly renormalized electronic bands in the gap region. Comparing these observations to the expected temperature and doping evolution of Mott gaps and Hubbard bands provides clear evidence that the insulating state does not originate from Mott correlations. We instead propose a correlated band insulator picture, where antiferromagnetic correlations play a key role in the gap opening. More broadly, our results demonstrate that energy-momentum-resolved nonequilibrium dynamics can be used to clarify the nature of equilibrium states in correlated materials.

FEOpti-ACVP: identification of novel anti-coronavirus peptide sequences based on feature engineering and optimization.

Anti-coronavirus peptides (ACVPs) represent a relatively novel approach of inhibiting the adsorption and fusion of the virus with human cells. Several peptide-based inhibitors showed promise as potential therapeutic drug candidates. However, identifying such peptides in laboratory experiments is both costly and time consuming. Therefore, there is growing interest in using computational methods to predict ACVPs. Here, we describe a model for the prediction of ACVPs that is based on the combination of feature engineering (FE) optimization and deep representation learning. FEOpti-ACVP was pre-trained using two feature extraction frameworks. At the next step, several machine learning approaches were tested in to construct the final algorithm. The final version of FEOpti-ACVP outperformed existing methods used for ACVPs prediction and it has the potential to become a valuable tool in ACVP drug design. A user-friendly webserver of FEOpti-ACVP can be accessed at http://servers.aibiochem.net/soft/FEOpti-ACVP/.

The endoplasmic reticulum connects to the nucleus by constricted junctions that mature after mitosis.

Junctions between the endoplasmic reticulum (ER) and the outer membrane of the nuclear envelope (NE) physically connect both organelles. These ER-NE junctions are essential for supplying the NE with lipids and proteins synthesized in the ER. However, little is known about the structure of these ER-NE junctions. Here, we systematically study the ultrastructure of ER-NE junctions in cryo-fixed mammalian cells staged in anaphase, telophase, and interphase by correlating live cell imaging with three-dimensional electron microscopy. Our results show that ER-NE junctions in interphase cells have a pronounced hourglass shape with a constricted neck of 7-20 nm width. This morphology is significantly distinct from that of junctions within the ER network, and their morphology emerges as early as telophase. The highly constricted ER-NE junctions are seen in several mammalian cell types, but not in budding yeast. We speculate that the unique and highly constricted ER-NE junctions are regulated via novel mechanisms that contribute to ER-to-NE lipid and protein traffic in higher eukaryotes.

New approaches for low phototoxicity imaging of living cells and tissues.

Fluorescence microscopy is a powerful tool used in scientific and medical research, but it is inextricably linked to phototoxicity. Neglecting phototoxicity can lead to erroneous or inconclusive results. Recently, several reports have addressed this issue, but it is still underestimated by many researchers, even though it can lead to cell death. Phototoxicity can be reduced by appropriate microscopic techniques and carefully designed experiments. This review focuses on recent strategies to reduce phototoxicity in microscopic imaging of living cells and tissues. We describe digital image processing and new hardware solutions. We point out new modifications of microscopy methods and hope that this review will interest microscopy hardware engineers. Our aim is to underscore the challenges and potential solutions integral to the design of microscopy systems. Simultaneously, we intend to engage biologists, offering insight into the latest technological advancements in imaging that can enhance their understanding and practice.

A Light-Responsive Neural Circuit Suppresses Feeding.

Light plays an essential role in a variety of physiological processes, including vision, mood, and glucose homeostasis. However, the intricate relationship between light and an animal's feeding behavior has remained elusive. Here, we found that light exposure suppresses food intake, whereas darkness amplifies it in male mice. Interestingly, this phenomenon extends its reach to diurnal male Nile grass rats and healthy humans. We further show that lateral habenula (LHb) neurons in mice respond to light exposure, which in turn activates 5-HT neurons in the dorsal Raphe nucleus (DRN). Activation of the LHb→5-HTDRN circuit in mice blunts darkness-induced hyperphagia, while inhibition of the circuit prevents light-induced anorexia. Together, we discovered a light-responsive neural circuit that relays the environmental light signals to regulate feeding behavior in mice.

Tadpoles rely on mechanosensory stimuli for communication when visual capabilities are poor.

The ways in which animals sense the world changes throughout development. For example, young of many species have limited visual capabilities, but still make social decisions, likely based on information gathered through other sensory modalities. Poison frog tadpoles display complex social behaviors that have been suggested to rely on vision despite a century of research indicating tadpoles have poorly-developed visual systems relative to adults. Alternatively, other sensory modalities, such as the lateral line system, are functional at hatching in frogs and may guide social decisions while other sensory systems mature. Here, we examined development of the mechanosensory lateral line and visual systems in tadpoles of the mimic poison frog (Ranitomeya imitator) that use vibrational begging displays to stimulate egg feeding from their mothers. We found that tadpoles hatch with a fully developed lateral line system. While begging behavior increases with development, ablating the lateral line system inhibited begging in pre-metamorphic tadpoles, but not in metamorphic tadpoles. We also found that the increase in begging and decrease in reliance on the lateral line co-occurs with increased retinal neural activity and gene expression associated with eye development. Using the neural tracer neurobiotin, we found that axonal innervations from the eye to the brain proliferate during metamorphosis, with few retinotectal connections in recently-hatched tadpoles. We then tested visual function in a phototaxis assay and found tadpoles prefer darker environments. The strength of this preference increased with developmental stage, but eyes were not required for this behavior, possibly indicating a role for the pineal gland. Together, these data suggest that tadpoles rely on different sensory modalities for social interactions across development and that the development of sensory systems in socially complex poison frog tadpoles is similar to that of other frog species.

Structure of the antenna complex expressed during far-red light photoacclimation in Synechococcus sp. PCC 7335.

Far-red light photoacclimation, or FaRLiP, is a facultative response exhibited by some cyanobacteria that allows them to absorb and utilize lower energy light (700-800 nm) than the wavelengths typically used for oxygenic photosynthesis (400-700 nm). During this process, three essential components of the photosynthetic apparatus are altered: photosystem I, photosystem II, and the phycobilisome. In all three cases, at least some of the chromophores found in these pigment-protein complexes are replaced by chromophores that have red-shifted absorbance relative to the analogous complexes produced in visible light. Recent structural and spectroscopic studies have elucidated important features of the two photosystems when altered to absorb and utilize far-red light, but much less is understood about the modified phycobiliproteins made during FaRLiP. We used single-particle, cryo-EM to determine the molecular structure of a phycobiliprotein core complex comprising allophycocyanin variants that absorb far-red light during FaRLiP in the marine cyanobacterium Synechococcus sp. PCC 7335. The structure reveals the arrangement of the numerous red-shifted allophycocyanin variants and the probable locations of the chromophores that serve as the terminal emitters in this complex. It also suggests how energy is transferred to the photosystem II complexes produced during FaRLiP. The structure additionally allows comparisons with other previously studied allophycocyanins to gain insights into how phycocyanobilin chromophores can be tuned to absorb far-red light. These studies provide new insights into how far-red light is harvested and utilized during FaRLiP, a widespread cyanobacterial photoacclimation mechanism.