Studying RAS Interactions in Live Cells with BRET.

Bioluminescence resonance energy transfer (BRET) is a valuable technique for studying protein-protein interactions (PPIs) within live cells (Pfleger and Eidne, Nat Methods 3:165-174, 2006). Among the various BRET methodologies, a recent addition called NanoBRET has emerged, leveraging advancements in donor and acceptor technologies (Machleidt and Woodroofe, ACS Chem Biol 10:1797-1804, 2015). In this study, we present a developed methodology designed to measure PPIs involving the RAS protein family and their effectors and interactors at the plasma membrane. By utilizing the NanoLuc and HaloTag BRET pair, we provide evidence of a saturable interaction between KRAS4b-G12D and full-length RAF1. Conversely, the RAF1 R89L mutant, known to impede RAF1 binding to active RAS, exhibits nonspecific interactions. The assay exhibits remarkable signal-to-background ratios and is highly suitable for investigating the interactions of RAS with effectors, as well as for high-throughput screening assays.

Can species guilds act as hubs for energy transfer in macrophyte meadows of Amazonian floodplain lakes?

Aquatic macrophytes are the main autochthonous component of primary production in the Amazon Basin. Floating meadows of these plants support habitats with highly diverse animal communities. Fishes inhabiting these habitats have been assumed to use a broad range of food items and compose a particular food web. We employed carbon (δ13C) and nitrogen (δ15N) stable isotope analysis to draw the trophic structure of these habitats and to trace the energy flow by its trophic levels. Fishes and other animals from 18 independent macrophyte meadows of a floodplain lake of the Solimões River (Amazonia, Brazil) were analyzed. The food web of macrophyte meadows consists of four trophic levels above autotrophic sources. In general, primary consumers exhibited a broader range of food sources than the upper trophic levels. Some fish species depended on a large number of food sources and at the same time are consumed by several predators. The energy transfer from one trophic level to the next was then mainly accomplished by these species concentrating a high-energy flux and acting as hubs in the food web. The broad range of δ13C values observed indicates that the organisms living in the macrophyte meadows utilize a great diversity of autotrophic sources.

Construction of an autofluorescence interference-free phosphorescence biosensor for the specific detection of TK1 mRNA.

The anti-interference ability of biosensors is critical for detection in biological samples. Fluorescence-based sensors are subject to interference from self-luminescent substances in biological matrices. Therefore, phosphorescent sensors stand out among biosensors due to their lack of self-luminescence background. In this study, a phosphorescent sensor was constructed, which can accurately detect thymidine kinase 1 (TK1) mRNA in biological samples and avoid autofluorescence interference. When there is no target, polydopamine (PDA) is used as the phosphorescence resonance energy transfer (PRET) acceptor to quench the phosphorescence of the persistently luminescent (PL) nanomaterial. When there is a target, the DNA modified by the PL nanomaterial is replaced by the hairpin H and removed away from the PDA, resulting in a rebound in phosphorescence. The phosphorescent sensor exhibits a good linear relationship in the TK1 mRNA concentration range of 0-200 nM, and the detection limit was 1.74 nM. The sensor fabricated in this study can effectively avoid interference from spontaneous fluorescence in complex biological samples, and sensitively and precisely detect TK1 mRNA in serum samples, providing a powerful tool to more accurately detect biomarkers in biological samples.

Energy Transfer-Based Recognition of Membrane Cholesterol by Controlling Intradistance of Linker.

Gold nanoparticles (AuNPs) are good candidates for donor material in energy transfer systems and can easily be functionalized with various ligands on the surface with Au-S bonding. Cyclodextrin (CD) forms inclusion complexes with fluorophores due to its unique structure for host-guest interaction. In this study, we fabricated ßCD-functionalized AuNPs using different lengths of thiol ligands and recognized cholesterol to confirm the energy-transfer-based turn-on fluorescence mechanism. AuNP-ßCD conjugated with various thiol ligands and quenched the fluorescein (Fl) dye, forming ßCD-Fl inclusion complexes. As the distance between AuNPs and ßCD decreased, the quenching efficiency became higher. The quenched fluorescence was recovered when the cholesterol replaced the Fl because of the stronger binding affinity of the cholesterol with ßCD. The efficiency of cholesterol recognition was also affected by the energy transfer effect because the shorter ßCD ligand had a higher fluorescence recovery. Furthermore, we fabricated a liposome with cholesterol embedded in the lipid bilayer membrane to mimic the cholesterol coexisting with lipids in human serum. These cellular cholesterols accelerated the replacement of the Fl molecules, resulting in a fluorescence recovery higher than that of pure lipid. These discoveries are expected to give guidance towards cholesterol sensors or energy-transfer-based biosensors using AuNPs.

High-Resolution Frequency-Domain Spectroscopic and Modeling Studies of Photosystem I (PSI), PSI Mutants and PSI Supercomplexes.

Photosystem I (PSI) is one of the two main pigment-protein complexes where the primary steps of oxygenic photosynthesis take place. This review describes low-temperature frequency-domain experiments (absorption, emission, circular dichroism, resonant and non-resonant hole-burned spectra) and modeling efforts reported for PSI in recent years. In particular, we focus on the spectral hole-burning studies, which are not as common in photosynthesis research as the time-domain spectroscopies. Experimental and modeling data obtained for trimeric cyanobacterial Photosystem I (PSI3), PSI3 mutants, and PSI3-IsiA18 supercomplexes are analyzed to provide a more comprehensive understanding of their excitonic structure and excitation energy transfer (EET) processes. Detailed information on the excitonic structure of photosynthetic complexes is essential to determine the structure-function relationship. We will focus on the so-called "red antenna states" of cyanobacterial PSI, as these states play an important role in photochemical processes and EET pathways. The high-resolution data and modeling studies presented here provide additional information on the energetics of the lowest energy states and their chlorophyll (Chl) compositions, as well as the EET pathways and how they are altered by mutations. We present evidence that the low-energy traps observed in PSI are excitonically coupled states with significant charge-transfer (CT) character. The analysis presented for various optical spectra of PSI3 and PSI3-IsiA18 supercomplexes allowed us to make inferences about EET from the IsiA18 ring to the PSI3 core and demonstrate that the number of entry points varies between sample preparations studied by different groups. In our most recent samples, there most likely are three entry points for EET from the IsiA18 ring per the PSI core monomer, with two of these entry points likely being located next to each other. Therefore, there are nine entry points from the IsiA18 ring to the PSI3 trimer. We anticipate that the data discussed below will stimulate further research in this area, providing even more insight into the structure-based models of these important cyanobacterial photosystems.

Energy Transfer and Radical-Pair Dynamics in Photosystem I with Different Red Chlorophyll a Pigments.

We establish a general kinetic scheme for the energy transfer and radical-pair dynamics in photosystem I (PSI) of Chlamydomonas reinhardtii, Synechocystis PCC6803, Thermosynechococcus elongatus and Spirulina platensis grown under white-light conditions. With the help of simultaneous target analysis of transient-absorption data sets measured with two selective excitations, we resolved the spectral and kinetic properties of the different species present in PSI. WL-PSI can be described as a Bulk Chl a in equilibrium with a higher-energy Chl a, one or two Red Chl a and a reaction-center compartment (WL-RC). Three radical pairs (RPs) have been resolved with very similar properties in the four model organisms. The charge separation is virtually irreversible with a rate of ≈900 ns-1. The second rate, of RP1 → RP2, ranges from 70-90 ns-1 and the third rate, of RP2 → RP3, is ≈30 ns-1. Since RP1 and the Red Chl a are simultaneously present, resolving the RP1 properties is challenging. In Chlamydomonas reinhardtii, the excited WL-RC and Bulk Chl a compartments equilibrate with a lifetime of ≈0.28 ps, whereas the Red and the Bulk Chl a compartments equilibrate with a lifetime of ≈2.65 ps. We present a description of the thermodynamic properties of the model organisms at room temperature.

Efficient photochemical conversion of naproxen by butanedione: Role of energy transfer.

Photochemical active species generated from photosensitizers, e.g., dissolved organic matter (DOM), play vital roles in the transformation of micropollutants in water. Here, butanedione (BD), a redox-active moiety in DOM and widely found in nature, was employed to photo-transform naproxen (NPX) with peracetic acid (PAA) and H2O2 as contrasts. The results obtained showed that the BD exhibited more applicable on NPX degradation. It works in the lake or river water under UV and solar irradiation, and its NPX degradation efficiency was 10-30 times faster than that of PAA and H2O2. The reason for the efficient transformation of pollutants is that the BD system was proved to be a non-free radical dominated mechanism. The quantum yield of BD (Ф254 nm) was calculated to be 0.064, which indicates that photophysical process is the dominant mode of BD conversion. By adding trapping agents, direct energy transfer from 3BD* to NPX (in anoxic environment) or dissolved oxygen (in aerobic environment) was proved to play a major role (> 91 %). Additionally, the BD process reduces the toxicity of NPX and promotes microbial growth after irradiation. Overall, this study significantly deepened the understanding of the transformation between BD and micropollutants, and provided a potential BD-based process for micropollutants removal under solar irradiation.

Synthesis and study of optical properties of a Gd3+-doped NaYF4 phosphor for phototherapy lamp application.

In recent trends, radiation falls under the narrowband ultraviolet-B region (305-315 nm) widely used in phototherapy lamp applications in the treatment of skin diseases. In this paper, we report a Gd3+-doped NaYF4 luminescent material synthesized for the first time using the low-temperature co-precipitation method. It crystallized into a face-centred cubic structure, as confirmed by X-ray diffraction characterization techniques and Rietveld refinement. The photoluminescence property of the as-prepared sample shows a highly intense, sharp emission band obtained at 311 nm, which belongs to the narrowband ultraviolet-B region and corresponds to the transition of the 6P7/2→8S7/2 level of the Gd3+ ions under 272 nm excitation (8S7/2 to 6IJ). The transitions of the Gd3+ ions are detected entirely with different concentrations of Gd3+ ions. Scanning electron microscopy analysis indicated that the average particle was 288 nm. The critical distance for energy transfer was calculated to be equal to 11.5017 Å. Dipole-dipole interaction is responsible for energy transfer, as analyzed by Dexter theory. These excellent optical characteristics, together with their highly efficient and low-cost synthesis approach, indicate that synthesized NaYF4:Gd3+ phosphors have excessive potential for phototherapeutic lamp applications.

Bioluminescence Resonance Energy Transfer (BRET)-based Assay for Measuring Interactions of CRAF with 14-3-3 Proteins in Live Cells.

CRAF is a primary effector of RAS GTPases and plays a critical role in the tumorigenesis of several KRAS-driven cancers. In addition, CRAF is a hotspot for germline mutations, which are shown to cause the developmental RASopathy, Noonan syndrome. All RAF kinases contain multiple phosphorylation-dependent binding sites for 14-3-3 regulatory proteins. The differential binding of 14-3-3 to these sites plays essential roles in the formation of active RAF dimers at the plasma membrane under signaling conditions and in maintaining RAF autoinhibition under quiescent conditions. Understanding how these interactions are regulated and how they can be modulated is critical for identifying new therapeutic approaches that target RAF function. Here, I describe a bioluminescence resonance energy transfer (BRET)-based assay for measuring the interactions of CRAF with 14-3-3 proteins in live cells. Specifically, this assay measures the interactions of CRAF fused to a Nano luciferase donor and 14-3-3 fused to a Halo tag acceptor, where the interaction of RAF and 14-3-3 results in donor-to-acceptor energy transfer and the generation of the BRET signal. The protocol further shows that this signal can be disrupted by mutations shown to prevent 14-3-3 binding to each of its high-affinity RAF docking sites. This protocol describes the procedures for seeding, transfecting, and replating the cells, along with detailed instructions for reading BRET emissions, performing data analysis, and confirming protein expression levels. In addition, example assay results, along with optimization and troubleshooting steps, are provided.

Human and Small Animal Detection Using Multiple Millimeter-Wave Radars and Data Fusion: Enabling Safe Applications.

Millimeter-wave (mmWave) radars attain high resolution without compromising privacy while being unaffected by environmental factors such as rain, dust, and fog. This study explores the challenges of using mmWave radars for the simultaneous detection of people and small animals, a critical concern in applications like indoor wireless energy transfer systems. This work proposes innovative methodologies for enhancing detection accuracy and overcoming the inherent difficulties posed by differences in target size and volume. In particular, we explore two distinct positioning scenarios that involve up to four mmWave radars in an indoor environment to detect and track both humans and small animals. We compare the outcomes achieved through the implementation of three distinct data-fusion methods. It was shown that using a single radar without the application of a tracking algorithm resulted in a sensitivity of 46.1%. However, this sensitivity significantly increased to 97.10% upon utilizing four radars using with the optimal fusion method and tracking. This improvement highlights the effectiveness of employing multiple radars together with data fusion techniques, significantly enhancing sensitivity and reliability in target detection.

Single-Nucleobase-Resolved Nanoruler Determines the Surface Energy Transfer Radius on the Living Cell Membrane.

Investigations about surface energy transfer radius (r0) are limited to the aqueous solution system, and it is quite limited on experimental values of r0 between dyes and the corresponding gold particle (AuNP) sizes, especially for living cell systems. Hence, the selection of suitable AuNP-dye pairs is restricted when designing nanometal surface energy transfer (NSET) strategies in analytical sciences. Here, we developed a single-nucleobase-resolved NSET strategy to in situ measure the r0 value between a specific dye and different-sized AuNPs on the living cell membrane. Using the aptamer-dye complex (XQ-2d-nTA-FAM) and antiCD71 antibody-coupled AuNP conjugate (Au@antiCD71) as two working elements to bind two different sites on CD71 receptors on living cell membranes, we modified the nTA spacer between FAM and the terminal of aptamer to change the distance (r) from FAM to AuNP center and further adjusted the quenching efficiency (Φ) between them. Different r0 values of various AuNP-FAM pairs in living cells are determined by this in situ detection strategy. Based on this single-nucleobase-resolved NSET strategy, we established a simple and efficient universal method for measuring r0 in the living cell system, which greatly expanded the selection range of AuNP-dye pairs during the construction of the NSET model at the nanoscale.

Efficient two-step excitation energy transfer in artificial light-harvesting antenna based on bacteriochlorophyll aggregates.

Chlorosomes of green photosynthetic bacteria are large light-harvesting complexes enabling these organisms to survive at extremely low-light conditions. Bacteriochlorophylls found in chlorosomes self-organize and are ideal candidates for use in biomimetic light-harvesting in artificial photosynthesis and other applications for solar energy utilization. Here we report on the construction and characterization of an artificial antenna consisting of bacteriochlorophyll c co-aggregated with ß-carotene, which is used to extend the light-harvesting spectral range, and bacteriochlorophyll a, which acts as a final acceptor for excitation energy. Efficient energy transfer between all three components was observed by means of fluorescence spectroscopy. The efficiency varies with the ß-carotene content, which increases the average distance between the donor and acceptor in both energy transfer steps. The efficiency ranges from 89 to 37% for the transfer from ß-carotene to bacteriochlorophyll c, and from 93 to 69% for the bacteriochlorophyll c to bacteriochlorophyll a step. A significant part of this study was dedicated to a development of methods for determination of energy transfer efficiency. These methods may be applied also for study of chlorosomes and other pigment complexes.

Photo-induced processes in photosynthesis-from femtoseconds to seconds.

Photosynthesis nourishes nearly all life on Earth. Therefore, a deeper understanding of the processes by which sunlight is converted into stored chemical energy presents an important and continuing challenge for fundamental scientific research. This Special Issue is dedicated to academician Vladimir A. Shuvalov (1943-2022). We are delighted to present 15 manuscripts in the Special Issue, including two review articles and 13 research papers. These papers are contributed by 67 authors from 8 countries, including China (9), Germany (8), Hungary (4), Italy (6), Japan (2), Russia (24), Taiwan (9), and USA (5). This Special Issue provides some of the recent updates on the dynamical aspects of the initial steps of photosynthesis, including excitation energy transfer, electron transport, and dissipation of energy across time domains from femtoseconds to seconds. We hope that the readers will benefit from the work presented in this Special Issue in honor of Prof. Shuvalov in many ways. We hope that the Special Issue will provide a valued resource to stimulate research efforts, initiate potential collaboration, and promote new directions in the photosynthesis community.

Site-Directed Mutagenesis of the Chlorophyll-Binding Sites Modulates Excited-State Lifetime and Chlorophyll-Xanthophyll Energy Transfer in the Monomeric Light-Harvesting Complex CP29.

We combine site-directed mutagenesis with picosecond time-resolved fluorescence and femtosecond transient absorption (TA) spectroscopies to identify excitation energy transfer (EET) processes between chlorophylls (Chls) and xanthophylls (Xant) in the minor antenna complex CP29 assembled inside nanodiscs, which result in quenching. When compared to WT CP29, a longer lifetime was observed in the A2 mutant, missing Chl a612, which closely interacts with Xant Lutein in site L1. Conversely, a shorter lifetime was obtained in the A5 mutant, in which the interaction between Chl a603 and Chl a609 is strengthened, shifting absorption to lower energy and enhancing Chl-Xant EET. Global analysis of TA data indicated that EET from Chl a Qy to a Car dark state S* is active in both the A2 and A5 mutants and that their rate constants are modulated by mutations. Our study provides experimental evidence that multiple Chl-Xant interactions are involved in the quenching activity of CP29.

Dual "on-off" signal conversion strategy based on surface plasmon coupling and resonance energy transfer for visual electrochemiluminescence ratiometric analysis of MiRNA-141.

An electrochemiluminescence (ECL) biosensor with a pair of new ECL emitters and a novel sensing mechanism was designed for the high-sensitivity detection of microRNA-141 (miRNA-141). Sulfur-doped boron nitrogen quantum dots (S-BN QDs) were initially employed to modify the cathode of the bipolar electrode (BPE), while the anode reservoir was [Ir(dfppy)2(bpy)]PF6/TPrA system. The next step involved attaching H1-bound ultra-small WO3-x nanodots (WO3-x NDs) to the S-BN QDs-modified BPE cathode via DNA hybridization. A strong surface plasmon coupling (SPC) effect was observed between S-BN QDs and WO3-x NDs, which allowed for the enhancement of the red and visible ECL emission from S-BN QDs. After target-induced cyclic amplification to produce abundant Zn2+ and Au NPs-DNA3-Au NPs (Au NPs-S3-Au NPs), Zn2+ could cleave DNA at a nucleotide sequence-specific recognition site to release the WO3-x NDs, resulting in the first diminution of cathode ECL signal and the first enhancement of anode ECL signal. Moreover, the ECL signal at cathode decreased for the second time and the emission of [Ir(dfppy)2(bpy)]PF6 was continuously enhanced after the introduction of Au nanoparticles-S3-Au nanoparticles on the cathode surface. Our sensing mode with a dual "on-off" signal conversion strategy shows a good detection capability for miRNAs ranging from 10-17 to 10-10 M, with a limit of detection (LOD) as low as 10-17 M, which has great application potential in biomedical research and clinical diagnosis.

MOF-mediated dual energy transfer nanoprobe integrated with exonuclease III amplification strategy for highly sensitive detection of DNA.

Accurate quantitative detection of DNA is an advanced strategy in various fields (such as disease diagnosis and environmental monitoring), but the classical DNA detection method usually suffers from low sensitivity, expensive thermal cyclers, or strict annealing conditions. Herein, a MOF-ERA platform for ultrasensitive HBV-DNA detection is constructed by integrating metal-organic framework (MOF)-mediated double energy transfer nanoprobe with exonuclease III (Exo III)-assisted target recycling amplification. The proposed double energy transfer containing a donor and two receptors is simply composed of MOFs (UiO-66-NH2, a well-studied MOF) modified with a signal probe formed by the hybridization of carboxyuorescein (FAM)-labeled DNA (FDNA) and black hole quencher (BHQ1)-terminated DNA (QDNA), resulting in low fluorescence signal. After the addition of HBV-DNA, Exo III degradation to FDNA is activated, leading to the liberation of the numerous FAM molecules, followed by the generation of a significant fluorescence signal owing to the negligible binding of MOFs with free FAM molecules. The results certify that the MOF-ERA platform can be successfully used to assay HBV-DNA in the range of 1.0-25.0 nM with a detection limit of 97.2 pM, which is lower than that without BHQ1 or Exo III. The proposed method with the superiorities of low background signal and high selectivity holds promise for early disease diagnosis and clinical biomedicine applications.

A novel n-UV convertible colour-tunable emitting oxynitride phosphor: Realization based on Ce3+ -Tb3+ energy transfer.

In the present work, a novel n-UV convertible colour-tunable emitting phosphor was obtained based on the efficient Ce3+ -Tb3+ energy transfer in the Y10 Al2 Si3 O18 N4 host. By properly controlling the ratio of Ce3+ /Tb3+ , the colour hue of the obtained powder covered the blue and green regions, under excitation of 365 nm. The steady-state and dynamic-state luminescence measurement was performed to shed light on the related mechanism, which was justified by the electronic dipole-quadrupole dominating the related energy transfer process. Preliminary studies showed that Y10 Al2 Si3 O18 N4 :Ce3+ ,Tb3+ can be promising as an inorganic phosphor for white LED applications.

Inter-subunit energy transfer processes in a minimal plant photosystem II supercomplex.

Photosystem II (PSII) is an integral part of the photosynthesis machinery, in which several light-harvesting complexes rely on inter-complex excitonic energy transfer (EET) processes to channel energy to the reaction center. In this paper, we report on a direct observation of the inter-complex EET in a minimal PSII supercomplex from plants, containing the trimeric light-harvesting complex II (LHCII), the monomeric light-harvesting complex CP26, and the monomeric PSII core complex. Using two-dimensional (2D) electronic spectroscopy, we measure an inter-complex EET timescale of 50 picoseconds for excitations from the LHCII-CP26 peripheral antenna to the PSII core. The 2D electronic spectra also reveal that the transfer timescale is nearly constant over the pump spectrum of 600 to 700 nanometers. Structure-based calculations reveal the contribution of each antenna complex to the measured inter-complex EET time. These results provide a step in elucidating the full inter-complex energy transfer network of the PSII machinery.

Synthesis of silica-encapsulated tetraphenylethylene with aggregation-induced electrochemiluminescence resonance energy transfer for sensitively sensing microcystin-LR.

The reported organic electrochemiluminescence (ECL) luminophors for the detection of various markers often suffer from intermolecular π-π stacking-induced luminophore quenching. Herein, we demonstrate one-pot synthesis of a new aggregation-induced electrochemiluminescence (AIECL) emitter (i.e., TPE@SiO2/rGO composite) for sensitive measurement of microcystin-leucine arginine (MC-LR). The TPE@SiO2/rGO composite is constructed by embedding the silica-encapsuled 1,1,2,2-tetra(4-carboxylphenyl)ethylene (TPE) in the reduced graphene oxide. In comparison with the monomer TPE, this composite exhibit high luminescence efficiency and strong ECL emission, because the AIECL phenomenon triggered by the spatial confinement effect in the SiO2 cage induces the restriction of the internal motion and vibration of molecules. Notably, this composite has distinct advantages of easy preparation, simple functionalization, and stable luminescence. Especially, the TPE@SiO2/rGO-based ECL-RET system exhibits a high quenching efficiency (ΦET) of 69.7%. When target MC-LR is present, it triggers DNA strand displacement reaction (SDR), inducing the quenching of the ECL signal of TPE@SiO2/rGO composite due to ECL resonance energy transfer between TPE@SiO2/rGO composite and methylene blue (MB). The proposed biosensor enables highly sensitive, low-cost, and robust measurement of MC-LR with a large dynamic range of 7 orders of magnitude and a detection limit of 3.78 fg/mL, and it displays excellent detection performance in complex biological matrices, holding potential applications in food safety and water monitoring.

Measuring sub-nanometer undulations at microsecond temporal resolution with metal- and graphene-induced energy transfer spectroscopy.

Out-of-plane fluctuations, also known as stochastic displacements, of biological membranes play a crucial role in regulating many essential life processes within cells and organelles. Despite the availability of various methods for quantifying membrane dynamics, accurately quantifying complex membrane systems with rapid and tiny fluctuations, such as mitochondria, remains a challenge. In this work, we present a methodology that combines metal/graphene-induced energy transfer (MIET/GIET) with fluorescence correlation spectroscopy (FCS) to quantify out-of-plane fluctuations of membranes with simultaneous spatiotemporal resolution of approximately one nanometer and one microsecond. To validate the technique and spatiotemporal resolution, we measure bending undulations of model membranes. Furthermore, we demonstrate the versatility and applicability of MIET/GIET-FCS for studying diverse membrane systems, including the widely studied fluctuating membrane system of human red blood cells, as well as two unexplored membrane systems with tiny fluctuations, a pore-spanning membrane, and mitochondrial inner/outer membranes.