ApcE plays an important role in light-induced excitation energy dissipation in the Synechocystis PCC6803 phycobilisomes.

Phycobilisomes (PBs) play an important role in cyanobacterial photosynthesis. They capture light and transfer excitation energy to the photosynthetic reaction centres. PBs are also central to some photoprotective and photoregulatory mechanisms that help sustain photosynthesis under non-optimal conditions. Amongst the mechanisms involved in excitation energy dissipation that are activated in response to excessive illumination is a recently discovered light-induced mechanism that is intrinsic to PBs and has been the least studied. Here, we used single-molecule spectroscopy and developed robust data analysis methods to explore the role of a terminal emitter subunit, ApcE, in this intrinsic, light-induced mechanism. We isolated the PBs from WT Synechocystis PCC 6803 as well as from the ApcE-C190S mutant of this strain and compared the dynamics of their fluorescence emission. PBs isolated from the mutant (i.e., ApcE-C190S-PBs), despite not binding some of the red-shifted pigments in the complex, showed similar global emission dynamics to WT-PBs. However, a detailed analysis of dynamics in the core revealed that the ApcE-C190S-PBs are less likely than WT-PBs to enter quenched states under illumination but still fully capable of doing so. This result points to an important but not exclusive role of the ApcE pigments in the light-induced intrinsic excitation energy dissipation mechanism in PBs.

Investigation into aggregation types in a benzodithiophene-isoindigo copolymer.

The type of aggregation in conjugated polymers determines their use in electronic devices. H-type aggregates are most suitable for solar cell applications, while J-type aggregates are recommended for light-emitting diodes. In this work, we used three methods to determine the type of aggregates in a benzodithiophene-isoindigo-based (PBDTI-DT) copolymer, namely, Huang-Rhys factor evolution with temperature, Franck-Condon analysis, and relative quantum yield (QY) calculation. All three methods indicate that both aggregation types are present, and the QY calculation clearly indicates that H-aggregates are more dominant. Time-dependent density functional theory was used to identify the two absorption bands of PBDTI-DT as local π - π* and intramolecular charge-transfer transitions.

Real-Time Feedback-Driven Single-Particle Tracking: A Survey and Perspective.

Real-time feedback-driven single-particle tracking (RT-FD-SPT) is a class of techniques in the field of single-particle tracking that uses feedback control to keep a particle of interest in a detection volume. These methods provide high spatiotemporal resolution on particle dynamics and allow for concurrent spectroscopic measurements. This review article begins with a survey of existing techniques and of applications where RT-FD-SPT has played an important role. Each of the core components of RT-FD-SPT are systematically discussed in order to develop an understanding of the trade-offs that must be made in algorithm design and to create a clear picture of the important differences, advantages, and drawbacks of existing approaches. These components are feedback tracking and control, ranging from simple proportional-integral-derivative control to advanced nonlinear techniques, estimation to determine particle location from the measured data, including both online and offline algorithms, and techniques for calibrating and characterizing different RT-FD-SPT methods. Then a collection of metrics for RT-FD-SPT is introduced to help guide experimentalists in selecting a method for their particular application and to help reveal where there are gaps in the techniques that represent opportunities for further development. Finally, this review is concluded with a discussion on future perspectives in the field.

Theoretical comparison of real-time feedback-driven single-particle tracking techniques.

Real-time feedback-driven single-particle tracking is a technique that uses feedback control to enable single-molecule spectroscopy of freely diffusing particles in native or near-native environments. A number of different real-time feedback-driven single-particle tracking (RT-FD-SPT) approaches exist, and comparisons between methods based on experimental results are of limited use due to differences in samples and setups. In this study, we used statistical calculations and dynamical simulations to directly compare the performance of different methods. The methods considered were the orbital method, the knight's tour (grid scan) method, and MINFLUX, and we considered both fluorescence-based and interferometric scattering (iSCAT) approaches. There is a fundamental trade-off between precision and speed, with the knight's tour method being able to track the fastest diffusion but with low precision, and MINFLUX being the most precise but only tracking slow diffusion. To compare iSCAT and fluorescence, different biological samples were considered, including labeled and intrinsically fluorescent samples. The success of iSCAT as compared to fluorescence is strongly dependent on the particle size and the density and photophysical properties of the fluorescent particles. Using a wavelength for iSCAT that is negligibly absorbed by the tracked particle allows for an increased illumination intensity, which results in iSCAT providing better tracking for most samples. This work highlights the fundamental aspects of performance in RT-FD-SPT and should assist with the selection of an appropriate method for a particular application. The approach used can easily be extended to other RT-FD-SPT methods.

Sub-lithic photosynthesis in hot desert habitats.

In hyper-arid soil environments, photosynthetic microorganisms are largely restricted to hypolithic (sub-lithic) habitats: i.e., on the ventral surfaces of translucent pebbles in desert pavements. Here, we combined fluorometric, spectroscopic, biochemical and metagenomic approaches to investigate in situ the light transmission properties of quartz stones in the Namib Desert, and assess the photosynthetic activity of the underlying hypolithic cyanobacterial biofilms. Quartz pebbles greatly reduced the total photon flux to the ventral surface biofilms and filtered out primarily the short wavelength portion of the solar spectrum. Chlorophylls d and f were not detected in biofilm pigment extracts; however, hypolithic cyanobacterial communities showed some evidence of adaptation to sub-lithic conditions, including the prevalence of genes encoding Helical Carotenoid Proteins, which are associated with desiccation stress. Under water-saturated conditions, hypolithic communities showed no evidence of light stress, even when the quartz stones were exposed to full midday sunlight. This initial study creates a foundation for future in-situ and laboratory exploration of various adaptation mechanisms employed by photosynthetic organisms forming hypolithic microbial communities.

What to feed or what not to feed-that is still the question.

INTRODUCTION: This review addresses metabolic diversities after grain feeding of cattle using artificial total mixed ration (TMR), in place of pasture-based feeding. OBJECTIVES: To determine how grain feeding impairs the deuterium-depleting functions of the anaplerotic mitochondrial matrix during milk and meat production. METHODS: Based on published data we herein evaluate how grain-fed animals essentially follow a branched-chain amino acid and odd-chain fatty acid-based reductive carboxylation-dependent feedstock, which is also one of the mitochondrial deuterium-accumulating dysfunctions in human cancer. RESULTS: It is now evident that food-based intracellular deuterium exchange reactions, especially that of glycogenic substrate oxidation, are significant sources of deuterium-enriched (2H; D) metabolic water with a significant impact on animal and human health. The burning of high deuterium nutritional dairy products into metabolic water upon oxidation in the human body may contribute to similar metabolic conditions and diseases as described in state-of-the-art articles for cows. Grain feeding also limits oxygen delivery to mitochondria for efficient deuterium-depleted metabolic water production by glyphosate herbicide exposure used in genetically modified crops of TMR constituents. CONCLUSION: Developments in medical metabolomics, biochemistry and deutenomics, which is the science of biological deuterium fractionation and discrimination warrant urgent critical reviews in order to control the epidemiological scale of population diseases such as diabetes, obesity and cancer by a thorough understanding of how the compromised metabolic health of grain-fed dairy cows impacts human consumers.

Photoelectrochemical performance and ultrafast dynamics of photogenerated electrons and holes in highly titanium-doped hematite.

Elemental doping of hematite has been widely performed to improve its mobility, electrical conductivity as well as to suppress electron-hole recombination in photoelectrochemical applications. When hematite is doped with high titanium concentrations, above 5%, pseudobrookite layers may be formed as overlayers leading to improved photocurrent while further doping beyond 15% could lead to the formation of a titania overlayer which has an effect of suppressing photocurrent. In this study, we observed that doping hematite with titanium improves photocurrent, reaching a maximum of 1.83 mA cm-2 at a titanium concentration of 15%, the highest achieved photocurrent with spin coating method. Further titanium incorporation to 20% resulted in a decrease of the photocurrent. XRD measurements shows that a Fe2TiO5 layer formed at 15% Ti concentration which resulted in the observed increase in photocurrent while a reduction in photocurrent at 20% Ti concentration could have resulted from the formation of a TiO2 layer. Analysis of the transient absorption spectroscopy data was achieved using a four-component sequential analysis scheme in the Glotaran software. We observed major doping concentration dependent lifetimes in the τ3 and τ4 values where the 15% doped samples had the slowest recombination rates. We also observed a blueshift in the spectra with increasing doping concentration, suggesting the occurance of the Burstein-Moss effect. This work shows that doping hematite with titanium leads to structural changes of the photoanodes at Ti concentrations of over 10%, in addition to the well documented conductivity enhancement.

How reduced excitonic coupling enhances light harvesting in the main photosynthetic antennae of diatoms.

Strong excitonic interactions are a key design strategy in photosynthetic light harvesting, expanding the spectral cross-section for light absorption and creating considerably faster and more robust excitation energy transfer. These molecular excitons are a direct result of exceptionally densely packed pigments in photosynthetic proteins. The main light-harvesting complexes of diatoms, known as fucoxanthin-chlorophyll proteins (FCPs), are an exception, displaying surprisingly weak excitonic coupling between their chlorophyll (Chl) a's, despite a high pigment density. Here, we show, using single-molecule spectroscopy, that the FCP complexes of Cyclotella meneghiniana switch frequently into stable, strongly emissive states shifted 4-10 nm toward the red. A few percent of isolated FCPa complexes and ∼20% of isolated FCPb complexes, on average, were observed to populate these previously unobserved states, percentages that agree with the steady-state fluorescence spectra of FCP ensembles. Thus, the complexes use their enhanced sensitivity to static disorder to increase their light-harvesting capability in a number of ways. A disordered exciton model based on the structure of the main plant light-harvesting complex explains the red-shifted emission by strong localization of the excitation energy on a single Chl a pigment in the terminal emitter domain due to very specific pigment orientations. We suggest that the specific construction of FCP gives the complex a unique strategy to ensure that its light-harvesting function remains robust in the fluctuating protein environment despite limited excitonic interactions.

Apoprotein heterogeneity increases spectral disorder and a step-wise modification of the B850 fluorescence peak position.

It has already been established that the quaternary structure of the main light-harvesting complex (LH2) from the photosynthetic bacterium Rhodopseudomonas palustris is a nonameric 'ring' of PucAB heterodimers and under low-light culturing conditions an increased diversity of PucB synthesis occurs. In this work, single molecule fluorescence emission studies show that different classes of LH2 'rings' are present in "low-light" adapted cells and that an unknown chaperon process creates multiple sub-types of 'rings' with more conformational sub-states and configurations. This increase in spectral disorder significantly augments the cross-section for photon absorption and subsequent energy flow to the reaction centre trap when photon availability is a limiting factor. This work highlights yet another variant used by phototrophs to gather energy for cellular development.

Orthonormal vector general polynomials derived from the Cartesian gradient of the orthonormal Zernike-based polynomials.

The concept of orthonormal vector circle polynomials is revisited by deriving a set from the Cartesian gradient of Zernike polynomials in a unit circle using a matrix-based approach. The heart of this model is a closed-form matrix equation of the gradient of Zernike circle polynomials expressed as a linear combination of lower-order Zernike circle polynomials related through a gradient matrix. This is a sparse matrix whose elements are two-dimensional standard basis transverse Euclidean vectors. Using the outer product form of the Cholesky decomposition, the gradient matrix is used to calculate a new matrix, which we used to express the Cartesian gradient of the Zernike circle polynomials as a linear combination of orthonormal vector circle polynomials. Since this new matrix is singular, the orthonormal vector polynomials are recovered by reducing the matrix to its row echelon form using the Gauss-Jordan elimination method. We extend the model to derive orthonormal vector general polynomials, which are orthonormal in a general pupil by performing a similarity transformation on the gradient matrix to give its equivalent in the general pupil. The outer form of the Gram-Schmidt procedure and the Gauss-Jordan elimination method are then applied to the general pupil to generate the orthonormal vector general polynomials from the gradient of the orthonormal Zernike-based polynomials. The performance of the model is demonstrated with a simulated wavefront in a square pupil inscribed in a unit circle.

Strehl ratio and amplitude-weighted generalized orthonormal Zernike-based polynomials.

The concept of orthonormal polynomials is revisited by developing a Zernike-based orthonormal set for a non-circular pupil that is transmitting an aberrated, non-uniform field. We refer to this pupil as a general pupil. The process is achieved by using the matrix form of the Gram-Schmidt procedure on Zernike circle polynomials and is interpreted as a process of balancing each Zernike circle polynomial by adding those of lower order in the general pupil, a procedure which was previously performed using classical aberrations. We numerically demonstrate this concept by comparing the representation of phase in a square-Gaussian pupil using the Zernike-Gauss square and Zernike circle polynomials. As expected, using the Strehl ratio, we show that only specific lower-order aberrations can be used to balance specific aberrations, for example, tilt cannot be used to balance spherical aberration. In the process, we present a possible definition of the Maréchal criterion for the analysis of the tolerance of systems with apodized pupils.

Controlling Light Harvesting with Light.

When exposed to intense sunlight, all organisms performing oxygenic photosynthesis implement various photoprotective strategies to prevent potentially lethal photodamage. The rapidly responding photoprotective mechanisms, occurring in the light-harvesting pigment-protein antennae, take effect within tens of seconds, while the dramatic and potentially harmful light intensity fluctuations manifest also on shorter time scales. Here we show that, upon illumination, individual phycobilisomes from Synechocystis PCC 6803, which, in vivo under low-light conditions, harvest solar energy, and have the built-in capacity to switch rapidly and reversibly into light-activated energy-dissipating states. Simultaneously measured fluorescence intensity, lifetime, and spectra, compared with a multicompartmental kinetic model, revealed that essentially any subunit of a phycobilisome can be quenched, and that the core complexes were targeted most frequently. Our results provide the first evidence for fluorescence blinking from a biologically active system at physiological light intensities and suggest that the light-controlled switches to intrinsically available energy-dissipating states are responsible for a novel type of photoprotection in cyanobacteria. We anticipate other photosynthetic organisms to employ similar strategies to respond instantly to rapid solar light intensity fluctuations. A detailed understanding of the photophysics of photosynthetic antenna complexes is of great interest for bioinspired solar energy technologies.

Dynamic quenching in single photosystem II supercomplexes.

Photosystem II (PSII) is a huge pigment-protein supercomplex responsible for the primary steps of photosynthesis in green plants. Its light-harvesting antenna exhibits efficient transfer of the absorbed excitation energy to the reaction center and also contains a well-regulated protection mechanism against over-excitation in strong light conditions. The latter is based on conformational changes in antenna complexes that open up excitation decay channels resulting in considerable fluorescence quenching. Meanwhile, fluorescence blinking, observed in single antennas, is likely caused by a similar mechanism. Thus the question arises whether this effect is also present in and relevant to the native supramolecular organization of a fully assembled PSII. To further investigate energy transfer and quenching in single PSII, we performed single-molecule experiments on PSII supercomplexes at 5 °C. Analysis of the fluorescence intensity and mean lifetime allowed us to distinguish detached antennas and specifically analyze PSII supercomplexes. The average fluorescence lifetime in PSII of about 100-150 ps, measured under our extreme excitation conditions, is surprisingly similar to published ensemble lifetime data of photochemical quenching in PSII of a similar size. In our case, this lifetime is nevertheless caused by either one or multiple quenched antennas or by a quencher in the reaction center. The observed reversible light-induced changes in fluorescence intensity on a millisecond timescale are reminiscent of blinking subunits. Our results therefore directly illustrate how environmental control over a fluctuating antenna can regulate light-harvesting in plant photosynthesis.

Conformational switching in a light-harvesting protein as followed by single-molecule spectroscopy.

Among the ultimate goals of protein physics, the complete, experimental description of the energy paths leading to protein conformational changes remains a challenge. Single protein fluorescence spectroscopy constitutes an approach of choice for addressing protein dynamics, and, among naturally fluorescing proteins, light-harvesting (LH) proteins from purple bacteria constitute an ideal object for such a study. LHs bind bacteriochlorophyll a molecules, which confer on them a high intrinsic fluorescence yield. Moreover, the electronic properties of these pigment-proteins result from the strong excitonic coupling between their bound bacteriochlorophyll a molecules in combination with the large energetic disorder due to slow fluctuations in their structure. As a result, the position and probability of their fluorescence transition delicately depends on the precise realization of the disorder of the set of bound pigments, which is governed by the LH protein dynamics. Analysis of these parameters using time-resolved single-molecule fluorescence spectroscopy thus yields direct access to the protein dynamics. Applying this technique to the LH2 protein from Rhodovulum (Rdv.) sulfidophilum, the structure-and consequently the fluorescence properties-of which depends on pH, allowed us to follow a single protein, pH-induced, reversible, conformational transition. Hence, for the first time, to our knowledge, a protein transition can be visualized through changes in the electronic structure of the intrinsic cofactors, at a level of a single LH protein, which opens a new, to our knowledge, route for understanding the changes in energy landscape that underlie protein function and adaptation to the needs of living organisms.

The role of exciton delocalization in the major photosynthetic light-harvesting antenna of plants.

In the major peripheral plant light-harvesting complex LHCII, excitation energy is transferred between chlorophylls along an energetic cascade before it is transmitted further into the photosynthetic assembly to be converted into chemical energy. The efficiency of these energy transfer processes involves a complicated interplay of pigment-protein structural reorganization and protein dynamic disorder, and the system must stay robust within the fluctuating protein environment. The final, lowest energy site has been proposed to exist within a trimeric excitonically coupled chlorophyll (Chl) cluster, comprising Chls a610-a611-a612. We studied an LHCII monomer with a site-specific mutation resulting in the loss of Chls a611and a612, and find that this mutant exhibits two predominant overlapping fluorescence bands. From a combination of bulk measurements, single-molecule fluorescence characterization, and modeling, we propose the two fluorescence bands originate from differing conditions of exciton delocalization and localization realized in the mutant. Disruption of the excitonically coupled terminal emitter Chl trimer results in an increased sensitivity of the excited state energy landscape to the disorder induced by the protein conformations. Consequently, the mutant demonstrates a loss of energy transfer efficiency. On the contrary, in the wild-type complex, the strong resonance coupling and correspondingly high degree of excitation delocalization within the Chls a610-a611-a612 cluster dampens the influence of the environment and ensures optimal communication with neighboring pigments. These results indicate that the terminal emitter trimer is thus an essential design principle for maintaining the efficient light-harvesting function of LHCII in the presence of protein disorder.

Disentangling the low-energy states of the major light-harvesting complex of plants and their role in photoprotection.

The ability to dissipate large fractions of their absorbed light energy as heat is a vital photoprotective function of the peripheral light-harvesting pigment-protein complexes in photosystem II of plants. The major component of this process, known as qE, is characterised by the appearance of low-energy (red-shifted) absorption and fluorescence bands. Although the appearance of these red states has been established, the molecular mechanism, their site and particularly their involvement in qE are strongly debated. Here, room-temperature single-molecule fluorescence spectroscopy was used to study the red emission states of the major plant light-harvesting complex (LHCII) in different environments, in particular conditions mimicking qE. It was found that most states correspond to peak emission at around 700nm and are unrelated to energy dissipative states, though their frequency of occurrence increased under conditions that mimicked qE. Longer-wavelength emission appeared to be directly related to energy dissipative states, in particular emission beyond 770nm. The ensemble average of the red emission bands shares many properties with those obtained from previous bulk in vitro and in vivo studies. We propose the existence of at least three excitation energy dissipating mechanisms in LHCII, each of which is associated with a different spectral signature and whose contribution to qE is determined by environmental control of protein conformational disorder. Emission at 700nm is attributed to a conformational change in the Lut 2 domain, which is facilitated by the conformational change associated with the primary quenching mechanism involving Lut 1.

Singlet-triplet annihilation in single LHCII complexes.

In light harvesting complex II (LHCII) of higher plants and green algae, carotenoids (Cars) have an important function to quench chlorophyll (Chl) triplet states and therefore avoid the production of harmful singlet oxygen. The resulting Car triplet states lead to a non-linear self-quenching mechanism called singlet-triplet (S-T) annihilation that strongly depends on the excitation density. In this work we investigated the fluorescence decay kinetics of single immobilized LHCIIs at room temperature and found a two-exponential decay with a slow (3.5 ns) and a fast (35 ps) component. The relative amplitude fraction of the fast component increases with increasing excitation intensity, and the resulting decrease in the fluorescence quantum yield suggests annihilation effects. Modulation of the excitation pattern by means of an acousto-optic modulator (AOM) furthermore allowed us to resolve the time-dependent accumulation and decay rate (∼7 µs) of the quenching species. Inspired by singlet-singlet (S-S) annihilation studies, we developed a stochastic model and then successfully applied it to describe and explain all the experimentally observed steady-state and time-dependent kinetics. That allowed us to distinctively identify the quenching mechanism as S-T annihilation. Quantitative fitting resulted in a conclusive set of parameters validating our interpretation of the experimental results. The obtained stochastic model can be generalized to describe S-T annihilation in small molecular aggregates where the equilibration time of excitations is much faster than the annihilation-free singlet excited state lifetime.

Conformational switching explains the intrinsic multifunctionality of plant light-harvesting complexes.

The light-harvesting complexes of photosystem I and II (Lhcas and Lhcbs) of plants display a high structural homology and similar pigment content and organization. Yet, the spectroscopic properties of these complexes, and accordingly their functionality, differ substantially. This difference is primarily due to the charge-transfer (CT) character of a chlorophyll dimer in all Lhcas, which mixes with the excitonic states of these complexes, whereas this CT character is generally absent in Lhcbs. By means of single-molecule spectroscopy near room temperature, we demonstrate that the presence or absence of such a CT state in Lhcas and Lhcbs can occasionally be reversed; i.e., these complexes are able to interconvert conformationally to quasi-stable spectral states that resemble the Lhcs of the other photosystem. The high structural similarity of all the Lhca and Lhcb proteins suggests that the stable conformational states that give rise to the mixed CT-excitonic state are similar for all these proteins, and similarly for the conformations that involve no CT state. This indicates that the specific functions related to Lhca and Lhcb complexes are realized by different stable conformations of a single generic protein structure. We propose that this functionality is modulated and controlled by the protein environment.

Energetic Landscape and Terminal Emitters of Phycobilisome Cores from Quantum Chemical Modeling.

Phycobilisomes (PBs) are giant antenna supercomplexes of cyanobacteria that use phycobilin pigments to capture sunlight and transfer the collected energy to membrane-bound photosystems. In the PB core, phycobilins are bound to particular allophycocyanin (APC) proteins. Some phycobilins are thought to be terminal emitters (TEs) with red-shifted fluorescence. However, the precise identification of TEs is still under debate. In this work, we employ multiscale quantum-mechanical calculations to disentangle the excitation energy landscape of PB cores. Using the recent atomistic PB structures from Synechoccoccus PCC 7002 and Synechocystis PCC 6803, we compute the spectral properties of different APC trimers and assign the low-energy pigments. We show that the excitation energy of APC phycobilins is determined by geometric and electrostatic factors and is tuned by the specific protein-protein interactions within the core. Our findings challenge the simple picture of a few red-shifted bilins in the PB core and instead suggest that the red-shifts are established by the entire TE-containing APC trimers. Our work provides a theoretical microscopic basis for the interpretation of energy migration and time-resolved spectroscopy in phycobilisomes.