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At least 127 records · Page 7

Inference of photosynthetic capacity parameters from chlorophyll a fluorescence is affected by redox state of PSII reaction centers

Solar-induced chlorophyll fluorescence (SIF) has been used to infer photosynthetic capacity parameters (e.g., the maximum carboxylation rate V cmax , and the maximum electron transport rate J max ). However, the precise mechanism and practical utility of such approach under dynamic environments remain unclear. In this study, we used the balance between the light and carbon reactions to derive theoretical equations relating chlorophyll a fluorescence (ChlF) emission and photosynthetic capacity parameters, and formulated testable hypotheses regarding the dynamic relationships between the true total ChlF emitted from PSII (SIF PSII ) and V cmax and J max . We employed concurrent measurements of gas exchanges and ChlF parameters for 15 species from six biomes to test the formulated hypotheses across species, temperatures, and limitation state of carboxylation. Our results revealed that SIF PSII alone is incapable of informing the variations in V cmax and J max across species, even when SIF PSII is determined under the same environmental conditions. In contrast, the product of SIF PSII and the fraction of open PSII reactions q L , which indicates the redox state of PSII, is a strong predictor of both V cmax and J max , although their precise relationships vary somewhat with environmental conditions. Our findings suggest the redox state of PSII strongly influences the relationship between SIF PSII and V cmax and J max .

59 BASIC BIOLOGICAL SCIENCES↗

Foliar elemental distribution in Blepharidium guatemalense assessed by synchrotron X-ray fluorescence spectroscopy and colorimetric optical microscopy

The hyperaccumulation phenomenon holds significant potential for Ni agromining in ultramafic areas; however, data on tropical hyperaccumulator species, particularly regarding metal distribution and tolerance mechanisms, remain scarce. Here, this study characterized the foliar elemental distribution of Blepharidium guatemalense, analyzed its metal localization at both tissue and cellular levels, and quantified its Ni accumulation when grown in Brazilian ultramafic soil. Plants were grown in pots for 90 days, and Ni concentrations in the aerial biomass and bio-ore were determined. Synchrotron-based micro-X-ray fluorescence (S-µXRF) was used to assess metal distribution in tissues, supplemented by microscopic examination with dimethylglyoxime (DMG) to visualize Ni accumulation in specific cell types. B. guatemalense reached 19,000 mg kg −1 Ni in leaves. Processing leaf biomass produced ash containing 24 wt% Ni, indicating promising metal-recovery potential for the species. S-µXRF revealed that Ni was predominantly localized in the central and secondary veins of the leaves, suggesting efficient vascular transport. Microscopic analysis using the colorimetric reagent DMG further showed that Ni accumulation occurs near the epidermis and phloem, suggesting that B. guatemalense employs specific physiological mechanisms for Ni translocation, potentially supporting both defense and growth functions. These results establish B. guatemalense as a promising candidate for large-scale Ni agromining in tropical regions.

36 MATERIALS SCIENCE↗

Open-source electrochemical cell for in situ X-ray absorption spectroscopy in transmission and fluorescence modes

X-ray spectroscopy is a valuable technique for the study of many materials systems. Characterizing reactions in situ and operando can reveal complex reaction kinetics, which is crucial to understanding active site composition and reaction mechanisms. In this project, the design, fabrication and testing of an open-source and easy-to-fabricate electrochemical cell for in situ electrochemistry compatible with X-ray absorption spectroscopy in both transmission and fluorescence modes are accomplished via windows with large opening angles on both the upstream and downstream sides of the cell. Using a hobbyist computer numerical control machine and free 3D CAD software, anyone can make a reliable electrochemical cell using this design. Onion-like carbon nanoparticles, with a 1:3 iron-to-cobalt ratio, were drop-coated onto carbon paper for testing in situ X-ray absorption spectroscopy. Cyclic voltammetry of the carbon paper showed the expected behavior, with no increased ohmic drop, even in sandwiched cells. Chronoamperometry was used to apply 0.4 V versus reversible hydrogen electrode, with and without 15 min of oxygen purging to ensure that the electrochemical cell does not provide any artefacts due to gas purging. The XANES and EXAFS spectra showed no differences with and without oxygen, as expected at 0.4 V, without any artefacts due to gas purging. The development of this open-source electrochemical cell design allows for improved collection of in situ X-ray absorption spectroscopy data and enables researchers to perform both transmission and fluorescence simultaneously. It additionally addresses key practical considerations including gas purging, reduced ionic resistance and leak prevention.

08 HYDROGEN↗

Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp

Abstract Nucleoid-associated proteins (NAPs) play central roles in bacterial chromosome organization and DNA processes. The Escherichia coli YejK protein is a highly abundant, yet poorly understood NAP. YejK proteins are conserved among Gram-negative bacteria but show no homology to any previously characterized DNA-binding protein. Hence, how YejK binds DNA is unknown. To gain insight into YejK structure and its DNA binding mechanism we performed biochemical and structural analyses on the E. coli YejK protein. Biochemical assays demonstrate that, unlike many NAPs, YejK does not show a preference for AT-rich DNA and binds non-sequence specifically. A crystal structure revealed YejK adopts a novel fold comprised of two domains. Strikingly, each of the domains harbors an extended arm that mediates dimerization, creating an asymmetric clamp with a 30 Å diameter pore. The lining of the pore is electropositive and mutagenesis combined with fluorescence polarization assays support DNA binding within the pore. Finally, our biochemical analyses on truncated YejK proteins suggest a mechanism for YejK clamp loading. Thus, these data reveal YejK contains a newly described DNA-binding motif that functions as a novel clamp.

Biochemistry & Molecular Biology↗

Mechanical Regulation of Photosynthesis in Cyanobacteria

Photosynthetic organisms regulate their responses to many diverse stimuli in an effort to balance light harvesting with utilizable light energy for carbon fixation and growth (source–sink regulation). This balance is critical to prevent the formation of reactive oxygen species that can lead to cell death. However, investigating the molecular mechanisms that underlie the regulation of photosynthesis in cyanobacteria using ensemble-based measurements remains a challenge due to population heterogeneity. Here, to address this problem, we used long-term quantitative time-lapse fluorescence microscopy, transmission electron microscopy, mathematical modelling and genetic manipulation to visualize and analyse the growth and subcellular dynamics of individual wild-type and mutant cyanobacterial cells over multiple generations. We reveal that mechanical confinement of actively growing Synechococcus sp. PCC 7002 cells leads to the physical disassociation of phycobilisomes and energetic decoupling from the photosynthetic reaction centres. We suggest that the mechanical regulation of photosynthesis is a critical failsafe that prevents cell expansion when light and nutrients are plentiful, but when space is limiting. These results imply that cyanobacteria must convert a fraction of the available light energy into mechanical energy to overcome frictional forces in the environment, providing insight into the regulation of photosynthesis and how microorganisms navigate their physical environment.

BASIC BIOLOGICAL SCIENCES,BIOMASS FUELS↗

Pressure-Induced Stacking of Rhodamine 6G Molecules

Extended conjugation of molecular π systems are of great significance for solar cells and organic light-emitting diodes as these can serve as new light absorbing and emitting chromophores. This research demonstrates the potential of using pressure and solvent environment to create larger assemblies of molecular π-conjugated systems. Here, we selected rhodamine 6G (Rh6G) to study the pressure-induced stacking of molecules in three different solvents: methanol (MeOH), isopropanol (IPA), and 16:3:1 mixture of methanol: ethanol: water (MEW). Absorption, emission, and fluorescence lifetime were studied at pressures up to 11.38 GPa. We found that pressure-induced stacking mechanisms can present solvent dependence: high pressures tend to create emissive Haggregates in MeOH and MEW, but excimers in IPA. This work guides and demonstrates routes to stacking of organic molecules using high pressures and provides fundamental insights into the formation of extended conjugation π systems.

Johnson, Kade [Univ. of Texas at San Antonio, TX (↗

N-Terminal domain homologs of the orange carotenoid protein increase quenching of cyanobacterial phycobilisomes

Stress exerted by excess captured light energy in cyanobacteria is prevented by the photoprotective activity of the orange carotenoid protein (OCP). Under high light, the OCP converts from an orange, inactive form (OCP O ) into the red form (OCP R ) that binds to and quenches the phycobilisome (PBS). Structurally, the OCP consists of 2 domains: the N-terminal effector domain and a C-terminal regulatory domain. Structural analysis of the OCP-PBS complex showed that the N-terminal domains of an OCP dimer interact with the PBS core. These N-terminal OCP domains have single-domain protein paralogs known as helical carotenoid proteins (HCPs). Using PBS quenching assays, we show that the HCP4 and HCP5 homologs efficiently quench PBS fluorescence in vitro, surpassing the quenching ability of the OCP. This is consistent with computational quantum mechanics/molecular mechanics results. Interestingly, when using a maximum quenching concentration of OCP with PBSs, HCP5 addition further increases PBS quenching. Our results provide mechanistic insight into the quenching capacity and roles of HCP4 and HCP5 in cyanobacteria, suggesting that they are more than simply functionally redundant to the OCP.

Sheppard, Damien I.↗

Correlative nano-imaging of metals and proteins in primary neurons by synchrotron X-ray fluorescence and STED super resolution microscopy: Experimental validation

It is becoming increasingly clear that biological metals such as iron, copper or zinc are involved in synaptic functions, and in particular in the mechanisms of synaptogenesis and subsequent plasticity. Understanding the role of metals on synaptic functions is a difficult challenge due to the very low concentration of these elements in neurons and to the submicrometer size of synaptic compartments. To address this challenge we have developed a correlative nano-imaging approach combining metal and protein detection. First, stimulated emission depletion (STED) microscopy, a super resolution optical microscopy technique, is applied to locate fluorescently labeled proteins. Then, synchrotron radiation induced X-ray fluorescence (SXRF) is performed on the same regions of interest, e.g. synaptic compartments. Here, we present here the principle scheme that allows this correlative nano-imaging and its experimental validation. We applied this correlative nano-imaging to the study of the physiological distribution of metals in synaptic compartments of primary rat hippocampal neurons. We thus compared the nanometric distribution of metals with that of synaptic proteins, such as PSD95 or cytoskeleton proteins. Compared to correlative imaging approaches currently used to characterize synaptic structures, such as electron microscopy correlated with optical fluorescence, our approach allows for ultra-sensitive detection of trace metals using highly focused synchrotron radiation beams. We provide proof-of-principle for correlative imaging of metals and proteins at the synaptic scale and discuss the present limitations and future developments in this area.

59 BASIC BIOLOGICAL SCIENCES↗

Quantum Light Imaging of the Plant Root─Rhizobacteria─System Using iLOV Fluorescence

It has been demonstrated recently that the use of specific quantum states of light for two-photon microscopy can lead to a substantial reduction of the intensity of light needed for the imaging of biological objects. This opens new ways to better understand the delicate mechanisms of the interactions of living organisms in the rhizosphere on an extended time scale without optical damage or alteration of their native behavior. Herein, we report a successful realization of entangled two-photon excited fluorescence microscopy of wheat plant roots and a set of biological samples, including purified iLOV protein, bacterial cells expressing iLOV, and combination of these under an extremely low excitation intensity. The entangled two-photon coupling strength of iLOV was modeled using electronic structure calculations which demonstrated that the FMN chromophore in the iLOV protein has an entangled two-photon absorption (ETPA) cross section that is large enough for imaging using weak quantum light for fluorescence excitation. Successful imaging of plant-associated Pantoea sp. YR343 cells expressing iLOV validates the feasibility of using iLOV as a molecular label for characterizing plant-microbe interactions based on entangled photon imaging. In conclusion, the results demonstrate the advantageous use of entangled photon imaging under noninvasive and nondestructive conditions.

Varnavksi, Oleg [Univ. of Michigan, Ann Arbor, MI ↗

Sensing Plant Photosynthesis Using Solar-Induced Chlorophyll Fluorescence: From Chloroplasts to the Globe

Photosynthesis is the fundamental biological process that introduced oxygen into Earth's atmosphere and continues to power life, from the earliest single-celled organisms to entire global ecosystems. Yet, measuring photosynthesis across scales has been challenging because traditional techniques have not transcended scales. The emergence of remote-sensing techniques to measure solar-induced chlorophyll fluorescence (SIF) provides a unique approach to estimate photosynthesis across spatiotemporal scales, representing a new age for optical remote sensing to study photosynthesis and shaping the decades of satellite SIF research. Here, focusing on spatiotemporal scales, we review the mechanisms that drive the relationship between SIF and photosynthesis. Remotely sensed SIF is modulated by biological drivers, environmental drivers, the interaction between biological and environmental drivers, and the viewing geometry. Studying fluorescence at small scales provides the ecophysiological understanding needed to disentangle the biological and environmental drivers of SIF at larger scales. Leveraging progress in satellite SIF, future research should focus on cross-scale mechanistic understanding of the drivers of SIF and using SIF as a metric for plant function beyond photosynthesis.

ecophysiology↗

Conservation of model degraded pine wood with selected organosilicons studied by XFM and nanoindentation

Previous research found that some organosilicon treatments proved effective in stabilizing waterlogged wood dimensions during drying. The present research aimed to determine the mechanism of wood stabilization by these chemicals to understand their mode of action. Here, the study used chemically (ChP) and biologically degraded (BP) model Scots pine wood treated with Methyltrimethoxysilane (MTMS), (3-Mercaptopropyl) trimethoxysilane (MPTMS), or 1,3-Bis(diethylamino)-3-propoxypropanol)-1,1,3,3-tetramethyldisiloxane (DEAPTMDS). Synchrotron-based X-ray fluorescence microscopy (XFM) was used to investigate the penetration of organosilicons into the wood cellular structure and cell walls, and nanoindentation was used to study the mechanical properties of the treated wood cell walls. All treatments resulted in high volumetric anti-shrink efficiency (ASE V ) values of 74-82%, except for MTMS-treated ChP with an ASE V of 52%. The multiscale XFM results revealed that all applied organosilicons penetrated throughout the whole wooden blocks and deposited in both cell lumina and cell walls. The retention of all applied organosilicons was highest in BP wood, and so was the dimensional stabilization effect. MTMS-treated ChP had the lowest measured cell wall infiltration, which likely contributed to its lower ASE v . DEAPTMDS treatments plasticized the cell walls and resulted in lowered nanoindentation elastic modulus (E s NI ) and hardness (H) for all types of wood. MTMS and MPTMS had modest effects on cell wall mechanical properties, and the effect depended on the type of wood. The final effect of organosilicon treatment on the dimensional wood stabilization and mechanical properties of wood cell walls depended not only on the type of the applied organosilicon but also the type of wood degradation. This means that the treatment cannot be considered universal, and specific approaches are needed for the conservation of individual wooden objects. Although some mechanisms are now better understood, such as the need for organosilicons to infiltrate the cell walls and the plasticizing effect of DEAPTMDS, other aspects will benefit from a more detailed analysis of the molecular interactions between organosilicons and wood polymers.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular catalyst coordinatively bonded to organic semiconductors for selective light-driven CO 2 reduction in water

The selective photoreduction of CO 2 in aqueous media based on earth-abundant elements only, is today a challenging topic. Here we present the anchoring of discrete molecular catalysts on organic polymeric semiconductors via covalent bonding, generating molecular hybrid materials with well-defined active sites for CO 2 photoreduction, exclusively to CO in purely aqueous media. The molecular catalysts are based on aryl substituted Co phthalocyanines that can be coordinated by dangling pyridyl attached to a polymeric covalent triazine framework that acts as a light absorber. This generates a molecular hybrid material that efficiently and selectively achieves the photoreduction of CO 2 to CO in KHCO 3 aqueous buffer, giving high yields in the range of 22 mmol g -1 (458 μmol g -1 h -1 ) and turnover numbers above 550 in 48 h, with no deactivation and no detectable H 2 . The electron transfer mechanism for the activation of the catalyst is proposed based on the combined results from time-resolved fluorescence spectroscopy, in situ spectroscopies and quantum chemical calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatiotemporal measurements of striations in a glow discharge’s positive column using laser-collisional induced fluorescence

Here we have observed the behavior of striations caused by ionization waves propagating in low-pressure helium DC discharges using the non-invasive laser-collision induced fluorescence (LCIF) diagnostic. To achieve this, we developed an analytic fit of collisional radiative model (CRM) predictions to interpret the LCIF data and recover quantitative two-dimensional spatial maps of the electron density, n e , and the ratios of LCIF emission states that can be correlated with T e with the use of accurate distribution functions at localized positions within striated helium discharges at 500 mTorr, 750 mTorr, and 1 Torr. To our knowledge, these are the first spatiotemporal, laser-based, experimental measurements of n e in DC striations. The n e and 447:588 ratio distributions align closely with striation theory. Constriction of the positive column appears to occur with decreased gas pressure, as shown by the radial n e distribution. We identify a transition from a slow ionization wave to a fast ionization wave between 750 mTorr and 1 Torr. These experiments validate our analytic fit of n e , allowing the implementation of an LCIF diagnostic in helium without the need to develop a CRM.

42 ENGINEERING↗

Imaging the structural organization of chemical elements in growth cones of developing hippocampal neurons

Abstract During neurodevelopment, neurons form growth cones, F-actin rich extensions located at the distal end of the neurites. Growth cones allow dendrites and axons to build synaptic connections through a process of neurite guidance whose mechanisms have not been fully elucidated. Calcium is an important element in this process by inducing F-actin reorganization. We hypothesized that other biologically active elements might be involved in the growth cone-mediated neurite guidance mechanisms. We performed super resolution and confocal microscopy of F-actin, followed by synchrotron X-ray fluorescence microscopy of phosphorous, sulfur, chlorine, potassium, calcium, iron and zinc on growth cones from primary rat hippocampal neurons. We identified two main patterns of element organization. First, active growth cones presenting an asymmetric distribution of Ca co-localized with the cytoskeleton protein F-actin. In active growth cones, we found that the distributions of P, S, Cl, K, and Zn are correlated with Ca. This correlation is lost in the second pattern, quiescent growth cones, exhibiting a spread elemental distribution. These results suggest that Ca is not the only element required in the F-actin rich active regions of growth cones. In addition, highly concentrated Fe spots of submicrometer size were observed in calcium-rich areas of active growth cones. These results reveal the need for biological active elements in growth cones during neural development and may help explain why early life deficiencies of elements, such as Fe or Zn, induce learning and memory deficits in children.

60 APPLIED LIFE SCIENCES↗

Entropy-defect synergy for dual luminescence mechanism in spinel: Time-resolved anti-counterfeiting and fingerprint visualization

Multimodal luminescent materials, while promising for anti-counterfeiting, often lack dynamic time-dependent responses and controllable spatial distribution, limiting their encryption capabilities in the spatiotemporal dimension. Here, this work presents a coordinated control strategy based on entropy and defect engineering, and uses a backpropagation (BP) neural network for material screening to successfully prepare spinel Mg 0.8 (Fe 0.04 Co 0.04 Ni 0.04 Cu 0.04 Zn 0.04 )Cr 2 O 4 (MgA 5 CO) phosphors with time-dependent dynamic luminescence behavior. This phosphor simultaneously activated the d-d transition luminescence (∼618 nm) derived from Co 2+ /Cr 3+ and the defect luminescence (∼398 nm) related to zinc vacancies (V Zn ) in a single-phase solid solution. The phosphor exhibits a time-dependent color evolution from pink to purple under fixed-wavelength excitation, due to the different excited-state dynamics and decay lifetimes associated with the d-d transition and defect luminescence. Structural characterization and spectral analysis confirmed the existence of V Zn and its significant role in defect luminescence process. The fluorescent and dynamic luminescent properties of entropy-based spinel oxide enable its use in advanced anti-counterfeiting applications like fingerprint recognition and color-changing dedicated anti-counterfeiting mark, showing promise in high-end and time-dynamic anti-counterfeiting fields. This research not only developed a new type of fluorescent dynamic anti-counterfeiting material, but also provided a new idea for constructing advanced optical functional materials with multiple luminescence mechanisms.

Defect project↗

(Towards) DNS of a Laboratory Lean CH4/H2 Low-Swirl Flame Impinging on an Inclined Wall

Due to downsizing trends, flame-wall interaction (FWI) is increasingly prominent in gas turbines (GTs). FWI has direct consequences on flame stabilization and pollutant emissions, but it is not well understood in turbulent flows representative of GTs. We present results from a direct numerical simulation (DNS) of a turbulent CH4/H2 model GT low-swirl laboratory-scale flame interacting with an inclined wall. The results from the laboratory flame include simultaneous measurements of velocity using stereo particle imaging velocimetry and OHxCH2O planar laser induced fluorescence. The adaptive-mesh refinement solver PeleLMeX is used, with 24-species, 105-reaction reduced Aramco chemical kinetics mechanism. The premixed fuel-air mixture consists of hydrogen-enriched methane with 70% hydrogen volume fraction and 0.4 equivalence ratio. The inflow is prescribed to match experimental measurements at the burner exit. Karlovitz and turbulent Reynolds numbers are 300 and 400, respectively. The simulation and experimental results show excellent agreement. The flame features a bowl-shape stabilization, with a corrugated, continuous flame front at the leading edge, followed by fragmented reaction zones downstream. A large diffuse cloud of CH2O is formed downstream of the quenching point. The simulation results indicate that the cloud of CH2O is the result of incomplete methane combustion, with CH2O "leaking" from the locally quenched reaction zones.The DNS provides fine-grain resolution of turbulence-flame-wall interaction that cannot be captured with experimental measurements. With access to the entire solution vector at each cell of the computational domain, the local quenching.

flame-wall interactions↗

Photoactivation Transition State and Dynamical Response of the Orange Carotenoid Protein

The orange carotenoid protein (OCP) regulates light harvesting in cyanobacteria by acting as a photoreceptor in its resting form, OCP O , and by effecting the quenching of bilin excitons upon binding to the core of the phycobilisome in its photoactivated red form, OCP R . We show herein using fluorescence anisotropy measurements and the action spectra for the rate constants of the two light-driven steps in the mechanism that the photoactivation of the OCP from Synechocystis sp. PCC 6803 is triggered by excited-state motions of the canthaxanthin chromophore that yield a twisted and bent conformation. Well-tempered metadynamics simulations reveal that a bicycle-pedal configuration, due to twisting of the two adjacent C=C bonds at the C13−C14 and C15−C15′ positions in the center of canthaxanthin’s π-conjugated isoprenoid backbone, can be accommodated by the binding site in the OCP, with the energy of a captured photon required to cross the local activation energy barriers from the dark equilibrium structure. The bicycle-pedal configuration breaks the conserved hydrogen-bonding interactions between the carbonyl substituent of the β-ionone end ring of canthaxanthin and the adjacent W288 and Y201 residues in the C-terminal domain. The action spectra are modulated by the vibronic excitation prepared by absorption transitions to the S 2 state, indicating that the photoactivation reactions are triggered by the canthaxanthin chromophore well prior to vibrational equilibration. These findings show that an ultrafast structural response of the OCP protein to the excited-state motions of the canthaxanthin chromophore controls the photoactivation yield and the sensing of blue light.

Fluorescence↗

Simultaneous Two- and Three-Photon Deep Imaging of Autofluorescence in Bacterial Communities

The intrinsic fluorescence of bacterial samples has a proven potential for label-free bacterial characterization, monitoring bacterial metabolic functions, and as a mechanism for tracking the transport of relevant components through vesicles. The reduced scattering and axial confinement of the excitation offered by multiphoton imaging can be used to overcome some of the limitations of single-photon excitation (e.g., scattering and out-of-plane photobleaching) to the imaging of bacterial communities. In this work, we demonstrate in vivo multi-photon microscopy imaging of Streptomyces bacterial communities, based on the excitation of blue endogenous fluorophores, using an ultrafast Yb-fiber laser amplifier. Its parameters, such as the pulse energy, duration, wavelength, and repetition rate, enable in vivo multicolor imaging with a single source through the simultaneous two- and three-photon excitation of different fluorophores. Three-photon excitation at 1040 nm allows fluorophores with blue and green emission spectra to be addressed (and their corresponding ultraviolet and blue single-photon excitation wavelengths, respectively), and two-photon excitation at the same wavelength allows fluorophores with yellow, orange, or red emission spectra to be addressed (and their corresponding green, yellow, and orange single-photon excitation wavelengths). We demonstrate that three-photon excitation allows imaging over a depth range of more than 6 effective attenuation lengths to take place, corresponding to an 800 micrometer depth of imaging, in samples with a high density of fluorescent structures.

59 BASIC BIOLOGICAL SCIENCES↗