Glotaran: A Java-Based Graphical User Interface for the R Package TIMP

In this work the software application called Glotaran is introduced as a Java-based graphical user interface to the R package TIMP, a problem solving environment for fitting superposition models to multi-dimensional data. TIMP uses a command-line user interface for the interaction with data, the specification of models and viewing of analysis results. Instead, Glotaran provides a graphical user interface which features interactive and dynamic data inspection, easier -- assisted by the user interface -- model specification and interactive viewing of results. The interactivity component is especially helpful when working with large, multi-dimensional datasets as often result from time-resolved spectroscopy measurements, allowing the user to easily pre-select and manipulate data before analysis and to quickly zoom in to regions of interest in the analysis results. Glotaran has been developed on top of the NetBeans rich client platform and communicates with R through the Java-to-R interface Rserve. The background and the functionality of the application are described here. In addition, the design, development and implementation process of Glotaran is documented in a generic way

Ultrafast Energy Transfer in an Artificial Photosynthetic Antenna

We temporally resolved energy transfer kinetics in an artificial light- harvesting dyad composed of a phthalocyanine covalently linked to a carotenoid. Upon carotenoid photo-excitation, energy transfers within ≈100fs (≈52% efficiency) to the phthalocyanine

Energy Transfer and Trapping in Red-Chlorophyll-Free Photosystem I from Synechococcus WH 7803

We report for the first time steady-state and time-resolved emission properties of photosystem I (PSI) complexes isolated from the cyanobacterial strain Synechococcus WH 7803. The PSI complexes from this strain display an extremely small fluorescence emission yield at 77 K, which we attribute to the absence of so-called red antenna chlorophylls, chlorophylls with absorption maxima at wavelengths longer than those of the primary electron donor P700. Emission measurements at room temperature with picosecond time resolution resulted in two main decay components with lifetimes of about 7.5 and 18 ps and spectra peaking at about 685 nm. Especially in the red flanks, these spectra show consistent differences, which means that earlier proposed models for the primary charge separation reactions based on ultrafast (∼1 ps) excitation equilibration processes cannot describe the data. We show target analyses of a number of alternative models and conclude that a simple model (Ant2)* (Ant1/RC)* → RP2 can explain the time-resolved emission data very well. In this model, (Ant2)* represents chlorophylls that spectrally equilibrate in about 7.5 ps and in which RP2 represents the "final" radical pair P70

Pennsylvania Folklife Vol. 18, No. 4

• Discord in the Garden • The Folk Festival Seminars: Crafts and Customs of the Year • What to Read on the Amish • Soup\u27s On! • Festival Highlights • Folk Festival Program • Folk Festival Geisinger • Four Interviews with Powwowers • The First Historian of the Pennsylvania Germans • The Public Sale Sixty Years Ago • The Long Shingle • Quilts and Quilting: Folk-Cultural Questionnaire No. 12https://digitalcommons.ursinus.edu/pafolklifemag/1036/thumbnail.jp

Complete Proton Transfer Cycle in GFP and Its T203V and S205V Mutants

Proton transfer is critical in many important biochemical reactions. The unique three‐step excited‐state proton transfer in avGFP allows observations of protein proton transport in real‐time. In this work we exploit femtosecond to microsecond transient IR spectroscopy to record, in D2O, the complete proton transfer photocycle of avGFP, and two mutants (T203V and S205V) which modify the structure of the proton wire. Striking differences and similarities are observed among the three mutants yielding novel information on proton transfer mechanism, rates, isotope effects, H‐bond strength and proton wire stability. These data provide a detailed picture of the dynamics of long‐range proton transfer in a protein against which calculations may be compared

Conservation of core complex subunits shaped the structure and function of photosystem I in the secondary endosymbiont alga Nannochloropsis gaditana

Photosystem I (PSI) is a pigment protein complex catalyzing the light-driven electron transport from plastocyanin to ferredoxin in oxygenic photosynthetic organisms. Several PSI subunits are highly conserved in cyanobacteria, algae and plants, whereas others are distributed differentially in the various organisms. Here we characterized the structural and functional properties of PSI purified from the heterokont alga Nannochloropsis gaditana, showing that it is organized as a supercomplex including a core complex and an outer antenna, as in plants and other eukaryotic algae. Differently from all known organisms, the N. gaditana PSI supercomplex contains five peripheral antenna proteins, identified by proteome analysis as type-R light-harvesting complexes (LHCr4-8). Two antenna subunits are bound in a conserved position, as in PSI in plants, whereas three additional antennae are associated with the core on the other side. This peculiar antenna association correlates with the presence of PsaF/J and the absence of PsaH, G and K in the N. gaditana genome and proteome. Excitation energy transfer in the supercomplex is highly efficient, leading to a very high trapping efficiency as observed in all other PSI eukaryotes, showing that although the supramolecular organization of PSI changed during evolution, fundamental functional properties such as trapping efficiency were maintained

Ultrafast photochemistry of the bc₁ complex

We present a full investigation of ultrafast light-induced events in the membraneous cytochrome bc 1 complex by transient absorption spectroscopy. This energy-transducing complex harbors four redox-active components per monomer: heme c 1 , two 6-coordinate b-hemes and a [2Fe-2S] cluster. Using excitation of these components in different ratios under various excitation conditions, probing in the full visible range and under three well-defined redox conditions, we demonstrate that for all ferrous hemes of the complex photodissociation of axial ligands takes place and that they rebind in 5-7 ps, as in other 6-coordinate heme proteins, including cytoglobin, which is included as a reference in this study. By contrast, the signals are not consistent with photooxidation of the b hemes. This conclusion contrasts with a recent assessment based on a more limited data set. The binding kinetics of internal and external ligands are indicative of a rigid heme environment, consistent with the electron transfer function. We also report, for the first time, photoactivity of the very weakly absorbing iron-sulfur center. This yields the unexpected perspective of studying photochemistry, initiated by excitation of iron-sulfur clusters, in a range of protein complexes