The aquatic biota of the now extinct lacustrine complex of the Mexico basin

The commonest organisms of the original Mexico lake complex are listed, including those that exist today in the Lago Viejo. In addition, a brief hydraulic history of this endorheic basin is given.

Models of the Oxygen-Evolving Complex of Photosystem II

In the five chapters that follow, I delineate my efforts over the last five years to synthesize structurally and chemically relevant models of the Oxygen Evolving Complex (OEC) of Photosystem II. The OEC is nature’s only water oxidation catalyst, in that it forms the dioxygen in our atmosphere necessary for oxygenic life. Therefore understanding its structure and function is of deep fundamental interest and could provide design elements for artificial photosynthesis and manmade water oxidation catalysts. Synthetic endeavors towards OEC mimics have been an active area of research since the mid 1970s and have mutually evolved alongside biochemical and spectroscopic studies, affording ever-refined proposals for the structure of the OEC and the mechanism of water oxidation. This research has culminated in the most recent proposal: a low symmetry Mn₄CaO₅ cluster with a distorted Mn₃CaO₄ cubane bridged to a fourth, dangling Mn. To give context for how my graduate work fits into this rich history of OEC research, Chapter 1 provides a historical timeline of proposals for OEC structure, emphasizing the role that synthetic Mn and MnCa clusters have played, and ending with our Mn₃CaO₄ heterometallic cubane complexes.

In Chapter 2, the triarylbenzene ligand framework used throughout my work is introduced, and trinuclear clusters of Mn, Co, and Ni are discussed. The ligand scaffold consistently coordinates three metals in close proximity while leaving coordination sites open for further modification through ancillary ligand binding. The ligands coordinated could be varied, with a range of carboxylates and some less coordinating anions studied. These complexes’ structures, magnetic behavior, and redox properties are discussed.

Chapter 3 explores the redox chemistry of the trimanganese system more thoroughly in the presence of a fourth Mn equivalent, finding a range of oxidation states and oxide incorporation dependent on oxidant, solvent, and Mn salt. Oxidation states from Mn^II₄ to Mn^IIIMn^IV₃ were observed, with 1-4 O^2– ligands incorporated, modeling the photoactivation of the OEC. These complexes were studied by X-ray diffraction, EPR, XAS, magnetometry, and CV.

As Ca²⁺ is a necessary component of the OEC, Chapter 4 discusses synthetic strategies for making highly structurally accurate models of the OEC containing both Mn and Ca in the Mn₃CaO₄ cubane + dangling Mn geometry. Structural and electrochemical characterization of the first Mn₃CaO₄ heterometallic cubane complex— and comparison to an all-Mn Mn₄O₄ analog—suggests a role for Ca²⁺ in the OEC. Modification of the Mn₃CaO₄ system by ligand substitution affords low symmetry Mn₃CaO₄ complexes that are the most accurate models of the OEC to date.

Finally, in Chapter 5 the reactivity of the Mn₃CaO₄ cubane complexes toward O- atom transfer is discussed. The metal M strongly affects the reactivity. The mechanisms of O-atom transfer and water incorporation from and into Mn₄O₄ and Mn₄O₃ clusters, respectively, are studied through computation and ¹⁸O-labeling studies. The μ3-oxos of the Mn₄O₄ system prove fluxional, lending support for proposals of O^2– fluxionality within the OEC.

MODIFIED DIRECT TWOS-COMPLEMENT PARALLEL ARRAY MULTIPLICATION ALGORITHM FOR COMPLEX MATRIX OPERATION

A direct twos-complement parallel array multiplication algorithm is introduced and modified for digital optical numerical computation. The modified version overcomes the problems encountered in the conventional optical twos-complement algorithm. In the array, all the summands are generated in parallel, and the relevant summands having the same weights are added simultaneously without carries, resulting in the product expressed in a mixed twos-complement system. In a two-stage array, complex multiplication is possible with using four real subarrays. Furthermore, with a three-stage array architecture, complex matrix operation is straightforwardly accomplished. In the experiment, parallel two-stage array complex multiplication with liquid-crystal panels is demonstrated.

Investigations of DNA-mediated protein oxidation

DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA π-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt π-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA π-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]^3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins.

Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding E. coli Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.

Further work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)₂, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)₂ is substituted with poly(dAdT)₂, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species.

We have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in E. coli Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at g = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate.

DNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.

While the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]^3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]³⁺ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells.

In conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.

Studies on the complex formation of iron with humic substances [Translation from: Vom Wasser 53, 243-247, 1979]

Most of the humic substances which occur in natural waters have an iron content of a few percent, indicated by the mg/1 content of organically-bonded carbon. This iron is apparently bound in a complex with the humic substances, for it quite plainly differs in its chemical and physico-chemical properties from what one would expect from the purely inorganic iron-water system. The deviations range from the solubility to the redox behaviour, and thus are frequently the basis of analytical and technical difficulties. The key to the solution of most of this problem lies in a better understanding of the aforementioned bonds between the iron and the humic substances. This paper studies the iron content of the humic substance concentration from a bog lake sample and the complexing of iron by humic substances from the surface of the bog lake.

Three-dimensional superresolution by three-zone complex pupil filters

Complex pupil filters are introduced to improve the three-dimensional resolving power of an optical imaging system. Through the design of the essential parameters of such filters, the transmittance and radius of the first zone, three-dimensional superresolution is realized. The Strehl ratio and the transverse and axial gains of such filters are analyzed in detail. A series of simulation examples of such filters are also presented that prove that three-dimensional superresolution can be realized. The advantage of such filters is that it is easy to realize three-dimensional superresolution, and the disadvantage is that the sidelobes of the axial intensity distribution are too high. But this can be overcome by the application of a confocal system. (C) 2005 Optical Society of America.

The complex angular momentum theory of the production of three particles in collisions of two strongly interacting particles at high energy

The problem of the continuation to complex values of the angular momentum of the partial wave amplitude is examined for the simplest production process, that of two particles → three particles. The presence of so-called "anomalous singularities" complicates the procedure followed relative to that used for quasi two-body scattering amplitudes. The anomalous singularities are shown to lead to exchange degenerate amplitudes with possible poles in much the same way as "normal" singularities lead to the usual signatured amplitudes. The resulting exchange-degenerate trajectories would also be expected to occur in two-body amplitudes.

The representation of the production amplitude in terms of the singularities of the partial wave amplitude is then developed and applied to the high energy region, with attention being paid to the emergence of "double Regge" terms. Certain new results are obtained for the behavior of the amplitude at zero momentum transfer, and some predictions of polarization and minima in momentum transfer distributions are made. A calculation of the polarization of the ρ^o meson in the reaction π ^- p → π ^- ρ^op at high energy with small momentum transfer to the proton is compared with data taken at 25 Gev by W. D. Walker and collaborators. The result is favorable, although limited by the statistics of the available data.

Ceratium hirundinella - ecology of a complex, mobile, and successful plant

Recent work carried out in the English Lake District (Esthwaite Water and Blelham Tarn) is reported. The seasonal growth cycle, diel growth cycle, photosynthesis, vertical distribution and migrations, horizontal distribution, and the interaction of environmental factors, were investigated.

One-shot parallel complex Fourier-domain optical coherence tomography using a spatial carrier frequency

We propose a novel method of one-shot parallel complex Fourier-domain optical coherence tomography using a spatial carrier frequency for full range imaging. The spatial carrier frequency is introduced into the 2-D spectral interferogram in the lateral direction by using a tilted reference wavefront. This spatial-carrier- contained 2-D spectral interferogram is recorded with one shot of a 2-D CCD camera, and is Fourier-transformed in the lateral direction to obtain a 2-D complex spectral interferogram by a spatial-carrier technique. A full-range tomogram is reconstructed from the 2-D complex spectral interferogram. The principle of this method is confirmed by cross-sectional imaging of a glass slip object. (c) 2008 Society of Photo-Optical Instrumentation Engineers.