Towards reverse engineering of Photosystem II: Synergistic Computational and Experimental Approaches

ABSTRACT Photosystem II (PSII) of oxygenic photosynthesis has the unique ability to photochemically oxidize water, extracting electrons from water to result in the evolution of oxygen gas while depositing these electrons to the rest of the photosynthetic machinery which in turn reduces CO2 to carbohydrate molecules acting as fuel for the cell. Unfortunately, native PSII is unstable and not suitable to be used in industrial applications. Consequently, there is a need to reverse-engineer the water oxidation photochemical reactions of PSII using solution-stable proteins. But what does it take to reverse-engineer PSII’s reactions? PSII has the pigment with the highest oxidation potential in nature known as P680. The high oxidation of P680 is in fact the driving force for water oxidation. P680 is made up of a chlorophyll a dimer embedded inside the relatively hydrophobic transmembrane environment of PSII. In this thesis, the electrostatic factors contributing to the high oxidation potential of P680 are described. PSII oxidizes water in a specialized metal cluster known as the Oxygen Evolving Complex (OEC). The pathways that water can take to enter the relatively hydrophobic region of PSII are described as well. A previous attempt to reverse engineer PSII’s reactions using the protein scaffold of E. coli’s Bacterioferritin (BFR) existed. The oxidation potential of the pigment used for the BFR ‘reaction centre’ was measured and the protein effects calculated in a similar fashion to how P680 potentials were calculated in PSII. The BFR-RC’s pigment oxidation potential was found to be 0.57 V, too low to oxidize water or tyrosine like PSII. We suggest that the observed tyrosine oxidation in BRF-RC could be driven by the ZnCe6 di-cation. In order to increase the efficiency of iii tyrosine oxidation, and ultimately oxidize water, the first potential of ZnCe6 would have to attain a value in excess of 0.8 V. The results were used to develop a second generation of BFR-RC using a high oxidation pigment. The hypervalent phosphorous porphyrin forms a radical pair that can be observed using Transient Electron Paramagnetic Resonance (TR-EPR). Finally, the results from this thesis are discussed in light of the development of solar fuel producing systems.

Photograph - Baie Comeau, Last Railway Spike

A photograph of the "last spike in the Baie Comeau railway. Photo shows, left to right; A.I.Cunningham, managing engineer of the Ontario Paper Company driving the spike: V.G. Younghusband, vice president of the Foundation Company of Canada; R.W. Shaver, construction manager for the paper company; K.W. Bash, general superintendent, Foundation Company; and His Lordship the Bishop of Quebec.

Association of Professional Engineers of Ontario records, 1948-1989

The Act to establish the Association of Professional Engineers of Ontario (APEO) was passed on June 14, 1922. The creation of the APEO was part of a larger movement in Canada to license the engineering profession. At first, membership in the APEO was not mandatory in order to work as an engineer, but this changed in 1937 when the Professional Engineers Act was amended so that licensing by the APEO was required. In 1945, the initials “P. Eng.” were adopted by the APEO as the official abbreviation of the professional engineer. Many other amendments have been made over the years in order to strengthen the APEO’s ability to regulate the profession. Members of the APEO must also abide by a Code of Ethics, which emphasizes the regard for public welfare as paramount. There are currently 36 chapters of the APEO. In 1993, the APEO’s name was changed to Professional Engineers of Ontario, in part to emphasize the group’s role as a licensing body for engineers as opposed to an association of member engineers.

Brass Surveying Compass

Brass Surveying Compass with a 6 1/2 inch diameter silvered brass dial signed E. and G.W. Blunt of New York. There is a fleur-de-lis at the north point and the outer needle ring is engraved 0-90 in four quadrants. There is an engraved central pattern, blue steel hand and brass lifter, shaped limbs and a brass dial cover. This belonged to Samuel DeVeaux Woodruff who was a Civil Engineer. It also belonged to R.D.W. Band who was also a Civil Engineer. Also, One 13 cm. brass spindle taper for the surveying compass, n.d

Report on Water Supply for Town of St. Catharines

Report (20 page booklet) on a water supply for the town of St. Catharines by Thomas Monro, civil engineer. This is addressed to Lucious S. Oille, M.D., chairman of the Water Committee of St. Catharines, June 10, 1875.

Letter to James Ingersoll from S.D. Woodruff

Letter to James Ingersoll from S.D. Woodruff asking for pay roll accounts for items such as nails and lumber for repairs to cattle guards and fencing. This letter is accompanied by an envelope and it is on “Engineer Department” letterhead, May 11, 1857.

Chart of estimate of work done on Port Dalhousie and Thorold Railway in the section between Geneva Street and Thorold Station of the Grantham Railway

Chart of estimate of work done on Port Dalhousie and Thorold Railway in the section between Geneva Street and Thorold Station of the Grantham Railway by John Brown for February, 1856. This is signed by S.D. Woodruff, engineer, March 1856.

Chart of estimate of work done on Port Dalhousie and Thorold Railway in the section between Geneva Street and Thorold Station of the Grantham Railway

Chart of estimate of work done on Port Dalhousie and Thorold Railway in the section between Geneva Street and Thorold Station of the Grantham Railway by John Brown for May, 1856. This is signed by S.D. Woodruff, engineer, June 3, 1856.

Letter to S.D. Woodruff from John Frazer

Letter to S.D. Woodruff from John Frazer of Fonthill stating that the cheques for engineer services are enclosed, Sept. 5, 1855.

Extract from the minutes of a session of the Provisional Municipal Council of the County of Welland

Extract from the minutes of a session of the Provisional Municipal Council of the County of Welland held on Nov. 3rd, 1855. It was decided that the petition of Andrew Drew and others be laid over until the engineer could make a survey of the premises and report to the council. This was signed by Dexter Deverardo, 1855

Letter to S.D. Woodruff from Fred Holmes

Letter to S.D. Woodruff from Fred Holmes saying that he received a letter from Mr. Greybell of Marshville stating that a cheque for A. Mains was waiting for a certificate of the engineer, Oct. 31, 1856.

Letter to S.D. Woodruff from Dexter Deverardo

Letter to S.D. Woodruff from Dexter Deverardo stating that a cheque is enclosed for the services of the engineers and a resolution is also provided to continue the services of the engineer, Jan. 20, 1858.

Estimate of work done on marsh lands drainage by Alexander Cook and Andrew Mains

Estimate of work done on marsh lands drainage by Alexander Cook and Andrew Mains. This is signed by S.D. Woodruff. Also on this sheet is pay roll for engineer services for the months of September, October and November, 1855. This was paid to Frederick Holmes, Thomas Baird, Joseph Simpson and Len [illegible name], Nov.30, 1855.

Drivers of Local Firms’ Focus on Internal R&D in Emerging Economies and Their International Performance

Grounded on the resource-based view of the firm, the study of this thesis investigates the effect of four internal and external factors – engineer intensity, location, affiliation with the government, government funding – on Chinese firms’ decision to either invest in internal R&D activities or external R&D and the effect of this decision on the firms’ international market success. In addition, the moderating role of the presence of foreign firms in China is examined. To understand these relationships, the thesis’ theorization focuses on the issue of how firms can combine optimally the two options – “internal R&D” and “external R&D”. In this regard I juxtapose internal R&D and external R&D and compare their advantages and disadvantages. To test my model, I apply panel data from the Annual Industrial Survey Database provided by the Chinese National Bureau of Statistics. My results show that three of the four investigated factors affect Chinese firms’ resource allocation decisions; and effective resource allocation decisions lead effectively to international market success, strengthened by the presence of foreign firms in China. Moreover the findings bear several theoretical and managerial contributions. First I propose the last dimension of the “VRIO framework” – “organization” – as an endogenous component of the VRIO framework, as my study investigated how firms can effectively combine resources to generate a competitive advantage in terms of international market success. Previous academic literature so far focused on examining whether internal and external R&D are complements or substitutes. My study fills a gap in the literature by investigating the determinants of the efficient combination of the two strategies and the outcome of the combination. One of the managerial implications is that Chinese firms can learn from foreign companies that are present in China.

Structure et dynamique des communautés multi-espèces : le rôle de l’espace

Cette thèse porte sur le rôle de l’espace dans l’organisation et dans la dynamique des communautés écologiques multi-espèces. Deux carences peuvent être identifiées dans les études théoriques actuelles portant sur la dimension spatiale des communautés écologiques : l’insuffisance de modèles multi-espèces représentant la dimension spatiale explicitement, et le manque d’attention portée aux interactions positives, tel le mutualisme, en dépit de la reconnaissance de leur ubiquité dans les systèmes écologiques. Cette thèse explore cette problématique propre à l’écologie des communautés, en utilisant une approche théorique s’inspirant de la théorie des systèmes complexes et de la mécanique statistique. Selon cette approche, les communautés d’espèces sont considérées comme des systèmes complexes dont les propriétés globales émergent des interactions locales entre les organismes qui les composent, et des interactions locales entre ces organismes et leur environnement. Le premier objectif de cette thèse est de développer un modèle de métacommunauté multi-espèces, explicitement spatial, orienté à l’échelle des individus et basé sur un réseau d’interactions interspécifiques générales comprenant à la fois des interactions d’exploitation, de compétition et de mutualisme. Dans ce modèle, les communautés locales sont formées par un processus d’assemblage des espèces à partir d’un réservoir régional. La croissance des populations est restreinte par une capacité limite et leur dynamique évolue suivant des mécanismes simples de reproduction et de dispersion des individus. Ces mécanismes sont dépendants des conditions biotiques et abiotiques des communautés locales et leur effet varie en fonction des espèces, du temps et de l’espace. Dans un deuxième temps, cette thèse a pour objectif de déterminer l’impact d’une connectivité spatiale croissante sur la dynamique spatiotemporelle et sur les propriétés structurelles et fonctionnelles de cette métacommunauté. Plus précisément, nous évaluons différentes propriétés des communautés en fonction du niveau de dispersion des espèces : i) la similarité dans la composition des communautés locales et ses patrons de corrélations spatiales; ii) la biodiversité locale et régionale, et la distribution locale de l’abondance des espèces; iii) la biomasse, la productivité et la stabilité dynamique aux échelles locale et régionale; et iv) la structure locale des interactions entre les espèces. Ces propriétés sont examinées selon deux schémas spatiaux. D’abord nous employons un environnement homogène et ensuite nous employons un environnement hétérogène où la capacité limite des communautés locales évoluent suivant un gradient. De façon générale, nos résultats révèlent que les communautés écologiques spatialement distribuées sont extrêmement sensibles aux modes et aux niveaux de dispersion des organismes. Leur dynamique spatiotemporelle et leurs propriétés structurelles et fonctionnelles peuvent subir des changements profonds sous forme de transitions significatives suivant une faible variation du niveau de dispersion. Ces changements apparaissent aussi par l’émergence de patrons spatiotemporels dans la distribution spatiale des populations qui sont typiques des transitions de phases observées généralement dans les systèmes physiques. La dynamique de la métacommunauté présente deux régimes. Dans le premier régime, correspondant aux niveaux faibles de dispersion des espèces, la dynamique d’assemblage favorise l’émergence de communautés stables, peu diverses et formées d’espèces abondantes et fortement mutualistes. La métacommunauté possède une forte diversité régionale puisque les communautés locales sont faiblement connectées et que leur composition demeure ainsi distincte. Par ailleurs dans le second régime, correspondant aux niveaux élevés de dispersion, la diversité régionale diminue au profit d’une augmentation de la diversité locale. Les communautés locales sont plus productives mais leur stabilité dynamique est réduite suite à la migration importante d’individus. Ce régime est aussi caractérisé par des assemblages incluant une plus grande diversité d’interactions interspécifiques. Ces résultats suggèrent qu’une augmentation du niveau de dispersion des organismes permet de coupler les communautés locales entre elles ce qui accroît la coexistence locale et favorise la formation de communautés écologiques plus riches et plus complexes. Finalement, notre étude suggère que le mutualisme est fondamentale à l’organisation et au maintient des communautés écologiques. Les espèces mutualistes dominent dans les habitats caractérisés par une capacité limite restreinte et servent d’ingénieurs écologiques en facilitant l’établissement de compétiteurs, prédateurs et opportunistes qui bénéficient de leur présence.