Thesis (M. Phil.)--University of Hong Kong, 2006. / Title proper from title frame. Also available in printed format.

Probably no group of organisms has been as important as bacteriophages when it comes to the understanding of fundamental biological processes like transcriptional control, DNA replication, site-specific recombination, e.t.c. The work presented in this thesis is a contribution towards the complete understanding of these organisms. Two proteins, integrase, and Cox, which are important for the choice of the life mode of bacteriophage P2, are investigated. P2 is a temperate phage, i.e. it can either insert its DNA into the host chromosome (by site-specific recombination) and wait (lysogeny), or it can produce new progeny with the help of the host protein machinery and thereafter lyse the cell (lytic cycle). The integrase protein is necessary for the integration and excision of the phage genome. The Cox protein is involved as a directional factor in the site-specific recombination, where it stimulates excision and inhibits integration. It has been shown that the Cox protein also is important for the choice of the lytic cycle. The choice of life mode is regulated on a transcriptional level, where two mutually exclusive promoters direct whether the lytic cycle (Pe) or lysogeny (Pc) is chosen. The Cox pro-tein has been shown to repress the Pc promoter and thereby making tran-scription from the Pe promoter possible, leading to the lytic cycle. Further, the Cox protein can function as a transcriptional activator on the parasite phage, P4. P4 has gained the ability to adopt the P2 protein machinery to its own purposes. In this work the importance of the native size for biologically active integrase and Cox proteins has been determined. Further, structure-function analyses of the two proteins have been performed with focus on the protein-protein interfaces. In addition it is shown that P2 Cox and the P2 relative Wphi Cox changes the DNA topology upon specific binding. From the obtained results a mechanism for P2 Cox-DNA interaction is discussed. The results from this thesis can be used in the development of a gene delivery system based on the P2 site-specific recombination system.

P2-like bacteriophages integrate their genome into the E. coli host cell by a site-specific recombination event upon lysogenization. The integrative recombination occurs between a specific sequence in the phage genome, attP, and a specific sequence in the host genome, attB, generating the host-phage junctions attL and attR. The integration is mediated by the phage enzyme integrase (Int) and the host factor IHF. The excisive recombination takes place between attL and attR, and is mediated by Int, IHF and phage encoded protein Cox. For safe integration of foreign genes into eukaryotic chromosome a recombinases is necessary which can perform the integration site-specifically. P2-like phage integrases have the potential to become tools for safe gene therapy. Their target is simple but specific, and once integration has occurred it is very stable in the absence of the Cox protein. The site-specific recombination mechanism has to be understood at the molecular level. Therefore, I have initiated the characterization of the site-specific recombination system of the P2-like phage ΦD145. In this work, Int and IHF are shown to bind to the different attachment sites cooperatively. One of two possible inverted repeats in attP is shown to be the Int core recognition site. The attP core of this phage has high identity with a site on human chromosome, denoted as ΨattB. In this study we have shown that in in vivo recombination ΦD145 Int can accept ΨattB in both bacteria and in eukaryotic cells. Also shown that Int consists of an intrinsic nuclear localization signal. A study also reveled that ΦD145 Int activity was affected by the Tyr-phosphorylation. Attempts have been made to change the specificity of the other P2-like phage P2 and WΦ integrases and also structural and functional analysis was done. A study on comparative analysis of Cox proteins and Cox binding sites gave us the basic information about the recombination mechanism. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript.

Dye-sensitized solar cells (DSCs) convert sunlight to electricity at a low cost. In the DSC, a dye anchored to a mesoporous TiO2 semiconductor is responsible for capturing the sunlight. The resulting excited dye injects an electron into the conduction band of the TiO2 and is in turn regenerated by a redox mediator, normally iodide/triiodide, in a surrounding electrolyte. The success of the iodide/triiodide redox couple is mainly attributed to its slow interception of electrons at the TiO2 surface, which suppresses recombination losses in the DSC. One of the main limitations with the iodide/triiodide redox couple is, however, the large driving force needed for regeneration, which minimizes the open circuit voltage and thus the energy conversion efficiency. In this thesis, alternative redox couples to the iodide/triiodide redox couple have been investigated. These redox couples include the one-electron transition metal complexes, ferrocene and cobalt polypyridine complexes. The use of one-electron redox couples in the DSC has previously been shown to lead to poor photovoltaic performances, because of increased recombination. Cobalt redox couples were here found to give surprisingly high efficiencies in combination with the triphenylamine-based organic dye, D35. The success of the D35 dye, in combination with cobalt redox couples, was mainly attributed to the introduction of steric alkoxy chains on the dye, which supress recombination losses. By introducing steric substituents on the dye, rather than on the redox couple, mass transport limitations could in addition be avoided, which previously has been suggested to limit the performance of cobalt complexes in the DSC. The result of this study formed the basis for the world record efficiency of DSCs of 12.3 % using cobalt redox couples. Interfacial electron-transfer processes in cobalt-based DSCs were investigated to gain information of advantages and limitations using cobalt redox couples in the DSC. The redox potentials of cobalt redox couples are easily tuned by changing the coordination sphere of the complexes, and regeneration and recombination kinetics were systematically investigated by increasing the redox potential of the cobalt complexes. Our hope is that this thesis can be a guideline for future design of new redox systems in DSCs.

Fanconi anaemia (FA) is an inherited disorder characterized by bone marrow failure, cancer predisposition and congenital abnormalities. The 12 known FA genes have been implicated in homologous recombination (HR), a process involved in telomere maintenance. A complex of at least 7 FA proteins promotes FANCD2 monoubiquitination and nuclear foci formation. FANCD2 colocalizes and interacts with HR proteins, however the role of FANCD2 in HR is unclear. Telomeres in dividing human somatic cells shorten until they reach a critical length, triggering most cells to undergo senescence or apoptosis. Rare immortal cells escape this crisis by expressing telomerase, or activating the Alternative Lengthening of Telomeres (ALT) pathway, which involves HR. FA core complex proteins and FANCD2 colocalize with telomeric foci in ALT, but not telomerase positive cells. Localization of FANCD2 to ALT telomeric foci requires monoubiquitination by the FA core complex, but is independent of ATM and ATR. FANCD2 primarily colocalizes with ALT telomeric DNA within ALT-associated PML bodies (APBs). Electron spectroscopic imaging and FISH experiments show that APBs contain extra-chromosomal telomeric repeat (ECTR) DNA that is non-nucleosomal. Depletion of FANCD2 causes marked increases in ECTR in ALT, but not telomerase positive cells. Overexpression of BLM, the helicase mutated in Bloom syndrome, also causes an ALT-specific increase in ECTR DNA. FANCD2 coimmunoprecipitates with BLM in ALT cells, and FANCD2 localization to ALT telomeric foci requires BLM expression. FANCD2-depleted ALT cells have reduced viability, signs of mitotic catastrophe, and multiple types of telomeric abnormalities, including increases in telomeric recombination, entanglements, colocalization with DNA repair proteins, and expression of fragile site characteristics. SiRNA depletion of FANCD2 does not cause overexpression of BLM, however codepletion of BLM with FANCD2 suppresses the telomere phenotypes caused by FANCD2 knockdown. Together this suggests that FANCD2 regulates BLM-dependent recombination and amplification of telomeric DNA within ALT cells.

Multijunction solar cells made from a combination of CQDs of differing sizes and thus bandgaps are a promising means by which to increase the energy harvested from the Sun’s broad spectrum. In this dissertation, we first report the systematic engineering of 1.6 eV PbS CQD solar cells, optimal as the front cell responsible for visible wavelength harvesting in tandem photovoltaics. We rationally optimize each of the device’s collecting electrodes—the heterointerface with electron accepting TiO2 and the deep-work-function hole-collecting MoO3 for ohmic contact—for maximum efficiency. Room-temperature processing enables flexible substrates, and permits tandem solar cells that integrate a small-bandgap back cell atop a low thermal-budget larger-bandgap front cell. We report an electrode strategy that enables a depleted heterojunction CQD PV device to be fabricated entirely at room temperature. We develop a two-layer donor-supply electrode (DSE) in which a highly doped, shallow work function layer supplies a high density of free electrons to an ultrathin TiO2 layer via charge-transfer doping. Using the DSE we build all-room-temperature-processed small-bandgap (1 eV) colloidal quantum dot solar cells suitable for use as the back junction in tandem solar cells. We further report in this work the first efficient CQD tandem solar cells. We use a graded recombination layer (GRL) to provide a progression of work functions from the hole-accepting electrode in the bottom cell to the electron-accepting electrode in the top cell. The recombination layers must allow the hole current from one cell to recombine, with high efficiency and low voltage loss, with the electron current from the next cell. We conclude our dissertation by presenting the generalized conditions for design of efficient graded recombination layer solar devices. We demonstrate a family of new GRL designs experimentally and highlight the benefits of the progression of dopings and work functions in the interlayers.

The persistence of sex is a recurrent conundrum in evolutionary biology because sex is costly. These costs may be accounted for by looking at the outcome of sex, namely that sex causes genetic mixing. Recombination is one of the processes by which sex causes genetic mixing; determining when recombination is advantageous may alleviate some of the costs of sex. The advantages of recombination are in the effects of recombination and the influences thereupon. The first experiment focuses on the effects of recombination on the mean fitness and variance in fitness. A second experiment examines the influences on recombination by addressing whether recombination is a general response to poor condition. Specifically, the impact on recombination rate of genotypes with variable fitness is investigated. Differing fitness effects are not correlated to recombination rates. Conversely, coincidence, a recombination related trait, is positively correlated with fitness.

The persistence of sex is a recurrent conundrum in evolutionary biology because sex is costly. These costs may be accounted for by looking at the outcome of sex, namely that sex causes genetic mixing. Recombination is one of the processes by which sex causes genetic mixing; determining when recombination is advantageous may alleviate some of the costs of sex. The advantages of recombination are in the effects of recombination and the influences thereupon. The first experiment focuses on the effects of recombination on the mean fitness and variance in fitness. A second experiment examines the influences on recombination by addressing whether recombination is a general response to poor condition. Specifically, the impact on recombination rate of genotypes with variable fitness is investigated. Differing fitness effects are not correlated to recombination rates. Conversely, coincidence, a recombination related trait, is positively correlated with fitness.

Fanconi anaemia (FA) is an inherited disorder characterized by bone marrow failure, cancer predisposition and congenital abnormalities. The 12 known FA genes have been implicated in homologous recombination (HR), a process involved in telomere maintenance. A complex of at least 7 FA proteins promotes FANCD2 monoubiquitination and nuclear foci formation. FANCD2 colocalizes and interacts with HR proteins, however the role of FANCD2 in HR is unclear. Telomeres in dividing human somatic cells shorten until they reach a critical length, triggering most cells to undergo senescence or apoptosis. Rare immortal cells escape this crisis by expressing telomerase, or activating the Alternative Lengthening of Telomeres (ALT) pathway, which involves HR. FA core complex proteins and FANCD2 colocalize with telomeric foci in ALT, but not telomerase positive cells. Localization of FANCD2 to ALT telomeric foci requires monoubiquitination by the FA core complex, but is independent of ATM and ATR. FANCD2 primarily colocalizes with ALT telomeric DNA within ALT-associated PML bodies (APBs). Electron spectroscopic imaging and FISH experiments show that APBs contain extra-chromosomal telomeric repeat (ECTR) DNA that is non-nucleosomal. Depletion of FANCD2 causes marked increases in ECTR in ALT, but not telomerase positive cells. Overexpression of BLM, the helicase mutated in Bloom syndrome, also causes an ALT-specific increase in ECTR DNA. FANCD2 coimmunoprecipitates with BLM in ALT cells, and FANCD2 localization to ALT telomeric foci requires BLM expression. FANCD2-depleted ALT cells have reduced viability, signs of mitotic catastrophe, and multiple types of telomeric abnormalities, including increases in telomeric recombination, entanglements, colocalization with DNA repair proteins, and expression of fragile site characteristics. SiRNA depletion of FANCD2 does not cause overexpression of BLM, however codepletion of BLM with FANCD2 suppresses the telomere phenotypes caused by FANCD2 knockdown. Together this suggests that FANCD2 regulates BLM-dependent recombination and amplification of telomeric DNA within ALT cells.

Hierarchy is widely observed in biological systems. In this thesis, evidence from nature is presented to show that protein interactions have became increasingly modular as evolution has proceeded over the last four billion years. The evolution of animal body plan development is considered. Results show the genes that determine the phylum and superphylum characters evolve slowly, while those genes that determine classes, families, and speciation evolve more rapidly. This result furnishes support to the hypothesis that the hierarchical structure of developmental regulatory networks provides an organizing structure that guides the evolution of aspects of the body plan. Next, the world trade network is treated as an evolving system. The theory of modularity predicts that the trade network is more sensitive to recessionary shocks and recovers more slowly from them now than it did 40 years ago, due to structural changes in the world trade network induced by globalization. Economic data show that recession-induced change to the world trade network leads to an increased hierarchical structure of the global trade network for a few years after the recession. In the study of influenza virus evolution, an approach for early detection of new dominant strains is presented. This method is shown to be able to identify a cluster around an incipient dominant strain before it becomes dominant. Recently, CRISPR has been suggested to provide adaptive immune response to bacteria. A population dynamics model is proposed that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is less diversifed. Finally, the creation of diversity of antibody repertoire is investigated. It is commonly believed that a heavy chain is generated by randomly combining V, D and J gene segments. However, using high throughput sequence data in this study, the naive VDJ repertoire is shown to be strongly correlated between individuals, which suggest VDJ recombination involves regulated mechanisms.