Thesis Abstracts

Mark Daly

Supervisor: Professor Síle Nic Chormaic

Research Unit: Light-Matter Interactions Unit

Thesis: Light-induced interactions using optical near-field devices


Optical near-fields are generated when light passes through components with wavelength, or subwavelength features. The near-fields generated at the surfaces of devices are often neglected, in part because the far-fields have more applications and are more readily accessible. Near-fields, as one might expect, occur very close to the surface of the material through which the light passes. However, near-fields present an interesting method of overcoming Rayleigh's diffraction limit. For example, the evanescent field at the surface of a prism or ultrathin fibre rapidly decays, but can exist in sub-diffraction limited areas. Similarly, the field generated by a subwavelength aperture or a plasmonic particle can have local field distributions with minute dimensions, allowing one to confine light to areas otherwise unattainable, extremely close to the surface of the material in question. By exploiting this aspect of optical near-fields we apply them to problems in atom and particle trapping.

Our main focus is on ultrathin optical fibres. These fibres differ from telecommunications fibre due to their lack of cladding material and their wavelength-scale dimensions. These two factors combine to produce a significant evanescent field at their waist. This field is readily accessible and can be used to trap particle or atoms through the optical forces which arise in such light-matter interactions. We can also use such devices to passively collect light which is emitted into the available guided mode. Here, we demonstrate how an ultrathin fibre can be used as a probe to determine the temperature of a cold atom cloud.

Ultrathin fibres, while extremely useful, have some limiting factors related to the strength and distribution of their evanescent fields. To improve upon the design, we also investigated how one can nanostructure an optical fibre using focussed ion beam milling techniques or combine optical fibres with gold dimer arrays to produce localised field enhancements. We used nanostructured fibres to trap 100 and 200 nm dielectric spheres within the structured region. Various numerical techniques were employed to characterise both the nanostructured fibre and the plasmonic-enhanced fibre.

Aside from optical fibres, we also briefy discuss how an array of Fresnel microlenses can be packaged with other atom chip designs to produce a device which could trap atoms microns away from a gold surface. We discuss the theory and fabrication technique for such a Fresnel microlens array atom chip.

Lee O'Riordan

Supervisor: Professor Thomas Busch

Research Unit: Quantum Systems Unit

Thesis: Non-equilibrium vortex dynamics in rapidly rotating Bose-Einstein condensates


This body of work examines the non-equilibrium dynamics of vortex lattice carrying Bose– Einstein condensates. We solve the mean-field Gross–Pitaevskii equation for a two-dimensional pancake geometry, in the co-rotating frame within the limit of high rotation frequencies. The condensate responds to this by creating a large periodic lattice of vortices with 6-fold triangular symmetry. By applying two distinct perturbations to this lattice, we examine the resulting effects on the vortices during time evolution. The first perturbation involves applying an optical potential with matching geometry to the vortex lattice. We observe the appearance of interference fringes, and we show that these can be described by moiré interference theory. This is backed up by a decomposition of the kinetic energy spectra of the condensate. The applied perturbation only modifies the condensate density, with the vortex positions largely unaffected. From this we conclude that the vortex lattice is very stable and robust against phononic disturbances.

Next, by removing vortices at predefined positions in the lattice using phase imprinting techniques, we examine the resulting order of the lattice. By performing this we generate stable topological defects in the crystal structure. The resulting lattice remains highly ordered in the presence of low numbers of these defects, where crystal structure and order of the lattice shows to be highly robust. By varying the type of imprinted phases we can create controllable degrees of disorder in the lattice. This disorder is analysed using orientational correlations, Delaunay triangulation, and Voronoi diagrams of the vortex lattice, and demonstrates a method for examining order and generating disorder in vortex lattices in Bose–Einstein condensates.

All work described makes extensive use of GPU computing techniques, and allows for the simulation of these systems to be realised in short times. The implementation of the calculations using GPU computing are also discussed, where the software is shown to be the fastest of its kind out of the independently tested software suites.


Faisal Mahmood

Supervisor: Professor Ulf Skoglund

Research Unit: Structural Cellular Biology Unit

Thesis: Algorithmic and architectural developments for cryo-electron tomography


Molecular structure determination is important for understanding functionalities and dynamics of macromolecules, such as proteins and nucleic acids. Cryo-electron tomography (Cryo-ET) is a technique that can be used to determine structures of individual macromolecules, thus providing snapshots of their native conformations. Such 3D reconstructions encounter several types of imperfections due to missing, corrupted and low-contrast data. This thesis focuses on the algorithmic and architectural aspects of improving and accelerating reconstructions for Cryo-ET specifically and the tomographic image reconstruction in general. The thesis explores modern compressed sensing and graph-based approaches for noise removal and recovering the missing wedge which act as a proof-of-concept for the applicability of sparsity exploiting methods to tomographic image reconstruction. The thesis also explores, analyses and explains an extended field (EF)-based noise removal method. When used in conjunction with a variety of reconstruction procedures with a regularization capability it proved to be computationally efficient, reliable and stable. Through extensive empirical simulations it was shown that extending the reconstruction space reduces the error at a relatively lower regularization parameter thus allowing a better fit with the projections and preventing over-smoothing. Computational constraints are a major issue in speeding up tomographic reconstruction and refinement. One of the fundamental components, which often become a bottleneck in a variety of reconstruction procedures, is the fast Fourier transform (FFT), specifically for analytical reconstructions. Generally, FFTs suffer from edge artifacts or series termination errors, which stem from the fact that two opposing edges of an image are often not periodic. These artifacts can propagate
to next stages of processing and appear as errors in reconstructions. This thesis also explores simultaneous 2D FFTs and edge artifact removal for real-time applications. This was accomplished on a multi-FPGA (Field Programmable Gate Array) reconfigurable computing system with a high-speed bus. The algorithmic optimization and architecture are general and can be replicated to a variety of different hardware


Märt Toots

Supervisor: Professor Ulf Skoglund

Research Unit: Structural Cellular Biology Unit

Thesis: Exploring the potential of cryo-electron tomography on protein nanocrystals for molecular structure determination


The three-dimensional structure of a protein molecule, challenging to determine and close to impossible to predict, plays a key role in understanding protein function and has implications in drug design. When it comes to structure determination, there exist many complementary methods, each with their specific advantages and disadvantages. Most of those methods rely on a combined signal from thousands of individuals and cannot be used for directly reconstructing an actual 3d volume as it appears inside the sample.

This thesis focuses on developing the methodology and providing proof of concept for a novel approach in structure determination by reconstructing small protein nanocrystals via cryo-electron tomography. Real-space imaging gets past the phase problem that is a challenging companion of conventional diffraction-based methods. With electron tomography we can reconstruct and visualize a 3d nanocrystal in its entirety and study the properties of small biological crystal from a new perspective.

Being a relatively unexplored territory, nanocrystal tomography sets several challenges, such as creating nanocrystals small enough for imaging with transmission electron microscope and developing algorithms for going from a tilt-series to a 3d structure. For a proof of concept we create, image and reconstruct nanocrystals of hen egg white lysozyme that, having molecular weight of only 15 kDa, is generally considered unfeasible for electron tomography. Nanocrystals make finding and determining the relative orientations of the individual molecules possible, symmetry relations help reduce the effects of missing information, and by averaging we are able to reconstruct a molecular structure at a medium resolution of around 13 Å. Using Fourier Transform (FFT) we get a direct objective measure of the resolution of details within the reconstruction in the form of a diffraction pattern and show that in specific directions the resolution reaches as high as 7Å in a single tomogram.

Additionally, this work explores two other tightly related ideas. First, we study the concept of extended field and show with extensive simulations that extending the reconstruction space in various regularized iterative reconstruction procedures helps reduce the overall error and prevent over-smoothing. Second, calculating FFT of an image comes at a computational cost, and when the image is not periodic, the discontinuity of the opposing edges causes undesirable strong artifacts in the FFT that could obstruct important details. In this project we implemented a simultaneous 2d FFT and edge artifact removal for real-time applications on a Field Programmable Gate Array (FPGA) reconfigurable computing system.


Dongxin Zhang

Supervisor: Professor Fujie Tanaka

Research Unit: Chemistry and Chemical Bioengineering Unit

Thesis: Amine catalyzed functionalization of enolizable ketones


Development of efficient methods for the synthesis of biologically important molecules in safe, atom economical, and environmentally friendly ways is a significant goal of modern organic chemistry. In this thesis, efficient methods using amines as catalysts for functionalization of enolizable ketones and synthesis of potential biologically active molecules have been developed. First, 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) was indentified to be an efficient catalyst for fast regioselective aldol reactions. Molecules containing tertiary alcohols were concisely obtained through the aldol reactions. The developed DBU-catalysis was applied for the synthesis of spirooxindoles and trifluoromethyl-substituted alcohols. Although the DBU-catalyzed aldol reactions are not enantioselective, the enantiomerically pure forms of the aldol products derived from -keto esters were obtained by the resolution of the enamines of the aldol products with a homochiral amine. Second, deuteration studies were carried out to elucidate the mechanism of the regioselective formation of the products in the aldol reactions catalyzed by DBU and to understand the relationship between the formation of carbanion or its equivalents and the bond-formation. Finally, enantioselective oxa-hetero-Diels-Alder reaction of enones with aryl trifluoromethyl ketones catalyzed by a novel amine catalyst system was developed. Tetrasubstituted carbon centers bearing a trifluoromethyl group were concisely constructed with the formation of the tetrahydropyranone ring. The hetero-Diels-Alder products were further transformed to various trifluoromethyl-substituted tetrahydropyran derivatives.


Yi-Jyun Luo

Supervisor: Professor Noriyuki Satoh

Research Unit: Marine Genomics Unit

Thesis: Insights into lophotrochozoan evolution and the origin of morphological novelties from brachiopod, phoronid, and nemertean genomes


Brachiopods, phoronids, and nemerteans are closely related lophotrochozoans, yet they carry distinct feeding apparatuses and lifestyles. They are poorly studied despite their importance in ecology, evolution, and paleontology. As a result, the genetic basis of their evolutionary origins and body plans have been obscure. Since the Cambrian explosion ~540 million years ago, animal forms have greatly diversified. One fundamental question of animal evolution is how these diverse morphologies are formed. While animals share many developmental toolkit genes, they also possess novel genes and expansion of gene families in a lineage-specific manner. How lineage-specific genes and changes of genomic features contribute to morphological novelties is still a challenge in understanding animal evolution. Also, whether common toolkit genes are involved in patterning these novelties at the genomic level is not well understood. Here I present the genomes of the brachiopod Lingula anatina, the phoronid Phoronis australis, and the nemertean Notospermus geniculatus, together with multiple transcriptomes, providing a comparative platform to understand the evolution of animal genomes and the origin of lophotrochozoans.

Using genomic, transcriptomic, and proteomic approaches, I show that although Lingula and vertebrates have superficially similar hard tissue components, Lingula lacks genes involved in bone formation, suggesting an independent origin of their phosphate biominerals. Several genes involved in Lingula shell formation are shared by molluscs. However, Lingula has independently undergone domain combinations to produce shell matrix collagens with epidermal growth factor domains and carries lineage-specific shell matrix proteins. Gene family expansion, domain shuffling, and co-option of genes appear to be the genomic background of Lingula’s unique biomineralization. Genome-based phylogenetic analyses place Nemertea sister to the group of Brachiopoda and Phoronida. Lophotrochozoans share many gene families with deuterostomes, suggesting that lophotrochozoans retain a core set of bilaterian gene repertoire rather than ecdysozoans or remaining spiralians. Comparative transcriptomics demonstrates that lophophores of brachiopods and phoronids have resemblance not only morphologically but also at the molecular level. Despite lophophores are dissimilar from head structures, lophophores highly express vertebrate head organizer and neuronal marker genes, probably indicating a common origin of bilaterian head patterning. Together, this study reveals a dual nature of lophotrochozoans in which bilaterian-conserved and lineage-specific features shape the evolution of their genomes.


Kenneth Baughman

Supervisor: Professor Noriyuki Satoh

Research Unit: Marine Genomics Unit

Thesis:  Decoding and analysis of the Crown-of-Thorns Starfish Acanthaster planci genome


Echinoderms are at the base of the deuterostome clade, yet have radial body plans, a watervascular system, and exoskeletons. In order to investigate how genomes control development, I studied the “Crown-of-Thorns Starfish” (COTS) or Acanthaster planci genome. I made four discoveries from sequencing two COTS specimens, one from the Great Barrier Reef, Australia (‘GBR’) and the other from Okinawa, Japan (‘OKI’). Separate 384 megabase (Mb) assemblies containing ~24,500 genes were generated. Firstly, I discovered that both genomes displayed unexpectedly low heterozygosity; reciprocal BLAST alignment of scaffolds longer than 10 kilobases (Kb) revealed 98.8% nucleotide identity, consistent with a single pacific COTS clade undergoing a recent population expansion. Secondly, although the unique Hox gene order in sea urchins was hypothesized to be related to pentaradial body plans, I discovered that COTS Hox and ParaHox clusters resemble hemichordate and chordate clusters. The COTS Hox cluster shares with sea urchins the transposition of even-skipped (Evx), as well as posterior Hox reorganization. I thus proposed an evolutionary scenario for how shuffling of the Hox cluster in urchins may have arisen. Thirdly, recent studies show that hemichordates possess a deuterostome-specific cluster of transcription factors associated with development of pharyngeal gill slits. Although extant echinoderms do not have pharyngeal gill slits, I found the cluster in the COTS genome, supporting an ancient origin for pharyngeal gill slits as a deuterostome-defining morphological feature. Fourthly, using systems biology notation, I mapped COTS candidate genes for 1-methlyadenine (1-MA)-mediated oocyte maturation. This thesis confirms that the high quality of the COTS genome is biologically significant, and amendable to future studies. Although COTS are famous for decimating coral reefs, this thesis shows that COTS can also be used for genomic and evolutionary developmental research.


Rico Pohle

Supervisor: Professor Nic Shannon

Research Unit: Theory of Quantum Matter Unit

Thesis:  Signatures of novel spin liquids in kagome-like lattices


The phenomenon of magnetism in solids aroused the curiosity of scientists already in ancient times. While quantum mechanical effects on a single–particle level are well understood, magnets offer phenomena caused by collective interactions between many electrons and provide the opportunity to find novel states of matter. In this context, frustrated magnets play a central role, since interactions between local magnetic moments on a crystallographic lattice cannot be satisfied at the same time. This can prevent the systems to order even at very low temperatures, creating a magnetic state similar to those of liquids, which gives them the name spin liquids. Within this field, the kagome lattice — a two–dimensional network of corner–sharing triangles — has played a particularly iconic role and continues to provide rich inspiration to theoreticians and experimentalists alike.
In this thesis, we first explore the thermodynamic properties and signatures of classical spin liquids on kagome–like lattices, by the use of complementary analytical Husimi tree and numerical Monte Carlo simulation techniques. The emerging phenomenon ofa Curie–law crossover, reflecting a crossover between a high–temperature paramagnet and a low–temperature collective paramagnet, turns out to be a powerful signature of exotic physics in classical spin liquids, and explains the difficulty of making a precise estimate of the Curie–Weiss temperature in experiments.
But spin liquids do not necessarily need to show just one Curie–law crossover. The anisotropic Ising model on the shuriken, or square–kagome lattice, shows a succession of multiple Curie–law crossovers due to a rich phase diagram with many disordered ground states. Hereby, low–and high–temperature regimes are less correlated than the intervening classical spin liquid, allowing to extend the definition of reentrant phenomena to disordered systems.
Furthermore, we also study dynamical properties of the nearest–neighbour Heisenberg model on the bilayer breathing kagome lattice, which has been motivated by recent experiments on Ca10Cr7O28. Using semi–classical molecular–dynamics simulations, we are able to reproduce many features seen by inelastic neutron scattering experiments and provide a first explanation of its spin–liquid origin. Surprisingly, we find that excitations encode not one, but two distinct types of spin liquids at different time scales. Fast fluctuations reveal a Coulombic spin liquid, as known from the classical kagome–lattice antiferromagnet, while slow fluctuations reveal a spiral spin liquid, which can be understood by a mapping onto an effective spin-3/2 honeycomb model.


Zafer Hawash

Supervisor: Professor Yabing Qi 

Research Unit: Energy Materials and Surface Sciences Unit 

Thesis: Surface science studies of perovskite solar cells: spiro-MeOTAD hole transport material and perovskite absorber


The past few years have witnessed an emergence of an outstanding class of thin film solar cells, which are based on organic-inorganic light absorbers, namely, perovskite solar cells (PSCs).   PSCs possess energy conversion efficiencies (PCEs) comparable to traditional silicon and other solar cell technologies. To achieve high efficiencies, typically perovskite materials are sandwiched between selective contacts, which significantly facilitate charge carries extraction. These contacts  are made of either electron or hole selective material and are called electron transport material  (ETM) and hole transport material (HTM). This thesis discusses surface science aspects of the  doping mechanism of spiro-MeOTAD HTM, and an engineering approach of the perovskite/spiroMeOTAD HTM interface for enhanced energy level alignment, efficiency, and reproducibility.
In this thesis surface science techniques (i.e., photoemission spectroscopy (PES), atomic force microscopy (AFM), and scanning electron microscopy(SEM)) combined with currentdensity voltage (J-V) measurements on hole only devices and PSCs are employed. PES measurements revealed that ambient air-exposure results in the migration of the commonly used Li-salt dopants from the bottom to the bulk (including top surface) of the spiro-MeOTAD HTM film. AFM and SEM images revealed the presence of pinholes with an average diameter of ~135nm, with a density of ~3.72 holes/µm2, and these pinholes form channels wiggling across the doped  spiro-MeOTAD film. Under controlled environments of H2O (relative humidity 90%) and dry O2, PES measurements revealed that H2O is the constituent component in ambient air that leads to the V redistribution of the LiTFSI dopants. In addition, the J-V measurement results on hole only devices revealed that H2O vapor exposure results in an irreversible enhancement of LiTFSI-doped HTM conductivity due to redistribution of the LiTFSI dopants across the HTM film, which was examined by PES measurements. On the contrary, O2 exposure results in a reversible enhancement of the HTM film under applied bias, in which this enhancement is mainly due to O2 doping, which was confirmed by PES measurements.
In addition, to achieve better energy level alignment between the HTM and the perovskite absorber, an intentional deposition of an ultrathin layer of methylammonium iodide (MAI) on top of a methylammonium lead iodide (MAPI) perovskite film was implemented. Using PES measurements, it was found that the deposition of small amount of MAI on top of MAPI results in an interfacial, favorable, energy-level tuning of the MAPI film. XPS measurements revealed that the enhanced energy-level tuning was from MAI dissociated species, not the MAI itself. Furthermore, the optimized energetics were verified using perovskite solar cells. Substantially enhanced stabilized-PCE and reproducibility was achieved (from 15 ± 2% to 17.2 ± 0.4%).


Caroline Starzynski

Supervisor: Professor Mitsuhiro Yanagida

Research Unit: G0 Cell Unit

Thesis: Investigating an evolutionarily conserved metabolic mechanism contributing to G0 quiescence survival in S. pombe


Since all living organism rely on assimilating environmental nitrogen (N) to promote cell divisions, an efficient system to deal with N scarcity is deterministic for survival. For example, the fission yeast Schizosaccharomyces pombe (S. pombe) withstands long-term N starvation by induction of growth arrest and quiescence entry (G0 phase). In past studies 89 S. pombe genes were found to be required for survival upon G0 phase. Because these are involved in diverse intracellular functions, a clear mechanism for quiescence was difficult to assign. Therefore, we developed a BLAST-based approach to generate phylogenetic profiles and characterize evolutionary conserved metabolic reactions by comparative analysis using prokaryotic databases of Escherichia coli and Bacillus subtilis. We report fourteen proteins fulfilling this study’s homology criteria, half of which (7/14) are localized to the mitochondria. Subsequent in silico analysis suggests the involvement of two functional response mechanisms which comprise oxygen-consuming and glutamate-metabolic reactions. Among these, ∆sod2 showed abnormally low oxygen consumption upon quiescence and loss of regenerative capability. We report that the conserved mechanisms to survive N starvation comprise enzymes which are associated with the regulation of oxygen and glutamateoxoglutarate metabolism.


Cong Liu

Supervisor: Professor Evan Economo

Research Unit: Biodiversity and Biocomplexity Unit

Thesis: Understanding the ecological and evolutionary processes shaping ant biodiversity across spatiotemporal scales


Ecological and historical evolutionary processes together generate biodiversity patterns across geographies and across the tree of life. However, understanding the relative importance of, and the interplay between ecological mechanisms and evolutionary processes in shaping biodiversity patterns is still a challenge due to the different spatiotemporal scales on which they are operating. Therefore, a fundamental goal of biodiversity research is to use different research approaches to investigate how the ecological processes (dispersal, competition, and environmental filtering), as well as long-term evolutionary processes (adaptation and speciation), contribute to the community assembly and biodiversity patterns. In this thesis, I investigate ant biodiversity patterns and underlying eco-evolutionary processes across multiple systems (tropical agroecosystem, complex mountainous landscape, and Pacific archipelago), providing a comparative framework to understand the eco-evolutionary processes driving biodiversity patterns. I first present results from an ant biodiversity survey in Xishuangbanna, Yunnan, China, where I found 213 species/morphospecies of ants from 10 subfamilies and 61 genera. Forty species represent new records for Yunnan province and 17 species are newly recorded for China. In addition, I describe one new species, Aenictus yangi. When examining the changes in taxonomic, functional, and phylogenetic ant biodiversity after conversion to rubber plantation, I found a sharp decline of species richness in rubber plantation with lower than expected taxonomic and functional beta diversity. This suggested a strong environmental filtering driving ant biodiversity in the rubber plantation. I then investigate the variation in taxonomic and phylogenetic ant diversity patterns along a geographic transect spanning 5000m in elevational range in the Hengduan mountains, where environmental gradients and spatial connectivity are intertwined as a complex process that might shape biodiversity patterns. I found that environmental gradients dominate variation in both alpha and beta diversity in this landscape, with alpha diversity strongly declining with elevation and beta diversity driven by elevational differences. Finally, I apply a comparative phylogeographic framework to examine the evolution of the hyperdiverse ant genus Strumigenys in Fiji archipelago using RAD sequencing. My results revealed the history of Strumigenys species that colonized to Fiji archipelagoes in Miocene (10.5-7.5 Ma), following by two independent radiations across the whole archipelago, leading to the emergence of 11 endemic species. The population structure and demographic history of each endemic species consistently support the idea of deterministic macroevolutionary processes that drive the diversity dynamic of ants in Fiji archipelago. Together, this study highlights the need for a pluralistic framework that integrates different approaches to understanding the eco-evolutionary drivers of biodiversity patterns across scales.


Nino Espinas

Supervisor: Professor Hidetoshi Saze

Research Unit: Plant Epigenetics Unit

Thesis: rCBP-dependent regulation in rice innate immunity


Plant  innate immunity against bacterial  attacks is a two-tiered inducible system capable  of defense responses at local and systemic areas.These systems are the PTI and ETI. During infection, PTI has the ability to recognize microbial signatures upon bacterial contact, while ETI recognizes microbial protein secretions called effectors delivered inside the cell.The activation  of  PTI  and  ETI  confers  systemic tissues  of  infected  plants a  broad-spectrum immunity against later pathogen attacks termed systemic acquired resistance (SAR). Defense priming  is an  adaptive component  of  SAR that regulates the molecular storage of defense memory for a more effective defense response.
The main aim of this work is finding a novel molecular defense signaling pathway that is controlled by acetylation at the infected (local defense) and systemic tissues (priming defense).
To investigate the role of histone acetyltransferase-dependent pathway in plant immunity, I have isolated transgenic and mutant lines of rCBP, [rice Cyclic adenosine monophosphate response  element-binding  protein (CREB) Binding Protein], under Nipponbare cultivar background  using  RNAi silencing and gRNA/Cas9-mediated genome editing. Animal CBP was initially described as both  transcriptional  coactivator  and  histone  acetyltransferase. The rCBP-RNAi lines with mistargeting of the other members of CBP family are characterized by massive  sterility  and  impairment  of  the  number  of  effective  grains. On  the  other  hand,  the CRISPR/Cas9 mutant lines have wild-type number of effective grains.
To  profile  the  global  acetylation  of  histone lysine-sites via rCBP, I performed mass spectrometry-based  proteomics  in  data dependent  acquisition (DDA)  and  parallel  reaction monitoring  (PRM)  modes.  My results  showed  that  H3  lysine sites  are possibly targeted by rCBP with very high acetylation specificity on H3K9.
To  implicate  the  role  of  rCBP  in  rice  innate  immunity,  I  conducted  a pathogenesis assay with  bacterial  pathogen, Pseudomonas  syringiae pv. oryzae (Pso). Pathogenesisassay showed that rCBP-/-mutants are resistant to Pso infection compared to segregated wild-type control.
I  also  performed transcriptome  analysis on local and systemic  tissues with Pso to investigate  the  genome-wide effects of rCBP mutation and to  identify  factors with roles in both basal and systemic immune response. As a result, I have identified seven putative rCBP-dependent transcriptional repressors that possibly explain the resistance phenotype of rCBP mutant lines.
Overall,  these  data  preliminary  indicate  that rCBP is both a positive regulator of developmental processes and a negative regulator of rice immunity. These data also suggest that  rCBP may execute this dual regulatory function either through  H3K9ac and/or  co-transcriptional activity on target gene loci.


Keita Ikegami

Supervisor: Professor Noriyuki Satoh

Research Unit: Marine Genomics Unit

Thesis: Comparative transcriptomeanalysisof basal deuterostomes and its implications for the phylotypic stage


The modification of embryogenesis in animals is an interesting research subject in evolutionary developmental biology. The phylotypic stage was originally described as a developmental period shared across vertebrates, where embryos resemble each other, andis represented by a narrowing waist of the developmental “hourglass” model. Recent studies of comprehensive gene expression have found support for this model in other metazoans, plants, and fungus. However, the existence of the phylotypic stage remains unresolved in deuterostomes. Thus, this study examines whether the phylotypic stage can be found across four deuterostome taxa, namely Ciona intestinalis from the Phylum Urochordata, Branchiostoma floridae from the Phylum Cephalochordata, Ptychodera flava from the Phylum Hemichordata, and Acanthaster planci from the Phylum Echinodermata. Comparison of gene expression profiles was carried out by microarray analysis of RNA across predetermined developmental time points. In this thesis, I developed a method of microarray probe design in A. planci, and proposed guidelines for the technology for use with other marine invertebrates. Next, I compared the gene expression profile with this microarray method. I found that the overall gene expression somewhat resembled each other in A. planci, P. flava and B. floridae, while C. intestinalis exhibited a unique pattern. The gene expression profiles of A. planci, P. flava and B. floridae showed narrowing waist-like pattern from the blastula to gastrula stages up to early larval stages; these stages were more conserved during embryogenesis in deuterostome taxa. However, I failed to find evidence for a typical vertebrate-like phylotypic stage in the four deuterostome taxa. 


Daisuke Takahashi

Thesis Supervisor: Professor Hirotaka Sugawara

Research Unit: Advanced Medical Instrumentation Unit

Thesis: Minimal Gauged U(1) Extension of the Standard Model with Classical Scale Invariance and Phenomenology


Although the Standard Model(SM) is the best theory in describing phenomena among elementary particles, it suffers from several problems, such as the gauge hierarchy problem, origin of the electroweak symmetry breaking, non-zero neutrino mass, and no candidate of dark matter. For solving these problems, we consider minimal U(1) extension of the SM with the classically conformal invariance, where an anomaly-free U(1) gauge symmetry is introduced along with a U(1) Higgs field and three right-handed neutrinos(RHNs) for the seesaw mechanism generating neutrino masses. With no mass term allowed by the classically conformal invariance, the U(1) gauge symmetry is broken through the Coleman-Weinberg mechanism, which subsequently triggers the electroweak symmetry breaking. We perform parameter scan and identify regions resolving the SM Higgs vacuum in stability, while satisfying the LHC Run-2 bound on the U(1) gauge boson production and the naturalness constraint. We also investigate cosmological aspects of the model. Introducing Z2 parity, one RHN being an unique parity-odd particle in the model serves as dark matter. A successful inflation scenario is possible by identifying the U(1) Higgs boson with inflation and introducing its non-minimal gravitational coupling. Interestingly, the LHC physics and cosmological observations are complementary narrowing down the model parameter space.