Simple gene assembly as a rewriting of directed overlap-inclusion graphs

The simple intramolecular model for gene assembly in ciliates consists of three molecular operations, simple Id, simple hi and simple dlad. Mathematical models in terms of signed permutations and signed strings proved limited in capturing some of the combinatorial details of the simple gene assembly process. Brijder and Hoogeboom introduced a new model in terms of overlap-inclusion graphs which could describe two of the three operations of the model and their combinatorial properties. To capture the third operation, we extended their framework to directed overlap-inclusion (DOI) graphs in Azimi et al. (2011) [1]. In this paper we introduce DOI graph-based rewriting rules that capture all three operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. (C) 2012 Elsevier B.V. All rights reserved

Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum

The marine ciliate Mesodinium rubrum is famous for its ability to acquire and exploit chloroplasts and other cell organelles from some cryptophyte algal species. We sequenced genomes and transcriptomes of free-swimming Teleaulax amphioxeia, as well as well-fed and starved M. rubrum in order to understand cellular processes upon sequestration under different prey and light conditions. From its prey, the ciliate acquires the ability to photosynthesize as well as the potential to metabolize several essential compounds including lysine, glycan, and vitamins that elucidate its specific prey dependency. M. rubrum does not express photosynthesis-related genes itself, but elicits considerable transcriptional control of the acquired cryptophyte organelles. This control is limited as light-dependent transcriptional changes found in free-swimming T. amphioxeia got lost after sequestration. We found strong transcriptional rewiring of the cryptophyte nucleus upon sequestration, where 35% of the T. amphioxeia genes were significantly differentially expressed within well-fed M. rubrum. Qualitatively, 68% of all genes expressed within well-fed M. rubrum originated from T. amphioxeia. Quantitatively, these genes contributed up to 48% to the global transcriptome in well-fed M. rubrum and down to 11% in starved M. rubrum. This tertiary endosymbiosis system functions for several weeks, when deprived of prey. After this point in time, the ciliate dies if not supplied with fresh prey cells. M. rubrum represents one evolutionary way of acquiring photosystems from its algal prey, and might represent a step on the evolutionary way towards a permanent tertiary endosymbiosis

Models of natural computation : gene assembly and membrane systems

This thesis is concerned with two research areas in natural computing: the computational nature of gene assembly and membrane computing. Gene assembly is a process occurring in unicellular organisms called ciliates. During this process genes are transformed through cut-and-paste operations. We study this process from a theoretical point of view. More specifically, we relate the theory of gene assembly to sorting by reversal, which is another well-known theory of DNA transformation. In this way we obtain a novel graph-theoretical representation that provides new insights into the nature of gene assembly. Membrane computing is a computational model inspired by the functioning of membranes in cells. Membrane systems compute in a parallel fashion by moving objects, through membranes, between compartments. We study the computational power of various classes of membrane systems, and also relate them to other well-known models of computation.Netherlands Organisation for Scientific Research (NWO), Institute for Programming research and Algorithmics (IPA)UBL - phd migration 201

Rewriting the genome of Escherichia coli

Our recently acquired ability to synthesize DNA at large scale is opening the door to writing entire genomes; this constitutes a powerful approach to address fundamental biological questions, and may enable the creation of designer organisms with useful properties. One interesting avenue for investigation is the creation of recoded genomes, where codons are substituted by their synonyms. Compression of synonymous codon boxes may provide blank spaces in the quasi-universal genetic code, and these may be amenable for reassignment into unnatural amino acids, in synergy with parallel efforts to engineer the protein translation machinery. Recoding genomes is subject to both biological and technical challenges. First, synonymous codon choice genome-wide is not trivial, and identifying suitable synonymous replacements is challenging. Second, synthetic DNA pieces need to be assembled into fragments of increasing size, and ultimately implemented inside a target host. Here, recently reported strategies for genome engineering in E. coli (REXER and GENESIS) are extended and used to create a synthetic, recoded E. coli genome. Chapter 2 describes a strategy for assembling large natural genomic DNA pieces into BACs that are substrates for genome replacement. Experiments with these BACs serve to validate and improve REXER and GENESIS, and lay out a strategy for genome replacement. Chapter 3 employs these strategies for the synthesis and assembly of a recoded E. coli genome where all annotated instances of serine codons TCG and TCA, and stop codon TAG, are systematically replaced by their synonyms. The resulting strain, Syn61, provides a unique platform for exploring sense codon reassignment in vivo, and reassignment of the TCG codon to both natural and unnatural amino acids is demonstrated. Finally, Chapter 4 extends the toolkit for genome engineering in E. coli, and provides technologies for splitting the genome into pairs of chromosomes, as well as performing precise inversions and translocations. These technologies are used to precisely combine synthetic sections from distinct strains into a single genome. Together, these technologies may provide a foundation for future genome synthesis endeavours

Microscale Testing in Aquatic Toxicology

Bioassays are among the ecotoxicologist's most effective weapons in the evaluation of water quality and the assessment of ecological impacts of effluents, chemicals, discharges, and emissions on the aquatic environment. Information on these assessment aids is needed throughout the international scientific and environmental management community. This comprehensive reference provides an excellent overview of the small-scale aquatic bioassay techniques and applications currently in use around the world. This special volume is the result of several years of collaboration between Environment Canada and Fisheries and Oceans Canada. Internationally recognized research scientists at many institutions have contributed to this state-of-the-art examination of the exciting, environmentally important field of microscale testing in aquatic toxicology. Microscale Testing in Aquatic Toxicology contains over forty chapters covering relevant principles, new techniques and recent advancements, and applications in scientific research, environmental management, academia, and the private sector

The role of waterbirds in the dispersal of aquatic organisms in southern Africa

Dispersal is a fundamental process with far-reaching ecological and evolutionary consequences. Not all organisms are capable of dispersing on their own and instead produce propagules that must be transported to new habitat by a vector. Propagule dispersal by frugivorous bird species is well researched, but only very recently has the capacity of highly mobile waterbirds to disperse aquatic organisms received similar attention in the dispersal literature. Dispersal is important for the organisation of communities, and therefore understanding the frequency and scale of waterbird-mediated dispersal provides insight into the structure of wetland communities. Additionally, the study of waterbird-mediated dispersal in arid southern Africa provides an opportunity to expand our knowledge on the persistence of populations of aquatic organisms in heterogeneous environments. Recently, field and laboratory studies have demonstrated the remarkable ability of waterbirds to disperse the propagules of both plants and aquatic invertebrates. However, these studies have largely been based in the northern hemisphere and many have focussed on long-distance dispersal by migratory waterbirds. Therefore, it is difficult to generalise how waterbird-mediated dispersal plays out in different landscapes and throughout the annual cycle. Furthermore, there is still little knowledge of the spatial patterns of propagule dispersal and the mechanisms that cause these patterns to vary in space and over time. This thesis aims to addresses several of these knowledge gaps in waterbird-mediated dispersal and presents the first detailed study of propagule dispersal by waterbirds anywhere in Africa. In Chapters 2 - 5, I adopt a field- and experimental-based approach to develop a general understanding of waterbird-mediated dispersal in southern Africa. Firstly, making use of faecal samples and feather brushings collected from several waterfowl (duck) species at three locations in South Africa, I determine the quantity and viability of propagules transported via endozoochory and ectozoochory. I then assess the relative contributions of each dispersal mode to the dispersal of plants and aquatic invertebrates in the field. I show that endozoochory is the dominant dispersal mechanism, but it may be complementary to ectozoochory as different propagules are transported via this mode. Secondly, by making use of an experimental feeding trial with two captive waterfowl species, Egyptian Goose and Red-billed Teal, I explore how seed traits mediate a trade-off in recoverability and germinability against gut retention times. I show that small, hard-seeded species are retained for longer and therefore may be dispersed further. Thirdly, I incorporate gut retention time data and Egyptian Goose and Red-billed Teal movement data, acquired from GPS satellite transmitters across five study populations in southern Africa, into a mechanistic model to explore spatial patterns of seed dispersal. The model demonstrates that waterfowl generally facilitate dispersal on the local scale of below 5 km, but on occasion can transport seeds as far as 500 km from a seed source. There was variation in dispersal distances between the vectors and across the study populations and the results indicate that dispersal is affected by both intrinsic and extrinsic drivers of animal movement. In Chapters 6 and 7, I apply the concept of waterbird-mediated dispersal more broadly to address (1) the role of waterbirds in the dispersal of aquatic invaders; and (2) the determination of seed dispersal functional groups amongst a waterfowl community. I conducted a literature review to objectively describe the role of waterbirds in the dispersal of aquatic weeds. Waterbirds are important vectors of aquatic invasive species and consideration of the spatially explicit manner in which birds move is imperative to our understanding of invasive spread. In the second case, I used diet data from the 16 waterfowl species indigenous to southern Africa to explore whether finer level seed dispersal functional groups were evident. I found support for several functional groups of seed disperser based on unique plant families in the diet and suggest that important functional differences do occur between groups of waterfowl species

A Model-Based Development and Verification Framework for Distributed System-on-Chip Architecture

The capabilities and thus, design complexity of VLSI-based embedded systems have increased tremendously in recent years, riding the wave of Moore’s law. The time-to-market requirements are also shrinking, imposing challenges to the designers, which in turn, seek to adopt new design methods to increase their productivity. As an answer to these new pressures, modern day systems have moved towards on-chip multiprocessing technologies. New architectures have emerged in on-chip multiprocessing in order to utilize the tremendous advances of fabrication technology. Platform-based design is a possible solution in addressing these challenges. The principle behind the approach is to separate the functionality of an application from the organization and communication architecture of hardware platform at several levels of abstraction. The existing design methodologies pertaining to platform-based design approach don’t provide full automation at every level of the design processes, and sometimes, the co-design of platform-based systems lead to sub-optimal systems. In addition, the design productivity gap in multiprocessor systems remain a key challenge due to existing design methodologies. This thesis addresses the aforementioned challenges and discusses the creation of a development framework for a platform-based system design, in the context of the SegBus platform - a distributed communication architecture. This research aims to provide automated procedures for platform design and application mapping. Structural verification support is also featured thus ensuring correct-by-design platforms. The solution is based on a model-based process. Both the platform and the application are modeled using the Unified Modeling Language. This thesis develops a Domain Specific Language to support platform modeling based on a corresponding UML profile. Object Constraint Language constraints are used to support structurally correct platform construction. An emulator is thus introduced to allow as much as possible accurate performance estimation of the solution, at high abstraction levels. VHDL code is automatically generated, in the form of “snippets” to be employed in the arbiter modules of the platform, as required by the application. The resulting framework is applied in building an actual design solution for an MP3 stereo audio decoder application.Siirretty Doriast

Local Structure for Vertex-Minors

This thesis is about a conjecture of Geelen on the structure of graphs with a forbidden vertex-minor; the conjecture is like the Graph Minors Structure Theorem of Robertson and Seymour but for vertex-minors instead of minors. We take a step towards proving the conjecture by determining the "local structure''. Our first main theorem is a grid theorem for vertex-minors, and our second main theorem is more like the Flat Wall Theorem of Robertson and Seymour. We believe that the results presented in this thesis provide a path towards proving the full conjecture. To make this area more accessible, we have organized the first chapter as a survey on "structure for vertex-minors''

Investigations into extracellular ATP signalling and FB1-induced cell death in Arabidopsis thaliana.

Extracellular ATP (eATP) is an important signalling molecule involved in regulation of plant growth and development, interactions with other organisms and responses to several environmental stimuli. The molecular targets mediating the physiological effects of eATP in plants remain to be identified. The work presented in this thesis focuses on identifying the signalling components that underlie the physiological roles of eATP in plants, with a strong emphasis on cell death control. An Arabidopsis thaliana (Arabidopsis) cell culture system combined with 2-dimensional difference in-gel electrophoresis (2D-DIGE) and mass spectrometry was used to identify proteins differentially expressed following ATP treatment. Twenty four putative cell death proteins were identified using the cell death-inducing toxin Fumonisin B1 (FB1) in combination with an ATP reversal filter. The potential role of these candidates in eATP- regulated cell death was tested using a variety of cell death assays on Arabidopsis T-DNA insertion KO mutants. The mitochondrial ATP synthase β-subunit, AT5G08690, was shown to be a novel cell death gene. The early effects of eATP on global protein and transcript abundance were also investigated. 2D-DiGE identified 53 proteins differentially regulated by ATP and bioinformatic analysis revealed new effects of eATP on general metabolism. Re- examination of a previously acquired DNA chip experiment that used ATP and FB1 treatments identified 10 genes that are differentially expressed within minutes by eATP that can be used as molecular markers. 2D-DiGE proteomics was also used to investigate the specific toxic effects of FB1 on Arabidopsis. A subset of proteins that were specifically regulated by FB1 treatment were tested for a role in FB1-induced cell death using cell death assays on Arabidopsis T-DNA insertion KO mutants. The UDP-glucose pyrophosphorylase, AT3G03250, was identified as a cell death gene responsive to FB1