GTB – An Online Genome Tolerance Browser

BACKGROUND: Accurate methods capable of predicting the impact of single nucleotide variants (SNVs) are assuming ever increasing importance. There exists a plethora of in silico algorithms designed to help identify and prioritize SNVs across the human genome for further investigation. However, no tool exists to visualize the predicted tolerance of the genome to mutation, or the similarities between these methods. RESULTS: We present the Genome Tolerance Browser (GTB, http://gtb.biocompute.org.uk): an online genome browser for visualizing the predicted tolerance of the genome to mutation. The server summarizes several in silico prediction algorithms and conservation scores: including 13 genome-wide prediction algorithms and conservation scores, 12 non-synonymous prediction algorithms and four cancer-specific algorithms. CONCLUSION: The GTB enables users to visualize the similarities and differences between several prediction algorithms and to upload their own data as additional tracks; thereby facilitating the rapid identification of potential regions of interest. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1436-4) contains supplementary material, which is available to authorized users

Prediction of driver variants in the cancer genome via machine learning methodologies

Sequencing technologies have led to the identification of many variants in the human genome which could act as disease-drivers. As a consequence, a variety of bioinformatics tools have been proposed for predicting which variants may drive disease, and which may be causatively neutral. After briefly reviewing generic tools, we focus on a subset of these methods specifically geared toward predicting which variants in the human cancer genome may act as enablers of unregulated cell proliferation. We consider the resultant view of the cancer genome indicated by these predictors and discuss ways in which these types of prediction tools may be progressed by further research

Functional characterization of AtGLP5 and AtSUC7, and their role in plant defense and development trade-offs in Arabidopsis thaliana

This study utilized the Arabidopsis thaliana-Sclerotinia sclerotiorum pathosystem to discover valuable rapeseed stem rot disease resistance engineering traits with activation-tagging, transgenic overexpressing, and T-DNA insertion knock-out mutants. By comparing their different disease resistance phenotypes and analyzing the expression of several pathway associated genes, we have got a relatively detailed knowledge about the molecular mechanism for the anti-pathogen function of the two proteins, AtGLP5 and AtSUC7. AtGLP5 is also further demonstrated to possess SOD activity and has a pivotal role in FLS2-associated flg22 signaling particularly. AtSUC7, previously regarded as a pseudogene encoding non-functional sucrose transporter, is proved to be involved in disease resistance and flowering time control

Combinatorial biological complexity: a study of amino acid side chains and alternative splicing

Both, laymen and experts have always been intrigued by nature’s vast complexity and variety. Often, these phenomena arise from combination of parts, as for example, cell types of the human body, or the diverse proteins of a cell. In this thesis I investigate three instances of combinatorial complexity: combinations of aliphatic amino acid side chains, alternative mRNA splicing in fungi, and mutually exclusively spliced exons in human and mouse. In the first part the number of aliphatic amino acid side chains is studied. Structural combinations yield a vast theoretical number, yet we find that only a fraction of them is realized in nature. Reasons especially with respect to restrictions by the genetic code are discussed. Moreover, strategies for the need for increased diversity are examined. In the second part, the extent of alternative splicing (AS) in fungi is investigated. A genome-wide, comparative multi-species study is conducted. I find that AS is common in fungi, but with lower frequency compared to plants and animals. AS is more common in more complex fungi, and is over-represented in pathogens. It is hypothesized that AS contributes to multi-cellular complexity in fungi. In the third part, mutually exclusive exons (MXEs) of mouse and human are detected and characterized. Rather unexpected patterns arose: the majority of MXEs originate from non-adjacent exons and frequently appear in clusters. Known regulatory mechanisms of MXE splicing are unsuitable for these MXEs, and thus, new mechanisms have to be sought. Summarizing it is hypothesized that complexity from combinations constitutes a universal principle in biology. However, there seems to be a need to restrict the combinatorial potential. This is highlighted by the interdependence of MXEs and the low number of realized amino acids in the genetic code. Combinatorial complexity and its restriction are discussed with respect to other biological systems to further substantiate the hypotheses

Incorporating standardised drift-tube ion mobility to enhance non-targeted assessment of the wine metabolome (LC×IM-MS)

Liquid chromatography with drift-tube ion mobility spectrometry-mass spectrometry (LCxIM-MS) is emerging as a powerful addition to existing LC-MS workflows for addressing a diverse range of metabolomics-related questions [1,2]. Importantly, excellent precision under repeatability and reproducibility conditions of drift-tube IM separations [3] supports the development of non-targeted approaches for complex metabolome assessment such as wine characterisation [4]. In this work, fundamentals of this new analytical metabolomics approach are introduced and application to the analysis of 90 authentic red and white wine samples originating from Macedonia is presented. Following measurements, intersample alignment of metabolites using non-targeted extraction and three-dimensional alignment of molecular features (retention time, collision cross section, and high-resolution mass spectra) provides confidence for metabolite identity confirmation. Applying a fingerprinting metabolomics workflow allows statistical assessment of the influence of geographic region, variety, and age. This approach is a state-of-the-art tool to assess wine chemodiversity and is particularly beneficial for the discovery of wine biomarkers and establishing product authenticity based on development of fingerprint libraries

Doctor of Philosophy

dissertationThere are many bacteria that associate with insects in a mutualistic manner and offer their hosts distinct fitness advantages, and thus have likely played an important role in shaping the ecology and evolution of insects. Therefore, there is much interest in understanding how these relationships are initiated and maintained and the molecular mechanisms involved in this process, as well as interest in developing symbionts as platforms for paratransgenesis to combat disease transmission by insect hosts. However, this research has been hampered by having only a limited number of systems to work with, due to the difficulties in isolating and modifying bacterial symbionts in the lab. In this dissertation, I present my work in developing a recently described insect-bacterial symbiosis, that of the louse fly, Pseudolynchia canariensis, and its bacterial symbiont, Candidatus Arsenophonus arthropodicus, into a new model system with which to investigate the mechanisms and evolution of symbiosis. This included generating and analyzing the complete genome sequence of Ca. A. arthropodicus, which provided some evidence that Ca. A. arthropodicus has become recently associated with insects and may have evolved from an ancestor that was an insect pathogen. Additionally, I describe the development of methods for genetic modification of this bacterial symbiont and for introducing recombinant symbionts into louse fly hosts, as well as a new microinjection technique that enables the complete replacement of native symbionts with recombinant symbionts. With the generation of the symbiont genome sequence along with strategies for engineering recombinant symbionts and establishing them in an insect host, this work provides an interesting new system with which to investigate the function of specific genes in symbiosis as well as a promising new avenue of research involving paratransgenesis

PRIMATE/HUMAN-SPECIFIC FEATURES AND FUNCTION OF TROPHOBLAST LINEAGE

Ph.DDOCTOR OF PHILOSOPH

Thermal stress in the Antarctic clam Laternula and the temperate mussel Mytilus.

There is ample evidence that a period of global warming is already affecting ecosystems worldwide. In order to predict the effects of a warming climate on organism physiology and biogeography, a description of the mechanisms involved in species responses to elevated temperatures is needed. Comparative studies examining species inhabiting different environments provide important information on the relative susceptibility of ecosystems to climate change. Antarctic marine ectotherms have evolved in a stable cold environment. They live within a narrow thermal window and experience stress with small elevations in temperature. In contrast, temperate intertidal species experience considerable temperature changes on a daily basis. The Antarctic clam Lateniula elliptica and temperate mussel Mytilus edulis were selected as representative species for their respective environments. This thesis presents i) a description of the construction of a cDNA microarray for L. elliptica, ii) analysis of gene expression in L. elliptica upon acute exposure to 3°C, iii) a comparative study between the two species at the protein level via two dimensional electrophoresis, and iv) analysis of corticosteroid synthesis in Mytiliis. Significant changes in the expression of 294 clones, representing 160 transcripts were observed. Of these, 33 were identified by sequence similarity searches and classified to a variety of cellular functions including protein turnover, folding and chaperoning, intracellular signalling and trafficking and cytoskeletal activity. In addition, the expression of 264 and 375 proteins in L. elliptica and M. edulis respectively was studied, 14 and 26 of which presented changes in expression between treatments. Only changes in proteins involved in energy metabolism were detected in both species. A higher level of biological variation in response to stress was observed in M. echilis at the protein level. The relevance of the observed results in determining the relative susceptibility of these species to climate change is discussed