Mammalian reverse genetics without crossing reveals Nr3a as a short-sleeper gene

The identification of molecular networks at the system level in mammals is accelerated by next-generation mammalian genetics without crossing, which requires both the efficient production of whole-body biallelic knockout (KO) mice in a single generation and high-performance phenotype analyses. Here, we show that the triple targeting of a single gene using the CRISPR/Cas9 system achieves almost perfect KO efficiency (96%–100%). In addition, we developed a respiration-based fully automated noninvasive sleep phenotyping system, the Snappy Sleep Stager (SSS), for high-performance (95.3% accuracy) sleep/wake staging. Using the triple-target CRISPR and SSS in tandem, we reliably obtained sleep/wake phenotypes, even in double-KO mice. By using this system to comprehensively analyze all of the N-methyl-D-aspartate (NMDA) receptor family members, we found Nr3a as a short-sleeper gene, which is verified by an independent set of triple-target CRISPR. These results demonstrate the application of mammalian reverse genetics without crossing to organism-level systems biology in sleep research.

Cell death control : the interplay of apoptosis and autophagy in the pathogenicity of sclerotinia sclerotiorum

Programmed cell death is characterized by a cascade of tightly controlled events that culminate in the orchestrated death of the cell. In multicellular organisms autophagy and apoptosis are recognized as two principal means by which these genetically determined cell deaths occur. During plant-microbe interactions cell death programs can mediate both resistant and susceptible events. Via oxalic acid (OA), the necrotrophic phytopathogen Sclerotinia sclerotiorum hijacks host pathways and induces cell death in host plant tissue resulting in hallmark apoptotic features in a time and dose dependent manner. OA-deficient mutants are non-pathogenic and trigger a restricted cell death phenotype in the host that unexpectedly exhibits markers associated with the plant hypersensitive response including callose deposition and a pronounced oxidative burst, suggesting the plant can recognize and in this case respond, defensively. The details of this plant directed restrictive cell death associated with OA deficient mutants is the focus of this work. Using a combination of electron and fluorescence microscopy, chemical effectors and reverse genetics, we show that this restricted cell death is autophagic. Inhibition of autophagy rescued the non-pathogenic mutant phenotype. These findings indicate that autophagy is a defense response in this necrotrophic fungus/plant interaction and suggest a novel function associated with OA; namely, the suppression of autophagy. These data suggest that not all cell deaths are equivalent, and though programmed cell death occurs in both situations, the outcome is predicated on who is in control of the cell death machinery. Based on our data, we suggest that it is not cell death per se that dictates the outcome of certain plant-microbe interactions, but the manner by which cell death occurs that is crucial.

Development of reverse phase protein microarrays for clinical applications and patient-tailored therapy

While genomics provide important information about the somatic genetic changes, and RNA transcript profiling can reveal important expression changes that correlate with outcome and response to therapy, it is the proteins that do the work in the cell. At a functional level, derangements within the proteome, driven by post-translational and epigenetic modifications, such as phosphorylation, is the cause of a vast majority of human diseases. Cancer, for instance, is a manifestation of deranged cellular protein molecular networks and cell signaling pathways that are based on genetic changes at the DNA level. Importantly, the protein pathways contain the drug targets in signaling networks that govern overall cellular survival, proliferation, invasion and cell death. Consequently, the promise of proteomics resides in the ability to extend analysis beyond correlation to causality. A critical gap in the information knowledge base of molecular profiling is an understanding of the ongoing activity of protein signaling in human tissue: what is activated and “in use” within the human body at any given point in time. To address this gap, we have invented a new technology, called reverse phase protein microarrays, that can generate a functional read-out of cell signaling networks or pathways for an individual patient obtained directly from a biopsy specimen. This “wiring diagram” can serve as the basis for both, selection of a therapy and patient stratification.

Latent variable models in statistical genetics

Understanding the complexities that are involved in the genetics of multifactorial diseases is still a monumental task. In addition to environmental factors that can influence the risk of disease, there is also a number of other complicating factors. Genetic variants associated with age of disease onset may be different from those variants associated with overall risk of disease, and variants may be located in positions that are not consistent with the traditional protein coding genetic paradigm. Latent Variable Models are well suited for the analysis of genetic data. A latent variable is one that we do not directly observe, but which is believed to exist or is included for computational or analytic convenience in a model. This thesis presents a mixture of methodological developments utilising latent variables, and results from case studies in genetic epidemiology and comparative genomics. Epidemiological studies have identified a number of environmental risk factors for appendicitis, but the disease aetiology of this oft thought useless vestige remains largely a mystery. The effects of smoking on other gastrointestinal disorders are well documented, and in light of this, the thesis investigates the association between smoking and appendicitis through the use of latent variables. By utilising data from a large Australian twin study questionnaire as both cohort and case-control, evidence is found for the association between tobacco smoking and appendicitis. Twin and family studies have also found evidence for the role of heredity in the risk of appendicitis. Results from previous studies are extended here to estimate the heritability of age-at-onset and account for the eect of smoking. This thesis presents a novel approach for performing a genome-wide variance components linkage analysis on transformed residuals from a Cox regression. This method finds evidence for a dierent subset of genes responsible for variation in age at onset than those associated with overall risk of appendicitis. Motivated by increasing evidence of functional activity in regions of the genome once thought of as evolutionary graveyards, this thesis develops a generalisation to the Bayesian multiple changepoint model on aligned DNA sequences for more than two species. This sensitive technique is applied to evaluating the distributions of evolutionary rates, with the finding that they are much more complex than previously apparent. We show strong evidence for at least 9 well-resolved evolutionary rate classes in an alignment of four Drosophila species and at least 7 classes in an alignment of four mammals, including human. A pattern of enrichment and depletion of genic regions in the profiled segments suggests they are functionally significant, and most likely consist of various functional classes. Furthermore, a method of incorporating alignment characteristics representative of function such as GC content and type of mutation into the segmentation model is developed within this thesis. Evidence of fine-structured segmental variation is presented.

Reverse immigration

This book (256 pages, written in Korean) is a critical essay that reviews, questions, and criticises Korean and Eastern immigrants’ thinking and behaviour styles in Australia from their cultural perspectives, and discuss and proposes a creative cultural dimension for their better life in a multicultural context. Multiculturalism is not supportive of Eastern cultures because of individualistic collection of cultures, while transculturalism facilitates nurture of their culture in a community-oriented way within multicultural circumstances. Korean and Eastern immigrants, sharing oriental cultural systems and values, should approach to the Australian multicultural context with transculturalism which allows creating new cultural values in collaboration with and by participation into local communities. ------------------------------------------------------------ Many Eastern immigrants live in their own ethnic communities without or less interacting with Australian (communities). The author defines this phenomenon as “reverse immigration”. Reverse immigration refers to re-immigrating to their ethnic community in Australia or to their birth country despite they did not anticipate that this would happen to them before immigration to Australia. The author argues that Easterners’ collectivistic culture often devalues individuality and vice versa. Cultural clash between West and East often forces the immigrants to choose reverse immigration because of their lack of understanding of Western culture and their cultural characteristics such as low individuality, high power distance, and high uncertainty avoidance. For example, a vague boundary between individualist and collectivist in a collectivistic context (within their ethnic group) often leads to maladjustment to local communities and enhancement of cultural conservatism. The author proposes that the cultural clash can be overcome by cross-cultural activities named “transculturalism”. To Eastern immigrants, transculturalism can be achieved by acculturation of their two predominant cultures, the third-person perspective and generalised others. In a multicultural context, the former refers to the ability to share another person's feelings and emotions as if they were your own, and the latter does the ability to manage community and public expectations. When both cultural values are used for quality interactions between East and West, they allow Eastern immigrants to be more creative and critical and Australian to be more socially inclusive and culturally tolerant. With these discussions, the author discusses cultural differences throughout the book with four topics (chapters) and proposes transculturalism as a solution to the reverse immigration. ------------------------------------------------------------ Chapter 1 criticises Koreans’ attitudes and methods towards learning English that is less pragmatic and practical, but more likely to be a scholarly study. The author explains that Koreans’ non-pragmatic towards learning English has been firmly built based on their traditional systems and values that Koreans view English as a discipline and an aim of academic achievements rather than a means of communication. Within their cultural context, English can be perceived as more than a language, but something like vastly superior to their language and culture. Their collectivistic culture regards English as an unreachable and heterogeneous one that may threaten their cultural identity, so that “scholarly studying” is only the way to achieve (not learn) it. This discourages the immigrants to engage and involve in daily dialogues by “using” English as a second language. The author further advises the readers to be aware of Eastern collectivistic culture in communication and interaction that sometimes completely reverses private and public topics in a Western context. This leads them to feel that they have no content to talk to natives. ------------------------------------------------------------ Chapter 2 compares between Korea and Australia in terms of their educational systems and values, and proposes how Eastern overseas students can achieve critical and creative thinking within a Western educational setting. Interestingly, this chapter includes an explanation of why Eastern overseas students easily fail assessments including essay writing, oral presentations and discussions. One of the reasons the author explains is that Eastern students are not familiar to criticise others and think creatively, especially when they recognise that their words and ideas may harm the collectivistic harmony. Western educational systems focuses on enhancement of individuality such as self-confidence, self-esteem, and self-expression, while Eastern educational systems foster group-oriented values such as interpersonal relationship, and strong moral and spiritual values. Yet, the author argues that the collectivistic approach to criticism and creativity is often more critical and creative than Western individuals when they know what they are supposed to do for a group (or a community). Therefore, Eastern students need to think their cultural merits and demerits by using an individual perspective rather than generalised others’ perspective. The latter often discourages individual participation in a community, and the generalised others in a Western culture is weaker than Eastern. Furthermore, Western educational systems do not educate students to transform (loose) their individuality to fit into a group or a community. Rather they cultivate individuality for community prosperity. ------------------------------------------------------------ Chapter 3 introduces various cases of reverse immigration in workplaces that many immigrants return to their country or their ethnic community after many trials for acculturation. Reverse immigration is unexpected and not planned before immigration, so that its emotional embarrassment increases such severe social loneliness. Most Eastern immigrant workers have tried to adjust themselves in this new cultural environment at the early stages of immigration. However, their cultural features of collectivism, high power distance, high uncertainty avoidance, and long-term oriented cultures suppress individual initiative and eliminate the space for experiments in ways of acculturation. The author argues that returning to their ethnic community (physically and psychologically) leads to two significant problems: their distorted parenting and becoming more conservatives. The former leads the first generation of immigrants to pressure their children to pursue extrinsic or materialist values, such as financial success, fame and physical appearance, rather than on intrinsic values, while the latter refers to their isolated conservative characters because of their remoteness from the changes of their own country. The author also warns that their ethnic and religious groups actively strengthens immigrants’ social loneliness and systematically discourages immigrants’ interests and desire to be involving into local communities. The ethnic communities and leaders have not been interacting with Australian local communities and, as a result, are eager to conserve outdated cultural systems values. Even they have a tendency to weed out those people who wish to settle down within Australian local communities. They believe that those people can threaten their community’s survival and continuity. ------------------------------------------------------------ Chapter 4 titled multiculturalism argues that Korean and Eastern immigrants should more precisely understand Australia as a multicultural society in a way of collaboratively creating new cultural values. The author introduces multiculturalism with its definitions and history in Australia and argues the limitations of multiculturalism from an Easterner’s perspective. With well known tragedies of the second generations of U.S. immigrants, Cho Seung-Hui, a university student, massacred 32 people on the Virginia Tech before committing suicide and Hidal Hassan, an Army psychiatrist, killed 13 people at Fort Hood and the responses of ethnic community, the author explains that their mental illness may be derived from their parents’ (or ethnic group) culturally isolated attitude and socially static viewpoint of U.S. (Western system and values). The author insists that multiculturalism may restrict Eastern immigrants’ engagement and involvement in local communities. Multiculturalism has been systematically and historically developed based on Western systems and cultural values. In other words, multiculturalism requires high self-confidence and self-esteem that Eastern immigrants less prioritise them. It has been generally known that Easterners put more weight on human relationship than Westerners, but the author claims that this is not true. Within an individualistic culture, Westerners are more interested in building person-to-person connections and relationships. While Easterners are more interested in how individuals can achieve a sense of belonging within a group and a community. Therefore, multiculturalism is an ideology which forces Eastern immigrants to discard their strong desire to be part of a group and does not give a sense of belonging. In a consequence, the author advises that Eastern immigrants should aim towards “transculturalism” which allows them to actively participate in and contribute to their multicultural community. Transculturalism does not ask Easterners to discard their cultural values, but enables them to be a collectivistic individualist (a community leader) who is capable of developing new cultural values in a more creative and productive way. Furthermore, transculturalism encourages Western Australians in a multicultural context to collaborate with ethnic minorities to build a better community.

Reverse engineering and finite element analysis of a 3-wheeler automotive structure

Auto rickshaws (3-wheelers) are the most sought after transport among the urban and rural poor in India. The assembly of the vehicle involves assemblies of several major components. The L-angle is the component that connects the front panel with the vehicle floor. Current L-angle part has been observed to experience permanent deformation failure over period of time. This paper studies the effect of the addition of stiffeners on the L-angle to increase the strength of the component. A physical model of the L-angle was reversed engineered and modelled in CAD before static loading analysis were carried out on the model using finite element analysis. The modified L-angle fitted with stiffeners was shown to be able to withstand more load compare to previous design.

Bayesian methodology for genetics of complex diseases

Genetic research of complex diseases is a challenging, but exciting, area of research. The early development of the research was limited, however, until the completion of the Human Genome and HapMap projects, along with the reduction in the cost of genotyping, which paves the way for understanding the genetic composition of complex diseases. In this thesis, we focus on the statistical methods for two aspects of genetic research: phenotype definition for diseases with complex etiology and methods for identifying potentially associated Single Nucleotide Polymorphisms (SNPs) and SNP-SNP interactions. With regard to phenotype definition for diseases with complex etiology, we firstly investigated the effects of different statistical phenotyping approaches on the subsequent analysis. In light of the findings, and the difficulties in validating the estimated phenotype, we proposed two different methods for reconciling phenotypes of different models using Bayesian model averaging as a coherent mechanism for accounting for model uncertainty. In the second part of the thesis, the focus is turned to the methods for identifying associated SNPs and SNP interactions. We review the use of Bayesian logistic regression with variable selection for SNP identification and extended the model for detecting the interaction effects for population based case-control studies. In this part of study, we also develop a machine learning algorithm to cope with the large scale data analysis, namely modified Logic Regression with Genetic Program (MLR-GEP), which is then compared with the Bayesian model, Random Forests and other variants of logic regression.