Bayesian Repulsive Gaussian Mixture Model

We develop a general class of Bayesian repulsive Gaussian mixture models that encourage well-separated clusters, aiming at reducing potentially redundant components produced by independent priors for locations (such as the Dirichlet process). The asymptotic results for the posterior distribution of the proposed models are derived, including posterior consistency and posterior contraction rate in the context of nonparametric density estimation. More importantly, we show that compared to the independent prior on the component centers, the repulsive prior introduces additional shrinkage effect on the tail probability of the posterior number of components, which serves as a measurement of the model complexity. In addition, an efficient and easy-to-implement blocked-collapsed Gibbs sampler is developed based on the exchangeable partition distribution and the corresponding urn model. We evaluate the performance and demonstrate the advantages of the proposed model through extensive simulation studies and real data analysis. The R code is available at https://drive.google.com/open?id=0B_zFse0eqxBHZnF5cEhsUFk0cVE

Genetic Analysis of Dog Congenital Deafness and Herding Behavior

Strong artificial selections of canine morphological and behavioral traits lead to the formation of more than 400 modern dog (Canis familiaris, CFA) breeds within the past 300 years. Most dog breeds are derived from small numbers of founders, and this closed genetic pool within each breed results in the high frequency of occurrence of canine congenital disorders. The majority of these heredopathies share common clinical signs with corresponding human diseases. Therefore, dogs are appropriate spontaneous models for studying human diseases. Congenital deafness can cause both health and welfare problems in dogs, and it is quite prevalent among several dog breeds such as Dalmatian, Australian Cattle Dog, English Setter and Australian Stumpy Tail Cattle Dog (ASCD). However, hearing loss causative or associated genes in these dog breeds are not yet identified. The purpose of the study in Chapter 2 was to identify congenital deafness related genes in ASCD. Three bilateral deaf and one normal hearing ASCDs were whole genome sequenced. The publicly available 722 canine whole genome sequences were also used to investigate potential causative mutations in this study. A case-control genome-wide association study (GWAS) was conducted by setting three deafness affected ASCDs as cases, and one unaffected ASCD and 43 additional herding group dogs were used as controls. The GWAS identified several loci on six chromosomes with potential canine deafness association (CFA3, 8, 17, 23, 28 and 37), and most (7 out of 13) of the significantly associated loci were located within CFA37. The private variants unique to three deaf ASCD were filtered by comparison to 722 canine controls of over 144 modern breeds. Subsequent annotation of these variants was performed, only potentially functional variants were filtered resulting in four remaining missense mutations. A missense mutation in the Kruppel-like factor 7 (KLF7) gene (NC_006619.3: g.15562684G>A; XP_022270984.1: p.Leu173Phe) on CFA37 could be emphasized to be associated considering the variant effect prediction and gene function. KLF7 inner ear expression and a corresponding functional impact in development of inner ear and sensory neurons is known. Further genotyping of the KLF7 variant in 28 affected and 27 normal hearing ASCDs still supported its association with ASCD congenital deafness. Dogs have been selectively bred to intensify the performance abilities in regard to diverse tasks such as herding, hunting or companionship. Finally, modern dog breeds vary diversely in not only morphological but also behavioral traits. GWAS analysis of dog morphological traits using breed standard values have been well studied, and many auspicious genes were identified. However, due to the complexity of dog behavior traits, research progress on this topic is still limited. The study of Chapter 3 was intended to elucidate the candidate genes underlying dog behavior traits including herding, predation, temperament and trainability. The phenotype information of these behavioral traits was obtained from American Kennel Club, which classified dog breeds into seven groups (Herding, Hound, Working, Terrier, Toy, Sporting and Non-sporting) based on the behavior, heritage and historical roles. 268 publicly available dog whole genome sequences of 130 modern breeds were used in this study. Four GWASs were performed to investigate potential candidate genes. Dogs with herding behavior were compared with the other dog categories by GWAS. Candidate neurological genes such as THOC1, ASIC2, MSRB3, LLPH, RFX8 and CHL1 were detected within or nearest to the significant loci of herding GWAS. Regarding dog predation behavior, herding behavior is the modified predatory behavior like repression of killing instinct, while hound dogs were selectively bred to enhance predation behaviors. We then use hound and herding group dogs in GWAS to analyze the dog predation behavior. Three neural genes JAK2, MEIS1 and LRRTM4 that were nearest to the significant loci of predation GWAS were revealed as candidates. In temperament GWAS, candidate neurological gene ACSS3 was significantly associated with dog temperament trait. Dog behaviors were reported to be associated with body mass, so we repeated the four GWASs with incorporating dog breed standard body size as covariates. Similar results except for the significant associations of ASIC2, JAK2 and MEIS1 were observed, while these three candidate genes could contribute to dog behaviors through their effects on dog brain architecture. Linkage disequilibrium (LD) analysis of the herding GWAS significant associated signals were also conducted. Promising neurological processes or cellular components were disclosed in GO analysis of potentially functional private genes of herding dogs. In the study described in Chapter 4, one loss of function mutation in ABHD16B was identified to be associated with bull infertility. However, the exact gene function of ABHD16B remains unknown. Western blot was applied to locate ABHD16B protein expression, uncovering its occurrence in bull testis tissue but not in sperm cells. ABHD16B protein owns a function domain of α/β-hydrolase (ABHD) and several ABHD members are involved in lipid metabolism. It is assumed that ABHD16B could play roles in biosynthesis of sperm membrane lipids. Lipidomes of heterozygous and homozygous wild-type bull sperms were analyzed to explore potential aberrations. Several lipid components including PC, DAG, Cer, SM and PC were found significantly altered which verified our hypothesis. Therefore, the imbalanced lipid homeostasis of sperm membrane could be responsible for the bull infertility problem subjected in this study.2021-10-1

A “FRONTIER” OR A “SPHERE”: AN ESSAY ON A LEGACY OF EUROPEAN COLONIALISM

As a historical phenomenon, European colonialism has, from its beginning through the present day, a tremendous influence on the history of human beings, and has long been studied by students and scholars from all parts of the world. Traditional understandings of the motivations and impacts of European colonialism has focused on the economic, political, and religious areas, which, without doubts, are true and sound. However, the mentality behind the decisions and actions of colonialism was not commonly understood. This paper focus on exploring this type of predatory “frontier” mentality, as well as its antithesis the “sphere” mentality, through interpreting and understanding the human mind behind the various causes and consequences of European colonialism. Given the current global situation, the growth of the “sphere” mentality and the decline of its antithesis is likely to be the general trend as a product of the evolution of human civilization in the twenty first century. This shift in human mentality from competition to cooperation is the biggest legacy of European colonialism.&nbsp

MAMMALIAN ADAPTATION MECHANISM OF INFLUENZA A VIRUS REPLICATION MECHINERY

ABSTRACT The incompatibility between avian influenza viruses and host factors within mammalian hosts constitutes the major host restriction on influenza A virus polymerase complex. To overcome restrictions of viral polymerase complex, the virus has evolved diverse adaptive strategies. The PB1 gene segment originated from avian strains has recurrently appeared in 1918, 1957, and 1968 pandemic viruses. Although this recurrent selection of the avian-origin PB1 segment has been correlated with enhanced viral polymerase activity in mammalian cells, the underlying mechanism behinds this phenomenon is still enigmatic. Using 2009 pH1N1 virus which naturally lacks the avian-origin PB1 segment and the canonical mammalian-signature PB2 E627K mutation, we demonstrate that the avian-origin PB1 can markedly enhance functions (both replication and transcription) of pH1N1 polymerase in human cells even in the absence of canonical PB2-associated adaptive mutations (E627K and G590S/Q591R). Mechanistically, acquisition of avian-origin PB1 does not change the interaction between polymerase subunits, or assembly of polymerase complex and viral ribonucleoprotein. In viral replication, acquisition of the avian-origin PB1 specifically facilitates the vRNA synthesis of 2009 pH1N1 polymerase by stimulating the trans-activation on cRNA-associated polymerase, thereby leading to the enhanced overall replication and polymerase activity. We extrapolate our finding to the function of acidic nuclear phosphoprotein 32 family member A (ANP32A), the major host factor underlying host restrictions on viral polymerase complex. We substantiate that the SR polymorphism (G590S/Q591R) is also deployed by viruses to accommodate the species difference in ANP32A, which is like the function of PB2 E627K. Our results also indicate that chicken ANP32A can specifically enhance vRNA synthesis of avian-like (PB2 627E) polymerase by promoting the trans-activating effect in replication without altering the genuine vRNP assembly capacity. Collectively, our results suggest that the trans-activation process in vRNA synthesis of un-adapted avian influenza polymerase is a defective step that needs to be restored via mammalian adaptation of viral polymerase complex