A genetic analysis of Escherichia coli using bioinformatic methods

Escherichia coli is the best-known species of Enterobacteriaceae. The species is genetically diverse and includes both commensal pathogenic strains and plays a significant role in veterinarian, environmental, and medical science. Despite the significance of E. coli, many aspects of the species biology, such as its genetic diversity and the pathogenesis are yet to be truly understood. To understand the diversity of E. coli as a whole, genome data of E. coli derived from variety of sources: humans, animals, and environment are essential. The aims of the research are to take the outstanding opportunity provided by the availability of many new E. coli genomes and to make use of a variety of bioinformatics tools to investigate the genetic diversity and reconstruct the evolutionary history of E. coli based on a genetic analysis and a comparative genomic approach. The thesis includes three main themes. Firstly, "Distribution of extra-intestinal virulence traits among E. coli isolated from native Australian vertebrates with those isolated from humans living in Australia". The frequency and distribution of extra-intestinal virulence traits in a collection of E. coli isolated from native Australian vertebrates as compared to E. coli isolated from humans living in Australia were reported. The result shows that the frequency and distribution of some traits varies with the source of isolation, human versus animal, and that there are traits typically associated with pathogenicity islands that are absent or very rare in animal isolates. The detected high rates of recombination in phylo-group B2 strains suggest that this is an important evolutionary adaptation for attaining virulence. Secondly, "Investigation of the evolution of conjugative plasmids in E. coli and their changing role in E. coli ecology". Conjugative plasmids: key agents in the adaptation of E. coli populations were investigated. Comparing between IncI1 and IncF plasmids, IncI1 plasmids were found to be more homogeneous and genetically conserved than IncF plasmids. These plasmids have changed their role as mediators of intra- and interspecies interactions to become associated with E. coli virulence. Lastly, "Genetic and metabolic characteristics of phylo-group F". In this study, phylo-group F: a recently described group of E. coli strains was investigated. Strains belonging to phylo-group F were found to be closely related to phylo-group D strains known to be responsible for extra-intestinal infection. Whilst a high degree of strain-specific genome differences were identified among F strains, some of genes shared by F strains (absent in D, B2, and H299) were also present in other phylo-groups (A, B1, and E). All together the outcomes of this project lead to significant advances in our understanding presented in E. coli species

Minor intron splicing is critical for survival of lethal prostate cancer.

The evolutionarily conserved minor spliceosome (MiS) is required for protein expression of ∼714 minor intron-containing genes (MIGs) crucial for cell-cycle regulation, DNA repair, and MAP-kinase signaling. We explored the role of MIGs and MiS in cancer, taking prostate cancer (PCa) as an exemplar. Both androgen receptor signaling and elevated levels of U6atac, a MiS small nuclear RNA, regulate MiS activity, which is highest in advanced metastatic PCa. siU6atac-mediated MiS inhibition in PCa in vitro model systems resulted in aberrant minor intron splicing leading to cell-cycle G1 arrest. Small interfering RNA knocking down U6atac was ∼50% more efficient in lowering tumor burden in models of advanced therapy-resistant PCa compared with standard antiandrogen therapy. In lethal PCa, siU6atac disrupted the splicing of a crucial lineage dependency factor, the RE1-silencing factor (REST). Taken together, we have nominated MiS as a vulnerability for lethal PCa and potentially other cancers

NOVEL MECHANISMS OF β-ADRENERGIC SIGNALING IN PROSTATE CANCER PROGRESSION

Prostate cancer is the second leading cause of cancer death among American men. The American Cancer Society estimates that 180,890 men will be will be diagnosed with prostate cancer in 2016 in the USA. (http://www.cancer.org/cancer/prostatecancer/detailedguide/prostate-cancer-key-statistics). Androgen deprivation therapy (ADT) is the standard treatment for early stage prostate cancer. But most patients relapse with aggressive variants of prostate cancer, with survival time between 1-3 years. In order to develop cure for such aggressive variants of prostate cancer, our present understanding of the mechanisms underlying its progression needs to be advanced. Recently, it has been found that activation of β-adrenergic signaling pathway leads to aggressive variants of prostate cancer. β-adrenergic signaling involves the activation of β-adrenergic receptors (ADRBs), eventually leading to increased activation of cAMP response element-binding protein (CREB). Downstream targets of CREB activation in neuroendocrine differentiation as well as in neoangiogenesis are largely unknown, indicating that the underlying mechanisms of β-adrenergic signaling in prostate cancer progression are far from completely understood. For instance, while the epigenetic regulation by histone deacetylases 2 (HDAC2) is necessary for stress to induce cardiac hypertrophy, its mechanism are unknown in cancer progression. Similarly, another regulator of β-adrenergic signaling, GRK3 was recently shown to be a new critical regulator of prostate cancer progressionand tumor angiogenesis. However, mechanisms of GRK3 in prostate cancer progression and its regulation by ADRB2 signaling remain unknown. Our hypothesis is that GRK3 and HDAC2 are critical downstream effectors of β-adrenergic signaling-activated CREB in promoting prostate cancer progression. Here, we show that CREB directly activates GRK3 transcription by binding to its promoter and this up-regulation of GRK3 expression by ADRB2/CREB pathway is sufficient as well as necessary to induce the neuroendocrine differentiation of prostate cancer cells. We also show that downstream of chronic stress and ADRB2, CREB binds to HDAC2 promoter and activates its expression. HDAC2 further suppresses the expression of thrombospondin 1 (TSP1) in order to induce angiogenesis, thus acting as a mediator for the β-adrenergic signaling pathway. Here, we have introduced two new pathways acting downstream of the ADRB2/CREB axis. We show that the CREB/GRK3 axis leads to neuroendocrine prostate cancer progression. We have introduced a new paradigm that β-adrenergic signaling and epigenetic gene expression regulation may be working synergistically resulting in cancer progression

Narrow, Fast, and "Cool" Mantle Plumes Caused by Strain-Weakening Rheology in Earth's Lower Mantle

The rheological properties of Earth's lower mantle are key for mantle dynamics and planetary evolution. The main rock-forming minerals in the lower mantle are bridgmanite (Br) and smaller amounts of ferropericlase (Fp). Previous work has suggested that the large differences in viscosity between these minerals greatly affect the bulk rock rheology. The resulting effective rheology becomes highly strain-dependent as weaker Fp minerals become elongated and eventually interconnected. This implies that strain localization may occur in Earth's lower mantle. So far, there have been no studies on global-scale mantle convection in the presence of such strain-weakening (SW) rheology. Here, we present 2D numerical models of thermo-chemical convection in spherical annulus geometry including a new strain-dependent rheology formulation for lower mantle materials, combining rheological weakening and healing terms. We find that SW rheology has several direct and indirect effects on mantle convection. The most notable direct effect is the changing dynamics of weakened plume channels as well as the formation of larger thermochemical piles at the base of the mantle. The weakened plume conduits act as lubrication channels in the mantle and exhibit a lower thermal anomaly. SW rheology also reduces the overall viscosity, notable in terms of increasing convective vigor and core-mantle boundary heat flux. Finally, we put our results into context with existing hypotheses on the style of mantle convection and mixing. Most importantly, we suggest that the new kind of plume dynamics may explain the discrepancy between expected and observed thermal anomalies of deep-seated mantle plumes on Earth

Opposing transcriptional programs of KLF5 and AR emerge during therapy for advanced prostate cancer.

Endocrine therapies for prostate cancer inhibit the androgen receptor (AR) transcription factor. In most cases, AR activity resumes during therapy and drives progression to castration-resistant prostate cancer (CRPC). However, therapy can also promote lineage plasticity and select for AR-independent phenotypes that are uniformly lethal. Here, we demonstrate the stem cell transcription factor Krüppel-like factor 5 (KLF5) is low or absent in prostate cancers prior to endocrine therapy, but induced in a subset of CRPC, including CRPC displaying lineage plasticity. KLF5 and AR physically interact on chromatin and drive opposing transcriptional programs, with KLF5 promoting cellular migration, anchorage-independent growth, and basal epithelial cell phenotypes. We identify ERBB2 as a point of transcriptional convergence displaying activation by KLF5 and repression by AR. ERBB2 inhibitors preferentially block KLF5-driven oncogenic phenotypes. These findings implicate KLF5 as an oncogene that can be upregulated in CRPC to oppose AR activities and promote lineage plasticity

Gaussian quadrature rules for C1 quintic splines with uniform knot vectors

We provide explicit quadrature rules for spaces of C1 quintic splines with uniform knot sequences over finite domains. The quadrature nodes and weights are derived via an explicit recursion that avoids numerical solvers. Each rule is optimal, that is, requires the minimal number of nodes, for a given function space. For each of n subintervals, generically, only two nodes are required which reduces the evaluation cost by 2/3 when compared to the classical Gaussian quadrature for polynomials over each knot span. Numerical experiments show fast convergence, as n grows, to the “two-third” quadrature rule of Hughes et al. (2010) for infinite domains

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data

We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing of transcript fragments, and it ranks candidates according to several statistics. It also has a module to identify exact sequences at breakpoint junctions. FusionSeq detected known and novel fusions in a specially sequenced calibration data set, including eight cancers with and without known rearrangements