Novel organoid models for the functional validation of pancreatic cancer genomic variants

With a five-year survival rate of 9%, pancreatic ductal adenocarcinoma (PDAC) has the one of the worst prognoses of all cancers. Some limitations in the understanding of the disease are due to the lack of representative in vitro patient tumour models. In order to overcome this unmet preclinical need, this thesis outlines the establishment of a method for the development of organoid and isogenic matched primary cancer cell line models from patient derived xenograft (PDX) tumours. In order to create a patient-reflective yet versatile in vitro model, the matched primary cell line was developed further and subsequently generated organoids, termed cell line organoids (CLOs). These CLOs represent the phenotypic and transcriptomic profile of the original organoids and PDX tumour. Recent genome wide association studies (GWAS) and pathway analyses have implicated genes and single nucleotide polymorphisms (SNPs) from the maturity onset diabetes of the young (MODY) gene set and the Pujana ATM Pearson correlation coefficient (PCC) network in the development of PDAC. The biological functionality of the genomic variants identified from the GWAS-enriched pathways were assessed using in silico methods and experimental dual luciferase reporter assays. Genes in the MODY pathway such as hepatocyte nuclear factor-1 alpha/beta (HNF1A and HNF1B) act as transcription factors. Their role in cancer progression was assessed through single and double CRISPR knockouts in PDAC primary cell cultures. CUT&RUN (cleavage under targets and release using nuclease) was performed to identify genes regulated by HNF1A and HNF1B TFs. Additionally, targeting the DNA damage response (DDR) pathway in non-BRCA mutated PDAC was assessed using a novel drug which mimics the effect of a BRCA2 mutation. In conclusion, this thesis shows the development of novel, adaptable organoid models for functional validation of genomic variants in PDAC. Furthermore, biological investigation of GWAS pathway identified SNPs and genes from the MODY and Pujana ATM PCC pathways highlights the powerful nature of these tools in identifying genomic variants associated with PDAC. It also highlights the importance of functional experimental analysis to provide better understanding of their role in the development and progression of PDAC

Information Content of Spontaneous Symmetry Breaking

We propose a measure of order in the context of nonequilibrium field theory and argue that this measure, which we call relative configurational entropy (RCE), may be used to quantify the emergence of coherent low-entropy configurations, such as time-dependent or time-independent topological and nontopological spatially-extended structures. As an illustration, we investigate the nonequilibrium dynamics of spontaneous symmetry-breaking in three spatial dimensions. In particular, we focus on a model where a real scalar field, prepared initially in a symmetric thermal state, is quenched to a broken-symmetric state. For a certain range of initial temperatures, spatially-localized, long-lived structures known as oscillons emerge in synchrony and remain until the field reaches equilibrium again. We show that the RCE correlates with the number-density of oscillons, thus offering a quantitative measure of the emergence of nonperturbative spatiotemporal patterns that can be generalized to a variety of physical systems.Comment: LaTeX, 9 pages, 5 figures, 1 tabl

Most \u3cem\u3eCaenorhabditis elegans\u3c/em\u3e MicroRNAs are Individually Not Essential for Development or Viability

MicroRNAs (miRNAs), a large class of short noncoding RNAs found in many plants and animals, often act to post-transcriptionally inhibit gene expression. We report the generation of deletion mutations in 87 miRNA genes in Caenorhabditis elegans, expanding the number of mutated miRNA genes to 95, or 83% of known C. elegans miRNAs. We find that the majority of miRNAs are not essential for the viability or development of C. elegans, and mutations in most miRNA genes do not result in grossly abnormal phenotypes. These observations are consistent with the hypothesis that there is significant functional redundancy among miRNAs or among gene pathways regulated by miRNAs. This study represents the first comprehensive genetic analysis of miRNA function in any organism and provides a unique, permanent resource for the systematic study of miRNAs

Plasticity of face processing in infancy

Experience plays a crucial role for the normal development of many perceptual and cognitive functions, such as speech perception. For example, between 6 and 10 months of age, the infant's ability to discriminate among native speech sounds improves, whereas the ability to discriminate among foreign speech sounds declines. However, a recent investigation suggests that some experience with nonnative languages from 9 months of age facilitates the maintenance of this ability at 12 months. Nelson has suggested that the systems underlying face processing may be similarly sculpted by experience with different kinds of faces. In the current investigation, we demonstrate that, in human infants between 6 and 9 months of age, exposure to nonnative faces, in this case, faces of Barbary macaques (Macaca sylvanus), facilitates the discrimination of monkey faces, an ability that is otherwise lost around 9 months of age. These data support, and further elucidate, the role of early experience in the development of face processing

A maximum rupture model for the central and southern Cascadia subduction zone—reassessing ages for coastal evidence of megathrust earthquakes and tsunamis

A new history of great earthquakes (and their tsunamis) for the central and southern Cascadia subduction zone shows more frequent (17 in the past 6700 yr) megathrust ruptures than previous coastal chronologies. The history is based on along-strike correlations of Bayesian age models derived from evaluation of 554 radiocarbon ages that date earthquake evidence at 14 coastal sites. We reconstruct a history that accounts for all dated stratigraphic evidence with the fewest possible ruptures by evaluating the sequence of age models for earthquake or tsunami contacts at each site, comparing the degree of temporal overlap of correlated site age models, considering evidence for closely spaced earthquakes at four sites, and hypothesizing only maximum-length megathrust ruptures. For the past 6700 yr, recurrence for all earthquakes is 370–420 yr. But correlations suggest that ruptures at ∼1.5 ka and ∼1.1 ka were of limited extent (<400 km). If so, post-3-ka recurrence for ruptures extending throughout central and southern Cascadia is 510–540 yr. But the range in the times between earthquakes is large: two instances may be ∼50 yr, whereas the longest are ∼550 and ∼850 yr. The closely spaced ruptures about 1.6 ka may illustrate a pattern common at subduction zones of a long gap ending with a great earthquake rupturing much of the subduction zone, shortly followed by a rupture of more limited extent. The ruptures of limited extent support the continued inclusion of magnitude-8 earthquakes, with longer ruptures near magnitude 9, in assessments of seismic hazard in the region

Feature selection for chemical sensor arrays using mutual information

We address the problem of feature selection for classifying a diverse set of chemicals using an array of metal oxide sensors. Our aim is to evaluate a filter approach to feature selection with reference to previous work, which used a wrapper approach on the same data set, and established best features and upper bounds on classification performance. We selected feature sets that exhibit the maximal mutual information with the identity of the chemicals. The selected features closely match those found to perform well in the previous study using a wrapper approach to conduct an exhaustive search of all permitted feature combinations. By comparing the classification performance of support vector machines (using features selected by mutual information) with the performance observed in the previous study, we found that while our approach does not always give the maximum possible classification performance, it always selects features that achieve classification performance approaching the optimum obtained by exhaustive search. We performed further classification using the selected feature set with some common classifiers and found that, for the selected features, Bayesian Networks gave the best performance. Finally, we compared the observed classification performances with the performance of classifiers using randomly selected features. We found that the selected features consistently outperformed randomly selected features for all tested classifiers. The mutual information filter approach is therefore a computationally efficient method for selecting near optimal features for chemical sensor arrays

Particle fluxes associated with mesoscale eddies in the Sargasso Sea

Author Posting. © Elsevier B.V., 2008. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 55 (2008): 1426-1444, doi:10.1016/j.dsr2.2008.02.007.We examined the impact of a cyclonic eddy and mode-water eddy on particle flux in the Sargasso Sea. The primary method used to quantify flux was based upon measurements of the natural radionuclide, 234Th, and these flux estimates were compared to results from sediment traps in both eddies, and a 210Po/210Pb flux method in the mode-water eddy. Particulate organic carbon (POC) fluxes at 150m ranged from 1 to 4 mmol C m-2 d-1 and were comparable between methods, especially considering differences in integration times scales of each approach. Our main conclusion is that relative to summer mean conditions at the Bermuda Atlantic Time-series Study (BATS) site, eddy-driven changes in biogeochemistry did not enhance local POC fluxes during this later, more mature stage of the eddy life cycle (>6 months old). The absence of an enhancement in POC flux puts a constraint on the timing of higher POC flux events, which are thought to have caused the local O2 minima below each eddy, and must have taken place >2 months prior to our arrival. The mode-water eddy did enhance preferentially diatom biomass in its center where we estimated a factor of 3 times higher biogenic Si flux than the BATS summer average. An unexpected finding in the highly depth resolved 234Th data sets are narrow layers of particle export and remineralization within the eddy. In particular, a strong excess 234Th signal is seen below the deep chlorophyll maxima which we attribute to remineralization of 234Th bearing particles. At this depth below the euphotic zone, de novo particle production in the euphotic zone has stopped, yet particle remineralization continues via consumption of labile sinking material by bacteria and/or zooplankton. These data suggest that further study of processes in ocean layers is warranted not only within, but below the euphotic zone.The EDDIES project was funded by the National Science Foundation Chemical, Biological, and Physical Oceanography Programs. Additional support for HPLC pigment analysis (Dr. Charles Trees, CHORS) was provided by NASA

"Open Innovation" and "Triple Helix" Models of Innovation: Can Synergy in Innovation Systems Be Measured?

The model of "Open Innovations" (OI) can be compared with the "Triple Helix of University-Industry-Government Relations" (TH) as attempts to find surplus value in bringing industrial innovation closer to public R&D. Whereas the firm is central in the model of OI, the TH adds multi-centeredness: in addition to firms, universities and (e.g., regional) governments can take leading roles in innovation eco-systems. In addition to the (transversal) technology transfer at each moment of time, one can focus on the dynamics in the feedback loops. Under specifiable conditions, feedback loops can be turned into feedforward ones that drive innovation eco-systems towards self-organization and the auto-catalytic generation of new options. The generation of options can be more important than historical realizations ("best practices") for the longer-term viability of knowledge-based innovation systems. A system without sufficient options, for example, is locked-in. The generation of redundancy -- the Triple Helix indicator -- can be used as a measure of unrealized but technologically feasible options given a historical configuration. Different coordination mechanisms (markets, policies, knowledge) provide different perspectives on the same information and thus generate redundancy. Increased redundancy not only stimulates innovation in an eco-system by reducing the prevailing uncertainty; it also enhances the synergy in and innovativeness of an innovation system.Comment: Journal of Open Innovations: Technology, Market and Complexity, 2(1) (2016) 1-12; doi:10.1186/s40852-016-0039-

Hematopoietic reconstitution by multipotent adult progenitor cells: precursors to long-term hematopoietic stem cells

For decades, in vitro expansion of transplantable hematopoietic stem cells (HSCs) has been an elusive goal. Here, we demonstrate that multipotent adult progenitor cells (MAPCs), isolated from green fluorescent protein (GFP)-transgenic mice and expanded in vitro for >40–80 population doublings, are capable of multilineage hematopoietic engraftment of immunodeficient mice. Among MAPC-derived GFP+CD45.2+ cells in the bone marrow of engrafted mice, HSCs were present that could radioprotect and reconstitute multilineage hematopoiesis in secondary and tertiary recipients, as well as myeloid and lymphoid hematopoietic progenitor subsets and functional GFP+ MAPC-derived lymphocytes that were functional. Although hematopoietic contribution by MAPCs was comparable to control KTLS HSCs, approximately 103-fold more MAPCs were required for efficient engraftment. Because GFP+ host-derived CD45.1+ cells were not observed, fusion is not likely to account for the generation of HSCs by MAPCs

An Information-Theoretic Link Between Spacetime Symmetries and Quantum Linearity

A nonlinear generalisation of Schrodinger's equation is obtained using information-theoretic arguments. The nonlinearities are controlled by an intrinsic length scale and involve derivatives to all orders thus making the equation mildly nonlocal. The nonlinear equation is homogeneous, separable, conserves probability, but is not invariant under spacetime symmetries. Spacetime symmetries are recovered when a dimensionless parameter is tuned to vanish, whereby linearity is simultaneously established and the length scale becomes hidden. It is thus suggested that if, in the search for a more basic foundation for Nature's Laws, an inference principle is given precedence over symmetry requirements, then the symmetries of spacetime and the linearity of quantum theory might both be emergent properties that are intrinsically linked. Supporting arguments are provided for this point of view and some testable phenomenological consequences highlighted. The generalised Klien-Gordon and Dirac equations are also studied, leading to the suggestion that nonlinear quantum dynamics with intrinsically broken spacetime symmetries might be relevant to understanding the problem of neutrino mass(lessness) and oscillations: Among other observations, this approach hints at the existence of a hidden discrete family symmetry in the Standard Model of particle physics.Comment: 43 pages; minor revisions. essentially journal versio