<div> <p>Pancreatic ductal adenocarcinoma (PDAC) is a poorly immune responsive, treatment refractory disease, representing the fourth leading cause of cancer deaths in the United States. A lack of significant improvements in patient prognoses over the last few decades highlights the necessity for a more basic understanding of how PDAC develops and progresses. To this end, the research outlined here investigates the contributions of SOX9 and PAR1 in PDAC initiation and tumor immune evasion, respectively. </p> <p>SOX9 is a developmental transcription factor important for proper pancreas development that is restricted to only a small subset of cells in the adult organ. However, SOX9 is aberrantly expressed in precancerous lesions of the pancreas and throughout PDAC development. Using genetically engineered mouse models we demonstrated that PDAC precursor lesions cannot form in the absence of SOX9 and conversely formed at an accelerated rate when SOX9 was ectopically expressed. Surprisingly deletion of SOX9 in primary mouse PDAC cell lines had no impact on tumor growth in subcutaneous allograft experiments, indicating that although SOX9 expression is necessary for PDAC initiation, it is dispensable in many cases for tumor maintenance and growth. Research investigating the transcriptional changes induced by SOX9 prior to lesion formation is ongoing to identify additional downstream factors critical for disease initiation. </p> <p>Previous research has shown that PDAC tumors frequently display low levels of immune infiltration, which is a major limitation for the use of immune-based therapeutics and is generally an unfavorable prognostic factor. We show that in primary mouse tumor cells ablation of the thrombin receptor PAR1 caused a significant increase in the infiltration of tumor targeting CD8a⁺T cells which in turn were found to eliminate PAR1 knockout tumors. When PAR1^KO and PAR1 expressing PDAC tumor cells were co-injected into wild type mice, cells lacking PAR1 were preferentially targeted and eliminated by the immune system, indicating that PAR1 provides cell autonomous protection during an active anti-tumor adaptive immune response. Furthermore, we identified a previously underappreciated association between PAR1-mediated expression of <i>Csf2</i> and <i>Ptgs2</i>, and PDAC tumor immune evasion. Together these findings provide novel insights into the mechanisms and drivers of PDAC initiation and immune evasion.</p> </div> <br>

<p>Within the last few decades, swine breeding programs have been refined to include pork quality and novel carcass traits alongside growth, feed efficiency, and carcass leanness in the selection programs for terminal sire lines with a goal to produce high quality and efficient pork product for consumers. In order to accurately select for multiple traits at once, it becomes imperative to explore their genetic and biological architecture. The genetic architecture of traits can be explored through the estimation of genetic parameters, genome-wide association studies (GWAS), gene networks and metabolic pathways. An alternative approach to explore the genetic and biological connection between traits is based on principal component analysis (PCA), which generates novel “pseudo-phenotypes” and biological types (biotypes). In this context, the main objective of this thesis was to understand the genetic and biological relationship between three growth, eight conventional carcass, 10 pork quality, and 18 novel carcass traits included in two studies. The phenotypic data set included 2,583 records from female Duroc pigs from a terminal sire line. The pedigree file contained 193,764 animals and the genotype file included 21,344 animals with 35,651 single nucleotide polymorphisms (SNPs). The results of the first study indicate that genetic progress can be achieved for all 39 traits. In general, the heritability estimates were moderate, while most genetic correlations were generally moderate to high and favorable. Some antagonisms were observed but those genetic correlations were low to moderate in nature. Thus, these relationships can be considered when developing selection indexes. The second study showed that there are strong links between traits through their principal components (PCs). The main PCs identified are linked to biotypes related to growth, muscle and fat deposition, pork color, and body composition. The PCs were also used as pseudo-phenotypes in the GWAS analysis, which identified important candidate genes and metabolic pathways linked to each biotype. All of this evidence links valuable variables such as belly, color, marbling, and leanness traits. Our findings greatly contribute to the optimization of genetic and genomic selection for the inclusion of valuable and novel traits to improve productive efficiency, novel carcass, and meat quality traits in terminal sire lines.<br></p><p></p>

Adult mammalian <a></a><a>cardiomyocytes </a>(CMs, or heart muscle cells) have little, if any, ability to proliferate in response to injury, and after myocardial infarction this defect underlies the poor regenerative ability of human hearts. In contrast, early stage of CMs (such as fetal CMs) still have some ability to proliferate, and we seek to identify novel gene regulators as potential therapeutic targets for heart regeneration. Here we use human pluripotent stem cells (hPSCs) as an in vitro human model to investigate the roles of emerging long non-coding RNAs (lncRNAs), with the lengths of over 200 nucleotides are able to be transcribed but not translated into protein, for heart regeneration. With public available RNA-sequencing data, we identified several human genes, including lncRNAs, that are highly enriched in fetal CMs. We generated targeted gene knockout hPSC lines using CRISPR/Cas9-mediated genome editing and will use them to study the roles of selected genes in regulating CM proliferation. To identify more therapeutic targets, we also generated a fluorescence ubiquitination cell cycle indicator (FUCCI) reporter cell line that express either green (indicating dividing cells) or red fluorescence (indicating non-dividing cells), on which we’ll perform unbiased genome-wide screening to identity genes that regulate CM proliferation. High-throughput chemical screening will also be performed on FUCCI reporter lines to identify potential therapeutic drugs for heart regeneration.

<p>Systemic dehydration negatively alters epithelial cell junction markers and inflammatory mediators  in  vocal  fold  tissue.  In other  organs,  dehydration canhave the  following  suboptimal outcomes; prolonged inflammation and delayed re-epithelization.It is surprising that the adverse role  of  systemic  dehydration  in  vocal  fold  healing  has  not  been  directly  demonstrated  when dehydration has the potential to alter recovery following injury. The similarities between healing in dermal and mucosal tissue indicate an increased need to understand the effects of dehydration onvocal fold recovery.</p> <p>Suboptimal vocal fold healing can have downstream consequences on vibratory function. Before functional voice changes can be delineated, there is a need to characterize the cellular interactions of  systemic  dehydration  and  vocal  fold  healing.   The  overarching  research  aim  of  this dissertation is to investigate the interaction of systemic dehydration and vocal fold healing on the gene expression of inflammatory and epithelial cell junction markers, following acute vocal  fold  injury.Gene expressionoutcomes werecompared  in four  groups;systemically-dehydrated,and  euhydrated  rats with minor,  bilateral  vocal  fold  injuriesand  systemically-dehydrated  and  euhydrated  rats  without  vocal  fold  injuries (N=9/group). We  hypothesized  that systemic  dehydration(compared  to  euhydration)would  cause an upregulation  of  pro  and  anti-inflammatory mediators with injury, but adownregulation of these inflammatory markers in the absence  of  injury.  We  also  hypothesized  that  systemic  dehydration(compared  to  euhydration)would cause a downregulation of epithelial cell junction markers with and without injury, butthat the effects of dehydration would be exacerbated with injury. </p> <p>We  found  that  the  gene  expression  of  pro-inflammatory  cytokines  was  differentially expressed  in  systemically-dehydrated  injured  vocal  old  tissue  when  compared  to  systemically-euhydrated injured vocal  fold  tissue, 24  hours  after  vocal  fold  injury. These  data  lay  the groundwork for future studies characterizing the later stages of interaction of systemic dehydration and injury.</p>

Despite major advances in treatment, pediatric cancers in the 5-16 age group remain the most common cause of disease death, and one out of eight children with cancer will not survive. Among children that do survive, some 60% suffer from late effects such as cancer recurrence and increased risk of obesity. This paper will provide a broad overview of pediatric oncology in the context of systems medicine. Systems medicine utilizes an integrative approach that relies on patient information gained from omics technology. A major goal of a systems medicine is to provide personalized medicine that optimizes positive outcomes while minimizing deleterious short and long-term sideeffects. There is an ever increasing development of effective cancer drugs, but a major challenge lies in picking the most effective drug for a particular patient. As detailed below, high-throughput omics technology holds the promise of solving this problem. Omics includes genomics, epigenomics, and proteomics. System medicine integrates omics information and provides detailed insights into disease mechanisms which can then inform the optimal treatment strategy.

Nitrogen (N) is a central nutrient in cropping systems. However, a considerable N fraction is lost through runoffs and leaching with detrimental consequences for environment and controversial effects on human health. Increasing the plant N uptake by optimizing the degree of root branching for exploring a larger soil volume in search of the mobile nitrate resource may contribute to limit soil leaching and subsequently to rely more efficiently on the soil mineralization and fertilizer inputs. Rapeseed (Brassica napus L.) is a major oil crop that highly depends on N fertilization. This doctoral thesis aims at exploring the diversity of root morphology in recently selected cultivars and in a large set of rapeseed inbred lines, and at understanding the genetic control on root morphology and how it is impacted by N nutrition.Firstly, a panel of twenty-eight European recently selected cultivars of winter oilseed rape were tested in laboratory and field conditions. Upon hydroponic culture, these hybrids showed a great diversity for biomass production and root morphological traits. Differences in root and shoot dry biomasses and lateral root length were mainly explained by the genotype, while differences in primary root length by the nutrition. The cultivars were tested in a pluriannual field trial. The observed variation for yield and seed quality traits attributed to the genotype was more important than the year or the genotype x year interaction effects. The total root length measured in laboratory could predict the proportion of nitrogen taken-up from the field and reallocated to the seeds. The genetic interrelationship between cultivars, established with polymorphic markers, indicated a very narrow genetic base. Positive correlations were found between the genetic distance measures, root morphological trait distances during nitrogen depletion conditions, and agronomic performance. Secondly, three cultivars previously selected from a root morphology screen at a young developmental stage were field tested with two nitrogen applications. The purpose was to examine the relationship between root morphology and Nitrogen Uptake Efficiency (NUpE) and to test the predictiveness of canopy optical indices for seed quality and yield. A tube-rhizotron system was used to incorporate below-ground root growth information. One-meter length clear tubes were installed in soil at an angle of 45°. The root development was followed with a camera at key growth stages in autumn (leaf development) and spring (stem elongation and flowering). Autumn was a critical time window to observe the root development and exploration in deeper horizons (36-48 cm) was faster without any fertilization treatment. Analysis of the rhizotron images was challenging and it was not possible to clearly discriminate between cultivars. Canopy reflectance and leaf optical indices were measured with proximal sensors. The Normalized Difference Vegetation Index (NDVI) was a positive indicator of biomass and seed yield while the Nitrogen Balance Index (NBI) was a positive indicator of above-ground biomass N concentration at flowering and seed N concentration at harvest.Thirdly, the natural variability offered by a diversity set of 392 inbred lines was screened to apprehend the genetic control of root morphology in rapeseed and how it is impacted by nitrogen nutrition. Seedlings grew hydroponically with low (0.2 mM) or elevated (5 mM) nitrate supplies. Low nitrate supply triggered the primary root and lateral root growth, while elevated supply promoted shoot biomass production. A considerable variation degree in the root morphological traits was observed across the diversity set, and there was no trade-off between abundant lateral root branching and shoot biomass production. Root traits were mainly dependent on the genotype and highly heritable. A genome wide association study identified some genomic regions associated with biomass production and root morphological traits. A total of fifty-nine QTLs were identified and thirty of them were integrated into seven clusters on chromosomes A01 and C07. Some candidate genes were identified with Arabidopsis orthologs related to root growth and development, nitrogen nutrition or hormone regulation.This study provides promising routes for redesigning the root system architecture by uncovering nitrogen-interactive genomic regions shaping root morphology. A perspective is to develop genetic markers associated with root morphological traits that could be used for assisted breeding. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

No description available.

<p> Obesity is a growing concern as 42.3% of people in the U.S were considered obese in the years 2017- 2018. Little is known about the genetic components that contribute to weight gain. In humans, the hormone glucagon is a major contributor to the body’s energy demand as it helps break down lipids. Therefore, learning more about this pathway could enable a range of therapeutics. In fact, studies have shown that glucagon treatments have helped patients with both weight loss and appetite suppression. In this project, we analyzed candidate genes that modify the glucagon pathway in <em>Drosophila melanogaster.</em> We reduced the expression of the fly version of the glucagon receptor (AKHR) in our model. This induces fat retention in the L3 larvae, which mimics obesity in humans. We then crossed our model to the DGRP and looked for natural variation in fat content using a density assay. The density assay examines the relative fat levels of the larvae by slowly increasing the amount of sucrose in water. This enables us to observe whether we have lean larvae which float later or fat larvae which float early on. We used the variation in floating concentration to identify candidate modifier genes through GWA or genome-wide association study. We crossed our <em>AKHR</em> RNAi model to RNAi for various candidate modifier genes that may enhance or suppress fat retention. We screened these candidates initially with the same density assay used in the original study. This resulted in four candidate genes that significantly impacted the density of the larvae: <em>THADA</em>, <em>AmyD</em>, <em>GluRIIC</em>, and <em>CG9826</em>. We further characterized these candidates using biochemical assays to analyze stored metabolites such as triglycerides, glucose, glycogen, and protein. These have been further analyzed under control, high sugar, and high fat conditions to see if the larvae are resistant to environmental changes. <em>CG9826</em> showed significant increase in stored fats across all environments. <em>THADA</em> RNAi showed an increase in fat in the high fat environment. Overexpression of <em>THADA</em> showed a decrease in fat storage in the high fat environment. Our goal is to advance our understanding of the glucagon signaling pathway, obesity, and lipid metabolism. We are also hopeful to provide candidate genes that can be regarded as future therapeutic targets. </p>

Assortative Mating, the tendency for mate selection to occur on the basis of similar traits, plays an essential role in understanding the genetic variation on academic achievements and intelligence (IQ). It is an important mechanism explaining spousal concordance. We used principal component analysis (PCA) for spousal correlation. There is a significant positive correlation between spouses by the new variable PC1 (correlation coefficient=0.515, p<0.0001). We further research the genetic factor that affects IQ by using the same data. We performed a low density genome-wide association (GWA) analysis with a family-based association test to identify genetic variants that associated with intelligence as measured by WAIS full-score IQ (FSIQ). NTM at 11q25 (rs411280, p=0.000764) and NR3C2 at 4q31.23 (rs3846329, p=0.000675) were 2 novel genes that haven't been associated with IQ from other studies. This study may serve as a resource for replication in other populations and a foundation for future investigations.

No description available.