Biology subjects

Quillen, E.

Publications and source records attributed to Quillen, E..

3 recordsLinked to original sources

bioRxiv2026

The Non-Human Primate Sample Size Calculator: a design tool for longitudinal research projects

Nonhuman primates (NHP) are crucial models of human health and disease and offer the opportunity to bridge the gap between basic research and the clinic. Given the ethical considerations, high costs, and logistical constraints associated with NHP studies, careful planning is essential to maximize scientific rigor while minimizing animal use. Statistical power calculations, to determine optimal sample size, require knowing the expected number of animals at each timepoint, a challenge for longitudinal studies that must account for natural deaths or disease during a study. Here, we leveraged data from a recent study detailing NHP life- and healthspans to develop a web-based NHP study design tool, available at midas.wakehealth.edu. For 11 NHP species relevant to biomedical research, users can provide study details to generate estimates of sample counts based on natural healthspan trajectories. We envision this tool being used by colony managers and investigators for both study design and monitoring colony health over the course of a study.

physiology↗

bioRxiv2021

Integrated Omics Analysis Reveals Sirtuin Signaling is Central to Hepatic Response to a High Fructose Diet

BackgroundDietary high fructose (HFr) is a known metabolic disruptor contributing to development of obesity and diabetes in Western societies. Initial molecular changes from exposure to HFr on liver metabolism may be essential to understand the perturbations leading to insulin resistance and abnormalities in lipid and carbohydrate metabolism. We studied vervet monkeys (Clorocebus aethiops sabaeus) fed a HFr (n=5) or chow diet (n=5) for 6 weeks, and obtained clinical measures of liver function, blood insulin, cholesterol and triglycerides. In addition, we performed untargeted global transcriptomics, proteomics, and metabolomics analyses on liver biopsies to determine the molecular impact of a HFr diet on coordinated pathways and networks that differed by diet. ResultsWe show that integration of omics data sets improved statistical significance for some pathways and networks, and decreased significance for others, suggesting that multiple omics datasets enhance confidence in relevant pathway and network identification. Specifically, we found that sirtuin signaling and a peroxisome proliferator activated receptor alpha (PPARA) regulatory network were significantly altered in hepatic response to HFr. Integration of metabolomics and miRNAs data further strengthened our findings. ConclusionsOur integrated analysis of three types of omics data with pathway and regulatory network analysis demonstrates the usefulness of this approach for discovery of molecular networks central to a biological response. In addition, metabolites aspartic acid and docosahexaenoic acid (DHA), protein ATG3, and genes ATG7, HMGCS2 link sirtuin signaling and the PPARA network suggesting molecular mechanisms for altered hepatic gluconeogenesis from consumption of a HFr diet.

systems biology↗

bioRxiv2020

Dichloroacetate improves hepatic and systemic energy metabolism during sepsis

Dramatic metabolic reprogramming between an anabolic resistance and catabolic tolerance state occurs within the immune system in response to systemic infection with the sepsis syndrome. While metabolic tissues such as the liver are subject to end-organ damage during sepsis and are the primary cause of sepsis death, how their metabolic and energy reprogramming during sepsis state ensures survival is unclear. Employing comprehensive metabolomic screening, targeted lipidomic screening, and transcriptional profiling in a mouse model of septic shock, we show that hepatocyte lipid metabolism, mitochondrial TCA energetics, and redox balance are significantly reprogramed after cecal ligation and puncture (CLP). We identify increases in TCA cycle metabolites citrate, cis-aconitate, and itaconate with reduced fumarate and triglyceride accumulation in septic hepatocytes. Transcription analysis of liver tissue supports and extends the hepatocyte findings. Strikingly, the administration of the pyruvate dehydrogenase kinase (PDK) inhibitor dichloroacetate (DCA) reverses dysregulated hepatocyte metabolism and mitochondrial dysfunction. Our data indicate sepsis promotes hepatic metabolic dysfunction. Furthermore, our data indicate that targeting the mitochondrial PDC/PDK energy home-ostat rebalances transcriptional and metabolic manifestations of sepsis within the liver.

immunology↗