Digital Commons Network^™

Association Of Social Determinants, Lifestyle, And Metabolic Factors With Mortality In Chinese Adults: A Nationwide 10-Year Prospective Cohort Study, Jieli Lu, Mian Li, Jiang He, Yu Xu, Ruizhi Zheng, Jie Zheng, Guijun Qin, Yingfen Qin, Yuhong Chen, Xulei Tang, Zhen Ye, Min Xu, Tiange Wang, Lixin Shi, Qing Su, Xuefeng Yu, Li Yan, Zhiyun Zhao, Qin Wan, Gang Chen, Zhengnan Gao, Guixia Wang, Feixia Shen, Xuejiang Gu, Zuojie Luo, Li Chen, Xinguo Hou, Yanan Huo, Qiang Li, Hong Qiao, Yinfei Zhang, Tianshu Zeng, Chunyan Hu, Qiuyu Cao, Xiaojing Jia, Chao Liu, Youmin Wang, Shengli Wu, Tao Yang, Huacong Deng, Hongyan Qi, Xueyan Wu, Di Zhang, Meng Dai, Donghui Li, Shenghan Lai, Lulu Chen, Jiajun Zhao, Yiming Mu, Weiguo Hu, Guang Ning, Ruying Hu, Yufang Bi, Weiqing Wang, 4c Study Group

Faculty, Staff and Student Publications

Nationwide estimates of the impact of common modifiable risk factors on mortality remain crucial. We aim to assess the influence of social determinants, lifestyle, and metabolic factors on mortality in 174,004 adults aged ≥40 years from the China Cardiometabolic Disease and Cancer Cohort (4C) Study. We reveal that 17 modifiable factors are independently associated with mortality, accounting for 64.8% of all-cause mortality, 77.4% of cardiovascular mortality, and 44.8% of cancer mortality. Low education emerges as the leading factor for both all-cause and cancer mortality, while hypertension is predominant for cardiovascular mortality. Moreover, low gross domestic product per capita and high …

Effect Of The Implementation Of A Multiple-Behavior Self-Monitoring Intervention On Dietary Intake In Type 2 Diabetes: Secondary Data Analysis, Jisook Ko, Jing Wang, Ngozi Mbue, Susan Schembre, Stanley Cron

Faculty, Staff and Student Publications

Background: An electronic diary embedded in a mobile device to monitor lifestyle can be as effective as traditional methods. However, the efficacy of self-monitoring multiple behaviors for dietary intake has not been well studied in people with diabetes.

Objective: This study aimed to compare the effect of using technology-assisted self-monitoring versus paper diaries on changes in dietary intake.

Methods: This is a secondary analysis of data collected from 39 people with type 2 diabetes as part of a 3-month pilot clinical trial. Changes in energy intake and the contribution of total fat intake and total carbohydrate intake to total calories …

Junctophilin-2 Regulates Mitochondrial Metabolism, Sasha Z Prisco, Lynn M Hartweck, Felipe Kazmirczak, Jenna B Mendelson, Stephanie L Deng, Madelyn Blake, Satadru K Lahiri, Xander H T Wehrens, Kurt W Prins

Faculty, Staff and Students Publications

No abstract provided.

Vitamin D And Metabolic Bone Disease In Prolonged Continuous Kidney Replacement Therapy: A Prospective Observational Study., Peace Dorothy Imani, Molly Vega, Naile Tufan Pekkucuksen, Poyyapakkam Srivaths, Ayse Akcan Arikan

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Complications of prolonged continuous kidney replacement therapy (CKRT) have not been well described. Our objective was to describe mineral metabolism and bone findings in children who required prolonged CKRT.

METHODS: In this single center prospective observational study, we enrolled 37 patients who required CKRT for ≥ 28 days with regional citrate anticoagulation. Exposure was duration on CKRT and outcomes were 25-hydroxy vitamin D and osteopenia and/or fractures.

RESULTS: The prevalence of vitamin D deficiency and insufficiency was 17.2% and 69.0%, respectively. 29.7% of patients had radiographic findings of osteopenia and/or fractures. There was no association between vitamin D deficiency …

Addressing Dermatologic Concerns And Teledermatology In Undomiciled And Sheltered Populations, Kennedy Gallagher, Sahithi Talasila, Anna Bistline, Rebecca Krain, Leena Ramani, Elizabeth Jones

Student Papers, Posters & Projects

Homelessness in the United States is a significant public health issue, with dermatologic disease being the most prevalent health concern among the undomiciled and sheltered populations. Despite a growing need for dermatologic care, the supply of dermatologists remains insufficient, contributing to disparities in healthcare access for this vulnerable group. This review aims to detail the spectrum of dermatologic conditions experienced by homeless individuals, identify barriers to adequate care, and explore teledermatology as a potential solution to bridge these gaps. A comprehensive literature review was conducted, analyzing studies and reports on dermatologic issues prevalent among the homeless population and the efficacy …

Preventive Effects Of Quercetin On The Leaky Gut By Suppression Of Il-1beta-Induced Transcription Factors Involved In An Inflammatory Pathway In Colonic Epithelial Cells, Wannaporn Chayalak, Sumpun Thammacharoen, Chatsri Deachapunya, Sutthasinee Poonyachoti

The Thai Journal of Veterinary Medicine

Flavonol quercetin (Q), found in vegetables and fruits, demonstrates the most potent anti-inflammatory effect. The preventive effect and cellular mechanisms of Q (Q1, Q10, and Q100 µM) on IL-1β induced leaky gut via the signaling molecules of inflammatory pathway, NF-κB p65-iκB/or p38/ERK1/2/MLCK/phospho(p)-MLC were investigated in Caco-2 cells. The cytotoxic effect of Q was initially determined by MTT assay. Transepithelial electrical resistance (TER) and apical-to-basolateral fluorescein isothiocyanate-labeled dextran (FD-4) flux were used to determine paracellular permeability. The protein expression of signaling molecules was examined by Western blot analysis, and their target MLCK mRNA expression was determined using real-time PCR. All Q …

In Vitro Antibacterial, Antibiofilm Activities, And Phytochemical Properties Of Posidonia Oceanica (L) Delile: An Endemic Mediterranean Seagrass, Ertugrul Ozbil, Mehmet Ilktac, Sultan Ogmen, Ovgu Isbilen, Jesus M Duran Ramirez, Jana Gomez, Jennifer N Walker, Ender Volkan

Faculty, Staff and Student Publications

In the antibiotic resistance era, utilizing understudied sources for novel antimicrobials or antivirulence agents can provide new advances against antimicrobial resistant pathogens. In this study, we aimed to investigate antibacterial and antibiofilm activities of Posidonia oceanica (L.) Delile against Enterococcus faecalis ATCC 29212, Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922 and Klebsiella pneumoniae ATCC 700603 and several S. aureus clinical isolates obtained from medical devices, including patient urinary catheters and breast implant infections, with varying antibiotic recalcitrance profiles. The ethanolic and methanolic extracts from P. oceanica rhizome exhibited significant antibacterial activity against E. faecalis and S. aureus, as well …

Factors Associated With Elevated Sars-Cov-2 Immune Response In Children And Adolescents, Sarah E Messiah, Rhiana Abbas, Emma Bergqvist, Harold W Kohl, Michael D Swartz, Yashar Talebi, Rachit Sabharwal, Haoting Han, Melissa A Valerio-Shewmaker, Stacia M Desantis, Ashraf Yaseen, Henal A Gandhi, Ximena Flandes Amavisca, Jessica A Ross, Lindsay N Padilla, Michael O Gonzalez, Leqing Wu, Mark A Silberman, David Lakey, Jennifer A Shuford, Stephen J Pont, Eric Boerwinkle

Faculty, Staff and Student Publications

BACKGROUND: Understanding the distinct immunologic responses to SARS-CoV-2 infection among pediatric populations is pivotal in navigating the COVID-19 pandemic and informing future public health strategies. This study aimed to identify factors associated with heightened antibody responses in children and adolescents to identify potential unique immune dynamics in this population.

METHODS: Data collected between July and December 2023 from the Texas Coronavirus Antibody REsponse Survey (Texas CARES), a statewide prospective population-based antibody survey among 1-to-19-year-old participants, were analyzed. Each participant had the following data available for analysis: (1) Roche Elecsys® Anti-SARS-CoV-2 Immunoassay for Nucleocapsid protein antibodies (Roche N-test), (2) qualitative and …

Regulatory Complexity Of Cellular Differentiation In Candida Albicans Revealed Through Systematic Screening Of Protein Kinase Mutants, Michael C Lorenz

Faculty, Staff and Student Publications

A recent study in mBio reports the construction and preliminary screening of a library containing mutants of 99 of the 119 predicted protein kinases in Candida albicans (the majority of the remaining 20 are probably essential) (J. Kramara, M.-J. Kim, T. L. Ollinger, L. C. Ristow, et al., mBio e01249-24, 2024, https://doi.org/10.1128/mbio.01249-24). Using a quantitative competition assay in 10 conditions that represent nutritional, osmotic, cell wall, and pH stresses that are considered to model various aspects of the host environment allowed them to phenotypically cluster kinases, which highlight both the integration and specialization of signaling pathways, suggesting novel functions …

Infant And Adult Human Intestinal Enteroids Are Morphologically And Functionally Distinct, Grace O Adeniyi-Ipadeola, Julia D Hankins, Amal Kambal, Xi-Lei Zeng, Ketki Patil, Victoria Poplaski, Carolyn Bomidi, Hoa Nguyen-Phuc, Sandra L Grimm, Cristian Coarfa, Fabio Stossi, Sue E Crawford, Sarah E Blutt, Allison L Speer, Mary K Estes, Sasirekha Ramani

Faculty, Staff and Students Publications

UNLABELLED: Human intestinal enteroids (HIEs) are gaining recognition as physiologically relevant models of the intestinal epithelium. While HIEs from adults are used extensively in biomedical research, few studies have used HIEs from infants. Considering the dramatic developmental changes that occur during infancy, it is important to establish models that represent infant intestinal characteristics and physiological responses. We established jejunal HIEs from infant surgical samples and performed comparisons to jejunal HIEs from adults using RNA sequencing (RNA-Seq) and morphologic analyses. We then validated differences in key pathways through functional studies and determined whether these cultures recapitulate known features of the infant …

Optimizing Nutrition Status And Patient Outcomes In Adults Receiving Post-Icu Care, Rachelle Pass

Theses and Graduate Projects

Background: Nutrition interventions for hospitalized patients can provide meaningful benefit on patient recovery outcome, length of hospital admission, and overall healthcare costs. Preventing and treating malnutrition is one aspect of optimizing patient outcomes following a prolonged clinical course, including stays in the intensive care unit (ICU).

Purpose: This literature review aims to address how nutrition status can be maximized for a patient’s post intensive care unit clinical course. While early enteral nutrition (EN) when appropriate is accepted as optimal care, there is little standardization for removal of devices to provide artificially administered nutrition and hydration (AANH).

Methods: A comprehensive literature …

Metal(Loid) Uptake And Physiological Response Of Coix Lacryma-Jobi L To Soil Potentially Toxic Elements In A Polluted Metal-Mining Area, Qun Zhao, Hongyan Liu, Longhua Wu, Peter Christie, Xuewen Wang, Ghulam Rasool, Guilan Peng

Faculty, Staff and Student Publications

Coix lacryma-jobi L. is a traditional medicinal plant in east Asia and is an important crop in Guizhou province, southwest China, where there are elevated levels of soil mercury and arsenic (As). Exposure to multiple potentially toxic elements (PTEs) may affect plant accumulation of metal(loid)s and food safety in regions with high geological metal concentrations. Field experiments were conducted to study the effects of PTEs on metal(loid) accumulation and physiological response of C. lacryma in different plant parts at three pollution levels. Total root length, number of root tips, number of branches, and number of root crosses increased with increasing …

The Case For Bisphosphonate Use In Astronauts Flying Long-Duration Missions, Reece Rosenthal, Victor S Schneider, Jeffrey A Jones, Jean D Sibonga

Faculty, Staff and Students Publications

Changes in the structure of bone can occur in space as an adaptive response to microgravity and on Earth due to the adaptive effects to exercise, to the aging of bone cells, or to prolonged disuse. Knowledge of cell-mediated bone remodeling on Earth informs our understanding of bone tissue changes in space and whether these skeletal changes might increase the risk for fractures or premature osteoporosis in astronauts. Comparisons of skeletal health between astronauts and aging humans, however, may be both informative and misleading. Astronauts are screened for a high level of physical fitness and health, are launched with high …

Barriers To Healthcare Faced By Individuals With Autism Spectrum Disorder And Their Families, Jennifer Lu

Theses and Graduate Projects

Background: Autism Spectrum Disorder (ASD) is a neurodevelopmental condition that is characterized by impairments in social interaction and communication as well as repetitive behaviors or interests that can affect daily functioning. ASD individuals are also more likely to experience poor physical and mental health along with reduced life expectancy compared to non-autistic people. Thus, it is crucial that those with ASD are able to obtain adequate healthcare. However, there is limited research on the barriers to medical care access faced by those with ASD and their families.

Purpose: Due to the lack of autism awareness in the general population and …

Efficacy Of Probiotics In Decreasing Rates Of Necrotizing Enterocolitis And Sepsis In Preterm Neonates, Valisa K. Teekadharry

Theses and Graduate Projects

Background: The incidence of preterm infants developing serious infections is a common finding in many neonatal intensive care units. Probiotics have been a supplement that has been used by numerous people to improve the microbiota of the intestine for prevention of infection.

Purpose: The purpose of this literature review is to explore the efficacy of using probiotics in preterm infants for prevention of serious infections such as necrotizing enterocolitis (NEC) and sepsis.

Methods: A comprehensive literature review was conducted using Lindell Library, Pub Med, Science Direct and Google Scholar. Using the search terms probiotics, probiotics in premature infants, probiotics and …

Clathrin Light Chains Negatively Regulate Plant Immunity By Hijacking The Autophagy Pathway, Hu-Jiao Lan, Jie Ran, Wen-Xu Wang, Lei Zhang, Ni-Ni Wu, Ya-Ting Zhao, Min-Jun Huang, Min Ni, Fen Liu, Ninghui Cheng, Paul A Nakata, Jianwei Pan, Steven A Whitham, Barbara J Baker, Jian-Zhong Liu

Faculty, Staff and Students Publications

The crosstalk between clathrin-mediated endocytosis (CME) and the autophagy pathway has been reported in mammals; however, the interconnection of CME with autophagy has not been established in plants. Here, we report that the Arabidopsis CLATHRIN LIGHT CHAIN (CLC) subunit 2 and 3 double mutant, clc2-1 clc3-1, phenocopies Arabidopsis AUTOPHAGY-RELATED GENE (ATG) mutants in both autoimmunity and nutrient sensitivity. Accordingly, the autophagy pathway is significantly compromised in the clc2-1 clc3-1 mutant. Interestingly, multiple assays demonstrate that CLC2 directly interacts with ATG8h/ATG8i in a domain-specific manner. As expected, both GFP-ATG8h/GFP-ATG8i and CLC2-GFP are subjected to autophagic degradation, and degradation of GFP-ATG8h is …

A Social Media Game To Increase Physical Activity Among Older Adult Women: Protocol Of A Randomized Controlled Trial To Evaluate Challenge, Michael C Robertson, Maria Chang Swartz, Karen M Basen-Engquist, Yisheng Li, Kristofer Jennings, Debbe Thompson, Tom Baranowski, Elena Volpi, Elizabeth J Lyons

Faculty, Staff and Student Publications

BACKGROUND: Older adult women often do not engage in sufficient physical activity (PA) and can encounter biological changes that exacerbate the negative effects of inadequate activity. Wearable activity monitors can facilitate PA initiation, but evidence of sustained behavior change is lacking. Supplementing wearable technologies with intervention content that evokes enjoyment, interest, meaning, and personal values associated with PA may support long term adherence. In this paper, we present the protocol of an NIA-funded study designed to evaluate the efficacy of CHALLENGE for increasing step count and motivation for PA in insufficiently active older women (Challenges for Healthy Aging: Leveraging Limits …

Cycle Syncing: Optimizing Women's Quality Of Life, Megan Francois

Theses and Graduate Projects

A woman’s hormones are in constant fluctuation throughout the menstrual cycle. This 28-day, on average, fluctuation can cause major shifts in mood, cognition, exercise tolerance, and nutrition needs. Because of this, there is potential to optimize quality of life if each phase is synced with diet, exercise, and complementary medicine utilizing holistic methods. Implications for further research include a need for additional longitudinal and prospective studies. Factors that need to be addressed include further analysis of the windows of vulnerability over the menstrual cycle according to female hormone fluctuations, effects of hormonal contraceptives, and effects of pathology on the cycle.

Preserving Pediatric Wellness: Enhanced Recovery After Surgery Protocols And Pain Management In Pediatric Surgery, Kimberly Kim

Theses and Graduate Projects

Background: Enhanced recovery after Surgery (ERAS) protocols and multimodal pain management strategies have revolutionized perioperative care in adult surgical practice by leading to improved postoperative outcomes and better pain management. However, the adoption of these protocols to pediatric surgical care remains underexplored.

Purpose: This systematic review aims to examine recent randomized clinical trials on the implementation of ERAS protocols and multimodal pain management strategies in pediatric surgical patients.

Methods: A computer-based literature search of databases through Google Scholar and PubMed with manual reference searches was used to identify eligible studies. The review includes randomized controlled trials focusing on multimodal pain …

Rheumatoid Arthritis Disease Activity Is Associated With Frailty In Veterans, Courtney N. Loecker

Theses & Dissertations

Frailty, a physiologic vulnerability to everyday stressors, affects approximately 30% of the 1.3 million Americans with rheumatoid arthritis (RA) and is associated with increased risk for adverse health outcomes. Active RA manifests as inflammation, pain, and joint damage leading to functional impairments and morbidity which cumulatively influences frailty. However, the relationship between RA disease activity and frailty is incompletely understood.

This study evaluated the relationship of RA disease activity and frailty at baseline and over up to five years in Veterans. A cohort study was performed using data from the Veterans Affairs Rheumatoid Arthritis registry. RA disease activity was measured …

The Impact Of Bariatric Surgery On Glutathione Synthesis In Individuals With Severe Obesity, Hong Chang Tan, Jean W Hsu, E Shyong Tai, Shaji Chacko, Jean-Paul Kovalik, Farook Jahoor

Faculty, Staff and Students Publications

Glycine is deficient in individuals with obesity but improves following bariatric surgery. Glycine deficiency could impair glutathione (GSH) synthesis and worsen oxidative stress. We examined the impact of obesity-associated glycine deficiency and bariatric surgery on GSH synthesis. Twenty-one participants with severe obesity and twenty-one healthy weight controls were recruited. [1,2-13C2] glycine was infused to measure the erythrocyte (RBC) GSH synthesis rate. Participants with obesity underwent bariatric surgery, and 19 were restudied six months post-surgery. Compared to healthy weight controls, individuals with obesity had significantly lower concentrations of RBC GSH (2.43 ± 0.23 vs. 2.63 ± 0.26 mmol/L, p < 0.01). However, there were no differences in GSH fractional synthesis rate [78.0 (51.4–123.7) vs. 76.9 (49.3–110.1) % pool/day, p = …

Sedation For Gi Endoscopy In The Morbidly Obese: Challenges And Possible Solutions, Lalitha Sundararaman, Basavana Goudra

Department of Anesthesiology Faculty Papers

With the increasing prevalence of obesity and morbid obesity, this subgroup's contribution to patients presenting for elective procedures requiring sedation is significant. Gastrointestinal (GI) procedures clearly form the largest group of such procedures. These procedures may be intended to treat obesity such as the insertion of an intragastric balloon or one or more unrelated procedures such as a screening colonoscopy and (or) diagnostic/therapeutic endoscopy. Regardless of the procedure, these patients pose significant challenges in terms of choice of sedatives, dosing, airway management, ventilation, and oxygenation. An understanding of dissimilarity in the handling of different groups of medications used by an …

Changing Landscape Of Liver Transplant In The United States—Time For A New Innovative Way To Define And Utilize The “Non-Standard Liver Allograft”—A Proposal, Rashmi Seth, Kenneth Andreoni

Department of Surgery Faculty Papers

Since the first liver transplant was performed over six decades ago, the landscape of liver transplantation in the US has seen dramatic evolution. Numerous advancements in perioperative and operative techniques have resulted in major improvements in graft and patient survival rates. Despite the increase in transplants performed over the years, the waitlist mortality rate continues to remain high. The obesity epidemic and the resultant metabolic sequelae continue to result in more marginal donors and challenging recipients. In this review, we aim to highlight the changing characteristics of liver transplant recipients and liver allograft donors. We focus on issues relevant in …

The Dna Methylome Of Pediatric Brain Tumors Appears Shaped By Structural Variation And Predicts Survival, Fengju Chen, Yiqun Zhang, Lanlan Shen, Chad J Creighton

Faculty, Staff and Students Publications

Structural variation heavily influences the molecular landscape of cancer, in part by impacting DNA methylation-mediated transcriptional regulation. Here, using multi-omic datasets involving >2400 pediatric brain and central nervous system tumors of diverse histologies from the Children's Brain Tumor Network, we report hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of somatic structural variant (SV) breakpoints is recurrently associated with altered expression or DNA methylation, respectively, including tumor suppressor genes ATRX and CDKN2A. Altered DNA methylation near enhancers associates with nearby somatic SV breakpoints, including MYC and MYCN. A subset of genes with SV-CGI methylation associations …

Translational Potential Of Mouse Models Of Human Metabolic Disease, I Sadaf Farooqi, Yong Xu

Children’s Nutrition Research Center Staff Publications

Obesity causes significant morbidity and mortality globally. Research in the last three decades has delivered a step-change in our understanding of the fundamental mechanisms that regulate energy homeostasis, building on foundational discoveries in mouse models of metabolic disease. However, not all findings made in rodents have translated to humans, hampering drug discovery in this field. Here, we review how studies in mice and humans have informed our current framework for understanding energy homeostasis, discuss their challenges and limitations, and offer a perspective on how human studies may play an increasingly important role in the discovery of disease mechanisms and identification …

Loss Of Transient Receptor Potential Channel 5 Causes Obesity And Postpartum Depression, Yongxiang Li, Tessa M Cacciottolo, Na Yin, Yang He, Hesong Liu, Hailan Liu, Yuxue Yang, Elana Henning, Julia M Keogh, Katherine Lawler, Edson Mendes De Oliveira, Eugene J Gardner, Katherine A Kentistou, Panayiotis Laouris, Rebecca Bounds, Ken K Ong, John R B Perry, Inês Barroso, Longlong Tu, Jonathan C Bean, Meng Yu, Kristine M Conde, Mengjie Wang, Olivia Ginnard, Xing Fang, Lydia Tong, Junying Han, Tia Darwich, Kevin W Williams, Yongjie Yang, Chunmei Wang, Shelagh Joss, Helen V Firth, Yong Xu, I Sadaf Farooqi

Duncan NRI Faculty and Staff Publications

Hypothalamic neural circuits regulate instinctive behaviors such as food seeking, the fight/flight response, socialization, and maternal care. Here, we identified microdeletions on chromosome Xq23 disrupting the brain-expressed transient receptor potential (TRP) channel 5 (TRPC5). This family of channels detects sensory stimuli and converts them into electrical signals interpretable by the brain. Male TRPC5 deletion carriers exhibited food seeking, obesity, anxiety, and autism, which were recapitulated in knockin male mice harboring a human loss-of-function TRPC5 mutation. Women carrying TRPC5 deletions had severe postpartum depression. As mothers, female knockin mice exhibited anhedonia and depression-like behavior with impaired care of offspring. Deletion of …

A Machine Learning Model For Risk Stratification Of Postdiagnosis Diabetic Ketoacidosis Hospitalization In Pediatric Type 1 Diabetes: Retrospective Study, Devika Subramanian, Rona Sonabend, Ila Singh

Faculty, Staff and Students Publications

BACKGROUND: Diabetic ketoacidosis (DKA) is the leading cause of morbidity and mortality in pediatric type 1 diabetes (T1D), occurring in approximately 20% of patients, with an economic cost of $5.1 billion/year in the United States. Despite multiple risk factors for postdiagnosis DKA, there is still a need for explainable, clinic-ready models that accurately predict DKA hospitalization in established patients with pediatric T1D.

OBJECTIVE: We aimed to develop an interpretable machine learning model to predict the risk of postdiagnosis DKA hospitalization in children with T1D using routinely collected time-series of electronic health record (EHR) data.

METHODS: We conducted a retrospective case-control …

Identification And Characterization Of A Skin Microbiome On Caenorhabditis Elegans Suggests Environmental Microbes Confer Cuticle Protection, Nadia B Haghani, Robert H Lampe, Buck S Samuel, Sreekanth H Chalasani, Molly A Matty

Faculty, Staff and Students Publications

In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The C. elegans cuticular surface serves as a barrier and first point of contact with their microbial environments. In this study, we identify microbes from C. elegans natural habitats that associate with its cuticle, constituting a simple “skin microbiome.” We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on the C. elegans surface. Furthermore, we conduct 16S rRNA gene sequencing studies …

Pkd1 Mutant Clones Within Cirrhotic Livers Inhibit Steatohepatitis Without Promoting Cancer, Min Zhu, Yunguan Wang, Tianshi Lu, Jason Guo, Lin Li, Meng-Hsiung Hsieh, Purva Gopal, Yi Han, Naoto Fujiwara, Darren P Wallace, Alan S L Yu, Xiangyi Fang, Crystal Ransom, Sara Verschleisser, David Hsiehchen, Yujin Hoshida, Amit G Singal, Adam Yopp, Tao Wang, Hao Zhu

Faculty, Staff and Student Publications

Somatic mutations in non-malignant tissues are selected for because they confer increased clonal fitness. However, it is uncertain whether these clones can benefit organ health. Here, ultra-deep targeted sequencing of 150 liver samples from 30 chronic liver disease patients revealed recurrent somatic mutations. PKD1 mutations were observed in 30% of patients, whereas they were only detected in 1.3% of hepatocellular carcinomas (HCCs). To interrogate tumor suppressor functionality, we perturbed PKD1 in two HCC cell lines and six in vivo models, in some cases showing that PKD1 loss protected against HCC, but in most cases showing no impact. However, Pkd1 haploinsufficiency …

Whole Genome Sequencing Based Analysis Of Inflammation Biomarkers In The Trans-Omics For Precision Medicine (Topmed) Consortium, Min-Zhi Jiang, Sheila M Gaynor, Xihao Li, Eric Van Buren, Adrienne Stilp, Erin Buth, Fei Fei Wang, Regina Manansala, Stephanie M Gogarten, Zilin Li, Linda M Polfus, Shabnam Salimi, Joshua C Bis, Nathan Pankratz, Lisa R Yanek, Peter Durda, Russell P Tracy, Stephen S Rich, Jerome I Rotter, Braxton D Mitchell, Joshua P Lewis, Bruce M Psaty, Katherine A Pratte, Edwin K Silverman, Robert C Kaplan, Christy Avery, Kari E North, Rasika A Mathias, Nauder Faraday, Honghuang Lin, Biqi Wang, April P Carson, Arnita F Norwood, Richard A Gibbs, Charles Kooperberg, Jessica Lundin, Ulrike Peters, Josée Dupuis, Lifang Hou, Myriam Fornage, Emelia J Benjamin, Alexander P Reiner, Russell P Bowler, Xihong Lin, Paul L Auer, Laura M Raffield, Nhlbi Trans-Omics For Precision Medicine (Topmed) Consortium, Topmed Inflammation Working Group

Faculty, Staff and Student Publications

Inflammation biomarkers can provide valuable insight into the role of inflammatory processes in many diseases and conditions. Sequencing based analyses of such biomarkers can also serve as an exemplar of the genetic architecture of quantitative traits. To evaluate the biological insight, which can be provided by a multi-ancestry, whole-genome based association study, we performed a comprehensive analysis of 21 inflammation biomarkers from up to 38 465 individuals with whole-genome sequencing from the Trans-Omics for Precision Medicine (TOPMed) program (with varying sample size by trait, where the minimum sample size was n = 737 for MMP-1). We identified 22 distinct single-variant …